├── .codecov.yml ├── .gitattributes ├── .github ├── CONTRIBUTING.md └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .idea ├── dictionaries │ ├── michael.xml │ └── mschauperl.xml ├── libraries │ └── R_User_Library.xml ├── misc.xml ├── modules.xml ├── resp2.iml ├── vcs.xml └── workspace.xml ├── .lgtm.yml ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── Studies ├── Charges │ ├── AAC_R2_0.mol2 │ ├── AAC_R2_100.mol2 │ ├── AAC_R2_60.mol2 │ ├── ACN_R1_100.mol2 │ ├── ACN_R2_0.mol2 │ ├── ACN_R2_100.mol2 │ ├── ACN_R2_60.mol2 │ ├── ACT_R1_100.mol2 │ ├── ACT_R2_0.mol2 │ ├── ACT_R2_100.mol2 │ ├── ACT_R2_60.mol2 │ ├── ANI_R1_100.mol2 │ ├── ANI_R2_0.mol2 │ ├── ANI_R2_100.mol2 │ ├── ANI_R2_60.mol2 │ ├── BAM_R1_100.mol2 │ ├── BAM_R2_0.mol2 │ ├── BAM_R2_100.mol2 │ ├── BAM_R2_60.mol2 │ ├── BUT_R1_100.mol2 │ ├── BUT_R2_0.mol2 │ ├── BUT_R2_100.mol2 │ ├── BUT_R2_60.mol2 │ ├── C00_R2_0.mol2 │ ├── C00_R2_100.mol2 │ ├── C00_R2_60.mol2 │ ├── C01_R1_100.mol2 │ ├── C01_R2_0.mol2 │ ├── C01_R2_100.mol2 │ ├── C01_R2_60.mol2 │ ├── C02_R1_100.mol2 │ ├── C02_R2_0.mol2 │ ├── C02_R2_100.mol2 │ ├── C02_R2_60.mol2 │ ├── C03_R1_100.mol2 │ ├── C03_R2_0.mol2 │ ├── C03_R2_100.mol2 │ ├── C03_R2_60.mol2 │ ├── C04_R2_0.mol2 │ ├── C04_R2_100.mol2 │ ├── C04_R2_60.mol2 │ ├── C05_R2_0.mol2 │ ├── C05_R2_100.mol2 │ ├── C05_R2_60.mol2 │ ├── C06_R2_0.mol2 │ ├── C06_R2_100.mol2 │ ├── C06_R2_60.mol2 │ ├── C07_R1_100.mol2 │ ├── C07_R2_0.mol2 │ ├── C07_R2_100.mol2 │ ├── C07_R2_60.mol2 │ ├── C08_R1_100.mol2 │ ├── C08_R2_0.mol2 │ ├── C08_R2_100.mol2 │ ├── C08_R2_60.mol2 │ ├── C09_R1_100.mol2 │ ├── C09_R2_0.mol2 │ ├── C09_R2_100.mol2 │ ├── C09_R2_60.mol2 │ ├── C10_R1_100.mol2 │ ├── C10_R2_0.mol2 │ ├── C10_R2_100.mol2 │ ├── C10_R2_60.mol2 │ ├── C11_R1_100.mol2 │ ├── C11_R2_0.mol2 │ ├── C11_R2_100.mol2 │ ├── C11_R2_60.mol2 │ ├── C12_R1_100.mol2 │ ├── C12_R2_0.mol2 │ ├── C12_R2_100.mol2 │ ├── C12_R2_60.mol2 │ ├── C13_R2_0.mol2 │ ├── C13_R2_100.mol2 │ ├── C13_R2_60.mol2 │ ├── C14_R1_100.mol2 │ ├── C14_R2_0.mol2 │ ├── C14_R2_100.mol2 │ ├── C14_R2_60.mol2 │ ├── C15_R1_100.mol2 │ ├── C15_R2_0.mol2 │ ├── C15_R2_100.mol2 │ ├── C15_R2_60.mol2 │ ├── C16_R1_100.mol2 │ ├── C16_R2_0.mol2 │ ├── C16_R2_100.mol2 │ ├── C16_R2_60.mol2 │ ├── C17_R1_100.mol2 │ ├── C17_R2_0.mol2 │ ├── C17_R2_100.mol2 │ ├── C17_R2_60.mol2 │ ├── C18_R1_100.mol2 │ ├── C18_R2_0.mol2 │ ├── C18_R2_100.mol2 │ ├── C18_R2_60.mol2 │ ├── C19_R1_100.mol2 │ ├── C19_R2_0.mol2 │ ├── C19_R2_100.mol2 │ ├── C19_R2_60.mol2 │ ├── C20_R1_100.mol2 │ ├── C20_R2_0.mol2 │ ├── C20_R2_100.mol2 │ ├── C20_R2_60.mol2 │ ├── C23_R1_100.mol2 │ ├── C23_R2_0.mol2 │ ├── C23_R2_100.mol2 │ ├── C23_R2_60.mol2 │ ├── C24_R1_100.mol2 │ ├── C24_R2_0.mol2 │ ├── C24_R2_100.mol2 │ ├── C24_R2_60.mol2 │ ├── C25_R1_100.mol2 │ ├── C25_R2_0.mol2 │ ├── C25_R2_100.mol2 │ ├── C25_R2_60.mol2 │ ├── C26_R1_100.mol2 │ ├── C26_R2_0.mol2 │ ├── C26_R2_100.mol2 │ ├── C26_R2_60.mol2 │ ├── C27_R1_100.mol2 │ ├── C27_R2_0.mol2 │ ├── C27_R2_100.mol2 │ ├── C27_R2_60.mol2 │ ├── C28_R1_100.mol2 │ ├── C28_R2_0.mol2 │ ├── C28_R2_100.mol2 │ ├── C28_R2_60.mol2 │ ├── C29_R1_100.mol2 │ ├── C29_R2_0.mol2 │ ├── C29_R2_100.mol2 │ ├── C29_R2_60.mol2 │ ├── C30_R1_100.mol2 │ ├── C30_R2_0.mol2 │ ├── C30_R2_100.mol2 │ ├── C30_R2_60.mol2 │ ├── C31_R1_100.mol2 │ ├── C31_R2_0.mol2 │ ├── C31_R2_100.mol2 │ ├── C31_R2_60.mol2 │ ├── C32_R1_100.mol2 │ ├── C32_R2_0.mol2 │ ├── C32_R2_100.mol2 │ ├── C32_R2_60.mol2 │ ├── C33_R1_100.mol2 │ ├── C33_R2_0.mol2 │ ├── C33_R2_100.mol2 │ ├── C33_R2_60.mol2 │ ├── C34_R1_100.mol2 │ ├── C34_R2_0.mol2 │ ├── C34_R2_100.mol2 │ ├── C34_R2_60.mol2 │ ├── C35_R1_100.mol2 │ ├── C35_R2_0.mol2 │ ├── C35_R2_100.mol2 │ ├── C35_R2_60.mol2 │ ├── C36_R1_100.mol2 │ ├── C36_R2_0.mol2 │ ├── C36_R2_100.mol2 │ ├── C36_R2_60.mol2 │ ├── C37_R1_100.mol2 │ ├── C37_R2_0.mol2 │ ├── C37_R2_100.mol2 │ ├── C37_R2_60.mol2 │ ├── C38_R1_100.mol2 │ ├── C38_R2_0.mol2 │ ├── C38_R2_100.mol2 │ ├── C38_R2_60.mol2 │ ├── C39_R1_100.mol2 │ ├── C39_R2_0.mol2 │ ├── C39_R2_100.mol2 │ ├── C39_R2_60.mol2 │ ├── C40_R1_100.mol2 │ ├── C40_R2_0.mol2 │ ├── C40_R2_100.mol2 │ ├── C40_R2_60.mol2 │ ├── C41_R1_100.mol2 │ ├── C41_R2_0.mol2 │ ├── C41_R2_100.mol2 │ ├── C41_R2_60.mol2 │ ├── C42_R1_100.mol2 │ ├── C42_R2_0.mol2 │ ├── C42_R2_100.mol2 │ ├── C42_R2_60.mol2 │ ├── C43_R1_100.mol2 │ ├── C43_R2_0.mol2 │ ├── C43_R2_100.mol2 │ ├── C43_R2_60.mol2 │ ├── C44_R1_100.mol2 │ ├── C44_R2_0.mol2 │ ├── C44_R2_100.mol2 │ ├── C44_R2_60.mol2 │ ├── C45_R1_100.mol2 │ ├── C45_R2_0.mol2 │ ├── C45_R2_100.mol2 │ ├── C45_R2_60.mol2 │ ├── C46_R1_100.mol2 │ ├── C46_R2_0.mol2 │ ├── C46_R2_100.mol2 │ ├── C46_R2_60.mol2 │ ├── C47_R1_100.mol2 │ ├── C47_R2_0.mol2 │ ├── C47_R2_100.mol2 │ ├── C47_R2_60.mol2 │ ├── C48_R1_100.mol2 │ ├── C48_R2_0.mol2 │ ├── C48_R2_100.mol2 │ ├── C48_R2_60.mol2 │ ├── C49_R1_100.mol2 │ ├── C49_R2_0.mol2 │ ├── C49_R2_100.mol2 │ ├── C49_R2_60.mol2 │ ├── C50_R1_100.mol2 │ ├── C50_R2_0.mol2 │ ├── C50_R2_100.mol2 │ ├── C50_R2_60.mol2 │ ├── C51_R1_100.mol2 │ ├── C51_R2_0.mol2 │ ├── C51_R2_100.mol2 │ ├── C51_R2_60.mol2 │ ├── C52_R1_100.mol2 │ ├── C52_R2_0.mol2 │ ├── C52_R2_100.mol2 │ ├── C52_R2_60.mol2 │ ├── C53_R1_100.mol2 │ ├── C53_R2_0.mol2 │ ├── C53_R2_100.mol2 │ ├── C53_R2_60.mol2 │ ├── C54_R1_100.mol2 │ ├── C54_R2_0.mol2 │ ├── C54_R2_100.mol2 │ ├── C54_R2_60.mol2 │ ├── C55_R1_100.mol2 │ ├── C55_R2_0.mol2 │ ├── C55_R2_100.mol2 │ ├── C55_R2_60.mol2 │ ├── C56_R1_100.mol2 │ ├── C56_R2_0.mol2 │ ├── C56_R2_100.mol2 │ ├── C56_R2_60.mol2 │ ├── C57_R1_100.mol2 │ ├── C57_R2_0.mol2 │ ├── C57_R2_100.mol2 │ ├── C57_R2_60.mol2 │ ├── C58_R1_100.mol2 │ ├── C58_R2_0.mol2 │ ├── C58_R2_100.mol2 │ ├── C58_R2_60.mol2 │ ├── C59_R1_100.mol2 │ ├── C59_R2_0.mol2 │ ├── C59_R2_100.mol2 │ ├── C59_R2_60.mol2 │ ├── C60_R1_100.mol2 │ ├── C60_R2_0.mol2 │ ├── C60_R2_100.mol2 │ ├── C60_R2_60.mol2 │ ├── C61_R1_100.mol2 │ ├── C61_R2_0.mol2 │ ├── C61_R2_100.mol2 │ ├── C61_R2_60.mol2 │ ├── C62_R1_100.mol2 │ ├── C62_R2_0.mol2 │ ├── C62_R2_100.mol2 │ ├── C62_R2_60.mol2 │ ├── C63_R1_100.mol2 │ ├── C63_R2_0.mol2 │ ├── C63_R2_100.mol2 │ ├── C63_R2_60.mol2 │ ├── C64_R1_100.mol2 │ ├── C64_R2_0.mol2 │ ├── C64_R2_100.mol2 │ ├── C64_R2_60.mol2 │ ├── C65_R1_100.mol2 │ ├── C65_R2_0.mol2 │ ├── C65_R2_100.mol2 │ ├── C65_R2_60.mol2 │ ├── C66_R1_100.mol2 │ ├── C66_R2_0.mol2 │ ├── C66_R2_100.mol2 │ ├── C66_R2_60.mol2 │ ├── DEE_R1_100.mol2 │ ├── DEE_R2_0.mol2 │ ├── DEE_R2_100.mol2 │ ├── DEE_R2_60.mol2 │ ├── FUR_R1_100.mol2 │ ├── FUR_R2_0.mol2 │ ├── FUR_R2_100.mol2 │ ├── FUR_R2_60.mol2 │ ├── IPP_R1_100.mol2 │ ├── IPP_R2_0.mol2 │ ├── IPP_R2_100.mol2 │ ├── IPP_R2_60.mol2 │ ├── ISO_R1_100.mol2 │ ├── ISO_R2_0.mol2 │ ├── ISO_R2_100.mol2 │ ├── ISO_R2_60.mol2 │ ├── MAA_R1_100.mol2 │ ├── MAA_R2_0.mol2 │ ├── MAA_R2_100.mol2 │ ├── MAA_R2_60.mol2 │ ├── MAC_R2_0.mol2 │ ├── MAC_R2_100.mol2 │ ├── MAC_R2_60.mol2 │ ├── MPE_R1_100.mol2 │ ├── MPE_R2_0.mol2 │ ├── MPE_R2_100.mol2 │ ├── MPE_R2_60.mol2 │ ├── MTH_R1_100.mol2 │ ├── MTH_R2_0.mol2 │ ├── MTH_R2_100.mol2 │ ├── MTH_R2_60.mol2 │ ├── NMM_R1_100.mol2 │ ├── NMM_R2_0.mol2 │ ├── NMM_R2_100.mol2 │ ├── NMM_R2_60.mol2 │ ├── PAC_R2_0.mol2 │ ├── PAC_R2_100.mol2 │ ├── PAC_R2_60.mol2 │ ├── PXY_R1_100.mol2 │ ├── PXY_R2_0.mol2 │ ├── PXY_R2_100.mol2 │ ├── PXY_R2_60.mol2 │ ├── TOL_R1_100.mol2 │ ├── TOL_R2_0.mol2 │ ├── TOL_R2_100.mol2 │ └── TOL_R2_60.mol2 ├── FF-files │ ├── LJ_opt_R1_100.offxml │ ├── LJ_opt_R2_50.offxml │ ├── LJ_opt_R2_60.offxml │ ├── smirnoff99Frosst.offxml │ ├── smirnoffFIVEMODEL.offxml │ └── smirnoffFOURMODEL.offxml ├── Results │ ├── dens_test_data.csv │ ├── dens_training_data.csv │ ├── hov_data.csv │ ├── hov_test_data.csv │ └── hov_training_data.csv └── example-input-files │ ├── ForceBalance │ ├── test.in │ └── training.in │ ├── HFE │ ├── DEE.pdb │ ├── DEE_experiment.yaml │ ├── DEE_solv.pdb │ ├── DEE_solv.prmtop │ ├── DEE_solv.xml │ ├── DEE_vacuum.pdb │ ├── DEE_vacuum.prmtop │ └── DEE_vacuum.xml │ └── respyte │ ├── benzene-RESP1 │ └── input │ │ ├── input.yml │ │ ├── molecules │ │ └── mol1 │ │ │ └── conf1 │ │ │ ├── grid.dat │ │ │ ├── mol1_conf1.espf │ │ │ ├── mol1_conf1.pdb │ │ │ └── mol1_conf1.xyz │ │ └── respyte.yml │ ├── benzene-RESP2GAS │ └── input │ │ ├── input.yml │ │ ├── molecules │ │ └── mol1 │ │ │ └── conf1 │ │ │ ├── grid.dat │ │ │ ├── mol1_conf1.espf │ │ │ ├── mol1_conf1.pdb │ │ │ └── mol1_conf1.xyz │ │ └── respyte.yml │ └── benzene-RESP2LIQUID │ └── input │ ├── input.yml │ ├── molecules │ └── mol1 │ │ └── conf1 │ │ ├── grid.dat │ │ ├── mol1_conf1.espf │ │ ├── mol1_conf1.pdb │ │ └── mol1_conf1.xyz │ └── respyte.yml ├── devtools ├── README.md ├── conda-envs │ ├── RESP2_environment.yaml │ └── env_save.yaml ├── scripts │ └── create_conda_env.py └── travis-ci │ ├── after_install.sh │ └── before_install.sh ├── docs ├── Makefile ├── README.md ├── _static │ └── README.md ├── _templates │ └── README.md ├── conf.py ├── environment.yml ├── index.rst ├── make.bat ├── readthedocs.yml ├── requirements.txt └── resp2.pdf ├── example └── Ethanol_Example.ipynb ├── readthedocs.yml ├── resp2 ├── __init__.py ├── _version.py ├── charge_calculation.py ├── create_mol2_pdb.py ├── data │ ├── CCO.smi │ ├── ETH-box.pdb │ ├── ETH-conformers.mol2 │ ├── ETH.mol2 │ ├── ETH.pdb │ ├── README.md │ └── look_and_say.dat ├── resp2.py ├── test_fb.in └── tests │ ├── __init__.py │ └── test_resp2.py ├── setup.cfg ├── setup.py └── versioneer.py /.codecov.yml: -------------------------------------------------------------------------------- 1 | # Codecov configuration to make it a bit less noisy 2 | coverage: 3 | status: 4 | patch: false 5 | project: 6 | default: 7 | threshold: 50% 8 | comment: 9 | layout: "header" 10 | require_changes: false 11 | branches: null 12 | behavior: default 13 | flags: null 14 | paths: null -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | resp2/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | ## Description 2 | Provide a brief description of the PR's purpose here. 3 | 4 | ## Todos 5 | Notable points that this PR has either accomplished or will accomplish. 6 | - [ ] TODO 1 7 | 8 | ## Questions 9 | - [ ] Question1 10 | 11 | ## Status 12 | - [ ] Ready to go -------------------------------------------------------------------------------- /.idea/dictionaries/michael.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | parameterization 5 | 6 | 7 | -------------------------------------------------------------------------------- /.idea/dictionaries/mschauperl.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | forcefield 5 | openeye 6 | resname 7 | respyte 8 | 9 | 10 | -------------------------------------------------------------------------------- /.idea/libraries/R_User_Library.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /.idea/misc.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 6 | 7 | -------------------------------------------------------------------------------- /.idea/modules.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -------------------------------------------------------------------------------- /.idea/resp2.iml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 16 | 17 | 18 | 20 | -------------------------------------------------------------------------------- /.idea/vcs.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /.lgtm.yml: -------------------------------------------------------------------------------- 1 | # Configure LGTM for this package 2 | 3 | extraction: 4 | python: # Configure Python 5 | python_setup: # Configure the setup 6 | version: 3 # Specify Version 3 7 | path_classifiers: 8 | library: 9 | - versioneer.py # Set Versioneer.py to an external "library" (3rd party code) 10 | - devtools/* 11 | generated: 12 | - resp2/_version.py 13 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: python 2 | 3 | # Run jobs on container-based infrastructure, can be overridden per job 4 | 5 | matrix: 6 | include: 7 | # Extra includes for OSX since python language is not available by default on OSX 8 | # - os: osx 9 | # language: generic 10 | # env: PYTHON_VER=3.6 11 | # - os: osx 12 | # language: generic 13 | # env: PYTHON_VER=3.7 14 | 15 | 16 | - os: linux 17 | language: generic # No need to set Python version since its conda 18 | env: PYTHON_VER=3.6 19 | - os: linux 20 | language: generic 21 | env: PYTHON_VER=3.7 22 | 23 | 24 | before_install: 25 | # Additional info about the build 26 | - uname -a 27 | - df -h 28 | - ulimit -a 29 | 30 | # Install the Python environment 31 | - source devtools/travis-ci/before_install.sh 32 | - python -V 33 | 34 | 35 | install: 36 | 37 | # Create test environment for package 38 | - python devtools/scripts/create_conda_env.py -n=RESP2 -p=$PYTHON_VER devtools/conda-envs/RESP2_environment.yaml 39 | # Activate the test environment 40 | - conda activate RESP2 41 | # Build and install package 42 | - python setup.py develop --no-deps 43 | # Install respyte 44 | - source devtools/travis-ci/after_install.sh 45 | 46 | 47 | script: 48 | - pytest -v --cov=resp2 resp2/tests/ 49 | 50 | notifications: 51 | email: false 52 | 53 | after_success: 54 | - codecov 55 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | 2 | MIT License 3 | 4 | Copyright (c) 2019 MSchauperl 5 | 6 | Permission is hereby granted, free of charge, to any person obtaining a copy 7 | of this software and associated documentation files (the "Software"), to deal 8 | in the Software without restriction, including without limitation the rights 9 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 | copies of the Software, and to permit persons to whom the Software is 11 | furnished to do so, subject to the following conditions: 12 | 13 | The above copyright notice and this permission notice shall be included in all 14 | copies or substantial portions of the Software. 15 | 16 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 22 | SOFTWARE. 23 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include LICENSE 2 | include MANIFEST.in 3 | include versioneer.py 4 | 5 | graft resp2 6 | global-exclude *.py[cod] __pycache__ *.soinclude resp2/_version.py 7 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | RESP2 2 | ============================== 3 | [//]: # (Badges) 4 | [![Travis Build Status](https://travis-ci.com/MSCHAUPERL/RESP2.png)](https://travis-ci.com/MSCHAUPERL/RESP2) 5 | [![codecov](https://codecov.io/gh/MSCHAUPERL/RESP2/branch/master/graph/badge.svg)](https://codecov.io/gh/MSCHAUPERL/RESP2/branch/master) 6 | [![Documentation Status](https://readthedocs.org/projects/resp2/badge/?version=latest)](https://resp2.readthedocs.io/en/latest/?badge=latest) 7 | [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MSchauperl/RESP2.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MSchauperl/RESP2/context:python) 8 | 9 | A template to create RESP2 charges 10 | 11 | 12 | ### Installation 13 | RESP 2 relies on the openeye-toolkits, ForceBalance, pybel, psi4 and respyte. 14 | We recommend to install all dependencies via conda (except for respyte). 15 | See Installation instructions: https://resp2.readthedocs.io 16 | 17 | 18 | ### Example 19 | 20 | The example folder contains a few useful example how you can use the python API to generate 21 | 22 | - conformations 23 | - optimize all your molecules with psi4 24 | - RESP1 charges 25 | - RESP2 charges 26 | - ForceBalance input files 27 | - PDB files necessary for ForceBalance 28 | 29 | 30 | ### Copyright 31 | 32 | Copyright (c) 2019, Michael Schauperl 33 | 34 | 35 | #### Acknowledgements 36 | 37 | Project based on the 38 | [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.0. 39 | -------------------------------------------------------------------------------- /Studies/Charges/AAC_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | AAC 3 | 8 7 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -1.5870 0.5730 1.2220 C.2 1 AAC 0.694000 9 | 2 C2 -1.0070 0.3070 -0.1430 C.3 1 AAC -0.459900 10 | 3 O1 -2.4270 -0.0960 1.7500 O.2 1 AAC -0.511200 11 | 4 O2 -1.0890 1.6600 1.8580 O.3 1 AAC -0.496100 12 | 5 H1 -1.1850 1.1620 -0.8080 H 1 AAC 0.141300 13 | 6 H2 0.0780 0.1540 -0.0750 H 1 AAC 0.141300 14 | 7 H3 -1.4720 -0.5840 -0.5660 H 1 AAC 0.141300 15 | 8 H4 -0.4270 2.0860 1.3010 H 1 AAC 0.349400 16 | @BOND 17 | 1 1 2 1 18 | 2 1 3 2 19 | 3 1 4 1 20 | 4 2 5 1 21 | 5 2 6 1 22 | 6 2 7 1 23 | 7 4 8 1 24 | -------------------------------------------------------------------------------- /Studies/Charges/AAC_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | AAC 3 | 8 7 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -1.5870 0.5730 1.2220 C.2 1 AAC 0.768700 9 | 2 C2 -1.0070 0.3070 -0.1430 C.3 1 AAC -0.447900 10 | 3 O1 -2.4270 -0.0960 1.7500 O.2 1 AAC -0.612200 11 | 4 O2 -1.0890 1.6600 1.8580 O.3 1 AAC -0.580400 12 | 5 H1 -1.1850 1.1620 -0.8080 H 1 AAC 0.148600 13 | 6 H2 0.0780 0.1540 -0.0750 H 1 AAC 0.148600 14 | 7 H3 -1.4720 -0.5840 -0.5660 H 1 AAC 0.148600 15 | 8 H4 -0.4270 2.0860 1.3010 H 1 AAC 0.426100 16 | @BOND 17 | 1 1 2 1 18 | 2 1 3 2 19 | 3 1 4 1 20 | 4 2 5 1 21 | 5 2 6 1 22 | 6 2 7 1 23 | 7 4 8 1 24 | -------------------------------------------------------------------------------- /Studies/Charges/AAC_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | AAC 3 | 8 7 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -1.5870 0.5730 1.2220 C.2 1 AAC 0.738820 9 | 2 C2 -1.0070 0.3070 -0.1430 C.3 1 AAC -0.452700 10 | 3 O1 -2.4270 -0.0960 1.7500 O.2 1 AAC -0.571800 11 | 4 O2 -1.0890 1.6600 1.8580 O.3 1 AAC -0.546680 12 | 5 H1 -1.1850 1.1620 -0.8080 H 1 AAC 0.145680 13 | 6 H2 0.0780 0.1540 -0.0750 H 1 AAC 0.145680 14 | 7 H3 -1.4720 -0.5840 -0.5660 H 1 AAC 0.145680 15 | 8 H4 -0.4270 2.0860 1.3010 H 1 AAC 0.395420 16 | @BOND 17 | 1 1 2 1 18 | 2 1 3 2 19 | 3 1 4 1 20 | 4 2 5 1 21 | 5 2 6 1 22 | 6 2 7 1 23 | 7 4 8 1 24 | -------------------------------------------------------------------------------- /Studies/Charges/ACN_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACN 3 | 6 5 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.2010 1.4630 1.5000 C.1 1 ACN 0.439300 10 | 2 C2 0.4490 0.2820 0.9560 C.3 1 ACN -0.423100 11 | 3 N1 -0.7190 2.4020 1.9340 N.1 1 ACN -0.500000 12 | 4 H1 -0.2920 -0.5020 0.7650 H 1 ACN 0.161200 13 | 5 H2 1.1920 -0.1000 1.6640 H 1 ACN 0.161200 14 | 6 H3 0.9520 0.5280 0.0160 H 1 ACN 0.161200 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 3 18 | 3 2 4 1 19 | 4 2 5 1 20 | 5 2 6 1 21 | @SUBSTRUCTURE 22 | 1 ACN 1 TEMP 0 **** **** 0 ROOT 23 | -------------------------------------------------------------------------------- /Studies/Charges/ACN_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACN 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.2010 1.4630 1.5000 C.1 1 MOL1 0.431300 9 | 2 C2 0.4490 0.2820 0.9560 C.3 1 MOL1 -0.461600 10 | 3 N1 -0.7190 2.4020 1.9340 N.1 1 MOL1 -0.486500 11 | 4 H1 -0.2920 -0.5020 0.7650 H 1 MOL1 0.172300 12 | 5 H2 1.1920 -0.1000 1.6640 H 1 MOL1 0.172300 13 | 6 H3 0.9520 0.5280 0.0160 H 1 MOL1 0.172300 14 | @BOND 15 | 1 1 2 1 16 | 2 1 3 3 17 | 3 2 4 1 18 | 4 2 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/ACN_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACN 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.2010 1.4630 1.5000 C.1 1 MOL1 0.440600 9 | 2 C2 0.4490 0.2820 0.9560 C.3 1 MOL1 -0.447900 10 | 3 N1 -0.7190 2.4020 1.9340 N.1 1 MOL1 -0.519100 11 | 4 H1 -0.2920 -0.5020 0.7650 H 1 MOL1 0.175500 12 | 5 H2 1.1920 -0.1000 1.6640 H 1 MOL1 0.175500 13 | 6 H3 0.9520 0.5280 0.0160 H 1 MOL1 0.175500 14 | @BOND 15 | 1 1 2 1 16 | 2 1 3 3 17 | 3 2 4 1 18 | 4 2 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/ACN_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACN 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.2010 1.4630 1.5000 C.1 1 MOL1 0.436880 9 | 2 C2 0.4490 0.2820 0.9560 C.3 1 MOL1 -0.453380 10 | 3 N1 -0.7190 2.4020 1.9340 N.1 1 MOL1 -0.506060 11 | 4 H1 -0.2920 -0.5020 0.7650 H 1 MOL1 0.174220 12 | 5 H2 1.1920 -0.1000 1.6640 H 1 MOL1 0.174220 13 | 6 H3 0.9520 0.5280 0.0160 H 1 MOL1 0.174220 14 | @BOND 15 | 1 1 2 1 16 | 2 1 3 3 17 | 3 2 4 1 18 | 4 2 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/ACT_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACT 3 | 10 9 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.0580 -0.4600 2.0950 C.2 1 ACT 0.766800 10 | 2 C2 -0.8150 -0.3980 0.7910 C.3 1 ACT -0.445100 11 | 3 C3 0.4950 0.8440 2.6150 C.3 1 ACT -0.445100 12 | 4 O1 0.1030 -1.5010 2.6880 O.2 1 ACT -0.572000 13 | 5 H1 -0.1710 0.0020 -0.0040 H 1 ACT 0.115900 14 | 6 H2 -1.1630 -1.3970 0.5170 H 1 ACT 0.115900 15 | 7 H3 -1.6710 0.2830 0.8790 H 1 ACT 0.115900 16 | 8 H4 -0.3170 1.5670 2.7700 H 1 ACT 0.115900 17 | 9 H5 1.1780 1.2880 1.8790 H 1 ACT 0.115900 18 | 10 H6 1.0230 0.6730 3.5560 H 1 ACT 0.115900 19 | @BOND 20 | 1 1 2 1 21 | 2 1 3 1 22 | 3 1 4 2 23 | 4 2 5 1 24 | 5 2 6 1 25 | 6 2 7 1 26 | 7 3 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | @SUBSTRUCTURE 30 | 1 ACT 1 TEMP 0 **** **** 0 ROOT 31 | -------------------------------------------------------------------------------- /Studies/Charges/ACT_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACT 3 | 10 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.0580 -0.4600 2.0950 C.2 1 MOL1 0.727400 9 | 2 C2 -0.8150 -0.3980 0.7910 C.3 1 MOL1 -0.454700 10 | 3 C3 0.4950 0.8440 2.6150 C.3 1 MOL1 -0.454700 11 | 4 O1 0.1030 -1.5010 2.6880 O.2 1 MOL1 -0.538300 12 | 5 H1 -0.1710 0.0020 -0.0040 H 1 MOL1 0.120100 13 | 6 H2 -1.1630 -1.3970 0.5170 H 1 MOL1 0.120100 14 | 7 H3 -1.6710 0.2830 0.8790 H 1 MOL1 0.120100 15 | 8 H4 -0.3170 1.5670 2.7700 H 1 MOL1 0.120100 16 | 9 H5 1.1780 1.2880 1.8790 H 1 MOL1 0.120100 17 | 10 H6 1.0230 0.6730 3.5560 H 1 MOL1 0.120100 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 1 21 | 3 1 4 2 22 | 4 2 5 1 23 | 5 2 6 1 24 | 6 2 7 1 25 | 7 3 8 1 26 | 8 3 9 1 27 | 9 3 10 1 28 | -------------------------------------------------------------------------------- /Studies/Charges/ACT_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACT 3 | 10 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.0580 -0.4600 2.0950 C.2 1 MOL1 0.760200 9 | 2 C2 -0.8150 -0.3980 0.7910 C.3 1 MOL1 -0.497500 10 | 3 C3 0.4950 0.8440 2.6150 C.3 1 MOL1 -0.497500 11 | 4 O1 0.1030 -1.5010 2.6880 O.2 1 MOL1 -0.630700 12 | 5 H1 -0.1710 0.0020 -0.0040 H 1 MOL1 0.144200 13 | 6 H2 -1.1630 -1.3970 0.5170 H 1 MOL1 0.144200 14 | 7 H3 -1.6710 0.2830 0.8790 H 1 MOL1 0.144200 15 | 8 H4 -0.3170 1.5670 2.7700 H 1 MOL1 0.144200 16 | 9 H5 1.1780 1.2880 1.8790 H 1 MOL1 0.144200 17 | 10 H6 1.0230 0.6730 3.5560 H 1 MOL1 0.144200 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 1 21 | 3 1 4 2 22 | 4 2 5 1 23 | 5 2 6 1 24 | 6 2 7 1 25 | 7 3 8 1 26 | 8 3 9 1 27 | 9 3 10 1 28 | -------------------------------------------------------------------------------- /Studies/Charges/ACT_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ACT 3 | 10 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.0580 -0.4600 2.0950 C.2 1 MOL1 0.747080 9 | 2 C2 -0.8150 -0.3980 0.7910 C.3 1 MOL1 -0.480380 10 | 3 C3 0.4950 0.8440 2.6150 C.3 1 MOL1 -0.480380 11 | 4 O1 0.1030 -1.5010 2.6880 O.2 1 MOL1 -0.593740 12 | 5 H1 -0.1710 0.0020 -0.0040 H 1 MOL1 0.134560 13 | 6 H2 -1.1630 -1.3970 0.5170 H 1 MOL1 0.134560 14 | 7 H3 -1.6710 0.2830 0.8790 H 1 MOL1 0.134560 15 | 8 H4 -0.3170 1.5670 2.7700 H 1 MOL1 0.134560 16 | 9 H5 1.1780 1.2880 1.8790 H 1 MOL1 0.134560 17 | 10 H6 1.0230 0.6730 3.5560 H 1 MOL1 0.134560 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 1 21 | 3 1 4 2 22 | 4 2 5 1 23 | 5 2 6 1 24 | 6 2 7 1 25 | 7 3 8 1 26 | 8 3 9 1 27 | 9 3 10 1 28 | -------------------------------------------------------------------------------- /Studies/Charges/ANI_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ANI 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8970 -1.0150 -0.1130 C.ar 1 MOL1 -0.065400 9 | 2 C2 0.8170 -0.4660 0.5710 C.ar 1 MOL1 -0.225200 10 | 3 C3 2.9130 -1.6230 0.6170 C.ar 1 MOL1 -0.225200 11 | 4 C4 0.7500 -0.5210 1.9560 C.ar 1 MOL1 -0.144400 12 | 5 C5 2.8550 -1.6840 2.0020 C.ar 1 MOL1 -0.144400 13 | 6 C6 1.7690 -1.1330 2.6950 C.ar 1 MOL1 0.214800 14 | 7 N1 1.6760 -1.2470 4.0770 N.pl3 1 MOL1 -0.698800 15 | 8 H1 1.9470 -0.9680 -1.1980 H 1 MOL1 0.107800 16 | 9 H2 0.0120 0.0170 0.0190 H 1 MOL1 0.146500 17 | 10 H3 3.7680 -2.0570 0.1030 H 1 MOL1 0.146500 18 | 11 H4 -0.1030 -0.0900 2.4780 H 1 MOL1 0.135300 19 | 12 H5 3.6560 -2.1660 2.5610 H 1 MOL1 0.135300 20 | 13 H6 1.1090 -0.5340 4.5160 H 1 MOL1 0.308500 21 | 14 H7 2.5660 -1.3390 4.5480 H 1 MOL1 0.308500 22 | @BOND 23 | 1 1 2 ar 24 | 2 1 3 ar 25 | 3 1 8 1 26 | 4 2 4 ar 27 | 5 2 9 1 28 | 6 3 5 ar 29 | 7 3 10 1 30 | 8 4 6 ar 31 | 9 4 11 1 32 | 10 5 6 ar 33 | 11 5 12 1 34 | 12 6 7 1 35 | 13 7 13 1 36 | 14 7 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/ANI_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ANI 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8970 -1.0150 -0.1130 C.ar 1 MOL1 -0.081600 9 | 2 C2 0.8170 -0.4660 0.5710 C.ar 1 MOL1 -0.245300 10 | 3 C3 2.9130 -1.6230 0.6170 C.ar 1 MOL1 -0.245300 11 | 4 C4 0.7500 -0.5210 1.9560 C.ar 1 MOL1 -0.149200 12 | 5 C5 2.8550 -1.6840 2.0020 C.ar 1 MOL1 -0.149200 13 | 6 C6 1.7690 -1.1330 2.6950 C.ar 1 MOL1 0.224600 14 | 7 N1 1.6760 -1.2470 4.0770 N.pl3 1 MOL1 -0.727300 15 | 8 H1 1.9470 -0.9680 -1.1980 H 1 MOL1 0.121600 16 | 9 H2 0.0120 0.0170 0.0190 H 1 MOL1 0.161500 17 | 10 H3 3.7680 -2.0570 0.1030 H 1 MOL1 0.161500 18 | 11 H4 -0.1030 -0.0900 2.4780 H 1 MOL1 0.142300 19 | 12 H5 3.6560 -2.1660 2.5610 H 1 MOL1 0.142300 20 | 13 H6 1.1090 -0.5340 4.5160 H 1 MOL1 0.322100 21 | 14 H7 2.5660 -1.3390 4.5480 H 1 MOL1 0.322100 22 | @BOND 23 | 1 1 2 ar 24 | 2 1 3 ar 25 | 3 1 8 1 26 | 4 2 4 ar 27 | 5 2 9 1 28 | 6 3 5 ar 29 | 7 3 10 1 30 | 8 4 6 ar 31 | 9 4 11 1 32 | 10 5 6 ar 33 | 11 5 12 1 34 | 12 6 7 1 35 | 13 7 13 1 36 | 14 7 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/ANI_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ANI 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8970 -1.0150 -0.1130 C.ar 1 MOL1 -0.075120 9 | 2 C2 0.8170 -0.4660 0.5710 C.ar 1 MOL1 -0.237260 10 | 3 C3 2.9130 -1.6230 0.6170 C.ar 1 MOL1 -0.237260 11 | 4 C4 0.7500 -0.5210 1.9560 C.ar 1 MOL1 -0.147280 12 | 5 C5 2.8550 -1.6840 2.0020 C.ar 1 MOL1 -0.147280 13 | 6 C6 1.7690 -1.1330 2.6950 C.ar 1 MOL1 0.220680 14 | 7 N1 1.6760 -1.2470 4.0770 N.pl3 1 MOL1 -0.715900 15 | 8 H1 1.9470 -0.9680 -1.1980 H 1 MOL1 0.116080 16 | 9 H2 0.0120 0.0170 0.0190 H 1 MOL1 0.155500 17 | 10 H3 3.7680 -2.0570 0.1030 H 1 MOL1 0.155500 18 | 11 H4 -0.1030 -0.0900 2.4780 H 1 MOL1 0.139500 19 | 12 H5 3.6560 -2.1660 2.5610 H 1 MOL1 0.139500 20 | 13 H6 1.1090 -0.5340 4.5160 H 1 MOL1 0.316660 21 | 14 H7 2.5660 -1.3390 4.5480 H 1 MOL1 0.316660 22 | @BOND 23 | 1 1 2 ar 24 | 2 1 3 ar 25 | 3 1 8 1 26 | 4 2 4 ar 27 | 5 2 9 1 28 | 6 3 5 ar 29 | 7 3 10 1 30 | 8 4 6 ar 31 | 9 4 11 1 32 | 10 5 6 ar 33 | 11 5 12 1 34 | 12 6 7 1 35 | 13 7 13 1 36 | 14 7 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/BAM_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BAM 3 | 13 12 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 1.0170 0.0970 -0.4400 C.3 1 BAM -0.062600 10 | 2 C2 1.2090 1.5170 -0.9420 C.3 1 BAM 0.027300 11 | 3 C3 2.5800 1.7550 -1.5490 C.3 1 BAM 0.346200 12 | 4 N1 2.6810 3.1110 -2.0690 N.3 1 BAM -0.949900 13 | 5 H1 1.1230 -0.6300 -1.2570 H 1 BAM 0.013400 14 | 6 H2 1.7590 -0.1610 0.3270 H 1 BAM 0.013400 15 | 7 H3 0.0230 -0.0440 -0.0000 H 1 BAM 0.013400 16 | 8 H4 1.0600 2.2260 -0.1120 H 1 BAM -0.006600 17 | 9 H5 0.4510 1.7690 -1.6960 H 1 BAM -0.006600 18 | 10 H6 3.3530 1.4940 -0.7990 H 1 BAM -0.042200 19 | 11 H7 2.7240 1.0600 -2.3900 H 1 BAM -0.042200 20 | 12 H8 3.5990 3.2510 -2.4840 H 1 BAM 0.348200 21 | 13 H9 2.6410 3.7680 -1.2910 H 1 BAM 0.348200 22 | @BOND 23 | 1 1 2 1 24 | 2 1 5 1 25 | 3 1 6 1 26 | 4 1 7 1 27 | 5 2 3 1 28 | 6 2 8 1 29 | 7 2 9 1 30 | 8 3 4 1 31 | 9 3 10 1 32 | 10 3 11 1 33 | 11 4 12 1 34 | 12 4 13 1 35 | @SUBSTRUCTURE 36 | 1 BAM 1 TEMP 0 **** **** 0 ROOT 37 | -------------------------------------------------------------------------------- /Studies/Charges/BAM_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BAM 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0170 0.0970 -0.4400 C.3 1 MOL1 -0.077000 9 | 2 C2 1.2090 1.5170 -0.9420 C.3 1 MOL1 0.048900 10 | 3 C3 2.5800 1.7550 -1.5490 C.3 1 MOL1 0.254200 11 | 4 N1 2.6810 3.1110 -2.0690 N.3 1 MOL1 -0.842400 12 | 5 H1 1.1230 -0.6300 -1.2570 H 1 MOL1 0.016900 13 | 6 H2 1.7590 -0.1610 0.3270 H 1 MOL1 0.016900 14 | 7 H3 0.0230 -0.0440 -0.0000 H 1 MOL1 0.016900 15 | 8 H4 1.0600 2.2260 -0.1120 H 1 MOL1 -0.005500 16 | 9 H5 0.4510 1.7690 -1.6960 H 1 MOL1 -0.005500 17 | 10 H6 3.3530 1.4940 -0.7990 H 1 MOL1 -0.023600 18 | 11 H7 2.7240 1.0600 -2.3900 H 1 MOL1 -0.023600 19 | 12 H8 3.5990 3.2510 -2.4840 H 1 MOL1 0.311800 20 | 13 H9 2.6410 3.7680 -1.2910 H 1 MOL1 0.311800 21 | @BOND 22 | 1 1 2 1 23 | 2 1 5 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 3 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 4 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | 12 4 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/BAM_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BAM 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0170 0.0970 -0.4400 C.3 1 MOL1 -0.062500 9 | 2 C2 1.2090 1.5170 -0.9420 C.3 1 MOL1 0.043300 10 | 3 C3 2.5800 1.7550 -1.5490 C.3 1 MOL1 0.326400 11 | 4 N1 2.6810 3.1110 -2.0690 N.3 1 MOL1 -1.043800 12 | 5 H1 1.1230 -0.6300 -1.2570 H 1 MOL1 0.013000 13 | 6 H2 1.7590 -0.1610 0.3270 H 1 MOL1 0.013000 14 | 7 H3 0.0230 -0.0440 -0.0000 H 1 MOL1 0.013000 15 | 8 H4 1.0600 2.2260 -0.1120 H 1 MOL1 -0.008100 16 | 9 H5 0.4510 1.7690 -1.6960 H 1 MOL1 -0.008100 17 | 10 H6 3.3530 1.4940 -0.7990 H 1 MOL1 -0.023000 18 | 11 H7 2.7240 1.0600 -2.3900 H 1 MOL1 -0.023000 19 | 12 H8 3.5990 3.2510 -2.4840 H 1 MOL1 0.379900 20 | 13 H9 2.6410 3.7680 -1.2910 H 1 MOL1 0.379900 21 | @BOND 22 | 1 1 2 1 23 | 2 1 5 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 3 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 4 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | 12 4 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/BAM_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BAM 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0170 0.0970 -0.4400 C.3 1 MOL1 -0.068300 9 | 2 C2 1.2090 1.5170 -0.9420 C.3 1 MOL1 0.045540 10 | 3 C3 2.5800 1.7550 -1.5490 C.3 1 MOL1 0.297520 11 | 4 N1 2.6810 3.1110 -2.0690 N.3 1 MOL1 -0.963240 12 | 5 H1 1.1230 -0.6300 -1.2570 H 1 MOL1 0.014560 13 | 6 H2 1.7590 -0.1610 0.3270 H 1 MOL1 0.014560 14 | 7 H3 0.0230 -0.0440 -0.0000 H 1 MOL1 0.014560 15 | 8 H4 1.0600 2.2260 -0.1120 H 1 MOL1 -0.007060 16 | 9 H5 0.4510 1.7690 -1.6960 H 1 MOL1 -0.007060 17 | 10 H6 3.3530 1.4940 -0.7990 H 1 MOL1 -0.023240 18 | 11 H7 2.7240 1.0600 -2.3900 H 1 MOL1 -0.023240 19 | 12 H8 3.5990 3.2510 -2.4840 H 1 MOL1 0.352660 20 | 13 H9 2.6410 3.7680 -1.2910 H 1 MOL1 0.352660 21 | @BOND 22 | 1 1 2 1 23 | 2 1 5 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 3 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 4 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | 12 4 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/BUT_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BUT 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.3970 -1.0360 -0.1160 C.3 1 MOL1 -0.200900 9 | 2 C2 -0.5810 -2.0200 0.5050 C.3 1 MOL1 0.144500 10 | 3 C3 -1.9340 -2.0260 -0.1880 C.3 1 MOL1 -0.050000 11 | 4 C4 -2.9130 -3.0020 0.4230 C.3 1 MOL1 0.150200 12 | 5 O1 -4.1220 -2.9170 -0.3000 O.3 1 MOL1 -0.539100 13 | 6 H1 0.0090 -0.0100 -0.0710 H 1 MOL1 0.043300 14 | 7 H2 1.3650 -1.0490 0.3990 H 1 MOL1 0.043300 15 | 8 H3 0.5790 -1.2720 -1.1730 H 1 MOL1 0.043300 16 | 9 H4 -0.1510 -3.0330 0.4760 H 1 MOL1 -0.017400 17 | 10 H5 -0.7170 -1.7800 1.5700 H 1 MOL1 -0.017400 18 | 11 H6 -2.3810 -1.0220 -0.1560 H 1 MOL1 0.021400 19 | 12 H7 -1.8140 -2.2770 -1.2520 H 1 MOL1 0.021400 20 | 13 H8 -2.4910 -4.0230 0.3850 H 1 MOL1 0.009800 21 | 14 H9 -3.0630 -2.7570 1.4910 H 1 MOL1 0.009800 22 | 15 H10 -4.7450 -3.5380 0.0890 H 1 MOL1 0.337900 23 | @BOND 24 | 1 1 2 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 3 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 3 4 1 32 | 9 3 11 1 33 | 10 3 12 1 34 | 11 4 5 1 35 | 12 4 13 1 36 | 13 4 14 1 37 | 14 5 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/BUT_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BUT 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.3970 -1.0360 -0.1160 C.3 1 MOL1 -0.194700 9 | 2 C2 -0.5810 -2.0200 0.5050 C.3 1 MOL1 0.160700 10 | 3 C3 -1.9340 -2.0260 -0.1880 C.3 1 MOL1 -0.042800 11 | 4 C4 -2.9130 -3.0020 0.4230 C.3 1 MOL1 0.188100 12 | 5 O1 -4.1220 -2.9170 -0.3000 O.3 1 MOL1 -0.649200 13 | 6 H1 0.0090 -0.0100 -0.0710 H 1 MOL1 0.041100 14 | 7 H2 1.3650 -1.0490 0.3990 H 1 MOL1 0.041100 15 | 8 H3 0.5790 -1.2720 -1.1730 H 1 MOL1 0.041100 16 | 9 H4 -0.1510 -3.0330 0.4760 H 1 MOL1 -0.022700 17 | 10 H5 -0.7170 -1.7800 1.5700 H 1 MOL1 -0.022700 18 | 11 H6 -2.3810 -1.0220 -0.1560 H 1 MOL1 0.018500 19 | 12 H7 -1.8140 -2.2770 -1.2520 H 1 MOL1 0.018500 20 | 13 H8 -2.4910 -4.0230 0.3850 H 1 MOL1 0.015800 21 | 14 H9 -3.0630 -2.7570 1.4910 H 1 MOL1 0.015800 22 | 15 H10 -4.7450 -3.5380 0.0890 H 1 MOL1 0.391300 23 | @BOND 24 | 1 1 2 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 3 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 3 4 1 32 | 9 3 11 1 33 | 10 3 12 1 34 | 11 4 5 1 35 | 12 4 13 1 36 | 13 4 14 1 37 | 14 5 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/BUT_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | BUT 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.3970 -1.0360 -0.1160 C.3 1 MOL1 -0.197180 9 | 2 C2 -0.5810 -2.0200 0.5050 C.3 1 MOL1 0.154220 10 | 3 C3 -1.9340 -2.0260 -0.1880 C.3 1 MOL1 -0.045680 11 | 4 C4 -2.9130 -3.0020 0.4230 C.3 1 MOL1 0.172940 12 | 5 O1 -4.1220 -2.9170 -0.3000 O.3 1 MOL1 -0.605160 13 | 6 H1 0.0090 -0.0100 -0.0710 H 1 MOL1 0.041980 14 | 7 H2 1.3650 -1.0490 0.3990 H 1 MOL1 0.041980 15 | 8 H3 0.5790 -1.2720 -1.1730 H 1 MOL1 0.041980 16 | 9 H4 -0.1510 -3.0330 0.4760 H 1 MOL1 -0.020580 17 | 10 H5 -0.7170 -1.7800 1.5700 H 1 MOL1 -0.020580 18 | 11 H6 -2.3810 -1.0220 -0.1560 H 1 MOL1 0.019660 19 | 12 H7 -1.8140 -2.2770 -1.2520 H 1 MOL1 0.019660 20 | 13 H8 -2.4910 -4.0230 0.3850 H 1 MOL1 0.013400 21 | 14 H9 -3.0630 -2.7570 1.4910 H 1 MOL1 0.013400 22 | 15 H10 -4.7450 -3.5380 0.0890 H 1 MOL1 0.369940 23 | @BOND 24 | 1 1 2 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 3 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 3 4 1 32 | 9 3 11 1 33 | 10 3 12 1 34 | 11 4 5 1 35 | 12 4 13 1 36 | 13 4 14 1 37 | 14 5 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C01_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C01 3 | 13 13 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.9480 -0.1920 0.8200 C.3 1 C01 -0.000400 10 | 2 C2 0.2390 0.7470 0.9960 C.3 1 C01 -0.000400 11 | 3 C3 -0.9370 -0.3990 -0.6860 C.3 1 C01 0.160200 12 | 4 C4 1.2140 0.1810 -0.0250 C.3 1 C01 0.160200 13 | 5 O1 0.4240 -0.3330 -1.0870 O.3 1 C01 -0.468700 14 | 6 H1 -0.7590 -1.1420 1.3380 H 1 C01 0.008600 15 | 7 H2 -1.8950 0.2160 1.1890 H 1 C01 0.008600 16 | 8 H3 -0.0460 1.7730 0.7250 H 1 C01 0.008600 17 | 9 H4 0.6450 0.7630 2.0130 H 1 C01 0.008600 18 | 10 H5 -1.3510 -1.3680 -0.9930 H 1 C01 0.028700 19 | 11 H6 -1.5130 0.3910 -1.1970 H 1 C01 0.028700 20 | 12 H7 1.9050 0.9330 -0.4270 H 1 C01 0.028700 21 | 13 H8 1.8170 -0.6300 0.4150 H 1 C01 0.028700 22 | @BOND 23 | 1 1 2 1 24 | 2 1 3 1 25 | 3 1 6 1 26 | 4 1 7 1 27 | 5 2 4 1 28 | 6 2 8 1 29 | 7 2 9 1 30 | 8 3 5 1 31 | 9 3 10 1 32 | 10 3 11 1 33 | 11 4 5 1 34 | 12 4 12 1 35 | 13 4 13 1 36 | @SUBSTRUCTURE 37 | 1 C01 1 TEMP 0 **** **** 0 ROOT 38 | -------------------------------------------------------------------------------- /Studies/Charges/C01_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C01 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.9480 -0.1920 0.8200 C.3 1 C011 0.003700 9 | 2 C2 0.2390 0.7470 0.9960 C.3 1 C011 0.003700 10 | 3 C3 -0.9370 -0.3990 -0.6860 C.3 1 C011 0.096800 11 | 4 C4 1.2140 0.1810 -0.0250 C.3 1 C011 0.096800 12 | 5 O1 0.4240 -0.3330 -1.0870 O.3 1 C011 -0.391000 13 | 6 H1 -0.7590 -1.1420 1.3380 H 1 C011 0.011100 14 | 7 H2 -1.8950 0.2160 1.1890 H 1 C011 0.011100 15 | 8 H3 -0.0460 1.7730 0.7250 H 1 C011 0.011100 16 | 9 H4 0.6450 0.7630 2.0130 H 1 C011 0.011100 17 | 10 H5 -1.3510 -1.3680 -0.9930 H 1 C011 0.036400 18 | 11 H6 -1.5130 0.3910 -1.1970 H 1 C011 0.036400 19 | 12 H7 1.9050 0.9330 -0.4270 H 1 C011 0.036400 20 | 13 H8 1.8170 -0.6300 0.4150 H 1 C011 0.036400 21 | @BOND 22 | 1 1 2 1 23 | 2 1 3 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 4 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 5 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 5 1 33 | 12 4 12 1 34 | 13 4 13 1 35 | -------------------------------------------------------------------------------- /Studies/Charges/C01_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C01 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.9480 -0.1920 0.8200 C.3 1 C011 0.016000 9 | 2 C2 0.2390 0.7470 0.9960 C.3 1 C011 0.016000 10 | 3 C3 -0.9370 -0.3990 -0.6860 C.3 1 C011 0.127800 11 | 4 C4 1.2140 0.1810 -0.0250 C.3 1 C011 0.127800 12 | 5 O1 0.4240 -0.3330 -1.0870 O.3 1 C011 -0.479700 13 | 6 H1 -0.7590 -1.1420 1.3380 H 1 C011 0.012700 14 | 7 H2 -1.8950 0.2160 1.1890 H 1 C011 0.012700 15 | 8 H3 -0.0460 1.7730 0.7250 H 1 C011 0.012700 16 | 9 H4 0.6450 0.7630 2.0130 H 1 C011 0.012700 17 | 10 H5 -1.3510 -1.3680 -0.9930 H 1 C011 0.035300 18 | 11 H6 -1.5130 0.3910 -1.1970 H 1 C011 0.035300 19 | 12 H7 1.9050 0.9330 -0.4270 H 1 C011 0.035300 20 | 13 H8 1.8170 -0.6300 0.4150 H 1 C011 0.035300 21 | @BOND 22 | 1 1 2 1 23 | 2 1 3 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 4 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 5 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 5 1 33 | 12 4 12 1 34 | 13 4 13 1 35 | -------------------------------------------------------------------------------- /Studies/Charges/C01_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C01 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.9480 -0.1920 0.8200 C.3 1 C011 0.011080 9 | 2 C2 0.2390 0.7470 0.9960 C.3 1 C011 0.011080 10 | 3 C3 -0.9370 -0.3990 -0.6860 C.3 1 C011 0.115400 11 | 4 C4 1.2140 0.1810 -0.0250 C.3 1 C011 0.115400 12 | 5 O1 0.4240 -0.3330 -1.0870 O.3 1 C011 -0.444220 13 | 6 H1 -0.7590 -1.1420 1.3380 H 1 C011 0.012060 14 | 7 H2 -1.8950 0.2160 1.1890 H 1 C011 0.012060 15 | 8 H3 -0.0460 1.7730 0.7250 H 1 C011 0.012060 16 | 9 H4 0.6450 0.7630 2.0130 H 1 C011 0.012060 17 | 10 H5 -1.3510 -1.3680 -0.9930 H 1 C011 0.035740 18 | 11 H6 -1.5130 0.3910 -1.1970 H 1 C011 0.035740 19 | 12 H7 1.9050 0.9330 -0.4270 H 1 C011 0.035740 20 | 13 H8 1.8170 -0.6300 0.4150 H 1 C011 0.035740 21 | @BOND 22 | 1 1 2 1 23 | 2 1 3 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 4 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 5 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 5 1 33 | 12 4 12 1 34 | 13 4 13 1 35 | -------------------------------------------------------------------------------- /Studies/Charges/C02_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C02 3 | 12 11 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 2.7900 -1.4380 0.2390 C.2 1 C02 0.346800 10 | 2 C2 0.8920 -0.0880 -0.4960 C.3 1 C02 -0.277700 11 | 3 C3 0.8430 -2.5550 -0.6760 C.3 1 C02 -0.277700 12 | 4 N1 1.5420 -1.3540 -0.2960 N.am 1 C02 0.003400 13 | 5 O1 3.4020 -2.4650 0.4380 O.2 1 C02 -0.533400 14 | 6 H1 3.1980 -0.4330 0.4800 H 1 C02 0.073000 15 | 7 H2 0.6570 0.0780 -1.5570 H 1 C02 0.110900 16 | 8 H3 1.5520 0.7180 -0.1580 H 1 C02 0.110900 17 | 9 H4 -0.0480 -0.0270 0.0720 H 1 C02 0.110900 18 | 10 H5 -0.0980 -2.6550 -0.1170 H 1 C02 0.110900 19 | 11 H6 1.4940 -3.4030 -0.4480 H 1 C02 0.110900 20 | 12 H7 0.6080 -2.5500 -1.7500 H 1 C02 0.110900 21 | @BOND 22 | 1 1 4 am 23 | 2 1 5 2 24 | 3 1 6 1 25 | 4 2 4 1 26 | 5 2 7 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 4 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 3 12 1 33 | @SUBSTRUCTURE 34 | 1 C02 1 TEMP 0 **** **** 0 ROOT 35 | -------------------------------------------------------------------------------- /Studies/Charges/C02_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C02 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.7900 -1.4380 0.2390 C.2 1 C021 0.256600 9 | 2 C2 0.8920 -0.0880 -0.4960 C.3 1 C021 -0.337500 10 | 3 C3 0.8430 -2.5550 -0.6760 C.3 1 C021 -0.337500 11 | 4 N1 1.5420 -1.3540 -0.2960 N.am 1 C021 0.119600 12 | 5 O1 3.4020 -2.4650 0.4380 O.2 1 C021 -0.488500 13 | 6 H1 3.1980 -0.4330 0.4800 H 1 C021 0.057700 14 | 7 H2 0.6570 0.0780 -1.5570 H 1 C021 0.121600 15 | 8 H3 1.5520 0.7180 -0.1580 H 1 C021 0.121600 16 | 9 H4 -0.0480 -0.0270 0.0720 H 1 C021 0.121600 17 | 10 H5 -0.0980 -2.6550 -0.1170 H 1 C021 0.121600 18 | 11 H6 1.4940 -3.4030 -0.4480 H 1 C021 0.121600 19 | 12 H7 0.6080 -2.5500 -1.7500 H 1 C021 0.121600 20 | @BOND 21 | 1 1 4 am 22 | 2 1 5 2 23 | 3 1 6 1 24 | 4 2 4 1 25 | 5 2 7 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 3 4 1 29 | 9 3 10 1 30 | 10 3 11 1 31 | 11 3 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C02_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C02 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.7900 -1.4380 0.2390 C.2 1 C021 0.295800 9 | 2 C2 0.8920 -0.0880 -0.4960 C.3 1 C021 -0.355100 10 | 3 C3 0.8430 -2.5550 -0.6760 C.3 1 C021 -0.355100 11 | 4 N1 1.5420 -1.3540 -0.2960 N.am 1 C021 0.126500 12 | 5 O1 3.4020 -2.4650 0.4380 O.2 1 C021 -0.600600 13 | 6 H1 3.1980 -0.4330 0.4800 H 1 C021 0.073500 14 | 7 H2 0.6570 0.0780 -1.5570 H 1 C021 0.135800 15 | 8 H3 1.5520 0.7180 -0.1580 H 1 C021 0.135800 16 | 9 H4 -0.0480 -0.0270 0.0720 H 1 C021 0.135800 17 | 10 H5 -0.0980 -2.6550 -0.1170 H 1 C021 0.135800 18 | 11 H6 1.4940 -3.4030 -0.4480 H 1 C021 0.135800 19 | 12 H7 0.6080 -2.5500 -1.7500 H 1 C021 0.135800 20 | @BOND 21 | 1 1 4 am 22 | 2 1 5 2 23 | 3 1 6 1 24 | 4 2 4 1 25 | 5 2 7 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 3 4 1 29 | 9 3 10 1 30 | 10 3 11 1 31 | 11 3 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C02_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C02 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.7900 -1.4380 0.2390 C.2 1 C021 0.280120 9 | 2 C2 0.8920 -0.0880 -0.4960 C.3 1 C021 -0.348060 10 | 3 C3 0.8430 -2.5550 -0.6760 C.3 1 C021 -0.348060 11 | 4 N1 1.5420 -1.3540 -0.2960 N.am 1 C021 0.123740 12 | 5 O1 3.4020 -2.4650 0.4380 O.2 1 C021 -0.555760 13 | 6 H1 3.1980 -0.4330 0.4800 H 1 C021 0.067180 14 | 7 H2 0.6570 0.0780 -1.5570 H 1 C021 0.130120 15 | 8 H3 1.5520 0.7180 -0.1580 H 1 C021 0.130120 16 | 9 H4 -0.0480 -0.0270 0.0720 H 1 C021 0.130120 17 | 10 H5 -0.0980 -2.6550 -0.1170 H 1 C021 0.130120 18 | 11 H6 1.4940 -3.4030 -0.4480 H 1 C021 0.130120 19 | 12 H7 0.6080 -2.5500 -1.7500 H 1 C021 0.130120 20 | @BOND 21 | 1 1 4 am 22 | 2 1 5 2 23 | 3 1 6 1 24 | 4 2 4 1 25 | 5 2 7 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 3 4 1 29 | 9 3 10 1 30 | 10 3 11 1 31 | 11 3 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C03_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C03 3 | 9 8 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 2.0750 -1.2230 2.3870 C.1 1 C03 0.280800 10 | 2 C2 0.5970 -0.7600 0.4420 C.3 1 C03 -0.108200 11 | 3 C3 1.2000 -0.2450 1.7460 C.3 1 C03 0.083900 12 | 4 N1 2.7650 -2.0080 2.8820 N.1 1 C03 -0.466700 13 | 5 H1 1.3800 -1.0020 -0.2840 H 1 C03 0.044600 14 | 6 H2 0.0010 -1.6630 0.6150 H 1 C03 0.044600 15 | 7 H3 -0.0540 0.0050 0.0060 H 1 C03 0.044600 16 | 8 H4 0.4110 0.0210 2.4620 H 1 C03 0.038200 17 | 9 H5 1.7860 0.6670 1.5710 H 1 C03 0.038200 18 | @BOND 19 | 1 1 3 1 20 | 2 1 4 3 21 | 3 2 3 1 22 | 4 2 5 1 23 | 5 2 6 1 24 | 6 2 7 1 25 | 7 3 8 1 26 | 8 3 9 1 27 | @SUBSTRUCTURE 28 | 1 C03 1 TEMP 0 **** **** 0 ROOT 29 | -------------------------------------------------------------------------------- /Studies/Charges/C03_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | mol1_conf1 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0750 -1.2230 2.3870 C.1 1 MOL1 0.266400 9 | 2 C2 0.5970 -0.7600 0.4420 C.3 1 MOL1 -0.119300 10 | 3 C3 1.2000 -0.2450 1.7460 C.3 1 MOL1 0.065100 11 | 4 N1 2.7650 -2.0080 2.8820 N.1 1 MOL1 -0.451300 12 | 5 H1 1.3800 -1.0020 -0.2840 H 1 MOL1 0.049900 13 | 6 H2 0.0010 -1.6630 0.6150 H 1 MOL1 0.049900 14 | 7 H3 -0.0540 0.0050 0.0060 H 1 MOL1 0.049900 15 | 8 H4 0.4110 0.0210 2.4620 H 1 MOL1 0.044700 16 | 9 H5 1.7860 0.6670 1.5710 H 1 MOL1 0.044700 17 | @BOND 18 | 1 1 3 1 19 | 2 1 4 3 20 | 3 2 3 1 21 | 4 2 5 1 22 | 5 2 6 1 23 | 6 2 7 1 24 | 7 3 8 1 25 | 8 3 9 1 26 | -------------------------------------------------------------------------------- /Studies/Charges/C03_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | mol1_conf1 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0750 -1.2230 2.3870 C.1 1 MOL1 0.334100 9 | 2 C2 0.5970 -0.7600 0.4420 C.3 1 MOL1 -0.103800 10 | 3 C3 1.2000 -0.2450 1.7460 C.3 1 MOL1 0.041500 11 | 4 N1 2.7650 -2.0080 2.8820 N.1 1 MOL1 -0.568900 12 | 5 H1 1.3800 -1.0020 -0.2840 H 1 MOL1 0.050400 13 | 6 H2 0.0010 -1.6630 0.6150 H 1 MOL1 0.050400 14 | 7 H3 -0.0540 0.0050 0.0060 H 1 MOL1 0.050400 15 | 8 H4 0.4110 0.0210 2.4620 H 1 MOL1 0.072800 16 | 9 H5 1.7860 0.6670 1.5710 H 1 MOL1 0.072800 17 | @BOND 18 | 1 1 3 1 19 | 2 1 4 3 20 | 3 2 3 1 21 | 4 2 5 1 22 | 5 2 6 1 23 | 6 2 7 1 24 | 7 3 8 1 25 | 8 3 9 1 26 | -------------------------------------------------------------------------------- /Studies/Charges/C03_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | mol1_conf1 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0750 -1.2230 2.3870 C.1 1 MOL1 0.307020 9 | 2 C2 0.5970 -0.7600 0.4420 C.3 1 MOL1 -0.110000 10 | 3 C3 1.2000 -0.2450 1.7460 C.3 1 MOL1 0.050940 11 | 4 N1 2.7650 -2.0080 2.8820 N.1 1 MOL1 -0.521860 12 | 5 H1 1.3800 -1.0020 -0.2840 H 1 MOL1 0.050200 13 | 6 H2 0.0010 -1.6630 0.6150 H 1 MOL1 0.050200 14 | 7 H3 -0.0540 0.0050 0.0060 H 1 MOL1 0.050200 15 | 8 H4 0.4110 0.0210 2.4620 H 1 MOL1 0.061560 16 | 9 H5 1.7860 0.6670 1.5710 H 1 MOL1 0.061560 17 | @BOND 18 | 1 1 3 1 19 | 2 1 4 3 20 | 3 2 3 1 21 | 4 2 5 1 22 | 5 2 6 1 23 | 6 2 7 1 24 | 7 3 8 1 25 | 8 3 9 1 26 | -------------------------------------------------------------------------------- /Studies/Charges/C04_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C04 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.6510 -0.7370 0.4880 C.3 1 C041 0.223900 9 | 2 N1 -1.8790 -0.6960 -0.2900 N.3 1 C041 -0.859700 10 | 3 H1 -0.3540 -1.7270 0.8790 H 1 C041 -0.003300 11 | 4 H2 -0.7390 -0.0580 1.3460 H 1 C041 -0.003300 12 | 5 H3 0.1800 -0.3640 -0.1240 H 1 C041 -0.003300 13 | 6 H4 -2.6430 -1.0650 0.2740 H 1 C041 0.322900 14 | 7 H5 -1.8020 -1.3440 -1.0710 H 1 C041 0.322900 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C04_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C04 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.6510 -0.7370 0.4880 C.3 1 C041 0.326300 9 | 2 N1 -1.8790 -0.6960 -0.2900 N.3 1 C041 -1.051100 10 | 3 H1 -0.3540 -1.7270 0.8790 H 1 C041 -0.017400 11 | 4 H2 -0.7390 -0.0580 1.3460 H 1 C041 -0.017400 12 | 5 H3 0.1800 -0.3640 -0.1240 H 1 C041 -0.017400 13 | 6 H4 -2.6430 -1.0650 0.2740 H 1 C041 0.388400 14 | 7 H5 -1.8020 -1.3440 -1.0710 H 1 C041 0.388400 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C04_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C04 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.6510 -0.7370 0.4880 C.3 1 C041 0.285340 9 | 2 N1 -1.8790 -0.6960 -0.2900 N.3 1 C041 -0.974540 10 | 3 H1 -0.3540 -1.7270 0.8790 H 1 C041 -0.011760 11 | 4 H2 -0.7390 -0.0580 1.3460 H 1 C041 -0.011760 12 | 5 H3 0.1800 -0.3640 -0.1240 H 1 C041 -0.011760 13 | 6 H4 -2.6430 -1.0650 0.2740 H 1 C041 0.362200 14 | 7 H5 -1.8020 -1.3440 -1.0710 H 1 C041 0.362200 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C05_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C05 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.3970 -1.0360 -0.1160 C.3 1 C051 -0.201000 9 | 2 C2 -0.5810 -2.0200 0.5050 C.3 1 C051 0.145000 10 | 3 C3 -1.9340 -2.0260 -0.1880 C.3 1 C051 -0.050100 11 | 4 C4 -2.9130 -3.0020 0.4230 C.3 1 C051 0.151000 12 | 5 O1 -4.1220 -2.9170 -0.3000 O.3 1 C051 -0.539300 13 | 6 H1 0.0090 -0.0100 -0.0710 H 1 C051 0.043300 14 | 7 H2 1.3650 -1.0490 0.3990 H 1 C051 0.043300 15 | 8 H3 0.5790 -1.2720 -1.1730 H 1 C051 0.043300 16 | 9 H4 -0.1510 -3.0330 0.4760 H 1 C051 -0.017600 17 | 10 H5 -0.7170 -1.7800 1.5700 H 1 C051 -0.017600 18 | 11 H6 -2.3810 -1.0220 -0.1560 H 1 C051 0.021300 19 | 12 H7 -1.8140 -2.2770 -1.2520 H 1 C051 0.021300 20 | 13 H8 -2.4910 -4.0230 0.3850 H 1 C051 0.009500 21 | 14 H9 -3.0630 -2.7570 1.4910 H 1 C051 0.009500 22 | 15 H10 -4.7450 -3.5380 0.0890 H 1 C051 0.337900 23 | @BOND 24 | 1 1 2 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 3 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 3 4 1 32 | 9 3 11 1 33 | 10 3 12 1 34 | 11 4 5 1 35 | 12 4 13 1 36 | 13 4 14 1 37 | 14 5 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C05_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C05 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.3970 -1.0360 -0.1160 C.3 1 C051 -0.194900 9 | 2 C2 -0.5810 -2.0200 0.5050 C.3 1 C051 0.161200 10 | 3 C3 -1.9340 -2.0260 -0.1880 C.3 1 C051 -0.042900 11 | 4 C4 -2.9130 -3.0020 0.4230 C.3 1 C051 0.188700 12 | 5 O1 -4.1220 -2.9170 -0.3000 O.3 1 C051 -0.649300 13 | 6 H1 0.0090 -0.0100 -0.0710 H 1 C051 0.041100 14 | 7 H2 1.3650 -1.0490 0.3990 H 1 C051 0.041100 15 | 8 H3 0.5790 -1.2720 -1.1730 H 1 C051 0.041100 16 | 9 H4 -0.1510 -3.0330 0.4760 H 1 C051 -0.022800 17 | 10 H5 -0.7170 -1.7800 1.5700 H 1 C051 -0.022800 18 | 11 H6 -2.3810 -1.0220 -0.1560 H 1 C051 0.018500 19 | 12 H7 -1.8140 -2.2770 -1.2520 H 1 C051 0.018500 20 | 13 H8 -2.4910 -4.0230 0.3850 H 1 C051 0.015600 21 | 14 H9 -3.0630 -2.7570 1.4910 H 1 C051 0.015600 22 | 15 H10 -4.7450 -3.5380 0.0890 H 1 C051 0.391300 23 | @BOND 24 | 1 1 2 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 3 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 3 4 1 32 | 9 3 11 1 33 | 10 3 12 1 34 | 11 4 5 1 35 | 12 4 13 1 36 | 13 4 14 1 37 | 14 5 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C05_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C05 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.3970 -1.0360 -0.1160 C.3 1 C051 -0.197340 9 | 2 C2 -0.5810 -2.0200 0.5050 C.3 1 C051 0.154720 10 | 3 C3 -1.9340 -2.0260 -0.1880 C.3 1 C051 -0.045780 11 | 4 C4 -2.9130 -3.0020 0.4230 C.3 1 C051 0.173620 12 | 5 O1 -4.1220 -2.9170 -0.3000 O.3 1 C051 -0.605300 13 | 6 H1 0.0090 -0.0100 -0.0710 H 1 C051 0.041980 14 | 7 H2 1.3650 -1.0490 0.3990 H 1 C051 0.041980 15 | 8 H3 0.5790 -1.2720 -1.1730 H 1 C051 0.041980 16 | 9 H4 -0.1510 -3.0330 0.4760 H 1 C051 -0.020720 17 | 10 H5 -0.7170 -1.7800 1.5700 H 1 C051 -0.020720 18 | 11 H6 -2.3810 -1.0220 -0.1560 H 1 C051 0.019620 19 | 12 H7 -1.8140 -2.2770 -1.2520 H 1 C051 0.019620 20 | 13 H8 -2.4910 -4.0230 0.3850 H 1 C051 0.013160 21 | 14 H9 -3.0630 -2.7570 1.4910 H 1 C051 0.013160 22 | 15 H10 -4.7450 -3.5380 0.0890 H 1 C051 0.369940 23 | @BOND 24 | 1 1 2 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 3 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 3 4 1 32 | 9 3 11 1 33 | 10 3 12 1 34 | 11 4 5 1 35 | 12 4 13 1 36 | 13 4 14 1 37 | 14 5 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C06_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C06 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0720 0.0330 0.2010 C.3 1 C061 -0.329700 9 | 2 C2 2.8230 1.0340 1.7120 C.3 1 C061 -0.329700 10 | 3 C3 1.3450 0.9030 1.4150 C.3 1 C061 0.530800 11 | 4 O1 0.8650 2.2230 1.2150 O.3 1 C061 -0.651900 12 | 5 H1 1.5530 0.4630 -0.6870 H 1 C061 0.080000 13 | 6 H2 1.4490 -0.9870 0.3460 H 1 C061 0.080000 14 | 7 H3 -0.0060 -0.0380 0.0040 H 1 C061 0.080000 15 | 8 H4 3.3420 1.4720 0.8500 H 1 C061 0.080000 16 | 9 H5 3.2680 0.0560 1.9310 H 1 C061 0.080000 17 | 10 H6 2.9790 1.6920 2.5740 H 1 C061 0.080000 18 | 11 H7 0.8480 0.4510 2.2940 H 1 C061 -0.072300 19 | 12 H8 -0.0710 2.1610 1.0000 H 1 C061 0.372900 20 | @BOND 21 | 1 1 3 1 22 | 2 1 5 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 3 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 2 10 1 29 | 9 3 4 1 30 | 10 3 11 1 31 | 11 4 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C06_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C06 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0720 0.0330 0.2010 C.3 1 C061 -0.412900 9 | 2 C2 2.8230 1.0340 1.7120 C.3 1 C061 -0.412900 10 | 3 C3 1.3450 0.9030 1.4150 C.3 1 C061 0.586500 11 | 4 O1 0.8650 2.2230 1.2150 O.3 1 C061 -0.755300 12 | 5 H1 1.5530 0.4630 -0.6870 H 1 C061 0.102800 13 | 6 H2 1.4490 -0.9870 0.3460 H 1 C061 0.102800 14 | 7 H3 -0.0060 -0.0380 0.0040 H 1 C061 0.102800 15 | 8 H4 3.3420 1.4720 0.8500 H 1 C061 0.102800 16 | 9 H5 3.2680 0.0560 1.9310 H 1 C061 0.102800 17 | 10 H6 2.9790 1.6920 2.5740 H 1 C061 0.102800 18 | 11 H7 0.8480 0.4510 2.2940 H 1 C061 -0.049700 19 | 12 H8 -0.0710 2.1610 1.0000 H 1 C061 0.427700 20 | @BOND 21 | 1 1 3 1 22 | 2 1 5 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 3 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 2 10 1 29 | 9 3 4 1 30 | 10 3 11 1 31 | 11 4 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C06_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C06 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0720 0.0330 0.2010 C.3 1 C061 -0.379620 9 | 2 C2 2.8230 1.0340 1.7120 C.3 1 C061 -0.379620 10 | 3 C3 1.3450 0.9030 1.4150 C.3 1 C061 0.564220 11 | 4 O1 0.8650 2.2230 1.2150 O.3 1 C061 -0.713940 12 | 5 H1 1.5530 0.4630 -0.6870 H 1 C061 0.093680 13 | 6 H2 1.4490 -0.9870 0.3460 H 1 C061 0.093680 14 | 7 H3 -0.0060 -0.0380 0.0040 H 1 C061 0.093680 15 | 8 H4 3.3420 1.4720 0.8500 H 1 C061 0.093680 16 | 9 H5 3.2680 0.0560 1.9310 H 1 C061 0.093680 17 | 10 H6 2.9790 1.6920 2.5740 H 1 C061 0.093680 18 | 11 H7 0.8480 0.4510 2.2940 H 1 C061 -0.058740 19 | 12 H8 -0.0710 2.1610 1.0000 H 1 C061 0.405780 20 | @BOND 21 | 1 1 3 1 22 | 2 1 5 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 3 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 2 10 1 29 | 9 3 4 1 30 | 10 3 11 1 31 | 11 4 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C08_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C08 3 | 10 9 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.9010 0.4430 0.4510 C.3 1 C08 0.178300 10 | 2 C2 -2.1380 -0.2020 -0.1140 C.3 1 C08 0.178300 11 | 3 O1 -0.9500 0.3490 1.8560 O.3 1 C08 -0.614000 12 | 4 O2 -2.0130 -1.5990 0.0200 O.3 1 C08 -0.614000 13 | 5 H1 -0.8660 1.4950 0.1130 H 1 C08 0.020600 14 | 6 H2 -0.0230 -0.0770 0.0320 H 1 C08 0.020600 15 | 7 H3 -2.2420 0.0990 -1.1720 H 1 C08 0.020600 16 | 8 H4 -3.0090 0.1890 0.4380 H 1 C08 0.020600 17 | 9 H5 -0.0840 0.5870 2.1990 H 1 C08 0.394600 18 | 10 H6 -2.8710 -1.9920 -0.1630 H 1 C08 0.394600 19 | @BOND 20 | 1 1 2 1 21 | 2 1 3 1 22 | 3 1 5 1 23 | 4 1 6 1 24 | 5 2 4 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 4 10 1 29 | @SUBSTRUCTURE 30 | 1 C08 1 TEMP 0 **** **** 0 ROOT 31 | -------------------------------------------------------------------------------- /Studies/Charges/C08_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C08 3 | 10 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.9010 0.4430 0.4510 C.3 1 C081 0.100500 9 | 2 C2 -2.1380 -0.2020 -0.1140 C.3 1 C081 0.100500 10 | 3 O1 -0.9500 0.3490 1.8560 O.3 1 C081 -0.533400 11 | 4 O2 -2.0130 -1.5990 0.0200 O.3 1 C081 -0.533400 12 | 5 H1 -0.8660 1.4950 0.1130 H 1 C081 0.039900 13 | 6 H2 -0.0230 -0.0770 0.0320 H 1 C081 0.039900 14 | 7 H3 -2.2420 0.0990 -1.1720 H 1 C081 0.039900 15 | 8 H4 -3.0090 0.1890 0.4380 H 1 C081 0.039900 16 | 9 H5 -0.0840 0.5870 2.1990 H 1 C081 0.353000 17 | 10 H6 -2.8710 -1.9920 -0.1630 H 1 C081 0.353000 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 1 21 | 3 1 5 1 22 | 4 1 6 1 23 | 5 2 4 1 24 | 6 2 7 1 25 | 7 2 8 1 26 | 8 3 9 1 27 | 9 4 10 1 28 | -------------------------------------------------------------------------------- /Studies/Charges/C08_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C08 3 | 10 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.9010 0.4430 0.4510 C.3 1 C081 0.119000 9 | 2 C2 -2.1380 -0.2020 -0.1140 C.3 1 C081 0.119000 10 | 3 O1 -0.9500 0.3490 1.8560 O.3 1 C081 -0.644400 11 | 4 O2 -2.0130 -1.5990 0.0200 O.3 1 C081 -0.644400 12 | 5 H1 -0.8660 1.4950 0.1130 H 1 C081 0.053200 13 | 6 H2 -0.0230 -0.0770 0.0320 H 1 C081 0.053200 14 | 7 H3 -2.2420 0.0990 -1.1720 H 1 C081 0.053200 15 | 8 H4 -3.0090 0.1890 0.4380 H 1 C081 0.053200 16 | 9 H5 -0.0840 0.5870 2.1990 H 1 C081 0.419000 17 | 10 H6 -2.8710 -1.9920 -0.1630 H 1 C081 0.419000 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 1 21 | 3 1 5 1 22 | 4 1 6 1 23 | 5 2 4 1 24 | 6 2 7 1 25 | 7 2 8 1 26 | 8 3 9 1 27 | 9 4 10 1 28 | -------------------------------------------------------------------------------- /Studies/Charges/C08_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C08 3 | 10 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.9010 0.4430 0.4510 C.3 1 C081 0.111600 9 | 2 C2 -2.1380 -0.2020 -0.1140 C.3 1 C081 0.111600 10 | 3 O1 -0.9500 0.3490 1.8560 O.3 1 C081 -0.600000 11 | 4 O2 -2.0130 -1.5990 0.0200 O.3 1 C081 -0.600000 12 | 5 H1 -0.8660 1.4950 0.1130 H 1 C081 0.047880 13 | 6 H2 -0.0230 -0.0770 0.0320 H 1 C081 0.047880 14 | 7 H3 -2.2420 0.0990 -1.1720 H 1 C081 0.047880 15 | 8 H4 -3.0090 0.1890 0.4380 H 1 C081 0.047880 16 | 9 H5 -0.0840 0.5870 2.1990 H 1 C081 0.392600 17 | 10 H6 -2.8710 -1.9920 -0.1630 H 1 C081 0.392600 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 1 21 | 3 1 5 1 22 | 4 1 6 1 23 | 5 2 4 1 24 | 6 2 7 1 25 | 7 2 8 1 26 | 8 3 9 1 27 | 9 4 10 1 28 | -------------------------------------------------------------------------------- /Studies/Charges/C10_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C10 3 | 6 5 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 0.2070 0.6160 -0.1570 C.2 1 C10 0.661900 10 | 2 N1 -0.2030 -0.6330 0.1700 N.am 1 C10 -0.943700 11 | 3 O1 1.1280 1.2000 0.3620 O.2 1 C10 -0.566300 12 | 4 H1 -0.4110 1.0530 -0.9730 H 1 C10 0.011400 13 | 5 H2 0.2830 -1.1330 0.9000 H 1 C10 0.418300 14 | 6 H3 -0.9790 -1.0730 -0.2970 H 1 C10 0.418300 15 | @BOND 16 | 1 1 2 am 17 | 2 1 3 2 18 | 3 1 4 1 19 | 4 2 5 1 20 | 5 2 6 1 21 | @SUBSTRUCTURE 22 | 1 C10 1 TEMP 0 **** **** 0 ROOT 23 | -------------------------------------------------------------------------------- /Studies/Charges/C10_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C10 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.2070 0.6160 -0.1570 C.2 1 C101 0.586200 9 | 2 N1 -0.2030 -0.6330 0.1700 N.am 1 C101 -0.853600 10 | 3 O1 1.1280 1.2000 0.3620 O.2 1 C101 -0.514000 11 | 4 H1 -0.4110 1.0530 -0.9730 H 1 C101 -0.000200 12 | 5 H2 0.2830 -1.1330 0.9000 H 1 C101 0.390800 13 | 6 H3 -0.9790 -1.0730 -0.2970 H 1 C101 0.390800 14 | @BOND 15 | 1 1 2 am 16 | 2 1 3 2 17 | 3 1 4 1 18 | 4 2 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/C10_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C10 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.2070 0.6160 -0.1570 C.2 1 C101 0.598900 9 | 2 N1 -0.2030 -0.6330 0.1700 N.am 1 C101 -0.834600 10 | 3 O1 1.1280 1.2000 0.3620 O.2 1 C101 -0.629400 11 | 4 H1 -0.4110 1.0530 -0.9730 H 1 C101 0.033300 12 | 5 H2 0.2830 -1.1330 0.9000 H 1 C101 0.415800 13 | 6 H3 -0.9790 -1.0730 -0.2970 H 1 C101 0.415800 14 | @BOND 15 | 1 1 2 am 16 | 2 1 3 2 17 | 3 1 4 1 18 | 4 2 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/C10_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C10 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.2070 0.6160 -0.1570 C.2 1 C101 0.593820 9 | 2 N1 -0.2030 -0.6330 0.1700 N.am 1 C101 -0.842200 10 | 3 O1 1.1280 1.2000 0.3620 O.2 1 C101 -0.583240 11 | 4 H1 -0.4110 1.0530 -0.9730 H 1 C101 0.019900 12 | 5 H2 0.2830 -1.1330 0.9000 H 1 C101 0.405800 13 | 6 H3 -0.9790 -1.0730 -0.2970 H 1 C101 0.405800 14 | @BOND 15 | 1 1 2 am 16 | 2 1 3 2 17 | 3 1 4 1 18 | 4 2 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/C11_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C11 3 | 8 7 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.5880 -0.4560 -0.8180 C.2 1 C11 -0.347400 10 | 2 C2 -0.7480 -1.7770 -0.9020 C.2 1 C11 -0.185900 11 | 3 C3 -0.1440 -2.6720 0.0970 C.2 1 C11 0.496600 12 | 4 O1 -0.2470 -3.8740 0.0840 O.2 1 C11 -0.479200 13 | 5 H1 -1.0230 0.2290 -1.5430 H 1 C11 0.194400 14 | 6 H2 -0.0060 -0.0180 -0.0060 H 1 C11 0.194400 15 | 7 H3 -1.3210 -2.2510 -1.6970 H 1 C11 0.136600 16 | 8 H4 0.4350 -2.1460 0.8950 H 1 C11 -0.009600 17 | @BOND 18 | 1 1 2 2 19 | 2 1 5 1 20 | 3 1 6 1 21 | 4 2 3 1 22 | 5 2 7 1 23 | 6 3 4 2 24 | 7 3 8 1 25 | @SUBSTRUCTURE 26 | 1 C11 1 TEMP 0 **** **** 0 ROOT 27 | -------------------------------------------------------------------------------- /Studies/Charges/C11_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C11 3 | 8 7 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.5880 -0.4560 -0.8180 C.2 1 C111 -0.308600 9 | 2 C2 -0.7480 -1.7770 -0.9020 C.2 1 C111 -0.174200 10 | 3 C3 -0.1440 -2.6720 0.0970 C.2 1 C111 0.455600 11 | 4 O1 -0.2470 -3.8740 0.0840 O.2 1 C111 -0.434500 12 | 5 H1 -1.0230 0.2290 -1.5430 H 1 C111 0.174600 13 | 6 H2 -0.0060 -0.0180 -0.0060 H 1 C111 0.174600 14 | 7 H3 -1.3210 -2.2510 -1.6970 H 1 C111 0.132200 15 | 8 H4 0.4350 -2.1460 0.8950 H 1 C111 -0.019600 16 | @BOND 17 | 1 1 2 2 18 | 2 1 5 1 19 | 3 1 6 1 20 | 4 2 3 1 21 | 5 2 7 1 22 | 6 3 4 2 23 | 7 3 8 1 24 | -------------------------------------------------------------------------------- /Studies/Charges/C11_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C11 3 | 8 7 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.5880 -0.4560 -0.8180 C.2 1 C111 -0.301800 9 | 2 C2 -0.7480 -1.7770 -0.9020 C.2 1 C111 -0.192500 10 | 3 C3 -0.1440 -2.6720 0.0970 C.2 1 C111 0.489700 11 | 4 O1 -0.2470 -3.8740 0.0840 O.2 1 C111 -0.536400 12 | 5 H1 -1.0230 0.2290 -1.5430 H 1 C111 0.188500 13 | 6 H2 -0.0060 -0.0180 -0.0060 H 1 C111 0.188500 14 | 7 H3 -1.3210 -2.2510 -1.6970 H 1 C111 0.150100 15 | 8 H4 0.4350 -2.1460 0.8950 H 1 C111 0.013900 16 | @BOND 17 | 1 1 2 2 18 | 2 1 5 1 19 | 3 1 6 1 20 | 4 2 3 1 21 | 5 2 7 1 22 | 6 3 4 2 23 | 7 3 8 1 24 | -------------------------------------------------------------------------------- /Studies/Charges/C11_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C11 3 | 8 7 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.5880 -0.4560 -0.8180 C.2 1 C111 -0.304520 9 | 2 C2 -0.7480 -1.7770 -0.9020 C.2 1 C111 -0.185180 10 | 3 C3 -0.1440 -2.6720 0.0970 C.2 1 C111 0.476060 11 | 4 O1 -0.2470 -3.8740 0.0840 O.2 1 C111 -0.495640 12 | 5 H1 -1.0230 0.2290 -1.5430 H 1 C111 0.182940 13 | 6 H2 -0.0060 -0.0180 -0.0060 H 1 C111 0.182940 14 | 7 H3 -1.3210 -2.2510 -1.6970 H 1 C111 0.142940 15 | 8 H4 0.4350 -2.1460 0.8950 H 1 C111 0.000500 16 | @BOND 17 | 1 1 2 2 18 | 2 1 5 1 19 | 3 1 6 1 20 | 4 2 3 1 21 | 5 2 7 1 22 | 6 3 4 2 23 | 7 3 8 1 24 | -------------------------------------------------------------------------------- /Studies/Charges/C12_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C12 3 | 11 11 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 0.4000 0.1090 1.1400 C.3 1 C12 0.117200 10 | 2 C2 0.2340 1.1870 0.0920 C.3 1 C12 0.117200 11 | 3 C3 -0.3960 -0.8090 -0.7700 C.3 1 C12 0.307200 12 | 4 O1 0.4120 -1.0650 0.3530 O.3 1 C12 -0.441100 13 | 5 O2 -0.6530 0.5730 -0.8220 O.3 1 C12 -0.441100 14 | 6 H1 1.3400 0.1620 1.6980 H 1 C12 0.056400 15 | 7 H2 -0.4460 0.1090 1.8480 H 1 C12 0.056400 16 | 8 H3 -0.2310 2.1080 0.4600 H 1 C12 0.056400 17 | 9 H4 1.1980 1.4300 -0.3850 H 1 C12 0.056400 18 | 10 H5 0.1480 -1.1560 -1.6630 H 1 C12 0.057400 19 | 11 H6 -1.3660 -1.3300 -0.7010 H 1 C12 0.057400 20 | @BOND 21 | 1 1 2 1 22 | 2 1 4 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 5 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 3 4 1 29 | 9 3 5 1 30 | 10 3 10 1 31 | 11 3 11 1 32 | @SUBSTRUCTURE 33 | 1 C12 1 TEMP 0 **** **** 0 ROOT 34 | -------------------------------------------------------------------------------- /Studies/Charges/C12_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C12 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.4000 0.1090 1.1400 C.3 1 C121 0.047000 9 | 2 C2 0.2340 1.1870 0.0920 C.3 1 C121 0.047000 10 | 3 C3 -0.3960 -0.8090 -0.7700 C.3 1 C121 0.206800 11 | 4 O1 0.4120 -1.0650 0.3530 O.3 1 C121 -0.357900 12 | 5 O2 -0.6530 0.5730 -0.8220 O.3 1 C121 -0.357900 13 | 6 H1 1.3400 0.1620 1.6980 H 1 C121 0.069800 14 | 7 H2 -0.4460 0.1090 1.8480 H 1 C121 0.069800 15 | 8 H3 -0.2310 2.1080 0.4600 H 1 C121 0.069800 16 | 9 H4 1.1980 1.4300 -0.3850 H 1 C121 0.069800 17 | 10 H5 0.1480 -1.1560 -1.6630 H 1 C121 0.067900 18 | 11 H6 -1.3660 -1.3300 -0.7010 H 1 C121 0.067900 19 | @BOND 20 | 1 1 2 1 21 | 2 1 4 1 22 | 3 1 6 1 23 | 4 1 7 1 24 | 5 2 5 1 25 | 6 2 8 1 26 | 7 2 9 1 27 | 8 3 4 1 28 | 9 3 5 1 29 | 10 3 10 1 30 | 11 3 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C12_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C12 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.4000 0.1090 1.1400 C.3 1 C121 0.079100 9 | 2 C2 0.2340 1.1870 0.0920 C.3 1 C121 0.079100 10 | 3 C3 -0.3960 -0.8090 -0.7700 C.3 1 C121 0.247700 11 | 4 O1 0.4120 -1.0650 0.3530 O.3 1 C121 -0.424700 12 | 5 O2 -0.6530 0.5730 -0.8220 O.3 1 C121 -0.424700 13 | 6 H1 1.3400 0.1620 1.6980 H 1 C121 0.074900 14 | 7 H2 -0.4460 0.1090 1.8480 H 1 C121 0.074900 15 | 8 H3 -0.2310 2.1080 0.4600 H 1 C121 0.074900 16 | 9 H4 1.1980 1.4300 -0.3850 H 1 C121 0.074900 17 | 10 H5 0.1480 -1.1560 -1.6630 H 1 C121 0.071900 18 | 11 H6 -1.3660 -1.3300 -0.7010 H 1 C121 0.071900 19 | @BOND 20 | 1 1 2 1 21 | 2 1 4 1 22 | 3 1 6 1 23 | 4 1 7 1 24 | 5 2 5 1 25 | 6 2 8 1 26 | 7 2 9 1 27 | 8 3 4 1 28 | 9 3 5 1 29 | 10 3 10 1 30 | 11 3 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C12_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C12 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.4000 0.1090 1.1400 C.3 1 C121 0.066260 9 | 2 C2 0.2340 1.1870 0.0920 C.3 1 C121 0.066260 10 | 3 C3 -0.3960 -0.8090 -0.7700 C.3 1 C121 0.231340 11 | 4 O1 0.4120 -1.0650 0.3530 O.3 1 C121 -0.397980 12 | 5 O2 -0.6530 0.5730 -0.8220 O.3 1 C121 -0.397980 13 | 6 H1 1.3400 0.1620 1.6980 H 1 C121 0.072860 14 | 7 H2 -0.4460 0.1090 1.8480 H 1 C121 0.072860 15 | 8 H3 -0.2310 2.1080 0.4600 H 1 C121 0.072860 16 | 9 H4 1.1980 1.4300 -0.3850 H 1 C121 0.072860 17 | 10 H5 0.1480 -1.1560 -1.6630 H 1 C121 0.070300 18 | 11 H6 -1.3660 -1.3300 -0.7010 H 1 C121 0.070300 19 | @BOND 20 | 1 1 2 1 21 | 2 1 4 1 22 | 3 1 6 1 23 | 4 1 7 1 24 | 5 2 5 1 25 | 6 2 8 1 26 | 7 2 9 1 27 | 8 3 4 1 28 | 9 3 5 1 29 | 10 3 10 1 30 | 11 3 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C13_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C13 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.0020 -0.8550 -0.6890 C.2 1 C131 -0.248300 9 | 2 C2 0.4410 -2.0830 -0.4280 C.2 1 C131 -0.282500 10 | 3 C3 0.9930 -2.3980 0.9070 C.2 1 C131 0.660400 11 | 4 O1 1.0930 -1.6260 1.8290 O.2 1 C131 -0.484700 12 | 5 O2 1.3850 -3.6830 0.9870 O.3 1 C131 -0.477500 13 | 6 H1 -0.4090 -0.5870 -1.6600 H 1 C131 0.163500 14 | 7 H2 0.0540 -0.0910 0.0850 H 1 C131 0.163500 15 | 8 H3 0.4160 -2.8870 -1.1600 H 1 C131 0.167200 16 | 9 H4 1.7280 -3.7960 1.8870 H 1 C131 0.338300 17 | @BOND 18 | 1 1 2 2 19 | 2 1 6 1 20 | 3 1 7 1 21 | 4 2 3 1 22 | 5 2 8 1 23 | 6 3 4 2 24 | 7 3 5 1 25 | 8 5 9 1 26 | -------------------------------------------------------------------------------- /Studies/Charges/C13_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C13 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.0020 -0.8550 -0.6890 C.2 1 C131 -0.268600 9 | 2 C2 0.4410 -2.0830 -0.4280 C.2 1 C131 -0.276100 10 | 3 C3 0.9930 -2.3980 0.9070 C.2 1 C131 0.717900 11 | 4 O1 1.0930 -1.6260 1.8290 O.2 1 C131 -0.589200 12 | 5 O2 1.3850 -3.6830 0.9870 O.3 1 C131 -0.547300 13 | 6 H1 -0.4090 -0.5870 -1.6600 H 1 C131 0.184300 14 | 7 H2 0.0540 -0.0910 0.0850 H 1 C131 0.184300 15 | 8 H3 0.4160 -2.8870 -1.1600 H 1 C131 0.181700 16 | 9 H4 1.7280 -3.7960 1.8870 H 1 C131 0.412800 17 | @BOND 18 | 1 1 2 2 19 | 2 1 6 1 20 | 3 1 7 1 21 | 4 2 3 1 22 | 5 2 8 1 23 | 6 3 4 2 24 | 7 3 5 1 25 | 8 5 9 1 26 | -------------------------------------------------------------------------------- /Studies/Charges/C13_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C13 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.0020 -0.8550 -0.6890 C.2 1 C131 -0.260480 9 | 2 C2 0.4410 -2.0830 -0.4280 C.2 1 C131 -0.278660 10 | 3 C3 0.9930 -2.3980 0.9070 C.2 1 C131 0.694900 11 | 4 O1 1.0930 -1.6260 1.8290 O.2 1 C131 -0.547400 12 | 5 O2 1.3850 -3.6830 0.9870 O.3 1 C131 -0.519380 13 | 6 H1 -0.4090 -0.5870 -1.6600 H 1 C131 0.175980 14 | 7 H2 0.0540 -0.0910 0.0850 H 1 C131 0.175980 15 | 8 H3 0.4160 -2.8870 -1.1600 H 1 C131 0.175900 16 | 9 H4 1.7280 -3.7960 1.8870 H 1 C131 0.383000 17 | @BOND 18 | 1 1 2 2 19 | 2 1 6 1 20 | 3 1 7 1 21 | 4 2 3 1 22 | 5 2 8 1 23 | 6 3 4 2 24 | 7 3 5 1 25 | 8 5 9 1 26 | -------------------------------------------------------------------------------- /Studies/Charges/C14_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C14 3 | 13 12 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.5910 0.4780 -1.0650 C.2 1 C14 0.879300 10 | 2 C2 0.6980 -1.0790 0.2450 C.2 1 C14 0.879300 11 | 3 C3 -1.7400 1.3990 -0.8110 C.3 1 C14 -0.554400 12 | 4 C4 1.6660 -0.9810 1.3800 C.3 1 C14 -0.554400 13 | 5 O1 -0.1700 0.1290 -2.1230 O.2 1 C14 -0.538400 14 | 6 O2 0.5060 -2.0220 -0.4570 O.2 1 C14 -0.538400 15 | 7 O3 -0.0190 0.1050 0.1440 O.3 1 C14 -0.558100 16 | 8 H1 -2.5380 0.8490 -0.2970 H 1 C14 0.164200 17 | 9 H2 -1.4290 2.2140 -0.1490 H 1 C14 0.164200 18 | 10 H3 -2.1090 1.7940 -1.7590 H 1 C14 0.164200 19 | 11 H4 2.4270 -0.2280 1.1410 H 1 C14 0.164200 20 | 12 H5 2.1380 -1.9510 1.5430 H 1 C14 0.164200 21 | 13 H6 1.1500 -0.6460 2.2860 H 1 C14 0.164200 22 | @BOND 23 | 1 1 3 1 24 | 2 1 5 2 25 | 3 1 7 1 26 | 4 2 4 1 27 | 5 2 6 2 28 | 6 2 7 1 29 | 7 3 8 1 30 | 8 3 9 1 31 | 9 3 10 1 32 | 10 4 11 1 33 | 11 4 12 1 34 | 12 4 13 1 35 | @SUBSTRUCTURE 36 | 1 C14 1 TEMP 0 **** **** 0 ROOT 37 | -------------------------------------------------------------------------------- /Studies/Charges/C14_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C14 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.5910 0.4780 -1.0650 C.2 1 C141 0.791300 9 | 2 C2 0.6980 -1.0790 0.2450 C.2 1 C141 0.791300 10 | 3 C3 -1.7400 1.3990 -0.8110 C.3 1 C141 -0.572900 11 | 4 C4 1.6660 -0.9810 1.3800 C.3 1 C141 -0.572900 12 | 5 O1 -0.1700 0.1290 -2.1230 O.2 1 C141 -0.482800 13 | 6 O2 0.5060 -2.0220 -0.4570 O.2 1 C141 -0.482800 14 | 7 O3 -0.0190 0.1050 0.1440 O.3 1 C141 -0.500100 15 | 8 H1 -2.5380 0.8490 -0.2970 H 1 C141 0.171500 16 | 9 H2 -1.4290 2.2140 -0.1490 H 1 C141 0.171500 17 | 10 H3 -2.1090 1.7940 -1.7590 H 1 C141 0.171500 18 | 11 H4 2.4270 -0.2280 1.1410 H 1 C141 0.171500 19 | 12 H5 2.1380 -1.9510 1.5430 H 1 C141 0.171500 20 | 13 H6 1.1500 -0.6460 2.2860 H 1 C141 0.171500 21 | @BOND 22 | 1 1 3 1 23 | 2 1 5 2 24 | 3 1 7 1 25 | 4 2 4 1 26 | 5 2 6 2 27 | 6 2 7 1 28 | 7 3 8 1 29 | 8 3 9 1 30 | 9 3 10 1 31 | 10 4 11 1 32 | 11 4 12 1 33 | 12 4 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/C14_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C14 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.5910 0.4780 -1.0650 C.2 1 C141 0.840200 9 | 2 C2 0.6980 -1.0790 0.2450 C.2 1 C141 0.840200 10 | 3 C3 -1.7400 1.3990 -0.8110 C.3 1 C141 -0.570000 11 | 4 C4 1.6660 -0.9810 1.3800 C.3 1 C141 -0.570000 12 | 5 O1 -0.1700 0.1290 -2.1230 O.2 1 C141 -0.566300 13 | 6 O2 0.5060 -2.0220 -0.4570 O.2 1 C141 -0.566300 14 | 7 O3 -0.0190 0.1050 0.1440 O.3 1 C141 -0.503400 15 | 8 H1 -2.5380 0.8490 -0.2970 H 1 C141 0.182600 16 | 9 H2 -1.4290 2.2140 -0.1490 H 1 C141 0.182600 17 | 10 H3 -2.1090 1.7940 -1.7590 H 1 C141 0.182600 18 | 11 H4 2.4270 -0.2280 1.1410 H 1 C141 0.182600 19 | 12 H5 2.1380 -1.9510 1.5430 H 1 C141 0.182600 20 | 13 H6 1.1500 -0.6460 2.2860 H 1 C141 0.182600 21 | @BOND 22 | 1 1 3 1 23 | 2 1 5 2 24 | 3 1 7 1 25 | 4 2 4 1 26 | 5 2 6 2 27 | 6 2 7 1 28 | 7 3 8 1 29 | 8 3 9 1 30 | 9 3 10 1 31 | 10 4 11 1 32 | 11 4 12 1 33 | 12 4 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/C14_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C14 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.5910 0.4780 -1.0650 C.2 1 C141 0.820640 9 | 2 C2 0.6980 -1.0790 0.2450 C.2 1 C141 0.820640 10 | 3 C3 -1.7400 1.3990 -0.8110 C.3 1 C141 -0.571160 11 | 4 C4 1.6660 -0.9810 1.3800 C.3 1 C141 -0.571160 12 | 5 O1 -0.1700 0.1290 -2.1230 O.2 1 C141 -0.532900 13 | 6 O2 0.5060 -2.0220 -0.4570 O.2 1 C141 -0.532900 14 | 7 O3 -0.0190 0.1050 0.1440 O.3 1 C141 -0.502080 15 | 8 H1 -2.5380 0.8490 -0.2970 H 1 C141 0.178160 16 | 9 H2 -1.4290 2.2140 -0.1490 H 1 C141 0.178160 17 | 10 H3 -2.1090 1.7940 -1.7590 H 1 C141 0.178160 18 | 11 H4 2.4270 -0.2280 1.1410 H 1 C141 0.178160 19 | 12 H5 2.1380 -1.9510 1.5430 H 1 C141 0.178160 20 | 13 H6 1.1500 -0.6460 2.2860 H 1 C141 0.178160 21 | @BOND 22 | 1 1 3 1 23 | 2 1 5 2 24 | 3 1 7 1 25 | 4 2 4 1 26 | 5 2 6 2 27 | 6 2 7 1 28 | 7 3 8 1 29 | 8 3 9 1 30 | 9 3 10 1 31 | 10 4 11 1 32 | 11 4 12 1 33 | 12 4 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/C15_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C15 3 | 13 12 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 0.7850 -0.0210 -0.7970 C.3 1 C15 -0.094200 10 | 2 C2 0.3890 0.9300 -1.9020 C.3 1 C15 0.278500 11 | 3 C3 1.0070 -1.4340 -1.2840 C.3 1 C15 0.278500 12 | 4 O1 0.2110 2.2060 -1.3280 O.3 1 C15 -0.624000 13 | 5 O2 1.3680 -2.2200 -0.1690 O.3 1 C15 -0.624000 14 | 6 H1 1.7020 0.3440 -0.3180 H 1 C15 0.037300 15 | 7 H2 0.0020 -0.0240 -0.0270 H 1 C15 0.037300 16 | 8 H3 1.1740 0.9450 -2.6810 H 1 C15 -0.010900 17 | 9 H4 -0.5380 0.5740 -2.3880 H 1 C15 -0.010900 18 | 10 H5 1.7980 -1.4430 -2.0560 H 1 C15 -0.010900 19 | 11 H6 0.0860 -1.8140 -1.7620 H 1 C15 -0.010900 20 | 12 H7 -0.0400 2.8130 -2.0290 H 1 C15 0.377000 21 | 13 H8 1.5110 -3.1200 -0.4760 H 1 C15 0.377000 22 | @BOND 23 | 1 1 2 1 24 | 2 1 3 1 25 | 3 1 6 1 26 | 4 1 7 1 27 | 5 2 4 1 28 | 6 2 8 1 29 | 7 2 9 1 30 | 8 3 5 1 31 | 9 3 10 1 32 | 10 3 11 1 33 | 11 4 12 1 34 | 12 5 13 1 35 | @SUBSTRUCTURE 36 | 1 C15 1 TEMP 0 **** **** 0 ROOT 37 | -------------------------------------------------------------------------------- /Studies/Charges/C15_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C15 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.7850 -0.0210 -0.7970 C.3 1 C151 -0.102400 9 | 2 C2 0.3900 0.9300 -1.9030 C.3 1 C151 0.216700 10 | 3 C3 1.0070 -1.4340 -1.2830 C.3 1 C151 0.216700 11 | 4 O1 0.2120 2.2060 -1.3280 O.3 1 C151 -0.552400 12 | 5 O2 1.3670 -2.2200 -0.1690 O.3 1 C151 -0.552400 13 | 6 H1 1.7020 0.3440 -0.3180 H 1 C151 0.046200 14 | 7 H2 0.0020 -0.0240 -0.0270 H 1 C151 0.046200 15 | 8 H3 1.1750 0.9450 -2.6810 H 1 C151 0.002300 16 | 9 H4 -0.5380 0.5740 -2.3880 H 1 C151 0.002300 17 | 10 H5 1.7980 -1.4440 -2.0550 H 1 C151 0.002300 18 | 11 H6 0.0850 -1.8140 -1.7620 H 1 C151 0.002300 19 | 12 H7 -0.0390 2.8130 -2.0300 H 1 C151 0.336200 20 | 13 H8 1.5090 -3.1210 -0.4760 H 1 C151 0.336200 21 | @BOND 22 | 1 1 2 1 23 | 2 1 3 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 4 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 5 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | 12 5 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/C15_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C15 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.7850 -0.0210 -0.7970 C.3 1 C151 -0.078100 9 | 2 C2 0.3900 0.9300 -1.9030 C.3 1 C151 0.250200 10 | 3 C3 1.0070 -1.4340 -1.2830 C.3 1 C151 0.250200 11 | 4 O1 0.2120 2.2060 -1.3280 O.3 1 C151 -0.666100 12 | 5 O2 1.3670 -2.2200 -0.1690 O.3 1 C151 -0.666100 13 | 6 H1 1.7020 0.3440 -0.3180 H 1 C151 0.039900 14 | 7 H2 0.0020 -0.0240 -0.0270 H 1 C151 0.039900 15 | 8 H3 1.1750 0.9450 -2.6810 H 1 C151 0.009700 16 | 9 H4 -0.5380 0.5740 -2.3880 H 1 C151 0.009700 17 | 10 H5 1.7980 -1.4440 -2.0550 H 1 C151 0.009700 18 | 11 H6 0.0850 -1.8140 -1.7620 H 1 C151 0.009700 19 | 12 H7 -0.0390 2.8130 -2.0300 H 1 C151 0.395800 20 | 13 H8 1.5090 -3.1210 -0.4760 H 1 C151 0.395800 21 | @BOND 22 | 1 1 2 1 23 | 2 1 3 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 4 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 5 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | 12 5 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/C15_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C15 3 | 13 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.7850 -0.0210 -0.7970 C.3 1 C151 -0.087820 9 | 2 C2 0.3900 0.9300 -1.9030 C.3 1 C151 0.236800 10 | 3 C3 1.0070 -1.4340 -1.2830 C.3 1 C151 0.236800 11 | 4 O1 0.2120 2.2060 -1.3280 O.3 1 C151 -0.620620 12 | 5 O2 1.3670 -2.2200 -0.1690 O.3 1 C151 -0.620620 13 | 6 H1 1.7020 0.3440 -0.3180 H 1 C151 0.042420 14 | 7 H2 0.0020 -0.0240 -0.0270 H 1 C151 0.042420 15 | 8 H3 1.1750 0.9450 -2.6810 H 1 C151 0.006740 16 | 9 H4 -0.5380 0.5740 -2.3880 H 1 C151 0.006740 17 | 10 H5 1.7980 -1.4440 -2.0550 H 1 C151 0.006740 18 | 11 H6 0.0850 -1.8140 -1.7620 H 1 C151 0.006740 19 | 12 H7 -0.0390 2.8130 -2.0300 H 1 C151 0.371960 20 | 13 H8 1.5090 -3.1210 -0.4760 H 1 C151 0.371960 21 | @BOND 22 | 1 1 2 1 23 | 2 1 3 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 4 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 3 5 1 30 | 9 3 10 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | 12 5 13 1 34 | -------------------------------------------------------------------------------- /Studies/Charges/C20_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C20 3 | 11 10 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.3290 -0.5230 0.9100 C.3 1 C20 0.280500 10 | 2 C2 -0.3820 -2.0260 0.7490 C.3 1 C20 0.180800 11 | 3 N1 -1.6570 -0.0110 1.2110 N.3 1 C20 -0.964200 12 | 4 O1 0.9230 -2.4690 0.4500 O.3 1 C20 -0.623100 13 | 5 H1 0.4490 -0.2850 1.6580 H 1 C20 -0.005900 14 | 6 H2 0.0080 -0.0910 -0.0410 H 1 C20 -0.005900 15 | 7 H3 -1.1040 -2.2710 -0.0480 H 1 C20 0.007000 16 | 8 H4 -0.7610 -2.4800 1.6840 H 1 C20 0.007000 17 | 9 H5 -1.6410 1.0050 1.1920 H 1 C20 0.362800 18 | 10 H6 -1.9040 -0.2530 2.1680 H 1 C20 0.362800 19 | 11 H7 0.8890 -3.4200 0.3150 H 1 C20 0.398300 20 | @BOND 21 | 1 1 2 1 22 | 2 1 3 1 23 | 3 1 5 1 24 | 4 1 6 1 25 | 5 2 4 1 26 | 6 2 7 1 27 | 7 2 8 1 28 | 8 3 9 1 29 | 9 3 10 1 30 | 10 4 11 1 31 | @SUBSTRUCTURE 32 | 1 C20 1 TEMP 0 **** **** 0 ROOT 33 | -------------------------------------------------------------------------------- /Studies/Charges/C20_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C20 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.3290 -0.5230 0.9100 C.3 1 C201 0.104000 9 | 2 C2 -0.3820 -2.0260 0.7490 C.3 1 C201 0.138800 10 | 3 N1 -1.6570 -0.0110 1.2110 N.3 1 C201 -0.784500 11 | 4 O1 0.9230 -2.4690 0.4500 O.3 1 C201 -0.538400 12 | 5 H1 0.4490 -0.2850 1.6580 H 1 C201 0.037600 13 | 6 H2 0.0080 -0.0910 -0.0410 H 1 C201 0.037600 14 | 7 H3 -1.1040 -2.2710 -0.0480 H 1 C201 0.020900 15 | 8 H4 -0.7610 -2.4800 1.6840 H 1 C201 0.020900 16 | 9 H5 -1.6410 1.0050 1.1920 H 1 C201 0.307200 17 | 10 H6 -1.9040 -0.2530 2.1680 H 1 C201 0.307200 18 | 11 H7 0.8890 -3.4200 0.3150 H 1 C201 0.348900 19 | @BOND 20 | 1 1 2 1 21 | 2 1 3 1 22 | 3 1 5 1 23 | 4 1 6 1 24 | 5 2 4 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 4 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/C20_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C20 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.3290 -0.5230 0.9100 C.3 1 C201 0.195700 9 | 2 C2 -0.3820 -2.0260 0.7490 C.3 1 C201 0.161000 10 | 3 N1 -1.6570 -0.0110 1.2110 N.3 1 C201 -0.985000 11 | 4 O1 0.9230 -2.4690 0.4500 O.3 1 C201 -0.650500 12 | 5 H1 0.4490 -0.2850 1.6580 H 1 C201 0.032200 13 | 6 H2 0.0080 -0.0910 -0.0410 H 1 C201 0.032200 14 | 7 H3 -1.1040 -2.2710 -0.0480 H 1 C201 0.025600 15 | 8 H4 -0.7610 -2.4800 1.6840 H 1 C201 0.025600 16 | 9 H5 -1.6410 1.0050 1.1920 H 1 C201 0.376000 17 | 10 H6 -1.9040 -0.2530 2.1680 H 1 C201 0.376000 18 | 11 H7 0.8890 -3.4200 0.3150 H 1 C201 0.411100 19 | @BOND 20 | 1 1 2 1 21 | 2 1 3 1 22 | 3 1 5 1 23 | 4 1 6 1 24 | 5 2 4 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 4 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/C20_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C20 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.3290 -0.5230 0.9100 C.3 1 C201 0.159020 9 | 2 C2 -0.3820 -2.0260 0.7490 C.3 1 C201 0.152120 10 | 3 N1 -1.6570 -0.0110 1.2110 N.3 1 C201 -0.904800 11 | 4 O1 0.9230 -2.4690 0.4500 O.3 1 C201 -0.605660 12 | 5 H1 0.4490 -0.2850 1.6580 H 1 C201 0.034360 13 | 6 H2 0.0080 -0.0910 -0.0410 H 1 C201 0.034360 14 | 7 H3 -1.1040 -2.2710 -0.0480 H 1 C201 0.023720 15 | 8 H4 -0.7610 -2.4800 1.6840 H 1 C201 0.023720 16 | 9 H5 -1.6410 1.0050 1.1920 H 1 C201 0.348480 17 | 10 H6 -1.9040 -0.2530 2.1680 H 1 C201 0.348480 18 | 11 H7 0.8890 -3.4200 0.3150 H 1 C201 0.386220 19 | @BOND 20 | 1 1 2 1 21 | 2 1 3 1 22 | 3 1 5 1 23 | 4 1 6 1 24 | 5 2 4 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 4 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/C23_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C23 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.8570 -0.5570 -1.1910 C.2 1 C23 0.7690 9 | 2 C2 -0.5200 0.3050 0.6570 C.3 1 C23 0.0695 10 | 3 N1 -0.1520 -0.2710 -0.6010 N.2 1 C23 -0.5605 11 | 4 O1 1.7570 -0.8810 -1.8700 O.2 1 C23 -0.4766 12 | 5 H1 -0.1890 1.3490 0.7280 H 1 C23 0.0662 13 | 6 H2 -0.0920 -0.2560 1.4970 H 1 C23 0.0662 14 | 7 H3 -1.6090 0.2870 0.7540 H 1 C23 0.0662 15 | @BOND 16 | 1 1 3 2 17 | 2 1 4 2 18 | 3 2 3 1 19 | 4 2 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C23_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C23 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.8570 -0.5570 -1.1910 C.2 1 C23 0.5976 9 | 2 C2 -0.5200 0.3050 0.6570 C.3 1 C23 -0.0244 10 | 3 N1 -0.1520 -0.2710 -0.6010 N.2 1 C23 -0.4119 11 | 4 O1 1.7570 -0.8810 -1.8700 O.2 1 C23 -0.3996 12 | 5 H1 -0.1890 1.3490 0.7280 H 1 C23 0.0795 13 | 6 H2 -0.0920 -0.2560 1.4970 H 1 C23 0.0795 14 | 7 H3 -1.6090 0.2870 0.7540 H 1 C23 0.0795 15 | @BOND 16 | 1 1 3 2 17 | 2 1 4 2 18 | 3 2 3 1 19 | 4 2 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C23_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C23 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.8570 -0.5570 -1.1910 C.2 1 C23 0.6733 9 | 2 C2 -0.5200 0.3050 0.6570 C.3 1 C23 0.0216 10 | 3 N1 -0.1520 -0.2710 -0.6010 N.2 1 C23 -0.4778 11 | 4 O1 1.7570 -0.8810 -1.8700 O.2 1 C23 -0.4683 12 | 5 H1 -0.1890 1.3490 0.7280 H 1 C23 0.0838 13 | 6 H2 -0.0920 -0.2560 1.4970 H 1 C23 0.0838 14 | 7 H3 -1.6090 0.2870 0.7540 H 1 C23 0.0838 15 | @BOND 16 | 1 1 3 2 17 | 2 1 4 2 18 | 3 2 3 1 19 | 4 2 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C23_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C23 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.8570 -0.5570 -1.1910 C.2 1 C23 0.6430 9 | 2 C2 -0.5200 0.3050 0.6570 C.3 1 C23 0.0032 10 | 3 N1 -0.1520 -0.2710 -0.6010 N.2 1 C23 -0.4514 11 | 4 O1 1.7570 -0.8810 -1.8700 O.2 1 C23 -0.4408 12 | 5 H1 -0.1890 1.3490 0.7280 H 1 C23 0.0821 13 | 6 H2 -0.0920 -0.2560 1.4970 H 1 C23 0.0821 14 | 7 H3 -1.6090 0.2870 0.7540 H 1 C23 0.0821 15 | @BOND 16 | 1 1 3 2 17 | 2 1 4 2 18 | 3 2 3 1 19 | 4 2 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/C24_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C24 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.5080 1.3100 -0.6750 C.1 1 C24 -0.1429 9 | 2 C2 1.8870 2.1700 -1.4390 C.1 1 C24 -0.1429 10 | 3 C3 1.0890 0.2790 0.2770 C.3 1 C24 0.2407 11 | 4 C4 2.3260 3.2440 -2.3320 C.3 1 C24 0.2407 12 | 5 O1 1.1790 0.6940 1.6210 O.3 1 C24 -0.5772 13 | 6 O2 2.9150 4.3290 -1.6510 O.3 1 C24 -0.5772 14 | 7 H1 1.6720 -0.6390 0.0890 H 1 C24 0.0486 15 | 8 H2 0.0360 0.0250 0.1060 H 1 C24 0.0486 16 | 9 H3 1.4710 3.5630 -2.9540 H 1 C24 0.0486 17 | 10 H4 3.0910 2.8640 -3.0190 H 1 C24 0.0486 18 | 11 H5 2.0810 1.0030 1.7620 H 1 C24 0.3822 19 | 12 H6 2.2840 4.6190 -0.9830 H 1 C24 0.3822 20 | @BOND 21 | 1 1 2 3 22 | 2 1 3 1 23 | 3 2 4 1 24 | 4 3 5 1 25 | 5 3 7 1 26 | 6 3 8 1 27 | 7 4 6 1 28 | 8 4 9 1 29 | 9 4 10 1 30 | 10 5 11 1 31 | 11 6 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C24_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C24 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.5080 1.3100 -0.6750 C.1 1 C24 -0.1291 9 | 2 C2 1.8870 2.1700 -1.4390 C.1 1 C24 -0.1291 10 | 3 C3 1.0890 0.2790 0.2770 C.3 1 C24 0.1600 11 | 4 C4 2.3260 3.2440 -2.3320 C.3 1 C24 0.1600 12 | 5 O1 1.1790 0.6940 1.6210 O.3 1 C24 -0.4930 13 | 6 O2 2.9150 4.3290 -1.6510 O.3 1 C24 -0.4930 14 | 7 H1 1.6720 -0.6390 0.0890 H 1 C24 0.0626 15 | 8 H2 0.0360 0.0250 0.1060 H 1 C24 0.0626 16 | 9 H3 1.4710 3.5630 -2.9540 H 1 C24 0.0626 17 | 10 H4 3.0910 2.8640 -3.0190 H 1 C24 0.0626 18 | 11 H5 2.0810 1.0030 1.7620 H 1 C24 0.3369 19 | 12 H6 2.2840 4.6190 -0.9830 H 1 C24 0.3369 20 | @BOND 21 | 1 1 2 3 22 | 2 1 3 1 23 | 3 2 4 1 24 | 4 3 5 1 25 | 5 3 7 1 26 | 6 3 8 1 27 | 7 4 6 1 28 | 8 4 9 1 29 | 9 4 10 1 30 | 10 5 11 1 31 | 11 6 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C24_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C24 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.5080 1.3100 -0.6750 C.1 1 C24 -0.1691 9 | 2 C2 1.8870 2.1700 -1.4390 C.1 1 C24 -0.1691 10 | 3 C3 1.0890 0.2790 0.2770 C.3 1 C24 0.2174 11 | 4 C4 2.3260 3.2440 -2.3320 C.3 1 C24 0.2174 12 | 5 O1 1.1790 0.6940 1.6210 O.3 1 C24 -0.5965 13 | 6 O2 2.9150 4.3290 -1.6510 O.3 1 C24 -0.5965 14 | 7 H1 1.6720 -0.6390 0.0890 H 1 C24 0.0742 15 | 8 H2 0.0360 0.0250 0.1060 H 1 C24 0.0742 16 | 9 H3 1.4710 3.5630 -2.9540 H 1 C24 0.0742 17 | 10 H4 3.0910 2.8640 -3.0190 H 1 C24 0.0742 18 | 11 H5 2.0810 1.0030 1.7620 H 1 C24 0.3999 19 | 12 H6 2.2840 4.6190 -0.9830 H 1 C24 0.3999 20 | @BOND 21 | 1 1 2 3 22 | 2 1 3 1 23 | 3 2 4 1 24 | 4 3 5 1 25 | 5 3 7 1 26 | 6 3 8 1 27 | 7 4 6 1 28 | 8 4 9 1 29 | 9 4 10 1 30 | 10 5 11 1 31 | 11 6 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C24_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C24 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.5080 1.3100 -0.6750 C.1 1 C24 -0.1531 9 | 2 C2 1.8870 2.1700 -1.4390 C.1 1 C24 -0.1531 10 | 3 C3 1.0890 0.2790 0.2770 C.3 1 C24 0.1944 11 | 4 C4 2.3260 3.2440 -2.3320 C.3 1 C24 0.1944 12 | 5 O1 1.1790 0.6940 1.6210 O.3 1 C24 -0.5551 13 | 6 O2 2.9150 4.3290 -1.6510 O.3 1 C24 -0.5551 14 | 7 H1 1.6720 -0.6390 0.0890 H 1 C24 0.0696 15 | 8 H2 0.0360 0.0250 0.1060 H 1 C24 0.0696 16 | 9 H3 1.4710 3.5630 -2.9540 H 1 C24 0.0696 17 | 10 H4 3.0910 2.8640 -3.0190 H 1 C24 0.0696 18 | 11 H5 2.0810 1.0030 1.7620 H 1 C24 0.3747 19 | 12 H6 2.2840 4.6190 -0.9830 H 1 C24 0.3747 20 | @BOND 21 | 1 1 2 3 22 | 2 1 3 1 23 | 3 2 4 1 24 | 4 3 5 1 25 | 5 3 7 1 26 | 6 3 8 1 27 | 7 4 6 1 28 | 8 4 9 1 29 | 9 4 10 1 30 | 10 5 11 1 31 | 11 6 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/C25_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C25 3 | 10 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.7410 -2.8500 0.3490 C.1 1 C25 0.2958 9 | 2 C2 0.5750 -0.5360 -2.1080 C.2 1 C25 -0.2225 10 | 3 C3 0.0960 -0.7450 -0.7870 C.2 1 C25 -0.1831 11 | 4 C4 0.5100 -1.7480 -2.7250 C.2 1 C25 -0.0485 12 | 5 C5 -0.2220 -2.0710 -0.7100 C.2 1 C25 0.1524 13 | 6 N1 -1.1670 -3.4650 1.2350 N.1 1 C25 -0.4179 14 | 7 O1 0.0290 -2.6900 -1.8920 O.3 1 C25 -0.1616 15 | 8 H1 0.9220 0.3910 -2.5440 H 1 C25 0.1889 16 | 9 H2 -0.0060 -0.0200 0.0100 H 1 C25 0.1956 17 | 10 H3 0.7610 -2.0880 -3.7200 H 1 C25 0.2008 18 | @BOND 19 | 1 1 5 1 20 | 2 1 6 3 21 | 3 2 3 1 22 | 4 2 4 2 23 | 5 2 8 1 24 | 6 3 5 2 25 | 7 3 9 1 26 | 8 4 7 1 27 | 9 4 10 1 28 | 10 5 7 1 29 | -------------------------------------------------------------------------------- /Studies/Charges/C25_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C25 3 | 10 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.7410 -2.8500 0.3490 C.1 1 C25 0.2682 9 | 2 C2 0.5750 -0.5360 -2.1080 C.2 1 C25 -0.2006 10 | 3 C3 0.0960 -0.7450 -0.7870 C.2 1 C25 -0.1883 11 | 4 C4 0.5100 -1.7480 -2.7250 C.2 1 C25 -0.0643 12 | 5 C5 -0.2220 -2.0710 -0.7100 C.2 1 C25 0.1568 13 | 6 N1 -1.1670 -3.4650 1.2350 N.1 1 C25 -0.3977 14 | 7 O1 0.0290 -2.6900 -1.8920 O.3 1 C25 -0.1160 15 | 8 H1 0.9220 0.3910 -2.5440 H 1 C25 0.1787 16 | 9 H2 -0.0060 -0.0200 0.0100 H 1 C25 0.1813 17 | 10 H3 0.7610 -2.0880 -3.7200 H 1 C25 0.1820 18 | @BOND 19 | 1 1 5 1 20 | 2 1 6 3 21 | 3 2 3 1 22 | 4 2 4 2 23 | 5 2 8 1 24 | 6 3 5 2 25 | 7 3 9 1 26 | 8 4 7 1 27 | 9 4 10 1 28 | 10 5 7 1 29 | -------------------------------------------------------------------------------- /Studies/Charges/C25_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C25 3 | 10 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.7410 -2.8500 0.3490 C.1 1 C25 0.3556 9 | 2 C2 0.5750 -0.5360 -2.1080 C.2 1 C25 -0.2132 10 | 3 C3 0.0960 -0.7450 -0.7870 C.2 1 C25 -0.1662 11 | 4 C4 0.5100 -1.7480 -2.7250 C.2 1 C25 -0.0301 12 | 5 C5 -0.2220 -2.0710 -0.7100 C.2 1 C25 0.1130 13 | 6 N1 -1.1670 -3.4650 1.2350 N.1 1 C25 -0.5128 14 | 7 O1 0.0290 -2.6900 -1.8920 O.3 1 C25 -0.1454 15 | 8 H1 0.9220 0.3910 -2.5440 H 1 C25 0.1999 16 | 9 H2 -0.0060 -0.0200 0.0100 H 1 C25 0.1998 17 | 10 H3 0.7610 -2.0880 -3.7200 H 1 C25 0.1993 18 | @BOND 19 | 1 1 5 1 20 | 2 1 6 3 21 | 3 2 3 1 22 | 4 2 4 2 23 | 5 2 8 1 24 | 6 3 5 2 25 | 7 3 9 1 26 | 8 4 7 1 27 | 9 4 10 1 28 | 10 5 7 1 29 | -------------------------------------------------------------------------------- /Studies/Charges/C25_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C25 3 | 10 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.7410 -2.8500 0.3490 C.1 1 C25 0.3206 9 | 2 C2 0.5750 -0.5360 -2.1080 C.2 1 C25 -0.2082 10 | 3 C3 0.0960 -0.7450 -0.7870 C.2 1 C25 -0.1750 11 | 4 C4 0.5100 -1.7480 -2.7250 C.2 1 C25 -0.0438 12 | 5 C5 -0.2220 -2.0710 -0.7100 C.2 1 C25 0.1305 13 | 6 N1 -1.1670 -3.4650 1.2350 N.1 1 C25 -0.4668 14 | 7 O1 0.0290 -2.6900 -1.8920 O.3 1 C25 -0.1336 15 | 8 H1 0.9220 0.3910 -2.5440 H 1 C25 0.1914 16 | 9 H2 -0.0060 -0.0200 0.0100 H 1 C25 0.1924 17 | 10 H3 0.7610 -2.0880 -3.7200 H 1 C25 0.1924 18 | @BOND 19 | 1 1 5 1 20 | 2 1 6 3 21 | 3 2 3 1 22 | 4 2 4 2 23 | 5 2 8 1 24 | 6 3 5 2 25 | 7 3 9 1 26 | 8 4 7 1 27 | 9 4 10 1 28 | 10 5 7 1 29 | -------------------------------------------------------------------------------- /Studies/Charges/C26_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C26 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.9770 -0.8630 0.0040 C.ar 1 C26 -0.2357 9 | 2 C2 0.8120 -0.4090 -0.5700 C.ar 1 C26 -0.2558 10 | 3 C3 2.8340 -1.6000 -0.8120 C.ar 1 C26 0.3408 11 | 4 C4 0.5860 -0.7210 -1.9150 C.ar 1 C26 0.6055 12 | 5 C5 -0.6480 -0.2760 -2.6340 C.3 1 C26 -0.4269 13 | 6 N1 2.5780 -1.8720 -2.0850 N.ar 1 C26 -0.3492 14 | 7 N2 1.4570 -1.4330 -2.6340 N.ar 1 C26 -0.3451 15 | 8 H1 2.2260 -0.6630 1.0440 H 1 C26 0.1663 16 | 9 H2 0.0840 0.1740 -0.0070 H 1 C26 0.1537 17 | 10 H3 3.7760 -1.9960 -0.4350 H 1 C26 0.0279 18 | 11 H4 -0.7300 0.8180 -2.6370 H 1 C26 0.1061 19 | 12 H5 -0.6120 -0.6320 -3.6670 H 1 C26 0.1061 20 | 13 H6 -1.5510 -0.6710 -2.1520 H 1 C26 0.1061 21 | @BOND 22 | 1 1 2 ar 23 | 2 1 3 ar 24 | 3 1 8 1 25 | 4 2 4 ar 26 | 5 2 9 1 27 | 6 3 6 ar 28 | 7 3 10 1 29 | 8 4 5 1 30 | 9 4 7 ar 31 | 10 5 11 1 32 | 11 5 12 1 33 | 12 5 13 1 34 | 13 6 7 ar 35 | -------------------------------------------------------------------------------- /Studies/Charges/C26_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C26 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.9770 -0.8630 0.0040 C.ar 1 C26 -0.2309 9 | 2 C2 0.8120 -0.4090 -0.5700 C.ar 1 C26 -0.2318 10 | 3 C3 2.8340 -1.6000 -0.8120 C.ar 1 C26 0.3450 11 | 4 C4 0.5860 -0.7210 -1.9150 C.ar 1 C26 0.6040 12 | 5 C5 -0.6480 -0.2760 -2.6340 C.3 1 C26 -0.4496 13 | 6 N1 2.5780 -1.8720 -2.0850 N.ar 1 C26 -0.3416 14 | 7 N2 1.4570 -1.4330 -2.6340 N.ar 1 C26 -0.3355 15 | 8 H1 2.2260 -0.6630 1.0440 H 1 C26 0.1518 16 | 9 H2 0.0840 0.1740 -0.0070 H 1 C26 0.1350 17 | 10 H3 3.7760 -1.9960 -0.4350 H 1 C26 0.0162 18 | 11 H4 -0.7300 0.8180 -2.6370 H 1 C26 0.1125 19 | 12 H5 -0.6120 -0.6320 -3.6670 H 1 C26 0.1125 20 | 13 H6 -1.5510 -0.6710 -2.1520 H 1 C26 0.1125 21 | @BOND 22 | 1 1 2 ar 23 | 2 1 3 ar 24 | 3 1 8 1 25 | 4 2 4 ar 26 | 5 2 9 1 27 | 6 3 6 ar 28 | 7 3 10 1 29 | 8 4 5 1 30 | 9 4 7 ar 31 | 10 5 11 1 32 | 11 5 12 1 33 | 12 5 13 1 34 | 13 6 7 ar 35 | -------------------------------------------------------------------------------- /Studies/Charges/C26_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C26 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.9770 -0.8630 0.0040 C.ar 1 C26 -0.2336 9 | 2 C2 0.8120 -0.4090 -0.5700 C.ar 1 C26 -0.2197 10 | 3 C3 2.8340 -1.6000 -0.8120 C.ar 1 C26 0.4291 11 | 4 C4 0.5860 -0.7210 -1.9150 C.ar 1 C26 0.6543 12 | 5 C5 -0.6480 -0.2760 -2.6340 C.3 1 C26 -0.4531 13 | 6 N1 2.5780 -1.8720 -2.0850 N.ar 1 C26 -0.4528 14 | 7 N2 1.4570 -1.4330 -2.6340 N.ar 1 C26 -0.4202 15 | 8 H1 2.2260 -0.6630 1.0440 H 1 C26 0.1770 16 | 9 H2 0.0840 0.1740 -0.0070 H 1 C26 0.1601 17 | 10 H3 3.7760 -1.9960 -0.4350 H 1 C26 0.0115 18 | 11 H4 -0.7300 0.8180 -2.6370 H 1 C26 0.1159 19 | 12 H5 -0.6120 -0.6320 -3.6670 H 1 C26 0.1159 20 | 13 H6 -1.5510 -0.6710 -2.1520 H 1 C26 0.1159 21 | @BOND 22 | 1 1 2 ar 23 | 2 1 3 ar 24 | 3 1 8 1 25 | 4 2 4 ar 26 | 5 2 9 1 27 | 6 3 6 ar 28 | 7 3 10 1 29 | 8 4 5 1 30 | 9 4 7 ar 31 | 10 5 11 1 32 | 11 5 12 1 33 | 12 5 13 1 34 | 13 6 7 ar 35 | -------------------------------------------------------------------------------- /Studies/Charges/C26_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C26 3 | 13 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.9770 -0.8630 0.0040 C.ar 1 C26 -0.2325 9 | 2 C2 0.8120 -0.4090 -0.5700 C.ar 1 C26 -0.2245 10 | 3 C3 2.8340 -1.6000 -0.8120 C.ar 1 C26 0.3955 11 | 4 C4 0.5860 -0.7210 -1.9150 C.ar 1 C26 0.6342 12 | 5 C5 -0.6480 -0.2760 -2.6340 C.3 1 C26 -0.4517 13 | 6 N1 2.5780 -1.8720 -2.0850 N.ar 1 C26 -0.4083 14 | 7 N2 1.4570 -1.4330 -2.6340 N.ar 1 C26 -0.3863 15 | 8 H1 2.2260 -0.6630 1.0440 H 1 C26 0.1669 16 | 9 H2 0.0840 0.1740 -0.0070 H 1 C26 0.1501 17 | 10 H3 3.7760 -1.9960 -0.4350 H 1 C26 0.0134 18 | 11 H4 -0.7300 0.8180 -2.6370 H 1 C26 0.1145 19 | 12 H5 -0.6120 -0.6320 -3.6670 H 1 C26 0.1145 20 | 13 H6 -1.5510 -0.6710 -2.1520 H 1 C26 0.1145 21 | @BOND 22 | 1 1 2 ar 23 | 2 1 3 ar 24 | 3 1 8 1 25 | 4 2 4 ar 26 | 5 2 9 1 27 | 6 3 6 ar 28 | 7 3 10 1 29 | 8 4 5 1 30 | 9 4 7 ar 31 | 10 5 11 1 32 | 11 5 12 1 33 | 12 5 13 1 34 | 13 6 7 ar 35 | -------------------------------------------------------------------------------- /Studies/Charges/C27_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C27 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5740 -0.5360 -2.1150 C.2 1 C27 -0.2701 9 | 2 C2 0.4970 -1.7390 -2.7290 C.2 1 C27 -0.0695 10 | 3 C3 -0.2310 -2.0730 -0.7080 C.2 1 C27 -0.0425 11 | 4 C4 0.0960 -0.7480 -0.7810 C.2 1 C27 0.0282 12 | 5 C5 -0.0220 0.2410 0.2850 C.2 1 C27 0.3760 13 | 6 O1 0.2840 1.4040 0.1610 O.2 1 C27 -0.4573 14 | 7 O2 0.0070 -2.6840 -1.8780 O.3 1 C27 -0.1610 15 | 8 H1 0.9220 0.4000 -2.5300 H 1 C27 0.1970 16 | 9 H2 0.7370 -2.0900 -3.7230 H 1 C27 0.1935 17 | 10 H3 -0.6280 -2.6930 0.0850 H 1 C27 0.1853 18 | 11 H4 -0.4220 -0.1510 1.2480 H 1 C27 0.0203 19 | @BOND 20 | 1 1 2 2 21 | 2 1 4 1 22 | 3 1 8 1 23 | 4 2 7 1 24 | 5 2 9 1 25 | 6 3 4 2 26 | 7 3 7 1 27 | 8 3 10 1 28 | 9 4 5 1 29 | 10 5 6 2 30 | 11 5 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C27_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C27 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5740 -0.5360 -2.1150 C.2 1 C27 -0.2355 9 | 2 C2 0.4970 -1.7390 -2.7290 C.2 1 C27 -0.0682 10 | 3 C3 -0.2310 -2.0730 -0.7080 C.2 1 C27 -0.0509 11 | 4 C4 0.0960 -0.7480 -0.7810 C.2 1 C27 0.0217 12 | 5 C5 -0.0220 0.2410 0.2850 C.2 1 C27 0.3493 13 | 6 O1 0.2840 1.4040 0.1610 O.2 1 C27 -0.4186 14 | 7 O2 0.0070 -2.6840 -1.8780 O.3 1 C27 -0.1122 15 | 8 H1 0.9220 0.4000 -2.5300 H 1 C27 0.1754 16 | 9 H2 0.7370 -2.0900 -3.7230 H 1 C27 0.1734 17 | 10 H3 -0.6280 -2.6930 0.0850 H 1 C27 0.1617 18 | 11 H4 -0.4220 -0.1510 1.2480 H 1 C27 0.0038 19 | @BOND 20 | 1 1 2 2 21 | 2 1 4 1 22 | 3 1 8 1 23 | 4 2 7 1 24 | 5 2 9 1 25 | 6 3 4 2 26 | 7 3 7 1 27 | 8 3 10 1 28 | 9 4 5 1 29 | 10 5 6 2 30 | 11 5 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C27_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C27 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5740 -0.5360 -2.1150 C.2 1 C27 -0.2669 9 | 2 C2 0.4970 -1.7390 -2.7290 C.2 1 C27 -0.0593 10 | 3 C3 -0.2310 -2.0730 -0.7080 C.2 1 C27 -0.0445 11 | 4 C4 0.0960 -0.7480 -0.7810 C.2 1 C27 0.0293 12 | 5 C5 -0.0220 0.2410 0.2850 C.2 1 C27 0.3783 13 | 6 O1 0.2840 1.4040 0.1610 O.2 1 C27 -0.5203 14 | 7 O2 0.0070 -2.6840 -1.8780 O.3 1 C27 -0.1291 15 | 8 H1 0.9220 0.4000 -2.5300 H 1 C27 0.1954 16 | 9 H2 0.7370 -2.0900 -3.7230 H 1 C27 0.1924 17 | 10 H3 -0.6280 -2.6930 0.0850 H 1 C27 0.1808 18 | 11 H4 -0.4220 -0.1510 1.2480 H 1 C27 0.0439 19 | @BOND 20 | 1 1 2 2 21 | 2 1 4 1 22 | 3 1 8 1 23 | 4 2 7 1 24 | 5 2 9 1 25 | 6 3 4 2 26 | 7 3 7 1 27 | 8 3 10 1 28 | 9 4 5 1 29 | 10 5 6 2 30 | 11 5 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C27_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C27 3 | 11 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5740 -0.5360 -2.1150 C.2 1 C27 -0.2543 9 | 2 C2 0.4970 -1.7390 -2.7290 C.2 1 C27 -0.0629 10 | 3 C3 -0.2310 -2.0730 -0.7080 C.2 1 C27 -0.0471 11 | 4 C4 0.0960 -0.7480 -0.7810 C.2 1 C27 0.0263 12 | 5 C5 -0.0220 0.2410 0.2850 C.2 1 C27 0.3667 13 | 6 O1 0.2840 1.4040 0.1610 O.2 1 C27 -0.4796 14 | 7 O2 0.0070 -2.6840 -1.8780 O.3 1 C27 -0.1223 15 | 8 H1 0.9220 0.4000 -2.5300 H 1 C27 0.1874 16 | 9 H2 0.7370 -2.0900 -3.7230 H 1 C27 0.1848 17 | 10 H3 -0.6280 -2.6930 0.0850 H 1 C27 0.1732 18 | 11 H4 -0.4220 -0.1510 1.2480 H 1 C27 0.0279 19 | @BOND 20 | 1 1 2 2 21 | 2 1 4 1 22 | 3 1 8 1 23 | 4 2 7 1 24 | 5 2 9 1 25 | 6 3 4 2 26 | 7 3 7 1 27 | 8 3 10 1 28 | 9 4 5 1 29 | 10 5 6 2 30 | 11 5 11 1 31 | -------------------------------------------------------------------------------- /Studies/Charges/C29_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C29 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.6150 -0.5620 -2.0930 C.2 1 C29 -0.1660 9 | 2 C2 0.0740 -0.7580 -0.7950 C.2 1 C29 -0.2132 10 | 3 C3 0.5930 -1.7840 -2.6940 C.2 1 C29 -0.1032 11 | 4 C4 -0.2390 -2.0850 -0.7060 C.2 1 C29 0.0476 12 | 5 C5 -0.8240 -2.8670 0.3860 C.2 1 C29 0.6397 13 | 6 C6 -1.0360 -4.3360 0.1410 C.3 1 C29 -0.3921 14 | 7 O1 -1.1150 -2.3220 1.4320 O.2 1 C29 -0.5523 15 | 8 O2 0.0800 -2.7160 -1.8700 O.3 1 C29 -0.1478 16 | 9 H1 0.9750 0.3610 -2.5290 H 1 C29 0.1698 17 | 10 H2 -0.0770 -0.0300 -0.0090 H 1 C29 0.1896 18 | 11 H3 0.8970 -2.1330 -3.6720 H 1 C29 0.2025 19 | 12 H4 -0.0820 -4.8230 -0.0960 H 1 C29 0.1085 20 | 13 H5 -1.6890 -4.4870 -0.7270 H 1 C29 0.1085 21 | 14 H6 -1.4790 -4.7890 1.0300 H 1 C29 0.1085 22 | @BOND 23 | 1 1 2 1 24 | 2 1 3 2 25 | 3 1 9 1 26 | 4 2 4 2 27 | 5 2 10 1 28 | 6 3 8 1 29 | 7 3 11 1 30 | 8 4 5 1 31 | 9 4 8 1 32 | 10 5 6 1 33 | 11 5 7 2 34 | 12 6 12 1 35 | 13 6 13 1 36 | 14 6 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/C29_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C29 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.6150 -0.5620 -2.0930 C.2 1 C29 -0.1616 9 | 2 C2 0.0740 -0.7580 -0.7950 C.2 1 C29 -0.1979 10 | 3 C3 0.5930 -1.7840 -2.6940 C.2 1 C29 -0.1111 11 | 4 C4 -0.2390 -2.0850 -0.7060 C.2 1 C29 0.0580 12 | 5 C5 -0.8240 -2.8670 0.3860 C.2 1 C29 0.5778 13 | 6 C6 -1.0360 -4.3360 0.1410 C.3 1 C29 -0.4006 14 | 7 O1 -1.1150 -2.3220 1.4320 O.2 1 C29 -0.5136 15 | 8 O2 0.0800 -2.7160 -1.8700 O.3 1 C29 -0.1044 16 | 9 H1 0.9750 0.3610 -2.5290 H 1 C29 0.1639 17 | 10 H2 -0.0770 -0.0300 -0.0090 H 1 C29 0.1708 18 | 11 H3 0.8970 -2.1330 -3.6720 H 1 C29 0.1836 19 | 12 H4 -0.0820 -4.8230 -0.0960 H 1 C29 0.1117 20 | 13 H5 -1.6890 -4.4870 -0.7270 H 1 C29 0.1117 21 | 14 H6 -1.4790 -4.7890 1.0300 H 1 C29 0.1117 22 | @BOND 23 | 1 1 2 1 24 | 2 1 3 2 25 | 3 1 9 1 26 | 4 2 4 2 27 | 5 2 10 1 28 | 6 3 8 1 29 | 7 3 11 1 30 | 8 4 5 1 31 | 9 4 8 1 32 | 10 5 6 1 33 | 11 5 7 2 34 | 12 6 12 1 35 | 13 6 13 1 36 | 14 6 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/C29_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C29 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.6150 -0.5620 -2.0930 C.2 1 C29 -0.2877 9 | 2 C2 0.0740 -0.7580 -0.7950 C.2 1 C29 -0.1119 10 | 3 C3 0.5930 -1.7840 -2.6940 C.2 1 C29 0.0211 11 | 4 C4 -0.2390 -2.0850 -0.7060 C.2 1 C29 0.0261 12 | 5 C5 -0.8240 -2.8670 0.3860 C.2 1 C29 0.5738 13 | 6 C6 -1.0360 -4.3360 0.1410 C.3 1 C29 -0.2922 14 | 7 O1 -1.1150 -2.3220 1.4320 O.2 1 C29 -0.5649 15 | 8 O2 0.0800 -2.7160 -1.8700 O.3 1 C29 -0.1901 16 | 9 H1 0.9750 0.3610 -2.5290 H 1 C29 0.2012 17 | 10 H2 -0.0770 -0.0300 -0.0090 H 1 C29 0.1685 18 | 11 H3 0.8970 -2.1330 -3.6720 H 1 C29 0.1732 19 | 12 H4 -0.0820 -4.8230 -0.0960 H 1 C29 0.0943 20 | 13 H5 -1.6890 -4.4870 -0.7270 H 1 C29 0.0943 21 | 14 H6 -1.4790 -4.7890 1.0300 H 1 C29 0.0943 22 | @BOND 23 | 1 1 2 1 24 | 2 1 3 2 25 | 3 1 9 1 26 | 4 2 4 2 27 | 5 2 10 1 28 | 6 3 8 1 29 | 7 3 11 1 30 | 8 4 5 1 31 | 9 4 8 1 32 | 10 5 6 1 33 | 11 5 7 2 34 | 12 6 12 1 35 | 13 6 13 1 36 | 14 6 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/C29_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C29 3 | 14 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.6150 -0.5620 -2.0930 C.2 1 C29 -0.2373 9 | 2 C2 0.0740 -0.7580 -0.7950 C.2 1 C29 -0.1463 10 | 3 C3 0.5930 -1.7840 -2.6940 C.2 1 C29 -0.0318 11 | 4 C4 -0.2390 -2.0850 -0.7060 C.2 1 C29 0.0389 12 | 5 C5 -0.8240 -2.8670 0.3860 C.2 1 C29 0.5754 13 | 6 C6 -1.0360 -4.3360 0.1410 C.3 1 C29 -0.3356 14 | 7 O1 -1.1150 -2.3220 1.4320 O.2 1 C29 -0.5444 15 | 8 O2 0.0800 -2.7160 -1.8700 O.3 1 C29 -0.1558 16 | 9 H1 0.9750 0.3610 -2.5290 H 1 C29 0.1863 17 | 10 H2 -0.0770 -0.0300 -0.0090 H 1 C29 0.1694 18 | 11 H3 0.8970 -2.1330 -3.6720 H 1 C29 0.1774 19 | 12 H4 -0.0820 -4.8230 -0.0960 H 1 C29 0.1013 20 | 13 H5 -1.6890 -4.4870 -0.7270 H 1 C29 0.1013 21 | 14 H6 -1.4790 -4.7890 1.0300 H 1 C29 0.1013 22 | @BOND 23 | 1 1 2 1 24 | 2 1 3 2 25 | 3 1 9 1 26 | 4 2 4 2 27 | 5 2 10 1 28 | 6 3 8 1 29 | 7 3 11 1 30 | 8 4 5 1 31 | 9 4 8 1 32 | 10 5 6 1 33 | 11 5 7 2 34 | 12 6 12 1 35 | 13 6 13 1 36 | 14 6 14 1 37 | -------------------------------------------------------------------------------- /Studies/Charges/C32_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C32 3 | 14 15 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0950 -0.0620 -0.8510 C.2 1 C32 0.2204 9 | 2 C2 0.7130 -0.0630 -0.8240 C.2 1 C32 -0.6418 10 | 3 C3 1.5070 -0.2260 -2.8810 C.2 1 C32 0.2394 11 | 4 C4 1.3690 -0.3380 -4.2820 C.2 1 C32 0.2371 12 | 5 C5 -0.9040 -0.3310 -4.1090 C.2 1 C32 0.2564 13 | 6 C6 -0.8840 -0.2220 -2.7520 C.2 1 C32 -0.5736 14 | 7 N1 2.5830 -0.1620 -2.1080 N.2 1 C32 -0.6283 15 | 8 N2 0.2120 -0.3900 -4.8900 N.2 1 C32 -0.5761 16 | 9 N3 0.3340 -0.1690 -2.1300 N.pl3 1 C32 0.5698 17 | 10 H1 2.7560 0.0080 0.0050 H 1 C32 0.1396 18 | 11 H2 -0.0050 0.0000 -0.0180 H 1 C32 0.2808 19 | 12 H3 2.2760 -0.3850 -4.8830 H 1 C32 0.1085 20 | 13 H4 -1.8600 -0.3740 -4.6260 H 1 C32 0.1086 21 | 14 H5 -1.7710 -0.1740 -2.1290 H 1 C32 0.2595 22 | @BOND 23 | 1 1 2 2 24 | 2 1 7 1 25 | 3 1 10 1 26 | 4 2 9 1 27 | 5 2 11 1 28 | 6 3 4 1 29 | 7 3 7 2 30 | 8 3 9 1 31 | 9 4 8 2 32 | 10 4 12 1 33 | 11 5 6 2 34 | 12 5 8 1 35 | 13 5 13 1 36 | 14 6 9 1 37 | 15 6 14 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C32_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C32 3 | 14 15 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0950 -0.0620 -0.8510 C.2 1 C32 0.2542 9 | 2 C2 0.7130 -0.0630 -0.8240 C.2 1 C32 -0.6765 10 | 3 C3 1.5070 -0.2260 -2.8810 C.2 1 C32 0.1790 11 | 4 C4 1.3690 -0.3380 -4.2820 C.2 1 C32 0.2240 12 | 5 C5 -0.9040 -0.3310 -4.1090 C.2 1 C32 0.2613 13 | 6 C6 -0.8840 -0.2220 -2.7520 C.2 1 C32 -0.6030 14 | 7 N1 2.5830 -0.1620 -2.1080 N.2 1 C32 -0.6040 15 | 8 N2 0.2120 -0.3900 -4.8900 N.2 1 C32 -0.5571 16 | 9 N3 0.3340 -0.1690 -2.1300 N.pl3 1 C32 0.6884 17 | 10 H1 2.7560 0.0080 0.0050 H 1 C32 0.1204 18 | 11 H2 -0.0050 0.0000 -0.0180 H 1 C32 0.2693 19 | 12 H3 2.2760 -0.3850 -4.8830 H 1 C32 0.1006 20 | 13 H4 -1.8600 -0.3740 -4.6260 H 1 C32 0.0995 21 | 14 H5 -1.7710 -0.1740 -2.1290 H 1 C32 0.2437 22 | @BOND 23 | 1 1 2 2 24 | 2 1 7 1 25 | 3 1 10 1 26 | 4 2 9 1 27 | 5 2 11 1 28 | 6 3 4 1 29 | 7 3 7 2 30 | 8 3 9 1 31 | 9 4 8 2 32 | 10 4 12 1 33 | 11 5 6 2 34 | 12 5 8 1 35 | 13 5 13 1 36 | 14 6 9 1 37 | 15 6 14 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C32_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C32 3 | 14 15 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0950 -0.0620 -0.8510 C.2 1 C32 0.2854 9 | 2 C2 0.7130 -0.0630 -0.8240 C.2 1 C32 -0.6877 10 | 3 C3 1.5070 -0.2260 -2.8810 C.2 1 C32 0.1954 11 | 4 C4 1.3690 -0.3380 -4.2820 C.2 1 C32 0.2591 12 | 5 C5 -0.9040 -0.3310 -4.1090 C.2 1 C32 0.2941 13 | 6 C6 -0.8840 -0.2220 -2.7520 C.2 1 C32 -0.6127 14 | 7 N1 2.5830 -0.1620 -2.1080 N.2 1 C32 -0.7236 15 | 8 N2 0.2120 -0.3900 -4.8900 N.2 1 C32 -0.6619 16 | 9 N3 0.3340 -0.1690 -2.1300 N.pl3 1 C32 0.7329 17 | 10 H1 2.7560 0.0080 0.0050 H 1 C32 0.1284 18 | 11 H2 -0.0050 0.0000 -0.0180 H 1 C32 0.3022 19 | 12 H3 2.2760 -0.3850 -4.8830 H 1 C32 0.0996 20 | 13 H4 -1.8600 -0.3740 -4.6260 H 1 C32 0.1086 21 | 14 H5 -1.7710 -0.1740 -2.1290 H 1 C32 0.2802 22 | @BOND 23 | 1 1 2 2 24 | 2 1 7 1 25 | 3 1 10 1 26 | 4 2 9 1 27 | 5 2 11 1 28 | 6 3 4 1 29 | 7 3 7 2 30 | 8 3 9 1 31 | 9 4 8 2 32 | 10 4 12 1 33 | 11 5 6 2 34 | 12 5 8 1 35 | 13 5 13 1 36 | 14 6 9 1 37 | 15 6 14 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C32_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C32 3 | 14 15 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 2.0950 -0.0620 -0.8510 C.2 1 C32 0.2729 9 | 2 C2 0.7130 -0.0630 -0.8240 C.2 1 C32 -0.6832 10 | 3 C3 1.5070 -0.2260 -2.8810 C.2 1 C32 0.1888 11 | 4 C4 1.3690 -0.3380 -4.2820 C.2 1 C32 0.2451 12 | 5 C5 -0.9040 -0.3310 -4.1090 C.2 1 C32 0.2810 13 | 6 C6 -0.8840 -0.2220 -2.7520 C.2 1 C32 -0.6088 14 | 7 N1 2.5830 -0.1620 -2.1080 N.2 1 C32 -0.6758 15 | 8 N2 0.2120 -0.3900 -4.8900 N.2 1 C32 -0.6200 16 | 9 N3 0.3340 -0.1690 -2.1300 N.pl3 1 C32 0.7151 17 | 10 H1 2.7560 0.0080 0.0050 H 1 C32 0.1252 18 | 11 H2 -0.0050 0.0000 -0.0180 H 1 C32 0.2890 19 | 12 H3 2.2760 -0.3850 -4.8830 H 1 C32 0.1000 20 | 13 H4 -1.8600 -0.3740 -4.6260 H 1 C32 0.1050 21 | 14 H5 -1.7710 -0.1740 -2.1290 H 1 C32 0.2656 22 | @BOND 23 | 1 1 2 2 24 | 2 1 7 1 25 | 3 1 10 1 26 | 4 2 9 1 27 | 5 2 11 1 28 | 6 3 4 1 29 | 7 3 7 2 30 | 8 3 9 1 31 | 9 4 8 2 32 | 10 4 12 1 33 | 11 5 6 2 34 | 12 5 8 1 35 | 13 5 13 1 36 | 14 6 9 1 37 | 15 6 14 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/C49_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C49 3 | 12 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8850 -1.0360 -0.1090 C.ar 1 C49 -0.1360 9 | 2 C2 0.8090 -0.4650 0.5630 C.ar 1 C49 -0.1360 10 | 3 C3 2.9180 -1.6290 0.6100 C.ar 1 C49 -0.1360 11 | 4 C4 0.7670 -0.4860 1.9530 C.ar 1 C49 -0.1360 12 | 5 C5 2.8760 -1.6500 2.0000 C.ar 1 C49 -0.1360 13 | 6 C6 1.8000 -1.0790 2.6720 C.ar 1 C49 -0.1360 14 | 7 H1 1.9180 -1.0200 -1.1960 H 1 C49 0.1360 15 | 8 H2 0.0010 -0.0010 0.0010 H 1 C49 0.1360 16 | 9 H3 3.7600 -2.0770 0.0850 H 1 C49 0.1360 17 | 10 H4 -0.0750 -0.0380 2.4790 H 1 C49 0.1360 18 | 11 H5 3.6840 -2.1140 2.5620 H 1 C49 0.1360 19 | 12 H6 1.7660 -1.0950 3.7600 H 1 C49 0.1360 20 | @BOND 21 | 1 1 2 ar 22 | 2 1 3 ar 23 | 3 1 7 1 24 | 4 2 4 ar 25 | 5 2 8 1 26 | 6 3 5 ar 27 | 7 3 9 1 28 | 8 4 6 ar 29 | 9 4 10 1 30 | 10 5 6 ar 31 | 11 5 11 1 32 | 12 6 12 1 33 | -------------------------------------------------------------------------------- /Studies/Charges/C49_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C49 3 | 12 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8850 -1.0360 -0.1090 C.ar 1 C49 -0.1214 9 | 2 C2 0.8090 -0.4650 0.5630 C.ar 1 C49 -0.1214 10 | 3 C3 2.9180 -1.6290 0.6100 C.ar 1 C49 -0.1214 11 | 4 C4 0.7670 -0.4860 1.9530 C.ar 1 C49 -0.1214 12 | 5 C5 2.8760 -1.6500 2.0000 C.ar 1 C49 -0.1214 13 | 6 C6 1.8000 -1.0790 2.6720 C.ar 1 C49 -0.1214 14 | 7 H1 1.9180 -1.0200 -1.1960 H 1 C49 0.1214 15 | 8 H2 0.0010 -0.0010 0.0010 H 1 C49 0.1214 16 | 9 H3 3.7600 -2.0770 0.0850 H 1 C49 0.1214 17 | 10 H4 -0.0750 -0.0380 2.4790 H 1 C49 0.1214 18 | 11 H5 3.6840 -2.1140 2.5620 H 1 C49 0.1214 19 | 12 H6 1.7660 -1.0950 3.7600 H 1 C49 0.1214 20 | @BOND 21 | 1 1 2 ar 22 | 2 1 3 ar 23 | 3 1 7 1 24 | 4 2 4 ar 25 | 5 2 8 1 26 | 6 3 5 ar 27 | 7 3 9 1 28 | 8 4 6 ar 29 | 9 4 10 1 30 | 10 5 6 ar 31 | 11 5 11 1 32 | 12 6 12 1 33 | -------------------------------------------------------------------------------- /Studies/Charges/C49_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C49 3 | 12 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8850 -1.0360 -0.1090 C.ar 1 C49 -0.1393 9 | 2 C2 0.8090 -0.4650 0.5630 C.ar 1 C49 -0.1393 10 | 3 C3 2.9180 -1.6290 0.6100 C.ar 1 C49 -0.1393 11 | 4 C4 0.7670 -0.4860 1.9530 C.ar 1 C49 -0.1393 12 | 5 C5 2.8760 -1.6500 2.0000 C.ar 1 C49 -0.1393 13 | 6 C6 1.8000 -1.0790 2.6720 C.ar 1 C49 -0.1393 14 | 7 H1 1.9180 -1.0200 -1.1960 H 1 C49 0.1393 15 | 8 H2 0.0010 -0.0010 0.0010 H 1 C49 0.1393 16 | 9 H3 3.7600 -2.0770 0.0850 H 1 C49 0.1393 17 | 10 H4 -0.0750 -0.0380 2.4790 H 1 C49 0.1393 18 | 11 H5 3.6840 -2.1140 2.5620 H 1 C49 0.1393 19 | 12 H6 1.7660 -1.0950 3.7600 H 1 C49 0.1393 20 | @BOND 21 | 1 1 2 ar 22 | 2 1 3 ar 23 | 3 1 7 1 24 | 4 2 4 ar 25 | 5 2 8 1 26 | 6 3 5 ar 27 | 7 3 9 1 28 | 8 4 6 ar 29 | 9 4 10 1 30 | 10 5 6 ar 31 | 11 5 11 1 32 | 12 6 12 1 33 | -------------------------------------------------------------------------------- /Studies/Charges/C49_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C49 3 | 12 12 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.8850 -1.0360 -0.1090 C.ar 1 C49 -0.1321 9 | 2 C2 0.8090 -0.4650 0.5630 C.ar 1 C49 -0.1321 10 | 3 C3 2.9180 -1.6290 0.6100 C.ar 1 C49 -0.1321 11 | 4 C4 0.7670 -0.4860 1.9530 C.ar 1 C49 -0.1321 12 | 5 C5 2.8760 -1.6500 2.0000 C.ar 1 C49 -0.1321 13 | 6 C6 1.8000 -1.0790 2.6720 C.ar 1 C49 -0.1321 14 | 7 H1 1.9180 -1.0200 -1.1960 H 1 C49 0.1321 15 | 8 H2 0.0010 -0.0010 0.0010 H 1 C49 0.1321 16 | 9 H3 3.7600 -2.0770 0.0850 H 1 C49 0.1321 17 | 10 H4 -0.0750 -0.0380 2.4790 H 1 C49 0.1321 18 | 11 H5 3.6840 -2.1140 2.5620 H 1 C49 0.1321 19 | 12 H6 1.7660 -1.0950 3.7600 H 1 C49 0.1321 20 | @BOND 21 | 1 1 2 ar 22 | 2 1 3 ar 23 | 3 1 7 1 24 | 4 2 4 ar 25 | 5 2 8 1 26 | 6 3 5 ar 27 | 7 3 9 1 28 | 8 4 6 ar 29 | 9 4 10 1 30 | 10 5 6 ar 31 | 11 5 11 1 32 | 12 6 12 1 33 | -------------------------------------------------------------------------------- /Studies/Charges/C54_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C54 3 | 14 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0150 0.5130 -0.0290 C.3 1 C54 0.0933 9 | 2 C2 0.9020 0.2950 -2.5240 C.3 1 C54 0.0933 10 | 3 C3 1.1510 1.2250 -1.3520 C.3 1 C54 0.1959 11 | 4 O1 0.8910 1.4820 0.9840 O.3 1 C54 -0.5887 12 | 5 O2 1.1960 1.0540 -3.6840 O.3 1 C54 -0.5887 13 | 6 O3 2.4490 1.7580 -1.4500 O.3 1 C54 -0.5876 14 | 7 H1 1.9100 -0.1170 0.1080 H 1 C54 0.0446 15 | 8 H2 0.1300 -0.1500 -0.0660 H 1 C54 0.0446 16 | 9 H3 -0.1420 -0.0580 -2.5270 H 1 C54 0.0446 17 | 10 H4 1.5700 -0.5790 -2.4430 H 1 C54 0.0446 18 | 11 H5 0.3930 2.0300 -1.3780 H 1 C54 0.0346 19 | 12 H6 0.9880 1.0390 1.8310 H 1 C54 0.3920 20 | 13 H7 1.2990 0.4530 -4.4270 H 1 C54 0.3920 21 | 14 H8 2.5420 2.0000 -2.3820 H 1 C54 0.3858 22 | @BOND 23 | 1 1 3 1 24 | 2 1 4 1 25 | 3 1 7 1 26 | 4 1 8 1 27 | 5 2 3 1 28 | 6 2 5 1 29 | 7 2 9 1 30 | 8 2 10 1 31 | 9 3 6 1 32 | 10 3 11 1 33 | 11 4 12 1 34 | 12 5 13 1 35 | 13 6 14 1 36 | -------------------------------------------------------------------------------- /Studies/Charges/C54_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C54 3 | 14 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0150 0.5130 -0.0290 C.3 1 C54 0.0279 9 | 2 C2 0.9020 0.2950 -2.5240 C.3 1 C54 0.0279 10 | 3 C3 1.1510 1.2250 -1.3520 C.3 1 C54 0.1077 11 | 4 O1 0.8910 1.4820 0.9840 O.3 1 C54 -0.5066 12 | 5 O2 1.1960 1.0540 -3.6840 O.3 1 C54 -0.5066 13 | 6 O3 2.4490 1.7580 -1.4500 O.3 1 C54 -0.5092 14 | 7 H1 1.9100 -0.1170 0.1080 H 1 C54 0.0623 15 | 8 H2 0.1300 -0.1500 -0.0660 H 1 C54 0.0623 16 | 9 H3 -0.1420 -0.0580 -2.5270 H 1 C54 0.0623 17 | 10 H4 1.5700 -0.5790 -2.4430 H 1 C54 0.0623 18 | 11 H5 0.3930 2.0300 -1.3780 H 1 C54 0.0661 19 | 12 H6 0.9880 1.0390 1.8310 H 1 C54 0.3494 20 | 13 H7 1.2990 0.4530 -4.4270 H 1 C54 0.3494 21 | 14 H8 2.5420 2.0000 -2.3820 H 1 C54 0.3449 22 | @BOND 23 | 1 1 3 1 24 | 2 1 4 1 25 | 3 1 7 1 26 | 4 1 8 1 27 | 5 2 3 1 28 | 6 2 5 1 29 | 7 2 9 1 30 | 8 2 10 1 31 | 9 3 6 1 32 | 10 3 11 1 33 | 11 4 12 1 34 | 12 5 13 1 35 | 13 6 14 1 36 | -------------------------------------------------------------------------------- /Studies/Charges/C54_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C54 3 | 14 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0150 0.5130 -0.0290 C.3 1 C54 0.0578 9 | 2 C2 0.9020 0.2950 -2.5240 C.3 1 C54 0.0578 10 | 3 C3 1.1510 1.2250 -1.3520 C.3 1 C54 0.1287 11 | 4 O1 0.8910 1.4820 0.9840 O.3 1 C54 -0.6172 12 | 5 O2 1.1960 1.0540 -3.6840 O.3 1 C54 -0.6172 13 | 6 O3 2.4490 1.7580 -1.4500 O.3 1 C54 -0.6318 14 | 7 H1 1.9100 -0.1170 0.1080 H 1 C54 0.0749 15 | 8 H2 0.1300 -0.1500 -0.0660 H 1 C54 0.0749 16 | 9 H3 -0.1420 -0.0580 -2.5270 H 1 C54 0.0749 17 | 10 H4 1.5700 -0.5790 -2.4430 H 1 C54 0.0749 18 | 11 H5 0.3930 2.0300 -1.3780 H 1 C54 0.0839 19 | 12 H6 0.9880 1.0390 1.8310 H 1 C54 0.4123 20 | 13 H7 1.2990 0.4530 -4.4270 H 1 C54 0.4123 21 | 14 H8 2.5420 2.0000 -2.3820 H 1 C54 0.4140 22 | @BOND 23 | 1 1 3 1 24 | 2 1 4 1 25 | 3 1 7 1 26 | 4 1 8 1 27 | 5 2 3 1 28 | 6 2 5 1 29 | 7 2 9 1 30 | 8 2 10 1 31 | 9 3 6 1 32 | 10 3 11 1 33 | 11 4 12 1 34 | 12 5 13 1 35 | 13 6 14 1 36 | -------------------------------------------------------------------------------- /Studies/Charges/C54_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | C54 3 | 14 13 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0150 0.5130 -0.0290 C.3 1 C54 0.0458 9 | 2 C2 0.9020 0.2950 -2.5240 C.3 1 C54 0.0458 10 | 3 C3 1.1510 1.2250 -1.3520 C.3 1 C54 0.1203 11 | 4 O1 0.8910 1.4820 0.9840 O.3 1 C54 -0.5730 12 | 5 O2 1.1960 1.0540 -3.6840 O.3 1 C54 -0.5730 13 | 6 O3 2.4490 1.7580 -1.4500 O.3 1 C54 -0.5828 14 | 7 H1 1.9100 -0.1170 0.1080 H 1 C54 0.0699 15 | 8 H2 0.1300 -0.1500 -0.0660 H 1 C54 0.0699 16 | 9 H3 -0.1420 -0.0580 -2.5270 H 1 C54 0.0699 17 | 10 H4 1.5700 -0.5790 -2.4430 H 1 C54 0.0699 18 | 11 H5 0.3930 2.0300 -1.3780 H 1 C54 0.0768 19 | 12 H6 0.9880 1.0390 1.8310 H 1 C54 0.3871 20 | 13 H7 1.2990 0.4530 -4.4270 H 1 C54 0.3871 21 | 14 H8 2.5420 2.0000 -2.3820 H 1 C54 0.3864 22 | @BOND 23 | 1 1 3 1 24 | 2 1 4 1 25 | 3 1 7 1 26 | 4 1 8 1 27 | 5 2 3 1 28 | 6 2 5 1 29 | 7 2 9 1 30 | 8 2 10 1 31 | 9 3 6 1 32 | 10 3 11 1 33 | 11 4 12 1 34 | 12 5 13 1 35 | 13 6 14 1 36 | -------------------------------------------------------------------------------- /Studies/Charges/DEE_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | DEE 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.9030 1.4540 0.5560 C.3 1 MOL1 -0.148000 9 | 2 C2 1.9370 1.3290 -4.0520 C.3 1 MOL1 -0.148000 10 | 3 C3 1.9100 0.9070 -0.4250 C.3 1 MOL1 0.199700 11 | 4 C4 2.4230 0.8450 -2.7080 C.3 1 MOL1 0.199700 12 | 5 O1 1.5390 1.3090 -1.7190 O.3 1 MOL1 -0.370900 13 | 6 H1 0.8740 2.5480 0.5040 H 1 MOL1 0.044300 14 | 7 H2 -0.1000 1.0750 0.3250 H 1 MOL1 0.044300 15 | 8 H3 1.1600 1.1590 1.5800 H 1 MOL1 0.044300 16 | 9 H4 0.9280 0.9510 -4.2530 H 1 MOL1 0.044300 17 | 10 H5 1.9020 2.4240 -4.0740 H 1 MOL1 0.044300 18 | 11 H6 2.6040 0.9850 -4.8510 H 1 MOL1 0.044300 19 | 12 H7 1.9530 -0.1970 -0.3670 H 1 MOL1 0.000500 20 | 13 H8 2.9260 1.2760 -0.1880 H 1 MOL1 0.000500 21 | 14 H9 3.4460 1.2130 -2.5070 H 1 MOL1 0.000500 22 | 15 H10 2.4730 -0.2590 -2.6860 H 1 MOL1 0.000500 23 | @BOND 24 | 1 1 3 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 4 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 2 11 1 32 | 9 3 5 1 33 | 10 3 12 1 34 | 11 3 13 1 35 | 12 4 5 1 36 | 13 4 14 1 37 | 14 4 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/DEE_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | DEE 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.9030 1.4540 0.5560 C.3 1 MOL1 -0.221000 9 | 2 C2 1.9370 1.3290 -4.0520 C.3 1 MOL1 -0.221000 10 | 3 C3 1.9100 0.9070 -0.4250 C.3 1 MOL1 0.244900 11 | 4 C4 2.4230 0.8450 -2.7080 C.3 1 MOL1 0.244900 12 | 5 O1 1.5390 1.3090 -1.7190 O.3 1 MOL1 -0.468600 13 | 6 H1 0.8740 2.5480 0.5040 H 1 MOL1 0.063600 14 | 7 H2 -0.1000 1.0750 0.3250 H 1 MOL1 0.063600 15 | 8 H3 1.1600 1.1590 1.5800 H 1 MOL1 0.063600 16 | 9 H4 0.9280 0.9510 -4.2530 H 1 MOL1 0.063600 17 | 10 H5 1.9020 2.4240 -4.0740 H 1 MOL1 0.063600 18 | 11 H6 2.6040 0.9850 -4.8510 H 1 MOL1 0.063600 19 | 12 H7 1.9530 -0.1970 -0.3670 H 1 MOL1 0.009900 20 | 13 H8 2.9260 1.2760 -0.1880 H 1 MOL1 0.009900 21 | 14 H9 3.4460 1.2130 -2.5070 H 1 MOL1 0.009900 22 | 15 H10 2.4730 -0.2590 -2.6860 H 1 MOL1 0.009900 23 | @BOND 24 | 1 1 3 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 4 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 2 11 1 32 | 9 3 5 1 33 | 10 3 12 1 34 | 11 3 13 1 35 | 12 4 5 1 36 | 13 4 14 1 37 | 14 4 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/DEE_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | DEE 3 | 15 14 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.9030 1.4540 0.5560 C.3 1 MOL1 -0.191800 9 | 2 C2 1.9370 1.3290 -4.0520 C.3 1 MOL1 -0.191800 10 | 3 C3 1.9100 0.9070 -0.4250 C.3 1 MOL1 0.226820 11 | 4 C4 2.4230 0.8450 -2.7080 C.3 1 MOL1 0.226820 12 | 5 O1 1.5390 1.3090 -1.7190 O.3 1 MOL1 -0.429520 13 | 6 H1 0.8740 2.5480 0.5040 H 1 MOL1 0.055880 14 | 7 H2 -0.1000 1.0750 0.3250 H 1 MOL1 0.055880 15 | 8 H3 1.1600 1.1590 1.5800 H 1 MOL1 0.055880 16 | 9 H4 0.9280 0.9510 -4.2530 H 1 MOL1 0.055880 17 | 10 H5 1.9020 2.4240 -4.0740 H 1 MOL1 0.055880 18 | 11 H6 2.6040 0.9850 -4.8510 H 1 MOL1 0.055880 19 | 12 H7 1.9530 -0.1970 -0.3670 H 1 MOL1 0.006140 20 | 13 H8 2.9260 1.2760 -0.1880 H 1 MOL1 0.006140 21 | 14 H9 3.4460 1.2130 -2.5070 H 1 MOL1 0.006140 22 | 15 H10 2.4730 -0.2590 -2.6860 H 1 MOL1 0.006140 23 | @BOND 24 | 1 1 3 1 25 | 2 1 6 1 26 | 3 1 7 1 27 | 4 1 8 1 28 | 5 2 4 1 29 | 6 2 9 1 30 | 7 2 10 1 31 | 8 2 11 1 32 | 9 3 5 1 33 | 10 3 12 1 34 | 11 3 13 1 35 | 12 4 5 1 36 | 13 4 14 1 37 | 14 4 15 1 38 | -------------------------------------------------------------------------------- /Studies/Charges/FUR_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | FUR 3 | 9 9 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 0.5750 -0.5370 -2.1130 C.2 1 FUR -0.198600 10 | 2 C2 0.0970 -0.7450 -0.7820 C.2 1 FUR -0.198600 11 | 3 C3 0.5060 -1.7460 -2.7260 C.2 1 FUR -0.058200 12 | 4 C4 -0.2220 -2.0620 -0.7030 C.2 1 FUR -0.058200 13 | 5 O1 0.0220 -2.6840 -1.8790 O.3 1 FUR -0.169500 14 | 6 H1 0.9230 0.3890 -2.5520 H 1 FUR 0.166600 15 | 7 H2 0.0030 -0.0110 0.0080 H 1 FUR 0.166600 16 | 8 H3 0.7530 -2.0910 -3.7200 H 1 FUR 0.175000 17 | 9 H4 -0.6170 -2.6860 0.0870 H 1 FUR 0.175000 18 | @BOND 19 | 1 1 2 1 20 | 2 1 3 2 21 | 3 1 6 1 22 | 4 2 4 2 23 | 5 2 7 1 24 | 6 3 5 1 25 | 7 3 8 1 26 | 8 4 5 1 27 | 9 4 9 1 28 | @SUBSTRUCTURE 29 | 1 FUR 1 TEMP 0 **** **** 0 ROOT 30 | -------------------------------------------------------------------------------- /Studies/Charges/FUR_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | FUR 3 | 9 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5750 -0.5370 -2.1130 C.2 1 MOL1 -0.182900 9 | 2 C2 0.0970 -0.7450 -0.7820 C.2 1 MOL1 -0.182900 10 | 3 C3 0.5060 -1.7460 -2.7260 C.2 1 MOL1 -0.068600 11 | 4 C4 -0.2220 -2.0620 -0.7030 C.2 1 MOL1 -0.068600 12 | 5 O1 0.0220 -2.6840 -1.8790 O.3 1 MOL1 -0.118000 13 | 6 H1 0.9230 0.3890 -2.5520 H 1 MOL1 0.154000 14 | 7 H2 0.0030 -0.0110 0.0080 H 1 MOL1 0.154000 15 | 8 H3 0.7530 -2.0910 -3.7200 H 1 MOL1 0.156400 16 | 9 H4 -0.6170 -2.6860 0.0870 H 1 MOL1 0.156400 17 | @BOND 18 | 1 1 2 1 19 | 2 1 3 2 20 | 3 1 6 1 21 | 4 2 4 2 22 | 5 2 7 1 23 | 6 3 5 1 24 | 7 3 8 1 25 | 8 4 5 1 26 | 9 4 9 1 27 | -------------------------------------------------------------------------------- /Studies/Charges/FUR_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | FUR 3 | 9 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5750 -0.5370 -2.1130 C.2 1 MOL1 -0.192800 9 | 2 C2 0.0970 -0.7450 -0.7820 C.2 1 MOL1 -0.192800 10 | 3 C3 0.5060 -1.7460 -2.7260 C.2 1 MOL1 -0.072500 11 | 4 C4 -0.2220 -2.0620 -0.7030 C.2 1 MOL1 -0.072500 12 | 5 O1 0.0220 -2.6840 -1.8790 O.3 1 MOL1 -0.120100 13 | 6 H1 0.9230 0.3890 -2.5520 H 1 MOL1 0.163900 14 | 7 H2 0.0030 -0.0110 0.0080 H 1 MOL1 0.163900 15 | 8 H3 0.7530 -2.0910 -3.7200 H 1 MOL1 0.161400 16 | 9 H4 -0.6170 -2.6860 0.0870 H 1 MOL1 0.161400 17 | @BOND 18 | 1 1 2 1 19 | 2 1 3 2 20 | 3 1 6 1 21 | 4 2 4 2 22 | 5 2 7 1 23 | 6 3 5 1 24 | 7 3 8 1 25 | 8 4 5 1 26 | 9 4 9 1 27 | -------------------------------------------------------------------------------- /Studies/Charges/FUR_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | FUR 3 | 9 9 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.5750 -0.5370 -2.1130 C.2 1 MOL1 -0.188840 9 | 2 C2 0.0970 -0.7450 -0.7820 C.2 1 MOL1 -0.188840 10 | 3 C3 0.5060 -1.7460 -2.7260 C.2 1 MOL1 -0.070940 11 | 4 C4 -0.2220 -2.0620 -0.7030 C.2 1 MOL1 -0.070940 12 | 5 O1 0.0220 -2.6840 -1.8790 O.3 1 MOL1 -0.119260 13 | 6 H1 0.9230 0.3890 -2.5520 H 1 MOL1 0.159940 14 | 7 H2 0.0030 -0.0110 0.0080 H 1 MOL1 0.159940 15 | 8 H3 0.7530 -2.0910 -3.7200 H 1 MOL1 0.159400 16 | 9 H4 -0.6170 -2.6860 0.0870 H 1 MOL1 0.159400 17 | @BOND 18 | 1 1 2 1 19 | 2 1 3 2 20 | 3 1 6 1 21 | 4 2 4 2 22 | 5 2 7 1 23 | 6 3 5 1 24 | 7 3 8 1 25 | 8 4 5 1 26 | 9 4 9 1 27 | -------------------------------------------------------------------------------- /Studies/Charges/IPP_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | IPP 3 | 12 11 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 1.0720 0.0330 0.2010 C.3 1 IPP -0.275000 10 | 2 C2 2.8230 1.0340 1.7120 C.3 1 IPP -0.275000 11 | 3 C3 1.3450 0.9030 1.4150 C.3 1 IPP 0.591100 12 | 4 O1 0.8650 2.2230 1.2150 O.3 1 IPP -0.719800 13 | 5 H1 1.5530 0.4630 -0.6870 H 1 IPP 0.060900 14 | 6 H2 1.4490 -0.9870 0.3460 H 1 IPP 0.060900 15 | 7 H3 -0.0060 -0.0380 0.0040 H 1 IPP 0.060900 16 | 8 H4 3.3420 1.4720 0.8500 H 1 IPP 0.060900 17 | 9 H5 3.2680 0.0560 1.9310 H 1 IPP 0.060900 18 | 10 H6 2.9790 1.6920 2.5740 H 1 IPP 0.060900 19 | 11 H7 0.8480 0.4510 2.2940 H 1 IPP -0.097400 20 | 12 H8 -0.0710 2.1610 1.0000 H 1 IPP 0.410700 21 | @BOND 22 | 1 1 3 1 23 | 2 1 5 1 24 | 3 1 6 1 25 | 4 1 7 1 26 | 5 2 3 1 27 | 6 2 8 1 28 | 7 2 9 1 29 | 8 2 10 1 30 | 9 3 4 1 31 | 10 3 11 1 32 | 11 4 12 1 33 | @SUBSTRUCTURE 34 | 1 IPP 1 TEMP 0 **** **** 0 ROOT 35 | -------------------------------------------------------------------------------- /Studies/Charges/IPP_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | IPP 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0720 0.0330 0.2010 C.3 1 MOL1 -0.329700 9 | 2 C2 2.8230 1.0340 1.7120 C.3 1 MOL1 -0.329700 10 | 3 C3 1.3450 0.9030 1.4150 C.3 1 MOL1 0.530800 11 | 4 O1 0.8650 2.2230 1.2150 O.3 1 MOL1 -0.651900 12 | 5 H1 1.5530 0.4630 -0.6870 H 1 MOL1 0.080000 13 | 6 H2 1.4490 -0.9870 0.3460 H 1 MOL1 0.080000 14 | 7 H3 -0.0060 -0.0380 0.0040 H 1 MOL1 0.080000 15 | 8 H4 3.3420 1.4720 0.8500 H 1 MOL1 0.080000 16 | 9 H5 3.2680 0.0560 1.9310 H 1 MOL1 0.080000 17 | 10 H6 2.9790 1.6920 2.5740 H 1 MOL1 0.080000 18 | 11 H7 0.8480 0.4510 2.2940 H 1 MOL1 -0.072300 19 | 12 H8 -0.0710 2.1610 1.0000 H 1 MOL1 0.372900 20 | @BOND 21 | 1 1 3 1 22 | 2 1 5 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 3 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 2 10 1 29 | 9 3 4 1 30 | 10 3 11 1 31 | 11 4 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/IPP_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | IPP 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0720 0.0330 0.2010 C.3 1 MOL1 -0.412900 9 | 2 C2 2.8230 1.0340 1.7120 C.3 1 MOL1 -0.412900 10 | 3 C3 1.3450 0.9030 1.4150 C.3 1 MOL1 0.586500 11 | 4 O1 0.8650 2.2230 1.2150 O.3 1 MOL1 -0.755300 12 | 5 H1 1.5530 0.4630 -0.6870 H 1 MOL1 0.102800 13 | 6 H2 1.4490 -0.9870 0.3460 H 1 MOL1 0.102800 14 | 7 H3 -0.0060 -0.0380 0.0040 H 1 MOL1 0.102800 15 | 8 H4 3.3420 1.4720 0.8500 H 1 MOL1 0.102800 16 | 9 H5 3.2680 0.0560 1.9310 H 1 MOL1 0.102800 17 | 10 H6 2.9790 1.6920 2.5740 H 1 MOL1 0.102800 18 | 11 H7 0.8480 0.4510 2.2940 H 1 MOL1 -0.049700 19 | 12 H8 -0.0710 2.1610 1.0000 H 1 MOL1 0.427700 20 | @BOND 21 | 1 1 3 1 22 | 2 1 5 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 3 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 2 10 1 29 | 9 3 4 1 30 | 10 3 11 1 31 | 11 4 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/IPP_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | IPP 3 | 12 11 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0720 0.0330 0.2010 C.3 1 MOL1 -0.379620 9 | 2 C2 2.8230 1.0340 1.7120 C.3 1 MOL1 -0.379620 10 | 3 C3 1.3450 0.9030 1.4150 C.3 1 MOL1 0.564220 11 | 4 O1 0.8650 2.2230 1.2150 O.3 1 MOL1 -0.713940 12 | 5 H1 1.5530 0.4630 -0.6870 H 1 MOL1 0.093680 13 | 6 H2 1.4490 -0.9870 0.3460 H 1 MOL1 0.093680 14 | 7 H3 -0.0060 -0.0380 0.0040 H 1 MOL1 0.093680 15 | 8 H4 3.3420 1.4720 0.8500 H 1 MOL1 0.093680 16 | 9 H5 3.2680 0.0560 1.9310 H 1 MOL1 0.093680 17 | 10 H6 2.9790 1.6920 2.5740 H 1 MOL1 0.093680 18 | 11 H7 0.8480 0.4510 2.2940 H 1 MOL1 -0.058740 19 | 12 H8 -0.0710 2.1610 1.0000 H 1 MOL1 0.405780 20 | @BOND 21 | 1 1 3 1 22 | 2 1 5 1 23 | 3 1 6 1 24 | 4 1 7 1 25 | 5 2 3 1 26 | 6 2 8 1 27 | 7 2 9 1 28 | 8 2 10 1 29 | 9 3 4 1 30 | 10 3 11 1 31 | 11 4 12 1 32 | -------------------------------------------------------------------------------- /Studies/Charges/MAA_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAA 3 | 7 6 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 -0.6500 -0.7370 0.4880 C.3 1 MAA 0.314000 10 | 2 N1 -1.8790 -0.6980 -0.2890 N.3 1 MAA -0.983200 11 | 3 H1 -0.3540 -1.7270 0.8800 H 1 MAA -0.019500 12 | 4 H2 -0.7400 -0.0580 1.3460 H 1 MAA -0.019500 13 | 5 H3 0.1800 -0.3640 -0.1250 H 1 MAA -0.019500 14 | 6 H4 -2.6440 -1.0630 0.2740 H 1 MAA 0.363800 15 | 7 H5 -1.8020 -1.3430 -1.0720 H 1 MAA 0.363800 16 | @BOND 17 | 1 1 2 1 18 | 2 1 3 1 19 | 3 1 4 1 20 | 4 1 5 1 21 | 5 2 6 1 22 | 6 2 7 1 23 | @SUBSTRUCTURE 24 | 1 MAA 1 TEMP 0 **** **** 0 ROOT 25 | -------------------------------------------------------------------------------- /Studies/Charges/MAA_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAA 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.6500 -0.7370 0.4880 C.3 1 MOL1 0.221800 9 | 2 N1 -1.8790 -0.6980 -0.2890 N.3 1 MOL1 -0.861600 10 | 3 H1 -0.3540 -1.7270 0.8800 H 1 MOL1 -0.002600 11 | 4 H2 -0.7400 -0.0580 1.3460 H 1 MOL1 -0.002600 12 | 5 H3 0.1800 -0.3640 -0.1250 H 1 MOL1 -0.002600 13 | 6 H4 -2.6440 -1.0630 0.2740 H 1 MOL1 0.323900 14 | 7 H5 -1.8020 -1.3430 -1.0720 H 1 MOL1 0.323900 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/MAA_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAA 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.6500 -0.7370 0.4880 C.3 1 MOL1 0.324900 9 | 2 N1 -1.8790 -0.6980 -0.2890 N.3 1 MOL1 -1.053400 10 | 3 H1 -0.3540 -1.7270 0.8800 H 1 MOL1 -0.016900 11 | 4 H2 -0.7400 -0.0580 1.3460 H 1 MOL1 -0.016900 12 | 5 H3 0.1800 -0.3640 -0.1250 H 1 MOL1 -0.016900 13 | 6 H4 -2.6440 -1.0630 0.2740 H 1 MOL1 0.389500 14 | 7 H5 -1.8020 -1.3430 -1.0720 H 1 MOL1 0.389500 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/MAA_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAA 3 | 7 6 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.6500 -0.7370 0.4880 C.3 1 MOL1 0.283660 9 | 2 N1 -1.8790 -0.6980 -0.2890 N.3 1 MOL1 -0.976680 10 | 3 H1 -0.3540 -1.7270 0.8800 H 1 MOL1 -0.011180 11 | 4 H2 -0.7400 -0.0580 1.3460 H 1 MOL1 -0.011180 12 | 5 H3 0.1800 -0.3640 -0.1250 H 1 MOL1 -0.011180 13 | 6 H4 -2.6440 -1.0630 0.2740 H 1 MOL1 0.363260 14 | 7 H5 -1.8020 -1.3430 -1.0720 H 1 MOL1 0.363260 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | 6 2 7 1 22 | -------------------------------------------------------------------------------- /Studies/Charges/MAC_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAC 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -1.7450 -0.5420 -1.1650 C.2 1 MAC1 0.847100 9 | 2 C2 -0.9920 -0.5210 0.1300 C.3 1 MAC1 -0.632500 10 | 3 C3 -2.4660 0.7440 -2.9700 C.3 1 MAC1 -0.163300 11 | 4 O1 -2.2730 -1.5040 -1.6610 O.2 1 MAC1 -0.562100 12 | 5 O2 -1.7660 0.6790 -1.7310 O.3 1 MAC1 -0.355500 13 | 6 H1 0.0350 -0.1810 -0.0430 H 1 MAC1 0.173600 14 | 7 H2 -0.9900 -1.5210 0.5670 H 1 MAC1 0.173600 15 | 8 H3 -1.4580 0.1920 0.8190 H 1 MAC1 0.173600 16 | 9 H4 -2.3950 1.7820 -3.2990 H 1 MAC1 0.115200 17 | 10 H5 -3.5130 0.4510 -2.8390 H 1 MAC1 0.115200 18 | 11 H6 -2.0100 0.0740 -3.7070 H 1 MAC1 0.115200 19 | @BOND 20 | 1 1 2 1 21 | 2 1 4 2 22 | 3 1 5 1 23 | 4 2 6 1 24 | 5 2 7 1 25 | 6 2 8 1 26 | 7 3 5 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 3 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/MAC_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAC 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -1.7450 -0.5420 -1.1650 C.2 1 MAC1 0.902900 9 | 2 C2 -0.9920 -0.5210 0.1300 C.3 1 MAC1 -0.666500 10 | 3 C3 -2.4660 0.7440 -2.9700 C.3 1 MAC1 -0.137400 11 | 4 O1 -2.2730 -1.5040 -1.6610 O.2 1 MAC1 -0.644700 12 | 5 O2 -1.7660 0.6790 -1.7310 O.3 1 MAC1 -0.387800 13 | 6 H1 0.0350 -0.1810 -0.0430 H 1 MAC1 0.191300 14 | 7 H2 -0.9900 -1.5210 0.5670 H 1 MAC1 0.191300 15 | 8 H3 -1.4580 0.1920 0.8190 H 1 MAC1 0.191300 16 | 9 H4 -2.3950 1.7820 -3.2990 H 1 MAC1 0.119800 17 | 10 H5 -3.5130 0.4510 -2.8390 H 1 MAC1 0.119800 18 | 11 H6 -2.0100 0.0740 -3.7070 H 1 MAC1 0.119800 19 | @BOND 20 | 1 1 2 1 21 | 2 1 4 2 22 | 3 1 5 1 23 | 4 2 6 1 24 | 5 2 7 1 25 | 6 2 8 1 26 | 7 3 5 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 3 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/MAC_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MAC 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -1.7450 -0.5420 -1.1650 C.2 1 MAC1 0.880580 9 | 2 C2 -0.9920 -0.5210 0.1300 C.3 1 MAC1 -0.652900 10 | 3 C3 -2.4660 0.7440 -2.9700 C.3 1 MAC1 -0.147760 11 | 4 O1 -2.2730 -1.5040 -1.6610 O.2 1 MAC1 -0.611660 12 | 5 O2 -1.7660 0.6790 -1.7310 O.3 1 MAC1 -0.374880 13 | 6 H1 0.0350 -0.1810 -0.0430 H 1 MAC1 0.184220 14 | 7 H2 -0.9900 -1.5210 0.5670 H 1 MAC1 0.184220 15 | 8 H3 -1.4580 0.1920 0.8190 H 1 MAC1 0.184220 16 | 9 H4 -2.3950 1.7820 -3.2990 H 1 MAC1 0.117960 17 | 10 H5 -3.5130 0.4510 -2.8390 H 1 MAC1 0.117960 18 | 11 H6 -2.0100 0.0740 -3.7070 H 1 MAC1 0.117960 19 | @BOND 20 | 1 1 2 1 21 | 2 1 4 2 22 | 3 1 5 1 23 | 4 2 6 1 24 | 5 2 7 1 25 | 6 2 8 1 26 | 7 3 5 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 3 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/MTH_R1_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MTH 3 | 6 5 1 0 0 4 | SMALL 5 | No Charge or Current Charge 6 | 7 | 8 | @ATOM 9 | 1 C1 0.2850 0.7820 0.7000 C.3 1 MTH 0.159700 10 | 2 O1 -0.3170 2.0050 0.3560 O.3 1 MTH -0.655500 11 | 3 H1 -0.0840 0.5090 1.6950 H 1 MTH 0.024500 12 | 4 H2 1.3850 0.8430 0.7560 H 1 MTH 0.024500 13 | 5 H3 0.0220 -0.0380 0.0100 H 1 MTH 0.024500 14 | 6 H4 0.0020 2.2510 -0.5170 H 1 MTH 0.422300 15 | @BOND 16 | 1 1 2 1 17 | 2 1 3 1 18 | 3 1 4 1 19 | 4 1 5 1 20 | 5 2 6 1 21 | @SUBSTRUCTURE 22 | 1 MTH 1 TEMP 0 **** **** 0 ROOT 23 | -------------------------------------------------------------------------------- /Studies/Charges/MTH_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MTH 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.2850 0.7820 0.7000 C.3 1 MOL1 0.099900 9 | 2 O1 -0.3170 2.0050 0.3560 O.3 1 MOL1 -0.578400 10 | 3 H1 -0.0840 0.5090 1.6950 H 1 MOL1 0.032100 11 | 4 H2 1.3850 0.8430 0.7560 H 1 MOL1 0.032100 12 | 5 H3 0.0220 -0.0380 0.0100 H 1 MOL1 0.032100 13 | 6 H4 0.0020 2.2510 -0.5170 H 1 MOL1 0.382300 14 | @BOND 15 | 1 1 2 1 16 | 2 1 3 1 17 | 3 1 4 1 18 | 4 1 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/MTH_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MTH 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.2850 0.7820 0.7000 C.3 1 MOL1 0.139300 9 | 2 O1 -0.3170 2.0050 0.3560 O.3 1 MOL1 -0.675300 10 | 3 H1 -0.0840 0.5090 1.6950 H 1 MOL1 0.033200 11 | 4 H2 1.3850 0.8430 0.7560 H 1 MOL1 0.033200 12 | 5 H3 0.0220 -0.0380 0.0100 H 1 MOL1 0.033200 13 | 6 H4 0.0020 2.2510 -0.5170 H 1 MOL1 0.436500 14 | @BOND 15 | 1 1 2 1 16 | 2 1 3 1 17 | 3 1 4 1 18 | 4 1 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/MTH_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | MTH 3 | 6 5 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 0.2850 0.7820 0.7000 C.3 1 MOL1 0.123540 9 | 2 O1 -0.3170 2.0050 0.3560 O.3 1 MOL1 -0.636540 10 | 3 H1 -0.0840 0.5090 1.6950 H 1 MOL1 0.032760 11 | 4 H2 1.3850 0.8430 0.7560 H 1 MOL1 0.032760 12 | 5 H3 0.0220 -0.0380 0.0100 H 1 MOL1 0.032760 13 | 6 H4 0.0020 2.2510 -0.5170 H 1 MOL1 0.414820 14 | @BOND 15 | 1 1 2 1 16 | 2 1 3 1 17 | 3 1 4 1 18 | 4 1 5 1 19 | 5 2 6 1 20 | -------------------------------------------------------------------------------- /Studies/Charges/PAC_R2_0.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | PAC 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.8920 -1.5300 -2.1300 C.2 1 PAC1 0.595600 9 | 2 C2 0.7840 -0.5940 -0.5060 C.3 1 PAC1 -0.107300 10 | 3 C3 0.4210 -0.7980 -1.9630 C.3 1 PAC1 -0.039500 11 | 4 O1 -1.5750 -1.9090 -1.2230 O.2 1 PAC1 -0.495100 12 | 5 O2 -1.2770 -1.7460 -3.4080 O.3 1 PAC1 -0.496100 13 | 6 H1 0.8640 -1.5570 0.0090 H 1 PAC1 0.041500 14 | 7 H2 1.7360 -0.0630 -0.4100 H 1 PAC1 0.041500 15 | 8 H3 0.0060 -0.0180 0.0070 H 1 PAC1 0.041500 16 | 9 H4 0.3430 0.1640 -2.4930 H 1 PAC1 0.038100 17 | 10 H5 1.1980 -1.3710 -2.4910 H 1 PAC1 0.038100 18 | 11 H6 -0.6160 -1.3790 -4.0080 H 1 PAC1 0.341800 19 | @BOND 20 | 1 1 3 1 21 | 2 1 4 2 22 | 3 1 5 1 23 | 4 2 3 1 24 | 5 2 6 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 5 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/PAC_R2_100.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | PAC 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.8920 -1.5300 -2.1300 C.2 1 PAC1 0.669500 9 | 2 C2 0.7840 -0.5940 -0.5060 C.3 1 PAC1 -0.106200 10 | 3 C3 0.4210 -0.7980 -1.9630 C.3 1 PAC1 -0.028500 11 | 4 O1 -1.5750 -1.9090 -1.2230 O.2 1 PAC1 -0.605200 12 | 5 O2 -1.2770 -1.7460 -3.4080 O.3 1 PAC1 -0.573600 13 | 6 H1 0.8640 -1.5570 0.0090 H 1 PAC1 0.042800 14 | 7 H2 1.7360 -0.0630 -0.4100 H 1 PAC1 0.042800 15 | 8 H3 0.0060 -0.0180 0.0070 H 1 PAC1 0.042800 16 | 9 H4 0.3430 0.1640 -2.4930 H 1 PAC1 0.048800 17 | 10 H5 1.1980 -1.3710 -2.4910 H 1 PAC1 0.048800 18 | 11 H6 -0.6160 -1.3790 -4.0080 H 1 PAC1 0.418200 19 | @BOND 20 | 1 1 3 1 21 | 2 1 4 2 22 | 3 1 5 1 23 | 4 2 3 1 24 | 5 2 6 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 5 11 1 30 | -------------------------------------------------------------------------------- /Studies/Charges/PAC_R2_60.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | PAC 3 | 11 10 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 -0.8920 -1.5300 -2.1300 C.2 1 PAC1 0.639940 9 | 2 C2 0.7840 -0.5940 -0.5060 C.3 1 PAC1 -0.106640 10 | 3 C3 0.4210 -0.7980 -1.9630 C.3 1 PAC1 -0.032900 11 | 4 O1 -1.5750 -1.9090 -1.2230 O.2 1 PAC1 -0.561160 12 | 5 O2 -1.2770 -1.7460 -3.4080 O.3 1 PAC1 -0.542600 13 | 6 H1 0.8640 -1.5570 0.0090 H 1 PAC1 0.042280 14 | 7 H2 1.7360 -0.0630 -0.4100 H 1 PAC1 0.042280 15 | 8 H3 0.0060 -0.0180 0.0070 H 1 PAC1 0.042280 16 | 9 H4 0.3430 0.1640 -2.4930 H 1 PAC1 0.044520 17 | 10 H5 1.1980 -1.3710 -2.4910 H 1 PAC1 0.044520 18 | 11 H6 -0.6160 -1.3790 -4.0080 H 1 PAC1 0.387640 19 | @BOND 20 | 1 1 3 1 21 | 2 1 4 2 22 | 3 1 5 1 23 | 4 2 3 1 24 | 5 2 6 1 25 | 6 2 7 1 26 | 7 2 8 1 27 | 8 3 9 1 28 | 9 3 10 1 29 | 10 5 11 1 30 | -------------------------------------------------------------------------------- /Studies/Results/dens_training_data.csv: -------------------------------------------------------------------------------- 1 | RESP2_0.50 LJ opt. [g/l],RESP2_0.60 LJ opt. [g/l],RESP2_0.50 SMIRNOFF [g/l],RESP2_0.60 SMIRNOFF [g/l], RESP1 LJ opt. [g/l], RESP1 SMIRNOFF [g/l] 2 | 1,OC,786.600,767.353,757.599,792.749,796.375,758.069,802.935 3 | 2,C-C#N,787.450,728.954,725.356,787.917,789.598,716.318,783.968 4 | 3,CCCN,732.700,723.452,724.142,741.904,746.511,718.976,745.106 5 | 4,COCCC,735.600,706.233,709.144,747.599,748.663,714.048,746.104 6 | 5,CCOCC,713.400,705.471,709.324,739.983,741.083,712.639,738.035 7 | 6,CC1=CC=CC=C1,862.300,855.730,856.425,840.550,840.190,856.764,844.127 8 | 7,Cc1ccc(C)cc1,861.000,847.960,849.227,835.365,835.906,849.479,836.623 9 | 8,N1(C)CCOCC1,919.000,962.577,964.015,1031.889,1033.995,960.188,1029.226 10 | 9,c1cocc1,973.100,972.402,969.973,975.953,976.528,984.538,994.303 11 | 10,c1ccccc1N,1021.700,1032.144,1030.051,1028.398,1031.828,1038.741,1049.269 12 | 11,CCCCO,809.800,794.006,789.795,794.427,796.870,791.496,797.663 13 | 12,CC(C)CC,620.100,615.128,615.181,617.142,616.515,614.948,616.814 14 | 13,CN,662.400,681.513,680.787,725.559,734.926,674.169,736.558 15 | 14,CC(=O)C,784.500,800.583,798.004,795.232,799.460,777.589,783.586 16 | 15,CC(C)O,785.100,816.663,813.679,813.149,815.305,809.847,809.122 17 | -------------------------------------------------------------------------------- /Studies/Results/hov_training_data.csv: -------------------------------------------------------------------------------- 1 | RESP2_0.50 LJ opt. [kJ/mol],RESP2_0.60 LJ opt. [kJ/mol],RESP2_0.50 SMIRNOFF [kJ/mol],RESP2_0.60 SMIRNOFF [kJ/mol], RESP1 LJ opt. [kJ/mol], RESP1 SMIRNOFF [kJ/mol] 2 | 1,OC,37.830,38.340,37.086,34.147,35.105,38.358,36.971 3 | 2,C-C#N,33.400,34.232,34.196,40.303,40.679,31.836,39.229 4 | 3,CCCN,35.840,33.307,33.891,34.553,35.563,31.570,35.219 5 | 4,COCCC,27.900,28.494,28.754,31.604,31.976,28.907,31.728 6 | 5,CCOCC,27.370,28.467,29.179,31.705,31.739,28.691,31.339 7 | 6,CC1=CC=CC=C1,38.060,38.043,38.597,35.748,35.868,38.248,36.407 8 | 7,Cc1ccc(C)cc1,42.420,42.528,42.624,40.630,40.601,42.704,40.822 9 | 8,N1(C)CCOCC1,40.000,36.618,37.161,39.500,39.987,34.107,39.504 10 | 9,c1cocc1,27.710,30.795,30.966,30.182,30.514,33.675,32.304 11 | 10,c1ccccc1N,55.830,54.139,54.770,50.355,50.756,55.204,53.790 12 | 11,CCCCO,52.000,45.249,44.490,42.962,44.319,45.233,45.059 13 | 12,CC(C)CC,25.220,26.117,26.270,27.918,27.588,25.147,27.355 14 | 13,CN,23.850,26.548,27.084,27.506,28.636,26.140,28.814 15 | 14,CC(=O)C,31.270,35.112,35.612,36.240,37.062,32.401,34.332 16 | 15,CC(C)O,45.500,51.598,50.543,47.741,48.914,50.232,49.191 17 | -------------------------------------------------------------------------------- /Studies/example-input-files/HFE/DEE_experiment.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | version: '1.3' 3 | options: 4 | anisotropic_dispersion_cutoff: 10.0*angstroms 5 | checkpoint_interval: 50 6 | default_number_of_iterations: 1000 7 | experiments_dir: DEE_result 8 | minimize: true 9 | output_dir: . 10 | pressure: 1*atmosphere 11 | resume_setup: true 12 | resume_simulation: true 13 | temperature: 298.15*kelvin 14 | verbose: false 15 | 16 | systems: 17 | hydration-system: 18 | phase1_path: [./DEE_solv.xml, ./DEE_solv.pdb] 19 | phase2_path: [./DEE_vacuum.xml, ./DEE_vacuum.pdb] 20 | protocols: 21 | hydration-protocol: 22 | solvent1: 23 | alchemical_path: 24 | lambda_electrostatics: [1.0, 0.75, 0.5, 0.25, 0.0, 0.0, 0.0, 0.0, 25 | 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 26 | lambda_sterics: [1.0, 1.0, 1.0, 1.0, 1.0, 0.95, 0.9, 0.8, 0.7, 0.6, 27 | 0.5, 0.4, 0.35, 0.3, 0.25, 0.2, 0.15, 0.1, 0.05, 0.0] 28 | solvent2: 29 | alchemical_path: 30 | lambda_electrostatics: [1.0, 0.75, 0.5, 0.25, 0.0] 31 | lambda_sterics: [1.0, 1.0, 1.0, 1.0, 1.0] 32 | experiments: 33 | protocol: hydration-protocol 34 | system: hydration-system 35 | -------------------------------------------------------------------------------- /Studies/example-input-files/HFE/DEE_solv.prmtop: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSchauperl/RESP2/f97bc6b51563228bc0085af0b1b3dec09761da69/Studies/example-input-files/HFE/DEE_solv.prmtop -------------------------------------------------------------------------------- /Studies/example-input-files/HFE/DEE_vacuum.prmtop: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSchauperl/RESP2/f97bc6b51563228bc0085af0b1b3dec09761da69/Studies/example-input-files/HFE/DEE_vacuum.prmtop -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP1/input/input.yml: -------------------------------------------------------------------------------- 1 | molecules: 2 | mol1 : 1 3 | charges : 4 | mol1 : 0 5 | cheminformatics : openeye 6 | 7 | grid_setting : 8 | forcegen : Y 9 | type : msk # msk(default)/ extendedmsk/ fcc/ newfcc/ vdwfactors/ vdwconstants 10 | radii : bondi # bondi(default)/ modbondi 11 | method : HF 12 | basis : 6-31G* 13 | pcm : N 14 | space : 0.4 15 | innner : 1.6 16 | outer : 2.1 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP1/input/molecules/mol1/conf1/mol1_conf1.pdb: -------------------------------------------------------------------------------- 1 | REMARK 1 CREATED WITH FORCEBALANCE 2019-08-07 2 | HETATM 1 C1 MOL A 1 1.885 -1.036 -0.109 1.00 0.00 C 3 | HETATM 2 C2 MOL A 1 0.809 -0.465 0.563 1.00 0.00 C 4 | HETATM 3 C3 MOL A 1 2.918 -1.629 0.610 1.00 0.00 C 5 | HETATM 4 C4 MOL A 1 0.767 -0.486 1.953 1.00 0.00 C 6 | HETATM 5 C5 MOL A 1 2.876 -1.650 2.000 1.00 0.00 C 7 | HETATM 6 C6 MOL A 1 1.800 -1.079 2.672 1.00 0.00 C 8 | HETATM 7 H7 MOL A 1 1.918 -1.020 -1.196 1.00 0.00 H 9 | HETATM 8 H8 MOL A 1 0.001 -0.001 0.001 1.00 0.00 H 10 | HETATM 9 H9 MOL A 1 3.760 -2.077 0.085 1.00 0.00 H 11 | HETATM 10 H10 MOL A 1 -0.075 -0.038 2.479 1.00 0.00 H 12 | HETATM 11 H11 MOL A 1 3.684 -2.114 2.562 1.00 0.00 H 13 | HETATM 12 H12 MOL A 1 1.766 -1.095 3.760 1.00 0.00 H 14 | TER 13 MOL A 1 15 | CONECT 1 2 3 7 16 | CONECT 2 1 4 8 17 | CONECT 3 1 5 9 18 | CONECT 4 2 6 10 19 | CONECT 5 3 6 11 20 | CONECT 6 4 5 12 21 | CONECT 7 1 22 | CONECT 8 2 23 | CONECT 9 3 24 | CONECT 10 4 25 | CONECT 11 5 26 | CONECT 12 6 27 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP1/input/molecules/mol1/conf1/mol1_conf1.xyz: -------------------------------------------------------------------------------- 1 | 12 2 | 3 | C 1.885029877247 -1.036403422015 -0.108881615340 4 | C 0.809306769384 -0.464566107916 0.562920378479 5 | C 2.918130715572 -1.629341594800 0.609885338196 6 | C 0.766685491531 -0.485659380533 1.953331425936 7 | C 2.875509648951 -1.650434496433 2.000296145245 8 | C 1.799787844384 -1.078594348988 2.672098348649 9 | H 1.918360480719 -1.019904434950 -1.196326355070 10 | H 0.001259473654 -0.000801373604 0.000860591758 11 | H 3.759508223725 -2.076610198502 0.084562986057 12 | H -0.074692556944 -0.038391419677 2.478653455469 13 | H 3.683556314844 -2.114200016482 2.562356196897 14 | H 1.766457716933 -1.095093206100 3.759543103725 15 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP1/input/respyte.yml: -------------------------------------------------------------------------------- 1 | 2 | molecules : 3 | mol1 : 1 4 | charges : 5 | mol1 : 0 6 | 7 | cheminformatics : openeye 8 | 9 | boundary_select: 10 | radii : bondi 11 | inner : 1.3 12 | outer : 2.1 13 | 14 | restraint : 15 | penalty : 2-stg-fit 16 | matrices : 17 | - esp 18 | a1 : 0.0005 19 | a2 : 0.001 20 | b : 0.1 21 | 22 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2GAS/input/input.yml: -------------------------------------------------------------------------------- 1 | molecules: 2 | mol1 : 1 3 | charges : 4 | mol1 : 0 5 | cheminformatics : openeye 6 | 7 | grid_setting : 8 | forcegen : Y 9 | type : msk # msk(default)/ extendedmsk/ fcc/ newfcc/ vdwfactors/ vdwconstants 10 | radii : bondi # bondi(default)/ modbondi 11 | method : PW6B95 12 | basis : aug-cc-pV(D+d)Z 13 | pcm : N 14 | space : 0.4 15 | innner : 1.6 16 | outer : 2.1 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2GAS/input/molecules/mol1/conf1/mol1_conf1.pdb: -------------------------------------------------------------------------------- 1 | REMARK 1 CREATED WITH FORCEBALANCE 2019-08-08 2 | HETATM 1 C1 MOL A 1 1.885 -1.036 -0.109 1.00 0.00 C 3 | HETATM 2 C2 MOL A 1 0.809 -0.465 0.563 1.00 0.00 C 4 | HETATM 3 C3 MOL A 1 2.918 -1.629 0.610 1.00 0.00 C 5 | HETATM 4 C4 MOL A 1 0.767 -0.486 1.953 1.00 0.00 C 6 | HETATM 5 C5 MOL A 1 2.876 -1.650 2.000 1.00 0.00 C 7 | HETATM 6 C6 MOL A 1 1.800 -1.079 2.672 1.00 0.00 C 8 | HETATM 7 H7 MOL A 1 1.918 -1.020 -1.196 1.00 0.00 H 9 | HETATM 8 H8 MOL A 1 0.001 -0.001 0.001 1.00 0.00 H 10 | HETATM 9 H9 MOL A 1 3.760 -2.077 0.085 1.00 0.00 H 11 | HETATM 10 H10 MOL A 1 -0.075 -0.038 2.479 1.00 0.00 H 12 | HETATM 11 H11 MOL A 1 3.684 -2.114 2.562 1.00 0.00 H 13 | HETATM 12 H12 MOL A 1 1.766 -1.095 3.760 1.00 0.00 H 14 | TER 13 MOL A 1 15 | CONECT 1 2 3 7 16 | CONECT 2 1 4 8 17 | CONECT 3 1 5 9 18 | CONECT 4 2 6 10 19 | CONECT 5 3 6 11 20 | CONECT 6 4 5 12 21 | CONECT 7 1 22 | CONECT 8 2 23 | CONECT 9 3 24 | CONECT 10 4 25 | CONECT 11 5 26 | CONECT 12 6 27 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2GAS/input/molecules/mol1/conf1/mol1_conf1.xyz: -------------------------------------------------------------------------------- 1 | 12 2 | 3 | C 1.885029877247 -1.036403422015 -0.108881615340 4 | C 0.809306769384 -0.464566107916 0.562920378479 5 | C 2.918130715572 -1.629341594800 0.609885338196 6 | C 0.766685491531 -0.485659380533 1.953331425936 7 | C 2.875509648951 -1.650434496433 2.000296145245 8 | C 1.799787844384 -1.078594348988 2.672098348649 9 | H 1.918360480719 -1.019904434950 -1.196326355070 10 | H 0.001259473654 -0.000801373604 0.000860591758 11 | H 3.759508223725 -2.076610198502 0.084562986057 12 | H -0.074692556944 -0.038391419677 2.478653455469 13 | H 3.683556314844 -2.114200016482 2.562356196897 14 | H 1.766457716933 -1.095093206100 3.759543103725 15 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2GAS/input/respyte.yml: -------------------------------------------------------------------------------- 1 | 2 | molecules : 3 | mol1 : 1 4 | charges : 5 | mol1 : 0 6 | 7 | cheminformatics : openeye 8 | 9 | boundary_select: 10 | radii : bondi 11 | inner : 1.3 12 | outer : 2.1 13 | 14 | restraint : 15 | penalty : 2-stg-fit 16 | matrices : 17 | - esp 18 | a1 : 0.0005 19 | a2 : 0.001 20 | b : 0.1 21 | 22 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2LIQUID/input/input.yml: -------------------------------------------------------------------------------- 1 | molecules: 2 | mol1 : 1 3 | charges : 4 | mol1 : 0 5 | cheminformatics : openeye 6 | 7 | grid_setting : 8 | forcegen : Y 9 | type : msk # msk(default)/ extendedmsk/ fcc/ newfcc/ vdwfactors/ vdwconstants 10 | radii : bondi # bondi(default)/ modbondi 11 | method : PW6B95 12 | basis : aug-cc-pV(D+d)Z 13 | pcm : Y 14 | solvent : water 15 | space : 0.4 16 | innner : 1.6 17 | outer : 2.1 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2LIQUID/input/molecules/mol1/conf1/mol1_conf1.pdb: -------------------------------------------------------------------------------- 1 | REMARK 1 CREATED WITH FORCEBALANCE 2019-08-08 2 | HETATM 1 C1 MOL A 1 1.885 -1.036 -0.109 1.00 0.00 C 3 | HETATM 2 C2 MOL A 1 0.809 -0.465 0.563 1.00 0.00 C 4 | HETATM 3 C3 MOL A 1 2.918 -1.629 0.610 1.00 0.00 C 5 | HETATM 4 C4 MOL A 1 0.767 -0.486 1.953 1.00 0.00 C 6 | HETATM 5 C5 MOL A 1 2.876 -1.650 2.000 1.00 0.00 C 7 | HETATM 6 C6 MOL A 1 1.800 -1.079 2.672 1.00 0.00 C 8 | HETATM 7 H7 MOL A 1 1.918 -1.020 -1.196 1.00 0.00 H 9 | HETATM 8 H8 MOL A 1 0.001 -0.001 0.001 1.00 0.00 H 10 | HETATM 9 H9 MOL A 1 3.760 -2.077 0.085 1.00 0.00 H 11 | HETATM 10 H10 MOL A 1 -0.075 -0.038 2.479 1.00 0.00 H 12 | HETATM 11 H11 MOL A 1 3.684 -2.114 2.562 1.00 0.00 H 13 | HETATM 12 H12 MOL A 1 1.766 -1.095 3.760 1.00 0.00 H 14 | TER 13 MOL A 1 15 | CONECT 1 2 3 7 16 | CONECT 2 1 4 8 17 | CONECT 3 1 5 9 18 | CONECT 4 2 6 10 19 | CONECT 5 3 6 11 20 | CONECT 6 4 5 12 21 | CONECT 7 1 22 | CONECT 8 2 23 | CONECT 9 3 24 | CONECT 10 4 25 | CONECT 11 5 26 | CONECT 12 6 27 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2LIQUID/input/molecules/mol1/conf1/mol1_conf1.xyz: -------------------------------------------------------------------------------- 1 | 12 2 | 3 | C 1.885029877247 -1.036403422015 -0.108881615340 4 | C 0.809306769384 -0.464566107916 0.562920378479 5 | C 2.918130715572 -1.629341594800 0.609885338196 6 | C 0.766685491531 -0.485659380533 1.953331425936 7 | C 2.875509648951 -1.650434496433 2.000296145245 8 | C 1.799787844384 -1.078594348988 2.672098348649 9 | H 1.918360480719 -1.019904434950 -1.196326355070 10 | H 0.001259473654 -0.000801373604 0.000860591758 11 | H 3.759508223725 -2.076610198502 0.084562986057 12 | H -0.074692556944 -0.038391419677 2.478653455469 13 | H 3.683556314844 -2.114200016482 2.562356196897 14 | H 1.766457716933 -1.095093206100 3.759543103725 15 | -------------------------------------------------------------------------------- /Studies/example-input-files/respyte/benzene-RESP2LIQUID/input/respyte.yml: -------------------------------------------------------------------------------- 1 | 2 | molecules : 3 | mol1 : 1 4 | charges : 5 | mol1 : 0 6 | 7 | cheminformatics : openeye 8 | 9 | boundary_select: 10 | radii : bondi 11 | inner : 1.3 12 | outer : 2.1 13 | 14 | restraint : 15 | penalty : 2-stg-fit 16 | matrices : 17 | - esp 18 | a1 : 0.0005 19 | a2 : 0.001 20 | b : 0.1 21 | 22 | -------------------------------------------------------------------------------- /devtools/conda-envs/RESP2_environment.yaml: -------------------------------------------------------------------------------- 1 | name: RESP2 2 | channels: 3 | - conda-forge 4 | - openeye 5 | - rdkit 6 | - omnia 7 | - psi4 8 | - bioconda 9 | - openbabel 10 | dependencies: 11 | # Base depends 12 | - python 13 | - pip 14 | - typing 15 | - scipy 16 | - numpy 17 | - openeye-toolkits 18 | - rdkit 19 | - openforcefield 20 | - pint 21 | - psi4 22 | - pymbar 23 | - forcebalance 24 | - pandas 25 | - pyyaml 26 | - matplotlib 27 | - future 28 | - openmoltools 29 | - gromacs 30 | - openbabel 31 | 32 | 33 | # Testing 34 | - pytest 35 | - pytest-cov 36 | - codecov 37 | -------------------------------------------------------------------------------- /devtools/conda-envs/env_save.yaml: -------------------------------------------------------------------------------- 1 | name: test-delete 2 | channels: 3 | - conda-forge 4 | - openeye 5 | - rdkit 6 | - psi4 7 | - bioconda 8 | - openbabel 9 | dependencies: 10 | # Base depends 11 | - python 12 | - pip 13 | - typing 14 | - scipy 15 | - numpy 16 | - openeye-toolkits 17 | - rdkit 18 | - openforcefield 19 | - pint 20 | - psi4 21 | - pymbar 22 | - forcebalance 23 | - pandas 24 | - pyyaml 25 | - matplotlib 26 | - future 27 | - openmoltools 28 | - gromacs 29 | - openbabel 30 | 31 | 32 | # Testing 33 | - pytest 34 | - pytest-cov 35 | - codecov 36 | -------------------------------------------------------------------------------- /devtools/travis-ci/after_install.sh: -------------------------------------------------------------------------------- 1 | # Temporarily change directory to $HOME to install software 2 | pushd . 3 | cd $HOME 4 | git clone https://github.com/lpwgroup/respyte.git 5 | export RESPYTEHOME=$HOME/respyte 6 | cd $RESPYTEHOME 7 | python setup.py install 8 | 9 | # Restore original directory 10 | popd 11 | -------------------------------------------------------------------------------- /devtools/travis-ci/before_install.sh: -------------------------------------------------------------------------------- 1 | # Temporarily change directory to $HOME to install software 2 | pushd . 3 | cd $HOME 4 | # Make sure some level of pip is installed 5 | python -m ensurepip 6 | 7 | # Install Miniconda 8 | if [ "$TRAVIS_OS_NAME" == "osx" ]; then 9 | # Make OSX md5 mimic md5sum from linux, alias does not work 10 | md5sum () { 11 | command md5 -r "$@" 12 | } 13 | MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh 14 | else 15 | MINICONDA=Miniconda3-latest-Linux-x86_64.sh 16 | fi 17 | MINICONDA_HOME=$HOME/miniconda 18 | MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') 19 | wget -q https://repo.continuum.io/miniconda/$MINICONDA 20 | if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then 21 | echo "Miniconda MD5 mismatch" 22 | exit 1 23 | fi 24 | bash $MINICONDA -b -p $MINICONDA_HOME 25 | 26 | # Configure miniconda 27 | export PIP_ARGS="-U" 28 | # New to conda >=4.4 29 | echo ". $MINICONDA_HOME/etc/profile.d/conda.sh" >> ~/.bashrc # Source the profile.d file 30 | echo "conda activate" >> ~/.bashrc # Activate conda 31 | source ~/.bashrc # source file to get new commands 32 | #export PATH=$MINICONDA_HOME/bin:$PATH # Old way, should not be needed anymore 33 | 34 | conda config --add channels conda-forge 35 | 36 | conda config --set always_yes yes 37 | conda install conda conda-build jinja2 anaconda-client 38 | conda update --quiet --all 39 | 40 | # Restore original directory 41 | popd 42 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = resp2 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- 1 | # Compiling RESP2's Documentation 2 | 3 | The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/). 4 | To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed. 5 | 6 | 7 | ```bash 8 | conda install sphinx sphinx_rtd_theme 9 | ``` 10 | 11 | 12 | Once installed, you can use the `Makefile` in this directory to compile static HTML pages by 13 | ```bash 14 | make html 15 | ``` 16 | 17 | The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself 18 | be inside a directory called `html/` depending on what version of Sphinx is installed). -------------------------------------------------------------------------------- /docs/_static/README.md: -------------------------------------------------------------------------------- 1 | # Static Doc Directory 2 | 3 | Add any paths that contain custom static files (such as style sheets) here, 4 | relative to the `conf.py` file's directory. 5 | They are copied after the builtin static files, 6 | so a file named "default.css" will overwrite the builtin "default.css". 7 | 8 | The path to this folder is set in the Sphinx `conf.py` file in the line: 9 | ```python 10 | templates_path = ['_static'] 11 | ``` 12 | 13 | ## Examples of file to add to this directory 14 | * Custom Cascading Style Sheets 15 | * Custom JavaScript code 16 | * Static logo images 17 | -------------------------------------------------------------------------------- /docs/_templates/README.md: -------------------------------------------------------------------------------- 1 | # Templates Doc Directory 2 | 3 | Add any paths that contain templates here, relative to 4 | the `conf.py` file's directory. 5 | They are copied after the builtin template files, 6 | so a file named "page.html" will overwrite the builtin "page.html". 7 | 8 | The path to this folder is set in the Sphinx `conf.py` file in the line: 9 | ```python 10 | html_static_path = ['_templates'] 11 | ``` 12 | 13 | ## Examples of file to add to this directory 14 | * HTML extensions of stock pages like `page.html` or `layout.html` 15 | -------------------------------------------------------------------------------- /docs/environment.yml: -------------------------------------------------------------------------------- 1 | name: documentation 2 | channels: 3 | - omnia 4 | - conda-forge 5 | - default 6 | dependencies: 7 | # Base depends 8 | - python 9 | - pip 10 | - typing 11 | - scipy 12 | - numpy 13 | - numpydoc 14 | - nbsphinx 15 | - m2r >=0.2.1 16 | #- forcebalance 17 | #- openmoltools 18 | #- openbabel 19 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=. 11 | set BUILDDIR=_build 12 | set SPHINXPROJ=resp2 13 | 14 | if "%1" == "" goto help 15 | 16 | %SPHINXBUILD% >NUL 2>NUL 17 | if errorlevel 9009 ( 18 | echo. 19 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 20 | echo.installed, then set the SPHINXBUILD environment variable to point 21 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 22 | echo.may add the Sphinx directory to PATH. 23 | echo. 24 | echo.If you don't have Sphinx installed, grab it from 25 | echo.http://sphinx-doc.org/ 26 | exit /b 1 27 | ) 28 | 29 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 30 | goto end 31 | 32 | :help 33 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 34 | 35 | :end 36 | popd 37 | -------------------------------------------------------------------------------- /docs/readthedocs.yml: -------------------------------------------------------------------------------- 1 | conda: 2 | file: environment.yml 3 | python: 4 | setup_py_install: true 5 | version: 3.5 6 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSchauperl/RESP2/f97bc6b51563228bc0085af0b1b3dec09761da69/docs/requirements.txt -------------------------------------------------------------------------------- /docs/resp2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSchauperl/RESP2/f97bc6b51563228bc0085af0b1b3dec09761da69/docs/resp2.pdf -------------------------------------------------------------------------------- /readthedocs.yml: -------------------------------------------------------------------------------- 1 | conda: 2 | file: docs/environment.yml 3 | python: 4 | setup_py_install: true 5 | version: 3.6 6 | -------------------------------------------------------------------------------- /resp2/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | RESP2 3 | A template to create RESP2 charges 4 | """ 5 | 6 | # Add imports here 7 | from .resp2 import * 8 | 9 | # Handle versioneer 10 | from ._version import get_versions 11 | versions = get_versions() 12 | __version__ = versions['version'] 13 | __git_revision__ = versions['full-revisionid'] 14 | del get_versions, versions 15 | 16 | from ._version import get_versions 17 | __version__ = get_versions()['version'] 18 | del get_versions 19 | -------------------------------------------------------------------------------- /resp2/data/CCO.smi: -------------------------------------------------------------------------------- 1 | CCO 2 | -------------------------------------------------------------------------------- /resp2/data/ETH.mol2: -------------------------------------------------------------------------------- 1 | @MOLECULE 2 | ***** 3 | 9 8 0 0 0 4 | SMALL 5 | USER_CHARGES 6 | 7 | @ATOM 8 | 1 C1 1.0616 -0.2681 -0.0006 C.3 1 ETH1 0.0000 9 | 2 C2 1.9101 0.9126 -0.4220 C.3 1 ETH1 0.2800 10 | 3 O1 1.5170 1.3236 -1.7228 O.3 1 ETH1 -0.6800 11 | 4 H1 1.6590 0.5652 -2.3129 H 1 ETH1 0.4000 12 | 5 H2 1.3393 -0.6108 1.0001 H 1 ETH1 0.0000 13 | 6 H3 -0.0000 -0.0002 -0.0006 H 1 ETH1 0.0000 14 | 7 H4 1.1801 -1.0990 -0.7040 H 1 ETH1 0.0000 15 | 8 H5 2.9684 0.6361 -0.4446 H 1 ETH1 0.0000 16 | 9 H6 1.7730 1.7499 0.2687 H 1 ETH1 0.0000 17 | @BOND 18 | 1 1 2 1 19 | 2 2 3 1 20 | 3 1 5 1 21 | 4 1 6 1 22 | 5 1 7 1 23 | 6 2 8 1 24 | 7 2 9 1 25 | 8 3 4 1 26 | -------------------------------------------------------------------------------- /resp2/data/ETH.pdb: -------------------------------------------------------------------------------- 1 | HETATM 1 C1 ETH 1 1.062 -0.268 -0.001 1.00 20.00 C 2 | HETATM 2 C2 ETH 1 1.910 0.913 -0.422 1.00 20.00 C 3 | HETATM 3 O1 ETH 1 1.517 1.324 -1.723 1.00 20.00 O 4 | HETATM 4 H1 ETH 1 1.659 0.565 -2.313 1.00 20.00 H 5 | HETATM 5 H2 ETH 1 1.339 -0.611 1.000 1.00 20.00 H 6 | HETATM 6 H3 ETH 1 -0.000 -0.000 -0.001 1.00 20.00 H 7 | HETATM 7 H4 ETH 1 1.180 -1.099 -0.704 1.00 20.00 H 8 | HETATM 8 H5 ETH 1 2.968 0.636 -0.445 1.00 20.00 H 9 | HETATM 9 H6 ETH 1 1.773 1.750 0.269 1.00 20.00 H 10 | TER 10 ETH 1 11 | CONECT 1 2 5 6 7 12 | CONECT 2 1 3 8 9 13 | CONECT 3 2 4 14 | CONECT 4 3 15 | CONECT 5 1 16 | CONECT 6 1 17 | CONECT 7 1 18 | CONECT 8 2 19 | CONECT 9 2 20 | END 21 | -------------------------------------------------------------------------------- /resp2/data/README.md: -------------------------------------------------------------------------------- 1 | # Sample Package Data 2 | 3 | This directory contains sample additional data you may want to include with your package. 4 | This is a place where non-code related additional information (such as data files, molecular structures, etc.) can 5 | go that you want to ship alongside your code. 6 | 7 | Please note that it is not recommended to place large files in your git directory. If your project requires files larger 8 | than a few megabytes in size it is recommended to host these files elsewhere. This is especially true for binary files 9 | as the `git` structure is unable to correctly take updates to these files and will store a complete copy of every version 10 | in your `git` history which can quickly add up. As a note most `git` hosting services like GitHub have a 1 GB per repository 11 | cap. 12 | 13 | ## Including package data 14 | 15 | Modify your package's `setup.py` file and the `setup()` command. Include the 16 | [`package_data`](http://setuptools.readthedocs.io/en/latest/setuptools.html#basic-use) keyword and point it at the 17 | correct files. 18 | 19 | ## Manifest 20 | 21 | * `look_and_say.dat`: first entries of the "Look and Say" integer series, sequence [A005150](https://oeis.org/A005150) 22 | -------------------------------------------------------------------------------- /resp2/data/look_and_say.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSchauperl/RESP2/f97bc6b51563228bc0085af0b1b3dec09761da69/resp2/data/look_and_say.dat -------------------------------------------------------------------------------- /resp2/test_fb.in: -------------------------------------------------------------------------------- 1 | $options 2 | 3 | wp_port 3333 4 | asynchronous 5 | penalty_type L2 6 | jobtype single 7 | forcefield smirnoff99Frosst.offxml ETH-resp2.mol2 8 | maxstep 100 9 | PENALTY_ADDITIVE 10 10 | 11 | convergence_step 0.001 12 | convergence_objective 30 13 | convergence_gradient 30 14 | criteria 2 15 | 16 | eig_lowerbound 0.01 17 | finite_difference_h 0.001 18 | penalty_additive 1.0 19 | trust0 0.15 20 | mintrust 0.05 21 | error_tolerance 1.0 22 | adaptive_factor 0.2 23 | adaptive_damping 1.0 24 | normalize_weights no 25 | print_hessian 26 | constrain_charge false 27 | backup false 28 | 29 | priors 30 | NonbondedForce/Atom/epsilon : 0.1 31 | NonbondedForce/Atom/rmin_half : 1.0 32 | /priors 33 | 34 | 35 | 36 | $target 37 | name data/ethanol-liquid 38 | type Liquid_SMIRNOFF 39 | weight 1.0 40 | liquid_coords ETH-box.pdb 41 | liquid_eq_steps 50000 42 | liquid_prod_steps 5000000 43 | liquid_timestep 1.0 44 | liquid_interval 1.0 45 | save_traj 2 46 | gas_coords ETH.pdb 47 | gas_eq_steps 5000000 48 | gas_prod_steps 20000000 49 | gas_timestep 0.5 50 | $end 51 | -------------------------------------------------------------------------------- /resp2/tests/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Empty init file in case you choose a package besides PyTest such as Nose which may look for such a file 3 | """ 4 | -------------------------------------------------------------------------------- /resp2/tests/test_resp2.py: -------------------------------------------------------------------------------- 1 | """ 2 | Unit and regression test for the resp2 package. 3 | """ 4 | 5 | # Import package, test suite, and other packages as needed 6 | import resp2 7 | import pytest 8 | import sys 9 | 10 | def test_resp2_imported(): 11 | """Sample test, will always pass so long as import statement worked""" 12 | assert "resp2" in sys.modules 13 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | # Helper file to handle all configs 2 | 3 | [coverage:run] 4 | # .coveragerc to control coverage.py and pytest-cov 5 | omit = 6 | # Omit the tests 7 | */tests/* 8 | # Omit generated versioneer 9 | resp2/_version.py 10 | 11 | [yapf] 12 | # YAPF, in .style.yapf files this shows up as "[style]" header 13 | COLUMN_LIMIT = 119 14 | INDENT_WIDTH = 4 15 | USE_TABS = False 16 | 17 | [flake8] 18 | # Flake8, PyFlakes, etc 19 | max-line-length = 119 20 | 21 | [versioneer] 22 | # Automatic version numbering scheme 23 | VCS = git 24 | style = pep440 25 | versionfile_source = resp2/_version.py 26 | versionfile_build = resp2/_version.py 27 | tag_prefix = '' 28 | 29 | [aliases] 30 | test = pytest 31 | --------------------------------------------------------------------------------