├── water.png ├── alkanes ├── butane.png ├── decane.png ├── dodecane.png ├── eicosane.png ├── 2-methylpropane.png └── eicosane.cjson ├── alkenes ├── ethene.png ├── propene.png ├── but-1-ene.png ├── hept-1-ene.png ├── hex-1-ene.png ├── oct-1-ene.png ├── pent-1-ene.png ├── E-but-2-ene.png ├── E-hept-2-ene.png ├── E-hept-3-ene.png ├── E-hex-2-ene.png ├── E-hex-3-ene.png ├── E-oct-2-ene.png ├── E-oct-3-ene.png ├── E-oct-4-ene.png ├── E-pent-2-ene.png ├── Z-but-2-ene.png ├── Z-hept-2-ene.png ├── Z-hept-3-ene.png ├── Z-hex-2-ene.png ├── Z-hex-3-ene.png ├── Z-oct-2-ene.png ├── Z-oct-3-ene.png ├── Z-oct-4-ene.png ├── Z-pent-2-ene.png ├── 2-methylbut-2-ene.png ├── 3E-penta-1_3-diene.png ├── 3Z-penta-1_3-diene.png ├── 2-methylbuta-1_3-diene.png ├── 3Z_3-ethylhepta-1_3-diene.png └── ethene.cjson ├── alkynes ├── propyne.png ├── acetylene.png └── acetylene.cjson ├── amides ├── oxamide.png ├── acetamide.png ├── ethyl_carbamate.png ├── N_N-dimethylacetamide.png └── N_N-dimethylformamide.png ├── amines ├── ammonia.png ├── azepane.png ├── 1H-azepine.png ├── ethylamine.png ├── methylamine.png ├── piperazine.png ├── piperidine.png ├── pyrrolidine.png ├── diethylamine.png ├── dimethylamine.png ├── triethylamine.png ├── 2-aminopropane.png ├── S-sec-butylamine.png ├── tert-butylamine.png ├── trimethylamine.png ├── triethylenediamine.png └── ammonia.cjson ├── carbamides └── urea.png ├── fullerenes ├── C180.png ├── C20.png ├── C24.png ├── C240.png ├── C26.png ├── C28.png ├── C30.png ├── C32.png ├── C36.png ├── C50.png ├── C70.png ├── C76.png ├── C78.png ├── C80.png ├── PCBM.png ├── PC70BM.png ├── C60-buckminsterfullerene.png ├── C20.cjson ├── C50.cjson └── C60-buckminsterfullerene.cjson ├── ketones ├── acetone.png ├── butanone.png ├── cyclohexanone.png ├── p-benzoquinone.png └── methyl_vinyl_ketone.png ├── alcohols ├── ethanol.png ├── methanol.png ├── propan-1-ol.png ├── propan-2-ol.png ├── 2-aminoethanol.png ├── cyclohexanol.png ├── cyclopentanol.png ├── ethane-1_2-diol.png ├── but-2-yne-1_4-diol.png ├── propane-1_2_3-triol.png └── methanol.cjson ├── aromatics ├── acridine.png ├── aniline.png ├── anisole.png ├── benzene.png ├── caffeine.png ├── chromone.png ├── coumarin.png ├── phenol.png ├── tetralin.png ├── toluene.png ├── 1H-indene.png ├── 1H-indole.png ├── 7H-purine.png ├── anthracene.png ├── benzofuran.png ├── cinnoline.png ├── quinoline.png ├── uric_acid.png ├── 2H-chromene.png ├── 4H-chromene.png ├── 9H-carbazole.png ├── 9H-fluorene.png ├── 9H-xanthene.png ├── acenaphthene.png ├── benzaldehyde.png ├── benzoic_acid.png ├── isoquinoline.png ├── naphthalene.png ├── nitrobenzene.png ├── phenanthrene.png ├── phthalimide.png ├── quinazoline.png ├── acenaphthylene.png ├── benzothiophene.png ├── 1_8-naphthyridine.png ├── benzoyl_chloride.png ├── 1_10-phenanthroline.png └── acenaphthenequinone.png ├── ethers ├── 1_4-dioxane.png ├── dibutylether.png ├── diethylether.png ├── dimethylether.png ├── dipropylether.png ├── diisopropylether.png ├── ethylmethylether.png ├── tetrahydrofuran.png ├── tetrahydropyran.png └── di-tert-butylether.png ├── nucleobases ├── uracil.png ├── adenine.png ├── cytosine.png ├── guanine.png └── thymine.png ├── steroids ├── estradiol.png ├── cholesterol.png └── testosterone.png ├── thiols ├── ethanethiol.png ├── methanethiol.png ├── R_butane-2-thiol.png ├── butane-1-thiol.png ├── heptane-1-thiol.png ├── hexane-1-thiol.png ├── octane-1-thiol.png ├── pentane-1-thiol.png ├── proprane-1-thiol.png ├── proprane-2-thiol.png ├── ethane-1_2-dithiol.png ├── 2-methylproprane-2-thiol.png └── methanethiol.cjson ├── amino_acids ├── D-lysine.png ├── D-serine.png ├── D-valine.png ├── L-lysine.png ├── L-serine.png ├── L-valine.png ├── glycine.png ├── D-alanine.png ├── D-arginine.png ├── D-cysteine.png ├── D-glutamine.png ├── D-histidine.png ├── D-leucine.png ├── D-proline.png ├── D-threonine.png ├── D-tyrosine.png ├── L-alanine.png ├── L-arginine.png ├── L-cysteine.png ├── L-glutamine.png ├── L-histidine.png ├── L-leucine.png ├── L-proline.png ├── L-threonine.png ├── L-tyrosine.png ├── D-asparagine.png ├── D-isoleucine.png ├── D-methionine.png ├── D-tryptophan.png ├── L-asparagine.png ├── L-isoleucine.png ├── L-methionine.png ├── L-tryptophan.png ├── D-allo-threonine.png ├── D-aspartic_acid.png ├── D-glutamic_acid.png ├── D-phenylalanine.png ├── L-aspartic_acid.png ├── L-glutamic_acid.png ├── L-phenylalanine.png ├── L-allo-isoleucine.png └── L-4-nitrophenylalanine.png ├── macrocycles ├── porphin.png └── phthalocyanine.png ├── aldehydes ├── acetaldehyde.png ├── formaldehyde.png └── formaldehyde.cjson ├── carbohydrates ├── d-allose.png ├── d-altrose.png ├── d-glucose.png ├── d-gulose.png ├── d-idose.png ├── d-lyxose.png ├── d-mannose.png ├── d-psicose.png ├── d-ribose.png ├── d-sorbose.png ├── d-talose.png ├── d-threose.png ├── d-xylose.png ├── d-arabinose.png ├── d-erythrose.png ├── d-fructose.png ├── d-galactose.png ├── d-ribulose.png ├── d-tagatose.png ├── d-xylulose.png ├── d-erythrulose.png ├── d-glyceraldehyde.png ├── dihydroxyacetone.png └── d-erythrose.cjson ├── coordination ├── 4-planar.png ├── 6-octahedral.png ├── 4-tetrahedral.png ├── 3-trigonal-planar.png ├── 3-trigonal-pyramidal.png ├── 5-square-pyramidal.png ├── 5-trigonal-bipyramidal.png ├── 5-square-pyramidal.cjson ├── 6-octahedral.cjson ├── 3-trigonal-planar.cjson ├── 3-trigonal-pyramidal.cjson ├── 4-planar.cjson ├── 4-tetrahedral.cjson └── 5-trigonal-bipyramidal.cjson ├── cyclic_alkanes ├── cubane.png ├── 1R-camphor.png ├── adamantane.png ├── norbornane.png ├── 1R-camphene.png ├── abietic_acid.png ├── cyclobutane.png ├── cyclodecane.png ├── cycloheptane.png ├── cyclohexane.png ├── cyclononane.png ├── cyclooctane.png ├── cyclopentane.png ├── cyclopropane.png ├── cyclohexane-boat.png ├── cyclohexane-chair.png ├── cyclohexane-twist-boat.png ├── cis-decahydronaphthalene.png ├── trans-decahydronaphthalene.png └── adamantane.cjson ├── fatty_acids ├── lauric_acid.png ├── oleic_acid.png ├── cervonic_acid.png ├── decanoic_acid.png ├── hexanoic_acid.png ├── linoleic_acid.png ├── myristic_acid.png ├── octanoic_acid.png ├── palmitic_acid.png ├── stearic_acid.png ├── arachidonic_acid.png ├── linolenic_acid.png ├── pentanoic_acid.png ├── linoleic_acid.cjson ├── arachidonic_acid.cjson ├── oleic_acid.cjson ├── cervonic_acid.cjson └── stearic_acid.cjson ├── halogenated ├── halothane.png ├── iodomethane.png ├── isoflurane.png ├── triclofos.png ├── allyl_bromide.png ├── bromoacetone.png ├── bromomethane.png ├── chloromethane.png ├── fluoroacetone.png ├── fluoromethane.png ├── vinyl_bromide.png ├── vinyl_iodide.png ├── benzal_chloride.png ├── benzyl_bromide.png ├── benzyl_chloride.png ├── bromoacetic_acid.png ├── vinyl_chloride.png ├── vinyl_fluoride.png ├── 1,1_difluoroethene.png ├── chloroacetic_acid.png ├── fluoroacetic_acid.png ├── hexachloroacetone.png ├── tetrachloroethylene.png ├── 2_bromo_1_chloropropane.png ├── bis_chloromethyl_ketone.png ├── dichlorodiphenyltrichloroethane.png ├── bromomethane.cjson ├── chloromethane.cjson ├── iodomethane.cjson ├── fluoromethane.cjson ├── vinyl_bromide.cjson ├── vinyl_chloride.cjson ├── tetrachloroethylene.cjson ├── vinyl_iodide.cjson ├── vinyl_fluoride.cjson ├── 1,1_difluoroethene.cjson ├── halothane.cjson ├── chloroacetic_acid.cjson ├── bromoacetic_acid.cjson ├── fluoroacetic_acid.cjson ├── allyl_bromide.cjson ├── bromoacetone.cjson ├── hexachloroacetone.cjson ├── bis_chloromethyl_ketone.cjson ├── fluoroacetone.cjson ├── 2_bromo_1_chloropropane.cjson ├── isoflurane.cjson ├── triclofos.cjson ├── benzyl_chloride.cjson ├── benzyl_bromide.cjson ├── benzal_chloride.cjson └── dichlorodiphenyltrichloroethane.cjson ├── heteroaromatics ├── furan.png ├── 1H-indole.png ├── pyridine.png ├── thiophene.png ├── 1H-pyrazole.png ├── 1H-pyrrole.png ├── 1_2-oxazole.png ├── 1_2-thiazole.png ├── 1_3-oxazole.png ├── 1_3-thiazole.png ├── benzofuran.png ├── nicotinamide.png ├── picolinamide.png ├── benzothiophene.png ├── nicotinic_acid.png ├── picolinic_acid.png ├── isonicotinamide.png └── isonicotinic_acid.png ├── nitriles ├── acetonitrile.png ├── butyronitrile.png ├── propionitrile.png ├── isobutyronitrile.png ├── 1_1_1-trichloroacetonitrile.png ├── acetonitrile.cjson └── 1_1_1-trichloroacetonitrile.cjson ├── carboxylic_acids ├── acetic_acid.png ├── citric_acid.png ├── formic_acid.png ├── oxalic_acid.png ├── D-lactic_acid.png ├── D-malic_acid.png ├── L-lactic_acid.png ├── L-malic_acid.png ├── butanoic_acid.png ├── D-tartaric_acid.png ├── E-butanoic_acid.png ├── L-ascorbic_acid.png ├── L-tartaric_acid.png ├── isobutyric_acid.png ├── propanoic_acid.png ├── E-butenedioic_acid.png ├── 2_2-dichloroacetic_acid.png ├── 2_2_2-trichloroacetic_acid.png ├── 2_2_2-trifluoroacetic_acid.png └── formic_acid.cjson ├── cyclic_alkenes ├── Z-cyclooctene.png ├── cyclohexene.png ├── cyclopentene.png ├── Z-cycloheptene.png ├── cyclohepta-1_3-diene.png ├── cyclohepta-1_4-diene.png ├── cyclohexa-1_3-diene.png ├── cyclohexa-1_4-diene.png ├── cycloocta-1_3-diene.png ├── cyclopenta-1_3-diene.png ├── cyclohepta-1_3_5-triene.png ├── cycloocta-1_3_5-triene.png └── cycloocta-1_3_5_7-tetraene.png ├── furanose ├── alpha-D-idofuranose.png ├── beta-D-allofuranose.png ├── beta-D-gulofuranose.png ├── beta-D-idofuranose.png ├── beta-D-lyxofuranose.png ├── beta-D-ribofuranose.png ├── beta-D-talofuranose.png ├── beta-D-xylofuranose.png ├── alpha-D-allofuranose.png ├── alpha-D-altrofuranose.png ├── alpha-D-glucofuranose.png ├── alpha-D-gulofuranose.png ├── alpha-D-lyxofuranose.png ├── alpha-D-mannofuranose.png ├── alpha-D-ribofuranose.png ├── alpha-D-sorbofuranose.png ├── alpha-D-talofuranose.png ├── alpha-D-xylofuranose.png ├── alpha-L-altrofuranose.png ├── beta-D-altrofuranose.png ├── beta-D-fructofuranose.png ├── beta-D-glucofuranose.png ├── beta-D-mannofuranose.png ├── beta-D-sorbofuranose.png ├── beta-L-altrofuranose.png ├── alpha-D-arabinofuranose.png ├── alpha-D-fructofuranose.png ├── alpha-D-galactofuranose.png ├── beta-D-arabinofuranose.png └── beta-D-galactofuranose.png ├── ligands ├── Cp-cyclopentadienyl.png └── Cp-cyclopentadienyl.cjson ├── pyranose ├── alpha-D-idopyranose.png ├── beta-D-allopyranose.png ├── beta-D-fucopyranose.png ├── beta-D-gulopyranose.png ├── beta-D-idopyranose.png ├── beta-D-lyxopyranose.png ├── beta-D-talopyranose.png ├── beta-L-lyxopyranose.png ├── beta-L-ribopyranose.png ├── beta-L-xylopyranose.png ├── alpha-D-allopyranose.png ├── alpha-D-altropyranose.png ├── alpha-D-fucopyranose.png ├── alpha-D-glucopyranose.png ├── alpha-D-gulopyranose.png ├── alpha-D-lyxopyranose.png ├── alpha-D-mannopyranose.png ├── alpha-D-psicopyranose.png ├── alpha-D-talopyranose.png ├── alpha-L-altropyranose.png ├── alpha-L-fucopyranose.png ├── alpha-L-lyxopyranose.png ├── alpha-L-ribopyranose.png ├── alpha-L-sorbopyranose.png ├── alpha-L-xylopyranose.png ├── beta-D-altropyranose.png ├── beta-D-fructopyranose.png ├── beta-D-glucopyranose.png ├── beta-D-mannopyranose.png ├── 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https://raw.githubusercontent.com/OpenChemistry/molecules/HEAD/halogenated/dichlorodiphenyltrichloroethane.png -------------------------------------------------------------------------------- /plugin.json: -------------------------------------------------------------------------------- 1 | { 2 | "author": "Geoffrey Hutchison", 3 | "version": 1.0, 4 | "name": "molecules", 5 | "url": "https://github.com/openchemistry/molecules", 6 | "description": "Set of over 300 common molecules.", 7 | "type": "data" 8 | } 9 | -------------------------------------------------------------------------------- /halogenated/bromomethane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.913088, -0.06208, 0.024203, 2.867162, -0.062094, 0.02417, 0.580677, -0.669025, -0.807471, 0.580668, 0.961642, -0.085556, 0.580605, -0.478843, 0.965654] 6 | }, 7 | "elements": { 8 | "number": [6, 35, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.439071, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [2, 0, 3, 0, 1, 0, 0, 4] 18 | }, 19 | "order": [1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "bromomethane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/chloromethane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.062699, 0.061476, -0.033352, 2.865821, 0.061495, -0.033372, 0.719742, -0.519286, 0.814371, 0.719654, -0.382273, -0.960148, 0.719684, 1.085987, 0.045701] 6 | }, 7 | "elements": { 8 | "number": [6, 17, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.404483, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 0, 1, 0, 0, 4, 0, 2] 18 | }, 19 | "order": [1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "chloromethane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/iodomethane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.07349, 0.008335, 0.03268, 3.230452, 0.008281, 0.032725, 0.748933, 0.677937, 0.816883, 0.748948, -1.005613, 0.220505, 0.748877, 0.35266, -0.939294] 6 | }, 7 | "elements": { 8 | "number": [6, 53, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.527224, -0.07648, 0.201237, 0.201227, 0.201241] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [4, 0, 0, 1, 0, 3, 0, 2] 18 | }, 19 | "order": [1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "iodomethane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/fluoromethane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.945553, 0.046058, 0.07706, 2.334874, 0.04609, 0.077049, 0.587975, -0.578352, 0.895295, 0.58789, -0.350354, -0.872781, 0.587908, 1.066858, 0.208678] 6 | }, 7 | "elements": { 8 | "number": [6, 9, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.193934, -0.287788, 0.160577, 0.160573, 0.160572] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 0, 1, 0, 0, 4, 0, 2] 18 | }, 19 | "order": [1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "fluoromethane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/vinyl_bromide.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.982262, -0.070419, -0.009697, 2.878634, -0.023451, -0.100466, 3.546575, 0.500107, -1.110283, 3.337924, -0.472639, 0.765872, 3.061939, 0.944292, -1.967034, 4.628567, 0.491409, -1.093392] 6 | }, 7 | "elements": { 8 | "number": [35, 6, 6, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [4, 2, 2, 5, 2, 1, 1, 0, 1, 3] 18 | }, 19 | "order": [1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "vinyl_bromide.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/vinyl_chloride.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.0844, -0.122317, -0.072785, 2.829464, -0.052388, -0.000729, 3.492737, 0.741741, 0.818215, 3.296601, -0.729579, -0.69904, 2.998626, 1.410152, 1.507409, 4.573672, 0.732191, 0.80833] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 6, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 1, 0, 1, 1, 2, 5, 2, 2, 4] 18 | }, 19 | "order": [1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "vinyl_chloride.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/tetrachloroethylene.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.979496, 0.049358, -0.062322, 2.705011, 0.061204, 0.007655, 3.506268, -0.194257, -1.500699, 3.374856, 0.254997, 1.151645, 2.573598, 0.510457, 2.659999, 5.100371, 0.266841, 1.221622] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 17, 6, 17, 17] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [2, 1, 0, 1, 1, 3, 3, 5, 3, 4] 18 | }, 19 | "order": [1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "tetrachloroethylene.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /coordination/5-square-pyramidal.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [-0.596634, -0.248879, 0.349136, -1.405765, -0.191054, -1.1179, 0.249523, -0.363861, 1.786692, -0.058552, 1.41804, 0.138912, -1.776952, 0.683616, 1.081665, 0.863561, -0.388861, -0.483575] 6 | }, 7 | "elements": { 8 | "number": [16, 9, 9, 9, 9, 9] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [1, 0, 5, 0, 3, 0, 0, 4, 0, 2] 18 | }, 19 | "order": [1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "5-square-pyramidal.out.gz", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 2 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/vinyl_iodide.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.126449, 0.103781, 0.020829, 3.22652, -0.012873, 0.034262, 3.897336, -1.141415, 0.163769, 3.687772, 0.955973, -0.076917, 3.41943, -2.103996, 0.27418, 4.980693, -1.122671, 0.161576] 6 | }, 7 | "elements": { 8 | "number": [53, 6, 6, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.035093, -0.214827, -0.315903, 0.208181, 0.187401, 0.170242] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 1, 0, 1, 1, 2, 5, 2, 2, 4] 18 | }, 19 | "order": [1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "vinyl_iodide.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/vinyl_fluoride.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.994176, -0.004165, 0.060492, 2.341895, -0.074517, 0.090027, 2.987814, -1.133154, 0.534898, 2.795788, 0.830815, -0.290415, 2.4699, -2.006472, 0.901839, 4.066628, -1.133407, 0.535059] 6 | }, 7 | "elements": { 8 | "number": [9, 6, 6, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.236266, 0.11395, -0.37099, 0.140109, 0.17908, 0.174117] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 1, 0, 1, 1, 2, 2, 5, 2, 4] 18 | }, 19 | "order": [1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "vinyl_fluoride.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/1,1_difluoroethene.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.057972, -0.073498, 0.027734, 2.373673, -0.073496, 0.027737, 3.13714, 0.828583, -0.576104, 3.137136, -0.975586, 0.631571, 0.517838, 0.699775, -0.490172, 0.517842, -0.846777, 0.545635] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 9, 9, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.464787, 0.503214, -0.213183, -0.213184, 0.19397, 0.19397] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [2, 1, 4, 0, 0, 1, 0, 5, 1, 3] 18 | }, 19 | "order": [1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "1,1_difluoroethene.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /coordination/6-octahedral.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [-0.564443, -0.177023, 0.171241, -1.984105, -0.470025, -1.500157, 0.856063, 0.111996, 1.84184, 0.07751, 1.749496, -0.719407, -1.208165, -2.105454, 1.06067, -2.146042, 0.880182, 1.322386, 1.015393, -1.241462, -0.976563] 6 | }, 7 | "elements": { 8 | "number": [26, 17, 17, 17, 17, 17, 17] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [1, 0, 6, 0, 3, 0, 0, 4, 0, 5, 0, 2] 18 | }, 19 | "order": [1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "6-octahedral.out.gz", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Molecules 2 | 3 | Common molecule fragments including a variety of organic functional groups: 4 | 5 | - alcohols 6 | - aldehydes 7 | - alkanes 8 | - alkenes 9 | - alkynes 10 | - amides 11 | - amines 12 | - amino acids 13 | - aromatics 14 | - carbamides 15 | - carbohydrates 16 | - carboxylic acids 17 | - coordination 18 | - cyclic alkanes 19 | - cyclic alkenes 20 | - cyclic sugars 21 | - ethers 22 | - fatty acids 23 | - fullerenes 24 | - heteroaromatics 25 | - ketones 26 | - ligands 27 | - macrocycles 28 | - nitriles 29 | - nucleobases 30 | - steroids 31 | - sulfoxides 32 | - thiols 33 | 34 | All molecules are made available the BSD license. Most are from the 35 | [Blue Obelisk Chemical Structures](http://chem-file.sourceforge.net/) set. 36 | Where possible, optimized geometries are made available using the 37 | [Pitt Quantum Repository](https://pqr.pitt.edu/) 38 | -------------------------------------------------------------------------------- /halogenated/halothane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.058232, 0.094102, 0.033438, 3.008271, 0.00079, 0.057794, 3.723224, 1.622697, 0.218683, 3.552166, -0.985697, 1.143231, 2.591469, -1.747616, 1.682963, 4.43786, -1.812635, 0.537571, 4.186731, -0.365596, 2.143976, 3.295747, -0.381146, -0.911656] 6 | }, 7 | "elements": { 8 | "number": [35, 6, 17, 6, 9, 9, 9, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [7, 1, 0, 1, 1, 2, 1, 3, 5, 3, 3, 4, 3, 6] 18 | }, 19 | "order": [1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "halothane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/chloroacetic_acid.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.019804, 0.035476, 0.082863, 2.832916, 0.120601, -0.012332, 3.386856, 1.046539, -1.081396, 2.527371, 1.718222, -1.856364, 4.580365, 1.148429, -1.197835, 3.194793, -0.883877, -0.200163, 3.192932, 0.451235, 0.955286, 1.617264, 1.491874, -1.59466] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 6, 8, 8, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 7, 3, 2, 4, 2, 2, 1, 5, 1, 1, 0, 1, 6] 18 | }, 19 | "order": [1, 1, 2, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "chloroacetic_acid.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/bromoacetic_acid.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.900151, -0.049035, -0.01562, 0.460815, 0.817599, -1.18029, -0.690396, 0.764025, -1.5292, 1.355769, 1.608646, -1.780794, 2.798469, 0.089623, 0.50369, 0.722193, -1.088732, -0.261909, 0.319501, 0.215453, 0.859718, 2.222198, 1.501721, -1.347496] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 8, 8, 35, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.290741, 0.381365, -0.34782, -0.502427, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 7, 3, 1, 2, 1, 1, 0, 5, 0, 0, 4, 0, 6] 18 | }, 19 | "order": [1, 1, 2, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "bromoacetic_acid.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/fluoroacetic_acid.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.973888, 0.064522, -0.074629, 2.375273, 0.063103, -0.092209, 2.926838, 0.032852, -1.504505, 2.020523, 0.012544, -2.496436, 4.112216, 0.027844, -1.704267, 2.728541, -0.813939, 0.446704, 2.729884, 0.961607, 0.409153, 1.130937, 0.021368, -2.106511] 6 | }, 7 | "elements": { 8 | "number": [9, 6, 6, 8, 8, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.276398, -0.068822, 0.351014, -0.505733, -0.352154, 0.19719, 0.197196, 0.457706] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 7, 3, 2, 4, 2, 2, 1, 1, 0, 1, 6, 1, 5] 18 | }, 19 | "order": [1, 1, 2, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "fluoroacetic_acid.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/allyl_bromide.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.9595, -0.104403, 0.033299, 2.28489, -0.035557, 0.009213, 3.05411, 1.07391, 0.597519, 4.140121, 0.439904, 2.148768, 0.426753, -0.924272, -0.4278, 0.357959, 0.656694, 0.514601, 2.86258, -0.819652, -0.466786, 2.425469, 1.864359, 0.989565, 3.793318, 1.484517, -0.081179] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 6, 35, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.348471, -0.094265, -0.308777, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [6, 1, 4, 0, 8, 2, 1, 0, 1, 2, 0, 5, 2, 7, 2, 3] 18 | }, 19 | "order": [1, 1, 1, 2, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "allyl_bromide.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/bromoacetone.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [3.619679, 1.76454, 0.08576, 2.964161, -0.090516, -0.000252, 3.472644, -0.788787, -1.241528, 2.677162, -1.282104, -2.013644, 4.958881, -0.872162, -1.454125, 1.883351, -0.048481, -0.005791, 3.331134, -0.572677, 0.901861, 5.53279, -0.590129, -0.57625, 5.235582, -0.199803, -2.265463, 5.216115, -1.880682, -1.768468] 6 | }, 7 | "elements": { 8 | "number": [35, 6, 6, 8, 6, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [8, 4, 3, 2, 9, 4, 4, 2, 4, 7, 2, 1, 5, 1, 1, 0, 1, 6] 18 | }, 19 | "order": [1, 2, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "bromoacetone.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/hexachloroacetone.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [3.930954, 0.192254, 1.520568, 2.87244, 0.097711, 0.087594, 2.672384, -1.621794, -0.437758, 1.278657, 0.775504, 0.512389, 3.415059, 0.832524, -1.187552, 2.647364, 1.368114, -1.926495, 4.949981, 0.874954, -1.507679, 5.856563, -0.591938, -1.049509, 5.169841, 1.156719, -3.254433, 5.559857, 2.307951, -0.587124] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 17, 17, 6, 8, 6, 17, 17, 17] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [8, 6, 5, 4, 6, 4, 6, 7, 6, 9, 4, 1, 2, 1, 1, 3, 1, 0] 18 | }, 19 | "order": [1, 2, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "hexachloroacetone.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/bis_chloromethyl_ketone.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.054041, -0.242367, -0.077492, 2.799574, -0.061969, 0.245836, 3.290886, 1.354514, 0.085539, 2.602721, 2.29226, -0.234213, 4.763275, 1.630829, 0.35035, 5.795463, 0.207211, 0.78547, 3.349461, -0.715971, -0.427114, 3.006197, -0.406807, 1.256519, 4.833593, 2.343631, 1.166431, 5.190188, 2.083468, -0.539026] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 6, 8, 6, 17, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [9, 4, 6, 1, 3, 2, 0, 1, 2, 1, 2, 4, 1, 7, 4, 5, 4, 8] 18 | }, 19 | "order": [1, 1, 2, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "bis_chloromethyl_ketone.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/fluoroacetone.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.082434, -0.06345, 0.024963, 2.577794, -0.098064, 0.035735, 3.233673, -1.072448, 0.341898, 3.329077, 1.16244, -0.359588, 2.493389, 2.225313, -0.693594, 0.690515, -1.027496, 0.330243, 0.717377, 0.193879, -0.969626, 0.717828, 0.719703, 0.690033, 3.966254, 0.935523, -1.215721, 3.965158, 1.465601, 0.473456] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 8, 6, 9, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.493186, 0.228801, -0.339327, -0.064649, -0.266206, 0.195605, 0.184371, 0.18434, 0.185115, 0.185137] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [8, 3, 6, 0, 4, 3, 3, 1, 3, 9, 0, 1, 0, 5, 0, 7, 1, 2] 18 | }, 19 | "order": [1, 1, 1, 1, 1, 1, 1, 1, 2] 20 | }, 21 | "properties": { 22 | "name": "fluoroacetone.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/2_bromo_1_chloropropane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.955517, 0.034064, -0.061056, 2.457922, 0.071092, -0.123618, 3.161165, -1.781029, -0.380617, 3.040155, 0.873248, -1.25839, 2.650505, 2.642183, -1.040593, 0.614946, -0.596098, 0.755185, 0.53257, -0.343875, -0.989351, 0.57784, 1.042529, 0.102936, 2.893473, 0.381424, 0.820451, 2.624455, 0.575411, -2.214694, 4.120153, 0.804152, -1.287953] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 35, 6, 17, 1, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.482733, -0.135397, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [9, 3, 10, 3, 3, 4, 3, 1, 6, 0, 2, 1, 1, 0, 1, 8, 0, 7, 0, 5] 18 | }, 19 | "order": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "2_bromo_1_chloropropane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/isoflurane.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.910433, -0.328523, -0.29674, 2.247247, -0.290579, -0.434571, 2.624798, -1.266245, -1.266004, 2.570999, 0.895148, -0.990044, 2.92232, -0.397337, 0.94459, 2.412299, -1.932902, 1.76762, 4.286563, -0.32289, 0.743281, 5.0587, 0.05261, 1.831212, 5.657072, -1.033616, 2.37112, 6.02602, 0.871145, 1.371709, 2.547365, 0.411172, 1.570016, 4.477682, 0.560917, 2.60301] 6 | }, 7 | "elements": { 8 | "number": [9, 6, 9, 9, 6, 17, 8, 6, 9, 9, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.197675, 0.632658, -0.188006, -0.202234, -0.115089, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [2, 1, 3, 1, 1, 0, 1, 4, 6, 4, 6, 7, 4, 10, 4, 5, 9, 7, 7, 8, 7, 11] 18 | }, 19 | "order": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "isoflurane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /water.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.617532, -0.027246, 0.481009, 0.156663, 0.031752, -0.362419, -0.774185, -0.004516, -0.11859] 6 | }, 7 | "elements": { 8 | "number": [1, 8, 1] 9 | }, 10 | "formalCharges": [0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.432255, -0.864515, 0.432259] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [1, 2, 1, 0] 18 | }, 19 | "order": [1, 1] 20 | }, 21 | "vibrations": { 22 | "frequencies": [1712.02, 3737.35, 3848.97], 23 | "modes": [1, 2, 3], 24 | "intensities": [0.014715, 4.7e-05, 0.006989], 25 | "eigenVectors": [ 26 | [-0.613847, -0.038639, 0.345241, 0.027998, 0.005675, -0.064767, 0.169469, -0.051434, 0.682738], 27 | [-0.381598, 0.040441, -0.592987, -0.019669, -0.003989, 0.045523, 0.693779, 0.022868, -0.129563], 28 | [0.337538, -0.043213, 0.61776, -0.064232, 0.001049, -0.027668, 0.681962, 0.026569, -0.178615] 29 | ] 30 | }, 31 | "properties": { 32 | "name": "water.out.gz", 33 | "totalCharge": 0, 34 | "totalSpinMultiplicity": 1 35 | } 36 | } -------------------------------------------------------------------------------- /halogenated/triclofos.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [4.057734, -1.183683, -0.124648, 2.934495, 0.133384, 0.315031, 1.277744, -0.256435, -0.257848, 2.910105, 0.318051, 2.115464, 3.341662, 1.440599, -0.346091, 4.657911, 1.788386, 0.051707, 4.942213, 3.328259, 0.496894, 4.532484, 4.371172, -0.459057, 4.24146, 3.463784, 1.932921, 6.508946, 3.219406, 0.835457, 2.611657, 2.201269, -0.073978, 3.314726, 1.297509, -1.424172, 4.235336, 2.630047, 2.424026, 7.035529, 3.649053, 0.149796] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 17, 17, 6, 8, 15, 8, 8, 8, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [11, 4, 7, 6, 4, 10, 4, 5, 4, 1, 2, 1, 0, 1, 5, 6, 13, 9, 1, 3, 6, 9, 6, 8, 8, 12] 18 | }, 19 | "order": [1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "triclofos.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/benzyl_chloride.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [3.572279, -0.818065, -1.531271, 2.744764, -0.055248, -0.07352, 3.189452, 1.343636, 0.142842, 2.503587, 2.402835, -0.446371, 2.922369, 3.709255, -0.250813, 4.034001, 3.971783, 0.537772, 4.725414, 2.922455, 1.127822, 4.304749, 1.617161, 0.931252, 2.992766, -0.70075, 0.761319, 1.683406, -0.12252, -0.283267, 1.640465, 2.199032, -1.067558, 2.379768, 4.523668, -0.711839, 4.360958, 4.991485, 0.6921, 5.591516, 3.122515, 1.74432, 4.849204, 0.798959, 1.385613] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [0, 1, 10, 3, 11, 4, 3, 4, 3, 2, 9, 1, 4, 5, 1, 2, 1, 8, 2, 7, 5, 12, 5, 6, 7, 6, 7, 14, 6, 13] 18 | }, 19 | "order": [1, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 2, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "benzyl_chloride.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/benzyl_bromide.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.143714, -0.854067, -0.201932, 2.94936, -0.034016, 0.073439, 3.404615, 0.711267, -1.120006, 3.098757, 2.062606, -1.270626, 3.527287, 2.761816, -2.38691, 4.267506, 2.117704, -3.369114, 4.575598, 0.771274, -3.229646, 4.146206, 0.07348, -2.112647, 3.58661, -0.875381, 0.314701, 2.820955, 0.597878, 0.943194, 2.51409, 2.563809, -0.50955, 3.285655, 3.81113, -2.490592, 4.602953, 2.663419, -4.240942, 5.152785, 0.265068, -3.991746, 4.379708, -0.978686, -2.009022] 6 | }, 7 | "elements": { 8 | "number": [35, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [12, 5, 13, 6, 5, 6, 5, 4, 6, 7, 11, 4, 4, 3, 7, 14, 7, 2, 3, 2, 3, 10, 2, 1, 0, 1, 1, 8, 1, 9] 18 | }, 19 | "order": [1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "benzyl_bromide.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /halogenated/benzal_chloride.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.854582, -1.474467, -0.850155, 2.807732, -0.110283, -0.123424, 4.186387, -0.782644, 0.849199, 3.276981, 0.848764, -1.156662, 2.847367, 2.168821, -1.089099, 3.267992, 3.090332, -2.038029, 4.119162, 2.695029, -3.057285, 4.550243, 1.374654, -3.126702, 4.132423, 0.455308, -2.182467, 2.146962, 0.356888, 0.593101, 2.182319, 2.480009, -0.293561, 2.928698, 4.115451, -1.978021, 4.4479, 3.411892, -3.797681, 5.214607, 1.063117, -3.921216, 4.466046, -0.571671, -2.234499] 6 | }, 7 | "elements": { 8 | "number": [17, 6, 17, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [13, 7, 12, 6, 7, 6, 7, 8, 6, 5, 14, 8, 8, 3, 5, 11, 5, 4, 3, 4, 3, 1, 4, 10, 0, 1, 1, 9, 1, 2] 18 | }, 19 | "order": [1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "benzal_chloride.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /carbohydrates/d-erythrose.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.399838, -0.340596, 0.04642, -0.435286, 0.960508, -0.0126, 1.358198, -0.10585, 0.525727, 0.708227, -0.915599, -1.211827, -0.317281, -1.378783, 0.902422, -0.434116, 1.643511, 1.223994, -1.475303, 0.673923, -0.191914, -0.044502, 1.844438, -1.176074, 0.452672, -2.554573, 1.025412, -1.295979, -1.582632, 0.448599, 0.299253, 2.864774, -0.913944, -0.09616, 1.462996, -2.325733, 0.667059, -2.831387, 0.124167, -0.481873, -0.99457, 1.907704, 0.475377, 1.713241, 1.539487, 0.219864, -0.459411, -1.911842] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 1, 8, 6, 8, 1, 6, 8, 1, 1, 8, 1, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.070563, -0.019679, 0.138533, -0.568357, -0.150632, -0.551699, 0.164088, 0.170855, -0.544786, 0.139763, 0.097263, -0.289396, 0.429495, 0.178688, 0.436207, 0.440219] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [11, 7, 15, 3, 3, 0, 7, 10, 7, 1, 6, 1, 1, 0, 1, 5, 0, 2, 0, 4, 12, 8, 9, 4, 4, 8, 4, 13, 5, 14] 18 | }, 19 | "order": [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "d-erythrose.out.gz", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /coordination/3-trigonal-planar.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [-0.242214, 0.199378, -0.0, 0.949348, 0.199379, 0.0, -0.837965, -0.832554, 0.0, -0.837969, 1.231307, 0.0] 6 | }, 7 | "elements": { 8 | "number": [5, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.077412, 0.025798, 0.025807, 0.025807] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [0, 1, 0, 2, 0, 3] 18 | }, 19 | "order": [1, 1, 1] 20 | }, 21 | "vibrations": { 22 | "frequencies": [1138.55, 1182.92, 1183.88, 2515.42, 2646.74, 2647.08], 23 | "modes": [1, 2, 3, 4, 5, 6], 24 | "intensities": [0.01828, 0.002978, 0.002922, 0.0, 0.027393, 0.02721], 25 | "eigenVectors": [ 26 | [0.0, -0.0, 0.159442, 0.0, 0.0, -0.569947, -0.0, 0.0, -0.569973, -0.0, -0.0, -0.569973], 27 | [-0.101155, -2.3e-05, 0.0, -0.084616, 0.000184, -0.0, 0.584623, -0.386513, -0.0, 0.584798, 0.386578, -0.0], 28 | [2.3e-05, -0.101141, -0.0, 1.8e-05, 0.807874, 0.0, -0.38666, 0.13848, -0.0, 0.386393, 0.138305, 0.0], 29 | [9e-06, -0.0, 0.0, -0.577497, -1e-06, -0.0, 0.2887, 0.499902, -0.0, 0.288701, -0.4999, -0.0], 30 | [-0.111417, -9.5e-05, 0.0, 0.811169, -1.2e-05, 0.0, 0.192149, 0.358269, -0.0, 0.191545, -0.357244, -0.0], 31 | [-9.5e-05, 0.11143, -0.0, 0.000686, 0.014623, 0.0, -0.357449, -0.604509, 0.0, 0.357776, -0.605115, -0.0] 32 | ] 33 | }, 34 | "properties": { 35 | "name": "3-trigonal-planar.out.gz", 36 | "totalCharge": 0, 37 | "totalSpinMultiplicity": 1 38 | } 39 | } -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2016, Geoffrey Hutchison, University of Pittsburgh 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | * Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | * Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | * Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /ligands/Cp-cyclopentadienyl.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "atoms": { 3 | "coords": { 4 | "3d": [-1.0963, -0.4179, -0.1293, -0.7943, 0.9338, 0.0286, 0.5925, 1.0681, 0.0281, 1.1481, -0.2005, -0.13, 0.1042, -1.1184, -0.2282, -2.0934, -0.8488, -0.17, -1.5152, 1.7406, 0.1346, 1.1453, 1.9983, 0.1338, 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31 | "locked": [false, false, false], 32 | "settings": { 33 | "Ball and Stick": ["true true 0.300000 0.100000"] 34 | }, 35 | "visible": [true, true, true] 36 | }, 37 | "properties": { 38 | "totalCharge": 0, 39 | "totalSpinMultiplicity": 2 40 | } 41 | } -------------------------------------------------------------------------------- /fullerenes/C20.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [1.147018, -0.417365, 1.562662, 0.000558, -1.293718, 1.629696, -1.227538, 1.627929, 0.365749, -1.224895, -0.399334, 1.624455, 1.145382, 1.575023, 0.330231, -0.74911, 0.961337, 1.56428, 1.932541, -0.665332, 0.368005, 0.68951, 0.947668, 1.54225, 0.005707, -2.017168, 0.426975, -1.921244, -0.618671, 0.424631, -0.005713, 2.017164, -0.426973, 1.921235, 0.618672, -0.424628, 1.22754, -1.627938, -0.365758, -1.145393, -1.575021, -0.330224, -1.932536, 0.665336, -0.368002, -0.00055, 1.293725, -1.6297, 1.224899, 0.399344, -1.624451, 0.749113, -0.961346, -1.564271, -0.689514, -0.947666, -1.542257, -1.14701, 0.417362, -1.562669] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 9 | }, 10 | "formalCharges": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.086699, 0.05896, 0.0582, 0.057427, 0.05876, -0.08733, 0.057817, 0.057902, -0.087531, -0.087478, -0.087514, -0.087505, 0.058188, 0.058745, 0.057789, 0.05887, 0.057517, -0.087371, 0.057904, -0.08665] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [15, 16, 15, 19, 15, 10, 16, 17, 16, 11, 17, 18, 17, 12, 19, 18, 19, 14, 18, 13, 10, 4, 10, 2, 11, 4, 11, 6, 14, 2, 14, 9, 12, 6, 12, 8, 13, 9, 13, 8, 4, 7, 2, 5, 6, 0, 9, 3, 8, 1, 7, 0, 7, 5, 0, 1, 5, 3, 3, 1] 18 | }, 19 | "order": [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 | }, 21 | "properties": { 22 | "name": "C20.out.gz", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /alkynes/acetylene.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.583595, 0.012481, 0.138157, -0.583573, -0.012497, -0.138248, 1.616059, 0.034583, 0.382905, -1.616081, -0.034577, -0.382815] 6 | }, 7 | "elements": { 8 | "number": [6, 6, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.242518, -0.242532, 0.242526, 0.242524] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 1, 1, 0, 0, 2] 18 | }, 19 | "order": [1, 3, 1] 20 | }, 21 | "vibrations": { 22 | "frequencies": [506.85, 660.52, 742.08, 2040.85, 3373.34, 3473.87], 23 | "modes": [1, 2, 3, 4, 5, 6], 24 | "intensities": [0.0, 0.014115, 0.023271, 0.0, 0.011907, 0.0], 25 | "eigenVectors": [ 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-------------------------------------------------------------------------------- /aldehydes/formaldehyde.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [0.491521, -0.157604, 0.983745, 0.004957, 0.00059, 0.000654, 0.693651, 0.187234, -0.847344, -1.190138, -0.03022, -0.137055] 6 | }, 7 | "elements": { 8 | "number": [1, 6, 1, 8] 9 | }, 10 | "formalCharges": [0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [0.123461, 0.047379, 0.123459, -0.294298] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [2, 1, 3, 1, 1, 0] 18 | }, 19 | "order": [1, 2, 1] 20 | }, 21 | "vibrations": { 22 | "frequencies": [1173.54, 1253.89, 1530.26, 1794.09, 2818.97, 2859.08], 23 | "modes": [1, 2, 3, 4, 5, 6], 24 | "intensities": [0.000416, 0.001944, 0.001776, 0.020798, 0.017151, 0.03404], 25 | "eigenVectors": [ 26 | [-0.029355, 0.683684, 0.124938, 0.007887, -0.171246, -0.030762, 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-------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [-0.16003, -0.199227, 0.129162, 0.155788, 0.513683, 0.773789, 0.669085, -0.592585, -0.296715, -0.664843, 0.278129, -0.606236] 6 | }, 7 | "elements": { 8 | "number": [7, 1, 1, 1] 9 | }, 10 | "formalCharges": [0, 0, 0, 0] 11 | }, 12 | "partialCharges": { 13 | "Gasteiger": [-0.946043, 0.315346, 0.315342, 0.315355] 14 | }, 15 | "bonds": { 16 | "connections": { 17 | "index": [3, 0, 2, 0, 0, 1] 18 | }, 19 | "order": [1, 1, 1] 20 | }, 21 | "vibrations": { 22 | "frequencies": [1104.49, 1722.74, 1723.0, 3418.51, 3556.99, 3557.28], 23 | "modes": [1, 2, 3, 4, 5, 6], 24 | "intensities": [0.041709, 0.005573, 0.005589, 0.000414, 6.7e-05, 6.4e-05], 25 | "eigenVectors": [ 26 | [0.064639, 0.080499, -0.052174, -0.276988, -0.275334, 0.419972, -0.165054, -0.516546, 0.186334, -0.456171, -0.326722, 0.118698], 27 | [-0.055567, 0.028891, -0.024229, 0.638699, 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21 | "properties": { 22 | "name": "eicosane.out", 23 | "totalCharge": 0, 24 | "totalSpinMultiplicity": 1 25 | } 26 | } -------------------------------------------------------------------------------- /fatty_acids/linoleic_acid.cjson: -------------------------------------------------------------------------------- 1 | { 2 | "chemicalJson": 1, 3 | "atoms": { 4 | "coords": { 5 | "3d": [3.532111, 0.325184, -1.371505, 2.316343, 0.367823, -0.83148, 1.187396, 1.28594, -1.19239, 0.963399, 2.306553, -0.117371, -0.106873, 2.452402, 0.660288, 4.063646, 1.149242, -2.495601, -1.36005, 1.64347, 0.662002, 4.230832, -0.403948, -0.969201, 2.102253, -0.303005, -0.005011, 0.285122, 0.696794, -1.355619, 1.395194, 1.796616, -2.133473, 1.80264, 2.976735, 0.041841, -0.077467, 3.244925, 1.403776, 4.419028, 0.315888, -3.725971, 4.965019, 1.670471, -2.157177, 3.355535, 1.927487, -2.779419, -2.211896, 2.305324, 0.474076, -1.593601, 0.920893, 1.987851, -1.35971, 0.915171, -0.148527, 4.985835, 1.14536, -4.866866, 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