Molecular descriptors
Datagrok supports calculation of the following descriptors:
EState.EState_VSA
Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
Descriptor | Description |
---|---|
EState_VSA1 | EState VSA Descriptor 1 (-inf < x < -0.39) |
EState_VSA10 | EState VSA Descriptor 10 ( 9.17 <= x < 15.00) |
EState_VSA11 | EState VSA Descriptor 11 ( 15.00 <= x < inf) |
EState_VSA2 | EState VSA Descriptor 2 ( -0.39 <= x < 0.29) |
EState_VSA3 | EState VSA Descriptor 3 ( 0.29 <= x < 0.72) |
EState_VSA4 | EState VSA Descriptor 4 ( 0.72 <= x < 1.17) |
EState_VSA5 | EState VSA Descriptor 5 ( 1.17 <= x < 1.54) |
EState_VSA6 | EState VSA Descriptor 6 ( 1.54 <= x < 1.81) |
EState_VSA7 | EState VSA Descriptor 7 ( 1.81 <= x < 2.05) |
EState_VSA8 | EState VSA Descriptor 8 ( 2.05 <= x < 4.69) |
EState_VSA9 | EState VSA Descriptor 9 ( 4.69 <= x < 9.17) |
VSA_EState1 | VSA EState Descriptor 1 (-inf < x < 4.78) |
VSA_EState10 | VSA EState Descriptor 10 ( 11.00 <= x < inf) |
VSA_EState2 | VSA EState Descriptor 2 ( 4.78 <= x < 5.00) |
VSA_EState3 | VSA EState Descriptor 3 ( 5.00 <= x < 5.41) |
VSA_EState4 | VSA EState Descriptor 4 ( 5.41 <= x < 5.74) |
VSA_EState5 | VSA EState Descriptor 5 ( 5.74 <= x < 6.00) |
VSA_EState6 | VSA EState Descriptor 6 ( 6.00 <= x < 6.07) |
VSA_EState7 | VSA EState Descriptor 7 ( 6.07 <= x < 6.45) |
VSA_EState8 | VSA EState Descriptor 8 ( 6.45 <= x < 7.00) |
VSA_EState9 | VSA EState Descriptor 9 ( 7.00 <= x < 11.00) |
QED
QED stands for quantitative estimation of drug-likeness
Descriptor | Description |
---|---|
qed | Weighted sum of ADS mapped properties |
GraphDescriptors
Topological/topochemical descriptors
Descriptor | Description |
---|---|
BalabanJ | Balaban's J value |
BertzCT | A topological index meant to quantify "complexity" |
Chi0 | From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) |
Chi0n | Similar to Hall Kier Chi0v, but uses nVal instead of valence. This makes a big difference after we get out of the first row |
Chi0v | From equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991) |
Chi1 | From equations (1),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991) |
Chi1n | Similar to Hall Kier Chi1v, but uses nVal instead of valence |
Chi1v | From equations (5),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991) |
Chi2n | Similar to Hall Kier Chi2v, but uses nVal instead of valence. This makes a big difference after we get out of the first row |
Chi2v | From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991) |
Chi3n | Similar to Hall Kier Chi3v, but uses nVal instead of valence. This makes a big difference after we get out of the first row |
Chi3v | From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991) |
Chi4n | Similar to Hall Kier Chi4v, but uses nVal instead of valence. This makes a big difference after we get out of the first row |
Chi4v | From equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991). |
HallKierAlpha | The Hall-Kier alpha value for a molecule |
Ipc | The information content of the coefficients of the characteristic polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule |
Kappa1 | Hall-Kier Kappa1 value |
Kappa2 | Hall-Kier Kappa2 value |
Kappa3 | Hall-Kier Kappa3 value |
General descriptors
General descriptors
Descriptor | Description |
---|---|
MinAbsPartialCharge | Minimal absolute partial charge |
NumRadicalElectrons | The number of radical electrons the molecule has (says nothing about spin state) |
FpDensityMorgan2 | Morgan fingerprint, radius 2 |
FpDensityMorgan3 | Morgan fingerprint, radius 3 |
FpDensityMorgan1 | Morgan fingerprint, radius 1 |
HeavyAtomMolWt | The average molecular weight of the molecule ignoring hydrogens |
MaxAbsPartialCharge | Maximum absolute partial charge |
MinPartialCharge | Minimal partial charge |
ExactMolWt | The exact molecular weight of the molecule |
MolWt | The average molecular weight of the molecule |
NumValenceElectrons | The number of valence electrons the molecule has |
MaxPartialCharge | Maximum partial charge |
Crippen
Atom-based calculation of LogP and MR using Crippen's approach
Descriptor | Description |
---|---|
MolLogP | Wildman-Crippen LogP value |
MolMR | Wildman-Crippen MR value |
MolSurf
MOE-like approximate molecular surface area descriptors
Descriptor | Description |
---|---|
LabuteASA | Labute's Approximate Surface Area (ASA from MOE) |
PEOE_VSA1 | MOE Charge VSA Descriptor 1 (-inf < x < -0.30) |
PEOE_VSA10 | MOE Charge VSA Descriptor 10 ( 0.10 <= x < 0.15) |
PEOE_VSA11 | MOE Charge VSA Descriptor 11 ( 0.15 <= x < 0.20) |
PEOE_VSA12 | MOE Charge VSA Descriptor 12 ( 0.20 <= x < 0.25) |
PEOE_VSA13 | MOE Charge VSA Descriptor 13 ( 0.25 <= x < 0.30) |
PEOE_VSA14 | MOE Charge VSA Descriptor 14 ( 0.30 <= x < inf) |
PEOE_VSA2 | MOE Charge VSA Descriptor 2 (-0.30 <= x < -0.25) |
PEOE_VSA3 | MOE Charge VSA Descriptor 3 (-0.25 <= x < -0.20) |
PEOE_VSA4 | MOE Charge VSA Descriptor 4 (-0.20 <= x < -0.15) |
PEOE_VSA5 | MOE Charge VSA Descriptor 5 (-0.15 <= x < -0.10) |
PEOE_VSA6 | MOE Charge VSA Descriptor 6 (-0.10 <= x < -0.05) |
PEOE_VSA7 | MOE Charge VSA Descriptor 7 (-0.05 <= x < 0.00) |
PEOE_VSA8 | MOE Charge VSA Descriptor 8 ( 0.00 <= x < 0.05) |
PEOE_VSA9 | MOE Charge VSA Descriptor 9 ( 0.05 <= x < 0.10) |
SMR_VSA1 | MOE MR VSA Descriptor 1 (-inf < x < 1.29) |
SMR_VSA10 | MOE MR VSA Descriptor 10 ( 4.00 <= x < inf) |
SMR_VSA2 | MOE MR VSA Descriptor 2 ( 1.29 <= x < 1.82) |
SMR_VSA3 | MOE MR VSA Descriptor 3 ( 1.82 <= x < 2.24) |
SMR_VSA4 | MOE MR VSA Descriptor 4 ( 2.24 <= x < 2.45) |
SMR_VSA5 | MOE MR VSA Descriptor 5 ( 2.45 <= x < 2.75) |
SMR_VSA6 | MOE MR VSA Descriptor 6 ( 2.75 <= x < 3.05) |
SMR_VSA7 | MOE MR VSA Descriptor 7 ( 3.05 <= x < 3.63) |
SMR_VSA8 | MOE MR VSA Descriptor 8 ( 3.63 <= x < 3.80) |
SMR_VSA9 | MOE MR VSA Descriptor 9 ( 3.80 <= x < 4.00) |
SlogP_VSA1 | MOE logP VSA Descriptor 1 (-inf < x < -0.40) |
SlogP_VSA10 | MOE logP VSA Descriptor 10 ( 0.40 <= x < 0.50) |
SlogP_VSA11 | MOE logP VSA Descriptor 11 ( 0.50 <= x < 0.60) |
SlogP_VSA12 | MOE logP VSA Descriptor 12 ( 0.60 <= x < inf) |
SlogP_VSA2 | MOE logP VSA Descriptor 2 (-0.40 <= x < -0.20) |
SlogP_VSA3 | MOE logP VSA Descriptor 3 (-0.20 <= x < 0.00) |
SlogP_VSA4 | MOE logP VSA Descriptor 4 ( 0.00 <= x < 0.10) |
SlogP_VSA5 | MOE logP VSA Descriptor 5 ( 0.10 <= x < 0.15) |
SlogP_VSA6 | MOE logP VSA Descriptor 6 ( 0.15 <= x < 0.20) |
SlogP_VSA7 | MOE logP VSA Descriptor 7 ( 0.20 <= x < 0.25) |
SlogP_VSA8 | MOE logP VSA Descriptor 8 ( 0.25 <= x < 0.30) |
SlogP_VSA9 | MOE logP VSA Descriptor 9 ( 0.30 <= x < 0.40) |
TPSA | The polar surface area of a molecule based upon fragments. |
Descriptors3D
Descriptors derived from a molecule's 3D structure
Descriptor | Description |
---|---|
PMI1 | First (smallest) principal moment of inertia |
PMI2 | Second principal moment of inertia |
PMI3 | Third (largest) principal moment of inertia |
NPR1 | Normalized principal moments ratio 1 (=I1/I3) |
NPR2 | Normalized principal moments ratio 2 (=I2/I3) |
RadiusOfGyration | Radius of gyration |
InertialShapeFactor | Inertial shape factor |
Eccentricity | Molecular eccentricity |
Asphericity | Molecular asphericity |
SpherocityIndex | Molecular spherocity index |
EState.EState
Basic EState descriptors
Descriptor | Description |
---|---|
MaxAbsEStateIndex | Maximum absolute EState index |
MaxEStateIndex | Maximum EState index |
MinEStateIndex | Minimum EState index |
MinAbsEStateIndex | Minimum absolute EState index |
Fragments
Bunch of fragment descriptors from a file
Descriptor | Description |
---|---|
fr_Al_COO | Number of aliphatic carboxylic acids |
fr_Al_OH | Number of aliphatic hydroxyl groups |
fr_Al_OH_noTert | Number of aliphatic hydroxyl groups excluding tert-OH |
fr_ArN | Number of N functional groups attached to aromatics |
fr_Ar_COO | Number of Aromatic carboxylic acide |
fr_Ar_N | Number of aromatic nitrogens |
fr_Ar_NH | Number of aromatic amines |
fr_Ar_OH | Number of aromatic hydroxyl groups |
fr_COO | Number of carboxylic acids |
fr_COO2 | Number of carboxylic acids |
fr_C_O | Number of carbonyl O |
fr_C_O_noCOO | Number of carbonyl O, excluding COOH |
fr_C_S | Number of thiocarbonyl |
fr_HOCCN | Number of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic |
fr_Imine | Number of Imines |
fr_NH0 | Number of Tertiary amines |
fr_NH1 | Number of Secondary amines |
fr_NH2 | Number of Primary amines |
fr_N_O | Number of hydroxylamine groups |
fr_Ndealkylation1 | Number of XCCNR groups |
fr_Ndealkylation2 | Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N) |
fr_Nhpyrrole | Number of H-pyrrole nitrogens |
fr_SH | Number of thiol groups |
fr_aldehyde | Number of aldehydes |
fr_alkyl_carbamate | Number of alkyl carbamates (subject to hydrolysis) |
fr_alkyl_halide | Number of alkyl halides |
fr_allylic_oxid | Number of allylic oxidation sites excluding steroid dienone |
fr_amide | Number of amides |
fr_amidine | Number of amidine groups |
fr_aniline | Number of anilines |
fr_aryl_methyl | Number of aryl methyl sites for hydroxylation |
fr_azide | Number of azide groups |
fr_azo | Number of azo groups |
fr_barbitur | Number of barbiturate groups |
fr_benzene | Number of benzene rings |
fr_benzodiazepine | Number of benzodiazepines with no additional fused rings |
fr_bicyclic | Bicyclic |
fr_diazo | Number of diazo groups |
fr_dihydropyridine | Number of dihydropyridines |
fr_epoxide | Number of epoxide rings |
fr_ester | Number of esters |
fr_ether | Number of ether oxygens (including phenoxy) |
fr_furan | Number of furan rings |
fr_guanido | Number of guanidine groups |
fr_halogen | Number of halogens |
fr_hdrzine | Number of hydrazine groups |
fr_hdrzone | Number of hydrazone groups |
fr_imidazole | Number of imidazole rings |
fr_imide | Number of imide groups |
fr_isocyan | Number of isocyanates |
fr_isothiocyan | Number of isothiocyanates |
fr_ketone | Number of ketones |
fr_ketone_Topliss | Number of ketones excluding diaryl, a,b-unsat |
fr_lactam | Number of beta lactams |
fr_lactone | Number of cyclic esters (lactones) |
fr_methoxy | Number of methoxy groups -OCH3 |
fr_morpholine | Number of morpholine rings |
fr_nitrile | Number of nitriles |
fr_nitro | Number of nitro groups |
fr_nitro_arom | Number of nitro benzene ring substituent |
fr_nitro_arom_nonortho | Number of non-ortho nitro benzene ring substituents |
fr_nitroso | Number of nitroso groups, excluding NO2 |
fr_oxazole | Number of oxazole rings |
fr_oxime | Number of oxime groups |
fr_para_hydroxylation | Number of para-hydroxylation sites |
fr_phenol | Number of phenols |
fr_phenol_noOrthoHbond | Number of phenolic OH excluding ortho intramolecular Hbond substituents |
fr_phos_acid | Number of phosphoric acid groups |
fr_phos_ester | Number of phosphoric ester groups |
fr_piperdine | Number of piperdine rings |
fr_piperzine | Number of piperzine rings |
fr_priamide | Number of primary amides |
fr_prisulfonamd | Number of primary sulfonamides |
fr_pyridine | Number of pyridine rings |
fr_quatN | Number of quarternary nitrogens |
fr_sulfide | Number of thioether |
fr_sulfonamd | Number of sulfonamides |
fr_sulfone | Number of sulfone groups |
fr_term_acetylene | Number of terminal acetylenes |
fr_tetrazole | Number of tetrazole rings |
fr_thiazole | Number of tetrazole rings |
fr_thiocyan | Number of thiocyanates |
fr_thiophene | Number of thiophene rings |
fr_unbrch_alkane | Number of unbranched alkanes of at least 4 members (excludes halogenated alkanes) |
fr_urea | Number of urea groups |
Lipinski
Lipinski parameters for molecules
Descriptor | Description |
---|---|
FractionCSP3 | The fraction of C atoms that are SP3 hybridized |
HeavyAtomCount | The number of heavy atoms a molecule |
NHOHCount | The number of NHs or OHs |
NOCount | The number of Nitrogens and Oxygens |
NumAliphaticCarbocycles | The number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule |
NumAliphaticHeterocycles | The number of aliphatic (containing at least one non-aromatic bond) heterocycles for a molecule |
NumAliphaticRings | The number of aliphatic (containing at least one non-aromatic bond) rings for a molecule |
NumAromaticCarbocycles | The number of aromatic carbocycles for a molecule |
NumAromaticHeterocycles | The number of aromatic heterocycles for a molecule |
NumAromaticRings | The number of aromatic rings for a molecule |
NumHAcceptors | The number of Hydrogen Bond Acceptors |
NumHDonors | The number of Hydrogen Bond Donors |
NumHeteroatoms | The number of Heteroatoms |
NumRotatableBonds | The number of Rotatable Bonds |
NumSaturatedCarbocycles | The number of saturated carbocycles for a molecule |
NumSaturatedHeterocycles | The number of saturated heterocycles for a molecule |
NumSaturatedRings | The number of saturated rings for a molecule |
RingCount | Ring count |
See also: