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: