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Molecular descriptors

Datagrok supports calculation of the following descriptors:

EState.EState_VSA

Hybrid EState-VSA descriptors (like the MOE VSA descriptors)

DescriptorDescription
EState_VSA1EState VSA Descriptor 1 (-inf < x < -0.39)
EState_VSA10EState VSA Descriptor 10 ( 9.17 <= x < 15.00)
EState_VSA11EState VSA Descriptor 11 ( 15.00 <= x < inf)
EState_VSA2EState VSA Descriptor 2 ( -0.39 <= x < 0.29)
EState_VSA3EState VSA Descriptor 3 ( 0.29 <= x < 0.72)
EState_VSA4EState VSA Descriptor 4 ( 0.72 <= x < 1.17)
EState_VSA5EState VSA Descriptor 5 ( 1.17 <= x < 1.54)
EState_VSA6EState VSA Descriptor 6 ( 1.54 <= x < 1.81)
EState_VSA7EState VSA Descriptor 7 ( 1.81 <= x < 2.05)
EState_VSA8EState VSA Descriptor 8 ( 2.05 <= x < 4.69)
EState_VSA9EState VSA Descriptor 9 ( 4.69 <= x < 9.17)
VSA_EState1VSA EState Descriptor 1 (-inf < x < 4.78)
VSA_EState10VSA EState Descriptor 10 ( 11.00 <= x < inf)
VSA_EState2VSA EState Descriptor 2 ( 4.78 <= x < 5.00)
VSA_EState3VSA EState Descriptor 3 ( 5.00 <= x < 5.41)
VSA_EState4VSA EState Descriptor 4 ( 5.41 <= x < 5.74)
VSA_EState5VSA EState Descriptor 5 ( 5.74 <= x < 6.00)
VSA_EState6VSA EState Descriptor 6 ( 6.00 <= x < 6.07)
VSA_EState7VSA EState Descriptor 7 ( 6.07 <= x < 6.45)
VSA_EState8VSA EState Descriptor 8 ( 6.45 <= x < 7.00)
VSA_EState9VSA EState Descriptor 9 ( 7.00 <= x < 11.00)

QED

QED stands for quantitative estimation of drug-likeness

DescriptorDescription
qedWeighted sum of ADS mapped properties

GraphDescriptors

Topological/topochemical descriptors

DescriptorDescription
BalabanJBalaban's J value
BertzCTA topological index meant to quantify "complexity"
Chi0From equations (1),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
Chi0nSimilar to Hall Kier Chi0v, but uses nVal instead of valence. This makes a big difference after we get out of the first row
Chi0vFrom equations (5),(9) and (10) of Rev. Comp. Chem. vol 2, 367-422, (1991)
Chi1From equations (1),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
Chi1nSimilar to Hall Kier Chi1v, but uses nVal instead of valence
Chi1vFrom equations (5),(11) and (12) of Rev. Comp. Chem. vol 2, 367-422, (1991)
Chi2nSimilar to Hall Kier Chi2v, but uses nVal instead of valence. This makes a big difference after we get out of the first row
Chi2vFrom equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
Chi3nSimilar to Hall Kier Chi3v, but uses nVal instead of valence. This makes a big difference after we get out of the first row
Chi3vFrom equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991)
Chi4nSimilar to Hall Kier Chi4v, but uses nVal instead of valence. This makes a big difference after we get out of the first row
Chi4vFrom equations (5),(15) and (16) of Rev. Comp. Chem. vol 2, 367-422, (1991).
HallKierAlphaThe Hall-Kier alpha value for a molecule
IpcThe information content of the coefficients of the characteristic polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule
Kappa1Hall-Kier Kappa1 value
Kappa2Hall-Kier Kappa2 value
Kappa3Hall-Kier Kappa3 value

General descriptors

General descriptors

DescriptorDescription
MinAbsPartialChargeMinimal absolute partial charge
NumRadicalElectronsThe number of radical electrons the molecule has (says nothing about spin state)
FpDensityMorgan2Morgan fingerprint, radius 2
FpDensityMorgan3Morgan fingerprint, radius 3
FpDensityMorgan1Morgan fingerprint, radius 1
HeavyAtomMolWtThe average molecular weight of the molecule ignoring hydrogens
MaxAbsPartialChargeMaximum absolute partial charge
MinPartialChargeMinimal partial charge
ExactMolWtThe exact molecular weight of the molecule
MolWtThe average molecular weight of the molecule
NumValenceElectronsThe number of valence electrons the molecule has
MaxPartialChargeMaximum partial charge

Crippen

Atom-based calculation of LogP and MR using Crippen's approach

DescriptorDescription
MolLogPWildman-Crippen LogP value
MolMRWildman-Crippen MR value

MolSurf

MOE-like approximate molecular surface area descriptors

DescriptorDescription
LabuteASALabute's Approximate Surface Area (ASA from MOE)
PEOE_VSA1MOE Charge VSA Descriptor 1 (-inf < x < -0.30)
PEOE_VSA10MOE Charge VSA Descriptor 10 ( 0.10 <= x < 0.15)
PEOE_VSA11MOE Charge VSA Descriptor 11 ( 0.15 <= x < 0.20)
PEOE_VSA12MOE Charge VSA Descriptor 12 ( 0.20 <= x < 0.25)
PEOE_VSA13MOE Charge VSA Descriptor 13 ( 0.25 <= x < 0.30)
PEOE_VSA14MOE Charge VSA Descriptor 14 ( 0.30 <= x < inf)
PEOE_VSA2MOE Charge VSA Descriptor 2 (-0.30 <= x < -0.25)
PEOE_VSA3MOE Charge VSA Descriptor 3 (-0.25 <= x < -0.20)
PEOE_VSA4MOE Charge VSA Descriptor 4 (-0.20 <= x < -0.15)
PEOE_VSA5MOE Charge VSA Descriptor 5 (-0.15 <= x < -0.10)
PEOE_VSA6MOE Charge VSA Descriptor 6 (-0.10 <= x < -0.05)
PEOE_VSA7MOE Charge VSA Descriptor 7 (-0.05 <= x < 0.00)
PEOE_VSA8MOE Charge VSA Descriptor 8 ( 0.00 <= x < 0.05)
PEOE_VSA9MOE Charge VSA Descriptor 9 ( 0.05 <= x < 0.10)
SMR_VSA1MOE MR VSA Descriptor 1 (-inf < x < 1.29)
SMR_VSA10MOE MR VSA Descriptor 10 ( 4.00 <= x < inf)
SMR_VSA2MOE MR VSA Descriptor 2 ( 1.29 <= x < 1.82)
SMR_VSA3MOE MR VSA Descriptor 3 ( 1.82 <= x < 2.24)
SMR_VSA4MOE MR VSA Descriptor 4 ( 2.24 <= x < 2.45)
SMR_VSA5MOE MR VSA Descriptor 5 ( 2.45 <= x < 2.75)
SMR_VSA6MOE MR VSA Descriptor 6 ( 2.75 <= x < 3.05)
SMR_VSA7MOE MR VSA Descriptor 7 ( 3.05 <= x < 3.63)
SMR_VSA8MOE MR VSA Descriptor 8 ( 3.63 <= x < 3.80)
SMR_VSA9MOE MR VSA Descriptor 9 ( 3.80 <= x < 4.00)
SlogP_VSA1MOE logP VSA Descriptor 1 (-inf < x < -0.40)
SlogP_VSA10MOE logP VSA Descriptor 10 ( 0.40 <= x < 0.50)
SlogP_VSA11MOE logP VSA Descriptor 11 ( 0.50 <= x < 0.60)
SlogP_VSA12MOE logP VSA Descriptor 12 ( 0.60 <= x < inf)
SlogP_VSA2MOE logP VSA Descriptor 2 (-0.40 <= x < -0.20)
SlogP_VSA3MOE logP VSA Descriptor 3 (-0.20 <= x < 0.00)
SlogP_VSA4MOE logP VSA Descriptor 4 ( 0.00 <= x < 0.10)
SlogP_VSA5MOE logP VSA Descriptor 5 ( 0.10 <= x < 0.15)
SlogP_VSA6MOE logP VSA Descriptor 6 ( 0.15 <= x < 0.20)
SlogP_VSA7MOE logP VSA Descriptor 7 ( 0.20 <= x < 0.25)
SlogP_VSA8MOE logP VSA Descriptor 8 ( 0.25 <= x < 0.30)
SlogP_VSA9MOE logP VSA Descriptor 9 ( 0.30 <= x < 0.40)
TPSAThe polar surface area of a molecule based upon fragments.

Descriptors3D

Descriptors derived from a molecule's 3D structure

DescriptorDescription
PMI1First (smallest) principal moment of inertia
PMI2Second principal moment of inertia
PMI3Third (largest) principal moment of inertia
NPR1Normalized principal moments ratio 1 (=I1/I3)
NPR2Normalized principal moments ratio 2 (=I2/I3)
RadiusOfGyrationRadius of gyration
InertialShapeFactorInertial shape factor
EccentricityMolecular eccentricity
AsphericityMolecular asphericity
SpherocityIndexMolecular spherocity index

EState.EState

Basic EState descriptors

DescriptorDescription
MaxAbsEStateIndexMaximum absolute EState index
MaxEStateIndexMaximum EState index
MinEStateIndexMinimum EState index
MinAbsEStateIndexMinimum absolute EState index

Fragments

Bunch of fragment descriptors from a file

DescriptorDescription
fr_Al_COONumber of aliphatic carboxylic acids
fr_Al_OHNumber of aliphatic hydroxyl groups
fr_Al_OH_noTertNumber of aliphatic hydroxyl groups excluding tert-OH
fr_ArNNumber of N functional groups attached to aromatics
fr_Ar_COONumber of Aromatic carboxylic acide
fr_Ar_NNumber of aromatic nitrogens
fr_Ar_NHNumber of aromatic amines
fr_Ar_OHNumber of aromatic hydroxyl groups
fr_COONumber of carboxylic acids
fr_COO2Number of carboxylic acids
fr_C_ONumber of carbonyl O
fr_C_O_noCOONumber of carbonyl O, excluding COOH
fr_C_SNumber of thiocarbonyl
fr_HOCCNNumber of C(OH)CCN-Ctert-alkyl or C(OH)CCNcyclic
fr_ImineNumber of Imines
fr_NH0Number of Tertiary amines
fr_NH1Number of Secondary amines
fr_NH2Number of Primary amines
fr_N_ONumber of hydroxylamine groups
fr_Ndealkylation1Number of XCCNR groups
fr_Ndealkylation2Number of tert-alicyclic amines (no heteroatoms, not quinine-like bridged N)
fr_NhpyrroleNumber of H-pyrrole nitrogens
fr_SHNumber of thiol groups
fr_aldehydeNumber of aldehydes
fr_alkyl_carbamateNumber of alkyl carbamates (subject to hydrolysis)
fr_alkyl_halideNumber of alkyl halides
fr_allylic_oxidNumber of allylic oxidation sites excluding steroid dienone
fr_amideNumber of amides
fr_amidineNumber of amidine groups
fr_anilineNumber of anilines
fr_aryl_methylNumber of aryl methyl sites for hydroxylation
fr_azideNumber of azide groups
fr_azoNumber of azo groups
fr_barbiturNumber of barbiturate groups
fr_benzeneNumber of benzene rings
fr_benzodiazepineNumber of benzodiazepines with no additional fused rings
fr_bicyclicBicyclic
fr_diazoNumber of diazo groups
fr_dihydropyridineNumber of dihydropyridines
fr_epoxideNumber of epoxide rings
fr_esterNumber of esters
fr_etherNumber of ether oxygens (including phenoxy)
fr_furanNumber of furan rings
fr_guanidoNumber of guanidine groups
fr_halogenNumber of halogens
fr_hdrzineNumber of hydrazine groups
fr_hdrzoneNumber of hydrazone groups
fr_imidazoleNumber of imidazole rings
fr_imideNumber of imide groups
fr_isocyanNumber of isocyanates
fr_isothiocyanNumber of isothiocyanates
fr_ketoneNumber of ketones
fr_ketone_ToplissNumber of ketones excluding diaryl, a,b-unsat
fr_lactamNumber of beta lactams
fr_lactoneNumber of cyclic esters (lactones)
fr_methoxyNumber of methoxy groups -OCH3
fr_morpholineNumber of morpholine rings
fr_nitrileNumber of nitriles
fr_nitroNumber of nitro groups
fr_nitro_aromNumber of nitro benzene ring substituent
fr_nitro_arom_nonorthoNumber of non-ortho nitro benzene ring substituents
fr_nitrosoNumber of nitroso groups, excluding NO2
fr_oxazoleNumber of oxazole rings
fr_oximeNumber of oxime groups
fr_para_hydroxylationNumber of para-hydroxylation sites
fr_phenolNumber of phenols
fr_phenol_noOrthoHbondNumber of phenolic OH excluding ortho intramolecular Hbond substituents
fr_phos_acidNumber of phosphoric acid groups
fr_phos_esterNumber of phosphoric ester groups
fr_piperdineNumber of piperdine rings
fr_piperzineNumber of piperzine rings
fr_priamideNumber of primary amides
fr_prisulfonamdNumber of primary sulfonamides
fr_pyridineNumber of pyridine rings
fr_quatNNumber of quarternary nitrogens
fr_sulfideNumber of thioether
fr_sulfonamdNumber of sulfonamides
fr_sulfoneNumber of sulfone groups
fr_term_acetyleneNumber of terminal acetylenes
fr_tetrazoleNumber of tetrazole rings
fr_thiazoleNumber of tetrazole rings
fr_thiocyanNumber of thiocyanates
fr_thiopheneNumber of thiophene rings
fr_unbrch_alkaneNumber of unbranched alkanes of at least 4 members (excludes halogenated alkanes)
fr_ureaNumber of urea groups

Lipinski

Lipinski parameters for molecules

DescriptorDescription
FractionCSP3The fraction of C atoms that are SP3 hybridized
HeavyAtomCountThe number of heavy atoms a molecule
NHOHCountThe number of NHs or OHs
NOCountThe number of Nitrogens and Oxygens
NumAliphaticCarbocyclesThe number of aliphatic (containing at least one non-aromatic bond) carbocycles for a molecule
NumAliphaticHeterocyclesThe number of aliphatic (containing at least one non-aromatic bond) heterocycles for a molecule
NumAliphaticRingsThe number of aliphatic (containing at least one non-aromatic bond) rings for a molecule
NumAromaticCarbocyclesThe number of aromatic carbocycles for a molecule
NumAromaticHeterocyclesThe number of aromatic heterocycles for a molecule
NumAromaticRingsThe number of aromatic rings for a molecule
NumHAcceptorsThe number of Hydrogen Bond Acceptors
NumHDonorsThe number of Hydrogen Bond Donors
NumHeteroatomsThe number of Heteroatoms
NumRotatableBondsThe number of Rotatable Bonds
NumSaturatedCarbocyclesThe number of saturated carbocycles for a molecule
NumSaturatedHeterocyclesThe number of saturated heterocycles for a molecule
NumSaturatedRingsThe number of saturated rings for a molecule
RingCountRing count

See also: