Examples of descriptors

Some examples that can be calculated using MOE


a_aro Number of aromatic atoms.
a_count Number of atoms (including implicit hydrogens). This is calculated as the sum of (1 + hi) over all non-trivial atoms i.
a_heavy Number of heavy atoms #{Zi | Zi > 1}.
a_ICM Atom information content (mean). This is the entropy of the element distribution in the molecule (including implicit hydrogens but not lone pair pseudo-atoms). Let ni be the number of occurrences of atomic number i in the molecule. Let pi = ni / n where n is the sum of the ni. The value of a_ICM is the negative of the sum over all i of pi log pi.
a_IC Atom information content (total). This is calculated to be a_ICM times n.
a_nH Number of hydrogen atoms (including implicit hydrogens). This is calculated as the sum of hi over all non-trivial atoms i plus the number of non-trivial hydrogen atoms.
a_nB Number of boron atoms: #{Zi | Zi = 5}.
a_nC Number of carbon atoms: #{Zi | Zi = 6}.
a_nN Number of nitrogen atoms: #{Zi | Zi = 7}.
a_nO Number of oxygen atoms: #{Zi | Zi = 8}.
a_nF Number of fluorine atoms: #{Zi | Zi = 9}.
a_nP Number of phosphorus atoms: #{Zi | Zi = 15}.
a_nS Number of sulfur atoms: #{Zi | Zi = 16}.
a_nCl Number of chlorine atoms: #{Zi | Zi = 17}.
a_nBr Number of bromine atoms: #{Zi | Zi = 35}.
a_nI Number of iodine atoms: #{Zi | Zi = 53}.
b_1rotN Number of rotatable single bonds. Conjugated single bonds are not included (e.g. ester and peptide bonds).
b_ar Number of aromatic bonds.
b_count Number of bonds (including implicit hydrogens). This is calculated as the sum of (di/2 + hi) over all non-trivial atoms i.
b_double Number of double bonds. Aromatic bonds are not considered to be double bonds.
b_heavy Number of bonds between heavy atoms.
b_rotN Number of rotatable bonds. A bond is rotatable if it has order 1, is not in a ring, and has at least two heavy neighbors.
b_single Number of single bonds (including implicit hydrogens). Aromatic bonds are not considered to be single bonds.
b_triple Number of triple bonds. Aromatic bonds are not considered to be triple bonds.
chiral The number of chiral centers.
lip_acc The number of O and N atoms.
lip_don The number of OH and NH atoms.
lip_druglike One if and only if lip_violation < 2 otherwise zero.
lip_violation The number of violations of Lipinski's Rule of Five
nmol The number of molecules (connected components).
opr_brigid The number of rigid bonds from [Oprea 2000].
opr_leadlike One if and only if opr_violation < 2 otherwise zero.
opr_nring The number of ring bonds from [Oprea 2000].
opr_nrot The number of rotatable bonds from [Oprea 2000].
opr_violation The number of violations of Oprea's lead-like test [Oprea 2000].
rings The number of rings.
Pharmacophore type counts
a_acc Number of hydrogen bond acceptor atoms (not counting acidic atoms but counting atoms that are both hydrogen bond donors and acceptors such as -OH).
a_acid Number of acidic atoms.
a_base Number of basic atoms.
a_don Number of hydrogen bond donor atoms (not counting basic atoms but counting atoms that are both hydrogen bond donors and acceptors such as -OH).
a_hyd Number of hydrophobic atoms.
vsa_acc Approximation to the sum of VDW surface areas (√Ö2) of pure hydrogen bond acceptors (not counting acidic atoms and atoms that are both hydrogen bond donors and acceptors such as -OH).
vsa_acid Approximation to the sum of VDW surface areas of acidic atoms (√Ö2).
vsa_base Approximation to the sum of VDW surface areas of basic atoms (√Ö2).
vsa_don Approximation to the sum of VDW surface areas of pure hydrogen bond donors (not counting basic atoms and atoms that are both hydrogen bond donors and acceptors such as -OH) (√Ö2).
vsa_hyd Approximation to the sum of VDW surface areas of hydrophobic atoms (√Ö2).
vsa_other Approximation to the sum of VDW surface areas (√Ö2) of atoms typed as "other".
vsa_pol Approximation to the sum of VDW surface areas (√Ö2) of polar atoms (atoms that are both hydrogen bond donors and acceptors), such as -OH
Charge based
ASA+ Water accessible surface area of all atoms with positive partial charge (strictly greater than 0).
ASA- Water accessible surface area of all atoms with negative partial charge (strictly less than 0).
ASA_H Water accessible surface area of all hydrophobic (|qi|<0.2) atoms.
ASA_P Water accessible surface area of all polar (|qi|>=0.2) atoms.
DASA Absolute value of the difference between ASA+ and ASA-.
CASA+ Positive charge weighted surface area, ASA+ times max { qi > 0 } [Stanton 1990].
CASA- Negative charge weighted surface area, ASA- times max { qi < 0 } [Stanton 1990].
DCASA Absolute value of the difference between CASA+ and CASA- [Stanton 1990].
dipole Dipole moment calculated from the partial charges of the molecule.

Examples available using ChemAxon cxcalc

atomcount, composition, dotdisconnectedformula,
dotdisconnectedisotopeformula, elemanal, elementalanalysistable,
exactmass, formula, icomposition, iformula, isotopecomposition,
isotopeformula, mass

Charge
atomicpolarizability, atompol, averagemolecularpolarizability,
averagepol, avgpol, axxpol, ayypol, azzpol, charge, formalcharge,
ioncharge, molecularpolarizability, molpol, oen,
orbitalelectronegativity, pol, polarizability, tholepolarizability,
tpol, tpolarizability

Conformation
conformers, hasvalidconformer, leconformer, lowestenergyconformer,
moldyn, moleculardynamics

Geometry
aliphaticatom, aliphaticatomcount, aliphaticbondcount,
aliphaticringcount, aliphaticringcountofsize, angle, aromaticatom,
aromaticatomcount, aromaticbondcount, aromaticringcount,
aromaticringcountofsize, asa, asymmetricatom, asymmetricatomcount,
asymmetricatoms, balabanindex, bondcount, bondtype,
carboaliphaticringcount, carboaromaticringcount, carboringcount,
chainatom, chainatomcount, chainbond, chainbondcount, chiralcenter,
chiralcentercount, chiralcenters, connected, connectedgraph,
cyclomaticnumber, dihedral, distance, distancedegree, dreidingenergy,
eccentricity, fragmentcount, fusedaliphaticringcount,
fusedaromaticringcount, fusedringcount, hararyindex,
heteroaliphaticringcount, heteroaromaticringcount, heteroringcount,
hindrance, hyperwienerindex, largestatomringsize, largestringsize,
largestringsystemsize, maximalprojectionarea, maximalprojectionradius,
maximalprojectionsize, minimalprojectionarea, minimalprojectionradius,
minimalprojectionsize, molecularsurfacearea, msa, plattindex,
polarsurfacearea, psa, randicindex, ringatom, ringatomcount, ringbond,
ringbondcount, ringcount, ringcountofatom, ringcountofsize,
ringsystemcount, ringsystemcountofsize, rotatablebond,
rotatablebondcount, shortestpath, smallestatomringsize,
smallestringsize, smallestringsystemsize, stereodoublebondcount,
stericeffectindex, sterichindrance, szegedindex, topanal,
topologyanalysistable, vdwsa, volume, wateraccessiblesurfacearea,
wienerindex, wienerpolarity

Isomers
canonicaltautomer, dominanttautomerdistribution,
doublebondstereoisomercount, doublebondstereoisomers, generictautomer,
majortautomer, moststabletautomer, stereoisomercount, stereoisomers,
tautomercount, tautomers, tetrahedralstereoisomercount,
tetrahedralstereoisomers

Markush Enumerations
enumerationcount, enumerations, markushenumerationcount,
markushenumerations, randommarkushenumerations

Name
name

Partitioning
logd, logp

Protonation
averagemicrospeciescharge, chargedistribution, isoelectricpoint,
majormicrospecies, majorms, microspeciesdistribution, msdistr, pi, pka

Other
acc, acceptor, acceptorcount, acceptormultiplicity, acceptorsitecount,
acceptortable, accsitecount, aromaticelectrophilicityorder,
aromaticnucleophilicityorder, canonicalresonant, chargedensity, don,
donor, donorcount, donormultiplicity, donorsitecount, donortable,
donsitecount, electrondensity, electrophilicityorder,
electrophiliclocalizationenergy, frameworks, hbda, hbonddonoracceptor,
hmochargedensity, hmoelectrondensity, hmoelectrophilicityorder,
hmoelectrophiliclocalizationenergy, hmohuckel, hmohuckeleigenvalue,
hmohuckeleigenvector, hmohuckelorbitals, hmohuckeltable,
hmolocalizationenergy, hmonucleophilicityorder,
hmonucleophiliclocalizationenergy, hmopienergy, huckel,
huckeleigenvalue, huckeleigenvector, huckelorbitals, huckeltable,
localizationenergy, msacc, msdon, nucleophilicityorder,
nucleophiliclocalizationenergy, pichargedensity, pienergy,
refractivity, resonantcount, resonants, totalchargedensity

Updated 24 February 2011

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