Table 2.
Categories and definitions of computed molecular descriptors [41].
| Categories of Descriptors | Definition | Categories of Descriptors | Definition | |
|---|---|---|---|---|
| Physico-Chemical Properties | LogP (o/w) | Log of the octanol/water partition coefficient (including implicit hydrogens) | MR | Molecular refractivity (including implicit hydrogens) |
| logS | Log of the aqueous solubility (mol/L) | TPSA | Polar surface area (Å2) calculated using group contributions to approximate the polar surface area from connection table information only | |
| apol | Sum of the atomic polarizabilities (including implicit hydrogens) | SlogP_VSA0 SlogP_VSA1 SlogP_VSA3 SlogP_VSA5 SlogP_VSA6 | Subdivided logP Surface Areas are descriptors based on an approximate accessible van der Waals surface area (in Å2) calculation for each atom along with its contribution to logP property | |
| Atom and Bond Counts | PEOE_RPC_− | Relative negative/positive partial charge: the smallest negative qi divided by the sum of the negative qi. Q_RPC−/Q_RPC+ is identical to RPC−/RPC+ which has been retained for compatibility | PEOE_VSA_0 | Sum of vi (a der Waals surface area of atom i) where qi (partial charge of atom i) is in the range (−0.05, 0.00) |
| PEOE_RPC_+ | PEOE_VSA_FPOS | Fractional positive van der Waals surface area. This is the sum of the vi such that qiis non-negative divided by the total surface area. The vi are calculated using a connection table approximation | ||
| Atom and Bond Counts | b_double | Number of double bonds. Aromatic bonds are not considered to be double bonds | lip_acc | The number of O and N atoms |
| 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) | lip_don | The number of OH and NH atoms | |
| b_count | Number of bonds (including implicit hydrogens) | lip_druglike | One if and only if Lipinski’s rules violation < 2 otherwise zero | |
| Pharmacophoric Features | 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) | 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) (Å2) |
| 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) | vsa_other | Approximation to the sum of VDW surface areas (Å2) of atoms typed as “other” | |
| Connectivity and Shape Indices | chi0 | Atomic connectivity index (order 0) | KierFlex | Kier molecular flexibility index |
| chil_C | Carbon connectivity index (order 1) | |||
| Adjacency and Distance Matrix Descriptors | VDistMa | If m is the sum of the distance matrix entries | BCUT_SLOGP_1 | The BCUT descriptors using atomic contribution to logP (using the Wildman and Crippen SlogP method) |
| WeinerPath | Wiener path number. | BCUT_SLOGP_3 | ||
| balabanJ | Balaban’s connectivity topological index | GCUT_SMR_1 | The GCUT descriptors using atomic contribution to molar refractivity (using the Wildman and Crippen SMR method) instead of partial charge | |
| BCUT_PEOE_3 | Adjacency and distance matrix descriptors. The BCUT descriptors are calculated from the eigenvalues of a modified adjacency matrix | GCUT_SMR_3 | ||
| BCUT_SMR_2 | The BCUT descriptors using atomic contribution to molar refractivity (using the Wildman and Crippen SMR method) instead of partial charge |