Atom type | Description | MOL2 types |
---|---|---|
C_l | Aliphatic carbon – sp3 hybridized | C.1, C.2, C.3 |
C_r | Aromatic carbon – sp2 hybridized, included in aromatic rings and in guanidine or carboxyl groups | C.ar, C.cat, C.2 |
N_+ | Positive nitrogen – sp 2 or sp 3 hybridized, protonated, forming a group with a positive charge (e.g. guanidine group) | N.4, N.pl3 |
N_d | Nitrogen donor of a hydrogen bond – sp 2 hybridized, protonated (e.g. amine group) | N.2, N.ar, N.am |
N_a | Nitrogen acceptor of hydrogen bond – not all valences covered by heavy atoms, not protonated | N.2, N.ar, N.3, N.1 |
N_r | Aromatic nitrogen – sp 2 hybridized, with all its valences covered by heavy atoms | N.ar, N.pl3 |
N_h | "Hydroxyl" nitrogen in histidines – sp 2 hybridized, undefined protonation | N.2 |
O_a | Oxygen acceptor of hydrogen bond – not protonated | O.2, O.3 |
O_- | Negative oxygen – negatively charged (e.g. nitro group, carboxyl group) | O.co2 |
O_h | Hydroxyl oxygen – protonated (OH group) | O.2, O.3 |