Table 1.
Atom types and descriptions
| Atom type | Description | Exampleb | On protein | On ligand |
|---|---|---|---|---|
| C2N | C, SP2, normal/non-polar | -C=C- | x | |
| C2P | C, SP2, polar | -C=O | x | x |
| C3N | C, SP3, normal/non-polar | -C-C- | x | x |
| C3P | C, SP3, polar | -C-OH | x | x |
| CRN | C, aromatic, normal/non-polar | a benzene carbon | x | x |
| CRP | C, aromatic, polar | a halogenated aromatic carbon | x | x |
| O2A | O, SP2, hydrogen bond acceptor | >C=O | x | x |
| O3A | O, SP3, hydrogen bond acceptor | C-O-C | x | |
| O3B | O, SP3, both | -OH | x | x |
| OLC | O, aliphatic, charged | -COO- | x | |
| ORA | O, aromatic, hydrogen bond acceptor | oxygen in furan | x | |
| NLA | N, aliphatic, hydrogen bond acceptor | -NR2 | x | x |
| NLB | N, aliphatic, hydrogen bond donor | -NH1or2 | x | x |
| NLC | N, aliphatic, charged | -NH3+ | x | |
| NRA | N, aromatic, hydrogen bond acceptor | a non-protonated aromatic nitrogen | x | |
| NRD | N, aromatic, hydrogen bond donor | a protonated aromatic nitrogen | x | x |
| NRE | N, aromatic, either H.B. donor or acceptor | nitrogen (protonated or not) of imidazole | x | |
| S3N | S, SP2, normal/non-polar | -SH | x | x |
| SRA | S, aromatic, hydrogen bond acceptor | sulfur in an aromatic ring | x | |
| SLC | S, aliphatic, charged | -SO4-2 | x | |
| PHO | Phosphorus | x | ||
| MET | Metala | x | ||
| HAL | Halogen | F, Cl, Br, I | x |
a Metal ions, such as Zn, were considered in this work as an extended interaction site of the protein molecule.
b See Fig. S3 in Additional file 1 for a representative chemical structure of the atom type CRN, CRP, ORA, NRA, NRD, NRE, and SRA.