| Atom | Description |
|---|---|
| C | sp2 carbonyl all-atom carbon and aromatic carbon with hydroxyl substituient in tyrosine |
| C* | sp2 aromatic all-atom carbon in 5-membered ring with 1 substituent |
| C2 | sp3 united carbon with 2 hydrogens |
| C3 | sp3 united carbon with 3 hydrogens |
| CA | sp2 aromatic all-atom carbon in 6-membered ring with 1 substituent |
| CB | sp2 aromatic all-atom carbon in junction between 5- and 6-membered rings |
| CC | sp2 aromatic all-atom carbon in 5-membered ring with 1 substituent and next to a nitrogen |
| CD | sp2 aromatic united carbon in 6-membered ring with 1 hydrogen |
| CE | sp2 aromatic united carbon in 5-membered ring between 2 nitrogens and with 1 hydrogen |
| CF | sp2 aromatic united carbon in 5-membered ring next to a nitrogen without a hydrogen |
| CG | sp2 aromatic united carbon in 5-membered ring next to a N-H |
| CH | sp3 united carbon with 1 hydrogen |
| CI | sp2 united carbon in 6-membered ring between 2 NC nitrogens |
| CJ | sp2 united carbon in pyrimidine at positions 5 or 6 |
| CK | sp2 aromatic carbon in 5-membered ring between 2 nitrogens and with 1 hydrogen |
| CM | sp2 all-atom carbon in pyrimidine at positions 5 or 6 |
| CN | sp2 aromatic junction all-atom carbon in between 5- and 6-membered rings |
| CP | sp2 aromatic united carbon in 5-membered ring between 2 nitrogens and with 1 hydrogen (in HIS) |
| CQ | sp2 all-atom carbon in 6-membered ring of purine between two NC nitrogens and with 1 hydrogen |
| CR | sp2 aromatic all-atom carbon in 5-membered ring between 2 nitrogens and with 1 hydrogen (in HIS) |
| CT | sp3 all-atom carbon with 4 explicit substituents |
| CV | sp2 aromatic all-atom carbon in 5-membered ring bonded to 1 N and 1 H |
| CW | sp2 aromatic all-atom carbon in 5-membered ring bonded to N-H and 1 H |
| H | amide or imino hydrogen |
| H2 | amino hydrogen in NH2 |
| H3 | hydrogen of lysine or arginine (positively charged) |
| HC | explicit hydrogen attached to carbon |
| HO | hydrogen in hydroxyl group |
| HS | hydrogen attached to sulfur |
| HW | hydrogen in water |
| LP | lone pair |
| N | sp2 nitrogen in amide |
| N* | sp2 nitrogen in purine or pyrimidine wiht alkyl group |
| N2 | sp2 nitrogen in base NH2 group or arginine NH2 |
| N3 | sp3 nitrogen with 4 substituents |
| NA | sp2 nitrogen in 5-membered ring with hydrogen attached |
| NB | sp2 nitrogen in 5-membered ring with lone pairs |
| NC | sp2 nitrogen in 6-membered ring with lone pairs |
| NP | |
| NT | sp3 nitrogen with 3 substituents |
| O | carbonyl oxygen |
| O2 | carboxyl or phosphate non-bonded oxygen |
| OH | alcohol oxygen |
| OS | ether or ester oxygen |
| OW | water oxygen |
| P | phosphorus in phosphate group |
| S | sulfur in disulfide linkage or methionine |
| SH | sulfur in thiol |
| C0 | calcium ion (+2) |
| IM | chlorine ion (-1) |
| CU | copper ion (+2) |
| I | Iodine ion (-1) |
| MG | Magnesium ion (+2) |
| QC | cesium ion (+1) |
| QK | potassium ion (+1) |
| QL | lithium ion (+1) |
| QN | sodium ion (+1) |
| QR | rubidium ion (+1) |
| CS | sp3 carbon |
| AC | alpha-anomeric carbon |
| BC | beta-anomeric carbon |
| HT | sp3 hydrogen |
| AH | alpha-anomeric hydrogen |
| BH | beta-anomeric hydrogen |
| HY | hydroxyl hydrogen |
| OT | hydroxyl oxygen |
| OA | alpha-anomeric oxygen |
| OB | beta-anomeric oxygen |
| OE | ring oxygen |
| h$ | atom for automatic parameter assignment |
| c$ | atom for automatic parameter assignment |
| n$ | atom for automatic parameter assignment |
| o$ | atom for automatic parameter assignment |
| s$ | atom for automatic parameter assignment |
| p$ | atom for automatic parameter assignment |
| ospc | in SPC water molecule - used for rattle routine |
| otip | in TIP3P water molecule - used for rattle routine |