| H | hydrogen on aliphatic carbon | 0 |
| H.ar | hydrogen on aromatic carbon | 0 |
| H.n | hydrogen on nitrogen | -1 |
| H.o | hydrogen on oxygen | -1 |
| H.p | hydrogen on phosphorus | ? |
| H.s | hydrogen on sulfur | ? |
| C.3 | sp3 carbon | 0 |
| C.3:1 | sp3 carbon with one implicit hydrogen | 0 |
| C.3:2 | sp3 carbon with two implicit hydrogens | 0 |
| C.3:3 | sp3 carbon with three implicit hydrogens | 0 |
| C.2 | sp2 carbon | 0 |
| C.2:1 | sp2 carbon with one implicit hydrogen | 0 |
| C.2:2 | sp2 carbon with two implicit hydrogens | 0 |
| C.ar | aromatic carbon | 0 |
| C.ar:1 | aromatic carbon with one implicit hydrogen | 0 |
| C.co | carbonyl carbon | -1 |
| C.co:1 | carbonyl carbon with one implicit hydrogen | -1 |
| C.1 | sp carbon | 0 |
| C.1:1 | sp carbon with one implicit hydrogen | 0 |
| C.cat | cationic carbon | +1 |
| N.3 | sp3 nitrogen | +1 |
| N.3:1 | sp3 nitrogen with one implicit hydrogen | +1 |
| N.3:2 | sp3 nitrogen with two implicit hydrogens | +1 |
| N.2 | sp2 nitrogen | +1 |
| N.2:1 | sp2 nitrogen with one implicit hydrogen | +1 |
| N.1 | sp nitrogen | +1|
| N.ar | aromatic nitrogen | +1 |
| N.ar:1 | aromatic nitrogen with one implicit hydrogen | +1 |
| N.am | amide nitrogen | +1 |
| N.am:1 | amide nitrogen with one implicit hydrogen | +1 |
| N.pl3 | trigonal planar nitrogen | +1 |
| N.pl3:2 | trigonal planar nitrogen with two implicit hydrogens | +1 |
| N.4 | quaternary sp3 nitrogen | -1 |
| N.4:1 | quaternary sp3 nitrogen with one implicit hydrogen | -1 |
| N.4:2 | quaternary sp3 nitrogen with two implicit hydrogens | -1 |
| N.4:3 | quaternary sp3 nitrogen with three implicit hydrogens | -1 |
| N.his | histidine nitrogen | +1 |
| N.his:1 | histidine nitrogen with one implicit hydrogen | +1 |
| O.3 | sp3 oxygen | +1 |
| O.3:1 | sp3 oxygen with one implicit hydrogen | +1 |
| O.3:2 | sp3 oxygen with two implicit hydrogens (water) | +1 |
| O.2 | sp2 oxygen | +1 |
| O.co2 | oxygen in carboxylate | +1 |
| O.ar | aromatic oxygen | +1 |
| O.m | anionic oxygen | +1 |
| S.3 | sp3 sulfur | +1 |
| S.3:1 | sp3 sulfur with one implicit hydrogen | +1 |
| S.2 | sp2 sulfur | -1 |
| S.o | sulfur in >S=O | -1 |
| S.o2 | sulfur in O=S=O | -1 |
| S.ar | aromatic sulfur | -1 |
| S.s | sulfur in dithio (-S-S-) | +1 |
| S.s:1 | sulfur in dithio with one implicit hydrogen (-S-SH) | +1 |
| P.3 | sp3 phosphorus | +1 |
| P.3:1 | sp3 phosphorus with one implicit hydrogen | +1 |
| F | fluorine | +1 |
| F.cf3 | fluorine in CF3 | +1 |
| Cl | chlorine | +1 |
| Br | bromine | +1 |
| I | iodine | +1 |
| Si | sp3 silicon | 0 |
| Si:1 | sp3 silicon with one implicit hydrogen | 0 |
| Si:2 | sp3 silicon with two implicit hydrogens | 0 |
| Si:3 | sp3 silicon with three implicit hydrogens | 0 |
| Du | dummy | 0 |