| Atom | Description |
|---|---|
| c | generic SP3 carbon |
| c3 | sp3 carbon with 3 hHs 1 heavy |
| c2 | sp3 carbon with 2 H's, 2 Heavy's |
| co | sp3 carbon in acetals |
| c3m | sp3 carbon in 3-membered ring |
| c4m | sp3 carbon in 4-membered ring |
| coh | sp3 carbon in acetals with hydrogen |
| c3h | sp3 carbon in 3-membered ring with hydrogens |
| c4h | sp3 carbon in 4-membered ring with hydrogens |
| c1 | sp3 carbon with 1 H 3 heavies |
| ca | general amino acid alpha carbon (sp3) |
| cg | sp3 alpha carbon in glycine |
| c= | non aromatic end doubly bonded carbon |
| c=1 | non aromatic, next to end doubly bonded carbon |
| c=2 | non aromatic doubly bonded carbon |
| c* | carbon in carbonyl group, non_amides |
| c" | carbon in carbonyl group, non_amides |
| c' | carbon in carbonyl group of amides |
| cp | sp2 aromatic carbon |
| c5 | sp2 aromatic carbon in 5-membered ring |
| c- | C in charged carboxylate |
| cr | C in neutral arginine |
| c+ | C in guanidinium group |
| cs | sp2 aromatic carbon in 5 membered ring next to S |
| ci | sp2 aromatic carbon in charged imidazole ring (His+) |
| ct | sp carbon involved in a triple bond |
| ct2 | sp carbon in CO2 |
| na | sp3 nitrogen in amines |
| n3m | sp3 nitrogen in 3- membered ring |
| n4m | sp3 nitrogen in 4- membered ring |
| n3n | sp2 nitrogen in 3- membered ring |
| n4n | sp2 nitrogen in 4- membered ring |
| nb | sp2 nitrogen in aromatic amines |
| nn | sp2 nitrogen in aromatic amines |
| n | generic sp2 nitrogen (in amids)) |
| np | sp2 nitrogen in 5- or 6- membered ring |
| npc | sp2 nitrogen in 5- or 6- membered ring bonded to a heavy atom |
| nh | sp2 nitrogen in 5-or 6- membered ring with hydrogen attached |
| nho | sp2 nitrogen in 6- membered ring next to a carbonyl group and with a hydrogen |
| nh+ | protonated nitrogen in 6- membered ring with hydrogen attached |
| n+ | sp3 nitrogen in protonated amines |
| n4 | sp3 nitrogen in protonated amines |
| nr | sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2) |
| n= | non aromatic end doubly bonded nitrogen |
| n=1 | non aromatic, next to end doubly bonded carbon |
| n=2 | non aromatic doubly bonded nitrogen |
| ni | nitrogen in charged imidazole ring |
| n1 | sp2 nitrogen in charged arginine |
| n2 | sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2) |
| nt | sp nitrogen involved in a triple bond |
| nz | sp nitrogen in N2 |
| o | generic SP3 oxygen |
| oh | oxygen bonded to hydrogen |
| oc | sp3 oxygen in ether or acetals |
| oe | sp3 oxygen in ester |
| o3e | sp3 oxygen in three membered ring |
| o4e | sp3 oxygen in four membered ring |
| o' | oxygen in carbonyl group |
| op | sp2 aromatic in 5 membered ring |
| o* | oxygen in water |
| o- | partial double oxygen bonded to something then bonded to another partial double oxygen |
| h | generic hydrogen bound to C, Si,or H |
| h* | hydrogen bonded to nitrogen, Oxygen |
| h+ | charged hydrogen in cations |
| hs | hydrogen bonded to sulfur |
| hc | hydrogen bonded to carbon |
| hp | hydrogen bonded to phosphorus |
| ho | hydrogen bonded to oxygen |
| hn | hydrogen bonded to nitrogen |
| hi | Hydrogen in charged imidazole ring |
| hw | hydrogen in water |
| dw | deuterium in heivy water |
| s | sp3 sulfur |
| sc | sp3 sulfur in methionines (C-S-C) group |
| s3e | sulfur in three membered ring |
| s4e | sulfur in four membered ring |
| s1 | sp3 sulfur involved in (S-S) group of disulfides |
| sh | sp3 sulfur in sulfhydryl (-SH) group (e.g. cysteine) |
| sp | sulfur in an aromatic ring (e.g. thiophene) |
| s' | S in thioketone group |
| s- | partial double sulfur bonded to something then bonded to another partial double oxygen or sulfur |
| p | general phosphorous atom |
| si | silicon atom |
| ca+ | calcium ion |
| f | fluorine atom |
| cl | chlorine atom |
| Cl | chlorine ion |
| br | bromine atom |
| Br | bromine ion |
| i | iodine atom |
| Na | sodium ion |
| lp | lone pair |
| ar | Argon atom |