| Atom | Description |
|---|---|
| h | Hydrogen bonded to C. Masses from CRC 1973/74 pages B-250 |
| d | General Deuterium |
| hn | Hydrogen bonded to N |
| ho | Hydrogen bonded to O |
| hp | Hydrogen bonded to P |
| hs | Hydrogen bonded to S |
| h* | Hydrogen in water molecule |
| hspc | Hydrogen in SPC water molecule |
| htip | Hydrogen in TIP water molecule |
| h$ | Hydrogen atom for automatic parameter assignment |
| lp | Lone Pair |
| lp | Lone Pair |
| h+ | Charged hydrogen in cations |
| hc | Hydrogen bonded to carbon |
| hi | Hydrogen in charged imidazole ring |
| hw | Hydrogen in water |
| dw | Deuterium in heivy water |
| c | Sp3 aliphatic carbon |
| cg | Sp3 alpha carbon in glycine |
| c' | Sp2 carbon in carbonyl (C=O) group |
| c* | Carbon in carbonyl group, non_amides |
| c" | Carbon in carbonyl group, non_amides |
| cp | Sp2 aromatic carbon (partial double bonds) |
| cr | Carbon in guanidinium group (HN=C(NH2)2) |
| c+ | C in guanidinium group |
| c- | Carbon in charged carboxylate (COO-) group |
| ca | General amino acid alpha carbon (sp3) |
| c3 | Sp3 carbon in methyl (CH3) group |
| cn | Sp3 Carbon bonded to N |
| c2 | Sp3 carbon bonded to 2 H's, 2 heavy atoms |
| c1 | Sp3 carbon bonded to 1 H, 3 Heavy atoms |
| c5 | Sp2 aromatic carbon in five membered ring |
| cs | Sp2 carbon involved in thiophene |
| c= | Non aromatic end doubly bonded carbon |
| c=1 | Non aromatic, next to end doubly bonded carbon |
| c=2 | Non aromatic doubly bonded carbon |
| ct | Sp carbon involved in triple bond |
| ci | Aromatic carbon in a charged imidazole ring (HIS+) |
| c$ | Carbon atom for automatic parameter assignment |
| 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 |
| ci | Sp2 aromatic carbon in charged imidazole ring (His+) |
| n | Sp2 nitrogen with 1 H, 2 heavy atoms (amide group) |
| no | Sp2 nitrogen in nitro group |
| n2 | Sp2 nitrogen (NH2 in the guanidinium group (HN=C(NH2)2)) |
| np | Sp2 aromatic nitrogen (partial double bonds) |
| n3 | Sp3 nitrogen with three substituents |
| n4 | Sp3 nitrogen with four substituents |
| n= | Non aromatic end double bonded nitrogen |
| n=1 | Non aromatic, next to end doubly bonded carbon |
| n=2 | Non aromatic doubly bonded nitrogen |
| nt | Sp nitrogen involved in triple bond |
| nz | Sp nitrogen in N2 |
| n1 | Sp2 nitrogen in charged arginine |
| ni | Sp2 nitrogen in a charged imidazole ring (HIS+) |
| n$ | Nitrogen atom for automatic parameter assignment |
| 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 |
| 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 |
| nr | sp2 nitrogen (NH2) in guanidinium group (HN=C(NH2)2) |
| o' | Oxygen in carbonyl (C=O) group |
| o | sp3 oxygen in ether or ester groups |
| oz | Oxygen stub for catalysis |
| o- | Oxygen in charged carboxylate (COO-) group |
| oh | Oxygen in hydroxyl (OH) group |
| o* | Oxygen in water molecule |
| ospc | Oxygen in SPC water molecule |
| otip | Oxygen in TIP3P water molecule |
| op | Oxygen in aromatic rings. e.g. furan |
| of | |
| o$ | Oxygen atom for automatic parameter assignment |
| 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 |
| s | Sulfur in methionine (C-S-C) group |
| s1 | Sulfu involved in S-S disulfide bond |
| sh | Sulfur in sulfhydryl (-SH) group |
| sp | Sulfur in thiophene |
| s' | Sulfur in thioketone (>C=S) group |
| s$ | Sulfur atom for automatic parameter assignment |
| sc | sp3 sulfur in methionines (C-S-C) group |
| s3e | sulfur in three membered ring |
| s4e | sulfur in four membered ring |
| s- | partial double sulfur bonded to something then bonded to another partial double oxygen |
| p | General phosphorous atom |
| pz | Phosphorous atom stub for catalysis |
| p$ | Phosphorous atom for automatic parameter assignment |
| ca+ | ion - Ca++, mass = mass of Ca - 2*electron mass. |
| f | Fluorine bonded to a carbon |
| cl | Chlorine bonded to a carbon |
| br | Bromine bonded to a carbon |
| i | Covalently bound Iodine |
| si | Silicon |
| sz | Silicon stub for catalysis |
| nu | atom for relative free energy |
| Cl | Chloride ion Cl- |
| Br | Bromide ion Br- |
| Na | Sodium ion |
| ar | Argon |