Sybyl atom type
Code | Definition | Code | Definition |
C.3 | carbon sp3 | H | hydrogen |
C.2 | carbon sp2 | H.spc | hydrogen in Single Point Charge (SPC) water model |
C.1 | carbon sp | H.t3p | hydrogen in Transferable intermolecular Potential (TIP3P) water model |
C.ar | carbon aromatic | LP | lone pair |
C.cat | carbocation (C+) used only in a guadinium group | Du | dummy atom |
N.3 | nitrogen sp3 | Du.C | dummy carbon |
N.2 | nitrogen sp2 | Any | any atom |
N.1 | nitrogen sp | Hal | halogen |
N.ar | nitrogen aromatic | Het | heteroatom = N, O, S, P |
N.am | nitrogen amide | Hev | heavy atom (non hydrogen) |
N.pl3 | nitrogen trigonal planar | Li | lithium |
N.4 | nitrogen sp3 positively charged | Na | sodium |
O.3 | oxygen sp3 | Mg | magnesium |
O.2 | oxygen sp2 | Al | aluminum |
O.co2 | oxygen in carboxylate and phosphate groups | Si | silicon |
O.spc | oxygen in Single Point Charge (SPC) water model | K | potassium |
O.t3p | oxygen in Transferable Intermolecular Potential (TIP3P) water model | Ca | calcium |
S.3 | sulfur sp3 | Cr.th | chromium (tetrahedral) |
S.2 | sulfur sp2 | Cr.oh | chromium (octahedral) |
S.O | sulfoxide sulfur | Mn | manganese |
S.O2 | sulfone sulfur | Fe | iron |
P.3 | phosphorous sp3 | Co.oh | cobalt (octahedral) |
F | fluorine | Cu | copper |
Cl | chlorine | Zn | zinc |
Br | bromine | Se | selenium |
I | iodine | Mo | molybdenum |
� | � | Sn | tin |
O.co2 只有在COO- 这种质子化状态才出现(否则就是O.2+O.3). 同理N.4也是(否则N.3).