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Sybyl原子类型

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).

Reference

  1. Tripos mol2 atom types


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