|
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
|
