The Atoms File

The atoms that are already defined.

H
Aliphatic Hydrogen
CH3OH
Hd
Hydrogen bonding H
CH3OH
C3
Sp3 Carbon
CH3OH
Ca
Aromatic Carbon
C6H6
C2
Sp2 isolated carbon
CH3COOH
C1
Sp1 carbon
HCCH
N3
Sp3 nitrogen
NH3
N2
Sp3 amide
?
Nm
Methyl nitrogen
CH3NH2
Nr
Ring Nitrogen
C5H5N
Np
Sp2 Amide (peptide) nitrogen
CH3CONHCH3
Nb
Strained ring nitrogen
C4H4N
N1
Sp1 nitrogen
HCN
Ow
Water oxygen
H2O
O3
Sp3 oxygen
CH3OH
O2
Sp2 oxygen
CH3CONHCH3
O1
Sp1 oxygen
CO
P35
Phosphate
H3PO4
S32
Reduced Sulfur
Disulfide Bonds
S34
Intermediate Sulfur
CH3SCH3
S36
Sulfate
SO4
Cl,Br,F
Halogens
CH3F
Mg
Mg ion

Fe2s
Iron Sulfur Cluster
Iron Sulfur proteins
Fe2
Iron +2
Heme
Fe3
Iron +3
Heme