C   sp2 C carbonyl group 
CA  sp2 C pure aromatic (benzene)
CB  sp2 aromatic C, 5&6 membered ring junction
CC  sp2 aromatic C, 5 memb. ring HIS
CD  sp2 C atom in the middle of: C=CD-CD=C
CK  sp2 C 5 memb.ring in purines
CM  sp2 C  pyrimidines in pos. 5 & 6
CN  sp2 C aromatic 5&6 memb.ring junct.(TRP)
CQ  sp2 C in 5 mem.ring of purines between 2 N
CR  sp2 arom as CQ but in HIS
CT  sp3 aliphatic C
CV  sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
CW  sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
C*  sp2 arom. 5 memb.ring w/1 subst. (TRP)
CY  nitrile C (Howard et al.JCC,16,243,1995)
CZ  sp C (Howard et al.JCC,16,243,1995)
C0  calcium
H   H bonded to nitrogen atoms
HC  H aliph. bond. to C without electrwd.group
H1  H aliph. bond. to C with 1 electrwd. group
H2  H aliph. bond. to C with 2 electrwd.groups
H3  H aliph. bond. to C with 3 eletrwd.groups
HA  H arom. bond. to C without elctrwd. groups
H4  H arom. bond. to C with 1 electrwd. group
H5  H arom.at C with 2 elctrwd. gr,+HCOO group
HO  hydroxyl group
HS  hydrogen bonded to sulphur (pol?)
HW  H in TIP3P water
HP  H bonded to C next to positively charged gr
HZ  H bond sp C (Howard et al.JCC,16,243,1995)
F   fluorine
Cl  chlorine  (Applequist)
Br  bromine  (Applequist)
I   iodine   (Applequist)
IM  assumed to be Cl- (ion minus)
IB  'big ion w/ waters' for vacuum (Na+, 6H2O)
MG  magnesium
N   sp2 nitrogen in amide groups
NA  sp2 N in 5 memb.ring w/H atom (HIS)
NB  sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
NC  sp2 N in 6 memb.ring w/LP (ADE,GUA)
N2  sp2 N in amino groups
N3  sp3 N for charged amino groups (Lys, etc)
NT  sp3 N for amino groups amino groups 
N*  sp2 N 
NY  nitrile N (Howard et al.JCC,16,243,1995)
O   carbonyl group oxygen
O2  carboxyl and phosphate group oxygen
OW  oxygen in TIP3P water
OH  oxygen in hydroxyl group
OS  ether and ester oxygen
P   phosphate,pol:JACS,112,8543,90,K.J.Miller
S   S in disulfide linkage,pol:JPC,102,2399,98
SH  S in cystine
CU  copper
FE  iron
Li  lithium, ions pol:J.PhysC,11,1541,(1978)
IP  assumed to be Na+ (ion plus)
Na  Na+, ions pol:J.PhysC,11,1541,(1978)
K   potassium
Rb  rubidium
Cs  cesium
Zn  Zn2+ 