Appendix D. GRUB table of recognized molecules
Energy Variables for the following Recognised Molecules are
included in the main Section of Datafile GRUB. It is important to
use the correct molecule name from this table, as the name of each
Recognised Molecule in the PDB input file, when the Target is
composed of ATOMS. This is essential if the ATOMS are to be
assigned correct Energy Variables for the GRID computation.
A ADENOSINE
ABU AMINO BUTYRIC ACID
ACE ACETYL
ADS AMINODEOXYSTATINE
AIB AMINO ISO-BUTYRIC ACID
ALA ALANINE
AMI AMIDE NH2 GROUP to be used at the C terminal of proteins
ARG ARGININE
ASN ASPARAGINE
ASP ASPARTIC ACID WITH IONIZED SIDE CHAIN
ASX ASPARAGINE OR ASPARTIC ACID
ASZ ASPARTIC ACID (with neutral -COOH group in side chain)
ASZ1 ASPARTIC ACID (neutral with alternative proton position)
AZT AZETIDINE
BAL BETA ALANINE
BOC BUTOXYCARBONYL
C CYTIDINE
CBZ BENZOXYCARBONYL
CER CERAMIDE (Saturated. Alpha-hydroxy fatty acid)
CE1 CERAMIDE (Saturated. Normal fatty acid)
CHA CYCLOHEXYL ALANINE
CUR CERAMIDE (Unsaturated. Normal fatty acid)
CU1 CERAMIDE (Unsaturated. Alpha-hydroxy fatty acid)
CYD CYSTINE (Deprotonated sulphur)
CYO CYSTINE (Ionised sulphite sulphur)
CYS CYSTINE
CYX CYSTINE (With oxydised sulphur making S-S bridge)
F6P FRUCTOSE-6-PHOSPHATE
FUC FUCOSE
FUM FUMARIC ACID
G GUANOSINE
GLA GAMMA-CARBOXY GLUTAMIC ACID
GLN GLUTAMINE
GLU GLUTAMIC ACID
GLX GLUTAMINE OR GLUTAMIC ACID
GLY GLYCINE
GLZ GLUTAMIC ACID (With neutral -COOH group in side chain)
GLZ1 GLUTAMIC ACID (Neutral with alternative proton position)
H2O WATER
HCX HOMOCYSTINE (With oxydised sulphur making S-S bridge)
HCY HOMOCYSTINE
HEM HAEM
HID HISTIDINE with ionisable proton fixed to ND1
HIE HISTIDINE with ionisable proton fixed to NE2
HIP HISTIDINE with two N-bonded side-chain protons
HIS HISTIDINE under normal physiological conditions
HI0 HISTIDINE without N-bonded side-chain protons
HOH WATER
HPH HOMOPHENYLALANINE
HSE HOMOSERINE
HYP HYDROXYPROLINE
ILE ISOLEUCINE
LEU LEUCINE
LOV LEUCINE HYDROXY VALINE
LRV LEUCINE REDUCED VALINE (NEUTRAL FORM)
LRVH LEUCINE REDUCED VALINE (CATIONIC FORM)
LYS LYSINE
LYSC LYSINE with anionic carbamylated side chain (NH.COO)
LYZ LYSINE with unionised NH2: at end of side chain
MAN MANNOSE
MET METHIONINE
NAD NICOTINAMIDE ADENINE DINUCLEOTIDE
NAG N-ACETYLGLUCOSEAMINE
NAL NAPHTHYL ALANINE
NAP NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE
NLE NORLEUCINE
NVA NORVALINE
OH2 WATER
ORN ORNITHINE
ORZ ORNITHINE with unionised NH2: at end of side chain
PCA PYROGLUTAMIC ACID (Pyrrolidone Carboxylic Acid)
PEN PENICILLAMINE
PHE PHENYLALANINE
PHG PHENYLGLYCINE
PIP PIPECOLIC ACID
PLP PYRIDOXAL PHOSPHATE BONDED TO LYSINE
PRO PROLINE
PSE PHOSPHOSERINE
PTH PHOSPHOTHREONINE
PTY PHOSPHOTYROSINE
RIB RIBOSE
SER SERINE
STA STATINE
SUC SUCCINIC ACID
T THYMIDINE
TCB TRICHLORO-BUTOXYCARBONYL
THR THREONINE
TRP TRYPTOPHAN
TYR TYROSINE
U URIDINE
VAL VALINE
WAT WATER |