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atom_nom.csv
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# Correlation of hydrogen atom naming systems, including diastereotopic
# protons. The original version of this table was created by Charles
# Hoogstraten.
#
# BMRB = System in use at BioMagResBank (IUPAC/IUB Biochemistry 9, 3471-3479
# [1970]).
#
# SC = Stereochemical designations
#
# UCSF = Mardigras-type software (peptide protonated with newhyd utility).
#
# XPLOR = Peptide protonated with XPLOR 3.1. Atom nomenclature is derived
# from the X-PLOR topology file topallhdg.pro.
#
# MSI = Artificial peptide created with InsightII. For the side chain
# protons attached to nitrogen in ASN, GLN, and ARG, the atom
# nomenclature does not reflect the potential stereoisomerism of the
# planar amide and guanidinium groups. The correlation with Z and E
# nomenclature listed here simply reflects the state of the artificial
# peptide generated as an example. The CG1 and CG2 atoms for VAL in a
# peptide generated by InsightII are not labeled according to IUPAC
# rules, while the CD1 and CD2 atoms for LEU are.
#
# PDB = PDB nomenclature (Taken from PDB entry 6I1B REVDAT 15-OCT-92.)
#
# SYBYL = The atom nomenclature was taken from the xxx.res files supplied with
# the software package Sybyl version 6.2 from Tripos, Inc.
#
# MIDAS = MidasPlus from the Computer Graphics Laboratory at UCSF. The atom
# nomenclature has been taken from the XXX.ins files supplied with the
# software. The prochiral atoms have not been correlated with the
# BMRB assignments at this time. Hydrogens are not included in the
# XXX.ins template files.
#
# Note-1: The prochiral methyl group names may reflect convention of code
# generating heavy atom names if protons are added later.
#
# Note-2: '*' The stereochemical assignments for the named atoms have not been
# determined for these software systems.
#
# Note-3: The Z and E nomenclature is defined in the paper by Blackwood, J.E.,
# Gladys, C.L., Loening, K.L., Petrarca, A.E., and Rush, J.E.,
# Unambiguous Specification of Stereoisomerism about a Double Bond,
# J. Amer. Chem. Soc. 90, 509-510 (1968).
#
# Note-3: For the terminal amine and carboxyl atoms, 'X' has been used as a
# dummy value for the amino acid type.
#
# Note-4: The terminal secondary amine protons for PRO have been included
# with the other PRO atoms.
#
# Note-5: Fields in the table are separated by tabs.
#
# Note-6: Please report errors, updates, or extensions to Eldon Ulrich
# (elu@nmrfam.wisc.edu)
# NX: Terminal amine protons
# CX: Terminal carboxyl atoms
# A.A. BMRB SC PDB UCSF MSI XPLOR SYBYL* MIDAS* DIANA
NX H1 1H HN1 HN1 HT1 HNCAP
NX H2 2H HN2 HN2 HT2
NX H3 3H HN3 HN3 HT3
CX H'' HOCAP
CX O' O O OT1 O O
CX O'' OXT OXT OT2 OXT OXT
A H H HN HN HN H HN
A HA HA HA HA HA HA HA
A HB1 1HB HB1 HB1 HB1 HB1 HB1
A HB2 2HB HB2 HB2 HB2 HB2 HB2
A HB3 3HB HB3 HB3 HB3 HB3 HB3
A C C C C C C C
A CA CA CA CA CA CA CA
A CB CB CB CB CB CB CB
A N N N N N N N
A O O O O O O O
R H H HN HN HN H HN
R HA HA HA HA HA HA HA
R HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
R HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
R HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2
R HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3
R HD2 pro-S 1HD HD1 HD1 HD2 HD2 HD2
R HD3 pro-R 2HD HD2 HD2 HD1 HD1 HD3
R HE HE HNE HE HE HE HE
R HH11 Z 1HH1 HN11 HH11 HH11 HH11 HH11
R HH12 E 2HH1 HN12 HH12 HH12 HH12 HH12
R HH21 Z 1HH2 HN21 HH22 HH21 HH21 HH21
R HH22 E 2HH2 HN22 HH21 HH22 HH22 HH22
R C C C C C C C
R CA CA CA CA CA CA CA
R CB CB CB CB CB CB CB
R CG CG CG CG CG CG CG
R CD CD CD CD CD CD CD
R CZ CZ CZ CZ CZ CZ CZ
R N N N N N N N
R NE NE NE NE NE NE NE
R NH1 Z NH1 NH1 NH1 NH1 NH1 NH1
R NH2 E NH2 NH2 NH2 NH2 NH2 NH2
R O O O O O O O
D H H HN HN HN H HN
D HA HA HA HA HA HA HA
D HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2
D HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3
D HD2 HD2 HD2
D C C C C C C C
D CA CA CA CA CA CA CA
D CB CB CB CB CB CB CB
D CG CG CG CG CG CG CG
D N N N N N N N
D O O O O O O O
D OD1 OD1 OD1 OD1 OD1 OD1 OD1
D OD2 OD2 OD2 OD2 OD2 OD2 OD2
N H H HN HN HN H HN
N HA HA HA HA HA HA HA
N HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2
N HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3
N HD21 E 1HD2 HN21 HD21 HD21 HD21 HD21
N HD22 Z 2HD2 HN22 HD22 HD22 HD22 HD22
N C C C C C C C
N CA CA CA CA CA CA CA
N CB CB CB CB CB CB CB
N CG CG CG CG CG CG CG
N N N N N N N N
N ND2 ND2 ND2 ND2 ND2 ND2 ND2
N O O O O O O O
N OD1 OD1 OD1 OD1 OD1 OD1 OD1
C H H HN HN HN H HN
C HA HA HA HA HA HA HA
C HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2
C HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3
C HG HG HSG HG HG HG HG
C C C C C C C C
C CA CA CA CA CA CA CA
C CB CB CB CB CB CB CB
C N N N N N N N
C O O O O O O O
C SG SG SG SG SG SG SG
E H H HN HN HN H HN
E HA HA HA HA HA HA HA
E HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
E HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
E HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2
E HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3
E HE2 HE2 HE2
E C C C C C C C
E CA CA CA CA CA CA CA
E CB CB CB CB CB CB CB
E CG CG CG CG CG CG CG
E CD CD CD CD CD CD CD
E N N N N N N N
E O O O O O O O
E OE1 OE1 OE1 OE1 OE1 OE1 OE1
E OE2 OE2 OE2 OE2 OE2 OE2 OE2
Q H H HN HN HN H HN
Q HA HA HA HA HA HA HA
Q HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
Q HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
Q HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2
Q HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3
Q HE21 E 1HE2 HN21 HE21 HE21 HE21 HE21
Q HE22 Z 2HE2 HN22 HE22 HE22 HE22 HE22
Q C C C C C C C
Q CA CA CA CA CA CA CA
Q CB CB CB CB CB CB CB
Q CG CG CG CG CG CG CG
Q CD CD CD CD CD CD CD
Q N N N N N N N
Q NE2 NE2 NE2 NE2 NE2 NE2 NE2
Q O O O O O O O
Q OE1 OE1 OE1 OE1 OE1 OE1 OE1
G H H HN HN HN H HN
G HA2 pro-R 1HA HA1 HA1 HA2 HA2 HA1
G HA3 pro-S 2HA HA2 HA2 HA1 HA1 HA2
G C C C C C C C
G CA CA CA CA CA CA CA
G N N N N N N N
G O O O O O O O
H H H HN HN HN H HN
H HA HA HA HA HA HA HA
H HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2
H HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3
H HD1 HD1 HND1 HD1 HD1 HD1 HD1
H HD2 HD2 HD2 HD2 HD2 HD2 HD2
H HE1 HE1 HE1 HE1 HE1 HE1 HE1
H HE2 HNE2 HE2 HE2
H C C C C C C C
H CA CA CA CA CA CA CA
H CB CB CB CB CB CB CB
H CG CG CG CG CG CG CG
H CD2 CD2 CD2 CD2 CD2 CD2 CD2
H CE1 CE1 CE1 CE1 CE1 CE1 CE1
H N N N N N N N
H ND1 ND1 ND1 ND1 ND1 ND1 ND1
H NE2 NE2 NE2 NE2 NE2 NE2 NE2
H O O O O O O O
I H H HN HN HN H HN
I HA HA HA HA HA HA HA
I HB HB HB HB HB HB HB
I HG12 pro-R 1HG1 HG11 HG11 HG12 HG12 HG12
I HG13 pro-S 2HG1 HG12 HG12 HG11 HG11 HG13
I HG21 1HG2 HG21 HG21 HG21 HG21 HG21
I HG22 2HG2 HG22 HG22 HG22 HG22 HG22
I HG23 3HG2 HG23 HG23 HG23 HG23 HG23
I HD11 1HD1 HD11 HD11 HD11 HD11 HD11
I HD12 2HD1 HD12 HD12 HD12 HD12 HD12
I HD13 3HD1 HD13 HD13 HD13 HD13 HD13
I C C C C C C C
I CA CA CA CA CA CA CA
I CB CB CB CB CB CB CB
I CG1 CG1 CG1 CG1 CG1 CG1 CG1
I CG2 CG2 CG2 CG2 CG2 CG2 CG2
I CD1 CD1 CD1 CD1 CD1 CD1 CD1
I N N N N N N N
I O O O O O O O
L H H HN HN HN H HN
L HA HA HA HA HA HA HA
L HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
L HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
L HG HG HG HG HG HG HG
L HD11 1HD1 HD11 HD11 HD11 HD11 HD11
L HD12 2HD1 HD12 HD12 HD12 HD12 HD12
L HD13 3HD1 HD13 HD13 HD13 HD13 HD13
L HD21 1HD2 HD21 HD21 HD21 HD21 HD21
L HD22 2HD2 HD22 HD22 HD22 HD22 HD22
L HD23 3HD2 HD23 HD23 HD23 HD23 HD23
L C C C C C C C
L CA CA CA CA CA CA CA
L CB CB CB CB CB CB CB
L CG CG CG CG CG CG CG
L CD1 pro-R CD1 CD1 CD1 CD1 CD1 CD1
L CD2 pro-S CD2 CD2 CD2 CD2 CD2 CD2
L N N N N N N N
L O O O O O O O
K H H HN HN HN H HN
K HA HA HA HA HA HA HA
K HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
K HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
K HG2 pro-R 1HG HG1 HG1 HG2 HG2 HG2
K HG3 pro-S 2HG HG2 HG2 HG1 HG1 HG3
K HD2 pro-S 1HD HD1 HD1 HD2 HD2 HD2
K HD3 pro-R 2HD HD2 HD2 HD1 HD1 HD3
K HE2 pro-S 1HE HE1 HE1 HE2 HE2 HE2
K HE3 pro-R 2HE HE2 HE2 HE1 HE1 HE3
K HZ1 1HZ HNZ1 HZ1 HZ1 HZ1 HZ1
K HZ2 2HZ HNZ2 HZ2 HZ2 HZ2 HZ2
K HZ3 3HZ HNZ3 HZ3 HZ3 HZ3 HZ3
K C C C C C C C
K CA CA CA CA CA CA CA
K CB CB CB CB CB CB CB
K CG CG CG CG CG CG CG
K CD CD CD CD CD CD CD
K CE CE CE CE CE CE CE
K N N N N N N N
K NZ NZ NZ NZ NZ NZ NZ
K O O O O O O O
M H H HN HN HN H HN
M HA HA HA HA HA HA HA
M HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2
M HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3
M HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2
M HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3
M HE1 1HE HE1 HE1 HE1 HE1 HE1
M HE2 2HE HE2 HE2 HE2 HE2 HE2
M HE3 3HE HE3 HE3 HE3 HE3 HE3
M C C C C C C C
M CA CA CA CA CA CA CA
M CB CB CB CB CB CB CB
M CG CG CG CG CG CG CG
M CE CE CE CE CE CE CE
M N N N N N N N
M O O O O O O O
M SD SD SD SD SD SD SD
F H H HN HN HN H HN
F HA HA HA HA HA HA HA
F HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
F HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
F HD1 HD1 HD1 HD1 HD1 HD1 HD1
F HD2 HD2 HD2 HD2 HD2 HD2 HD2
F HE1 HE1 HE1 HE1 HE1 HE1 HE1
F HE2 HE2 HE2 HE2 HE2 HE2 HE2
F HZ HZ HZ HZ HZ HZ HZ
F C C C C C C C
F CA CA CA CA CA CA CA
F CB CB CB CB CB CB CB
F CG CG CG CG CG CG CG
F CD1 CD1 CD1 CD1 CD1 CD1 CD1
F CD2 CD2 CD2 CD2 CD2 CD2 CD2
F CE1 CE1 CE1 CE1 CE1 CE1 CE1
F CE2 CE2 CE2 CE2 CE2 CE2 CE2
F CZ CZ CZ CZ CZ CZ CZ
F N N N N N N N
F O O O O O O O
P H2 pro-R H2 HN2 HT2
P H3 pro-S H1 HN1 HT1
P HA HA HA HA HA HA HA
P HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
P HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
P HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2
P HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3
P HD2 pro-S 1HD HD2 HD1 HD2 HD2 HD2
P HD3 pro-R 2HD HD1 HD2 HD1 HD1 HD3
P C C C C C C C
P CA CA CA CA CA CA CA
P CB CB CB CB CB CB CB
P CG CG CG CG CG CG CG
P CD CD CD CD CD CD CD
P N N N N N N N
P O O O O O O O
S H H HN HN HN H HN
S HA HA HA HA HA HA HA
S HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2
S HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3
S HG HG HOG HG HG HG HG
S C C C C C C C
S CA CA CA CA CA CA CA
S CB CB CB CB CB CB CB
S N N N N N N N
S O O O O O O O
S OG OG OG OG OG OG OG
T H H HN HN HN H HN
T HA HA HA HA HA HA HA
T HB HB HB HB HB HB HB
T HG1 HG1 HOG1 HG1 HG1 HG1 HG1
T HG21 1HG2 HG21 HG21 HG21 HG21 HG21
T HG22 2HG2 HG22 HG22 HG22 HG22 HG22
T HG23 3HG2 HG23 HG23 HG23 HG23 HG23
T C C C C C C C
T CA CA CA CA CA CA CA
T CB CB CB CB CB CB CB
T CG2 CG2 CG2 CG2 CG2 CG2 CG2
T N N N N N N N
T O O O O O O O
T OG1 OG1 OG1 OG1 OG1 OG1 OG1
W H H HN HN HN H HN
W HA HA HA HA HA HA HA
W HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
W HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
W HD1 HD1 HD1 HD1 HD1 HD1 HD1
W HE1 HE1 HNE1 HE1 HE1 HE1 HE1
W HE3 HE3 HE3 HE3 HE3 HE3 HE3
W HZ2 HZ2 HZ2 HZ2 HZ2 HZ2 HZ2
W HZ3 HZ3 HZ3 HZ3 HZ3 HZ3 HZ3
W HH2 HH2 HH2 HH2 HH2 HH2 HH2
W C C C C C C C
W CA CA CA CA CA CA CA
W CB CB CB CB CB CB CB
W CG CG CG CG CG CG CG
W CD1 CD1 CD1 CD1 CD1 CD1 CD1
W CD2 CD2 CD2 CD2 CD2 CD2 CD2
W CE2 CE2 CE2 CE2 CE2 CE2 CE2
W CE3 CE3 CE3 CE3 CE3 CE3 CE3
W CZ2 CZ2 CZ2 CZ2 CZ2 CZ2 CZ2
W CZ3 CZ3 CZ3 CZ3 CZ3 CZ3 CZ3
W CH2 CH2 CH2 CH2 CH2 CH2 CH2
W N N N N N N N
W NE1 NE1 NE1 NE1 NE1 NE1 NE1
W O O O O O O O
Y H H HN HN HN H HN
Y HA HA HA HA HA HA HA
Y HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2
Y HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3
Y HD1 HD1 HD1 HD1 HD1 HD1 HD1
Y HD2 HD2 HD2 HD2 HD2 HD2 HD2
Y HE1 HE1 HE1 HE1 HE1 HE1 HE1
Y HE2 HE2 HE2 HE2 HE2 HE2 HE2
Y HH HH HOH HH HH HH HH
Y C C C C C C C
Y CA CA CA CA CA CA CA
Y CB CB CB CB CB CB CB
Y CG CG CG CG CG CG CG
Y CD1 CD1 CD1 CD1 CD1 CD1 CD1
Y CD2 CD2 CD2 CD2 CD2 CD2 CD2
Y CE1 CE1 CE1 CE1 CE1 CE1 CE1
Y CE2 CE2 CE2 CE2 CE2 CE2 CE2
Y CZ CZ CZ CZ CZ CZ CZ
Y N N N N N N N
Y O O O O O O O
Y OH OH OH OH OH OH OH
V H H HN HN HN H HN
V HA HA HA HA HA HA HA
V HB HB HB HB HB HB HB
V HG11 1HG1 HG11 HG21 HG11 HG11 HG11
V HG12 2HG1 HG12 HG22 HG12 HG12 HG12
V HG13 3HG1 HG13 HG23 HG13 HG13 HG13
V HG21 1HG2 HG21 HG11 HG21 HG21 HG21
V HG22 2HG2 HG22 HG12 HG22 HG22 HG22
V HG23 3HG2 HG23 HG13 HG23 HG23 HG23
V C C C C C C C
V CA CA CA CA CA CA CA
V CB CB CB CB CB CB CB
V CG1 pro-R CG1 CG2 CG1 CG1 CG1 CG1
V CG2 pro-S CG2 CG1 CG2 CG2 CG2 CG2
V N N N N N N N
V O O O O O O O