1 # Correlation of hydrogen atom naming systems, including diastereotopic
2 # protons. The original version of this table was created by Charles
5 # BMRB = System in use at BioMagResBank (IUPAC/IUB Biochemistry 9, 3471-3479
8 # SC = Stereochemical designations
10 # UCSF = Mardigras-type software (peptide protonated with newhyd utility).
12 # XPLOR = Peptide protonated with XPLOR 3.1. Atom nomenclature is derived
13 # from the X-PLOR topology file topallhdg.pro.
15 # MSI = Artificial peptide created with InsightII. For the side chain
16 # protons attached to nitrogen in ASN, GLN, and ARG, the atom
17 # nomenclature does not reflect the potential stereoisomerism of the
18 # planar amide and guanidinium groups. The correlation with Z and E
19 # nomenclature listed here simply reflects the state of the artificial
20 # peptide generated as an example. The CG1 and CG2 atoms for VAL in a
21 # peptide generated by InsightII are not labeled according to IUPAC
22 # rules, while the CD1 and CD2 atoms for LEU are.
24 # PDB = PDB nomenclature (Taken from PDB entry 6I1B REVDAT 15-OCT-92.)
26 # SYBYL = The atom nomenclature was taken from the xxx.res files supplied with
27 # the software package Sybyl version 6.2 from Tripos, Inc.
29 # MIDAS = MidasPlus from the Computer Graphics Laboratory at UCSF. The atom
30 # nomenclature has been taken from the XXX.ins files supplied with the
31 # software. The prochiral atoms have not been correlated with the
32 # BMRB assignments at this time. Hydrogens are not included in the
33 # XXX.ins template files.
35 # Note-1: The prochiral methyl group names may reflect convention of code
36 # generating heavy atom names if protons are added later.
38 # Note-2: '*' The stereochemical assignments for the named atoms have not been
39 # determined for these software systems.
41 # Note-3: The Z and E nomenclature is defined in the paper by Blackwood, J.E.,
42 # Gladys, C.L., Loening, K.L., Petrarca, A.E., and Rush, J.E.,
43 # "Unambiguous Specification of Stereoisomerism about a Double Bond,"
44 # J. Amer. Chem. Soc. 90, 509-510 (1968).
46 # Note-3: For the terminal amine and carboxyl atoms, 'X' has been used as a
47 # dummy value for the amino acid type.
49 # Note-4: The terminal secondary amine protons for PRO have been included
50 # with the other PRO atoms.
52 # Note-5: Fields in the table are separated by tabs.
54 # Note-6: Please report errors, updates, or extensions to Eldon Ulrich
55 # (elu@nmrfam.wisc.edu)
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