Atom Nomenclature for CHO

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for CHO

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
O3 O3
C4 C4
C5 C5
C6 C6
C7 C7
O7 O7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
O24 O24
N25 N25
C26 C26
C27 C27
OT1 OT1
OT2 OT2
H11 H11
H12 H12
H21 H21
H22 H22
H3 H3
HO3 HO3
H41 H41
H42 H42
H5 H5
H61 H61
H62 H62
H7 H7
HO7 HO7
H8 H8
H9 H9
H111 H111
H112 H112
H121 H121
H122 H122
H14 H14
H151 H151
H152 H152
H161 H161
H162 H162
H17 H17
H181 H181
H182 H182
H183 H183
H191 H191
H192 H192
H193 H193
H20 H20
H211 H211
H212 H212
H213 H213
H221 H221
H222 H222
H231 H231
H232 H232
HN HN
H261 H261
H262 H262
HOT HOT