Atom Nomenclature for FAD

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 FAD

Atom Name (V3) Atom Name (V2)
PA AP
O1A AO1
O2A AO2
O5B AO5*
C5B AC5*
C4B AC4*
O4B AO4*
C3B AC3*
O3B AO3*
C2B AC2*
O2B AO2*
C1B AC1*
N9A AN9
C8A AC8
N7A AN7
C5A AC5
C6A AC6
N6A AN6
N1A AN1
C2A AC2
N3A AN3
C4A AC4
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C4X C4A
N5 N5
C5X C5A
C6 C6
C7 C7
C7M C7M
C8 C8
C8M C8M
C9 C9
C9A C9A
N10 N10
C10 C10
C1' C1*
C2' C2*
O2' O2*
C3' C3*
O3' O3*
C4' C4*
O4' O4*
C5' C5*
O5' O5*
P P
O1P O1P
O2P O2P
O3P O3P
HOA2 2HOA
H51A AH51
H52A AH52
H4B AH4*
H3B AH3*
HO3A AHO3
H2B AH2*
HO2A AHO2
H1B AH1*
H8A AH8
H61A AH61
H62A AH62
H2A AH2
HN3 HN3
H6 H6
HM71 1HM7
HM72 2HM7
HM73 3HM7
HM81 1HM8
HM82 2HM8
HM83 3HM8
H9 H9
H1'1 1H1*
H1'2 2H1*
H2' H2*
HO2' *HO2
H3' H3*
HO3' *HO3
H4' H4*
HO4' *HO4
H5'1 1H5*
H5'2 2H5*
HOP2 2HOP