Atom Nomenclature for EFD

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 EFD

Atom Name (V3) Atom Name (V2)
C10 C1
C11 C2
C01 C3
C02 C4
C03 C5
C04 C6
C05 C7
C06 C8
C07 C9
O08 O1
N09 N1
C12 C10
C13 C11
C14 C12
C15 C13
C16 C14
C17 C15
C18 C16
C19 C17
C20 C18
C21 C19
F22 F1
C23 C20
N24 N2
C25 C21
C26 C22
C27 C23
C28 C24
C29 C25
O30 O2
N31 N3
C32 C26
C33 C27
C34 C28
C35 C29
C36 C30
C37 C31
C38 C32
C39 C33
F40 F2
F41 F3
F42 F4
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35