Atom Nomenclature for IMZ

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 IMZ

Atom Name (V3) Atom Name (V2)
C4 C4
C40 C40
C45 C45
C44 C44
C41 C41
C42 C42
C43 C43
BR43 BR43
N3 N3
C2 C2
C20 C20
C26 C26
O26 O26
C27 C27
C28 C28
C25 C25
C21 C21
C22 C22
C23 C23
O23 O23
C24 C24
N1 N1
C10 C10
O10 O10
N10 N10
C15 C15
C14 C14
N13 N13
C13 C13
C16 C16
O17 O17
C11 C11
C12 C12
C5 C5
C50 C50
C51 C51
C52 C52
C55 C55
C54 C54
C53 C53
BR53 BR53
H4 H4
H45 H45
H44 H44
H41 H41
H42 H42
H271 1H27
H272 2H27
H281 1H28
H282 2H28
H283 3H28
H25 H25
H21 H21
H22 H22
H241 1H24
H242 2H24
H243 3H24
H151 1H15
H152 2H15
H141 1H14
H142 2H14
H131 1H13
H132 2H13
H161 1H16
H162 2H16
H17 H17
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H5 H5
H51 H51
H52 H52
H55 H55
H54 H54