OEPDBAtomName

The OEPDBAtomName namespace encodes symbolic constants representing PDB atom types returned by the OEGetPDBAtomIndex function.

PDB documentation can be found at http://www.wwpdb.org/documentation/file-format For diagrams of amino acid and nucleic acid naming conventions see: Markley, J.L., Bax, A., Arata, Y., Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüthrich, K., 1998. Recommendations for the presentation of NMR structures of proteins and nucleic acids (IUPAC Recommendations 1998). Pure and Applied Chemistry, 70(1), pp.117-142.

This namespace contains the following constants:

N

Peptide backbone amide nitrogen.

CA

Peptide backbone alpha carbon.

C

Peptide backbone carbonyl carbon.

O

Peptide backbone carbonyl oxygen.

CB

Peptide sidechain beta carbon (for example ALA).

CG

Peptide sidechain gamma carbon (for example LYS).

OG

Peptide sidechain gamma oxygen (for example SER).

SG

Peptide sidechain gamma sulfur (for example CYS).

CG1

Peptide sidechain beta carbon 1 (for example the long arm of ILE).

OG1

Peptide sidechain beta oxygen 1 (for example THR).

CG2

Peptide sidechain beta carbon 2 (for example the short arm of ILE).

CD

Peptide sidechain delta carbon (for example LYS).

OD

Peptide sidechain delta oxygen.

SD

Peptide sidechain delta sulfur (for example MET).

CD1

Peptide sidechain delta carbon 1 (for example ILE).

ND1

Peptide sidechain delta nitrogen 1 (for example HIS).

OD1

Peptide sidechain delta oxygen 1 (for example ASN).

CD2

Peptide sidechain delta carbon 2 (for example HIS).

ND2

Peptide sidechain delta nitrogen 2 (for example ASN).

OD2

Peptide sidechain delta oxygen 2 (for example ASP).

SE_

Peptide sidechain selenium (for example MSE).

CE

Peptide sidechain epsilon carbon (for example MET).

NE

Peptide sidechain epsilon nitrogen (for example ARG).

OE

Peptide sidechain epsilon oxygen.

CE1

Peptide sidechain epsilon carbon 1 (for example HIS).

NE1

Peptide sidechain epsilon nitrogen 1 (for example TRP).

OE1

Peptide sidechain epsilon oxygen 1 (for example GLN).

CE2

Peptide sidechain epsilon carbon 2 (for example TRP).

NE2

Peptide sidechain epsilon nitrogen 2 (for example GLN).

OE2

Peptide sidechain epsilon oxygen 2 (for example GLN).

CE3

Peptide sidechain epsilon carbon 3 (for example TRP).

OE3

Peptide sidechain epsilon oxygen 3.

OE4

Peptide sidechain epsilon oxygen 4.

CZ

Peptide sidechain zeta carbon (for example TYR).

NZ

Peptide sidechain zeta nitrogen (for example LYS).

CZ2

Peptide sidechain zeta carbon 2 (for example TRP).

CZ3

Peptide sidechain zeta carbon 3 (for example TRP).

OH

Peptide sidechain eta oxygen (for example TYR).

CH1

Peptide sidechain eta carbon 1.

NH1

Peptide sidechain eta nitrogen 1 (for example ARG).

CH2

Peptide sidechain eta carbon 2 (for example TRP).

NH2

Peptide sidechain eta nitrogen 2 (for example ARG).

CH3

Methyl carbon (for example ACE).

OXT

Peptide backbone C-terminal oxygen.

P

Nucleic acid backbone phosphate phosphorus.

O1P

Nucleic acid backbone phosphate oxygen 1.

O2P

Nucleic acid backbone phosphate oxygen 2.

O5_

Nucleic acid backbone ribose oxygen 5-prime.

C5_

Nucleic acid backbone ribose carbon 5-prime.

C4_

Nucleic acid backbone ribose carbon 4-prime.

O4_

Nucleic acid backbone ribose oxygen 4-prime.

C3_

Nucleic acid backbone ribose carbon 3-prime.

O3_

Nucleic acid backbone ribose oxygen 3-prime.

C2_

Nucleic acid backbone ribose carbon 2-prime.

O2_

Nucleic acid backbone ribose oxygen 2-prime.

C2A

Methylated nucleic acid base carbon 2A (for example 2MG).

C1_

Nucleic acid backbone ribose carbon 1-prime.

N9

Nucleic acid base nitrogen 9.

C8

Nucleic acid base carbon 2.

N7

Nucleic acid base nitrogen 7.

C5

Nucleic acid base carbon 5.

C6

Nucleic acid base carbon 6.

O6

Nucleic acid base oxygen 6.

N6

Nucleic acid base nitrogen 6.

N1

Nucleic acid base nitrogen 1.

C2

Nucleic acid base carbon 2.

O2

Nucleic acid base oxygen 2.

N2

Nucleic acid base nitrogen 2.

CM5

Methylated nucleic acid base carbon M5 (for example 5MC).

N3

Nucleic acid base nitrogen 3.

C3

Nucleic acid base carbon 3.

C4

Nucleic acid base carbon 4.

O4

Nucleic acid base oxygen 4.

N4

Nucleic acid base nitrogen 4.

CM7

Methylated nucleic acid base carbon M7 (for example 7MG).

C5M

Methylated nucleic acid base carbon 5M (for example methylated T).

O3P

Nucleic acid terminal phosphate oxygen 3P (for example 1MA).

CM1

Methylated nucleic acid base carbon M1 (for example 1MA).

CM2

Methylated nucleic acid base carbon M2 (for example 2MG).

C10

Modified nucleic acid base carbon 10 (for example YG).

C11

Modified nucleic acid base carbon 11 (for example YG).

C12

Modified nucleic acid base carbon 12 (for example YG).

C13

Modified nucleic acid base carbon 13 (for example YG).

C14

Modified nucleic acid base carbon 14 (for example YG).

C15

Modified nucleic acid base carbon 15 (for example YG).

C16

Modified nucleic acid base carbon 16 (for example YG).

O17

Modified nucleic acid base oxygen 17 (for example YG).

O18

Modified nucleic acid base oxygen 18 (for example YG).

C19

Modified nucleic acid base carbon 19 (for example YG).

N20

Modified nucleic acid base nitrogen 20 (for example YG).

C21

Modified nucleic acid base carbon 21 (for example YG).

O22

Modified nucleic acid base oxygen 22 (for example YG).

O23

Modified nucleic acid base oxygen 23 (for example YG).

C24

Modified nucleic acid base carbon 24 (for example YG).

Cprev

Refers to previous peptide backbone carbonyl carbon.

Nnext

Refers to next peptide backbone amide nitrogen.

CAnext

Refers to next peptide backbone alpha carbon.