International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, p. 169

Section 3.6.7.2.1. Molecular chemistry in the core CIF dictionary

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.7.2.1. Molecular chemistry in the core CIF dictionary

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The data items in these categories are as follows:

(a) CHEMICAL [Scheme scheme96]

(b) CHEMICAL_CONN_ATOM [Scheme scheme97]

(c) CHEMICAL_CONN_BOND [Scheme scheme98]

(d) CHEMICAL_FORMULA [Scheme scheme99]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_). Data items marked with a plus (+) have companion data names for the standard uncertainty in the reported value, formed by appending the string _esd to the data name listed.

Descriptions of molecular chemistry in an mmCIF are normally made using data items in the CHEM_COMP and CHEM_LINK category groups. The CHEMICAL category group is retained in the mmCIF dictionary solely for consistency with the core CIF dictionary and Section 3.2.4.2[link] may be consulted for details.

Two of the categories in this group, CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND, have existing category keys in the core dictionary. The formal keys _chemical.entry_id and _chemical_formula.entry_id have been added to CHEMICAL and CHEMICAL_FORMULA, respectively, to provide the category keys required by the DDL2 data model.

It is emphasized that these items will not appear in the description of a macromolecular structure, but they are retained to allow the representation of small-molecule or inorganic structures in the DDL2 formalism of mmCIF.








































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