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, pp. 172-174

Section 3.6.7.2.3. Chemical links

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

3.6.7.2.3. Chemical links

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The data items in these categories are as follows:

(a) CHEM_LINK [Scheme scheme112]

(b) CHEM_LINK_ANGLE [Scheme scheme113]

(c) CHEM_LINK_BOND [Scheme scheme114]

(d) CHEM_LINK_CHIR [Scheme scheme115]

(e) CHEM_LINK_CHIR_ATOM [Scheme scheme116]

(f) CHEM_LINK_PLANE [Scheme scheme117]

(g) CHEM_LINK_PLANE_ATOM [Scheme scheme118]

(h) CHEM_LINK_TOR [Scheme scheme119]

(i) CHEM_LINK_TOR_VALUE [Scheme scheme120]

(j) ENTITY_LINK [Scheme scheme121]

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. 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.

The geometry of the links between chemical components or entities can be described in the CHEM_LINK group of categories. Chemical components may be linked together according to the type of the component; defining the linking according to the type of the component rather than by each component in turn allows a type of polymer link for all the monomers in a polymer to be specified (e.g. L-peptide linking). The geometry of the links can be specified in the remaining CHEM_LINK categories. The relationships between categories used to describe links between chemical components are shown in Fig. 3.6.7.4[link], which also shows how information about the links is passed to the CHEM_COMP and CHEM_LINK categories. For simplicity, the categories CHEM_COMP_PLANE, CHEM_COMP_PLANE_ATOM, CHEM_COMP_CHIR, CHEM_COMP_CHIR_ATOM and ENTITY_LINK are not included in Fig. 3.6.7.4[link].

[Figure 3.6.7.4]

Figure 3.6.7.4 | top | pdf |

The family of categories used to describe the links between chemical components. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ([\bullet]). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

Note that this category group can be used to describe the links that connect the monomers within a macromolecular polymer (using the CHEM_LINK categories) and also the intramolecular links between separate molecules in the whole complex (using the ENTITY_LINK category). Intramolecular links, for example a covalent bond formed between a bound ligand and an amino-acid side chain, are usually discovered as a result of the structure determination, and it would therefore seem more appropriate to describe them in the STRUCT_CONN category. However, since one of the roles of the CHEM_LINK category group is to record target values used for restraints or constraints during the refinement of the model of the structure, ideal values for the geometry of any entity-to-entity links should be given here.

Data items in the CHEM_LINK category are used to assign a unique identifier to each link and allow the author to record any unusual aspects of each link. The other categories in the CHEM_LINK category group describe the geometric model of each link, and are closely analogous to the similarly named categories in the CHEM_COMP group.

The relationships among these categories are complex (see Fig. 3.6.7.4[link]). Each atom that participates in an aspect of the link (for example, a bond, an angle, a chiral centre, a torsion angle or a plane) must be identified and it must also be specified whether the atom is in the first or second of the components that form the link.

Data items in the CHEM_LINK_BOND category describe the bonds between atoms participating in an intermolecular link between chemical components. Bond restraints may be described by the distance between the bonded atoms, the bond order or both.

An angle at a link may be described in the CHEM_LINK_ANGLE category as either an angle at the vertex atom or as a distance between the atoms attached to the vertex. For data items in both the CHEM_LINK_BOND and CHEM_LINK_ANGLE categories, a target value and its associated standard uncertainty may be specified (Example 3.6.7.5[link]).

Example 3.6.7.5. A peptide bond described with data items in the CHEM_LINK_BOND and CHEM_LINK_ATOM categories.

[Scheme scheme122]

Data items in the CHEM_LINK_CHIR category can be used to describe the conformation of chiral centres in a link between two chemical components. The absolute configuration and the chiral volume may be specified, as well as the total number of atoms and the number of non-hydrogen atoms bonded to the chiral centre. There is also a flag to indicate whether a restrained chiral volume should match the target value in sign as well as in magnitude. Because chiral centres can involve a variable number of atoms, a separate list of the atoms should be given in CHEM_LINK_CHIR_ATOM.

Data items in the CHEM_LINK_PLANE category can be used to list planes defined across a link between two chemical components. Because planes can involve a variable number of atoms, a separate list of the atoms should be given in CHEM_LINK_PLANE_ATOM.

Data items in the CHEM_LINK_TOR category can be used to give details of the torsion angles across a link between two chemical components. The torsion angle may be described either as an angle or as a distance between the first and last atoms. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category.

The ENTITY_LINK category is used to identify the participants in links between distinct molecular entities. A pointer to the details of the link is given in _entity_link.link_id, which matches a value of _chem_link.id in the CHEM_LINK category.








































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