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. 169-172

Section 3.6.7.2.2. Chemical components

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

3.6.7.2.2. Chemical components

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Data items in these categories are as follows:

(a) CHEM_COMP [Scheme scheme100]

(b) CHEM_COMP_ANGLE [Scheme scheme101]

(c) CHEM_COMP_ATOM [Scheme scheme102]

(d) CHEM_COMP_BOND [Scheme scheme103]

(e) CHEM_COMP_CHIR [Scheme scheme104]

(f) CHEM_COMP_CHIR_ATOM [Scheme scheme105]

(g) CHEM_COMP_LINK [Scheme scheme106]

(h) CHEM_COMP_PLANE [Scheme scheme107]

(i) CHEM_COMP_PLANE_ATOM [Scheme scheme108]

(j) CHEM_COMP_TOR [Scheme scheme109]

(k) CHEM_COMP_TOR_VALUE [Scheme scheme110]

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.

Data items in the CHEM_COMP and related categories allow the covalent geometry, stereochemistry and Cartesian coordinates for the chemical components of the structure to be specified. These components may be monomers, e.g. the amino acids that form proteins, the nucleotides that form nucleic acids or the sugars that form oligosaccharides, or they may be the small-molecule compounds, ions or water molecules that co-crystallize with the macromolecule(s).

In a small-molecule structure determination, the chemistry is often deduced from the electron density distribution. In contrast, in macromolecular crystallography, the chemistry of the monomers that form a polymeric macromolecule is usually known in advance and is used to interpret the electron density. In many cases, the chemistry of the monomers is so well determined that it is not worth storing a copy of the geometric restraints used in every mmCIF that uses the same set of data for the monomers. In these cases, the data item _chem_comp.model_erf can be used to identify an external reference file (e.r.f.) that contains standard chemical data for these monomers. Although the present version of the mmCIF dictionary does not specify the form that the file identifier might take, it is likely that users will specify the location of the file in their local file system or the URL of files of reference data accessible over the Internet. In the long term, it would be helpful to have a standard repository of reference data for monomers with a stable identifier that is independent of file names or access protocols.

The relationships between the categories used to describe chemical components are shown in Fig. 3.6.7.3[link].

[Figure 3.6.7.3]

Figure 3.6.7.3 | top | pdf |

The family of categories used to describe the chemical and structural features of the monomers and small molecules used to build a model of a structure. 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.

The CHEM_COMP category provides data items for the chemical formula and formula weight of each component, the total number of atoms, the number of non-hydrogen atoms, and the name of the component. The name of the component will typically be a common name such as `alanine' or `valine'; it is recommended that the IUPAC name is used for components that are not among the usual monomers that make up proteins, nucleic acids or sugars.

The one-letter or three-letter code for a standard component may be given (using _chem_comp.one_letter_code and _chem_comp.three_letter_code, respectively). Values of X for the one-letter code or UNK for the three-letter code are used to indicate components that do not have a standard abbreviation. A component that has been formed by modification of a standard component can be indicated by prefixing the code with a plus sign. A value of ` .', which means `not applicable', should be used for components that are not monomers from which a polymeric macromolecule is built, for example co-crystallized small molecules, ions or water.

The data item _chem_comp.type can be used to describe the structural role of a monomer within a polymeric molecule. The types that are recognized are classified as linking monomers (for proteins, nucleic acids and sugars), monomers with an N-terminal or C-terminal cap (for proteins), and monomers with a 5′ or 3′ terminal cap (for nucleic acids). The specification of types for sugars is less complete than for proteins and nucleic acids and no types of terminal groups are currently specified for sugars. The values non-polymer and other are provided for types that have not been defined explicitly.

Information about the source of the model for the chemical component can be given using _chem_comp.model_source and _chem_comp.model_details. _chem_comp.model_source is a text field where the user might, for example, supply a reference to the Cambridge Structural Database or another small-molecule crystallographic database, or describe a molecular-modelling process. _chem_comp.model_details can be used to discuss any modification made to the model given in _chem_comp.model_source. As mentioned previously, _chem_comp.model_erf can be used to specify the location of an external reference file if the model is not described within the current data block.

Macromolecules often contain modifications of standard monomers, such as phosphorylated serines and threonines. In the mmCIF data model, a nonstandard monomer should be treated as a separate CHEM_COMP entry and described in full. However, it may be useful to refer to the standard monomer from which it was derived using the _chem_comp.mon_nstd_* data items. There are no fixed rules for what constitutes a `standard' or `nonstandard' monomer in this context, but any covalent modification of a standard amino acid or nucleotide would generally be considered nonstandard. Sometimes it is is difficult to decide whether a monomer is standard or nonstandard: seleno­methionine is not one of the standard 20 amino acids, but it is so commonly used that geometric restraints for it are included in many standard packages for protein structure refinement.

Data items in the CHEM_COMP_ATOM category can be used to describe the atoms in a component. The position of each atom is given in orthogonal ångström coordinates. These coordinates correspond to the atom positions in the model of the component used in the refinement, not to the final set of refined atom positions recorded in the ATOM_SITE list.

Other CHEM_COMP_ATOM data items can be used to specify what element the atom is and its formal electronic charge, or partial charge. A code may also be assigned to the atom to indicate its role within a substructural classification of the component. The allowed codes are main and side for the main-chain and side-chain parts of amino acids, and base, phos and sugar for the base, phosphate and sugar parts of nucleotides. Atoms that do not belong to a substructure may be assigned the code none.

Data items in the CHEM_COMP_BOND category can be used to describe the intramolecular bonds between atoms in a component. Bond restraints may be described by the distance between the bonded atoms, the bond order, or both. The recognized bond types are the same as those for the core CIF dictionary data item _chemical_conn_bond.type, and they fulfil the same role: to characterize a model that could be used for database substructure searching, rather than to give a detailed description of unusual bond types.

In the CHEM_COMP_ANGLE category, atom 2 defines the vertex of the angle involving atoms 1, 2 and 3. The angle may be described as either an angle at the vertex atom or as a distance between atoms 1 and 3.

Data items in the CHEM_COMP_CHIR category can be used to describe the conformation of chiral centres within the component. 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_COMP_CHIR_ATOM.

Data items in the CHEM_COMP_PLANE category can be used to define planes within a component. The number of non-hydrogen atoms and the total number of atoms in each plane can be recorded. The atoms defining each plane should be listed separately in CHEM_COMP_PLANE_ATOM.

Data items in the CHEM_COMP_TOR category can be used to give details about the torsion angles in a component. A torsion angle may be described either as an angle or as a distance between the first and last atoms. (A torsion angle cannot be completely described by a distance, but sometimes a distance restraint is used in refinement, where the value of the angle is assumed to be close to the target value.) As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category.

Data items in the CHEM_COMP_LINK category can be used to provide a table of links between the components of the structure. Each link is assigned an identifier ( _chem_comp_link.link_id) and the types of monomer at each end of the link are stated. The types are those allowed for the parent data item _chem_comp.type.

The use of many of these data items to describe a typical component is shown in Example 3.6.7.4[link].

Example 3.6.7.4. The description of a component (adriamycin) of a macromolecule with data items in the CHEM_COMP, CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_TOR and CHEM_COMP_TOR_VALUE categories (Leonard et al., 1993[link]).

[Scheme scheme111]

References

Leonard, G. A., Hambley, T. W., McAuley-Hecht, K., Brown, T. & Hunter, W. N. (1993). Anthracycline–DNA interactions at unfavourable base-pair triplet-binding sites: structures of d(CGGCCG)/dauno­mycin and d(TGGCCA)/adriamycin complexes. Acta Cryst. D49, 458–467.








































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