Section 3.6.7.2. Molecular chemistry

The data items in these categories are as follows:

(a) CHEMICAL

(b) CHEMICAL_CONN_ATOM

(c) CHEMICAL_CONN_BOND

(d) CHEMICAL_FORMULA

The 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 () 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 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.

Data items in these categories are as follows:

(a) CHEM_COMP

(b) CHEM_COMP_ANGLE

(c) CHEM_COMP_ATOM

(d) CHEM_COMP_BOND

(e) CHEM_COMP_CHIR

(f) CHEM_COMP_CHIR_ATOM

(g) CHEM_COMP_LINK

(h) CHEM_COMP_PLANE

(i) CHEM_COMP_PLANE_ATOM

(j) CHEM_COMP_TOR

(k) CHEM_COMP_TOR_VALUE

The 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 () 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.

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 (). 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.

The data items in these categories are as follows:

(a) CHEM_LINK

(b) CHEM_LINK_ANGLE

(c) CHEM_LINK_BOND

(d) CHEM_LINK_CHIR

(e) CHEM_LINK_CHIR_ATOM

(f) CHEM_LINK_PLANE

(g) CHEM_LINK_PLANE_ATOM

(h) CHEM_LINK_TOR

(i) CHEM_LINK_TOR_VALUE

(j) ENTITY_LINK

The 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 () 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, 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.

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 (). 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). 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).

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.