Section 3.2.4.3.1. Contents of the geometry-related categories

The data items in these categories are as follows:

(a) GEOM

(b) GEOM_ANGLE

(c) GEOM_BOND

(d) GEOM_CONTACT

(e) GEOM_HBOND

(f) GEOM_TORSION

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. *_symmetry_* items have a default value and may be omitted from the list. The arrow () is a reference to a parent data item.

Most categories within this group record distances or angles specified by atom-site labels and are well characterized. The GEOM category currently provides the single data name _geom_special_details in which any other details of the geometry that an author considers noteworthy may be stored. Examples of information that might be stored in this data item are least-squares equations of planes, out-of-plane distances, dihedral angles between planes and general comments about the calculation of standard uncertainties.

A subtlety in the geometry-related categories arises from the need to record geometric relationships that involve atoms that are not listed in the ATOM_SITE coordinate list, but that can be derived from the coordinates in this list by the application of a crystallographic symmetry transformation. Thus atom sites in the geometry lists are identified both by their atom-site labels (which must identically match one of the entries in the ATOM_SITE list) and by the code for the symmetry transformation that has been applied to the initial location. Since the atom-site labels may refer to atoms in their original location as well as to atoms in symmetry-related locations, the formal key for these categories involves the site labels as well as the symmetry codes. However, in many cases (as discussed further below) the symmetry codes may be absent from a list, and a parser must supply suitable default or null values for the missing components when constructing or checking a complete key.

In many cases, interest is focused on intramolecular distances and angles, and on intramolecular contacts within a single asymmetric unit. In such cases, the geometry lists would contain only atoms listed explicitly in the ATOM_SITE list and the symmetry codes all refer trivially to the identity transformation.

The examples in this section demonstrate various ways of handling geometry lists with trivial or non-trivial symmetry transformations. In Example 3.2.4.9, showing treatment of bond angles, the relevant data items (_geom_angle_site_symmetry_*) are absent, which is one method for indicating the identity transformation. Dictionary validation software must therefore be able to handle both the presence and absence of these components of the formal category key.

The symmetry transformations in this and related categories take the form of codes 'n klm' or n_klm, where n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. The value of n must match a number given in _symmetry_equiv_pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the contact. These translations (x, y, z) are related to (k, l, m) by

By adding 5 to the translations, the use of negative numbers is avoided. As an example, the symmetry code 7_645 means that the symmetry operation with label `7' in the _symmetry_equiv_pos_site_id list is applied and the resulting position is translated +1.0 × a along the x axis, −1.0 × b along the y axis and 0.0 × c along the z axis, where a, b and c are the unit-cell edges.

List entries with a _geom_angle_publ_flag value of yes are those that should be published.

The GEOM_BOND category records intramolecular bond distances. In Example 3.2.4.10, all the atoms are untransformed and are at the positions given in the ATOM_SITE list. The symmetry code is 1_555, where the trivial symmetry operation x, y, z is numbered `1' by _symmetry_equiv_pos_site_id.

The GEOM_CONTACT category records nonbonded interatomic contacts. In Example 3.2.4.11, all the atoms are untransformed and are at the positions given in the ATOM_SITE list, and therefore the symmetry codes all have the value ` .' (meaning `inapplicable'). This is another method for indicating the identity transformation.

The GEOM_HBOND category records details about hydrogen bonds. Unlike other categories in the GEOM group, the GEOM_HBOND category records information about both distances and angles, including donor–acceptor, donor–hydrogen and acceptor–hydrogen distances and the included angle at the hydrogen-atom site (see Example 3.2.4.12). The comments above about the interpretation of symmetry codes and their relevance in the formal assignment of the category key also apply to this category.

Note that, strictly speaking, this category should only be populated if coordinates for the hydrogen atom are available (because the mandatory component of the category key _geom_hbond_atom_site_label_H needs a parent label in the atom-site list). In practice, hydrogen bonds can be assumed between donor atoms and acceptors even if the hydrogen atom is not specifically located.

The items in the GEOM_TORSION category describe the torsion angle in degrees generated for the bonded sequence of four atom sites identified by the _geom_torsion_atom_site_label_* codes. As with other geometry-specific site labels, these must match labels specified as _atom_site_label in the atom list. The torsion angle definition is that of Klyne & Prelog (1960).

Example 3.2.4.13 includes two sites that have been generated by crystallographic symmetry operations and lattice translations from the parent sites in the atom list.