Volume 1 Chapter 7 Searching for Non-Bonded Contacts

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7.14.1 The CSD Reference Molecule(s) and the Extended Crystal Structure

A crystal structure consists of an infinite three-dimensional array of molecules and/or ions. The basic building block of this array is the crystallographic unit cell, and the complete crystal consists of many millions of these units.

Within the unit cell, individual molecules and ions are related to each other in 3D space according to the symmetry of the space group. Crystal structures can exist in any one of 230 possible space groups. Because the molecules of the unit cell are related by symmetry only part of the cell contents, the asymmetric unit, is required to describe the crystal structure. Frequently, but not always (see below), the asymmetric unit is a single molecule of the compound under study.

The example below shows the chemical diagram (a) and structural diagram (b) for entry AADMPY10. For this entry the crystal chemical unit is the same as the asymmetric unit. The position of the asymmetric unit in the unit cell can be seen in (b).


The space group of the crystal structure is o(P,`)1. If we denote the centroid of the asymmetric unit by the 3D coordinates x,y,z, then the space group symmetry will add a further two-residue asymmetric unit at :

-x, -y, -z

as shown in (c).


The positions of molecules in other unit cells can then be simply generated by adding unit cell translations along any or all of the axial directions.

During a non-bonded search, the crystal chemical unit is used as a reference point to search out into the extended crystal structure for intermolecular contacts. Sometimes the crystal chemical unit will be refered to as the reference molecule(s) when describing the operation of non-bonded commands. The extended crystal structure that results from searching AADMPY10 for hydrogen bonds is shown in (d). The non-bonded contacts are identified by dotted lines. Because diagrams of the extended crystal can quickly become large and difficult to visualize, the convention of the non-bonded search utility is to only add the atoms necessary to represent the contact. The actual display generated by the search is given in (e). Section 7.14.6 will provide more details about the display of non-bonded contacts.


Despite these apparent complications, all the user has to remember is that the CSD stores coordinate data for a single asymmetric unit consisting of bonded residues. This is known as the crystal chemical unit which is used as a reference for non-bonded searches. The CSD also stores the symmetry operators that are required to generate the extended crystal structure from these reference coordinates.

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Volume 1 Chapter 7 Searching for Specific Contact Types.