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. 2.4, p. 48

Section 2.4.7. Structural templates

F. H. Allen,a* J. M. Barnard,b A. P. F. Cookb and S. R. Hallc

aCambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, England,bBCI Ltd, 46 Uppergate Road, Stannington, Sheffield S6 6BX, England, and cSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia
Correspondence e-mail:  allen@ccdc.cam.ac.uk

2.4.7. Structural templates

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In many chemical information systems, it is standard practice to build complete 2D molecular representations through the use of a library of commonly referenced structural templates, e.g. ligands, functional groups, amino-acid units etc.

In a MIF, molecular templates can be encapsulated as save frames, either within a data block for a specific molecule, or within a global block that is accessible to many data blocks. A simple application of a MIF template is shown in Fig. 2.4.7.1[link], where a 4-methylcyclohexyl ligand is used to encode the molecule tris(methylcyclohexyl)phosphine. In this example a molecular fragment is constructed in the save frame mechex, where the `atom' sites and `bond' connections appear in _atom_* and _bond_* loops. The molecule (2-methylcyclohexyl)(3-methyl­cyclohexyl)(4-methylcyclohexyl)phosphine is encoded by referencing the template fragment as the save frame $mechex. In the `atom' loop, the item _atom_environment identifies the components of the target molecule as an `atom' or `frag' (fragment). If the component is a fragment, the items _atom_frag_key and _atom_frag_id are used to specify the frame code and the ID of the attached atom in the fragment, respectively. In the `bond' loop, the connections from the atom P(1) to the template are encoded simply in terms of the _atom_id values. The necessary redefinition of the hydrogen and non-hydrogen counts of the template atoms is accomplished using the _atom_attach_h and _atom_attach_nh items, respectively. The external values override any values that are contained in, or derived from, the data in the template.

[Figure 2.4.7.1]

Figure 2.4.7.1 | top | pdf |

MIF representation of (2-methylcyclohexyl)(3-methylcyclohexyl)(4-methylcyclohexyl)phosphine using a single global save frame that encapsulates the structure of methylcyclohexane, together with `external' referencing of save-frame atoms in _atom_ and _bond_ loops.

The same approach is used to construct the dipeptide alanyl­serine in Fig. 2.4.7.2[link]. This employs the template peptide units described by the atoms and bonds in the save frames $alanyl and $seryl. The complete dipeptide is specified in its `atom' list as the template peptides (identified by their save-frame names) and an additional carboxylate O atom. Note that only the atom sites affected by molecule formation are identified explicitly in this list, which gives the values of _atom_attach_nh, _atom_attach_h and _atom_charge for the modified sites in the zwitterionic form of alanylserine.

[Figure 2.4.7.2]

Figure 2.4.7.2 | top | pdf |

MIF representation of the dipeptide alanylserine constructed using alanyl and seryl templates encapsulated in global save frames.








































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