Volume 1 Chapter 7 Display of Hits from Non-Bonded Searches

Located non-bonded contacts are represented by dotted lines in the 3D displays as shown in the example below taken from a search for hydrogen bonds. In colour displays the dotted line is pale blue, the same colour used for non-bonded commands in the 3D-CONSTRAIN sub-menu. One line is generated for each CONTACT command.

When single atoms are used in the CONTACT command the atoms themselves are used as the endpoints of the contact line. If a GROUP is used in a CONTACT, the endpoint is determined by the search method applied to the GROUP. For centroid representations, the endpoint will be the centroid of the atoms of the GROUP. Note that this centroid cannot be selected with any of the MEASURE commands unless it is also declared with a SETUP command (see following section). The endpoint for GROUPs searched atom-by-atom will be the atom which is the shortest distance from the other search set of the CONTACT command.

For intramolecular contacts each dotted line will be within one of the molecule(s) of the crystal chemical unit. However, for intermolecular contacts it is sometimes necessary to add "extra" atoms to the 3D display in order to represent the nonbonded contact. These extra atoms are generated from the crystal chemical unit molecule(s) by symmetry operations and lattice translations. They may appear as small "floating" fragments at the end of a contact line. The labels of these atoms have % appended to indicate they are symmetry-generated for the non-bonded search. These atoms can be used with any of the MEASURE commands.

The first atom or GROUP of the first CONTACT command in a query will always be in the asymmetric unit molecule(s). From this starting point atoms are added as needed to build up the 3D display as each CONTACT command is processed. When a symmetry-generated atom is required the entire substructural fragment of which it is a part is also generated and added to the display.

The 3D display below shows the results of a search for intermolecular hydrogen bonds

The following contact required no addition of atoms since it occurs between molecules of the crystal chemical unit:

     N17-H172...O1   2.217 Å

However, atoms had to be added for these contacts:

     N1-H1...O3%     2.656 Å
     N1-H1...O3%     1.949 Å
     N17-H171...N3%  2.337 Å
     N18-H181...O1%  1.976 Å
     N18-H182...O3%  2.641 Å
     N18-H182...O2%  2.480 Å

Note that only the single acceptor atom was added to the display since the donor group was the first set of the CONTACT command. The PACK commands were used to generate the display below showing the entire molecules that participate in hydrogen bonding (see Volume 2 for a description of the PACK commands). Note that the O3 atom from two separate molecules participates in hydrogen bonding.

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Volume 1 Chapter 7 Geometric Surveys of Non-Bonded Fragments .

7.14.6 Display of Hits from Non-Bonded Searches