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

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7.14.7 Geometrical Surveys of Non-Bonded Fragments

A complete set of subfragments, linked together by non-bonded contacts, once located, can be treated in the same way as a bonded fragment. Thus, we may use the 3D-CONSTRAIN sub-menu to SETUP geometric objects, DEFINE and name geometrical parameters, TRANSFORM those parameters, and SELECT some subset of hits on the basis of geometrical parameter values.

The calculation of such geometric data is common in the systematic study of hydrogen bond interactions.

Ex. 11 We extend the study of amino-thiocarbonyl hydrogen bonding begun in Ex. 7 of section 7.14.3 to:

The setup of the search in the 3D-CONSTRAIN sub-menu and an example hit, and the summary statistics of all hits are given are shown below.

NFRAG   REFCOD     HBOND    HANG   THETA     PHI
     1  ABHYTZ     2.480 164.762 -20.906-106.093
     2  ACRTUR     2.589 157.488  32.379 106.570
     3  ACRTUR     2.561 170.452  -7.296-105.989
     4  ACTCBZ     2.931 137.567  46.311 121.393
   685  XANHYD     2.112 160.436  17.513 101.275
   686  XANHYD01   2.138 160.395 -18.660 100.561
   687  ZNDITZ02   2.856 124.215  34.757-151.824
   688  ZZZEII01   2.890 157.984 -54.200 160.643
   689  ZZZGEO01   2.546 169.119  -6.861-109.372
   690  ZZZMJK02   2.634 155.342 -17.372 108.877
   691  ZZZQMK10   2.520 140.496 -71.513 132.202
        Nobs         691     691     691     691
        Mean       2.604 156.226  -2.651  -5.224
        SDSample   0.176  14.416  38.270 111.815
        SDMean     0.007   0.548   1.456   4.254
        Minimum    2.058 120.578 -85.672-179.076
        Maximum    2.997 179.169  85.205 179.849

7.14.8 Efficiency of Non-Bonded Searches

It is obvious that the intermolecular non-bonded search mechanism is highly cpu-intensive, since it can involve the testing of an appreciable number of symmetry/translational variants of atomic positions. Even though the symmetry/translation search routine employs upper-bound tests and is as efficient as possible, the intermolecular searches are likely to take much longer than any comparable intramolecular search.

In the present database and software release, no 3D screening system exists to speed these intermolecular searches. The only screening procedures employed relate to the 2D chemical structures of the subfragments that make up the complete non-bonded search query. This lack of 3D intermolecular distance screens is currently being remedied.

For the present, several factors should be considered when composing non-bonded searches:

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Volume 1 Chapter 7 Further Examples of Non-Bonded Searches.