Volume 2 Chapter 3 3D-Constrain Sub-menu GROUP

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VDW-RAD

Function

VDW-RAD is used to modify the standard van der Waals radii and/or tolerance limit used in a non-bonded contact search.

Full details of non-bonded contact searching are given in chapter 7 of Vol.1 and users must read that chapter before attempting to formulate such a search.

Remarks

The distance criterion for a non-bonded contact, in terms of van der Waals radii, is as follows:

Suppose that:

The two atoms are considered to be in contact if: The default van der Waals radii are taken from A. Bondi (1964) "van der Waals Volumes and Radii "J.Phys.Chem. 68, 441-451. These values are shown in the table below (all values in Å).

Ag    1.72       Ar    1.88       As     1.85       Au     1.66
Br    1.85       C     1.70       Cd     1.58       Cl     1.75
Cu    1.40       F     1.47       Ga     1.87       H      1.20
He    1.40       Hg    1.55       I      1.98       In     1.93
K     2.75       Kr    2.02       Li     1.82       Mg     1.73
N     1.55       Na    2.27       Ne     1.54       Ni     1.63
O     1.52       P     1.80       Pb     2.02       Pd     1.63
Pt    1.72       S     1.80       Se     1.90       Si     2.10
Sn    2.17       Te    2.06       Tl     1.96       U      1.86
Xe    2.16       Zn    1.39
If an element does not appear in the table it is assigned a value of 2.0Å.

If the vander Waals radii and/or tolerance are to be changed from the standard values then the VDW-RAD command must be used before the CONTACT command is defined.

Suppose a fragment is AB==C where AB is defined by ELDEF as O or S or Se.

It is permissible, for example, to change the value of the van der Waals radius for S by a command VDW S 1.9.

However, it is not permissible to compose a command of the type VDW AB 1.9.

Ex.1 Suppose we wish to find all intermolecular contacts less than 3.9Å between a keto-oxygen atom and the hydrogen atom of a secondary amine.

The standard van der Waals radii for O and H are 1.52 and 1.20Å resp., allowing a non-bonded contact distance of 3.72Å. We will raise the van der Waals radius of O to 1.70Å to find the required contacts.

An example of a hit registered by this search is shown below.

Ex.2 Suppose we wish to find all intramolecular contacts less than 3.05Å between a carbonyl oxygen atom and the hydrogen atom of an NH group in peptide structures.

The standard van der Waals radii for O and H are 1.52 and 1.20Å resp., allowing a non-bonded contact distance of 3.72Å. We will lower the tolerance limit to 0.33Å to find the required contacts.

We will also require that the minimum path length be set to a value of 5.

An example of a hit registered by this search is below.

Three contacts have been established, viz. O3...H5, O3...H6, O6...H3.

If we repeat the calculation using 4 999 for the min. and. max. number of bonds then five contacts are established, viz. the above three plus O3...H3 and O6...H6.

If we repeat the calculation using 1 999 for the min. and. max. number of bonds then nine contacts

are established, viz. the above five plus O6...H1, O5...H6, O1...H2 and O2...H3.

Ex.3 Consider the fragment below, where RR is either nitrogen or oxygen.

Suppose we wish to find all intramolecular contacts H...N < 2.75Å and H...O < 2.72Å.

An example of a hit registered by this search is shown below.

Six contacts have been established as follows:

H2...N1 2.532Å  H3...O6 2.289Å  H3...N2 2.473Å
H5...N4 2.291Å  H6...N5 2.323Å  H6...O3 2.111Å

Related Commands

CONTACT, GROUP

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Volume 2 Chapter 3 3D-Constrain Sub-menu NUMBERS.