Volume 2 Chapter 3 3D-Constrain Sub-menu 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 distance between two non-bonded atoms i and j is dij
the van der Waals radii for atoms are ri and rj

The two atoms are considered to be in contact if:

dij < ri + rj +t
where t is a tolerance limit, set by default to 1.0Å

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.

Select VDW-RAD

Please type an element symbol and radius, or press
<RETURN>

Type O 1.70 <RETURN>

Please type an element symbol and radius, or press
<RETURN>

Press <RETURN>

If you want to change the TOLERANCE value, type a number and
press <RETURN>
Otherwise just press <RETURN> [No change]

Press <RETURN>
Select CONTACT

Select or type atoms for CONTACT. If necessary reselect CONTACT
to end input.
Select CANCEL to cancel command.

Select atom 4 and then atom 6

Type 1,2, or 3 to indicate type of contact:
          1 = INTRA-molecular contacts   2 = INTER-molecular contacts
          3 = ANY (ie, either INTRA or INTER-molecular contacts)  [Default = 3]

Type 2 <RETURN>

By default, a Van der Waals distance search will be used for this CONTACT.
To over-ride it with a minimum and maximum distance, enter the MIN. and MAX.
distances, separated by spaces or commas. Otherwise, press
<RETURN>.

Press <RETURN>
On the diagram a blue line is drawn between atoms 4 and 6.
In the summary area we now have the line:
```
INTER 4 A 6 A
```
This line is displayed in blue to indicate that it is a non-bonded command.
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
The resultant command in the instruction document is:
```
CONTACT INTER 4 A 6 A
```

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.

Select VDW-RAD

Please type an element symbol and radius, or press
<RETURN>

Press <RETURN>

If you want to change the TOLERANCE value, type a number and
press <RETURN>
Otherwise just press <RETURN> [No change]

Type 0.33 <RETURN>
```
 
```

In the summary area we now have the line:  
TOL 0.33

Select CONTACT

Select or type atoms for CONTACT. If necessary reselect CONTACT
to end input.
Select CANCEL to cancel command.

Select atom 2 and then atom 4

Type 1,2, or 3 to indicate type of contact:
          1 = INTRA-molecular contacts   2 = INTER-molecular contacts
          3 = ANY (ie, either INTRA or INTER-molecular contacts)  [Default = 3]

Type 1 <RETURN>

For "INTRA" and "ANY" searches, you must specify the minimum and maximum number
of bonds allowed in the shortest path between INTRAMOLECULAR contact atoms.
Enter MIN. and MAX. numbers of bonds, separated by spaces or commas [4  999]

Type 5 999 <RETURN>

By default, a Van der Waals distance search will be used for this CONTACT.
To over-ride it with a minimum and maximum distance, enter the MIN. and MAX.
distances, separated by spaces or commas. Otherwise, press
<RETURN>.

Press <RETURN>
On the diagram a blue line is drawn between atoms 2 and 4.
In the summary area we now have the line:
```
INTRA  5  999  2  A  4  A
```
This line is displayed in blue to indicate that it is a non-bonded command.

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.

In constructing the search fragments we use: ELDEF RR = N O

Select VDW-RAD

Please type an element symbol and radius, or press
<RETURN>

Press <RETURN>

If you want to change the TOLERANCE value, type a number and
press <RETURN>
Otherwise just press <RETURN> [No change]

Type 0.0 <RETURN>
```
 
```

In the summary area we now have the line:  
TOL 0.0

Select CONTACT

Select or type atoms for CONTACT. If necessary reselect CONTACT
to end input.
Select CANCEL to cancel command.

Select atom 2 and then atom 3

Type 1,2, or 3 to indicate type of contact:
          1 = INTRA-molecular contacts   2 = INTER-molecular contacts
          3 = ANY (ie, either INTRA or INTER-molecular contacts)  [Default = 3]

Type 1 <RETURN>

For "INTRA" and "ANY" searches, you must specify the minimum and maximum number
of bonds allowed in the shortest path between INTRAMOLECULAR contact atoms.
Enter MIN. and MAX. numbers of bonds, separated by spaces or commas [4  999]

Press <RETURN>

By default, a Van der Waals distance search will be used for this CONTACT.
To over-ride it with a minimum and maximum distance, enter the MIN. and MAX.
distances, separated by spaces or commas. Otherwise, press
<RETURN>.

Press <RETURN>
On the diagram a blue line is drawn between atoms 2 and 4.
In the summary area we now have the line:
```
INTRA  4  999  2  A  3  A
```
This line is displayed in blue to indicate that it is a non-bonded command.

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 .