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

Function

GROUP is used to define a set of atoms for use 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

If a set of atoms consists of a group of atoms then the set must be defined using the GROUP command before the NON-BONDED CONTACT is defined.
The atoms of a GROUP are required to be in the same fragment of the search query.
A specific atom can be a member of more than one GROUP.
GROUP can only be used in a non-bonded contact search and in no other geometrical test or calculation.
A maximum of 20 GROUPs may be defined.
The maximum number of atoms in a GROUP is 25.
The maximum number of atoms from all GROUPs must not exceed 250.

Ex.1 Suppose we wish to find intermolecular contacts between the carbon, hydrogen atoms of a phenyl group and the oxygen atom of a ketone. In this example we will use the standard van der Waals radii so that hits will be registered for C...O < 4.42Å and H...O < 3.72Å.

Select GROUP

Select or type items for GROUP. If necessary reselect GROUP to end
input.
Select CANCEL to cancel command.

Select in turn atoms 7 6 5 8 4 9 3 10 11 2
Select GROUP
On the diagram the group, labelled G1, is now indicated by blue lines drawn from each atom in the group to the centroid of the group.
In the summary area we now have:
```
G1   7  6  5  8  4  9  3  10  11  2
```
This line is displayed in blue to indicate that it is a NON-BONDED command.
In the dialogue area we now have the "home" prompt:
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
Select CONTACT

In the dialogue area we now have:

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

Select G1 and atom 15

In the dialogue area we now have:

Should contacts to FIRST group be calculated for each ATOM or for the CENTROID?
Type A or C  [A]

Type A <RETURN>

In the dialogue area we now have:

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>

In the dialogue area we now have:

At least one of your contact sets is centroid-based, so you MUST specify
the minimum and maximum distances for which a contact will be registered.
Please enter the MIN. and MAX. distances, separated by spaces or commas.

Press <RETURN>
On the diagram a blue line is now drawn between G1 and atom 15.
In the summary area we now have the line:
```
INTER  G1  A  15  A
```
This line is displayed in blue to indicate that it is a non-bonded command.
In this line G1 A 15 A indicates that G1 is represented by its constituent atoms and 15 is an atom.
In the dialogue area we now have the "home" prompt:
```
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  G1  A  15  A
```

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

H8 is linked by a dotted blue line to O1%.

If you use MEASURE DIST the contact distance is displayed as 2.598Å.

Ex.2 Suppose we wish to find all intramolecular contacts in the range 1.9-2.9Å between the centroid of a benzene ring and the hydrogen atom of an NH group.

Select GROUP

Select or type items for GROUP. If necessary reselect GROUP to end
input.
Select CANCEL to cancel command.

Select in turn atoms 1 2 3 4 5 6
Select GROUP
On the diagram the group is now indicated by blue lines drawn from each atom in the group to the centroid of the group, which is labelled G1.
In the summary area we now have:
```
G1   1  2  3  4  5  6
```
This line is displayed in blue to indicate that it is a NON-BONDED command.
In the dialogue area we now have the "home" prompt:
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
Select CONTACT

In the dialogue area we now have:

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

Select G1 and atom 8

In the dialogue area we now have:

Should contacts to FIRST group be calculated for each ATOM or for the CENTROID?
Type A or C  [A]

Type C <RETURN>

In the dialogue area we now have:

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>

In the dialogue area we now have:

At least one of your contact sets is centroid-based, so you MUST specify
the minimum and maximum distances for which a contact will be registered.
Please enter the MIN. and MAX. distances, separated by spaces or commas.

Type 1.9 2.9 <RETURN>
On the diagram a blue line is now drawn between the centroid G1 and atom 8.
In the summary area we now have the line:
```
INTRA  4  999  G1  C  8  A  1.9  2.9
```
This line is displayed in blue to indicate that it is a non-bonded command.
In the dialogue area we now have the "home" prompt:
```
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 INTRA  4  999  G1  C  8  A  1.9  2.9 
```
In this command G1 C 8 A indicates that G1 is represented by its centroid and 8 is an atom.

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

H41, attached to N5, is linked by a dotted blue line to the centroid of a benzene ring.

In this case you cannot use MEASURE DIST to display the actual value of the non-bonded contact distance since a GROUP centroid is involved. To do this you would have to also SETUP CENTROID in the 3D-CONSTRAIN sub-menu.

Ex.3 This example has been chosen to illustrate the use of multiple CONTACT commands in a single search.

Consider the search query represented by 4 fragments:

Suppose we wish to find the following non-bonded contacts:

(i): intramolecular contact between the centroid of the benzene ring and the sulfur atom
(ii): intermolecular contact between the centroid of the benzene ring and the carbonyl oxygen atom
(iii): intermolecular contact between the carbonyl oxygen atom and the hydrogen of the NH group
(iv): intramolecular contact between the nitrogen of the NH group and the sulfur atom.

Using the standard dialogues, the following commands are constructed:

SETUP X1 1 2 3 4 5 6
Since the centroid of the benzene ring is defined by SETUP we can use MEASURE DIST to display distances involving the centroid in hits.
GROUP G1 1 2 3 4 5 6
This defines the six atoms of the benzene ring as group G1.
CONTACT INTRA 5 8 G1 C 11 A 2.0 10.0
This command deals with contact (i).
Minimum and maximum bonds in shortest path are 5 and 8.
The contact distance lies in the range 2.0 - 10.0Å
CONTACT INTER G1 C 8 A 0.0 5.0
This command deals with contact (ii).
The contact distance lies in the range 0.0 - 5.0Å
CONTACT INTER 8 A 10 A
This command deals with contact (iii).
The contact distance is less than 3.72Å, using the standard van der Waals radii and tolerance limit
CONTACT INTRA 1 999 9 A 11 A 0.0 999.9
This command deals with contact (iv).
Minimum and maximum bonds in shortest path are 1 and 999.
The contact distance lies in the range 0.0 - 999.9Å

A search which satisfies all four CONTACT commands will hit, for example, the structure shown below.

The four contact distances are:

X1...S1   7.524Å  X1...O14% 4.591Å
O14%...H7 1.690Å  N7...S1   4.762Å

Related Commands

CONTACT, VDW-RAD

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Volume 2 Chapter 3 3D-Constrain Sub-menu VDW-RAD .