Volume 1 Chapter 7 Searching with Functional Groups

All of the contacts encountered up to now have been between single atoms. Sometimes we are interested in how a substructural fragment interacts with another as a whole. The non-bonded search mechanism allows groups of atoms to be defined for use with the CONTACT command. The command is called GROUP.

Ex.8 Suppose we wish to find intermolecular contacts between the carbon or 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 < 4.22Å 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:

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 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.

Obviously, the GROUP command must precede the CONTACT in which it will be used since the GROUP label is given in the CONTACT command to identify a set of atoms. The atoms contained in a GROUP must all be from the same substructural fragment. However, an atom may belong to more than one group. It should also be noted that GROUPs can not be used for other geometrical calculations, they relate only to the non-bonded search process (see Volume 2 for SETUP of centroids and other geometric objects).

The inclusion of a GROUP in the CONTACT command generates a question not seen in previous examples. The question prompts the user to indicate how the atoms of the GROUP are to be used in the non-bonded search. One choice is to use the atoms to define a centroid which will be used for the distance test. Obviously, a distance range must be supplied to CONTACT when centroids are used since no van der Waals radii are available for centroids. Alternatively, each atom can be used in turn, atom by atom, for the distance testing. In atom by atom testing, the use of van der Waals distance testing can be very powerful. The table below illustrates the various search options.

Table : Search Options for GROUPs

Consider the interaction between an aromatic ring and the hydrogen atoms of an amino group. The four sets of contacts are illustrated below:

(i) A : A

(ii) C : A

(iii) A : C

(iv) C : C

(i)
- Set 1 consists of the 6 atoms of the aromatic ring.
- Set 2 consists of the 2 H atoms of the amino group.
  The search process involves the calculation of the distance between each atom of set 1 and each atom of set 2, ie. 12 distances must be calculated. If any one of these distances satisfies the specified distance criterion then a non-bonded contact is declared and a hit is registered.
(ii)
- Set 1 consists of the centroid of the 6 atoms of the aromatic ring.
- Set 2 consists of the 2 H atoms.
  In this case 2 distances must be tested for a non-bonded contact.
(iii)
- Set 1 consists of the 6 atoms of the aromatic ring.
- Set 2 consists of the centroid of the 2 H atoms.
  In this case 6 distances must be tested for a non-bonded contact.
(iv)
- Set 1 consists of the centroid of the 6 atoms of the aromatic ring.
- Set 2 consists of the centroid of the 2 H atoms.
  In this case 1 distance must be tested for a non-bonded contact.

When the search mechanism locates an intramolecular contact the shortest bond path range test must be applied. If a GROUP is used in the CONTACT command the test is applied to only one atom - the atom that is the shortest bond path from the other search set in the CONTACT. Therefore, only the shortest path between the two sets of the CONTACT is used for the range test.

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Volume 1 Chapter 7 Searches Involving Multiple Contacts .

7.14.4 Searching with Functional Groups