Volume 2 Chapter 1 Build menu LIGAND

Function

LIGAND is used as a short-cut in generating multiple occurrences of a ligand.

Its most common application is in the generation of metal complex search fragments.

Example

Suppose we wish to search for structures containing (i) - see below.

We can reformulate (i) as (ii) where the acetamide ligand skeleton, is enclosed within square brackets. The ligand has a multiplier value of 2.

We might proceed as follows:

Select LIGAND

Please use the cursor to select the left -most point in your
ligand or repeat.

Select point a

Please use the cursor to select the right-most point in your
ligand or repeat.

Select point b mid-way between N and Cd

Please use the cursor to select the upper point in your ligand or
repeat.

Select point c

Please use the cursor to select the lower point in your ligand or
repeat.

Select point d below the O
A white + appears at the four points as you select them.
```
Please type the multiplier
```
Type 2 <R>

The fragment is now as in (iv).

The above example illustrates the use of LIGAND for a monodentate ligand.

It can also be used for polydentate ligands e.g. (vi).

The correct order of point selection is as shown in (v). Care should be taken if the fragment is rather complicated, involving ligands and non-ligand moieties. Judicious use of the four-point selection system, however, should allow you to select the parts of the fragment to be contained in the ligand.

If you get the points in the wrong order, the program sounds an alert and produces the error message:

ERROR - Points in wrong order. Operation cancelled.

The maximum number of different ligands allowed in one structure is 9. If you try to add ligands outside these limits, the program will sound an alert and produce an error message.

To edit and delete ligands see EDIT-LIG and DEL-LIG in the EDIT menu (chapter 5).

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