[ Enumerate Markush ]

To enumerate a library based on R-groups you first need to draw a sketch of the structure and display it in a chemical spreadsheet. To do this:

• Open up the ICM Molecular Editor.
• Draw the template structure with R-groups attached. Right click on an atom and select Element/R1, R2 ...

• In the Molecular Editor select File/Append to Table/New

The next step is to read into ICM or construct a table of substituents. You can read in an SDF, mol, smiles file or extract fragments. If you do not want the first atom of the substituents to be the attachment point you need to define the attachment point. Attachment points are automatically assigned when you extract fragments or you can define them manually by:

• Right click on the substituent sketch and select Edit Molecule
• Right click on the atom and select Attachment point.

Next enumerate the library

• Select the template structure (highlighted blue).
• Right click on the structure and select Chemistry/Enumerate R-groups or use the Chemistry menu and select Enumerate by Markush. If you use the menu option you will need to choose the table containing the scaffold from the drop down list of currently loaded tables. The index number refers to the row number in the scaffold table. In this example we only have one row containing the scaffold so the index number is 1.
• Select the R1, R2... table , labels and filters if necesary.

A new table will be produced called T_enum with the Template structure highlighted in red.

16.21.1 How to enumerate a Markush library.