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A quick start guide on how to work with small molecules and ICM Molecular Tables.

2.17.1 Constructing a new chemical

Draw new compounds by using the ICM Molecular Editor.

The molecular editor can be activated by:

• Clicking on the Open ICM Molecular Editor button shown below.

OR

• Select Tools/Chemistry/Molecular Editor and the editor as shown below will be displayed.

2.17.2 Using a SMILES string to generate a molecule

• Open the ICM Molecular Editor
• Select Edit in the ICM Molecular Editor
• Select Add Smiles and enter the string.

2.17.3 Loading small molecules into ICM

To load a small molecule into ICM:

• File/Open
• Small molecule files generally have the file type .mol, .mol2 or sdf
• Depending on the file type the chemical will either be loaded into an ICM Molecular Table or in the ICM Workspace.

2.17.4 Extracting a ligand from a PDB file into an ICM Molecular Table

• As an example we will use the PDB structure 1STP. Type 1STP in the pdb search tab and press return.
• Right click on the ligand (btn) in the ICM Workspace and select "Extract Ligand"
• You can choose whether to keep the 3D coordinates or just 2D
• The ligand is then extracted into an ICM Molecular Table.

2.17.5 Converting a chemical in an ICM Molecular Table into 3D

To do this:

• Select the chemical or chemicals in the ICM Molecular Table you wish to convert to 3D. You can do this by clicking on the row number whilst keeping the CTRL key pressed down.
• Right click on the chemical table and select Chemistry/Convert 2D to 3D
• The converted chemical will then become an object in the ICM Workspace.

2.17.6 Adding properties to a molecular table

To read a chemical table into ICM:

• File/Open and look for sdf files.

To add a chemical property to the table.

• Right click on the 'mol' column header and select Insert Column...

• Click on the drop down 'Function' button and select chemical.
• Select which property you wouls like to add and click OK.
• The property you selected will be displayed in the table.

2.17.7 Editing a molecule in an ICM molecular table

To edit a molecule in an ICM molecular table:

• Right click on the chemical sketch in the ICM Molecular Table.
• Select Edit Molecule ....
• The ICM Molecular Editor will be displayed.
• Edit the molecule and then select File/Save and Quit inside the ICM Molecular Editor window. Changes will then be added to the sketch in the table.

2.17.8 Editing a ligand in a 3D structure.

To edit a ligand in a 3D structure:

• As an example we will use the PDB structure 1STP. Type 1STP in the pdb search tab and press return.
• Right click on the ligand (btn) in the ICM Workspace and select "Edit Compound"
• The ICM Molecular Editor will be displayed.
• Edit the molecule and then select File/Save and Quit inside the ICM Molecular Editor window.

2.17.9 Make Tautomers

To generate the tautomeric structures of a chemical in an ICM Molecular Table.

• Right click on the chemical sketch in the ICM Molecular Table. More than one compound can be selected (see section on Table Selections).
• Select Chemistry/Enumerate Tautomers
• A new table will be generated.

2.17.10 Generate Stereoisomers

To generate the stereoisomers of a chemical in an ICM Molecular Table.

• Right click on the chemical sketch in the ICM Molecular Table. More than one compound can be selected (see section on Table Selections).
• Select Chemistry/Enumerate Stereoisomers
• A new table will be generated.

2.17.11 Saving an ICM molecular table as an SDF file

To save an ICM Molecular Table as an SDF file

• Right click on the table header and select "Save As.."

2.17.12 Chemical Clustering

To cluster a set of compounds in a an ICM Molecular Table:

• Select the rows of the table you wish to cluster. If you wish to cluster all the chemicals in the table there is no need to make any selection.
• Right click and select Clustering...

NOTE: More information regarding clustering can be found in the Tables section of the GUI manual.

2.17.13 3D Chemical Browsing

If you have an ICM molecular table (Chemical Spreadsheet) displayed you can browse the compounds in the graphical display by right clicking on the "mol" column header and select Set 3D Browse Mode.

See: Set Chemical Table 3D Browse Mode