[ New | Right Click Options | Chemical groups | Adding fragment | Property Monitor | Key chemical | Save/Append | Edit | Selections | Copy/Cut/Paste | SMILES | Undo/Redo | Isis ]

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

15.3.1 Drawing a New Chemical Structure

To draw a new chemical structure the ICM Molecular Editor should be loaded.

To do this:

• Select Chemistry/Molecular Editor

Now you can start drawing your structure.

• First select one of the appropriate buttons on the left hand side of the molecular editor.
• Then click in the white Molecular Editor Workspace and your element, ring or bond will be displayed.

• You can extend your structure by selecting another button from the left hand-side as before.
• Select where on the structure you would like to add the new group by hovering the mouse over the desired position. The position you will add to will be highlighted in a red box.

To change the direction of a bond:

• Right click on the bond and a menu as shown below will be displayed.
• Select which bond direction you desire from up, down or either.

Carry on drawing until your structure is complete! See the other sections in this chapter.

1. To save your structure read the save and append chemical structure section.
2. To append your structure to an existing SDF file read the save and append chemical structure section.
3. To save your structure to an ICM table read the save and append chemical structure section.
4. To edit your structure read the edit your structure section.

15.3.2 Right Click Options

There are a number of different options available when you right click on a bond or atom. These options are described in detail in the Chemical Searching part of the manual.

15.3.3 A dictionary of chemical groups.

The ICM Chemical Editor has a dictionary of chemical groups. These groups are stored in a table stored in CHEM_GROUPS.csv file. This file can be manually edited to remove or add new definitions. The group can be selected using the Grp button of the Editor.

15.3.4 Adding and rotating a fragment in molecular editor by clicking-holding-and-dragging.

The Chemical Editor allows one to add bonds (click the bond button), or chemical groups (the Grp button), Often one needs to re-orient the added bond or fragment. In this case press on the atom to which you are going to append the bond or the fragment and hold-and-drag the mouse it until you see added fragment rotating around the attachment point. While you keep the mouse button pressed you can rotate by dragging in the preferred direction.

If you add templates (the Templates menu, or paste fragments, the mechanism is somewhat different because the group is added in its default orientation. In this case you can press Ctrl to rotate the fragment to to be able to attach the fragment in the desired orientation.

15.3.5 Property Monitor

When drawing a compound in ICM you can monitor important ADME-Tox and drug-likeness properties.

To view the drug-likeness monitor

• ICM Molecular Editor/View/Chemical Monitor and a window as shown below will be displayed.

The following properties are monitored.

• Molecular Weight (MolWeight)
• Number of Hydrogen Bond Acceptors (HBA)
• Number of Hydrogen Bond Donators (HBD)
• Number of Rotatable Bonds (RotB)
• DrugLikeness value Druglikeness is not based on other properties, this is separate model built using Bayesian Classifier. http://www.molsoft.com/mpropdesc.html - Normaly Bayesian classifier returns either 1 ot -1 (positive ot negative) So, roughly speaking: positive values means drug-like, negative - not.
• Preidction model build for 'delta Hf in gas' property. using public NIST database. Description can be found: http://webbook.nist.gov A low dHf value means that the compound is more 'stable'.
• LogP
• LogS
• Polar Surface Area (PSA)
• Volume
• Formula
• Smiles String
• Bad ADME-Tox Groups

The rows in the monitor window are colored from green (good) to red (poor) ADME-Tox properties.

15.3.6 Editing structure using keyboard

You can select a fragment or simply position your mouse cursor over a bond or atom and use the following keystrokes for editing:

• Changing atom properties
• d set/unset heavy atom connectivity as drawn to avoid additional branches in chemical searches. Toggle.
• r set/unset the "in-ring" property of atoms. Toggle.
• y set/unset atom hybridization type ( sp1,sp2,sp3 ). Toggle.
• A set atomic property to be aliphatic
• a set atomic property to be aromatic
• * (asterisk) set atomic property to be any atom
• C Carbon
• H Hydrogen
• N Nitrogen
• O Oxygen
• F Fluorine
• P Phosphorus
• S Sulfur
• I Iodine
• Changing chemical bonds
• 1,- (dash) single bond.
• 2,= (equal) double bond.
• 3,# (hash) triple bond.
• 4,: (column) aromatic bond.
• 0,~ (tilde) any bond
• Changing R-Groups
• Press 1 to mark an atom as R1
• Press Ctrl-1 to preserve its type and create [C;R1]
• Press Ctrl-0 to remove the mark.

15.3.7 Save and Append Chemical Structures

Once you have drawn a chemical structure (see Drawing a New Chemical Structure) then you can save the structure in the following ways:

1. By saving the structure as a MOL file or SDF file on your machine or server.
2. Appending the structure to an already created SDF file.
3. Appending the structure to an ICM Molecular table.

To save the structure as a MOL or SDF file on your machine or server.

• In the Molecular Editor window select File/Save
• Enter a filename and select where you wish to save the file.

NOTE: Other save options can be found on the ICM Molecular Editor Toolbar.

To append the structure to an already created sdf file.

• In the Molecular Editor window select File/Append to SD file...
• Search for the SDF file you wish to append to and select OK. This SDF file can be read into ICM as described in Read Chemical Structure section of this manual.

To append your structure to an ICM table:

• In the Molecular Editor window select File/Append to table
• A list of loaded ICM tables will be displayed as shown below. If you dont have any ICM table loaded or you wish to add the structure to a new table select the "new" option.
• The structure will be automatically added to an ICM table and displayed in the GUI.

OR

• Click click on the append to table button in the editor (see below).

NOTE: For more information on how to manipulate standard ICM Tables and Molecular Tables see the Table section of this manual.

15.3.8 Editing a Chemical Structure

If you make a mistake whilst drawing a chemical structure or if you wish to change an already saved and loaded structure there are a number of editing tools and techniques which can be used.

To edit a structure which is in a loaded ICM molecular table:

• Right click on the structure in the table and a menu as shown below will be displayed.

• Select the Edit Mode and a black square will be displayed around the chemical you wish to edit.
• Double click on the structure and the ICM Molecular Editor will be activated.

To edit a bond or atom in the structure:

• First select the new bond, atom or ring from the buttons on the left of the ICM Molecular Editor.

• Hover over the element or bond you wish to change in the ICM Molecular Editor workspace. A red square will be displayed over the bond or element you select as shown below.

• Click on the bond or element and it will automatically change to your selection.

To delete parts of a structure:

• Select the eraser button on the ICM Molecular Editor Toolbar.

• Click on the regions you wish to delete.

Alternatively you can select the delete option in the ICM Molecular Editor "Edit" menu.

NOTE: A quick image can be constructed using the camera button A quick image can be constructed using the camera button as described in the TIPS section of this manual .

15.3.9 Molecular Editor Selections

Selections can be made in the ICM Molecular Editor using the two buttons shown below.

Selections are displayed in green.

15.3.10 Copy, Cut and Paste

To copy, cut and paste part or all of your structure.

• First select the parts you wish to copy or cut by reading the instructions in the Molecular Editor Selections section of this manual.
• Select copy or cut from the ICM Molecular Editor "Edit" menu.
• The selected regions will then be placed on the copy clipboard and can be pasted into the ICM Molecular Editor or any other program.

The copy and paste buttons and menus are shown below:

To copy your structure as a smiles string:

C1C=CC=C(C=1C(C)=O)CC(CC=C1)=C1

• Select the "Copy as SMILES" option in the ICM Molecular Editor "Edit" menu.

This will place the SMILES string on the clipboard which can then be pasted into any application.

15.3.11 How to use SMILES strings to sketch a chemical.

15.3.12 Undo and Redo

The undo and redo options for the ICM Molecular Editor are located in the Edit menu and on the toolbar as shown below.

15.3.13 Isis Draw Copy and Paste

Molecules drawn in ICM can be cut and pasted into ISIS-Draw and vice-versa molecules from ISIS-Draw can be cut and pasted into ICM.

To perform these functions the correct settings need to be turned on in ISIS-Draw so that the compound drawing is saved in the clipboard.

IN ISIS-DRAW - Go to Options/Settings/General/Copy Mol Rxn file to the clipboard.

Compounds drawn in ISIS Draw can be cut and pasted into the ICM Molecular Editor and into ICM tables. Compounds can be copied in ICM by:

• Right click on the compound in the chemical table and select Copy Molecule.