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Contents
 
Introduction
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
 Read
 Save
 Chemical Spreadsheets
 Editor
  New
  Stereo Bond
  Right Click Options
  Chemical Dictionary
  Chemical Groups
  Template Menu
  Free Radical
  Adding fragment
  Property Monitor
  Key chemical
  Edit Options
  Paste Smiles/InChi
  Save as Mol/RXN
  Save Chemical Spreadsheet
  Save SMILES
  Convert to 3D and Conformers
  Isis
 Chemical Search
 2D Interaction
 Convert to 3D
 Fragments
 Find Bioisostere
 Molcart
 Calculate Properties
 Standardize Table
 Annotate
 Align/Color by 2D Scaffold
 Formal Charges
 Enumerate Formal Charge States
 Convert
 Build Prediction Model
 Predict
 Generate 3D Conformers
 Generate Tautomers
 Generate Stereoisomers
 Prodrug
 Ligand Energetics
 Cluster Set
 PCA Analysis
 MCS Dendrogram
 Compare Two Sets
 Merge Two Sets
 Select Duplicates
 MPO
 Combinatorial Chemistry
 SAR Analysis
 Chemical Superposition
 APF Superposition
 APF Tools
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
9.4 Molecular Editor
Next

[ New | Stereo Bond | Right Click Options | Chemical Dictionary | Chemical Groups | Template Menu | Free Radical | Adding fragment | Property Monitor | Key chemical | Edit Options | Paste Smiles/InChi | Save as Mol/RXN | Save Chemical Spreadsheet | Save SMILES | Convert to 3D and Conformers | Isis ]

Available in the following product(s): ICM-Chemist | ICM-Chemist-Pro | ICM-VLS

| Video |

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.

9.4.1 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 an atom, bond or ring and then click in the white Molecular Editor Workspace to start skethching.

  • You can extend your structure by selecting another atom, bond or ring.
  • 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.

9.4.2 Stereo Bond


To set the stereo bond type:

  • 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.

9.4.3 Right Click Options


There are a number of different options available when you right click on a bond or atom. These can be used for editing bond and atom types and there are additional options for Chemical Searching.

9.4.4 Chemical Dictionary


There is an inbuilt chemical dictionary which enables you to import a 2D sketch quickly. To use it:

  • Click on the chemical dictionary button.
  • Start typing the name of the chemical.
  • Select the chemical from the drop down list.

9.4.5 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.

9.4.6 Template Menu


A set of chemical templates are available for:

  • amino acids
  • bases
  • bicyclics
  • rings

9.4.7 Set Free Radical Type


To set a free radical type (singlet, doublet or triplet) to an atom:

  • Sketch the ligand in the Molecular Editor.
  • Right click on the atom and select the free radical type.
  • Convert to 3D or add to a chemical table if needed for docking.

9.4.8 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.

9.4.9 Property Monitor


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

To view the monitor

  • ICM Molecular Editor/View/Chemical Monitor or click on the Chemical Monitor button and a window as shown below will be displayed.

The following properties are monitored.

  • Chemical Formula
  • SMILES string
  • Name/IUPAC Name
  • InChI
  • InChI Key
  • 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 (See: http://www.molsoft.com/mpropdesc.html). Normaly Bayesian classifier returns either 1 ot -1 (positive ot negative) therefore positive values means drug-like, negative - not.
  • Molecular Area (MolArea)
  • Prediction model build for 'delta Hf in gas' property using public NIST database (description can be found here: http://webbook.nist.gov).A low dHf value means that the compound is more 'stable'.
  • LogP (MolLogP)
  • LogS (MolLogS)
  • Polar Surface Area (PSA)
  • Volume
  • Chem Alert will flag any reactive group, PAINS or Bad ADME-TOX groups.
  • Groups option highlights chemical groups in the sketch.

The rows in the monitor window are colored from green (good) to red (poor). You can right click on the table to copy a value or add your own prediction model.

9.4.10 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.

9.4.11 Chemical Editing Options


Tools are provided to help editing your chemical sketch. These include buttons for selection, erasing, copy and paste.

9.4.12 Paste SMILES or InChi String


To paste a SMILES string into the Molecular Editor:

  • Open the Molecular Editor.
  • In the Molecular Editor window select Edit/Add Smiles/InChi.
  • Click on the canvas.

9.4.13 Save Chemical in Mol/RXN Format


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

  • Select File/Save As... in the Molecular Editor window
  • Enter a filename and select where you wish to save the file.
  • Save as type mol or rxn

9.4.14 Save to Chemical Spreadsheet


To save the chemical to a chemical spreadsheet:

  • Click on one of the buttons shown below. You can append to a new table or an existing one.

9.4.15 Save as SMILES or InChi


To save the chemical in SMILES format

  • Edit/Copy as Smiles

To save the chemical in InChi format

9.4.16 Convert Chemical to 3D or Generate Conformers


To convert the chemical to 3D or to generate conformers:

  • Click on the buttons shown below to convert to 3D or generate conformers in the Merck Molecular Force Field (MMFF)
  • The 3D chemical will be listed in the ICM workspace. If conformers are generated a table showing the conformers will be created.

9.4.17 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.


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