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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
 Read
 Save
 Chemical Spreadsheets
 Editor
 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
 Visualize Chemical Space
 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
10.6 2D Ligand Interaction Diagram
Next

To create a 2D interaction diagram between a ligand and receptor:

  • Read into ICM a PDB file containing the ligand and receptor. For correct hydrogen bond assignment you will need to convert to an ICM object.
  • Right click on the ligand and choose Tools/Ligand 2D Diagram.
  • A dialog box will be displayed. Select the receptor object from the drop down button and allow ICM to Auto Detect the ligand if needed.
  • The Hydrophobic Distance Cutoff is <= to the minimum distance between ligand and the closest atom in the residue. The Hydrogen Bond Strength is based on the GRAPHICS.hbondMinStrength parameter so lowering the value will identify weaker hydrogen bonds.
  • An option is available to match the 2D representation to a pre-calculated one saved in a chemical table loaded into ICM.

A guide to the coloring and representation of the 2D display:

  • Green shading represents hydrophobic region.
  • Blue shading represents hydrogen bond acceptor.
  • White dashed arrows represents hydrogen bonds.
  • Grey parabolas represents accessible surface for large areas.
  • Broken thick line around ligand shape indicates accessible surface.
  • Size of residue ellipse represents the strength of the contact.
  • 2D distance between residue label and ligand represents proximity.
  • Covalently bound residue represented with thick black line around ellipse. (C25 in the picture above)

To edit the 2D image (e.g. rotate a group):

  • Right click on the image and choose Edit Molecule and edit using the Molecular Editor.

To save the 2D interaction diagram to an image file:

  • Right click on the image and choose Save Export/Molecular Image


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