Use this extension to understand interactions between ligands and other molecules, including proteins, water, chemical groups, etc., as well as create and edit molecules in 2D.

Create interaction diagrams and molecules

The Interaction Designer has two main modes:

• Creating interaction diagrams: use the Home > Diagram command to automatically create an interaction diagram based on the current selection, or the whole document if nothing is selected.
• Creating new molecules in 2D: use the Edit > Design command to start a new molecule.

The Interaction Designer keeps the 2D documents synchronized with the 3D viewport: selecting, adding and removing atoms and fragments is performed in both 2D and 3D.

Everything is editable

Everything in the 2D diagram is editable:

• You can move all labels and interaction symbols to control the diagram layout, as well as the caption.
• You can hide and show interactions by clicking on their name in the caption.
• You can change the interaction colors by double-clicking on their name in the caption.

Easily export interaction diagrams

You can save your interaction diagrams in various image formats, including png, jpg, jpeg, bmp and svg.

Interactions

The following interactions are determined:

• Clashes
• Polar
• Water
• Carbonyl
• Amide–Amide
• Metal
• Hydrophobic
• Aromatic (general aromatic contacts)
• Pi–Pi (Aromatic ring–aromatic ring interactions)
• Cation–Pi (Positively charged group–aromatic ring)
• Donor–Pi (Hydrogen bond donor–aromatic ring)
• Amide–Pi (Amide group–aromatic ring)
• Carbon–Pi (Aliphatic carbon–aromatic ring)
• Sulfur–Pi (Sulfur atom–aromatic ring)
• Halogen–Pi (Halogen atom–aromatic ring)
• Halogen bonds

Documentation

User Guide: Interaction Designer