Ligand Analysis
Connect ligand chemistry, nearby residues, and interaction geometry across coordinated 2D, table, and 3D views.
Ligand analysis works best when you move between three complementary views instead of treating any single view as complete:
- The 2D Diagram summarizes chemistry and nearby partners.
- The Interactions Table provides filterable contact records.
- The 3D Diagram shows spatial geometry in the binding site.
Prepare the binding site
If more than one ligand is present, confirm which ligand the current view targets before recording a conclusion.
Open the ligand views
Use Applications → Ligand Interaction and choose the view that matches the question.
| View | Primary question | Best output |
|---|---|---|
| 2D Diagram | Which residues and interaction classes surround the ligand? | Compact schematic for discussion |
| Interactions Table | What are the exact contact partners, types, and distances? | Filterable evidence and validation |
| 3D Diagram | How are those contacts oriented in space? | Binding-site geometry and camera focus |
You can also use the bottom ligand utilities for quick access when they are available.
Read the 2D Diagram
The 2D view lays out the ligand with heteroatom labels, places nearby residues around it, and draws interaction lines by type.
| Visual cue | Meaning |
|---|---|
| Blue dashed line | Hydrogen bond |
| Gray dotted line | Hydrophobic contact |
| Violet dashed line | Aromatic or halogen contact, depending on the legend |
| Teal line | Cation–pi contact |
| Orange line | Ionic contact |
Emerald line with a W node | Water bridge |
| Amber solid line | Metal contact |
Always use the visible legend as the authority for the current diagram.
Navigate and clean the layout
- Scroll to zoom and drag the canvas to pan.
- Drag a residue node when labels or lines overlap.
- Use the
+and−controls for predictable zoom steps. - Toggle distances, atom names, and the legend according to the audience.
- Keep enough white space to distinguish separate interaction lines.
Use the Interactions Table for validation
The table is the best place to verify the molecular partners behind a diagram line.
Use the 3D Diagram for geometry
The 3D ligand view focuses on the real binding site and draws contacts as spatial connectors. Select an interaction to move the camera toward it, then rotate slightly to inspect whether the geometry is convincing.
Do not judge a contact from a single projection. A line that looks short in a flat view may be oriented toward or away from the camera.
Copy the ligand identifier
When available, copy the ligand's SMILES string for use in an authorized downstream workflow. Confirm protonation, stereochemistry, and source conventions before treating a copied string as a canonical chemical record.
A recommended review sequence
- Start with the 3D binding-site overview.
- Use the 2D Diagram to identify the interaction pattern.
- Validate individual contacts in the table.
- Return to 3D for spatial interpretation.
- Measure a critical distance if it supports the conclusion.
- Save a viewer session or story scene with a meaningful name.
A detected interaction is a candidate interpretation based on the available structure. Review source quality, atom identity, protonation, and geometry before using it in a decision.