Ligand structure and representation
Except for rotations around single bonds, the 3D structure of the ligand is not changed during the docking simulation.
Bond lengths and angles, as well as planarity around atoms participating in double and delocalized bonds and ring structures, should therefore be correct and sensible in the initial structure.
Some problems with the ligand structure and representation will give rise to Issues being raised on import. Right-click in the Molecule Table or Molecule Project and select:
Show | Issues
and sort the issues table by Molecule, to see if any issues are raised for the ligand.
Ligand structures can be imported to the workbench from PDB, Mol2, or SDF files holding 3D information about the molecules, or generated in the workbench from 2D information or from SMILES representation (see Import molecules). Many ligand 3D structures are available from http://zinc.docking.org/. If there are problems with the ligand structure, try one of the alternative options for importing or generating a ligand structure, and see if the situation improves.
Based on bond orders, atom hybridization and hydrogen atoms, all heavy atoms are assigned a type prior to the docking simulation. This type determines what target interactions are favorable. It is therefore important that the bond orders, atom hybridization and number of hydrogen atoms on the heavy atoms correspond to the expected chemical state of the ligand when interacting with the target.
The representation can be adjusted from the right-click context menu on individual atoms. This will not change the structure. Alternatively, the Ligand Optimizer (The Ligand Optimizer) can be used to change representation and structure of the ligand.