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Certain groups can be represented in more than one way (i.e. have more than one
canonical form), such as nitro, carboxylate and amidinium. In such cases, there is
usually a right and a wrong representation for use in GOLD. The conventions used
for some common difficult groups and further help on setting up the ligand is
provided (see Setting Up Ligands).

The phosphate and carboxylate groups are unprotonated and in each case the bond
to the O atom has been assigned as aromatic. In this case these groups have been
correctly handled by Hermes and so no editing is required. Had modifications been
required, editing functionality is available under Edit, Edit Structure.

Re-display all the Chains, Ligands and Metals tickboxes so that the 3D view displays
the entire protein structure.

In the Protein setup window, click on the Delete Ligands option beneath the
Extract/Delete Waters option. This window enables us to extract and delete a ligand
from the protein in order to set it up for docking. As we are going to be docking into
chain A we need to first remove the co-crystallised ligand from its active site:
activate the tickbox adjacent to A, underneath the Extract and Reload header:
GOLD User Guide