The geometry description for residues, monomers and links used by Coot are in the standard mmCIF format. Because this format alows multiple comp_ids (residue types) to be described within a cif loop, it is hard to tell when a dictionary entry needs to be overwritten when reading a new file. Therefore Coot makes this extra constraint: that the “chem_comp” loop should appear first in the comp list data item - if this is the case, then Coot can overwrite an old restraint table for a particular comp_id/residue-type when a new one is read.
By default, the geometry dictionary entries for only the standard residues are read in at the start 1. It may be that your particular ligand is not amongst these. To interactively add a dictionary entry use File -> Import CIF Dictionary. Alternatively, you can use the function:
(read-cif-dictionary filename)
and add this to your .coot file (this may be the preferred
method if you want to read the file on more than one occasion).
Note: the dictionary also provides the description of the ligand's torsions.