LigandExtractor can be used to find all ligands in a file from the PDB. In addition to finding all possible ligands, it annotates any problems or particularities as so-called “skip reasons”. All ligands found in PDB files can be specifically extracted, including their conformation. The extracted ligands can then be used in other tools, for example, to define a binding site or analyse their conformation.
It is part of the NAOMI ChemBio Suite details are here https://software.zbh.uni-hamburg.de/tools/availableSoftware