Permutation of ligands on a core skeleton

[JoshiGaurav11]

Dear admin,
This tool is outstanding for generating various metal complexes with different ligands. Using the provided commands, I can obtain the most favourable structures.

What I really want is ligand permutation across unique coordination sites-for instance, in square bipyramidal geometry with axial and basal positions. If I have 1 ammonia, 1 CO, and fill the remaining sites with water (3 for pentacoordination), I want all possible arrangements: ammonia on axial sites, water on axial, etc.

Is there a way to generate these permuted geometries directly with the tool? This would be incredibly helpful.

[JoshiGaurav11]

Dear admin,
To provide more detail on the issue I mentioned, here is an example: I can obtain the correct permutations in some cases using
inputDict = {'core': {'metal': 'Cu', 'coreCN': 6}, 'ligands': [{'smiles': 'NCC(=O)O', 'coordList': [3]}], 'parameters': {'fill_ligand': 'water', 'n_conformers': 10, 'n_symmetries': 10, 'relax': False}}
and then calling arch_out = build_complex(inputDict).

However, when I try a similar setup with a bidentate ligand using
inputDict = {'core': {'metal': 'Cu', 'coreCN': 5}, 'ligands': [{'smiles': 'NCC(=O)O', 'coordList': [0, 3]}], 'parameters': {'fill_ligand': 'water', 'n_conformers': 10, 'n_symmetries': 10, 'relax': False}}
and call arch_out = build_complex(inputDict),

I observed that for the trigonal bipyramidal geometry, permutations were generated correctly, but for the square bipyramidal case, I obtained only two conformers: one with glycine in a basal position, and another where the carboxylate (oxygen) arm is axial. I am unable to get a configuration where the amine (nitrogen) arm is in the axial position.

Could you please let me know if there is something missing or incorrect in my inputDict that prevents sampling this arrangement? This is a small test system, and I plan to extend the same approach to larger complexes, so I would like to ensure that all possible coordination permutations are captured.

Thank you!