Clean up `ligands.yaml` files

[IAlibay]

These are out of sync, we should clean them up before a release.

[David-Araripe]

Hi @IAlibay , do you have updates on this?

I checked the edges listed on kartograf_mapper_lomap_network.yml and compared the ligands there, in the ligands.sdf files and on the ligands.yml file.

From what I've seen, most of the ligands.yml files are up to date, with data/thrombin/00_data/ligands.yml being the only exception I could find. This ligand 7d (lines highlighted on the link) is not present in neither the network.yml or the ligands.sdf files.

Are there other changes coming to the repo for the starting ligands/protein starting coordinates? I'm working on benchmarking FEP too so would love to be up to date on incoming changes.