Fix PDB files

[IAlibay]

Essentially #58 but this time directly against main.

Need to fix:

• Make sure HETATM are applied properly, and make sure https://github.com/openforcefield/protein-ligand-benchmark/pull/52#issuecomment-1259610322 is fixed.
• Change the atom names for the caps to adhere to PDB naming conventions
• Remove ANISOU records for TYK2 and Thrombin
• Rename NMA caps to NME
• Don't have NME (or NMA) caps have icodes
• Make sure SSBOND entries are consistent (I believe this is already fine)
• Assign correct hydrogen name for histidines (need to double check if this is PDB compliant)

[IAlibay]

@ijpulidos I'm going to migrate that comment of yours re: POP in pfkfb3 here (https://github.com/openforcefield/protein-ligand-benchmark/pull/82#issuecomment-1329856207).

Seems like one we should have moved to a the cofactors sdf file. We should aim to deal with it alongside this once #82 is merged.