Consistent atom names PDB
You'd need to have some sort of ligand dictionary. For many PDB ligands, this exists, and you can look up the atom naming.

For example, the PDB ligand expo allow you to search for ligands by 3-letter code (e.g., HEM).

The PDBeChem also lets you find atom names based on 3-letter codes (the link is HEM).

However, as far as I know, there isn't (yet) any sort of pattern matching that would allow you to go through PDB files and automatically perceive your ligands, sort the atoms, and name them systematically.

If you find one, please let me know - it would be a great addition to programs like Open Babel