How can I determine hybridization state and bond order for all atoms in a protein pdb file? In general, how can I acquire the same information for a pdb file as a mol2 file format? Multiple research papers state that for proteins, bond orders can be easily deduced but for a ligand, it is not easy. I only care about the protein and I want to know the easy approach for it. I don't want any programs that can do the job for me but I want know how do they determine hybridization states, rings and bond orders.