The ligand (FRJ) was seperated from the protein (1T4J), but it couldn't be saved as ligand.sd File. So it was saved as ligand.msv file. I found the net formal charge was -0.5. So could the ligand not be saved as ligand.sd file for the charge? If the net formal charge of ligand is not zero, does the charge affect the docking in Ligandfit? How to dock in this condition?