[ this discussion is a follow up of this thread
the fact you have a positive energy means that there is some unfavorable interaction (i.e. overlap) of one or more ligand atoms with the target structure. while the other interaction seems to be very weak. I suggest you to double-check that the splitted structures obtained from the original one include all the atoms.
Also, it would be useful to visually inspect the structures to be sure the same atoms from each part are still in close contact with the ligand used in the EPDB calculation.