I did docking for an enzyme and I now want to rate the ligands with different scoring functions but the trouble is that I don't understand what are the values I get for all the scoring functions for example: is it energy values and if so what are its values or is it the negative of the energy value?

I am also not sure if I ran the protocol right: Should I put in the "input receptor" the receptor from the docking output file or the receptor molecule window with the binding site?