Ligand Building Explanations.

At left, several conformations of a ligand built with electrostatics off. At right the same ligand built with electrostatics on. The MMFF94S energies from OMEGA are shown below each pose. The bottom conformation on either side is the lowest energy conformation according to either energy function. The scales at either side are the differences in energy score from the best conformation to the shown conformation, this is the energy window used in construction.