In addition to looking at how much partial charges vary, we wanted to examine how these impact downstream calculations like free energy calculations. We selected the molecules for AHFE simulations by selecting 5 "good" molecules that produced low partial charge variation across 50 conformers, 5 "average" molecules that produced average partial charge variation across 50 conformers, and 5 "bad" molecules that produced high partial charge variation across 50 conformers. For all 126 molecules, we plotted the maximal partial charge di erences for each molecule as a histogram. We used the OpenEye AM1-BCC charges di erences distribution to select our molecules for simulation as this distribution was the most Gaussian. We selected 5 "good" molecules from the lower end of the distribution in