While it is well known that partial charge assignment can vary significantly depending on charging method, little investigation has been done to describe the downstream e ects of varied small molecule partial charge assignment on free energy estimates. Past studies have investigated the downstream e ect of assigned partial charges on absolute hydration free energies (AHFEs) on a limited set of small molecules. One study found di erent partial charge sets of a sucrose molecule resulted in maximal errors in the calculated AHFEs of 3.1 kcal/mol. Another study found that a relative hydration free energy calculation between ethanol and propanol di ered by up to 2.2 kcal/mol depending on the partial charge set used. Lastly, two studies compared RESP versus AM1-BCC charge models and the resulting e ect on free energy calculations, however the results were inconclusive. To an extent, it is hoped that these variations in partial charge sets have little functional importance for downstream applications such as free energy calculations. However, preliminary benchmarks from the Open Free Energy Project have shown that generating partial charges from di erent input conformers leads to high variability in calculated relative binding free energies of up to 9 kcal/mol (Figure ). Di erent partial charges used in di erent studies of the same molecule will lead to di erent "correct" answers for calculated free energy values. This can adversely a ect the rankings of compounds based on their calculated a nities and thus our recommendations we make to experimental researchers and pharmaceutical companies of compounds to prioritize in synthesis.