They can be obtained by assessing the population of orbitals in an electronic wavefunction, by partitioning the total electron density, by calculating the electrostatic potential, or by other means. In MPcules, we currently calculate atomic partial charges using four methods: Mulliken population analysis, 49 the restrained electrostatic potential (RESP), Bader charges 54 (obtained using the critic2 program), and natural atomic populations via NBO. When other methods are available, we recommend against Mulliken population analysis, as the Mulliken method is known to depend strongly on basis set and produce in some cases unphysical partial charges. We include Mulliken partial charges because they remain widely used in computational chemistry and because Mulliken population analysis is performed by default in Q-Chem DFT calculations. We provide a comparison of Mulliken and NBO atomic partial charges in the Supplementary Information.