The ground state electron densities of the dipeptides were computed using the ONETEP linear-scaling DFT code with the PBE exchange correlation functional and standard parameter settings, (Supporting Information S2.2). Since the reference QM potential energy scans are performed in the gas phase, we have decided to derive QUBE force field charges and Lennard-Jones parameters from the vacuum electron density (rather than in an implicit solvent). The assumption here is that the required correction to the MM potential energy surface is approximately the same in the gas and condensed phases.