This article discusses the relevance of the similarity of the molecular electrostatic potential for rational drug design and optimization of lead structures on the basis of a comparison of nine fluoroquinolone antibiotics. Molecular electrostatic potentials and dipole moments were calculated directly from the electron-density distribution after crystal structure refinement with invarioms, theoretical non-spherical scattering factors. Deposited, newly determined and re-measured single-crystal diffraction data of varying quality were evaluated in this manner. An in silico validation procedure for invariom database entries is presented. Despite differences in their substitution pattern, molecular electrostatic potentials for molecules with the same protonation states show a striking degree of similarity for the whole group of compounds studied. The rapid calculation of electrostatic potentials directly from the invariom database makes the procedure suitable for high-throughput screening.