The combined study of electron-density features in three substituted hydropyrimidines of the Biginelli compound family has been fulfilled. Results of the low-temperature X-ray diffraction measurements and density functional theory (DFT) B3LYP/6-311++G** calculations of these compounds are described. The experimentally derived atomic and bonding characteristics determined within the quantum-topological theory of atoms in molecules and crystals (QTAIMC) were demonstrated to be fully transferable within chemically similar structures such as the Biginelli compounds. However, for certain covalent bonds they differ significantly from the theoretical results because of insufficient flexibility of the atom-centered multipole electron density model. It was concluded that currently analysis of the theoretical electron density provides a more reliable basis for the determination of the transferability of QTAIMC descriptors for molecular structures. Empirical corrections making the experimentally derived QTAIMC bond descriptors more transferable are proposed.