Whitlockite is a calcium phosphate phase of crucial interest in various pathologies. It appears in abnormal calcification such as dental calculi, kidney stones, or dystrophic calcifications of tuberculous origin. It is a complex material which involves cation substitutions, cation vacancies, and protonation of phosphate groups. In the literature, there is a lack of theoretical characterization of such materials originating from biological calcifications. By means of DFT calculations, we were able to quantify the ability of whitlockite to hold these substitutions and vacancies in preferential sites. The impact of Ca2+/Mg2+ substitutions on characterizations (IR, RAMAN, and XRD) was also investigated in the scope of DFT.