Metal toxicity in human and animal organisms develops during accumulation which principally targets hard tissues. On the molecular level, incorporation of metals into bones depends on interactions with hydroxyapatite, their chief structural component. Bone hydroxyapatite is a natural compound exhibiting significant reactivity to metals. The immense surface of hydroxyapatite predisposes its chemical components to being displaced by other atoms with a similar atomic radius. Knowledge of spatial structure and energy data of the molecule helps to understand the binding of metals by hydroxyapatite and elucidate the chemical and physical properties of such complexes. We used HyperChem software to analyze the structure of hydroxyapatite when the central calcium atom is replaced by one of the metal ions (Pb, Cd, Hg). Our results show that hetero-ionic exchange affects composition and leads to deformation of hydroxyapatite crystals. Replacement was accompanied by changes in bond lengths between oxygen and calcium atoms in the hydroxyapatite molecule and by displacement of groups of atoms surrounding the central calcium atom. The use of molecular modeling as a computational tool enabled a preliminary and theoretical understanding of chemical structure without the need for laboratory tests.