Semi-empirical calculations were used to characterize the orotic acid structure. The structures optimised using the PM3, AM1, and CNDO methods were compared with the crystallographic data. Orotic acid is a polydentate ligand due to the net charge on the atoms from the functional group. A compound was synthesized by reacting orotic acid with zinc acetate dihydrated in a neutral and non-aqueous media. This compound was characterized by elemental analysis, spectroscopy, and thermal analysis. The orotic acid replaces water molecules from zinc acetate dihydrate and coordinates through an exo-cyclic oxygen. Based on the probable structure, PM3 semi-empirical calculations of the complex of Zn(II) were performed. The semi-empirical calculations suggest that the orotic acid coordinated through C2=O group, where acetate groups maintained the bidentate coordination and the Zn- H3Or distance is greater than that the Zn- H2O distance for the Zn(II) acetate dihydrate.