The pharmaceutical proprieties of the 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid compound have been studied and the relevant drug design has been considered. The investigated organic compound with formula (2,6-(CH3)C4H10N2)2(C2O4)2·H2C2O4 (2DPOA) has been synthesized by slow evaporation technique at room temperature of a molar ratio 3:2 mix of oxalic acid and 2,6-dimethylpiperazine. Then 2DPOA has been characterized by IR, 13C NMR, UV–visible and the DFT calculation at the B3LYP level of theory has been made. The molecular structure and parameters (bond angles and lengths) of the molecule have been optimized using the Gaussian 09 software and compared with the XRD data. The atoms-in-molecules (AIM), electron localization function (ELF), and localized orbital locator (LOL) methods have been utilized to determine the types and nature of noncovalent interactions present within the 2DPOA molecule. These methods offer insights into the characteristics and behavior of these interactions. Furthermore, the presence of these interactions has been confirmed through the Hirshfeld Surface (HS) and reduced density gradient (RDG) analysis. The NBO analysis is employed to assess the charge exchange occurring within the studied compound. The molecular reactive sites have been examined using the molecular potential surface and Mulliken atomic charges. The energy gap between HOMO–LUMO and chemical properties of 2DPOA have been determined within the frontier molecular orbital theory. The UV–Vis spectrum of the 2DPOA molecule has been recorded and examined. The calculated and experimental infrared absorption and nuclear magnetic resonance spectra of 2DPOA molecule have been investigated. Finally, the molecular docking simulation has been used to find novel inhibitors and drugs for the cancer and epilepsy disease treatment.