The hyaluronate molecule is a negatively charged polysaccharide that performs a plethora of physiological functions in many cell tissues depending on its conformation. In the present paper, molecular modeling at three levels of theory and two basis sets was used to gain a deeper insight in the complex molecular structure of calcium(II) and copper(II) hyaluronate. Simulation results were compared with the experimental data (EXAFS or X-ray). It was found that B3LYP does not properly reproduce the experimental data while the HF and M06 methods do. Simulation data confirm that the N-acetyl group of the N-acetylglucosamine residue does not participate in the coordination bonding to the calcium(II) or copper(II) ion, as evident from the experimental data.