High resolution electron energy loss spectroscopy (HREELS) measurements and density functional model cluster calculations are presented to clarify the vibrational structure of the adsorption system C6H6/Si(001). All vibrational modes of the adsorption complex, which previously was identified to exhibit a cyclohexadiene-like structure, have been calculated and characterized according to the motion of the different atoms of the adsorption complex. Special emphasis is placed on the low-frequency modes. The coupling between the adsorbate and the substrate modes is analyzed with the help of a model that represents various limiting situations. Different coupling variants are found to apply to different collective modes of the adsorbate. The A(1) and B-1 modes can be described rather well by a model that only encompasses the adsorbate and the Si dimer underneath; for the A(2) and B-2 modes a frozen substrate description of the adsorption complex is more appropriate.