As a prototypical case of a pi-conjugated organic overlayer on a semiconductor surface the adsorption of phenanthrenequinone (C14O2H8) on the Si(001) surface is studied by means of first principles calculations, using gradient-corrected density functional theory together with ultrasoft pseudopotentials and the projector augmented wave method. A thermodynamic phase diagram gives adsorption geometries depending on experimental conditions, the microscopically most favorable bonding configuration representing a "[4+2]-cycloaddition product". The surface electronic structure depends strongly on the respective adsorption configuration. Calculations of the surface optical signature show its sensitivity to molecular adsorption and are in agreement with experimental results. A detailed analysis illustrates that the bonding to the surface has to be taken into account accurately to unveil the molecule's contribution to the surface optical response.