Using normal incidence x-ray standing waves, we determined the geometric structure of the adsorption site of a large π -conjugated molecule with six rings, end-capped quaterthiophene (EC4T), on the Ag(111) surface in the commensurate monolayer. The S 1s absorption profiles were measured for the (111) and (111) Bragg reflections. The vertical coherent position D_co⁽¹¹¹⁾, i.e., the average distance between molecules and Ag surface, was determined to 3.15±0.05 Å. This is less than expected for van der Waals bonding and more than known for a local S-Ag bond, thus revealing that the surface bonding involves the entire conjugated π system, in agreement with earlier photoemission results. The lateral position of the EC4T molecule was obtained from a simulation of the experimental coherent position in [111] direction (1.02±0.1 Å). This results in the first complete determination of the adsorption geometry of a large flat-lying organic molecule on an inorganic surface.