The interaction of the strong electron-acceptor tetracyanoethylene with the Cu(100) surface is studied with scanning tunneling microscopy experiments and first-principles density functional theory calculations. We compare two different adsorption models with the experimental results and show that the molecular self-assembly is caused by a strong structural modification of the Cu(100) surface rather than the formation of a coordination network by diffusing Cu adatoms. Surface atoms become highly buckled, and the chemisorption of tetracyanoethylene is accompanied by a partial charge transfer.