The adsorption geometry of the planar 3, 4, 9, 10-perylene-tetracarboxylic-dianhydride (PTCDA) molecule in the commensurate $\mathrm{c}(8\times 8)$ structure on Ag(100) was determined from the analysis of the intensities in low-energy electron diffraction (LEED-IV). Using data from different angles of incidence and optimized computer code, we were able to overcome earlier challenges given by the limitations of the experimental data set and the calculation times required for the large unit cell with many atoms. Testing of different structures confirmed the on-top adsorption site for the center of the perylene core. The final Pendry $R$ factor of $R_{\mathrm{P}}=0.180$ for the on-top position is significantly lower than the one for the fourfold hollow position (minimum $R_{\mathrm{P}}=0.369$) that is hence excluded. The molecule shows archlike deformation with a downshift of the terminal carboxylic groups. Both the molecular structure and the adsorption height are in very good agreement with results from an earlier normal incidence x-ray standing wave (NIXSW) experiment and new density functional theory (DFT) calculations, which we performed in parallel for 0 K and in addition for 300 K. The LEED-IV analysis demonstrates that the PTCDA induces a relaxation ($-0.08$ versus $-0.04\AA$ of the clean surface) and buckling (0.33 Å) of the topmost Ag layer. Special attention was given to the Ag atom below the central ring of the PTCDA. The IV analysis was rather insensitive to its vertical position, and a small $R$ factor, close to the minimal, was also obtained when this Ag atom was moved upward ($R_{\mathrm{P}}=0.185$) or even an Ag vacancy site ($R_{\mathrm{P}}=0.171$) was assumed. However, these structures could be excluded on the basis of DFT calculations. The vacancy structure has a free adsorption energy that is 0.18 eV larger compared to the favored geometry where this central Ag atom is pushed downward, partly due to the energy cost for the vacancy formation. The discussion of adsorbate-induced formation of vacancy sites is important because it was reported for ${\mathrm{C}}_{60}$ on Ag(111). The up- and downward displacements of the first-layer Ag atoms support the understanding of the chemical bond of the PTCDA to the Ag substrate and reveal how the originally planar $\pi$ system is locally distorted. Our analysis proves that LEED-IV is a powerful technique for surface crystallography of large organic adsorbates.

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• Molecules
• Surfaces
• Density functional calculations
• Low-energy electron diffraction