(S)-Glutamic acid adsorbed on Ag(100) organizes in different self-assembled structures depending on surface temperature [Smerieri, M.; Vattuone, L.; Kravchuk, T.; Costa, D.; Savio, L. (S)-Glutamic Acid on Ag(100): Self-Assembly in the Nonzwitterionic Form. Langmuir2011, 27, 2393–2404]. In particular, two of these structures, referred to as “square” and “flower” geometries, are found to coexist on the surface upon deposition at T = 350 K. The former assembly was fully resolved at the atomic level in the work of Smerieri et al. [Smerieri, M.; Vattuone, L.; Costa, D.; Tielens, F.; Savio, L. Self-Assembly of (S)-Glutamic Acid on Ag(100): A Combined LT-STM and Ab Initio Investigation. Langmuir2010, 26, 7208–7215], in which we proved that the driving force for adsorption is the van der Waals interactions between the molecules and the Ag surface, that is, that molecules are in a physisorbed state. In this paper, we complete our work by presenting the characterization of the “flower” structure. In contrast to the case of the “square” assembly, a strong chemical bond between glutamic acid radicals and the surface is at the basis of the “flowers” geometry. Whereas the chemisorbed central GLU tetramer interacts strongly with the surface, the physisorbed surrounding GLU molecules conserve some degree of freedom in the layer which counterbalances the weak adsorption energy. The “flower” and the “square” assemblies have similar dispersion energy and H-bond interaction energy; as a consequence of the different chemical state of the GLU molecules, however, such contributions have a very different relative weight in the stabilization of the two structures.