Using density functional theory augmented with state-of-the-art van der Waals corrections, we studied the geometric and electronic properties of nonplanar chlorogallium-phthalocyanine GaClPc molecules adsorbed on Cu(111). Comparing these results with published experimental data for adsorption heights, we found indications for breaking of the metal-halogen bond when the molecule is heated during or after the deposition process. Interestingly, the work-function change induced by this dissociated geometry is the same as that computed for an intact adsorbate layer in the "Cl-down" configuration, with both agreeing well with the experimental photoemission data. This is unexpected, as the chemical natures of the adsorbates and the adsorption distances are markedly different in the two cases. The observation is explained as a consequence of Fermi-level pinning due to fractional charge transfer at the interface. Our results show that rationalizing the adsorption configurations on the basis of electronic interface properties alone can be ambiguous and that additional insight from dispersion-corrected DFT simulations is desirable.