To validate the IMOMM (integrated molecular orbitals/molecular mechanics) method for ligand-stabilized transition metal clusters, we compare results of this combined quantum mechanical and molecular mechanical (QM/MM) approach, as implemented in the program ParaGauss (Kerdcharoen, T.; Birkenheuer, U.; Krüger, S.; Woiterski, A.; Rösch, N. Theor. Chem. Acc. 2003, 109, 285), to a full density functional (DF) treatment. For this purpose, we have chosen a model copper ethylthiolate cluster, Cu13(SCH2CH3)8 in D4h symmetry. The evaluation is based on 16 conformers of the cluster which exhibit single and bridging coordination of the ligands at the Cu13 cluster as well as various ligand orientations. For corresponding isomers, we obtained moderate deviations between QM and QM/MM results: 0.01-0.06 Å for pertinent bond lengths and up to ∼15° for bond angles. Ligand binding energies of the two approaches deviated less than 6 kcal/mol. The largest discrepancies between full DF and IMOMM results were found for isomers exhibiting short Cu-H and H-H contacts. We traced this back to the localization of different minima, reflecting the unequal performance of the DF and the force-field methods for nonbonding interactions. Thus, QM/MM results can be considered as more reliable because of the well-known limitations of standard exchange-correlation functionals for the description of nonbonding interactions for this class of systems.