We then used the CSKDE95 set, in addition to good-quality structures from a previously published set (CS244), to assess a new covalent docking method implemented in our inhouse docking code, Attracting Cavities. AC reached high success rates for re-docking from randomized ligand conformations, up to 81% on the complexes of the CSKDE95 set and 79% on the CS244 set. In agreement with earlier studies, the RMSD of the best pose was found to be significantly dependent on three factors. First, the prediction of the correct binding mode depends on the buriedness of the ligand. The more contacts the ligand makes with the protein, the easier the prediction. This remains true despite the covalent anchoring point present in covalent ligands. Second, the existence of crystal contacts in the experimental structure impedes the prediction of the native binding mode, because these interactions are absent in the docking calculation. Third, the quality of the experimental data in the ligand binding site plays an important role, as a poorly defined ligand conformation is more difficult to correctly predict than a well-defined conformation. This highlights the importance of using high-quality structures for benchmarking purposes.