In order to investigate whether we correctly protonated the aspartyl dyad or not, we changed the protonation states of Asp32 and Asp228 for the BACE_18 protein structure and performed separate MD simulations on the modified protein-ligand complexes. Thus, in addition to the BACE_-18 complex bearing a protonated Asp32 and a deprotonated Asp228 (32p, 228d), we designed four BACE_18 complexes (Fig. ) with different orientations of the ligand's hydroxyl groups that interact with the aspartyl dyad for complex -A) protonated Asp32 and deprotonated Asp228 (32p1, 228d1) and tried all the reasonable protonation states of the aspartyl dyad at pH 4.5 on complexes: B) deprotonated Asp32 and protonated Asp228 (32d, 228p), C) protonated Asp32 and protonated Asp228 (32p1, 228p1), and D) protonated Asp32 and protonated Asp228 (32p2, 228p2). C and D are different by the orientation of the hydrogens and the oxygen (OD2) of the carboxyl group on their Asp32 and Asp228.