The recognition and association of donepezil with acetylcholinesterase (AChE) has been extensively studied in the past several decades because of the former's use as a palliative treatment for mild Alzheimer disease. Herein we examine the conformational properties of donepezil and we re-examine the donepezil-AChE crystal structure using combined quantum mechanical/molecular mechanical (QM/MM) X-ray refinement tools. Donepezil's conformational energy surface was explored using the M06 suite of density functionals and with the MP2/complete basis set (CBS) method using the aug-cc-pVXZ (X = D and T) basis sets. The donepezil-AChE complex (PDB 1EVE) was also re-refined through a parallel QM/MM X-ray refinement approach based on an in-house ab initio code QUICK, which uses the message passing interface (MPI) in a distributed SCF algorithm to accelerate the calculation via parallelization. In the QM/MM re-refined donepezil structure, coordinate errors that previously existed in the PDB deposited geometry were improved leading to an improvement of the modeling of the interaction between donepezil and the aromatic side chains located in the AChE active site gorge. As a result of the re-refinement there was a 93% reduction in the donepezil conformational strain energy versus the original PDB structure. The results of the present effort offer further detailed structural and biochemical inhibitor-AChE information for the continued development of more effective and palliative treatments of Alzheimer disease.