We used the attach-pull-release (APR) method, as implemented in the open source package pAPRika version 0.0.3, to calculate absolute binding free energies. A complete description of the APR method has been provided in the literature . The attachment and release phases each consisted of 15 independent windows. During the attachment phase, the force constants on the host and guest are scaled by a parameter that goes from , at which point all restraints are turned off, to , at which point all restraints are at their maximum force constant. The windows are more densely spaced where the force constant is smaller to improve sampling along highly curved regions of the potential of mean force. These restraints include a set of distance, angle, and torsion restraints that orient the host and guest along the long axis of the simulation box. A separate set of conformational restraints were applied between neighboring glucose units of the cyclodextrin to minimize deformations of the host molecule as the guest molecule is pulled out. The conformational restraints were applied along the pseudodihedrals O5 n -C1 n -C1 n -C4 n+1 and C1 n -O1 n -C4 n+1 -C5 n+1 to improve convergence and sampling of the bound state (Figure for atom names). To further improve sampling of weak-binding guests, we applied a hard wall restraint that confined the guest molecule to within a sphere of 12.3 and 13.5 Å of αCD and βCD, respectively, during the bound state.