Boresch-style restraints, as described in , were used to control the translation and orientation of the host molecule, while providing a frame of reference. After anchor atoms are defined, one distance, one angle, and one dihedral restraints are imposed via D1-L1, D2-D1-L1, and D3-D2-D1-L1, respectively. The orientation restraints were imposed by one angle and two dihedrals via D1-H1-H2, D2-D1-H1-H2, and D1-H1-H2-H3, respectively. Together these restraints were also called "static" restraints since they are constant throughout the entire APR simulations. Static restraints do not alter the internal coordinates of the host, therefore the static restraints free energy was not included since it does not contribute to the binding free energy.