Abstract
We have applied alchemical free energy calculation of theophylline with an RNA aptamer with one or more ligand docking poses. We find that the predicted binding affinity strongly depends on the anchor's position at the receptor using only distance restraints; it means that a ligand is trapped at the other metastable states during the decoupling process. We also demonstrate that the binding affinity of a fragment-like molecule such as theophylline to the receptor is obtained by phase space decomposition with orientational restraints.
