The Journal of Physical Chemistry B ARTICLE Figure 3. Hydrogen bond interactions for individual water molecules for the 1FTJ-Glu model system (A) WG, (B) W1, (C) W2, (D) W3, (E) W4, and (F) W5. can be described as in eq 1 ΔEInteraction ¼ ΔETotal ð ΔEFragment1 þ ΔEFragment2Þ 1 ð Þ 3. RESULTS 3.1. Basis Set Choice. We began by first assessing the influence of different levels of theory on the interaction energies. We selected two water molecules (WG and W5) from the 1FTJ-Glu system (see Figure 2A), and calculated the interaction energies with the MPW1B95 and B3LYP methods (Table 1) on unoptimized systems. The MPW1B9563 meta-hybrid method was first used in conjunction with three different basis sets. These included the more mathematically complete 6-31G* and 6-31G** basis sets66,67 as well as the locally dense basis set (LDBS)68 approach, where the model- system can be partitioned into two very different regions, which are assigned basis sets of different accuracy. Specifically, the atoms directly involved in the formation of hydrogen bonds (including the ligand and water molecules) were described by the 6-31G* basis set. The 3-21G57 59 basis set was chosen for all remaining atoms. We find that the basis set superimposition error (BSSE) was the smallest at the MPW1B95/6-31G** level of theory with compar- able interaction energy values for each water molecule (Table 1). The B3LYP/6-31G** level of theory was also investigated and in this context the BSSE is larger than the MPW1B95/6-31G** level of theory. However, although reportedly less accurate in its description of hydrogen-bond interactions than MPW1B9563 it still offers a good compromise between computational expe- dience and reliability of the values for BSSE. Thus we pursued B3LYP/6-31G** for the series of calculations for all fragments as detailed in Table 2. 3.2. Ligand Protein Interaction Energies. Analysis of the ligand to proteinþwater interaction energies (L-WsP cells, Table 2) reveals that glutamate is much more favorable in its crystallographically observed mode compared to AMPA in its crystal structure (1FTM-AMPA). Comparing glutamate in alter- native binding poses, we find that the L-WsP interaction energy for 1FTJ-Glu is more favorable than 1FTM-Glu by 75.32 kcal mol 1. However, the situation is not simply reversed for AMPA; in this instance the energies of interaction between AMPA and protein 7089 dx.doi.org/10.1021/jp200776t |J. Phys. Chem. B 2011, 115, 7085–7096