The Journal of Physical Chemistry B ARTICLE Figure 6. Hydrogen bond interactions for individual water molecules for the 1FTM-Glu model system (A) WA, (B) W1, (C) W2, (D) W3, (E) W4, and (F) W5. Leu 650, backbone NH of Lys 656 and backbone NH of Gly 653 in 1FTM-Glu. 3.4. Polarization. A method commonly employed to calculate partial charges for compounds that are not already parametrized in modern force-fields is to use the restricted electrostatic potential (RESP) fitting method.69 We performed RESP calculations on the ligands within the four models in order to assess to what extent polarization from the environment in the different binding modes might be a factor. The results are shown for the four models in Figure 7. The calculations show that there is reasonable agreement at the amino and carboxylic acid groups in all four systems (which is to be expected). The greatest variation is observed at the OE1 and OE2 atoms of Glu, which have an asymmetric charge distribution, presumably reflecting the local environment in each case (WG or WA). In contrast there is much less variation observed at the OE2 (or OE1) atoms of AMPA in 1FTM or 1FTJ. 3.5. Internal Energies. We also examined the internal en- ergies of the different fragments as isolated fragments in the gas phase. Differences between the internal gas-phase energies for the water molecules were all under 0.25 kcal mol 1. The results for the ligands suggest that gas-phase internal energy of gluta- mate is raised by 13.35 kcal mol 1 when placed in the AMPA- binding mode (1FTM-Glu system). Similarly, when AMPA is positioned in the glutamate binding mode, the internal energy of AMPA rises by 8.19 kcal mol 1. When using the polarizable continuum model (PCM) of solvent,70 the internal energy for glutamate in the 1FTM derived system is only 0.15 kcal mol 1 higher than the glutamate conformation observed crystallogra- phically in 1FTJ. However, AMPA in 1FTJ is still 2.06 kcal mol 1 more unfavorable compared to AMPA in 1FTM, suggesting that internal strain is a considerable factor in dictating the binding mode of AMPA, but is not a contributing factor to the glutamate mode of binding. 4. DISCUSSION The crystallographically determined binding pose of AMPA was rather contrary to expectation. Prior to structural knowledge it was anticipated that the 3-oxyanion and ring nitrogen of AMPA would superimpose on the γ-carboxylate oxygens of glutamate. 7092 dx.doi.org/10.1021/jp200776t |J. Phys. Chem. B 2011, 115, 7085–7096