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. Author manuscript; available in PMC: 2011 Dec 9.
Published in final edited form as: J Phys Chem B. 2010 Nov 15;114(48):16020–16028. doi: 10.1021/jp1086416

Figure 2.

Figure 2

(A) Ribbon diagram for the binding mode of the MD-simulated structure of compound 3 in the active site pocket of PDE2A. The intermolecular hydrogen bonds are highlighted in dashed red line. (B) Plots of MD-simulated internuclear distances and RMSD for atomic positions of the ligand versus the simulation time for PDE2A binding with compound 3. Traces D1 and D2 represent the H···O distances associated with a pair of hydrogen bonds (N-H···O) between the amide group in R4 and the amide group of Gln859 side chain. Trace D3 refers to the internuclear distance between the oxygen of the methoxy group (R2) and the hydrogen of the amine group of Asn704 side chain.