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. Author manuscript; available in PMC: 2010 Apr 13.
Published in final edited form as: J Phys Chem Lett. 2010 Jan 21;1(3):668–672. doi: 10.1021/jz100026k

Figure 1.

Figure 1

Optimized QM/MM geometries of (A) wildtype (WT) in red, (B) demethyl (DM) in black, (C) deprotonated (SBRcip) in the presence of protonated counterion Glu180 in green, and (D) deprotonated (SBRcidp) in the presence of deprotonated counterion Glu180 in cyan. Also shown are the distances (black dashed lines) between SBN+ or the SBN atom to the OH atom of Tyr111 (ochre), the OD1 atom of Asn87 (magenta), the OE2 atom of Glu180 (yellow), and the C5 atom of the retinal. Also shown are the two internal water molecules W1 and W2 (blue circles) near the SB.