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. Author manuscript; available in PMC: 2020 May 14.
Published in final edited form as: J Chem Theory Comput. 2019 Apr 12;15(5):3134–3152. doi: 10.1021/acs.jctc.9b00061

Figure 1.

Figure 1.

General scheme of a QM/MM ARM and a-ARM model, composed by (1) main chain (cyan cartoon), (2) chromophore rPSB (green ball-and-sticks), (3) Lys side chain covalently linked to the chromophore (blue ball-and-sticks), (4) main counterion MC (cyan tubes), (5) protonated residues GLH and ASH (violet tubes), (6) external Cl– (green balls) counterions, (7) water molecules (tubes), and the (8) residues of the chromophore cavity subsystem (red frames). Parts 1 and 6 form the environment subsystem. Parts 2 and 3 form the Lys-QM subsystem, which includes the H-link atom located along the only bond connecting blue and green atoms. Parts 4 and 8 form the cavity subsystem. Water molecules (Part 7) may be part of the environment or cavity subsystems. The external OS and IS charged residues are shown in frame representation. This figure, and all other protein structures presented in this work, were produced using PyMOL, version 1.2.59