Skip to main content
. Author manuscript; available in PMC: 2018 Jan 13.
Published in final edited form as: J Am Chem Soc. 2017 Nov 29;139(49):17945–17952. doi: 10.1021/jacs.7b08938

Figure 3. Thermodynamics cycle for calculating the relative binding free energy of the noncovalent (a) and covalent (b) states.

Figure 3

The structure on the right shows the scaffold of the binding complexes used for FEP/λ-REMD simulations. Protein backbones are shown in silver new cartoon mode. In noncovalent complex, the catalytic cysteine is shown in CPK mode with atom color code: yellow sulfur, red oxygen, blue nitrogen, and cyan carbon. Ligand 4 is shown in licorice mode with the same color code. In covalent complex, the catalytic cysteine is covalently linked to the ligand warhead. All hydrogen atoms are omitted for clarity.