Fig. 7: Quantum refinements of SARS-CoV-2 MPro. | Nature Communications

Fig. 7: Quantum refinements of SARS-CoV-2 MPro.

From: Accelerating reliable multiscale quantum refinement of protein–drug systems enabled by machine learning

Fig. 7

a Nirmatrelvir bonded to Cys145 in the X-ray structure and refined by M7 quantum refinement scheme, including the electron density maps. b Nirmatrelvir nonbonded to Cys145 and real-space Z-difference (RSZD) scores of the Cys145 residue and nirmatrelvir (4WI) in wild-type SARS-CoV-2 MPro refined by M7-based quantum refinement with different occupations (bonded: nonbonded). c Structures of the nirmatrelvir binding site in SARS-CoV-2 MPro refined by various quantum refinement schemes (M7, M8, and M10a) with an occupation ratio of 7:3 (bonded: nonbonded), including the electron density maps (2mFo-DFc maps, contoured at 1.0 σ (blue), mFo-DFc maps, contoured at + 3.0 σ (green), and mFo-DFc maps, contoured at −3.0 σ (red)). The X-ray results were taken from the experimental structure without further refinement. Source data of panel (b) are provided as a Source Data file.

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