Fig. 6: Structural comparison in the gas phase and in proteins. | Nature Communications

Fig. 6: Structural comparison in the gas phase and in proteins.

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

Fig. 6

Boxplots of root mean square deviation (RMSD) of structures optimized using the ANI-2x, AIQM1, and (SE) GFN2-xTB methods compared to the (DFT) ωB97X-D method for the neutral drugs/inhibitors (26 structures) in the gas phase (orange) and in the proteins after quantum refinement (blue) and for the charged drugs/inhibitors (26 structures) in the gas phase (red) and in the proteins after quantum refinements (pink). a Those with RMSD range from 0 to 3.5 Å; (b) Those with RMSD range from 0 to 0.1 Å. The boxplots indicate median values, interquartile range, minimum and maximum value, and individual data points. The black dots indicate the average values. The QR data by the M7, M8, M10 and M6R schemes (ONIOM3(DFT:SE:MM), ONIOM3(ANI-2x:SE:MM), ONIOM3(AIQM1:SE:MM) and ONIOM2(SE:MM), respectively) were used. Source data are provided as a Source Data file.

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