Table4 Geometric RMSD values of self-docked native ligands relative to their experimentally determined structures. All values are given in Å. The number in parentheses indicates which of the three retained docking poses-ranked by binding energy-exhibits the lowest RMSD value. The table above demonstrates that the vinardo scoring function, when used with the Smina program, yields remarkably low RMSD values for self-docked poses compared to the experimental structures. Interestingly, applying the identical vinardo scoring function within the Vina program does not produce such sharp results, leading to notably higher RMSD errors for the 2D0T and 7E0O targets. Except for the 7E0O case-where all three top-ranked docking poses deviate substantially from the experimental structure-the dkoes scoring function also generally aligns well with the experimental data. Note that the 7E0O PDB structure has the least precise X-ray diffraction data among the 16 targets considered. Consequently, this target may exhibit increased uncertainty in both self-docking assessments and final docking results compared to the other targets.