Conversely, the Hsp90-ligand 9 complex showed no significant changes in the ligand-binding site COM-COM distance throughout the simulation (Figure ). POVME2 (POcket Volume MEasurer 2) is a powerful computational tool designed to characterize and measure binding pockets within macromolecular and small-molecule complexes . POVME2 operates through a series of steps, including grid-based point generation, exclusion of points near receptor atoms, and optional removal of non-contiguous regions. We utilized the POVME2 algorithm to assess the binding pocket volumes for the two complexes for 10 µs of MD simulations. A 1.09 Å cutoff, corresponding to the van der Waals radius of the hydrogen atom, ensured the precise exclusion of non-pocket regions. Larger binding pocket volumes are observed for the Hsp90-ligand 1 complex compared to the Hsp90-ligand 9 complex (Figure ). Ligand 1 possesses a larger and more voluminous molecular structure and is expected to adopt conformations that extend into the binding pocket more than ligand 9 (Figure ), leading to an increased volume estimate for the binding pocket. Consequently, the Hsp90ligand 1 complex might exhibit a more expansive and accommodating binding pocket due to the specific interactions (Figure ) and spatial arrangements between the ligand and the receptor, resulting in a larger calculated binding volume. We analyzed interaction dynamics between ligand 1 and a set of key residues (within a cutoff distance of 4 Å) within the ligandbinding pocket of the Hsp90 receptor. Two distinct time intervals were selected (0 µs to 6.0 µs and 6.5 µs to 8.5 µs), where significant differences in the ligand-binding site distance were observed (Figure ). More ligand-residue contacts were prevalent during the 6.5 µs to 8.5 µs simulation interval, indicating a dynamic shift in the binding interactions (Figure and Supplementary Table ). Residues such as Glu32, Ser35, Asn36, Asp39, and Gly80 consistently exhibited higher ligand-residue contact frequencies throughout both intervals (Supplementary Table ), indicating their key roles in maintaining robust interactions with the ligand.