## 3 Results
### Analysis of MDS Trajectories
#### 3.7.5 Analysis of Intramolecular Bonds  
To elucidate the discrepancies between molecular docking data and the examination of intramolecular bonds during the 100-nanosecond molecular dynamics (MD) simulation, it is essential to acknowledge the fundamental contrasts between these two approaches. Molecular docking offers a static, short-term forecast of ligand-receptor interactions derived from a singular conformational snapshot of the ligand at the receptor's binding site. It emphasizes evaluating the most probable conformation and interactions, including hydrogen bonds, hydrophobic interactions, and ionic connections, at a specific moment. Nonetheless, these predictions are constrained by the inflexible or semi-inflexible characteristics of most docking algorithms, which fail to consider receptor flexibility or the temporal dynamics of solvent effects. Conversely, the intramolecular bond analysis derived from molecular dynamics simulation illustrates a dynamic system wherein the flexibility of the ligand, receptor, and solvent molecules is comprehensively accounted for. This offers a more accurate representation of the evolution of interactions throughout time. Hydrogen bonds can be ephemeral, forming and dissociating as the system investigates various conformations. Consequently, a hydrogen bond not detected during docking (for instance, between 1-Monolinolein (CID-25000608) and the receptor) may manifest in the molecular dynamic's simulation owing to the conformational flexibility of the binding site or ligand and vice versa. A hydrogen bond observed in molecular docking (e.g., CID-5366020 with Met528) may not endure throughout the simulation due to structural rearrangements or competing interactions within the dynamic environment (Figure 8). Figure 7: The polar surface area (PSA) of the simulated protein–ligand interactions molecules calculated using 100 ns simulated interaction graphs. The chosen chemicals CID-250006068, CID-5366020, CID-91696396, and CID-7311, together with CID-23725625 (control), are displayed as blue, orange, gray, yellow, and sky-blue in combination with the target protein, respectively. The presence of hydrogen bonds in the MD analysis but their absence in docking for CID-23725625 can be attributed to the time-dependent characteristics of bond formation during simulations. The MD simulation may uncover novel hydrogen bonds when the ligand adjusts to the receptor milieu and refines its interactions in a manner that docking alone cannot anticipate. Moreover, water-bridged hydrogen bonds and other solvent-mediated interactions, typically lacking in docking, are elucidated by molecular dynamics and can substantially enhance overall binding stability. The disparities between molecular docking and MD simulation illustrate the limitations of static docking models in contrast to the more comprehensive and dynamic representation offered by MD. The distinctions must be examined as a crucial component of comprehending ligand-receptor interactions, as molecular dynamics simulation provides a more comprehensive and precise representation of these complexes within a biological  
Figure 8: The relationships amongst ligands and protein molecules that were found throughout the 100 ns simulations depicted in layered bar diagrams. This section provides examples of the interactions between the chosen ligand molecules. Wherein CID-25000608, CID-5366020, CID-91696396, and CID-7311, CID-23725625 (control) are the five antagonists that were chosen and are associated with the corresponding protein. In this instance, CID-25000608, CID-5366020, CID-91696396, and CID-7311, CID-23725625 (control) are designated as (**A**–**E**), respectively. framework. The distinctions between docking and MD bond analysis highlight the necessity of employing both methodologies in a complementary manner.