Molecular Dynamics Simulation Data of the Glycycoumarin–IKKβ Complex

This dataset contains molecular dynamics simulation data for the glycycoumarin (GC)–IKKβ complex used in the study “Glycycoumarin alleviates IL-1β-induced OA-like changes in chondrocytes through modulation of IKKβ/NF-κB signaling and extracellular matrix metabolism.” A 100 ns molecular dynamics simulation was performed using GROMACS 2024.3. The protein was parameterized using the AMBER14 force field, while GC parameters were generated using Sobtop with the General AMBER Force Field. The system was solvated using the TIP3P water model and simulated under periodic boundary conditions at 300 K and 1 bar. The deposited files include the production trajectory, GROMACS run input, structure, energy and log files, checkpoint files, and MM/PBSA analysis outputs. The trajectory was used for RMSD, RMSF, radius of gyration, solvent-accessible surface area, hydrogen-bond, principal component/free-energy landscape, and MM/PBSA analyses. The complete 100 ns production trajectory is provided as 10 consecutive XTC segments covering the full simulation period. Trajectory coordinates were originally saved at 5 ps intervals. The first nine trajectory segments contain 2,000 frames each, and the final 90–100 ns segment contains 2,001 frames, including the final 100 ns frame. Together, the 10 XTC files contain all 20,001 trajectory frames. The trajectory files were split solely for data deposition and transfer purposes; no trajectory frames were omitted during splitting.