Short MD and 11 Å-fragmented Insulin–Receptor Complexes

The first part "01-MD" contains the three selected short 5ns-long MD trajectories of insulin-IR complex in binary XTC format and starting PDB files. The minimized model with the loops modeled based on 6HN5 cryo-EM structure is also provided as PDB file. The second part "02-QM" contains PDB files of 11 Å-fragmented insulin–IR complexes derived from three MD trajectories. For each trajectory, ten snapshots were selected for analysis, grouped into the following structure sets:
1. Non-optimized snapshots: Original snapshots directly extracted from MD simulations without further optimization.
2. MM/GB optimized snapshots: Snapshots optimized using the Molecular Mechanics/Generalized Born (MM/GB) solvent model.
3. SQM/COSMO optimized snapshots: Snapshots further refined using Semiempirical Quantum Mechanics (SQM) at the COSMO implicit solvent model level.
4. SQM/COSMO optimized snapshots with adjusted H-bond scaling: SQM/COSMO optimization performed with hydrogen-bond scaling turned off for charged groups (e.g., COO⁻, NH₃⁺).
This dataset offers insights into the influence of various optimization techniques and adjustments on the geometry and interactions within insulin–IR complexes.