This dataset contains simulation results and analyses related to the fluorescence modulation of a COX-2 specific fluorogenic probe.

METHODOLOGICAL INFORMATION

(1) Description of Methods Used for Collection-Generation of Data

The dataset was generated through a series of advanced computational simulations, combining molecular dynamics (MD), quantum mechanics/molecular mechanics (QM/MM), 
and Born-Oppenheimer Molecular Dynamics (BOMD) techniques.

(2) Methods for Processing the Data

Data analysis involved a range of software (cpptraj, MDAnalysis...) and scripting tools to process the MD and QM/MM simulation outputs. 
Bash and Python scripts were developed to automate trajectory processing and spectra plotting.

(3) Instrument- or Software-Specific Information Needed to Interpret the Data

H++ web-server for hydrogen atom topology
AutoDock Vina for molecular docking 
Amber20 for molecular dynamics simulations 
Gaussian9 and 16 for quantum mechanical calculations 
Additional QM/MM interface modifications were applied in Amber20 to support BOMD simulations.

All software used is widely available, though users may need institutional licenses for Amber20 and Gaussian16. 
Data is in a format compatible with open visualization software (e.g., VMD, PyMOL).

(4) Instruments, Calibration, and Standards Information

Computational simulations were executed on high-performance GPUs and cluster nodes. The MD simulations utilized an NVIDIA RTX 3090 GPU for enhanced computational 
speed and efficiency, the BOMD calculations were run on a CPUs of CSUC (2 Intel Xeon Platinum 8168) and QMMMpol calculations were performed on IQTC HPC cluster.

(5) Environmental or Experimental Conditions

Simulations were conducted under constant temperature (298.15 K) and pressure (1 atm) in water, using the OPC water model. QM/MM BOMD simulations used various 
functionals (B3LYP, CAM-B3LYP, M06, ωB97XD) to test and validate computational accuracy, with production runs based on the M06 functional.

(6) Quality-Assurance Procedures Performed on the Data

Extensive quality control was performed through multi-replicate MD and BOMD simulations, ensuring thorough sampling and stability of results across multiple frames. 
Additionally, consistency was checked by recomputing excitation energies using alternative functionals, and systematic error corrections were applied to match experimental spectra.