DFTB3-CH-CC-RPs_For_HydrideTransfers

This repository contains the data needed to replicate/evaluate our research work titled: "Adapted DFTB3 repulsive potentials reach DFT accuracy for hydride transfer reactions in enzymes"

If you need more technical information about our research, don't hesitate to contact us via email at [email protected].

Repository Structure

DFTB3_Fitted_Parameters

Folder containing the C-C and C-H fitted parameters to describe the hydride transfer reaction in Ccr.

IRC

Folder containing the output of the IRC calculations describing Ccr's hydride transfer reaction in vacuo.

String_Calculations

Folder containing the inputs and results from the Adaptive String Method's (ASM) calculations on Ccr and DHFR enzymes' hydride transfer reactions.

Ccr/

Contains all calculations related to the Crotonyl-CoA Carboxylase/Reductase enzyme:

• Ccr_DFT/: DFT-level calculations for the hydride transfer reaction
• Ccr_DFTB3_CH_CC_mod3/: Calculations using modified DFTB3 parameters (CH_4_CC_3)
• Ccr_DFTB3_CH_mod5/: Calculations using modified DFTB3 parameters (CH_5)
• Ccr_DFTB3_Original_parameters/: Calculations using original DFTB3 parameters
• INPUTS/: Input files for ASM calculations on Ccr hydride transfer reaction step

DHFR/

Contains all calculations related to the Dihydrofolate Reductase enzyme:

• DHFR_DFTB3_CH_CC_mod3/: Calculations using modified DFTB3 parameters (CH_4_CC_3)
• DHFR_DFTB3_Original_parameters/: Calculations using original DFTB3 parameters
• INPUTS/: Input files for ASM calculations on DHFR hydride transfer reaction

Parametrization

Contains the scripts and data used for DFTB3 parameter optimization:

• LIB/: Library folder containing the python clases in utils.py module
• PARAM/: Folder with DFTB3's original parameter files and for storing the modified parameters
• RUNS/: Calculation outputs using sqm program from AmberTools suite
• STRUCT/: Ordered IRC trajectory in xyz format
• AnalysisRepPot-DistDistrib-IRC.ipynb: Jupyter notebook for analyzing repulsive potentials and distance distributions from IRC calculations
• FitHrm_CH_EXP1_deltaE.ipynb: Jupyter notebook for fitting C-H using linear combinations of harmonic functions
• FitHrm_CH_CC_EXP1_deltaE.ipynb: Jupyter notebook for fitting C-H and C-C RPs using linear combinations of harmonic functions
• PlotGaussAndHarmonics.ipynb: Jupyter notebook for visualizing Gaussian and harmonic functions

Citation

If you use these parameters or data in your research, please cite our paper: (https://doi.org/10.26434/chemrxiv-2024-kkwwg-v2)