Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem

This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules.

All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas.

All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level.

0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.

0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.

1.eners.zip: The single point replica energies along all GES-5/IPM pathways.

1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways.

2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays.

3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers.

5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like.

6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations. 

p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work.

README.md: A markdown file that contains additional descriptions.

environment.yml: The Conda environment used for the graph-learning. 

Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. Electron. Struct. 2022, 4, 034001. DOI: 10.1088/2516-1075/ac7993