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2 results for “minimum energy pathways”
Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin
<p>This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin).</p> <p>These files are:</p> <ul> <li>toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level;</li> <li>chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level;</li> <li>farrys.zip: the featurzied NumPy arrays for model training;</li> <li>peephole.zip: an example file for how the optimized MEPs look like; </li> <li>dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. </li> </ul> <p>The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. </p> <p>All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. </p> <p>Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: <a href="https://doi.org/10.1021/acsphyschemau.2c00005">10.1021/acsphyschemau.2c00005</a></p>
Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem
<p>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.</p> <p>All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas.</p> <p>All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level.</p> <ul> <li>0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>1.eners.zip: The single point replica energies along all GES-5/IPM pathways.</li> <li>1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways.</li> <li>2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays.</li> <li>3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers.</li> <li>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.</li> <li>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. </li> <li>p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work.</li> <li>README.md: A markdown file that contains additional descriptions.</li> <li>environment.yml: The Conda environment used for the graph-learning. </li> </ul> <p>Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. <strong><em>Electron. Struct.</em></strong> 2022, <strong>4</strong>, 034001. DOI: <a href="https://doi.org/10.1088/2516-1075/ac7993">10.1088/2516-1075/ac7993</a></p>
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