Published May 12, 2022
| Version 1.0
Dataset
Open
Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem
Description
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.
Files
1.chrgs.zip
Files
(4.0 GB)
Name | Size | Download all |
---|---|---|
md5:2f2fd531d99ba12acfa72d08fda98fda
|
1.9 GB | Download |
md5:d3544335f9024d174603f59c2057204c
|
1.9 GB | Download |
md5:2263bf06e7d6d6bfc2cb1363c443e3a8
|
12.8 MB | Preview Download |
md5:674bf0c4bee53ff770a9aacc26af65e3
|
791.9 kB | Preview Download |
md5:96f7478faaba0e0e574214cd5d9f391f
|
840.0 kB | Preview Download |
md5:ef16848ad74df08ef80e0495f9fd8751
|
9.1 MB | Preview Download |
md5:e84eb16670c35243330ac6db9195c2c3
|
67.2 MB | Preview Download |
md5:55a86cb51a2d6da14dafbf3aa20ed230
|
21.5 MB | Preview Download |
md5:e57c2034c0d826ca2e335c7304eded10
|
124.9 MB | Preview Download |