Merge pull request #223 from openforcefield/jacs_fragment_update

Add version 2 of the benchmark ligand fragments

README.md

@@ -183,6 +183,7 @@ These are currently used perform a complete rotation of one or more selected bon
 | `OpenFF Gen3 Torsion Set v1.0` | [2021-04-09-OpenFF-Gen3-Torsion-Set-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-04-09-OpenFF-Gen3-Torsion-Set-v1.0) | This dataset is a simple-molecule-only torsiondrive dataset, aiming to avoid issue of torsion parameter contamination by large internal non-bonded interactions during a valece parameter optimization. Molecules with one effective rotating bond were generate by combining two simple substituents, which were identified by fragmenting small drug like molecules. Torsions from the generated molecule set were selected using clustering method, in a way that the dataset can allow a chemical diversity of molecules training each torsion parameter. | F ,N ,H ,Cl ,P ,S ,O ,Br ,C | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange)
 | `OpenFF Aniline 2D Impropers v1.0` | [2021-03-29-OpenFF-Aniline-2D-Impropers-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-03-29-OpenFF-Aniline-2D-Impropers-v1.0) | This dataset contains a set of aniline derivatives which have para-substituted groups of varying electron donating and withdrawing properties. This dataset was curated in an effort to improve and understand improper torsions in force fields. We will scan the improper and proper angle simultaneously to better understand the coupling and energetics of these torsions. | O, C, S, H, N | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange)
 | `OpenFF BCC Refit Study COH v2.0` | [2021-06-22-OpenFF-BCC-Refit-Study-COH-v2.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-06-22-OpenFF-BCC-Refit-Study-COH-v2.0) | A data set curated for the initial stage of the on-going OpenFF study which aims to co-optimize the AM1BCC bond charge correction (BCC) parameters against an experimental training set of density and enthalpy of mixing data points and a QM training set of electric field data. The initial data set is limited to only molecules composed of C, O, H. This limited scope significantly reduces the number of BCC parameters which must be retrained, thus allowing for easier convergence of the initial optimizations. The included molecules were combinatorially generated to cover a range of alcohol, ether, and carbonyl containing molecules. | O, C, S, H, N | [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange)
+| `OpenFF-benchmark-ligand-fragments-v2.0` | [2021-08-10-OpenFF-JACS-Fragments-v2.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-08-10-OpenFF-JACS-Fragments-v2.0) |  This is a torsiondrive dataset created from the [OpenFF FEP benchmark dataset](https://github.com/openmm/openmmforcefields/tree/master/openmmforcefields/data/perses_jacs_systems). The ligands are fragmented using openff-fragmenter with both ambertools and openeye before having key torsions driven. | S, N, Br, C, H, O, Cl, F, I| [![Running](https://img.shields.io/badge/Status-Running-orange)](https://img.shields.io/badge/Status-Running-orange)
 
 # GridOptimization Datasets
 These are currently used perform a scan of one or more internal coordinates (bond, angle, torsion), where optimizations are performed over a discrete set of values.