cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccxgy8k
title: CCDC 848509: Experimental Crystal Structure Determination

description: Related Article: S.A.Diener, A.Santoro, C.A.Kilner, J.J.Loughrey, M.A.Halcrow|2012|Dalton Trans.|41|3731|doi:10.1039/c2dt11911k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxgy9l
title: CCDC 848510: Experimental Crystal Structure Determination

description: Related Article: S.A.Diener, A.Santoro, C.A.Kilner, J.J.Loughrey, M.A.Halcrow|2012|Dalton Trans.|41|3731|doi:10.1039/c2dt11911k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvtfkm
title: CCDC 799011: Experimental Crystal Structure Determination

description: Related Article: V.Bocokic, M.Lutz, A.L.Spek, J.N.H.Reek|2012|Dalton Trans.|41|3740|doi:10.1039/c2dt12096h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxgybm
title: CCDC 848511: Experimental Crystal Structure Determination

description: Related Article: S.A.Diener, A.Santoro, C.A.Kilner, J.J.Loughrey, M.A.Halcrow|2012|Dalton Trans.|41|3731|doi:10.1039/c2dt11911k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccvtfln
title: CCDC 799012: Experimental Crystal Structure Determination

description: Related Article: V.Bocokic, M.Lutz, A.L.Spek, J.N.H.Reek|2012|Dalton Trans.|41|3740|doi:10.1039/c2dt12096h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx81qx
title: CCDC 841889: Experimental Crystal Structure Determination

description: Related Article: A.S.R.Chesman, D.R.Turner, B.Moubaraki, K.S.Murray, G.B.Deacon, S.R.Batten|2012|Dalton Trans.|41|3751|doi:10.1039/c2dt11905f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxmnms
title: CCDC 853046: Experimental Crystal Structure Determination

description: Related Article: Shaowei Zhang, Yuan Wang, Junwei Zhao, Pengtao Ma, Jingping Wang, Jingyang Niu|2012|Dalton Trans.|41|3764|doi:10.1039/c2dt12202b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.34371.99361
title: About Exploration of Abstract Dimensions and Energy Dynamics in a 0-Dimensional State
DOI: 10.5517/ccxmnnt
title: CCDC 853047: Experimental Crystal Structure Determination

description: Related Article: Shaowei Zhang, Yuan Wang, Junwei Zhao, Pengtao Ma, Jingping Wang, Jingyang Niu|2012|Dalton Trans.|41|3764|doi:10.1039/c2dt12202b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxmnpv
title: CCDC 853048: Experimental Crystal Structure Determination

description: Related Article: Shaowei Zhang, Yuan Wang, Junwei Zhao, Pengtao Ma, Jingping Wang, Jingyang Niu|2012|Dalton Trans.|41|3764|doi:10.1039/c2dt12202b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxmnqw
title: CCDC 853049: Experimental Crystal Structure Determination

description: Related Article: Shaowei Zhang, Yuan Wang, Junwei Zhao, Pengtao Ma, Jingping Wang, Jingyang Niu|2012|Dalton Trans.|41|3764|doi:10.1039/c2dt12202b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxc6p4
title: CCDC 844926: Experimental Crystal Structure Determination

description: Related Article: K.F.Konidaris, V.Bekiari, E.Katsoulakou, C.P.Raptopoulou, V.Psycharis, E.Manessi-Zoupa, G.E.Kostakis, S.P.Perlepes|2012|Dalton Trans.|41|3797|doi:10.1039/c2dt11853j
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxmnrx
title: CCDC 853050: Experimental Crystal Structure Determination

description: Related Article: Shaowei Zhang, Yuan Wang, Junwei Zhao, Pengtao Ma, Jingping Wang, Jingyang Niu|2012|Dalton Trans.|41|3764|doi:10.1039/c2dt12202b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.17155665
title: OpenFF 2.3.0rc1 Relative Binding Free Energy Benchmarks

description: Overview

Relative binding free energy benchmarks of the openff-2.3.0rc1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.3.0rc1_elf10`: simulations using OpenFF 2.3.0rc1 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.3.0rc1_nagl`: simulations using OpenFF 2.3.0rc1 and AshGC v0.1rc3 charges

RBFE data

The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can alsos be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following:  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent  * 2.5 ps HREX exchange rate  * 0.9 nm short range interaction cutoff
DOI: 10.5517/ccxfsmq
title: CCDC 847404: Experimental Crystal Structure Determination

description: Related Article: J.M.Klein, J.K.Clegg, V.Saggiomo, L.Reck, U.Luning, J.K.M.Sanders|2012|Dalton Trans.|41|3780|doi:10.1039/c2dt11861k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxfsnr
title: CCDC 847405: Experimental Crystal Structure Determination

description: Related Article: J.M.Klein, J.K.Clegg, V.Saggiomo, L.Reck, U.Luning, J.K.M.Sanders|2012|Dalton Trans.|41|3780|doi:10.1039/c2dt11861k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxfsps
title: CCDC 847406: Experimental Crystal Structure Determination

description: Related Article: J.M.Klein, J.K.Clegg, V.Saggiomo, L.Reck, U.Luning, J.K.M.Sanders|2012|Dalton Trans.|41|3780|doi:10.1039/c2dt11861k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxhnz0
title: CCDC 849213: Experimental Crystal Structure Determination

description: Related Article: A.Castineiras, N.Fernandez-Hermida, I.Garcia-Santos, J.L.Perez-Lustres, I.Rodriguez-Gonzalez|2012|Dalton Trans.|41|3787|doi:10.1039/c2dt12204a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.17408578
title: OpenFF 2.3.0rc1 Relative Binding Free Energy Benchmarks

description: Overview

Relative binding free energy benchmarks of the openff-2.3.0rc1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.3.0rc1_elf10`: simulations using OpenFF 2.3.0rc1 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.3.0rc1_nagl`: simulations using OpenFF 2.3.0rc1 and AshGC v0.1rc3 charges

RBFE data

The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can alsos be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following:  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent  * 2.5 ps HREX exchange rate  * 0.9 nm short range interaction cutoff
DOI: 10.5517/ccxhp02
title: CCDC 849214: Experimental Crystal Structure Determination

description: Related Article: A.Castineiras, N.Fernandez-Hermida, I.Garcia-Santos, J.L.Perez-Lustres, I.Rodriguez-Gonzalez|2012|Dalton Trans.|41|3787|doi:10.1039/c2dt12204a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxhwv3
title: CCDC 849426: Experimental Crystal Structure Determination

description: Related Article: A.Castineiras, N.Fernandez-Hermida, I.Garcia-Santos, J.L.Perez-Lustres, I.Rodriguez-Gonzalez|2012|Dalton Trans.|41|3787|doi:10.1039/c2dt12204a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.27084.39049
title: TERCERA EDAD Y HOME AND BUILDINGS ELECTRONIC SYSTEMS.
DOI: 10.13140/rg.2.2.32536.98569
title: Exploration of Abstract Dimensions and Energy Equivalence in a 0-Dimensional State: II
DOI: 10.5517/ccxm2zk
title: CCDC 852499: Experimental Crystal Structure Determination

description: Related Article: C.M.Sabate, E.Jeanneau, H.Delalu|2012|Dalton Trans.|41|3817|doi:10.1039/c2dt12100j
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxm30m
title: CCDC 852500: Experimental Crystal Structure Determination

description: Related Article: C.M.Sabate, E.Jeanneau, H.Delalu|2012|Dalton Trans.|41|3817|doi:10.1039/c2dt12100j
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxm31n
title: CCDC 852501: Experimental Crystal Structure Determination

description: Related Article: C.M.Sabate, E.Jeanneau, H.Delalu|2012|Dalton Trans.|41|3817|doi:10.1039/c2dt12100j
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwwqv9
title: CCDC 831012: Experimental Crystal Structure Determination

description: Related Article: M.D.Santana, R.Garcia-Bueno, G.Garcia, G.Sanchez, J.Garcia, A.R.Kapdi, M.Naik, S.Pednekar, J.Perez, L.Garcia, E.Perez, J.L.Serrano|2012|Dalton Trans.|41|3832|doi:10.1039/c2dt12187e
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwwqwb
title: CCDC 831013: Experimental Crystal Structure Determination

description: Related Article: M.D.Santana, R.Garcia-Bueno, G.Garcia, G.Sanchez, J.Garcia, A.R.Kapdi, M.Naik, S.Pednekar, J.Perez, L.Garcia, E.Perez, J.L.Serrano|2012|Dalton Trans.|41|3832|doi:10.1039/c2dt12187e
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwwqxc
title: CCDC 831014: Experimental Crystal Structure Determination

description: Related Article: M.D.Santana, R.Garcia-Bueno, G.Garcia, G.Sanchez, J.Garcia, A.R.Kapdi, M.Naik, S.Pednekar, J.Perez, L.Garcia, E.Perez, J.L.Serrano|2012|Dalton Trans.|41|3832|doi:10.1039/c2dt12187e
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxrbzy
title: CCDC 856591: Experimental Crystal Structure Determination

description: Related Article: T.Kogiso, K.Yamamoto, H.Suemune, K.Usui|2012|Org.Biomol.Chem.|10|2934|doi:10.1039/c2ob25223f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwlscl
title: CCDC 822410: Experimental Crystal Structure Determination

description: Related Article: K.Namitharan, K.Pitchumani|2012|Org.Biomol.Chem.|10|2937|doi:10.1039/c2ob25226k
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccy5vfc
title: CCDC 869563: Experimental Crystal Structure Determination

description: Related Article: M.V.Mijangos, J.Gonzalez-Marrero, L.D.Miranda, P.Vincent-Ruz, A.Lujan-Montelongo, D.Olivera-Diaz, E.Bautista, A.Ortega, M.de la L.Campos-Gonzalez, R.Gamez-Montano|2012|Org.Biomol.Chem.|10|2946|doi:10.1039/c2ob25249j
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx0r1p
title: CCDC 834862: Experimental Crystal Structure Determination

description: Related Article: V.O.Iaroshenko, I.Knepper, M.Zahid, R.Kuzora, S.Dudkin, A.Villinger, P.Langer|2012|Org.Biomol.Chem.|10|2955|doi:10.1039/c2ob07030h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx0r2q
title: CCDC 834863: Experimental Crystal Structure Determination

description: Related Article: V.O.Iaroshenko, I.Knepper, M.Zahid, R.Kuzora, S.Dudkin, A.Villinger, P.Langer|2012|Org.Biomol.Chem.|10|2955|doi:10.1039/c2ob07030h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx0r3r
title: CCDC 834864: Experimental Crystal Structure Determination

description: Related Article: V.O.Iaroshenko, I.Knepper, M.Zahid, R.Kuzora, S.Dudkin, A.Villinger, P.Langer|2012|Org.Biomol.Chem.|10|2955|doi:10.1039/c2ob07030h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx0r4s
title: CCDC 834865: Experimental Crystal Structure Determination

description: Related Article: V.O.Iaroshenko, I.Knepper, M.Zahid, R.Kuzora, S.Dudkin, A.Villinger, P.Langer|2012|Org.Biomol.Chem.|10|2955|doi:10.1039/c2ob07030h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx0r5t
title: CCDC 834866: Experimental Crystal Structure Determination

description: Related Article: V.O.Iaroshenko, I.Knepper, M.Zahid, R.Kuzora, S.Dudkin, A.Villinger, P.Langer|2012|Org.Biomol.Chem.|10|2955|doi:10.1039/c2ob07030h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx0r6v
title: CCDC 834867: Experimental Crystal Structure Determination

description: Related Article: V.O.Iaroshenko, I.Knepper, M.Zahid, R.Kuzora, S.Dudkin, A.Villinger, P.Langer|2012|Org.Biomol.Chem.|10|2955|doi:10.1039/c2ob07030h
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.