--- !ruby/object:ProtocolDataset::DataSet #=============================================================================== # Data set description #=============================================================================== description: !ruby/object:ProtocolDataset::DataSetDescription name: PL-REX_1k references: "10.1038/s41467-024-45431-8": "A. Pecina, J. Fanfrlík, M. Lepšík and J. Řezáč; Nature Communications 2024, 15, 1127." text: "PL-REX protein-ligand complexes - small model (~ 1000 atoms)" method_geometry: | PM6-D3H4X/MM optimization of ligand and surroundings method_energy: | wB97X-D3BJ/DZVP-DFT units: kcal/mol global_setup: job: interaction geometry_setup_from_file: yes groups: - 001-CA2 - 002-HIV-PR - 003-CK2 - 004-AR - 005-Cath-D - 006-BACE1 - 007-JAK1 - 008-Trypsin - 009-CDK2 - 010-MMP12 #=============================================================================== # Items #=============================================================================== items: - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NXG shortname: 001-CA2__5NXG geometry: PLREX_1k:001-CA2__5NXG reference_value: -211.986070 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NXI shortname: 001-CA2__5NXI geometry: PLREX_1k:001-CA2__5NXI reference_value: -212.762001 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NXO shortname: 001-CA2__5NXO geometry: PLREX_1k:001-CA2__5NXO reference_value: -207.566633 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NXP shortname: 001-CA2__5NXP geometry: PLREX_1k:001-CA2__5NXP reference_value: -220.995195 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NXV shortname: 001-CA2__5NXV geometry: PLREX_1k:001-CA2__5NXV reference_value: -209.193367 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NXW shortname: 001-CA2__5NXW geometry: PLREX_1k:001-CA2__5NXW reference_value: -209.312981 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NY1 shortname: 001-CA2__5NY1 geometry: PLREX_1k:001-CA2__5NY1 reference_value: -211.770575 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NY3 shortname: 001-CA2__5NY3 geometry: PLREX_1k:001-CA2__5NY3 reference_value: -209.830885 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NY6 shortname: 001-CA2__5NY6 geometry: PLREX_1k:001-CA2__5NY6 reference_value: -215.492711 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 001-CA2 / 5NYA shortname: 001-CA2__5NYA geometry: PLREX_1k:001-CA2__5NYA reference_value: -201.860703 group: '001-CA2' tags: 'zinc' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 1HSG shortname: 002-HIV-PR__1HSG geometry: PLREX_1k:002-HIV-PR__1HSG reference_value: -159.435575 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 1HXW shortname: 002-HIV-PR__1HXW geometry: PLREX_1k:002-HIV-PR__1HXW reference_value: -164.946378 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 1IZH shortname: 002-HIV-PR__1IZH geometry: PLREX_1k:002-HIV-PR__1IZH reference_value: -185.505719 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 1T3R shortname: 002-HIV-PR__1T3R geometry: PLREX_1k:002-HIV-PR__1T3R reference_value: -142.717734 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 2Q54 shortname: 002-HIV-PR__2Q54 geometry: PLREX_1k:002-HIV-PR__2Q54 reference_value: -148.951645 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 2Q55 shortname: 002-HIV-PR__2Q55 geometry: PLREX_1k:002-HIV-PR__2Q55 reference_value: -158.114394 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 2Q5K shortname: 002-HIV-PR__2Q5K geometry: PLREX_1k:002-HIV-PR__2Q5K reference_value: -154.372809 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 3EKX shortname: 002-HIV-PR__3EKX geometry: PLREX_1k:002-HIV-PR__3EKX reference_value: -147.016885 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 3EL1 shortname: 002-HIV-PR__3EL1 geometry: PLREX_1k:002-HIV-PR__3EL1 reference_value: -172.162621 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 3NU3 shortname: 002-HIV-PR__3NU3 geometry: PLREX_1k:002-HIV-PR__3NU3 reference_value: -134.549749 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 3OXC shortname: 002-HIV-PR__3OXC geometry: PLREX_1k:002-HIV-PR__3OXC reference_value: -168.251819 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / 5HVP shortname: 002-HIV-PR__5HVP geometry: PLREX_1k:002-HIV-PR__5HVP reference_value: -177.938239 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / model13a shortname: 002-HIV-PR__model13a geometry: PLREX_1k:002-HIV-PR__model13a reference_value: -156.857683 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / model13c shortname: 002-HIV-PR__model13c geometry: PLREX_1k:002-HIV-PR__model13c reference_value: -149.031132 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / model13d shortname: 002-HIV-PR__model13d geometry: PLREX_1k:002-HIV-PR__model13d reference_value: -150.287780 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / model16a shortname: 002-HIV-PR__model16a geometry: PLREX_1k:002-HIV-PR__model16a reference_value: -148.080949 group: '002-HIV-PR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 002-HIV-PR / model16e shortname: 002-HIV-PR__model16e geometry: PLREX_1k:002-HIV-PR__model16e reference_value: -141.467736 group: '002-HIV-PR' tags: '' - 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!ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 1F0Q shortname: 003-CK2__1F0Q geometry: PLREX_1k:003-CK2__1F0Q reference_value: -41.139106 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 1J91 shortname: 003-CK2__1J91 geometry: PLREX_1k:003-CK2__1J91 reference_value: -38.947121 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 1M2P shortname: 003-CK2__1M2P geometry: PLREX_1k:003-CK2__1M2P reference_value: -45.80861 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 1M2Q shortname: 003-CK2__1M2Q geometry: PLREX_1k:003-CK2__1M2Q reference_value: -49.295931 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 1M2R shortname: 003-CK2__1M2R geometry: PLREX_1k:003-CK2__1M2R reference_value: -51.229631 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 1ZOE shortname: 003-CK2__1ZOE geometry: PLREX_1k:003-CK2__1ZOE reference_value: -45.791032 group: '003-CK2' tags: '' - 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!ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 3KXH shortname: 003-CK2__3KXH geometry: PLREX_1k:003-CK2__3KXH reference_value: -134.643144 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 3KXM shortname: 003-CK2__3KXM geometry: PLREX_1k:003-CK2__3KXM reference_value: -58.056914 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 3KXN shortname: 003-CK2__3KXN geometry: PLREX_1k:003-CK2__3KXN reference_value: -35.021862 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 003-CK2 / 3PVG shortname: 003-CK2__3PVG geometry: PLREX_1k:003-CK2__3PVG reference_value: -75.016767 group: '003-CK2' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 1US0 shortname: 004-AR__1US0 geometry: PLREX_1k:004-AR__1US0 reference_value: -116.680655 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 2IKG shortname: 004-AR__2IKG geometry: PLREX_1k:004-AR__2IKG reference_value: -135.386865 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 2IKH shortname: 004-AR__2IKH geometry: PLREX_1k:004-AR__2IKH reference_value: -121.543611 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 2IKI shortname: 004-AR__2IKI geometry: PLREX_1k:004-AR__2IKI reference_value: -122.467019 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 2IKJ shortname: 004-AR__2IKJ geometry: PLREX_1k:004-AR__2IKJ reference_value: -125.205567 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4LAU shortname: 004-AR__4LAU geometry: PLREX_1k:004-AR__4LAU reference_value: -123.618057 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4LAZ shortname: 004-AR__4LAZ geometry: PLREX_1k:004-AR__4LAZ reference_value: -129.805655 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4LB3 shortname: 004-AR__4LB3 geometry: PLREX_1k:004-AR__4LB3 reference_value: -130.783351 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4LB4 shortname: 004-AR__4LB4 geometry: PLREX_1k:004-AR__4LB4 reference_value: -126.052267 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4LBR shortname: 004-AR__4LBR geometry: PLREX_1k:004-AR__4LBR reference_value: -133.005096 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4LBS shortname: 004-AR__4LBS geometry: PLREX_1k:004-AR__4LBS reference_value: -126.028743 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4QXI shortname: 004-AR__4QXI geometry: PLREX_1k:004-AR__4QXI reference_value: -134.458136 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4XZH shortname: 004-AR__4XZH geometry: PLREX_1k:004-AR__4XZH reference_value: -127.369693 group: '004-AR' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 004-AR / 4XZI shortname: 004-AR__4XZI geometry: PLREX_1k:004-AR__4XZI reference_value: -124.182738 group: '004-AR' tags: '' - 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!ruby/object:ProtocolDataset::DataSetItem name: 005-Cath-D / model25 shortname: 005-Cath-D__model25 geometry: PLREX_1k:005-Cath-D__model25 reference_value: -149.973598 group: '005-Cath-D' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 005-Cath-D / model31 shortname: 005-Cath-D__model31 geometry: PLREX_1k:005-Cath-D__model31 reference_value: -136.937643 group: '005-Cath-D' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 005-Cath-D / model35 shortname: 005-Cath-D__model35 geometry: PLREX_1k:005-Cath-D__model35 reference_value: -137.814556 group: '005-Cath-D' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 005-Cath-D / model36 shortname: 005-Cath-D__model36 geometry: PLREX_1k:005-Cath-D__model36 reference_value: -112.987377 group: '005-Cath-D' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCO shortname: 006-BACE1__5QCO geometry: PLREX_1k:006-BACE1__5QCO reference_value: -52.469598 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCP shortname: 006-BACE1__5QCP geometry: PLREX_1k:006-BACE1__5QCP reference_value: -53.010414 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCR shortname: 006-BACE1__5QCR geometry: PLREX_1k:006-BACE1__5QCR reference_value: -132.45281 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCT shortname: 006-BACE1__5QCT geometry: PLREX_1k:006-BACE1__5QCT reference_value: -138.47573 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCU shortname: 006-BACE1__5QCU geometry: PLREX_1k:006-BACE1__5QCU reference_value: -134.12098 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCV shortname: 006-BACE1__5QCV geometry: PLREX_1k:006-BACE1__5QCV reference_value: -43.668864 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCX shortname: 006-BACE1__5QCX geometry: PLREX_1k:006-BACE1__5QCX reference_value: -47.485104 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCY shortname: 006-BACE1__5QCY geometry: PLREX_1k:006-BACE1__5QCY reference_value: -63.324648 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QCZ shortname: 006-BACE1__5QCZ geometry: PLREX_1k:006-BACE1__5QCZ reference_value: -42.338148 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QD0 shortname: 006-BACE1__5QD0 geometry: PLREX_1k:006-BACE1__5QD0 reference_value: -51.837431 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QD1 shortname: 006-BACE1__5QD1 geometry: PLREX_1k:006-BACE1__5QD1 reference_value: -45.140959 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QD2 shortname: 006-BACE1__5QD2 geometry: PLREX_1k:006-BACE1__5QD2 reference_value: -47.053961 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QD3 shortname: 006-BACE1__5QD3 geometry: PLREX_1k:006-BACE1__5QD3 reference_value: -45.227926 group: '006-BACE1' tags: '' - !ruby/object:ProtocolDataset::DataSetItem name: 006-BACE1 / 5QD5 shortname: 006-BACE1__5QD5 geometry: PLREX_1k:006-BACE1__5QD5 reference_value: -48.822136 group: '006-BACE1' tags: '' - 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