data_XDO # _chem_comp.id XDO _chem_comp.name "(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-1,7~{a}-dimethyl-1-[6,6,6-tris(fluoranyl)-5-oxidanyl-5-(trifluoromethyl)hexa-1,3-diynyl]-2,3,3~{a},5,6,7-hexahydroinden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H30 F6 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Xe4MeCF3 analog" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-06 _chem_comp.pdbx_modified_date 2024-06-21 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 516.516 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XDO _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8P9W _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal XDO C7 C1 C 0 1 N N N N N N -1.975 34.559 37.335 2.090 2.345 -2.504 C7 XDO 1 XDO C8 C2 C 0 1 N N N N N N -1.156 33.285 37.531 0.999 2.996 -1.637 C8 XDO 2 XDO C9 C3 C 0 1 N N S N N N 0.289 33.531 37.994 0.986 2.279 -0.307 C9 XDO 3 XDO O1 O1 O 0 1 N N N N N N 3.584 40.674 38.194 5.024 -3.013 1.055 O1 XDO 4 XDO C1 C4 C 0 1 N N S N N N 1.096 32.321 38.578 -0.078 2.664 0.709 C1 XDO 5 XDO C5 C5 C 0 1 N N N N N N -0.528 35.707 38.961 3.398 1.982 -0.395 C5 XDO 6 XDO C6 C6 C 0 1 N N N N N N -1.951 35.464 38.561 3.465 2.434 -1.846 C6 XDO 7 XDO C4 C7 C 0 1 N N S N N N 0.194 34.418 39.267 2.315 2.620 0.424 C4 XDO 8 XDO C3 C8 C 0 1 N N N N N N 1.588 34.328 39.913 2.056 2.020 1.808 C3 XDO 9 XDO C2 C9 C 0 1 N N N N N N 2.194 32.998 39.409 0.585 2.435 2.092 C2 XDO 10 XDO F5 F1 F 0 1 N N N N N N 5.448 29.875 31.628 -5.977 -0.983 2.351 F5 XDO 11 XDO C26 C10 C 0 1 N N N N N N 5.240 30.148 32.914 -6.501 -0.835 1.062 C26 XDO 12 XDO F3 F2 F 0 1 N N N N N N 6.374 29.893 33.566 -7.627 -1.653 0.920 F3 XDO 13 XDO F4 F3 F 0 1 N N N N N N 5.001 31.457 33.002 -6.867 0.500 0.859 F4 XDO 14 XDO C24 C11 C 0 1 N N N N N N 4.054 29.298 33.393 -5.445 -1.238 0.032 C24 XDO 15 XDO O2 O2 O 0 1 N N N N N N 4.553 27.981 33.577 -5.072 -2.601 0.240 O2 XDO 16 XDO C25 C12 C 0 1 N N N N N N 2.997 29.241 32.289 -6.019 -1.075 -1.377 C25 XDO 17 XDO F2 F4 F 0 1 N N N N N N 2.767 30.456 31.787 -5.053 -1.444 -2.320 F2 XDO 18 XDO F1 F5 F 0 1 N N N N N N 3.417 28.473 31.291 -7.144 -1.894 -1.519 F1 XDO 19 XDO F F6 F 0 1 N N N N N N 1.837 28.754 32.709 -6.384 0.260 -1.581 F XDO 20 XDO C23 C13 C 0 1 N N N N N N 3.436 29.920 34.568 -4.260 -0.377 0.181 C23 XDO 21 XDO C22 C14 C 0 1 N N N N N N 2.958 30.498 35.510 -3.316 0.310 0.301 C22 XDO 22 XDO C21 C15 C 0 1 N N N N N N 2.330 31.094 36.567 -2.208 1.116 0.440 C21 XDO 23 XDO C20 C16 C 0 1 N N N N N N 1.772 31.610 37.493 -1.263 1.802 0.560 C20 XDO 24 XDO C C17 C 0 1 N N N N N N 0.218 31.305 39.337 -0.467 4.134 0.542 C XDO 25 XDO C10 C18 C 0 1 N N N N N N 1.077 34.235 36.883 0.933 0.769 -0.548 C10 XDO 26 XDO C11 C19 C 0 1 N N N N N N 0.106 36.886 38.878 4.242 1.084 0.113 C11 XDO 27 XDO C12 C20 C 0 1 N N N N N N -0.492 38.138 38.631 5.281 0.494 -0.734 C12 XDO 28 XDO C13 C21 C 0 1 N N N N N N 0.128 39.337 38.460 6.135 -0.415 -0.220 C13 XDO 29 XDO C18 C22 C 0 1 N N N N N N 1.580 39.417 38.274 6.055 -0.841 1.193 C18 XDO 30 XDO C19 C23 C 0 1 N N N N N N 2.267 38.509 37.605 5.858 0.036 2.177 C19 XDO 31 XDO C17 C24 C 0 1 N N S N N N 2.279 40.655 38.773 6.206 -2.324 1.468 C17 XDO 32 XDO C16 C25 C 0 1 N N N N N N 1.533 41.904 38.339 7.410 -2.842 0.675 C16 XDO 33 XDO C15 C26 C 0 1 N N R N N N 0.101 41.843 38.835 7.209 -2.560 -0.815 C15 XDO 34 XDO O O3 O 0 1 N N N N N N 0.116 41.766 40.257 8.261 -3.174 -1.561 O XDO 35 XDO C14 C27 C 0 1 N N N N N N -0.610 40.636 38.242 7.220 -1.053 -1.065 C14 XDO 36 XDO H1 H1 H 0 1 N N N N N N -1.564 35.114 36.479 1.839 1.296 -2.662 H1 XDO 37 XDO H2 H2 H 0 1 N N N N N N -3.018 34.279 37.124 2.124 2.850 -3.470 H2 XDO 38 XDO H3 H3 H 0 1 N N N N N N -1.659 32.664 38.286 1.227 4.051 -1.486 H3 XDO 39 XDO H4 H4 H 0 1 N N N N N N -1.124 32.744 36.574 0.029 2.893 -2.123 H4 XDO 40 XDO H5 H5 H 0 1 N N N N N N 4.051 41.446 38.491 4.220 -2.721 1.507 H5 XDO 41 XDO H6 H6 H 0 1 N N N N N N -2.435 36.422 38.321 4.164 1.798 -2.389 H6 XDO 42 XDO H7 H7 H 0 1 N N N N N N -2.489 34.978 39.388 3.816 3.466 -1.885 H7 XDO 43 XDO H8 H8 H 0 1 N N N N N N -0.472 33.866 39.947 2.461 3.698 0.483 H8 XDO 44 XDO H9 H9 H 0 1 N N N N N N 2.212 35.178 39.599 2.154 0.935 1.783 H9 XDO 45 XDO H10 H10 H 0 1 N N N N N N 1.503 34.320 41.010 2.732 2.451 2.547 H10 XDO 46 XDO H11 H11 H 0 1 N N N N N N 2.477 32.361 40.259 0.562 3.356 2.675 H11 XDO 47 XDO H12 H12 H 0 1 N N N N N N 3.079 33.193 38.786 0.069 1.639 2.629 H12 XDO 48 XDO H13 H13 H 0 1 N N N N N N 5.214 27.985 34.259 -4.699 -2.778 1.115 H13 XDO 49 XDO H14 H14 H 0 1 N N N N N N -0.304 31.814 40.161 -0.860 4.294 -0.462 H14 XDO 50 XDO H15 H15 H 0 1 N N N N N N -0.521 30.872 38.647 -1.229 4.394 1.276 H15 XDO 51 XDO H16 H16 H 0 1 N N N N N N 0.853 30.504 39.744 0.412 4.761 0.693 H16 XDO 52 XDO H17 H17 H 0 1 N N N N N N 2.110 34.409 37.219 1.815 0.460 -1.109 H17 XDO 53 XDO H18 H18 H 0 1 N N N N N N 1.086 33.603 35.983 0.910 0.250 0.410 H18 XDO 54 XDO H19 H19 H 0 1 N N N N N N 0.600 35.199 36.650 0.036 0.523 -1.116 H19 XDO 55 XDO H20 H20 H 0 1 N N N N N N 1.177 36.875 39.013 4.160 0.791 1.150 H20 XDO 56 XDO H21 H21 H 0 1 N N N N N N -1.570 38.147 38.570 5.363 0.787 -1.770 H21 XDO 57 XDO H22 H22 H 0 1 N N N N N N 3.321 38.657 37.420 5.754 1.087 1.951 H22 XDO 58 XDO H23 H23 H 0 1 N N N N N N 1.775 37.618 37.243 5.804 -0.304 3.201 H23 XDO 59 XDO H24 H24 H 0 1 N N N N N N 2.340 40.627 39.871 6.371 -2.484 2.534 H24 XDO 60 XDO H25 H25 H 0 1 N N N N N N 2.029 42.791 38.761 8.314 -2.340 1.020 H25 XDO 61 XDO H26 H26 H 0 1 N N N N N N 1.537 41.969 37.241 7.511 -3.916 0.830 H26 XDO 62 XDO H27 H27 H 0 1 N N N N N N -0.424 42.755 38.513 6.251 -2.969 -1.135 H27 XDO 63 XDO H28 H28 H 0 1 N N N N N N 0.563 42.526 40.611 8.199 -3.037 -2.516 H28 XDO 64 XDO H29 H29 H 0 1 N N N N N N -0.723 40.795 37.159 7.027 -0.855 -2.119 H29 XDO 65 XDO H30 H30 H 0 1 N N N N N N -1.604 40.554 38.706 8.191 -0.644 -0.786 H30 XDO 66 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal XDO F1 C25 SING N N 1 XDO F5 C26 SING N N 2 XDO F2 C25 SING N N 3 XDO C25 F SING N N 4 XDO C25 C24 SING N N 5 XDO C26 F4 SING N N 6 XDO C26 C24 SING N N 7 XDO C26 F3 SING N N 8 XDO C24 O2 SING N N 9 XDO C24 C23 SING N N 10 XDO C23 C22 TRIP N N 11 XDO C22 C21 SING N N 12 XDO C21 C20 TRIP N N 13 XDO C10 C9 SING N N 14 XDO C7 C8 SING N N 15 XDO C7 C6 SING N N 16 XDO C20 C1 SING N N 17 XDO C8 C9 SING N N 18 XDO C19 C18 DOUB N N 19 XDO C9 C1 SING N N 20 XDO C9 C4 SING N N 21 XDO O1 C17 SING N N 22 XDO C14 C13 SING N N 23 XDO C14 C15 SING N N 24 XDO C18 C13 SING N N 25 XDO C18 C17 SING N N 26 XDO C16 C17 SING N N 27 XDO C16 C15 SING N N 28 XDO C13 C12 DOUB N Z 29 XDO C6 C5 SING N N 30 XDO C1 C SING N N 31 XDO C1 C2 SING N N 32 XDO C12 C11 SING N N 33 XDO C15 O SING N N 34 XDO C11 C5 DOUB N E 35 XDO C5 C4 SING N N 36 XDO C4 C3 SING N N 37 XDO C2 C3 SING N N 38 XDO C7 H1 SING N N 39 XDO C7 H2 SING N N 40 XDO C8 H3 SING N N 41 XDO C8 H4 SING N N 42 XDO O1 H5 SING N N 43 XDO C6 H6 SING N N 44 XDO C6 H7 SING N N 45 XDO C4 H8 SING N N 46 XDO C3 H9 SING N N 47 XDO C3 H10 SING N N 48 XDO C2 H11 SING N N 49 XDO C2 H12 SING N N 50 XDO O2 H13 SING N N 51 XDO C H14 SING N N 52 XDO C H15 SING N N 53 XDO C H16 SING N N 54 XDO C10 H17 SING N N 55 XDO C10 H18 SING N N 56 XDO C10 H19 SING N N 57 XDO C11 H20 SING N N 58 XDO C12 H21 SING N N 59 XDO C19 H22 SING N N 60 XDO C19 H23 SING N N 61 XDO C17 H24 SING N N 62 XDO C16 H25 SING N N 63 XDO C16 H26 SING N N 64 XDO C15 H27 SING N N 65 XDO O H28 SING N N 66 XDO C14 H29 SING N N 67 XDO C14 H30 SING N N 68 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor XDO InChI InChI 1.06 "InChI=1S/C27H30F6O3/c1-17-19(15-20(34)16-22(17)35)9-8-18-7-6-12-24(3)21(18)10-14-23(24,2)11-4-5-13-25(36,26(28,29)30)27(31,32)33/h8-9,20-22,34-36H,1,6-7,10,12,14-16H2,2-3H3/b18-8+,19-9-/t20-,21+,22+,23+,24+/m1/s1" XDO InChIKey InChI 1.06 MVLLQZOKYYYEBT-ZUDXOIQDSA-N XDO SMILES_CANONICAL CACTVS 3.385 "C[C@@]1(CC[C@H]2C(/CCC[C@]12C)=C/C=C\3C[C@@H](O)C[C@H](O)C\3=C)C#CC#CC(O)(C(F)(F)F)C(F)(F)F" XDO SMILES CACTVS 3.385 "C[C]1(CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C[CH](O)C3=C)C#CC#CC(O)(C(F)(F)F)C(F)(F)F" XDO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@]1(CC[C@@H]\2[C@@]1(CCC/C2=C\C=C/3\C[C@H](C[C@@H](C3=C)O)O)C)C#CC#CC(C(F)(F)F)(C(F)(F)F)O" XDO SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C)C#CC#CC(C(F)(F)F)(C(F)(F)F)O" # _pdbx_chem_comp_identifier.comp_id XDO _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-1,7~{a}-dimethyl-1-[6,6,6-tris(fluoranyl)-5-oxidanyl-5-(trifluoromethyl)hexa-1,3-diynyl]-2,3,3~{a},5,6,7-hexahydroinden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XDO "Create component" 2023-06-06 PDBE XDO "Initial release" 2024-06-26 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XDO _pdbx_chem_comp_synonyms.name "Xe4MeCF3 analog" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #