data_6XM # _chem_comp.id 6XM _chem_comp.name "8,12-bis(2-morpholinoethyl)-8H-benzo[ij]xantheno[1,9,8-cdef][2,7]naphthyridin-12-iumhexafluorophosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H34 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-07-15 _chem_comp.pdbx_modified_date 2018-02-27 _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 510.627 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6XM _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 5LIG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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.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 6XM C1 C1 C 0 1 Y N N 19.814 25.841 24.287 -2.368 4.178 0.485 C1 6XM 1 6XM C2 C2 C 0 1 Y N N 20.015 24.987 25.366 -3.454 3.542 1.055 C2 6XM 2 6XM CA C3 C 0 1 N N N 20.892 20.908 24.482 -3.666 -0.727 0.928 CA 6XM 3 6XM CB C4 C 0 1 N N N 19.355 20.833 24.633 -4.165 -1.110 -0.466 CB 6XM 4 6XM CC1 C5 C 0 1 N N N 17.491 19.256 25.095 -5.811 -2.446 -1.638 CC1 6XM 5 6XM CD1 C6 C 0 1 N N N 16.621 20.011 26.130 -7.093 -3.263 -1.457 CD1 6XM 6 6XM O1 O1 O 0 1 N N N 17.094 19.728 27.475 -8.116 -2.422 -0.917 O1 6XM 7 6XM CD2 C7 C 0 1 N N N 18.487 20.091 27.684 -7.773 -1.832 0.340 CD2 6XM 8 6XM CC2 C8 C 0 1 N N N 19.388 19.344 26.669 -6.497 -1.001 0.177 CC2 6XM 9 6XM N2 N1 N 0 1 N N N 18.943 19.548 25.257 -5.424 -1.858 -0.348 N2 6XM 10 6XM N1 N2 N 0 1 N N N 21.366 22.024 23.630 -2.410 0.018 0.810 N1 6XM 11 6XM C6 C9 C 0 1 Y N N 20.929 23.308 23.868 -2.417 1.413 0.690 C6 6XM 12 6XM C7 C10 C 0 1 Y N N 20.743 24.186 22.801 -1.351 2.049 0.072 C7 6XM 13 6XM C3 C11 C 0 1 Y N N 20.593 23.737 25.156 -3.484 2.164 1.165 C3 6XM 14 6XM C8 C12 C 0 1 Y N N 20.184 25.445 23.008 -1.302 3.433 -0.003 C8 6XM 15 6XM O O2 O 0 1 N N N 19.987 26.296 21.941 -0.214 4.051 -0.530 O 6XM 16 6XM "C8'" C13 C 0 1 Y N N 20.402 25.931 20.677 0.982 3.409 -0.527 "C8'" 6XM 17 6XM "C1'" C14 C 0 1 Y N N 20.234 26.815 19.621 2.168 4.131 -0.564 "C1'" 6XM 18 6XM "C2'" C15 C 0 1 Y N N 20.693 26.488 18.353 3.383 3.472 -0.541 "C2'" 6XM 19 6XM "C3'" C16 C 0 1 Y N N 21.327 25.267 18.153 3.431 2.092 -0.471 "C3'" 6XM 20 6XM "C6'" C17 C 0 1 Y N N 21.487 24.347 19.198 2.250 1.362 -0.435 "C6'" 6XM 21 6XM "C7'" C18 C 0 1 Y N N 21.010 24.697 20.463 1.033 2.024 -0.494 "C7'" 6XM 22 6XM C11 C19 C 0 1 N N S 21.155 23.822 21.528 -0.248 1.237 -0.550 C11 6XM 23 6XM C10 C20 C 0 1 Y N N 21.822 22.624 21.344 -0.089 -0.071 0.172 C10 6XM 24 6XM C9 C21 C 0 1 Y N N 22.009 21.771 22.439 -1.182 -0.653 0.799 C9 6XM 25 6XM C4 C22 C 0 1 Y N N 22.831 20.651 22.283 -1.045 -1.889 1.417 C4 6XM 26 6XM C5 C23 C 0 1 Y N N 23.434 20.378 21.060 0.186 -2.519 1.434 C5 6XM 27 6XM "C4'" C24 C 0 1 Y N N 23.187 21.201 19.965 1.286 -1.918 0.851 "C4'" 6XM 28 6XM "C9'" C25 C 0 1 Y N N 22.359 22.325 20.085 1.155 -0.683 0.230 "C9'" 6XM 29 6XM "N1'" N3 N 0 1 N N N 22.058 23.109 18.991 2.273 -0.031 -0.302 "N1'" 6XM 30 6XM "CA'" C26 C 0 1 N N N 22.110 22.542 17.629 3.453 -0.796 -0.714 "CA'" 6XM 31 6XM "CB'" C27 C 0 1 N N N 23.393 22.907 16.856 4.415 -0.926 0.469 "CB'" 6XM 32 6XM "N2'" N4 N 0 1 N N N 23.153 22.839 15.393 5.597 -1.693 0.056 "N2'" 6XM 33 6XM "CC2'" C28 C 0 0 N N N 22.810 21.483 14.863 6.430 -2.043 1.216 "CC2'" 6XM 34 6XM "CD2'" C29 C 0 0 N N N 24.065 20.598 14.658 7.616 -2.891 0.749 "CD2'" 6XM 35 6XM "O1'" O3 O 0 1 N N N 25.046 21.296 13.844 8.349 -2.170 -0.246 "O1'" 6XM 36 6XM "CD1'" C30 C 0 0 N N N 25.457 22.575 14.405 7.568 -1.813 -1.390 "CD1'" 6XM 37 6XM "CC1'" C31 C 0 0 N N N 24.220 23.488 14.581 6.381 -0.955 -0.945 "CC1'" 6XM 38 6XM H1 H1 H 0 1 N N N 19.370 26.813 24.444 -2.349 5.255 0.414 H1 6XM 39 6XM H2 H2 H 0 1 N N N 19.725 25.291 26.361 -4.287 4.126 1.419 H2 6XM 40 6XM HA1 H3 H 0 1 N N N 21.241 19.964 24.039 -4.413 -0.105 1.423 HA1 6XM 41 6XM HA2 H4 H 0 1 N N N 21.331 21.028 25.483 -3.499 -1.630 1.516 HA2 6XM 42 6XM HB2 H5 H 0 1 N N N 19.015 21.666 25.266 -4.332 -0.208 -1.054 HB2 6XM 43 6XM HB1 H6 H 0 1 N N N 18.891 20.915 23.639 -3.418 -1.732 -0.961 HB1 6XM 44 6XM HC2 H7 H 0 1 N N N 17.180 19.558 24.084 -5.012 -3.097 -1.996 HC2 6XM 45 6XM HC1 H8 H 0 1 N N N 17.331 18.175 25.220 -5.985 -1.651 -2.363 HC1 6XM 46 6XM HD2 H9 H 0 1 N N N 16.686 21.093 25.941 -7.415 -3.654 -2.422 HD2 6XM 47 6XM HD1 H10 H 0 1 N N N 15.575 19.684 26.035 -6.904 -4.090 -0.773 HD1 6XM 48 6XM HD3 H11 H 0 1 N N N 18.785 19.817 28.707 -8.586 -1.189 0.675 HD3 6XM 49 6XM HD4 H12 H 0 1 N N N 18.605 21.176 27.546 -7.604 -2.618 1.077 HD4 6XM 50 6XM HC3 H13 H 0 1 N N N 19.360 18.268 26.897 -6.683 -0.183 -0.519 HC3 6XM 51 6XM HC4 H14 H 0 1 N N N 20.419 19.714 26.772 -6.201 -0.596 1.144 HC4 6XM 52 6XM H3 H16 H 0 1 N N N 20.784 23.090 26.000 -4.333 1.675 1.618 H3 6XM 53 6XM "H1'" H17 H 0 1 N N N 19.743 27.763 19.787 2.141 5.210 -0.611 "H1'" 6XM 54 6XM "H2'" H18 H 0 1 N N N 20.559 27.175 17.530 4.301 4.039 -0.579 "H2'" 6XM 55 6XM "H3'" H19 H 0 1 N N N 21.704 25.022 17.171 4.383 1.584 -0.445 "H3'" 6XM 56 6XM H7 H20 H 0 1 N N N 20.184 23.351 21.314 -0.498 1.031 -1.591 H7 6XM 57 6XM H4 H21 H 0 1 N N N 22.999 19.991 23.121 -1.898 -2.357 1.884 H4 6XM 58 6XM H5 H22 H 0 1 N N N 24.093 19.528 20.960 0.288 -3.485 1.905 H5 6XM 59 6XM "H4'" H23 H 0 1 N N N 23.639 20.971 19.012 2.247 -2.409 0.878 "H4'" 6XM 60 6XM "HA2'" H24 H 0 0 N N N 21.245 22.917 17.063 3.145 -1.788 -1.043 "HA2'" 6XM 61 6XM "HA1'" H25 H 0 0 N N N 22.051 21.446 17.706 3.952 -0.280 -1.533 "HA1'" 6XM 62 6XM "HB1'" H26 H 0 0 N N N 24.192 22.200 17.125 4.722 0.066 0.798 "HB1'" 6XM 63 6XM "HB2'" H27 H 0 0 N N N 23.700 23.928 17.126 3.915 -1.442 1.289 "HB2'" 6XM 64 6XM "HC3'" H29 H 0 0 N N N 22.298 21.600 13.897 6.797 -1.132 1.688 "HC3'" 6XM 65 6XM "HC4'" H30 H 0 0 N N N 22.138 20.984 15.576 5.836 -2.611 1.932 "HC4'" 6XM 66 6XM "HD3'" H31 H 0 0 N N N 23.773 19.665 14.154 8.267 -3.104 1.596 "HD3'" 6XM 67 6XM "HD4'" H32 H 0 0 N N N 24.507 20.363 15.637 7.251 -3.826 0.325 "HD4'" 6XM 68 6XM "HD2'" H33 H 0 0 N N N 25.932 22.410 15.383 8.184 -1.248 -2.089 "HD2'" 6XM 69 6XM "HD1'" H34 H 0 0 N N N 26.175 23.058 13.726 7.201 -2.717 -1.876 "HD1'" 6XM 70 6XM "HC2'" H35 H 0 0 N N N 24.533 24.415 15.083 5.752 -0.729 -1.806 "HC2'" 6XM 71 6XM "HC1'" H36 H 0 0 N N N 23.813 23.728 13.588 6.748 -0.026 -0.507 "HC1'" 6XM 72 # 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 6XM "O1'" "CD1'" SING N N 1 6XM "O1'" "CD2'" SING N N 2 6XM "CD1'" "CC1'" SING N N 3 6XM "CC1'" "N2'" SING N N 4 6XM "CD2'" "CC2'" SING N N 5 6XM "CC2'" "N2'" SING N N 6 6XM "N2'" "CB'" SING N N 7 6XM "CB'" "CA'" SING N N 8 6XM "CA'" "N1'" SING N N 9 6XM "C3'" "C2'" DOUB Y N 10 6XM "C3'" "C6'" SING Y N 11 6XM "C2'" "C1'" SING Y N 12 6XM "N1'" "C6'" SING N N 13 6XM "N1'" "C9'" SING N N 14 6XM "C6'" "C7'" DOUB Y N 15 6XM "C1'" "C8'" DOUB Y N 16 6XM "C4'" "C9'" SING Y N 17 6XM "C4'" C5 DOUB Y N 18 6XM "C9'" C10 DOUB Y N 19 6XM "C7'" "C8'" SING Y N 20 6XM "C7'" C11 SING N N 21 6XM "C8'" O SING N N 22 6XM C5 C4 SING Y N 23 6XM C10 C11 SING N N 24 6XM C10 C9 SING Y N 25 6XM C11 C7 SING N N 26 6XM O C8 SING N N 27 6XM C4 C9 DOUB Y N 28 6XM C9 N1 SING N N 29 6XM C7 C8 SING Y N 30 6XM C7 C6 DOUB Y N 31 6XM C8 C1 DOUB Y N 32 6XM N1 C6 SING N N 33 6XM N1 CA SING N N 34 6XM C6 C3 SING Y N 35 6XM C1 C2 SING Y N 36 6XM CA CB SING N N 37 6XM CB N2 SING N N 38 6XM CC1 N2 SING N N 39 6XM CC1 CD1 SING N N 40 6XM C3 C2 DOUB Y N 41 6XM N2 CC2 SING N N 42 6XM CD1 O1 SING N N 43 6XM CC2 CD2 SING N N 44 6XM O1 CD2 SING N N 45 6XM C1 H1 SING N N 46 6XM C2 H2 SING N N 47 6XM CA HA1 SING N N 48 6XM CA HA2 SING N N 49 6XM CB HB2 SING N N 50 6XM CB HB1 SING N N 51 6XM CC1 HC2 SING N N 52 6XM CC1 HC1 SING N N 53 6XM CD1 HD2 SING N N 54 6XM CD1 HD1 SING N N 55 6XM CD2 HD3 SING N N 56 6XM CD2 HD4 SING N N 57 6XM CC2 HC3 SING N N 58 6XM CC2 HC4 SING N N 59 6XM C3 H3 SING N N 60 6XM "C1'" "H1'" SING N N 61 6XM "C2'" "H2'" SING N N 62 6XM "C3'" "H3'" SING N N 63 6XM C11 H7 SING N N 64 6XM C4 H4 SING N N 65 6XM C5 H5 SING N N 66 6XM "C4'" "H4'" SING N N 67 6XM "CA'" "HA2'" SING N N 68 6XM "CA'" "HA1'" SING N N 69 6XM "CB'" "HB1'" SING N N 70 6XM "CB'" "HB2'" SING N N 71 6XM "CC2'" "HC3'" SING N N 72 6XM "CC2'" "HC4'" SING N N 73 6XM "CD2'" "HD3'" SING N N 74 6XM "CD2'" "HD4'" SING N N 75 6XM "CD1'" "HD2'" SING N N 76 6XM "CD1'" "HD1'" SING N N 77 6XM "CC1'" "HC2'" SING N N 78 6XM "CC1'" "HC1'" SING N N 79 # 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 6XM InChI InChI 1.03 "InChI=1S/C31H34N4O3/c1-4-22-28-23(5-1)35(13-11-33-16-20-37-21-17-33)25-7-3-9-27-30(25)31(28)29-24(6-2-8-26(29)38-27)34(22)12-10-32-14-18-36-19-15-32/h1-9,31H,10-21H2" 6XM InChIKey InChI 1.03 JDODSALIMITEDK-UHFFFAOYSA-N 6XM SMILES_CANONICAL CACTVS 3.385 "C1CN(CCO1)CCN2c3cccc4Oc5cccc6N(CCN7CCOCC7)c8cccc2c8[C@@H](c34)c56" 6XM SMILES CACTVS 3.385 "C1CN(CCO1)CCN2c3cccc4Oc5cccc6N(CCN7CCOCC7)c8cccc2c8[CH](c34)c56" 6XM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1cc2c3c(c1)N(c4cccc5c4C3c6c(cccc6O5)N2CCN7CCOCC7)CCN8CCOCC8" 6XM SMILES "OpenEye OEToolkits" 2.0.6 "c1cc2c3c(c1)N(c4cccc5c4C3c6c(cccc6O5)N2CCN7CCOCC7)CCN8CCOCC8" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 6XM "Create component" 2016-07-15 EBI 6XM "Initial release" 2016-09-14 RCSB 6XM "Other modification" 2018-02-27 EBI #