data_XE6 # _chem_comp.id XE6 _chem_comp.name "4-amino-1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidin-2(1H)-one" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-11-14 _chem_comp.pdbx_modified_date 2023-09-15 _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 337.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XE6 _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 8F5C _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 XE6 O2 O1 O 0 1 N N N 0.602 -14.312 6.427 3.847 -0.909 0.541 O2 XE6 1 XE6 C2 C1 C 0 1 N N N 0.794 -13.232 6.980 3.460 0.230 0.337 C2 XE6 2 XE6 N3 N1 N 0 1 N N N 1.882 -13.030 7.805 4.346 1.179 0.041 N3 XE6 3 XE6 C4 C2 C 0 1 N N N 2.122 -11.861 8.396 3.953 2.426 -0.187 C4 XE6 4 XE6 N4 N2 N 0 1 N N N 3.195 -11.749 9.130 4.877 3.398 -0.492 N4 XE6 5 XE6 C5 C3 C 0 1 N N N 1.254 -10.793 8.202 2.582 2.748 -0.115 C5 XE6 6 XE6 C6 C4 C 0 1 N N N 0.115 -11.005 7.449 1.694 1.772 0.187 C6 XE6 7 XE6 N1 N3 N 0 1 N N N -0.084 -12.221 6.805 2.145 0.505 0.408 N1 XE6 8 XE6 "C1'" C5 C 0 1 N N S -1.224 -12.501 5.922 1.194 -0.562 0.730 "C1'" XE6 9 XE6 "O4'" O2 O 0 1 N N N -2.266 -11.528 6.194 -0.159 -0.057 0.721 "O4'" XE6 10 XE6 "C4'" C6 C 0 1 N N S -2.468 -10.747 4.989 -1.027 -1.187 0.534 "C4'" XE6 11 XE6 "C5'" C7 C 0 1 N N N -2.858 -9.301 5.330 -2.247 -0.774 -0.293 "C5'" XE6 12 XE6 "O5'" O3 O 0 1 N N N -1.834 -8.707 6.089 -3.040 0.149 0.455 "O5'" XE6 13 XE6 P P1 P 0 1 N N N -2.092 -7.294 6.810 -4.403 0.793 -0.109 P XE6 14 XE6 OP1 O4 O 0 1 N N N -0.799 -6.849 7.312 -5.326 -0.288 -0.522 OP1 XE6 15 XE6 OP2 O5 O 0 1 N N N -2.864 -6.334 5.913 -5.095 1.679 1.043 OP2 XE6 16 XE6 "C3'" C8 C 0 1 N N S -1.118 -10.892 4.320 -0.222 -2.263 -0.220 "C3'" XE6 17 XE6 "O3'" O6 O 0 1 N N N -1.230 -10.507 2.914 -0.151 -3.465 0.550 "O3'" XE6 18 XE6 "C2'" C9 C 0 1 N N S -0.822 -12.332 4.485 1.185 -1.640 -0.384 "C2'" XE6 19 XE6 "O2'" O7 O 0 1 N N N -1.748 -13.059 3.634 2.204 -2.615 -0.157 "O2'" XE6 20 XE6 C22 C10 C 0 1 N N N -1.508 -14.464 3.510 2.631 -3.296 -1.339 C22 XE6 21 XE6 H1 H1 H 0 1 N N N 3.812 -12.529 9.237 5.819 3.173 -0.541 H1 XE6 22 XE6 H2 H2 H 0 1 N N N 3.401 -10.883 9.586 4.586 4.308 -0.658 H2 XE6 23 XE6 H3 H3 H 0 1 N N N 1.464 -9.823 8.628 2.246 3.758 -0.297 H3 XE6 24 XE6 H4 H4 H 0 1 N N N -0.624 -10.223 7.360 0.639 1.994 0.249 H4 XE6 25 XE6 H5 H5 H 0 1 N N N -1.595 -13.523 6.089 1.431 -1.007 1.697 H5 XE6 26 XE6 H6 H6 H 0 1 N N N -3.248 -11.199 4.358 -1.349 -1.571 1.502 H6 XE6 27 XE6 H7 H7 H 0 1 N N N -3.003 -8.731 4.400 -1.915 -0.302 -1.218 H7 XE6 28 XE6 H8 H8 H 0 1 N N N -3.792 -9.300 5.910 -2.841 -1.657 -0.528 H8 XE6 29 XE6 H10 H10 H 0 1 N N N -2.364 -5.534 5.801 -5.923 2.099 0.772 H10 XE6 30 XE6 H11 H11 H 0 1 N N N -0.367 -10.278 4.839 -0.668 -2.460 -1.195 H11 XE6 31 XE6 H12 H12 H 0 1 N N N -1.420 -9.578 2.854 -1.005 -3.898 0.683 H12 XE6 32 XE6 H13 H13 H 0 1 N N N 0.234 -12.582 4.304 1.297 -1.184 -1.367 H13 XE6 33 XE6 H14 H14 H 0 1 N N N -2.265 -14.909 2.847 3.405 -4.019 -1.083 H14 XE6 34 XE6 H15 H15 H 0 1 N N N -0.507 -14.629 3.086 1.783 -3.815 -1.786 H15 XE6 35 XE6 H16 H16 H 0 1 N N N -1.568 -14.935 4.502 3.030 -2.573 -2.050 H16 XE6 36 XE6 OP3 OP3 O 0 1 N Y N -3.077 -7.640 8.020 -4.070 1.727 -1.378 OP3 XE6 37 XE6 H9 H9 H 0 1 N Y N -2.631 -7.489 8.845 -3.469 2.459 -1.181 H9 XE6 38 # 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 XE6 "O3'" "C3'" SING N N 1 XE6 C22 "O2'" SING N N 2 XE6 "O2'" "C2'" SING N N 3 XE6 "C3'" "C2'" SING N N 4 XE6 "C3'" "C4'" SING N N 5 XE6 "C2'" "C1'" SING N N 6 XE6 "C4'" "C5'" SING N N 7 XE6 "C4'" "O4'" SING N N 8 XE6 "C5'" "O5'" SING N N 9 XE6 OP2 P SING N N 10 XE6 "C1'" "O4'" SING N N 11 XE6 "C1'" N1 SING N N 12 XE6 "O5'" P SING N N 13 XE6 O2 C2 DOUB N N 14 XE6 N1 C2 SING N N 15 XE6 N1 C6 SING N N 16 XE6 P OP1 DOUB N N 17 XE6 C2 N3 SING N N 18 XE6 C6 C5 DOUB N N 19 XE6 N3 C4 DOUB N N 20 XE6 C5 C4 SING N N 21 XE6 C4 N4 SING N N 22 XE6 N4 H1 SING N N 23 XE6 N4 H2 SING N N 24 XE6 C5 H3 SING N N 25 XE6 C6 H4 SING N N 26 XE6 "C1'" H5 SING N N 27 XE6 "C4'" H6 SING N N 28 XE6 "C5'" H7 SING N N 29 XE6 "C5'" H8 SING N N 30 XE6 OP2 H10 SING N N 31 XE6 "C3'" H11 SING N N 32 XE6 "O3'" H12 SING N N 33 XE6 "C2'" H13 SING N N 34 XE6 C22 H14 SING N N 35 XE6 C22 H15 SING N N 36 XE6 C22 H16 SING N N 37 XE6 P OP3 SING N N 38 XE6 OP3 H9 SING N N 39 # 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 XE6 SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(N2C=CC(N)=NC2=O)C(OC)C1O" XE6 InChI InChI 1.06 "InChI=1S/C10H16N3O8P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m0/s1" XE6 InChIKey InChI 1.06 USRXKJOTSNCJMA-ZITKLIBNSA-N XE6 SMILES_CANONICAL CACTVS 3.385 "CO[C@H]1[C@@H](O)[C@H](CO[P](O)(O)=O)O[C@@H]1N2C=CC(=NC2=O)N" XE6 SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N" XE6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@H]1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" XE6 SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier XE6 "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidin-2(1H)-one" XE6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{S},5~{S})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XE6 "Create component" 2022-11-14 RCSB XE6 "Initial release" 2023-09-20 RCSB #