data_A1IC1 # _chem_comp.id A1IC1 _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-4-methoxy-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-06-04 _chem_comp.pdbx_modified_date 2024-12-20 _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 352.234 _chem_comp.one_letter_code U _chem_comp.three_letter_code A1IC1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 9F67 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1IC1 "C5'" C1 C 0 1 N N N N N N 166.657 109.048 127.765 2.565 0.608 0.379 "C5'" A1IC1 1 A1IC1 O4 O1 O 0 1 N N N N N N 167.693 117.510 126.328 -4.986 -2.627 1.085 O4 A1IC1 2 A1IC1 "O5'" O2 O 0 1 N N N N N N 166.616 108.679 126.386 3.224 -0.333 -0.472 "O5'" A1IC1 3 A1IC1 OP3 O3 O 0 1 N Y N N N N 165.771 109.363 124.144 5.134 -1.925 -1.326 OP3 A1IC1 4 A1IC1 C55 C2 C 0 1 N N N N N N 168.000 115.692 124.406 -5.248 -1.511 -1.361 C55 A1IC1 5 A1IC1 C4 C3 C 0 1 N N N N N N 167.775 116.349 126.725 -4.078 -1.892 0.741 C4 A1IC1 6 A1IC1 "C4'" C4 C 0 1 N N R N N N 167.650 110.196 127.972 1.267 1.072 -0.285 "C4'" A1IC1 7 A1IC1 C50 C5 C 0 1 N N N N N N 167.405 113.609 131.131 -2.163 3.913 0.740 C50 A1IC1 8 A1IC1 N1 N1 N 0 1 N N N N N N 167.946 113.766 127.520 -2.058 -0.249 -0.033 N1 A1IC1 9 A1IC1 C5 C6 C 0 1 N N N N N N 167.699 116.073 128.076 -2.974 -1.670 1.599 C5 A1IC1 10 A1IC1 C6 C7 C 0 1 N N N N N N 167.797 114.755 128.474 -1.981 -0.850 1.194 C6 A1IC1 11 A1IC1 "C1'" C8 C 0 1 N N R N N N 168.064 112.364 127.963 -0.980 0.641 -0.474 "C1'" A1IC1 12 A1IC1 "C2'" C9 C 0 1 N N R N N N 167.481 112.155 129.317 -0.913 1.892 0.431 "C2'" A1IC1 13 A1IC1 "C3'" C10 C 0 1 N N R N N N 167.607 110.643 129.425 0.599 2.182 0.558 "C3'" A1IC1 14 A1IC1 O2 O4 O 0 1 N N N N N N 168.155 113.225 125.378 -3.155 0.068 -1.930 O2 A1IC1 15 A1IC1 C2 C11 C 0 1 N N N N N N 168.019 114.091 126.233 -3.110 -0.472 -0.842 C2 A1IC1 16 A1IC1 N3 N2 N 0 1 N N N N N N 167.932 115.362 125.845 -4.114 -1.285 -0.462 N3 A1IC1 17 A1IC1 "O4'" O5 O 0 1 N N N N N N 167.317 111.389 127.239 0.302 -0.002 -0.310 "O4'" A1IC1 18 A1IC1 "O2'" O6 O 0 1 N N N N N N 168.271 112.825 130.306 -1.584 2.993 -0.186 "O2'" A1IC1 19 A1IC1 OP1 O7 O 0 1 N N N N N N 164.222 108.291 125.865 5.629 0.013 0.214 OP1 A1IC1 20 A1IC1 "O3'" O8 O 0 1 N N N N N N 168.840 110.266 130.035 0.909 3.471 0.023 "O3'" A1IC1 21 A1IC1 P P1 P 0 1 N N N N N N 165.368 109.166 125.548 4.623 -1.031 -0.088 P A1IC1 22 A1IC1 "H5'" H1 H 0 1 N N N N N N 165.655 109.371 128.085 2.336 0.135 1.334 "H5'" A1IC1 23 A1IC1 "H5''" H2 H 0 0 N N N N N N 166.972 108.181 128.365 3.215 1.466 0.545 "H5''" A1IC1 24 A1IC1 HOP3 H3 H 0 0 N Y N N N N 165.197 108.862 123.576 5.974 -2.376 -1.165 HOP3 A1IC1 25 A1IC1 H4 H4 H 0 1 N N N N N N 167.912 116.781 124.274 -5.039 -2.368 -2.001 H4 A1IC1 26 A1IC1 H1 H5 H 0 1 N N N N N N 168.962 115.350 123.997 -6.144 -1.707 -0.772 H1 A1IC1 27 A1IC1 H2 H6 H 0 1 N N N N N N 167.177 115.191 123.876 -5.406 -0.626 -1.977 H2 A1IC1 28 A1IC1 "H4'" H7 H 0 1 N N N N N N 168.665 109.853 127.721 1.465 1.430 -1.295 "H4'" A1IC1 29 A1IC1 H8 H8 H 0 1 N N N N N N 167.999 114.130 131.896 -2.897 3.395 1.358 H8 A1IC1 30 A1IC1 H9 H9 H 0 1 N N N N N N 166.878 114.348 130.510 -1.382 4.329 1.377 H9 A1IC1 31 A1IC1 H10 H10 H 0 1 N N N N N N 166.672 112.952 131.621 -2.653 4.719 0.194 H10 A1IC1 32 A1IC1 H5 H11 H 0 1 N N N N N N 167.567 116.864 128.799 -2.927 -2.150 2.565 H5 A1IC1 33 A1IC1 H6 H12 H 0 1 N N N N N N 167.758 114.499 129.522 -1.131 -0.669 1.834 H6 A1IC1 34 A1IC1 "H1'" H13 H 0 1 N N N N N N 169.127 112.080 127.984 -1.131 0.932 -1.513 "H1'" A1IC1 35 A1IC1 "H2'" H14 H 0 1 N N N N N N 166.426 112.463 129.350 -1.345 1.680 1.409 "H2'" A1IC1 36 A1IC1 "H3'" H15 H 0 1 N N N N N N 166.736 110.213 129.942 0.915 2.113 1.599 "H3'" A1IC1 37 A1IC1 "HO3'" H17 H 0 0 N N N N N N 168.838 110.535 130.946 1.853 3.680 0.023 "HO3'" A1IC1 38 A1IC1 OP2 O9 O 0 1 N N N N N N ? ? ? 4.419 -1.969 1.204 OP2 A1IC1 39 A1IC1 HOP2 H19 H 0 0 N N N N N N ? ? ? 3.772 -2.677 1.078 HOP2 A1IC1 40 # 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 A1IC1 OP3 P SING N N 1 A1IC1 C55 N3 SING N N 2 A1IC1 O2 C2 DOUB N N 3 A1IC1 P OP1 DOUB N N 4 A1IC1 P "O5'" SING N N 5 A1IC1 N3 C2 SING N N 6 A1IC1 N3 C4 SING N N 7 A1IC1 C2 N1 SING N N 8 A1IC1 O4 C4 DOUB N N 9 A1IC1 "O5'" "C5'" SING N N 10 A1IC1 C4 C5 SING N N 11 A1IC1 "O4'" "C1'" SING N N 12 A1IC1 "O4'" "C4'" SING N N 13 A1IC1 N1 "C1'" SING N N 14 A1IC1 N1 C6 SING N N 15 A1IC1 "C5'" "C4'" SING N N 16 A1IC1 "C1'" "C2'" SING N N 17 A1IC1 "C4'" "C3'" SING N N 18 A1IC1 C5 C6 DOUB N N 19 A1IC1 "C2'" "C3'" SING N N 20 A1IC1 "C2'" "O2'" SING N N 21 A1IC1 "C3'" "O3'" SING N N 22 A1IC1 "O2'" C50 SING N N 23 A1IC1 "C5'" "H5'" SING N N 24 A1IC1 "C5'" "H5''" SING N N 25 A1IC1 OP3 HOP3 SING N N 26 A1IC1 C55 H4 SING N N 27 A1IC1 C55 H1 SING N N 28 A1IC1 C55 H2 SING N N 29 A1IC1 "C4'" "H4'" SING N N 30 A1IC1 C50 H8 SING N N 31 A1IC1 C50 H9 SING N N 32 A1IC1 C50 H10 SING N N 33 A1IC1 C5 H5 SING N N 34 A1IC1 C6 H6 SING N N 35 A1IC1 "C1'" "H1'" SING N N 36 A1IC1 "C2'" "H2'" SING N N 37 A1IC1 "C3'" "H3'" SING N N 38 A1IC1 "O3'" "HO3'" SING N N 39 A1IC1 P OP2 SING N N 40 A1IC1 OP2 HOP2 SING N N 41 # 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 A1IC1 InChI InChI 1.06 "InChI=1S/C11H17N2O9P/c1-12-7(14)3-4-13(11(12)16)10-9(20-2)8(15)6(22-10)5-21-23(17,18)19/h3-4,6,8-10,15H,5H2,1-2H3,(H2,17,18,19)/t6-,8-,9-,10-/m1/s1" A1IC1 InChIKey InChI 1.06 DXHZPCMDHBXXMJ-PEBGCTIMSA-N A1IC1 SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)N(C)C2=O" A1IC1 SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)N(C)C2=O" A1IC1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC" A1IC1 SMILES "OpenEye OEToolkits" 2.0.7 "CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC" # _pdbx_chem_comp_identifier.comp_id A1IC1 _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 "[(2~{R},3~{R},4~{R},5~{R})-4-methoxy-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-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 A1IC1 "Create component" 2024-06-04 PDBE A1IC1 "Modify linking type" 2024-06-07 PDBE A1IC1 "Modify parent residue" 2024-06-07 PDBE A1IC1 "Initial release" 2024-12-25 RCSB #