data_LHH # _chem_comp.id LHH _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-5-(4-acetamido-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H18 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-08-15 _chem_comp.pdbx_modified_date 2020-02-14 _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 379.260 _chem_comp.one_letter_code C _chem_comp.three_letter_code LHH _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 ? _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 LHH C4 C1 C 0 1 N N N ? ? ? -3.908 0.514 0.589 C4 LHH 1 LHH C5 C2 C 0 1 N N N ? ? ? -3.744 -0.490 1.563 C5 LHH 2 LHH C6 C3 C 0 1 N N N ? ? ? -2.559 -1.143 1.639 C6 LHH 3 LHH N1 N1 N 0 1 N N N ? ? ? -1.559 -0.813 0.774 N1 LHH 4 LHH C7 C4 C 0 1 N N N ? ? ? -5.262 2.152 -0.448 C7 LHH 5 LHH N3 N2 N 0 1 N N N ? ? ? -2.908 0.802 -0.232 N3 LHH 6 LHH N4 N3 N 0 1 N N N ? ? ? -5.108 1.192 0.486 N4 LHH 7 LHH C1 C5 C 0 1 N N N ? ? ? -1.041 -4.167 -1.603 C1 LHH 8 LHH C2 C6 C 0 1 N N N ? ? ? -1.748 0.152 -0.145 C2 LHH 9 LHH "C1'" C7 C 0 1 N N R ? ? ? -0.273 -1.510 0.846 "C1'" LHH 10 LHH "C2'" C8 C 0 1 N N R ? ? ? -0.025 -2.331 -0.445 "C2'" LHH 11 LHH "C3'" C9 C 0 1 N N R ? ? ? 1.520 -2.434 -0.472 "C3'" LHH 12 LHH "C4'" C10 C 0 1 N N R ? ? ? 1.991 -1.272 0.424 "C4'" LHH 13 LHH "C5'" C11 C 0 1 N N N ? ? ? 2.898 -0.333 -0.375 "C5'" LHH 14 LHH CM7 C12 C 0 1 N N N ? ? ? -6.570 2.891 -0.560 CM7 LHH 15 LHH O2 O1 O 0 1 N N N ? ? ? -0.842 0.435 -0.912 O2 LHH 16 LHH "O2'" O2 O 0 1 N N N ? ? ? -0.620 -3.626 -0.349 "O2'" LHH 17 LHH "O3'" O3 O 0 1 N N N ? ? ? 1.947 -3.686 0.067 "O3'" LHH 18 LHH "O4'" O4 O 0 1 N N N ? ? ? 0.818 -0.565 0.860 "O4'" LHH 19 LHH "O5'" O5 O 0 1 N N N ? ? ? 3.422 0.674 0.492 "O5'" LHH 20 LHH O7 O6 O 0 1 N N N ? ? ? -4.347 2.422 -1.197 O7 LHH 21 LHH OP1 O7 O 0 1 N N N ? ? ? 5.806 1.178 -0.496 OP1 LHH 22 LHH OP2 O8 O 0 1 N N N ? ? ? 3.795 2.560 -1.143 OP2 LHH 23 LHH P P1 P 0 1 N N N ? ? ? 4.417 1.835 -0.013 P LHH 24 LHH H1 H1 H 0 1 N N N ? ? ? -4.549 -0.735 2.239 H1 LHH 25 LHH H2 H2 H 0 1 N N N ? ? ? -2.408 -1.916 2.378 H2 LHH 26 LHH H3 H3 H 0 1 N N N ? ? ? -5.840 0.977 1.085 H3 LHH 27 LHH H4 H4 H 0 1 N N N ? ? ? -1.482 -5.151 -1.445 H4 LHH 28 LHH H5 H5 H 0 1 N N N ? ? ? -1.781 -3.505 -2.055 H5 LHH 29 LHH H6 H6 H 0 1 N N N ? ? ? -0.181 -4.257 -2.267 H6 LHH 30 LHH H7 H7 H 0 1 N N N ? ? ? -0.236 -2.156 1.724 H7 LHH 31 LHH H8 H8 H 0 1 N N N ? ? ? -0.394 -1.798 -1.322 H8 LHH 32 LHH H9 H9 H 0 1 N N N ? ? ? 1.893 -2.307 -1.488 H9 LHH 33 LHH H10 H10 H 0 1 N N N ? ? ? 2.532 -1.664 1.286 H10 LHH 34 LHH H11 H11 H 0 1 N N N ? ? ? 3.719 -0.903 -0.808 H11 LHH 35 LHH H12 H12 H 0 1 N N N ? ? ? 2.321 0.137 -1.171 H12 LHH 36 LHH H13 H13 H 0 1 N N N ? ? ? -6.546 3.773 0.080 H13 LHH 37 LHH H14 H14 H 0 1 N N N ? ? ? -6.727 3.198 -1.595 H14 LHH 38 LHH H15 H15 H 0 1 N N N ? ? ? -7.385 2.238 -0.248 H15 LHH 39 LHH H16 H16 H 0 1 N N N ? ? ? 2.907 -3.804 0.075 H16 LHH 40 LHH H17 H17 H 0 1 N N N ? ? ? 6.270 0.686 0.195 H17 LHH 41 LHH OP3 OP3 O 0 1 N N N ? ? ? 4.701 2.862 1.193 OP3 LHH 42 LHH H18 H18 H 0 1 N N N ? ? ? 5.294 3.589 0.960 H18 LHH 43 # # 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 LHH O2 C2 DOUB N N 1 LHH C1 "O2'" SING N N 2 LHH N3 C2 SING N N 3 LHH N3 C4 DOUB N N 4 LHH C2 N1 SING N N 5 LHH N4 C4 SING N N 6 LHH N4 C7 SING N N 7 LHH C4 C5 SING N N 8 LHH "O2'" "C2'" SING N N 9 LHH N1 "C1'" SING N N 10 LHH N1 C6 SING N N 11 LHH "C1'" "C2'" SING N N 12 LHH "C1'" "O4'" SING N N 13 LHH O7 C7 DOUB N N 14 LHH "C2'" "C3'" SING N N 15 LHH C7 CM7 SING N N 16 LHH C5 C6 DOUB N N 17 LHH "O4'" "C4'" SING N N 18 LHH "C3'" "C4'" SING N N 19 LHH "C3'" "O3'" SING N N 20 LHH "C4'" "C5'" SING N N 21 LHH "C5'" "O5'" SING N N 22 LHH "O5'" P SING N N 23 LHH P OP1 SING N N 24 LHH P OP2 DOUB N N 25 LHH C5 H1 SING N N 26 LHH C6 H2 SING N N 27 LHH N4 H3 SING N N 28 LHH C1 H4 SING N N 29 LHH C1 H5 SING N N 30 LHH C1 H6 SING N N 31 LHH "C1'" H7 SING N N 32 LHH "C2'" H8 SING N N 33 LHH "C3'" H9 SING N N 34 LHH "C4'" H10 SING N N 35 LHH "C5'" H11 SING N N 36 LHH "C5'" H12 SING N N 37 LHH CM7 H13 SING N N 38 LHH CM7 H14 SING N N 39 LHH CM7 H15 SING N N 40 LHH "O3'" H16 SING N N 41 LHH OP1 H17 SING N N 42 LHH P OP3 SING N N 43 LHH OP3 H18 SING N N 44 # # 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 LHH InChI InChI 1.03 "InChI=1S/C12H18N3O9P/c1-6(16)13-8-3-4-15(12(18)14-8)11-10(22-2)9(17)7(24-11)5-23-25(19,20)21/h3-4,7,9-11,17H,5H2,1-2H3,(H2,19,20,21)(H,13,14,16,18)/t7-,9-,10-,11-/m1/s1" LHH InChIKey InChI 1.03 XSIWUOJELZFTTR-QCNRFFRDSA-N LHH 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)NC(C)=O" LHH SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)NC(C)=O" LHH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC" LHH SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1=NC(=O)N(C=C1)C2C(C(C(O2)COP(=O)(O)O)O)OC" # _pdbx_chem_comp_identifier.comp_id LHH _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})-5-(4-acetamido-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 LHH "Create component" 2019-08-15 EBI LHH "Initial release" 2020-02-19 RCSB ##