data_LV2 # _chem_comp.id LV2 _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-[4-(dimethylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H18 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-09-10 _chem_comp.pdbx_modified_date 2020-07-24 _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 351.250 _chem_comp.one_letter_code C _chem_comp.three_letter_code LV2 _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 6SKG _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 LV2 P P1 P 0 1 N N N 205.474 279.251 190.612 4.525 1.375 0.128 P LV2 1 LV2 OP1 O1 O 0 1 N N N 205.961 279.758 189.279 5.642 0.579 -0.430 OP1 LV2 2 LV2 OP2 O2 O 0 1 N N N 206.378 279.326 191.815 4.033 2.449 -0.966 OP2 LV2 3 LV2 "O5'" O3 O 0 1 N N N 204.108 279.997 190.946 3.305 0.395 0.505 "O5'" LV2 4 LV2 "C5'" C1 C 0 1 N N N 203.040 280.025 190.009 2.710 -0.504 -0.433 "C5'" LV2 5 LV2 "C4'" C2 C 0 1 N N R 201.729 280.327 190.689 1.584 -1.282 0.250 "C4'" LV2 6 LV2 "O4'" O4 O 0 1 N N N 201.445 279.289 191.657 0.471 -0.407 0.538 "O4'" LV2 7 LV2 "C3'" C3 C 0 1 N N S 201.691 281.618 191.493 1.009 -2.349 -0.707 "C3'" LV2 8 LV2 "C2'" C4 C 0 1 N N R 200.638 281.335 192.558 -0.507 -2.348 -0.405 "C2'" LV2 9 LV2 "O2'" O5 O 0 1 N N N 199.333 281.546 192.041 -0.923 -3.629 0.072 "O2'" LV2 10 LV2 "C1'" C5 C 0 1 N N R 200.823 279.837 192.796 -0.668 -1.280 0.700 "C1'" LV2 11 LV2 N1 N1 N 0 1 N N N 201.668 279.526 193.971 -1.914 -0.533 0.509 N1 LV2 12 LV2 C2 C6 C 0 1 N N N 201.065 279.154 195.188 -2.097 0.189 -0.612 C2 LV2 13 LV2 O2 O6 O 0 1 N N N 199.820 279.118 195.281 -1.220 0.213 -1.460 O2 LV2 14 LV2 N3 N2 N 0 1 N N N 201.827 278.842 196.256 -3.220 0.877 -0.811 N3 LV2 15 LV2 C4 C7 C 0 1 N N N 203.170 278.873 196.164 -4.189 0.867 0.094 C4 LV2 16 LV2 N4 N3 N 0 1 N N N 203.942 278.546 197.280 -5.345 1.581 -0.123 N4 LV2 17 LV2 C5 C8 C 0 1 N N N 203.780 279.227 194.969 -4.029 0.121 1.280 C5 LV2 18 LV2 C6 C9 C 0 1 N N N 202.999 279.550 193.869 -2.884 -0.578 1.465 C6 LV2 19 LV2 CM4 C10 C 0 1 N N N 203.290 278.015 198.464 -5.460 2.449 -1.298 CM4 LV2 20 LV2 "O3'" O7 O 0 1 N N N 201.383 282.741 190.686 1.574 -3.631 -0.426 "O3'" LV2 21 LV2 C1 C11 C 0 1 N N N 205.386 278.720 197.256 -6.460 1.474 0.821 C1 LV2 22 LV2 H2 H2 H 0 1 N N N 207.208 279.714 191.564 3.302 3.007 -0.667 H2 LV2 23 LV2 H3 H3 H 0 1 N N N 202.971 279.045 189.514 2.305 0.061 -1.272 H3 LV2 24 LV2 H4 H4 H 0 1 N N N 203.242 280.802 189.257 3.465 -1.202 -0.796 H4 LV2 25 LV2 H5 H5 H 0 1 N N N 200.932 280.358 189.931 1.947 -1.750 1.165 H5 LV2 26 LV2 H6 H6 H 0 1 N N N 202.664 281.758 191.986 1.191 -2.069 -1.745 H6 LV2 27 LV2 H7 H7 H 0 1 N N N 200.833 281.910 193.475 -1.073 -2.067 -1.293 H7 LV2 28 LV2 H8 H8 H 0 1 N N N 198.691 281.365 192.717 -0.787 -4.347 -0.561 H8 LV2 29 LV2 H9 H9 H 0 1 N N N 199.831 279.383 192.938 -0.652 -1.747 1.684 H9 LV2 30 LV2 H10 H10 H 0 1 N N N 204.857 279.251 194.896 -4.809 0.104 2.026 H10 LV2 31 LV2 H11 H11 H 0 1 N N N 203.466 279.820 192.933 -2.739 -1.161 2.362 H11 LV2 32 LV2 H12 H12 H 0 1 N N N 204.044 277.815 199.240 -5.872 1.880 -2.131 H12 LV2 33 LV2 H13 H13 H 0 1 N N N 202.562 278.748 198.841 -6.120 3.286 -1.068 H13 LV2 34 LV2 H14 H14 H 0 1 N N N 202.770 277.080 198.208 -4.475 2.827 -1.568 H14 LV2 35 LV2 H15 H15 H 0 1 N N N 201.369 283.524 191.224 1.248 -4.339 -0.999 H15 LV2 36 LV2 H16 H16 H 0 1 N N N 205.809 278.409 198.222 -6.160 0.860 1.670 H16 LV2 37 LV2 H17 H17 H 0 1 N N N 205.816 278.104 196.452 -6.736 2.468 1.172 H17 LV2 38 LV2 H18 H18 H 0 1 N N N 205.625 279.778 197.075 -7.314 1.014 0.324 H18 LV2 39 LV2 OP3 OP3 O 0 1 N Y N 205.041 277.720 190.416 5.024 2.145 1.451 OP3 LV2 40 LV2 H1 H1 H 0 1 N N N 205.183 277.464 189.512 5.760 2.754 1.298 H1 LV2 41 # # 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 LV2 OP1 P DOUB N N 1 LV2 "C5'" "C4'" SING N N 2 LV2 "C5'" "O5'" SING N N 3 LV2 P "O5'" SING N N 4 LV2 P OP2 SING N N 5 LV2 "O3'" "C3'" SING N N 6 LV2 "C4'" "C3'" SING N N 7 LV2 "C4'" "O4'" SING N N 8 LV2 "C3'" "C2'" SING N N 9 LV2 "O4'" "C1'" SING N N 10 LV2 "O2'" "C2'" SING N N 11 LV2 "C2'" "C1'" SING N N 12 LV2 "C1'" N1 SING N N 13 LV2 C6 N1 SING N N 14 LV2 C6 C5 DOUB N N 15 LV2 N1 C2 SING N N 16 LV2 C5 C4 SING N N 17 LV2 C2 O2 DOUB N N 18 LV2 C2 N3 SING N N 19 LV2 C4 N3 DOUB N N 20 LV2 C4 N4 SING N N 21 LV2 C1 N4 SING N N 22 LV2 N4 CM4 SING N N 23 LV2 OP2 H2 SING N N 24 LV2 "C5'" H3 SING N N 25 LV2 "C5'" H4 SING N N 26 LV2 "C4'" H5 SING N N 27 LV2 "C3'" H6 SING N N 28 LV2 "C2'" H7 SING N N 29 LV2 "O2'" H8 SING N N 30 LV2 "C1'" H9 SING N N 31 LV2 C5 H10 SING N N 32 LV2 C6 H11 SING N N 33 LV2 CM4 H12 SING N N 34 LV2 CM4 H13 SING N N 35 LV2 CM4 H14 SING N N 36 LV2 "O3'" H15 SING N N 37 LV2 C1 H16 SING N N 38 LV2 C1 H17 SING N N 39 LV2 C1 H18 SING N N 40 LV2 P OP3 SING N N 41 LV2 OP3 H1 SING N N 42 # # 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 LV2 InChI InChI 1.03 "InChI=1S/C11H18N3O8P/c1-13(2)7-3-4-14(11(17)12-7)10-9(16)8(15)6(22-10)5-21-23(18,19)20/h3-4,6,8-10,15-16H,5H2,1-2H3,(H2,18,19,20)/t6-,8-,9-,10-/m1/s1" LV2 InChIKey InChI 1.03 PGVGGVCCRBGELR-PEBGCTIMSA-N LV2 SMILES_CANONICAL CACTVS 3.385 "CN(C)C1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" LV2 SMILES CACTVS 3.385 "CN(C)C1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" LV2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)C1=NC(=O)N(C=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" LV2 SMILES "OpenEye OEToolkits" 2.0.7 "CN(C)C1=NC(=O)N(C=C1)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id LV2 _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~{S},4~{R},5~{R})-5-[4-(dimethylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(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 LV2 "Create component" 2019-09-10 EBI LV2 "Initial release" 2020-07-29 RCSB ##