data_GMX # _chem_comp.id GMX _chem_comp.name "2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-01-06 _chem_comp.pdbx_modified_date 2020-11-13 _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 377.247 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GMX _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 6VEM _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 GMX OP2 O1 O 0 1 N N N 17.465 -10.915 -16.989 -6.262 -0.798 0.229 OP2 GMX 1 GMX P P1 P 0 1 N N N 16.700 -9.981 -17.996 -4.981 0.148 0.466 P GMX 2 GMX OP1 O2 O 0 1 N N N 16.851 -10.194 -19.576 -4.205 -0.323 1.796 OP1 GMX 3 GMX "O5'" O3 O 0 1 N N N 17.080 -8.456 -17.714 -3.992 0.038 -0.800 "O5'" GMX 4 GMX "C5'" C1 C 0 1 N N R 16.395 -7.360 -18.301 -2.815 0.836 -0.940 "C5'" GMX 5 GMX "C6'" C2 C 0 1 N N N 16.747 -7.194 -19.780 -2.917 1.675 -2.215 "C5''" GMX 6 GMX "C4'" C3 C 0 1 N N S 16.708 -6.109 -17.528 -1.588 -0.074 -1.024 "C4'" GMX 7 GMX "O4'" O4 O 0 1 N N N 16.128 -6.169 -16.213 -0.378 0.715 -1.057 "O4'" GMX 8 GMX "C1'" C4 C 0 1 N N R 17.012 -5.490 -15.306 0.673 -0.184 -0.641 "C1'" GMX 9 GMX "C2'" C5 C 0 1 N N R 18.132 -4.886 -16.144 0.056 -1.005 0.513 "C2'" GMX 10 GMX "O2'" O5 O 0 1 N N N 17.658 -3.632 -16.668 0.510 -2.359 0.462 "O2'" GMX 11 GMX "C3'" C6 C 0 1 N N S 18.202 -5.880 -17.296 -1.465 -0.932 0.255 "C3'" GMX 12 GMX "O3'" O6 O 0 1 N N N 18.867 -5.356 -18.489 -2.000 -2.238 0.035 "O3'" GMX 13 GMX N9 N1 N 0 1 Y N N 17.573 -6.499 -14.351 1.832 0.574 -0.164 N9 GMX 14 GMX C8 C7 C 0 1 Y N N 17.491 -7.857 -14.417 1.818 1.848 0.323 C8 GMX 15 GMX N7 N2 N 0 1 Y N N 18.091 -8.408 -13.340 3.027 2.202 0.652 N7 GMX 16 GMX C5 C8 C 0 1 Y N N 18.553 -7.345 -12.568 3.875 1.179 0.395 C5 GMX 17 GMX C6 C9 C 0 1 N N N 19.223 -7.231 -11.345 5.319 0.978 0.549 C6 GMX 18 GMX O6 O7 O 0 1 N N N 19.542 -8.235 -10.684 6.027 1.863 1.003 O6 GMX 19 GMX N1 N3 N 0 1 N N N 19.581 -6.009 -10.863 5.846 -0.200 0.181 N1 GMX 20 GMX C2 C10 C 0 1 N N N 19.271 -4.884 -11.551 5.095 -1.163 -0.309 C2 GMX 21 GMX N2 N4 N 0 1 N N N 19.615 -3.665 -11.053 5.689 -2.344 -0.668 N2 GMX 22 GMX N3 N5 N 0 1 N N N 18.608 -4.948 -12.739 3.753 -1.031 -0.473 N3 GMX 23 GMX C4 C11 C 0 1 Y N N 18.233 -6.160 -13.228 3.119 0.133 -0.121 C4 GMX 24 GMX H1 H1 H 0 1 N N N 16.843 -11.318 -16.395 -6.903 -0.781 0.953 H1 GMX 25 GMX H2 H2 H 0 1 N N N 15.992 -10.313 -19.963 -3.885 -1.234 1.763 H2 GMX 26 GMX H3 H3 H 0 1 N N N 15.311 -7.537 -18.234 -2.719 1.496 -0.078 H3 GMX 27 GMX H4 H4 H 0 1 N N N 16.196 -6.337 -20.194 -3.791 2.323 -2.155 H4 GMX 28 GMX H5 H5 H 0 1 N N N 17.828 -7.019 -19.882 -2.019 2.284 -2.322 H5 GMX 29 GMX H6 H6 H 0 1 N N N 16.470 -8.107 -20.327 -3.012 1.015 -3.077 H6 GMX 30 GMX H7 H7 H 0 1 N N N 16.303 -5.244 -18.073 -1.650 -0.713 -1.905 H7 GMX 31 GMX H8 H8 H 0 1 N N N 16.485 -4.696 -14.756 0.961 -0.839 -1.464 H8 GMX 32 GMX H9 H9 H 0 1 N N N 19.080 -4.811 -15.592 0.303 -0.557 1.475 H9 GMX 33 GMX H10 H10 H 0 1 N N N 17.606 -2.994 -15.966 0.154 -2.921 1.164 H10 GMX 34 GMX H11 H11 H 0 1 N N N 18.677 -6.813 -16.960 -1.971 -0.447 1.090 H11 GMX 35 GMX H12 H12 H 0 1 N N N 19.790 -5.227 -18.307 -1.949 -2.819 0.806 H12 GMX 36 GMX H13 H13 H 0 1 N N N 17.016 -8.411 -15.213 0.939 2.468 0.420 H13 GMX 37 GMX H14 H14 H 0 1 N N N 20.097 -3.600 -10.179 6.646 -2.458 -0.559 H14 GMX 38 GMX H15 H15 H 0 1 N N N 19.386 -2.835 -11.561 5.153 -3.066 -1.031 H15 GMX 39 GMX H16 H16 H 0 1 N N N 18.399 -4.112 -13.246 3.238 -1.767 -0.838 H16 GMX 40 GMX OP3 OP3 O 0 1 N Y N 15.161 -10.048 -17.656 -5.425 1.551 0.624 OP3 GMX 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 GMX "C6'" "C5'" SING N N 1 GMX OP1 P SING N N 2 GMX "O3'" "C3'" SING N N 3 GMX "C5'" "O5'" SING N N 4 GMX "C5'" "C4'" SING N N 5 GMX P "O5'" SING N N 6 GMX P OP2 SING N N 7 GMX "C4'" "C3'" SING N N 8 GMX "C4'" "O4'" SING N N 9 GMX "C3'" "C2'" SING N N 10 GMX "O2'" "C2'" SING N N 11 GMX "O4'" "C1'" SING N N 12 GMX "C2'" "C1'" SING N N 13 GMX "C1'" N9 SING N N 14 GMX C8 N9 SING Y N 15 GMX C8 N7 DOUB Y N 16 GMX N9 C4 SING Y N 17 GMX N7 C5 SING Y N 18 GMX C4 N3 SING N N 19 GMX C4 C5 DOUB Y N 20 GMX N3 C2 SING N N 21 GMX C5 C6 SING N N 22 GMX C2 N2 SING N N 23 GMX C2 N1 DOUB N N 24 GMX C6 N1 SING N N 25 GMX C6 O6 DOUB N N 26 GMX OP2 H1 SING N N 27 GMX OP1 H2 SING N N 28 GMX "C5'" H3 SING N N 29 GMX "C6'" H4 SING N N 30 GMX "C6'" H5 SING N N 31 GMX "C6'" H6 SING N N 32 GMX "C4'" H7 SING N N 33 GMX "C1'" H8 SING N N 34 GMX "C2'" H9 SING N N 35 GMX "O2'" H10 SING N N 36 GMX "C3'" H11 SING N N 37 GMX "O3'" H12 SING N N 38 GMX C8 H13 SING N N 39 GMX N2 H14 SING N N 40 GMX N2 H15 SING N N 41 GMX N3 H16 SING N N 42 GMX P OP3 DOUB N N 43 # # 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 GMX SMILES ACDLabs 12.01 "OP(OC(C1C(C(C(O1)n2c3c(nc2)C(N=C(N)N3)=O)O)O)C)(=O)O" GMX InChI InChI 1.03 "InChI=1S/C11H16N5O8P/c1-3(24-25(20,21)22)7-5(17)6(18)10(23-7)16-2-13-4-8(16)14-11(12)15-9(4)19/h2-3,5-7,10,17-18H,1H3,(H2,20,21,22)(H3,12,14,15,19)/t3-,5+,6-,7-,10-/m1/s1" GMX InChIKey InChI 1.03 QYBUIBIHUIWDID-KPCPHYELSA-N GMX SMILES_CANONICAL CACTVS 3.385 "C[C@@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)N=C(N)Nc23" GMX SMILES CACTVS 3.385 "C[CH](O[P](O)(O)=O)[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)N=C(N)Nc23" GMX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]([C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2NC(=NC3=O)N)O)O)OP(=O)(O)O" GMX SMILES "OpenEye OEToolkits" 2.0.7 "CC(C1C(C(C(O1)n2cnc3c2NC(=NC3=O)N)O)O)OP(=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 GMX "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one" GMX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(1~{R})-1-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl] 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 GMX "Create component" 2020-01-06 RCSB GMX "Initial release" 2020-11-18 RCSB ##