data_VC7 # _chem_comp.id VC7 _chem_comp.name "5'-O-[(R)-hydroxy(methyl)phosphoryl]guanosine" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-07-27 _chem_comp.pdbx_modified_date 2020-12-18 _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 361.248 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VC7 _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 7JJF _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 VC7 "C1'" C1 C 0 1 N N R -13.397 14.581 -0.667 0.481 0.711 0.328 "C1'" VC7 1 VC7 C2 C2 C 0 1 N N N -14.849 11.104 -2.492 4.944 0.486 0.619 C2 VC7 2 VC7 "C2'" C3 C 0 1 N N R -13.159 14.195 0.791 0.328 1.681 -0.871 "C2'" VC7 3 VC7 "C3'" C4 C 0 1 N N S -11.802 14.794 1.001 -1.086 2.266 -0.636 "C3'" VC7 4 VC7 C4 C5 C 0 1 Y N N -13.302 12.814 -2.297 2.807 -0.264 0.162 C4 VC7 5 VC7 "C4'" C6 C 0 1 N N R -12.173 16.121 0.490 -1.774 1.235 0.280 "C4'" VC7 6 VC7 C5 C7 C 0 1 Y N N -12.561 12.407 -3.343 3.316 -1.500 -0.255 C5 VC7 7 VC7 "C5'" C8 C 0 1 N N N -10.943 16.988 0.311 -3.044 0.708 -0.392 "C5'" VC7 8 VC7 C6 C9 C 0 1 N N N -12.937 11.300 -3.982 4.715 -1.703 -0.219 C6 VC7 9 VC7 C8 C10 C 0 1 Y N N -11.664 14.167 -2.526 1.161 -1.587 -0.467 C8 VC7 10 VC7 CP2 C11 C 0 1 N N N -8.772 16.378 -3.005 -5.597 -2.016 1.488 CP2 VC7 11 VC7 N1 N1 N 0 1 N N N -14.123 10.637 -3.581 5.499 -0.694 0.221 N1 VC7 12 VC7 N2 N2 N 0 1 N N N -15.942 10.486 -2.084 5.765 1.493 1.061 N2 VC7 13 VC7 N3 N3 N 0 1 N N N -14.423 12.202 -1.882 3.646 0.689 0.585 N3 VC7 14 VC7 N7 N4 N 0 1 Y N N -11.518 13.245 -3.481 2.260 -2.264 -0.627 N7 VC7 15 VC7 N9 N5 N 0 1 Y N N -12.736 13.887 -1.787 1.449 -0.344 0.018 N9 VC7 16 VC7 "O2'" O1 O 0 1 N N N -14.157 14.874 1.619 1.319 2.709 -0.824 "O2'" VC7 17 VC7 "O3'" O2 O 0 1 N N N -11.500 14.925 2.412 -1.001 3.535 0.015 "O3'" VC7 18 VC7 "O4'" O3 O 0 1 N N N -12.777 15.876 -0.766 -0.844 0.159 0.486 "O4'" VC7 19 VC7 "O5'" O4 O 0 1 N N N -10.092 16.428 -0.699 -3.736 -0.158 0.511 "O5'" VC7 20 VC7 O6 O5 O 0 1 N N N -12.303 10.890 -4.967 5.202 -2.762 -0.576 O6 VC7 21 VC7 OP1 O6 O 0 1 N N N -8.167 18.054 -1.171 -4.939 -1.671 -1.112 OP1 VC7 22 VC7 P P1 P 0 1 N N N -9.376 17.410 -1.765 -5.118 -0.893 0.134 P VC7 23 VC7 "H1'" H1 H 0 1 N N N -14.479 14.654 -0.853 0.780 1.253 1.225 "H1'" VC7 24 VC7 "H2'" H2 H 0 1 N N N -13.159 13.104 0.931 0.373 1.141 -1.816 "H2'" VC7 25 VC7 "H3'" H3 H 0 1 N N N -11.013 14.299 0.416 -1.623 2.358 -1.580 "H3'" VC7 26 VC7 "H4'" H4 H 0 1 N N N -12.876 16.613 1.179 -2.025 1.697 1.235 "H4'" VC7 27 VC7 "H5'" H5 H 0 1 N N N -10.393 17.041 1.262 -3.689 1.546 -0.658 "H5'" VC7 28 VC7 "H5''" H6 H 0 0 N N N -11.251 18.000 0.008 -2.776 0.155 -1.292 H5S VC7 29 VC7 H8 H7 H 0 1 N N N -11.010 15.013 -2.375 0.169 -1.953 -0.687 H8 VC7 30 VC7 HCP2 H8 H 0 0 N N N -9.611 15.863 -3.495 -4.816 -2.763 1.634 HP2 VC7 31 VC7 HCP3 H9 H 0 0 N N N -8.226 16.978 -3.748 -5.728 -1.444 2.406 H8L VC7 32 VC7 HCP1 H10 H 0 0 N N N -8.092 15.634 -2.564 -6.532 -2.514 1.233 H8M VC7 33 VC7 H1 H11 H 0 1 N N N -14.438 9.831 -4.083 6.462 -0.810 0.254 H1 VC7 34 VC7 H21 H12 H 0 1 N N N -16.459 10.845 -1.307 5.385 2.340 1.344 H21 VC7 35 VC7 H22 H13 H 0 1 N N N -16.253 9.659 -2.552 6.725 1.358 1.091 H22 VC7 36 VC7 "HO2'" H14 H 0 0 N N N -14.022 14.644 2.531 1.264 3.341 -1.554 H8O VC7 37 VC7 "HO3'" H15 H 0 0 N Y N -11.257 14.077 2.764 -0.525 4.207 -0.493 H2 VC7 38 VC7 OP3 OP3 O 0 1 N Y N -10.534 18.190 -2.466 -6.271 0.209 -0.082 OP3 VC7 39 VC7 HOP3 H16 H 0 0 N Y N -10.344 19.121 -2.451 -6.442 0.757 0.697 H3 VC7 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 VC7 O6 C6 DOUB N N 1 VC7 C6 N1 SING N N 2 VC7 C6 C5 SING N N 3 VC7 N1 C2 SING N N 4 VC7 N7 C5 SING Y N 5 VC7 N7 C8 DOUB Y N 6 VC7 C5 C4 DOUB Y N 7 VC7 CP2 P SING N N 8 VC7 C8 N9 SING Y N 9 VC7 C2 N2 SING N N 10 VC7 C2 N3 DOUB N N 11 VC7 C4 N3 SING N N 12 VC7 C4 N9 SING Y N 13 VC7 N9 "C1'" SING N N 14 VC7 P OP1 DOUB N N 15 VC7 P "O5'" SING N N 16 VC7 "O4'" "C1'" SING N N 17 VC7 "O4'" "C4'" SING N N 18 VC7 "O5'" "C5'" SING N N 19 VC7 "C1'" "C2'" SING N N 20 VC7 "C5'" "C4'" SING N N 21 VC7 "C4'" "C3'" SING N N 22 VC7 "C2'" "C3'" SING N N 23 VC7 "C2'" "O2'" SING N N 24 VC7 "C3'" "O3'" SING N N 25 VC7 "C1'" "H1'" SING N N 26 VC7 "C2'" "H2'" SING N N 27 VC7 "C3'" "H3'" SING N N 28 VC7 "C4'" "H4'" SING N N 29 VC7 "C5'" "H5'" SING N N 30 VC7 "C5'" "H5''" SING N N 31 VC7 C8 H8 SING N N 32 VC7 CP2 HCP2 SING N N 33 VC7 CP2 HCP3 SING N N 34 VC7 CP2 HCP1 SING N N 35 VC7 N1 H1 SING N N 36 VC7 N2 H21 SING N N 37 VC7 N2 H22 SING N N 38 VC7 "O2'" "HO2'" SING N N 39 VC7 "O3'" "HO3'" SING N N 40 VC7 P OP3 SING N N 41 VC7 OP3 HOP3 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 VC7 SMILES ACDLabs 12.01 "C1(C(C(O)C(COP(C)(=O)O)O1)O)n3c2N=C(N)NC(c2nc3)=O" VC7 InChI InChI 1.03 "InChI=1S/C11H16N5O7P/c1-24(20,21)22-2-4-6(17)7(18)10(23-4)16-3-13-5-8(16)14-11(12)15-9(5)19/h3-4,6-7,10,17-18H,2H2,1H3,(H,20,21)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1" VC7 InChIKey InChI 1.03 ZRTURURJQQBKIB-KQYNXXCUSA-N VC7 SMILES_CANONICAL CACTVS 3.385 "C[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N" VC7 SMILES CACTVS 3.385 "C[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)NC(=Nc23)N" VC7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2N=C(NC3=O)N)O)O" VC7 SMILES "OpenEye OEToolkits" 2.0.7 "CP(=O)(O)OCC1C(C(C(O1)n2cnc3c2N=C(NC3=O)N)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 VC7 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy(methyl)phosphoryl]guanosine" VC7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-methyl-phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VC7 "Create component" 2020-07-27 RCSB VC7 "Initial release" 2020-12-23 RCSB ##