data_V3L # _chem_comp.id V3L _chem_comp.name ;2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H23 N5 O14 P2" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-12-21 _chem_comp.pdbx_modified_date 2014-05-29 _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 559.316 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V3L _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 3V3L _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 V3L N1 N1 N 0 1 Y N N 28.211 58.899 82.245 -4.929 4.245 -0.019 N1 V3L 1 V3L C2 C2 C 0 1 Y N N 28.319 57.552 82.335 -3.902 4.069 -0.831 C2 V3L 2 V3L N3 N3 N 0 1 Y N N 27.257 56.733 82.413 -3.257 2.926 -0.917 N3 V3L 3 V3L C4 C4 C 0 1 Y N N 25.997 57.224 82.403 -3.622 1.885 -0.175 C4 V3L 4 V3L C5 C5 C 0 1 Y N N 25.787 58.667 82.310 -4.708 2.020 0.705 C5 V3L 5 V3L C6 C6 C 0 1 Y N N 26.994 59.507 82.257 -5.366 3.261 0.761 C6 V3L 6 V3L N6 N6 N 0 1 N N N 26.832 60.832 82.183 -6.443 3.454 1.608 N6 V3L 7 V3L N7 N7 N 0 1 Y N N 24.461 58.886 82.321 -4.867 0.829 1.330 N7 V3L 8 V3L C8 C8 C 0 1 Y N N 23.867 57.699 82.423 -3.968 -0.009 0.900 C8 V3L 9 V3L N9 N9 N 0 1 Y N N 24.775 56.712 82.436 -3.176 0.595 -0.030 N9 V3L 10 V3L P P P 0 1 N N N 19.716 56.794 82.543 -1.478 -5.770 0.006 P V3L 11 V3L PB PB P 0 1 N N N 24.488 54.108 91.278 5.999 -0.090 0.481 PB V3L 12 V3L C10 "C1''" C 0 1 N N R 25.041 55.306 86.244 0.597 2.217 0.528 C10 V3L 13 V3L "C1'" "C1'" C 0 1 N N R 24.458 55.279 82.613 -2.054 -0.020 -0.743 "C1'" V3L 14 V3L OP3 OP3 O 0 1 N Y N 18.517 56.028 83.082 -2.640 -6.627 -0.706 OP3 V3L 15 V3L O1B O1B O 0 1 N N N 25.321 55.169 91.928 6.189 -0.047 2.079 O1B V3L 16 V3L C12 "C2''" C 0 1 N N R 26.416 55.222 86.903 0.915 3.648 0.055 C12 V3L 17 V3L O12 "O2''" O 0 1 N N N 27.449 55.609 86.008 0.321 3.897 -1.221 O12 V3L 18 V3L "C2'" "C2'" C 0 1 N N R 23.976 55.101 84.057 -0.715 0.289 -0.026 "C2'" V3L 19 V3L "O2'" "O2'" O 0 1 N N N 25.115 54.848 84.894 -0.179 1.539 -0.463 "O2'" V3L 20 V3L OP1 OP1 O 0 1 N N N 19.750 56.971 81.034 -1.743 -5.692 1.460 OP1 V3L 21 V3L O2B O2B O 0 1 N N N 23.039 54.513 91.163 7.074 0.695 -0.165 O2B V3L 22 V3L C13 "C3''" C 0 1 N N S 26.520 53.755 87.309 2.460 3.678 -0.052 C13 V3L 23 V3L O13 "O3''" O 0 1 N N N 27.172 52.954 86.316 2.877 4.386 -1.221 O13 V3L 24 V3L "C3'" "C3'" C 0 1 N N R 22.966 53.952 83.949 0.179 -0.888 -0.488 "C3'" V3L 25 V3L "O3'" "O3'" O 0 1 N N N 23.518 52.668 84.245 1.002 -0.489 -1.586 "O3'" V3L 26 V3L OP2 OP2 O 0 1 N N N 20.039 58.031 83.341 -0.056 -6.482 -0.243 OP2 V3L 27 V3L O3B O3B O 0 1 N N N 24.673 52.708 91.802 6.070 -1.617 -0.027 O3B V3L 28 V3L C14 "C4''" C 0 1 N N R 25.070 53.316 87.455 2.806 2.171 -0.164 C14 V3L 29 V3L O14 "O4''" O 0 1 N N N 24.240 54.389 86.987 1.850 1.539 0.714 O14 V3L 30 V3L "C4'" "C4'" C 0 1 N N R 22.498 53.993 82.498 -0.822 -1.972 -0.930 "C4'" V3L 31 V3L "O4'" "O4'" O 0 1 N N N 23.393 54.860 81.791 -2.143 -1.460 -0.686 "O4'" V3L 32 V3L C15 "C5''" C 0 1 N N N 24.700 52.968 88.894 4.235 1.910 0.316 C15 V3L 33 V3L O15 "O5''" O 0 1 N N N 25.068 54.012 89.794 4.569 0.538 0.094 O15 V3L 34 V3L "C5'" "C5'" C 0 1 N N N 21.097 54.542 82.301 -0.598 -3.250 -0.119 "C5'" V3L 35 V3L "O5'" "O5'" O 0 1 N N N 20.963 55.849 82.897 -1.450 -4.284 -0.615 "O5'" V3L 36 V3L H2 H2 H 0 1 N N N 29.307 57.115 82.345 -3.580 4.896 -1.447 H2 V3L 37 V3L HN6 HN6 H 0 1 N N N 27.726 61.275 82.120 -6.888 4.316 1.638 HN6 V3L 38 V3L HN6A HN6A H 0 0 N N N 26.291 61.057 81.372 -6.752 2.729 2.172 HN6A V3L 39 V3L H8 H8 H 0 1 N N N 22.799 57.551 82.487 -3.866 -1.031 1.232 H8 V3L 40 V3L "H1''" "H1''" H 0 0 N N N 24.650 56.332 86.306 0.050 2.251 1.470 "H1''" V3L 41 V3L "H1'" "H1'" H 0 1 N N N 25.356 54.666 82.447 -2.024 0.324 -1.777 "H1'" V3L 42 V3L HOP3 HOP3 H 0 0 N N N 17.955 55.770 82.361 -2.715 -7.535 -0.381 HOP3 V3L 43 V3L HO1B HO1B H 0 0 N N N 24.772 55.912 92.150 5.518 -0.542 2.569 HO1B V3L 44 V3L "H2''" "H2''" H 0 0 N N N 26.425 55.851 87.806 0.570 4.378 0.787 "H2''" V3L 45 V3L "HO2'" "HO2'" H 0 0 N N N 28.289 55.546 86.447 -0.643 3.834 -1.225 "HO2'" V3L 46 V3L "H2'" "H2'" H 0 1 N N N 23.454 56.014 84.380 -0.843 0.279 1.056 "H2'" V3L 47 V3L "H3''" "H3''" H 0 0 N N N 27.032 53.675 88.279 2.903 4.113 0.844 "H3''" V3L 48 V3L HO13 HO3A H 0 0 N N N 27.213 52.052 86.613 2.603 5.313 -1.237 HO13 V3L 49 V3L "H3'" "H3'" H 0 1 N N N 22.112 54.164 84.609 0.793 -1.247 0.338 "H3'" V3L 50 V3L "HO3'" "HO3'" H 0 0 N Y N 22.843 52.005 84.160 1.583 -1.188 -1.915 "HO3'" V3L 51 V3L HOP2 HOP2 H 0 0 N N N 20.219 58.752 82.749 0.183 -6.568 -1.176 HOP2 V3L 52 V3L HO3B HO3B H 0 0 N N N 23.823 52.318 91.972 6.907 -2.059 0.173 HO3B V3L 53 V3L "H4''" "H4''" H 0 0 N N N 24.911 52.425 86.830 2.677 1.823 -1.189 "H4''" V3L 54 V3L "H4'" "H4'" H 0 1 N N N 22.546 52.977 82.080 -0.697 -2.181 -1.993 "H4'" V3L 55 V3L "H5''" "H5''" H 0 0 N N N 23.613 52.809 88.956 4.926 2.546 -0.237 "H5''" V3L 56 V3L H5AA H5AA H 0 0 N N N 25.223 52.045 89.184 4.307 2.133 1.380 H5AA V3L 57 V3L "H5'" "H5'" H 0 1 N N N 20.888 54.615 81.224 0.443 -3.561 -0.212 "H5'" V3L 58 V3L "H5'A" "H5'A" H 0 0 N N N 20.374 53.858 82.769 -0.829 -3.060 0.929 "H5'A" V3L 59 # 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 V3L N1 C6 DOUB Y N 1 V3L N1 C2 SING Y N 2 V3L C2 N3 DOUB Y N 3 V3L C2 H2 SING N N 4 V3L C4 N3 SING Y N 5 V3L C5 C4 DOUB Y N 6 V3L C4 N9 SING Y N 7 V3L C6 C5 SING Y N 8 V3L C5 N7 SING Y N 9 V3L N6 C6 SING N N 10 V3L N6 HN6 SING N N 11 V3L N6 HN6A SING N N 12 V3L N7 C8 DOUB Y N 13 V3L C8 N9 SING Y N 14 V3L C8 H8 SING N N 15 V3L N9 "C1'" SING N N 16 V3L OP1 P DOUB N N 17 V3L P "O5'" SING N N 18 V3L P OP3 SING N N 19 V3L P OP2 SING N N 20 V3L O15 PB SING N N 21 V3L O2B PB DOUB N N 22 V3L PB O3B SING N N 23 V3L PB O1B SING N N 24 V3L "O2'" C10 SING N N 25 V3L C10 C12 SING N N 26 V3L C10 O14 SING N N 27 V3L C10 "H1''" SING N N 28 V3L "O4'" "C1'" SING N N 29 V3L "C1'" "C2'" SING N N 30 V3L "C1'" "H1'" SING N N 31 V3L OP3 HOP3 SING N N 32 V3L O1B HO1B SING N N 33 V3L O12 C12 SING N N 34 V3L C12 C13 SING N N 35 V3L C12 "H2''" SING N N 36 V3L O12 "HO2'" SING N N 37 V3L "C3'" "C2'" SING N N 38 V3L "C2'" "O2'" SING N N 39 V3L "C2'" "H2'" SING N N 40 V3L O13 C13 SING N N 41 V3L C13 C14 SING N N 42 V3L C13 "H3''" SING N N 43 V3L O13 HO13 SING N N 44 V3L "C4'" "C3'" SING N N 45 V3L "C3'" "O3'" SING N N 46 V3L "C3'" "H3'" SING N N 47 V3L "O3'" "HO3'" SING N N 48 V3L OP2 HOP2 SING N N 49 V3L O3B HO3B SING N N 50 V3L O14 C14 SING N N 51 V3L C14 C15 SING N N 52 V3L C14 "H4''" SING N N 53 V3L "O4'" "C4'" SING N N 54 V3L "C5'" "C4'" SING N N 55 V3L "C4'" "H4'" SING N N 56 V3L C15 O15 SING N N 57 V3L C15 "H5''" SING N N 58 V3L C15 H5AA SING N N 59 V3L "C5'" "O5'" SING N N 60 V3L "C5'" "H5'" SING N N 61 V3L "C5'" "H5'A" SING N N 62 # 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 V3L SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(n1c2ncnc(N)c2nc1)C(OC3OC(C(O)C3O)COP(=O)(O)O)C4O" V3L InChI InChI 1.03 "InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(9(22)6(32-14)2-31-36(27,28)29)34-15-10(23)8(21)5(33-15)1-30-35(24,25)26/h3-6,8-11,14-15,21-23H,1-2H2,(H2,16,17,18)(H2,24,25,26)(H2,27,28,29)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" V3L InChIKey InChI 1.03 BHIWBSNWEZIHHL-KEOHHSTQSA-N V3L SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O[C@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O" V3L SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O" V3L SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O[C@@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)N" V3L SMILES "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)OC4C(C(C(O4)COP(=O)(O)O)O)O)N" # 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 V3L "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) ; V3L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-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 V3L "Create component" 2011-12-21 RCSB V3L "Modify atom id" 2014-05-29 RCSB #