data_VNR
# 
_chem_comp.id                                    VNR 
_chem_comp.name                                  "1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H35 N4 O16 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-06-15 
_chem_comp.pdbx_modified_date                    2011-10-28 
_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                        716.462 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VNR 
_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        3B03 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
VNR P      P      P 0 1 N N N 28.509 41.464 17.751 9.629  -2.083 -0.197 P      VNR 1  
VNR N1     N1     N 0 1 N N N 20.580 44.161 20.282 2.001  2.917  -0.422 N1     VNR 2  
VNR C2     C2     C 0 1 N N N 19.387 44.133 20.913 1.919  4.233  -0.191 C2     VNR 3  
VNR O2     O2     O 0 1 N N N 19.381 44.091 22.155 2.794  4.964  -0.616 O2     VNR 4  
VNR N3     N3     N 0 1 N N N 18.241 44.385 20.246 0.898  4.770  0.498  N3     VNR 5  
VNR C4     C4     C 0 1 N N N 18.190 44.381 18.901 -0.180 4.033  0.823  C4     VNR 6  
VNR O4     O4     O 0 1 N N N 17.083 44.479 18.317 -1.068 4.526  1.484  O4     VNR 7  
VNR N5     N5     N 0 1 N N N 19.534 43.950 16.897 -0.769 1.737  1.455  N5     VNR 8  
VNR C6     C6     C 0 1 Y N N 20.565 44.067 14.798 -1.564 -0.522 1.835  C6     VNR 9  
VNR C7     C7     C 0 1 Y N N 21.634 43.514 14.126 -1.468 -1.880 1.583  C7     VNR 10 
VNR C8     C8     C 0 1 Y N N 22.953 43.457 14.814 -0.494 -2.360 0.727  C8     VNR 11 
VNR C9     C9     C 0 1 Y N N 23.011 43.540 16.190 0.396  -1.491 0.122  C9     VNR 12 
VNR "C1'"  "C1'"  C 0 1 N N N 23.066 44.105 19.123 2.368  0.234  -0.967 "C1'"  VNR 13 
VNR C10    C10    C 0 1 N N N 20.625 44.253 18.932 1.040  2.092  -0.105 C10    VNR 14 
VNR N10    N10    N 0 1 N N N 21.855 43.980 18.306 1.220  0.755  -0.221 N10    VNR 15 
VNR C11    C11    C 0 1 N N N 19.362 46.074 17.582 -1.278 2.535  -0.791 C11    VNR 16 
VNR C12    C12    C 0 1 N N N 17.452 48.191 17.792 -4.389 1.331  -0.710 C12    VNR 17 
VNR C13    C13    C 0 1 N N N 18.438 48.073 18.964 -3.588 2.099  0.344  C13    VNR 18 
VNR C14    C14    C 0 1 N N N 19.576 47.160 18.582 -2.626 3.036  -0.341 C14    VNR 19 
VNR C15    C15    C 0 1 N N N 20.822 47.262 19.029 -2.962 4.286  -0.544 C15    VNR 20 
VNR O15    O15    O 0 1 N N N 17.295 49.549 17.344 -5.301 0.442  -0.061 O15    VNR 21 
VNR C16    C16    C 0 1 N N N 21.223 48.294 20.035 -4.310 4.786  -0.094 C16    VNR 22 
VNR O1P    O1P    O 0 1 N N N 28.846 39.995 17.916 10.540 -2.395 1.093  O1P    VNR 23 
VNR "C2'"  "C2'"  C 0 1 N N S 23.695 42.711 19.170 3.554  0.053  -0.018 "C2'"  VNR 24 
VNR "O2'"  "O2'"  O 0 1 N N N 22.804 41.846 19.859 3.896  1.314  0.562  "O2'"  VNR 25 
VNR O22    O22    O 0 1 N N N 12.586 48.795 17.516 -8.662 -2.873 -1.212 O22    VNR 26 
VNR O2P    O2P    O 0 1 N N N 29.745 42.316 17.719 10.372 -1.001 -1.130 O2P    VNR 27 
VNR "C3'"  "C3'"  C 0 1 N N S 25.065 42.707 19.851 4.753  -0.491 -0.797 "C3'"  VNR 28 
VNR "O3'"  "O3'"  O 0 1 N N N 24.914 43.075 21.236 4.411  -1.752 -1.377 "O3'"  VNR 29 
VNR O33    O33    O 0 1 N N N 13.127 51.043 18.581 -8.865 -3.051 1.297  O33    VNR 30 
VNR O3P    O3P    O 0 1 N N N 27.506 41.776 16.682 9.415  -3.331 -0.963 O3P    VNR 31 
VNR "C4'"  "C4'"  C 0 1 N N R 26.063 43.642 19.171 5.939  -0.672 0.153  "C4'"  VNR 32 
VNR "O4'"  "O4'"  O 0 1 N N N 25.805 43.618 17.758 6.281  0.588  0.733  "O4'"  VNR 33 
VNR O44    O44    O 0 1 N N N 13.164 48.923 19.975 -6.817 -4.083 0.012  O44    VNR 34 
VNR C4A    C4A    C 0 1 N N R 19.445 44.658 18.139 -0.291 2.609  0.376  C4A    VNR 35 
VNR "C5'"  "C5'"  C 0 1 N N N 27.532 43.259 19.466 7.138  -1.217 -0.626 "C5'"  VNR 36 
VNR "O5'"  "O5'"  O 0 1 N N N 27.810 41.885 19.146 8.208  -1.495 0.279  "O5'"  VNR 37 
VNR P55    P55    P 0 1 N N N 13.321 49.538 18.600 -7.875 -2.870 0.041  P55    VNR 38 
VNR C5A    C5A    C 0 1 Y N N 20.630 44.132 16.172 -0.682 0.352  1.227  C5A    VNR 39 
VNR O66    O66    O 0 1 N N N 14.906 49.323 18.255 -7.086 -1.473 0.175  O66    VNR 40 
VNR O77    O77    O 0 1 N N N 16.118 51.600 18.249 -7.369 0.366  -1.682 O77    VNR 41 
VNR C7M    C7M    C 0 1 N N N 21.576 43.480 12.617 -2.427 -2.837 2.243  C7M    VNR 42 
VNR O88    O88    O 0 1 N N N 15.329 50.499 16.027 -5.532 -1.361 -1.811 O88    VNR 43 
VNR C8M    C8M    C 0 1 N N N 24.209 43.050 14.070 -0.400 -3.838 0.452  C8M    VNR 44 
VNR P99    P99    P 0 1 N N N 15.885 50.343 17.423 -6.305 -0.525 -0.865 P99    VNR 45 
VNR C9A    C9A    C 0 1 Y N N 21.913 44.001 16.888 0.310  -0.129 0.370  C9A    VNR 46 
VNR HN3    HN3    H 0 1 N N N 17.408 44.580 20.764 0.938  5.702  0.764  HN3    VNR 47 
VNR HN5    HN5    H 0 1 N N N 19.486 42.975 17.113 -1.127 2.097  2.282  HN5    VNR 48 
VNR H6     H6     H 0 1 N N N 19.703 44.438 14.263 -2.325 -0.148 2.504  H6     VNR 49 
VNR H9     H9     H 0 1 N N N 23.907 43.247 16.716 1.156  -1.872 -0.543 H9     VNR 50 
VNR "H1'"  "H1'"  H 0 1 N N N 23.762 44.828 18.674 2.107  -0.728 -1.410 "H1'"  VNR 51 
VNR "H1'A" "H1'A" H 0 0 N N N 22.815 44.450 20.137 2.638  0.936  -1.756 "H1'A" VNR 52 
VNR H11    H11    H 0 1 N N N 18.357 46.206 17.156 -1.368 1.502  -1.126 H11    VNR 53 
VNR H11A   H11A   H 0 0 N N N 20.138 46.174 16.809 -0.916 3.153  -1.612 H11A   VNR 54 
VNR H12    H12    H 0 1 N N N 17.832 47.588 16.954 -4.945 2.035  -1.328 H12    VNR 55 
VNR H12A   H12A   H 0 0 N N N 16.472 47.816 18.121 -3.707 0.757  -1.337 H12A   VNR 56 
VNR H13    H13    H 0 1 N N N 18.835 49.069 19.209 -4.270 2.673  0.971  H13    VNR 57 
VNR H13A   H13A   H 0 0 N N N 17.916 47.660 19.840 -3.031 1.395  0.962  H13A   VNR 58 
VNR H15    H15    H 0 1 N N N 21.570 46.578 18.655 -2.273 4.957  -1.035 H15    VNR 59 
VNR H16    H16    H 0 1 N N N 22.296 48.193 20.257 -5.095 4.218  -0.594 H16    VNR 60 
VNR H16A   H16A   H 0 0 N N N 21.025 49.297 19.630 -4.403 4.661  0.985  H16A   VNR 61 
VNR H16B   H16B   H 0 0 N N N 20.643 48.151 20.958 -4.409 5.842  -0.347 H16B   VNR 62 
VNR HO1P   HO1P   H 0 0 N N N 28.348 39.483 17.290 11.413 -2.752 0.881  HO1P   VNR 63 
VNR "H2'"  "H2'"  H 0 1 N N N 23.859 42.368 18.138 3.284  -0.649 0.771  "H2'"  VNR 64 
VNR "HO2'" "HO2'" H 0 0 N N N 23.177 40.973 19.899 4.147  1.988  -0.083 "HO2'" VNR 65 
VNR HO2P   HO2P   H 0 0 N N N 29.685 42.935 17.001 10.544 -0.156 -0.692 HO2P   VNR 66 
VNR "H3'"  "H3'"  H 0 1 N N N 25.471 41.688 19.768 5.023  0.210  -1.586 "H3'"  VNR 67 
VNR "HO3'" "HO3'" H 0 0 N N N 25.764 43.073 21.659 4.160  -2.427 -0.732 "HO3'" VNR 68 
VNR HO33   HO33   H 0 0 N N N 12.553 51.280 17.862 -9.374 -3.873 1.282  HO33   VNR 69 
VNR "H4'"  "H4'"  H 0 1 N N N 25.928 44.657 19.573 5.669  -1.374 0.942  "H4'"  VNR 70 
VNR "HO4'" "HO4'" H 0 0 N N N 26.379 42.986 17.341 6.532  1.263  0.088  "HO4'" VNR 71 
VNR HO44   HO44   H 0 0 N N N 12.613 48.152 19.916 -6.265 -4.143 0.804  HO44   VNR 72 
VNR "H5'"  "H5'"  H 0 1 N N N 28.190 43.900 18.860 6.850  -2.133 -1.141 "H5'"  VNR 73 
VNR "H5'A" "H5'A" H 0 0 N N N 27.726 43.415 20.537 7.463  -0.476 -1.357 "H5'A" VNR 74 
VNR HO77   HO77   H 0 0 N N N 15.866 52.363 17.743 -7.911 0.940  -1.125 HO77   VNR 75 
VNR H7M    H7M    H 0 1 N N N 21.832 44.472 12.217 -3.304 -2.966 1.609  H7M    VNR 76 
VNR H7MA   H7MA   H 0 0 N N N 22.293 42.736 12.239 -1.938 -3.800 2.386  H7MA   VNR 77 
VNR H7MB   H7MB   H 0 0 N N N 20.560 43.207 12.295 -2.732 -2.437 3.209  H7MB   VNR 78 
VNR H8M    H8M    H 0 1 N N N 24.744 43.950 13.734 -1.022 -4.089 -0.407 H8M    VNR 79 
VNR H8MA   H8MA   H 0 0 N N N 24.858 42.466 14.739 0.636  -4.104 0.241  H8MA   VNR 80 
VNR H8MB   H8MB   H 0 0 N N N 23.936 42.438 13.197 -0.746 -4.392 1.325  H8MB   VNR 81 
# 
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 
VNR P     O1P    SING N N 1  
VNR P     O2P    SING N N 2  
VNR P     O3P    DOUB N N 3  
VNR P     "O5'"  SING N N 4  
VNR N1    C2     SING N N 5  
VNR N1    C10    DOUB N N 6  
VNR C2    O2     DOUB N N 7  
VNR C2    N3     SING N N 8  
VNR N3    C4     SING N N 9  
VNR C4    O4     DOUB N N 10 
VNR C4    C4A    SING N N 11 
VNR N5    C4A    SING N N 12 
VNR N5    C5A    SING N N 13 
VNR C6    C7     SING Y N 14 
VNR C6    C5A    DOUB Y N 15 
VNR C7    C8     DOUB Y N 16 
VNR C7    C7M    SING N N 17 
VNR C8    C9     SING Y N 18 
VNR C8    C8M    SING N N 19 
VNR C9    C9A    DOUB Y N 20 
VNR "C1'" N10    SING N N 21 
VNR "C1'" "C2'"  SING N N 22 
VNR C10   N10    SING N N 23 
VNR C10   C4A    SING N N 24 
VNR N10   C9A    SING N N 25 
VNR C11   C14    SING N N 26 
VNR C11   C4A    SING N N 27 
VNR C12   C13    SING N N 28 
VNR C12   O15    SING N N 29 
VNR C13   C14    SING N N 30 
VNR C14   C15    DOUB N Z 31 
VNR C15   C16    SING N N 32 
VNR O15   P99    SING N N 33 
VNR "C2'" "O2'"  SING N N 34 
VNR "C2'" "C3'"  SING N N 35 
VNR O22   P55    DOUB N N 36 
VNR "C3'" "O3'"  SING N N 37 
VNR "C3'" "C4'"  SING N N 38 
VNR O33   P55    SING N N 39 
VNR "C4'" "O4'"  SING N N 40 
VNR "C4'" "C5'"  SING N N 41 
VNR O44   P55    SING N N 42 
VNR "C5'" "O5'"  SING N N 43 
VNR P55   O66    SING N N 44 
VNR C5A   C9A    SING Y N 45 
VNR O66   P99    SING N N 46 
VNR O77   P99    SING N N 47 
VNR O88   P99    DOUB N N 48 
VNR N3    HN3    SING N N 49 
VNR N5    HN5    SING N N 50 
VNR C6    H6     SING N N 51 
VNR C9    H9     SING N N 52 
VNR "C1'" "H1'"  SING N N 53 
VNR "C1'" "H1'A" SING N N 54 
VNR C11   H11    SING N N 55 
VNR C11   H11A   SING N N 56 
VNR C12   H12    SING N N 57 
VNR C12   H12A   SING N N 58 
VNR C13   H13    SING N N 59 
VNR C13   H13A   SING N N 60 
VNR C15   H15    SING N N 61 
VNR C16   H16    SING N N 62 
VNR C16   H16A   SING N N 63 
VNR C16   H16B   SING N N 64 
VNR O1P   HO1P   SING N N 65 
VNR "C2'" "H2'"  SING N N 66 
VNR "O2'" "HO2'" SING N N 67 
VNR O2P   HO2P   SING N N 68 
VNR "C3'" "H3'"  SING N N 69 
VNR "O3'" "HO3'" SING N N 70 
VNR O33   HO33   SING N N 71 
VNR "C4'" "H4'"  SING N N 72 
VNR "O4'" "HO4'" SING N N 73 
VNR O44   HO44   SING N N 74 
VNR "C5'" "H5'"  SING N N 75 
VNR "C5'" "H5'A" SING N N 76 
VNR O77   HO77   SING N N 77 
VNR C7M   H7M    SING N N 78 
VNR C7M   H7MA   SING N N 79 
VNR C7M   H7MB   SING N N 80 
VNR C8M   H8M    SING N N 81 
VNR C8M   H8MA   SING N N 82 
VNR C8M   H8MB   SING N N 83 
# 
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 
VNR SMILES           ACDLabs              12.01 "O=P(O)(O)OCC(O)C(O)C(O)CN2C3=NC(=O)NC(=O)C3(Nc1cc(c(cc12)C)C)CC(=C/C)/CCOP(=O)(O)OP(=O)(O)O" 
VNR InChI            InChI                1.03  
;InChI=1S/C23H35N4O16P3/c1-4-14(5-6-41-46(39,40)43-45(36,37)38)9-23-20(24-22(32)25-21(23)31)27(16-8-13(3)12(2)7-15(16)26-23)10-17(28)19(30)18(29)11-42-44(33,34)35/h4,7-8,17-19,26,28-30H,5-6,9-11H2,1-3H3,(H,39,40)(H,25,31,32)(H2,33,34,35)(H2,36,37,38)/b14-4+/t17-,18+,19-,23+/m0/s1
;
VNR InChIKey         InChI                1.03  OAOWJIIZSRFUAL-QCJQWHCGSA-N 
VNR SMILES_CANONICAL CACTVS               3.370 "C/C=C(CCO[P](O)(=O)O[P](O)(O)=O)/C[C@@]12Nc3cc(C)c(C)cc3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)C1=NC(=O)NC2=O" 
VNR SMILES           CACTVS               3.370 "CC=C(CCO[P](O)(=O)O[P](O)(O)=O)C[C]12Nc3cc(C)c(C)cc3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)C1=NC(=O)NC2=O" 
VNR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C/C=C(\CCO[P@](=O)(O)OP(=O)(O)O)/C[C@]12C(=O)NC(=O)N=C1N(c3cc(c(cc3N2)C)C)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O" 
VNR SMILES           "OpenEye OEToolkits" 1.7.2 "CC=C(CCOP(=O)(O)OP(=O)(O)O)CC12C(=O)NC(=O)N=C1N(c3cc(c(cc3N2)C)C)CC(C(C(COP(=O)(O)O)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 
VNR "SYSTEMATIC NAME" ACDLabs              12.01 "1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol" 
VNR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(Z)-3-[[(4aR)-7,8-dimethyl-2,4-bis(oxidanylidene)-10-[(2S,3S,4R)-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-5H-benzo[g]pteridin-4a-yl]methyl]pent-3-enyl] phosphono hydrogen 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 
VNR "Create component" 2011-06-15 PDBJ 
# 
