data_VLO
# 
_chem_comp.id                                    VLO 
_chem_comp.name                                  "[[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H27 N9 O21 P4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-08-30 
_chem_comp.pdbx_modified_date                    2023-10-20 
_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                        853.371 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VLO 
_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        8EAE 
_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 
VLO N1  N1  N 0 1 N N N 3.500  -26.884 -21.289 3.715   -0.706 -2.904 N1  VLO 1  
VLO C1  C1  C 0 1 N N N 2.198  -26.877 -20.965 2.575   -0.057 -3.305 C1  VLO 2  
VLO N2  N2  N 0 1 N N N 1.590  -28.017 -20.621 1.629   0.176  -2.422 N2  VLO 3  
VLO C2  C2  C 0 1 Y N N 0.279  -27.830 -20.327 0.500   0.807  -2.768 C2  VLO 4  
VLO C3  C3  C 0 1 Y N N -0.439 -26.651 -20.345 0.318   1.227  -4.091 C3  VLO 5  
VLO N3  N3  N 0 1 Y N N -1.762 -26.880 -19.975 -0.894  1.828  -4.158 N3  VLO 6  
VLO C4  C4  C 0 1 Y N N -1.822 -28.174 -19.743 -1.454  1.803  -2.984 C4  VLO 7  
VLO N4  N4  N 0 1 Y N N -0.612 -28.806 -19.950 -0.629  1.181  -2.092 N4  VLO 8  
VLO C5  C5  C 0 1 N N R -0.330 -30.253 -19.763 -0.902  0.956  -0.671 C5  VLO 9  
VLO O1  O1  O 0 1 N N N 0.742  -30.373 -18.853 -2.326  0.964  -0.425 O1  VLO 10 
VLO C6  C6  C 0 1 N N R 1.673  -31.400 -19.278 -2.467  1.234  0.987  C6  VLO 11 
VLO C7  C7  C 0 1 N N N 3.001  -30.740 -19.559 -3.868  1.767  1.290  C7  VLO 12 
VLO O2  O2  O 0 1 N N N 3.998  -31.722 -19.951 -4.832  0.741  1.044  O2  VLO 13 
VLO P1  P1  P 0 1 N N N 5.398  -31.111 -20.449 -6.413  0.953  1.258  P1  VLO 14 
VLO O3  O3  O 0 1 N N N 6.285  -32.198 -20.965 -6.714  1.203  2.820  O3  VLO 15 
VLO O4  O4  O 0 1 N N N 5.141  -29.920 -21.310 -6.865  2.125  0.476  O4  VLO 16 
VLO O5  O5  O 0 1 N N N 5.980  -30.584 -19.055 -7.203  -0.359 0.763  O5  VLO 17 
VLO P2  P2  P 0 1 N N N 7.440  -30.221 -18.515 -8.725  -0.651 0.328  P2  VLO 18 
VLO O6  O6  O 0 1 N N N 7.411  -28.888 -17.830 -8.951  -0.167 -1.191 O6  VLO 19 
VLO O7  O7  O 0 1 N N N 8.447  -30.472 -19.589 -9.644  0.087  1.223  O7  VLO 20 
VLO O8  O8  O 0 1 N N N 7.563  -31.377 -17.413 -9.022  -2.230 0.438  O8  VLO 21 
VLO P3  P3  P 0 1 N N N 7.588  -32.990 -17.482 -10.365 -3.117 0.450  P3  VLO 22 
VLO O9  O9  O 0 1 N N N 8.777  -33.395 -16.649 -10.050 -4.558 1.096  O9  VLO 23 
VLO O10 O10 O 0 1 N N N 7.737  -33.413 -18.925 -11.401 -2.432 1.255  O10 VLO 24 
VLO O11 O11 O 0 1 N N N 6.264  -33.410 -16.889 -10.895 -3.309 -1.058 O11 VLO 25 
VLO C8  C8  C 0 1 N N R 0.991  -32.108 -20.458 -1.402  2.312  1.291  C8  VLO 26 
VLO O12 O12 O 0 1 N N N 0.306  -33.278 -20.024 -0.816  2.088  2.575  O12 VLO 27 
VLO C9  C9  C 0 1 N N R 0.057  -31.035 -21.017 -0.349  2.124  0.175  C9  VLO 28 
VLO O13 O13 O 0 1 N N N -1.087 -31.665 -21.618 0.919   1.779  0.736  O13 VLO 29 
VLO P4  P4  P 0 1 N N N -1.533 -31.230 -23.104 2.249   2.657  0.504  P4  VLO 30 
VLO O14 O14 O 0 1 N N N -1.990 -29.796 -23.115 2.063   4.103  1.186  O14 VLO 31 
VLO O15 O15 O 0 1 N N N -2.496 -32.263 -23.629 2.483   2.822  -0.948 O15 VLO 32 
VLO O16 O16 O 0 1 N N N -0.172 -31.313 -23.958 3.509   1.907  1.168  O16 VLO 33 
VLO C10 C10 C 0 1 N N N 0.608  -32.537 -24.027 4.852   2.382  1.042  C10 VLO 34 
VLO C11 C11 C 0 1 N N R 2.010  -32.209 -24.481 5.797   1.439  1.790  C11 VLO 35 
VLO O17 O17 O 0 1 N N N 1.957  -31.083 -25.391 5.887   0.170  1.106  O17 VLO 36 
VLO C12 C12 C 0 1 N N R 3.068  -30.233 -25.208 7.118   -0.426 1.570  C12 VLO 37 
VLO N5  N5  N 0 1 Y N N 2.572  -28.886 -24.905 7.576   -1.449 0.627  N5  VLO 38 
VLO C13 C13 C 0 1 Y N N 1.304  -28.523 -24.514 7.258   -1.526 -0.696 C13 VLO 39 
VLO N6  N6  N 0 1 Y N N 1.186  -27.226 -24.332 7.840   -2.562 -1.229 N6  VLO 40 
VLO C14 C14 C 0 1 Y N N 2.445  -26.712 -24.623 8.561   -3.207 -0.283 C14 VLO 41 
VLO C15 C15 C 0 1 N N N 2.920  -25.367 -24.598 9.379   -4.364 -0.280 C15 VLO 42 
VLO O18 O18 O 0 1 N N N 2.300  -24.349 -24.304 9.551   -5.012 -1.298 O18 VLO 43 
VLO N7  N7  N 0 1 N N N 4.273  -25.317 -24.967 9.964   -4.729 0.882  N7  VLO 44 
VLO C16 C16 C 0 1 N N N 5.033  -26.377 -25.295 9.766   -4.001 2.010  C16 VLO 45 
VLO N8  N8  N 0 1 N N N 4.613  -27.618 -25.323 9.016   -2.934 2.024  N8  VLO 46 
VLO C17 C17 C 0 1 Y N N 3.303  -27.728 -24.977 8.405   -2.499 0.913  C17 VLO 47 
VLO C18 C18 C 0 1 N N R 3.947  -30.829 -24.109 8.126   0.744  1.626  C18 VLO 48 
VLO O19 O19 O 0 1 N N N 5.074  -31.489 -24.645 8.990   0.606  2.755  O19 VLO 49 
VLO C19 C19 C 0 1 N N S 2.998  -31.788 -23.384 7.237   1.999  1.774  C19 VLO 50 
VLO O20 O20 O 0 1 N N N 3.702  -32.907 -22.856 7.526   2.675  2.999  O20 VLO 51 
VLO C20 C20 C 0 1 N N N 0.212  -25.442 -20.705 1.344   0.969  -5.030 C20 VLO 52 
VLO O21 O21 O 0 1 N N N -0.268 -24.302 -20.775 1.228   1.317  -6.193 O21 VLO 53 
VLO N9  N9  N 0 1 N N N 1.560  -25.657 -21.008 2.458   0.333  -4.606 N9  VLO 54 
VLO H1  H1  H 0 1 N N N 4.015  -27.741 -21.273 3.815   -0.986 -1.980 H1  VLO 55 
VLO H2  H2  H 0 1 N N N 3.956  -26.032 -21.546 4.420   -0.889 -3.544 H2  VLO 56 
VLO H3  H3  H 0 1 N N N -2.719 -28.685 -19.426 -2.425  2.212  -2.750 H3  VLO 57 
VLO H4  H4  H 0 1 N N N -1.225 -30.727 -19.335 -0.467  0.010  -0.346 H4  VLO 58 
VLO H5  H5  H 0 1 N N N 1.808  -32.131 -18.467 -2.270  0.333  1.567  H5  VLO 59 
VLO H6  H6  H 0 1 N N N 3.344  -30.221 -18.652 -3.922  2.074  2.335  H6  VLO 60 
VLO H7  H7  H 0 1 N N N 2.875  -30.011 -20.373 -4.078  2.624  0.649  H7  VLO 61 
VLO H8  H8  H 0 1 N N N 6.590  -31.972 -21.836 -6.443  0.474  3.395  H8  VLO 62 
VLO H9  H9  H 0 1 N N N 8.088  -28.330 -18.194 -8.381  -0.610 -1.834 H9  VLO 63 
VLO H10 H10 H 0 1 N N N 9.408  -33.848 -17.196 -10.816 -5.147 1.136  H10 VLO 64 
VLO H11 H11 H 0 1 N N N 5.756  -33.873 -17.544 -10.266 -3.753 -1.643 H11 VLO 65 
VLO H12 H12 H 0 1 N N N 1.749  -32.359 -21.215 -1.841  3.308  1.240  H12 VLO 66 
VLO H13 H13 H 0 1 N N N 0.934  -33.907 -19.688 -1.445  2.134  3.307  H13 VLO 67 
VLO H14 H14 H 0 1 N N N 0.592  -30.388 -21.728 -0.268  3.027  -0.429 H14 VLO 68 
VLO H15 H15 H 0 1 N N N -2.869 -29.746 -23.471 1.906   4.071  2.139  H15 VLO 69 
VLO H16 H16 H 0 1 N N N 0.142  -33.230 -24.743 5.128   2.413  -0.011 H16 VLO 70 
VLO H17 H17 H 0 1 N N N 0.644  -33.007 -23.033 4.925   3.382  1.468  H17 VLO 71 
VLO H18 H18 H 0 1 N N N 2.425  -33.084 -25.003 5.457   1.297  2.816  H18 VLO 72 
VLO H19 H19 H 0 1 N N N 3.660  -30.194 -26.134 6.981   -0.858 2.561  H19 VLO 73 
VLO H20 H20 H 0 1 N N N 0.496  -29.225 -24.372 6.620   -0.832 -1.223 H20 VLO 74 
VLO H21 H21 H 0 1 N N N 4.709  -24.417 -24.988 10.528  -5.518 0.911  H21 VLO 75 
VLO H22 H22 H 0 1 N N N 6.065  -26.192 -25.554 10.244  -4.315 2.925  H22 VLO 76 
VLO H23 H23 H 0 1 N N N 4.253  -30.031 -23.417 8.705   0.793  0.704  H23 VLO 77 
VLO H24 H24 H 0 1 N N N 5.598  -31.847 -23.938 9.644   1.314  2.839  H24 VLO 78 
VLO H25 H25 H 0 1 N N N 2.460  -31.247 -22.592 7.377   2.668  0.925  H25 VLO 79 
VLO H26 H26 H 0 1 N N N 4.303  -32.614 -22.182 8.417   3.046  3.043  H26 VLO 80 
VLO H27 H27 H 0 1 N N N 2.104  -24.862 -21.277 3.176   0.148  -5.231 H27 VLO 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 
VLO O17 C12 SING N N 1  
VLO O17 C11 SING N N 2  
VLO N8  C16 DOUB N N 3  
VLO N8  C17 SING N N 4  
VLO C16 N7  SING N N 5  
VLO C12 N5  SING N N 6  
VLO C12 C18 SING N N 7  
VLO C17 N5  SING Y N 8  
VLO C17 C14 DOUB Y N 9  
VLO N7  C15 SING N N 10 
VLO N5  C13 SING Y N 11 
VLO O19 C18 SING N N 12 
VLO C14 C15 SING N N 13 
VLO C14 N6  SING Y N 14 
VLO C15 O18 DOUB N N 15 
VLO C13 N6  DOUB Y N 16 
VLO C11 C10 SING N N 17 
VLO C11 C19 SING N N 18 
VLO C18 C19 SING N N 19 
VLO C10 O16 SING N N 20 
VLO O16 P4  SING N N 21 
VLO O15 P4  DOUB N N 22 
VLO C19 O20 SING N N 23 
VLO O14 P4  SING N N 24 
VLO P4  O13 SING N N 25 
VLO O13 C9  SING N N 26 
VLO O4  P1  DOUB N N 27 
VLO N1  C1  SING N N 28 
VLO C9  C8  SING N N 29 
VLO C9  C5  SING N N 30 
VLO N9  C1  SING N N 31 
VLO N9  C20 SING N N 32 
VLO C1  N2  DOUB N N 33 
VLO O3  P1  SING N N 34 
VLO O21 C20 DOUB N N 35 
VLO C20 C3  SING N N 36 
VLO N2  C2  SING N N 37 
VLO C8  O12 SING N N 38 
VLO C8  C6  SING N N 39 
VLO P1  O2  SING N N 40 
VLO P1  O5  SING N N 41 
VLO C3  C2  DOUB Y N 42 
VLO C3  N3  SING Y N 43 
VLO C2  N4  SING Y N 44 
VLO N3  C4  DOUB Y N 45 
VLO O2  C7  SING N N 46 
VLO N4  C5  SING N N 47 
VLO N4  C4  SING Y N 48 
VLO C5  O1  SING N N 49 
VLO O7  P2  DOUB N N 50 
VLO C7  C6  SING N N 51 
VLO C6  O1  SING N N 52 
VLO O5  P2  SING N N 53 
VLO O10 P3  DOUB N N 54 
VLO P2  O6  SING N N 55 
VLO P2  O8  SING N N 56 
VLO P3  O8  SING N N 57 
VLO P3  O11 SING N N 58 
VLO P3  O9  SING N N 59 
VLO N1  H1  SING N N 60 
VLO N1  H2  SING N N 61 
VLO C4  H3  SING N N 62 
VLO C5  H4  SING N N 63 
VLO C6  H5  SING N N 64 
VLO C7  H6  SING N N 65 
VLO C7  H7  SING N N 66 
VLO O3  H8  SING N N 67 
VLO O6  H9  SING N N 68 
VLO O9  H10 SING N N 69 
VLO O11 H11 SING N N 70 
VLO C8  H12 SING N N 71 
VLO O12 H13 SING N N 72 
VLO C9  H14 SING N N 73 
VLO O14 H15 SING N N 74 
VLO C10 H16 SING N N 75 
VLO C10 H17 SING N N 76 
VLO C11 H18 SING N N 77 
VLO C12 H19 SING N N 78 
VLO C13 H20 SING N N 79 
VLO N7  H21 SING N N 80 
VLO C16 H22 SING N N 81 
VLO C18 H23 SING N N 82 
VLO O19 H24 SING N N 83 
VLO C19 H25 SING N N 84 
VLO O20 H26 SING N N 85 
VLO N9  H27 SING N N 86 
# 
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 
VLO InChI            InChI                1.06  "InChI=1S/C20H27N9O21P4/c21-20-26-15-9(17(34)27-20)25-5-29(15)19-13(11(31)7(47-19)2-45-53(40,41)50-54(42,43)49-51(35,36)37)48-52(38,39)44-1-6-10(30)12(32)18(46-6)28-4-24-8-14(28)22-3-23-16(8)33/h3-7,10-13,18-19,30-32H,1-2H2,(H,38,39)(H,40,41)(H,42,43)(H,22,23,33)(H2,35,36,37)(H3,21,26,27,34)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1" 
VLO InChIKey         InChI                1.06  QIEFBLFMZQEZSF-INFSMZHSSA-N                                                                                                                                                                                                                                                                                                                
VLO SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC=Nc56"                                                                                                                                                                                      
VLO SMILES           CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC=Nc56"                                                                                                                                                                                                 
VLO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5N=C(NC6=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)N=CNC2=O"                                                                                                                                                                                             
VLO SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5N=C(NC6=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)N=CNC2=O"                                                                                                                                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           VLO 
_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~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 
VLO "Create component" 2022-08-30 RCSB 
VLO "Initial release"  2023-10-25 RCSB 
# 
