data_F5D
# 
_chem_comp.id                                    F5D 
_chem_comp.name                                  "5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H32 N7 O15 P3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-02-28 
_chem_comp.pdbx_modified_date                    2018-03-29 
_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                        735.492 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     F5D 
_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        6CK0 
_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 
F5D C10 C1  C 0 1 Y N N 17.472 0.819   36.830 -7.836  3.725  -0.872 C10 F5D 1  
F5D C13 C2  C 0 1 N N R 15.722 2.947   32.129 -4.477  -0.738 0.676  C13 F5D 2  
F5D C21 C3  C 0 1 N N N 13.185 -3.441  31.119 2.749   0.965  1.088  C21 F5D 3  
F5D C22 C4  C 0 1 N N N 13.814 -4.122  32.356 4.131   0.716  0.480  C22 F5D 4  
F5D C24 C5  C 0 1 N N N 15.082 -6.201  33.175 6.538   1.385  0.544  C24 F5D 5  
F5D C28 C6  C 0 1 N N R 16.194 -9.839  32.590 9.824   3.360  0.860  C28 F5D 6  
F5D C02 C7  C 0 1 Y N N 17.091 0.201   38.035 -8.911  4.629  -0.822 C02 F5D 7  
F5D C04 C8  C 0 1 Y N N 15.284 1.605   38.225 -9.690  3.546  1.062  C04 F5D 8  
F5D C06 C9  C 0 1 Y N N 16.690 1.845   36.371 -7.761  2.729  0.117  C06 F5D 9  
F5D C08 C10 C 0 1 Y N N 18.301 1.563   34.959 -6.065  2.542  -1.280 C08 F5D 10 
F5D C11 C11 C 0 1 N N R 16.668 3.354   34.428 -6.134  0.848  0.589  C11 F5D 11 
F5D C14 C12 C 0 1 N N N 16.132 1.658   31.378 -3.211  -1.245 -0.018 C14 F5D 12 
F5D C19 C13 C 0 1 N N N 12.885 -1.938  31.250 1.740   0.062  0.427  C19 F5D 13 
F5D C23 C14 C 0 1 N N N 14.096 -5.629  32.159 5.156   1.633  1.151  C23 F5D 14 
F5D C25 C15 C 0 1 N N S 15.025 -7.719  33.457 7.562   2.302  1.215  C25 F5D 15 
F5D C27 C16 C 0 1 N N N 15.967 -9.748  34.258 8.968   4.628  1.008  C27 F5D 16 
F5D C30 C17 C 0 1 N N R 17.878 -8.446  31.878 9.632   3.099  -1.446 C30 F5D 17 
F5D C33 C18 C 0 1 N N S 15.534 -8.683  32.090 8.968   2.105  0.603  C33 F5D 18 
F5D C43 C19 C 0 1 N N S 16.625 3.918   32.123 -5.714  -1.516 0.174  C43 F5D 19 
F5D C45 C20 C 0 1 N N R 17.510 3.791   33.527 -6.829  -0.448 0.115  C45 F5D 20 
F5D N01 N1  N 0 1 N N N 17.878 -0.880  38.547 -9.038  5.630  -1.769 N01 F5D 21 
F5D N03 N2  N 0 1 Y N N 16.016 0.600   38.698 -9.803  4.499  0.155  N03 F5D 22 
F5D N05 N3  N 0 1 Y N N 15.610 2.212   37.085 -8.700  2.678  1.055  N05 F5D 23 
F5D N07 N4  N 0 1 Y N N 17.231 2.289   35.228 -6.634  1.999  -0.167 N07 F5D 24 
F5D N09 N5  N 0 1 Y N N 18.459 0.673   35.926 -6.769  3.558  -1.689 N09 F5D 25 
F5D N29 N6  N 0 1 N N N 17.692 -9.744  32.118 10.613  3.488  -0.400 N29 F5D 26 
F5D N32 N7  N 0 1 N N N 16.527 -7.993  31.203 8.862   1.977  -0.863 N32 F5D 27 
F5D O12 O1  O 0 1 N N N 15.472 2.660   33.645 -4.732  0.636  0.313  O12 F5D 28 
F5D O15 O2  O 0 1 N N N 15.101 0.685   31.465 -2.068  -0.597 0.542  O15 F5D 29 
F5D O17 O3  O 0 1 N N N 14.509 0.833   29.033 -0.472  -0.675 -1.412 O17 F5D 30 
F5D O18 O4  O 0 1 N N N 13.258 -1.017  30.222 0.452   0.106  0.803  O18 F5D 31 
F5D O20 O5  O 0 1 N N N 12.302 -1.602  32.227 2.091   -0.703 -0.441 O20 F5D 32 
F5D O31 O6  O 0 1 N N N 18.999 -8.155  31.121 10.312  2.670  -2.628 O31 F5D 33 
F5D O34 O7  O 0 1 N N N 12.688 1.698   30.602 -0.174  -2.414 0.392  O34 F5D 34 
F5D O36 O8  O 0 1 N N N 13.470 4.187   31.133 1.250   -3.215 -1.532 O36 F5D 35 
F5D O37 O9  O 0 1 N N N 12.924 3.610   28.786 2.349   -3.067 0.736  O37 F5D 36 
F5D O38 O10 O 0 1 N N N 11.095 3.946   30.549 0.572   -4.928 0.194  O38 F5D 37 
F5D O40 O11 O 0 1 N N N 8.904  5.111   30.263 2.601   -6.371 -0.219 O40 F5D 38 
F5D O41 O12 O 0 1 N N N 9.181  2.876   29.213 0.519   -7.520 0.627  O41 F5D 39 
F5D O42 O13 O 0 1 N N N 10.260 4.851   28.210 0.673   -6.601 -1.831 O42 F5D 40 
F5D O44 O14 O 0 1 N N N 15.962 5.188   32.184 -6.061  -2.552 1.095  O44 F5D 41 
F5D O46 O15 O 0 1 N N N 17.999 5.086   33.910 -7.899  -0.793 0.997  O46 F5D 42 
F5D P16 P1  P 0 1 N N S 13.886 0.547   30.322 -0.563  -0.890 0.049  P16 F5D 43 
F5D P35 P2  P 0 1 N N N 12.588 3.344   30.236 1.005   -3.402 -0.084 P35 F5D 44 
F5D P39 P3  P 0 1 N N N 9.841  4.205   29.506 1.124   -6.355 -0.305 P39 F5D 45 
F5D S26 S1  S 0 1 N N N 15.994 -8.112  34.469 7.235   4.066  0.810  S26 F5D 46 
F5D H1  H1  H 0 1 N N N 14.772 3.296   31.698 -4.380  -0.835 1.758  H1  F5D 47 
F5D H2  H2  H 0 1 N N N 13.878 -3.573  30.275 2.780   0.755  2.157  H2  F5D 48 
F5D H3  H3  H 0 1 N N N 12.237 -3.954  30.899 2.465   2.005  0.930  H3  F5D 49 
F5D H4  H4  H 0 1 N N N 14.765 -3.618  32.584 4.416   -0.324 0.639  H4  F5D 50 
F5D H5  H5  H 0 1 N N N 13.124 -4.006  33.205 4.101   0.926  -0.589 H5  F5D 51 
F5D H6  H6  H 0 1 N N N 16.095 -5.972  32.814 6.823   0.345  0.702  H6  F5D 52 
F5D H7  H7  H 0 1 N N N 14.907 -5.683  34.130 6.508   1.595  -0.525 H7  F5D 53 
F5D H8  H8  H 0 1 N N N 15.740 -10.771 32.223 10.467  3.221  1.729  H8  F5D 54 
F5D H9  H9  H 0 1 N N N 14.413 1.933   38.773 -10.437 3.477  1.839  H9  F5D 55 
F5D H10 H10 H 0 1 N N N 18.940 1.676   34.095 -5.161  2.185  -1.751 H10 F5D 56 
F5D H11 H11 H 0 1 N N N 16.262 4.152   35.066 -6.295  0.996  1.656  H11 F5D 57 
F5D H12 H12 H 0 1 N N N 16.316 1.898   30.320 -3.125  -2.322 0.126  H12 F5D 58 
F5D H13 H13 H 0 1 N N N 17.051 1.253   31.827 -3.268  -1.025 -1.084 H13 F5D 59 
F5D H14 H14 H 0 1 N N N 13.146 -6.176  32.250 4.871   2.674  0.993  H14 F5D 60 
F5D H15 H15 H 0 1 N N N 14.510 -5.777  31.151 5.186   1.424  2.221  H15 F5D 61 
F5D H16 H16 H 0 1 N N N 14.003 -8.023  33.728 7.578   2.145  2.293  H16 F5D 62 
F5D H18 H18 H 0 1 N N N 15.003 -10.182 34.562 9.112   5.069  1.995  H18 F5D 63 
F5D H19 H19 H 0 1 N N N 16.781 -10.243 34.807 9.222   5.349  0.231  H19 F5D 64 
F5D H20 H20 H 0 1 N N N 17.945 -7.903  32.832 8.970   3.934  -1.672 H20 F5D 65 
F5D H21 H21 H 0 1 N N N 14.631 -8.948  31.520 9.452   1.224  1.026  H21 F5D 66 
F5D H23 H23 H 0 1 N N N 17.317 3.865   31.270 -5.528  -1.930 -0.817 H23 F5D 67 
F5D H24 H24 H 0 1 N N N 18.342 3.096   33.341 -7.195  -0.335 -0.905 H24 F5D 68 
F5D H25 H25 H 0 1 N N N 17.476 -1.210  39.401 -8.381  5.714  -2.477 H25 F5D 69 
F5D H26 H26 H 0 1 N N N 17.898 -1.624  37.879 -9.785  6.248  -1.724 H26 F5D 70 
F5D H27 H27 H 0 1 N N N 18.311 -10.064 32.835 10.928  4.437  -0.535 H27 F5D 71 
F5D H29 H29 H 0 1 N N N 16.417 -6.999  31.228 7.898   2.008  -1.159 H29 F5D 72 
F5D H31 H31 H 0 1 N N N 19.061 -7.216  30.995 10.866  3.352  -3.032 H31 F5D 73 
F5D H32 H32 H 0 1 N N N 13.621 4.253   28.735 2.262   -3.169 1.693  H32 F5D 74 
F5D H33 H33 H 0 1 N N N 8.299  2.875   29.567 0.810   -8.410 0.383  H33 F5D 75 
F5D H34 H34 H 0 1 N N N 9.847  5.703   28.132 -0.285  -6.603 -1.963 H34 F5D 76 
F5D H35 H35 H 0 1 N N N 15.071 5.096   31.867 -6.831  -3.072 0.829  H35 F5D 77 
F5D H36 H36 H 0 1 N N N 18.610 5.401   33.254 -8.371  -1.600 0.747  H36 F5D 78 
# 
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 
F5D C10 C02 DOUB Y N 1  
F5D C10 C06 SING Y N 2  
F5D C10 N09 SING Y N 3  
F5D C13 C14 SING N N 4  
F5D C13 C43 SING N N 5  
F5D C13 O12 SING N N 6  
F5D C21 C22 SING N N 7  
F5D C21 C19 SING N N 8  
F5D C22 C23 SING N N 9  
F5D C24 C23 SING N N 10 
F5D C24 C25 SING N N 11 
F5D C28 C27 SING N N 12 
F5D C28 C33 SING N N 13 
F5D C28 N29 SING N N 14 
F5D C02 N01 SING N N 15 
F5D C02 N03 SING Y N 16 
F5D C04 N03 DOUB Y N 17 
F5D C04 N05 SING Y N 18 
F5D C06 N05 DOUB Y N 19 
F5D C06 N07 SING Y N 20 
F5D C08 N07 SING Y N 21 
F5D C08 N09 DOUB Y N 22 
F5D C11 C45 SING N N 23 
F5D C11 N07 SING N N 24 
F5D C11 O12 SING N N 25 
F5D C14 O15 SING N N 26 
F5D C19 O18 SING N N 27 
F5D C19 O20 DOUB N N 28 
F5D C25 S26 SING N N 29 
F5D C27 S26 SING N N 30 
F5D C30 N29 SING N N 31 
F5D C30 N32 SING N N 32 
F5D C30 O31 SING N N 33 
F5D C33 N32 SING N N 34 
F5D C43 C45 SING N N 35 
F5D C43 O44 SING N N 36 
F5D C45 O46 SING N N 37 
F5D O15 P16 SING N N 38 
F5D O17 P16 DOUB N N 39 
F5D O18 P16 SING N N 40 
F5D O34 P16 SING N N 41 
F5D O34 P35 SING N N 42 
F5D O36 P35 DOUB N N 43 
F5D O37 P35 SING N N 44 
F5D O38 P35 SING N N 45 
F5D O38 P39 SING N N 46 
F5D O40 P39 DOUB N N 47 
F5D O41 P39 SING N N 48 
F5D O42 P39 SING N N 49 
F5D C13 H1  SING N N 50 
F5D C21 H2  SING N N 51 
F5D C21 H3  SING N N 52 
F5D C22 H4  SING N N 53 
F5D C22 H5  SING N N 54 
F5D C24 H6  SING N N 55 
F5D C24 H7  SING N N 56 
F5D C28 H8  SING N N 57 
F5D C04 H9  SING N N 58 
F5D C08 H10 SING N N 59 
F5D C11 H11 SING N N 60 
F5D C14 H12 SING N N 61 
F5D C14 H13 SING N N 62 
F5D C23 H14 SING N N 63 
F5D C23 H15 SING N N 64 
F5D C25 H16 SING N N 65 
F5D C27 H18 SING N N 66 
F5D C27 H19 SING N N 67 
F5D C30 H20 SING N N 68 
F5D C33 H21 SING N N 69 
F5D C43 H23 SING N N 70 
F5D C45 H24 SING N N 71 
F5D N01 H25 SING N N 72 
F5D N01 H26 SING N N 73 
F5D N29 H27 SING N N 74 
F5D N32 H29 SING N N 75 
F5D O31 H31 SING N N 76 
F5D O37 H32 SING N N 77 
F5D O41 H33 SING N N 78 
F5D O42 H34 SING N N 79 
F5D O44 H35 SING N N 80 
F5D O46 H36 SING N N 81 
F5D C33 C25 SING N N 82 
# 
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 
F5D SMILES           ACDLabs              12.01 "c12c(N)ncnc1n(cn2)C5C(C(C(COP(=O)(OC(CCCCC3SCC4C3NC(N4)O)=O)OP(=O)(O)OP(=O)(O)O)O5)O)O" 
F5D InChI            InChI                1.03  
;InChI=1S/C20H32N7O15P3S/c21-17-14-18(23-7-22-17)27(8-24-14)19-16(30)15(29)10(39-19)5-38-45(37,42-44(35,36)41-43(32,33)34)40-12(28)4-2-1-3-11-13-9(6-46-11)25-20(31)26-13/h7-11,13,15-16,19-20,25-26,29-31H,1-6H2,(H,35,36)(H2,21,22,23)(H2,32,33,34)/t9-,10+,11-,13?,15+,16+,19+,20+,45-/m0/s1
;
F5D InChIKey         InChI                1.03  KMVPKOZRCVFEFI-NSWRTZSASA-N 
F5D SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](=O)(OC(=O)CCCC[C@@H]4SC[C@@H]5N[C@@H](O)N[C@H]45)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" 
F5D SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](=O)(OC(=O)CCCC[CH]4SC[CH]5N[CH](O)N[CH]45)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" 
F5D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(OC(=O)CCCCC4C5[C@H](CS4)N[C@H](N5)O)OP(=O)(O)OP(=O)(O)O)O)O)N" 
F5D SMILES           "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(OC(=O)CCCCC4C5C(CS4)NC(N5)O)OP(=O)(O)OP(=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 
F5D "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" 
F5D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 
"[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl] 5-[(2~{R},6~{a}~{R})-2-oxidanyl-2,3,3~{a},4,6,6~{a}-hexahydro-1~{H}-thieno[3,4-d]imidazol-4-yl]pentanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
F5D "Create component" 2018-02-28 RCSB 
F5D "Initial release"  2018-04-04 RCSB 
# 
