data_U6F
# 
_chem_comp.id                                    U6F 
_chem_comp.name                                  "5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H18 N2 O24 P6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-15 
_chem_comp.pdbx_modified_date                    2023-12-15 
_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                        724.081 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     U6F 
_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        8FHM 
_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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
U6F "C1'"  C1  C 0 1 N N R N N N 36.364 6.302  20.336 -6.592 -1.866 -0.964 "C1'"  U6F 1  
U6F C2     C2  C 0 1 N N N N N N 35.604 4.514  21.970 -6.984 -1.596 1.420  C2     U6F 2  
U6F "C2'"  C3  C 0 1 N N R N N N 37.659 7.084  20.361 -7.793 -1.012 -1.445 "C2'"  U6F 3  
U6F "C3'"  C4  C 0 1 N N S N N N 37.431 8.100  19.286 -7.122 -0.051 -2.458 "C3'"  U6F 4  
U6F C4     C5  C 0 1 N N N N N N 36.501 2.247  21.634 -7.347 -3.409 2.849  C4     U6F 5  
U6F "C4'"  C6  C 0 1 N N R N N N 36.977 7.258  18.114 -5.632 -0.070 -2.066 "C4'"  U6F 6  
U6F C5     C7  C 0 1 N N N N N N 37.293 2.755  20.453 -7.220 -4.288 1.747  C5     U6F 7  
U6F "C5'"  C8  C 0 1 N N N N N N 38.105 6.599  17.396 -5.167 1.347  -1.723 "C5'"  U6F 8  
U6F C6     C9  C 0 1 N N N N N N 37.229 4.025  20.077 -6.967 -3.777 0.523  C6     U6F 9  
U6F N1     N1  N 0 1 N N N N N N 36.382 4.972  20.807 -6.855 -2.422 0.365  N1     U6F 10 
U6F N3     N2  N 0 1 N N N N N N 35.682 3.136  22.403 -7.225 -2.080 2.652  N3     U6F 11 
U6F O04    O1  O 0 1 N N N N N N 39.840 4.905  11.785 -0.772 3.516  1.381  O04    U6F 12 
U6F O05    O2  O 0 1 N N N N N N 38.310 3.316  12.365 0.385  4.171  -0.765 O05    U6F 13 
U6F O1A    O3  O 0 1 N N N N N N 37.843 3.817  16.166 -2.943 3.688  -2.301 O1A    U6F 14 
U6F O2     O4  O 0 1 N N N N N N 34.922 5.278  22.561 -6.876 -0.396 1.258  O2     U6F 15 
U6F "O2'"  O5  O 0 1 N N N N N N 37.859 7.643  21.656 -8.774 -1.827 -2.089 "O2'"  U6F 16 
U6F O2A    O6  O 0 1 N N N N N N 36.698 4.613  14.453 -3.562 3.300  0.115  O2A    U6F 17 
U6F "O3'"  O7  O 0 1 N N N N N N 36.400 9.032  19.701 -7.294 -0.532 -3.792 "O3'"  U6F 18 
U6F O3A    O8  O 0 1 N N N N N N 39.237 4.870  14.268 -1.416 2.257  -0.709 O3A    U6F 19 
U6F O3B    O9  O 0 1 N N N N N N 40.733 2.932  13.111 0.920  1.896  0.441  O3B    U6F 20 
U6F O4     O10 O 0 1 N N N N N N 36.595 1.093  21.858 -7.566 -3.847 3.964  O4     U6F 21 
U6F "O4'"  O11 O 0 1 N N N N N N 36.026 6.305  18.847 -5.503 -0.919 -0.913 "O4'"  U6F 22 
U6F "O5'"  O12 O 0 1 N N N N N N 37.802 6.416  16.026 -3.763 1.336  -1.458 "O5'"  U6F 23 
U6F P01    P1  P 0 1 N N N N N N 42.067 3.190  14.042 2.113  1.828  1.520  P01    U6F 24 
U6F P02    P2  P 0 1 N N N N N N 39.503 4.000  12.881 -0.233 2.972  0.115  P02    U6F 25 
U6F PA     P3  P 0 1 N N N N N N 37.892 4.934  15.230 -2.935 2.659  -1.062 PA     U6F 26 
U6F O01    O13 O 0 1 N N N N N N 42.043 4.401  14.933 1.524  1.353  2.941  O01    U6F 27 
U6F O02    O14 O 0 1 N N N N N N 43.377 -0.759 10.615 7.745  0.693  -0.640 O02    U6F 28 
U6F O03    O15 O 0 1 N N N N N N 43.158 3.600  13.159 2.727  3.167  1.663  O03    U6F 29 
U6F O06    O16 O 0 1 N N N N N N 42.085 0.328  12.537 5.493  -0.318 0.263  O06    U6F 30 
U6F O07    O17 O 0 1 N N N N N N 43.830 4.120  9.598  8.317  -4.065 -0.617 O07    U6F 31 
U6F O08    O18 O 0 1 N N N N N N 42.494 2.661  8.410  9.566  -2.138 -1.664 O08    U6F 32 
U6F O09    O19 O 0 1 N N N N N N 41.642 3.731  10.293 7.923  -3.379 -3.124 O09    U6F 33 
U6F O1B    O20 O 0 1 N N N N N N 44.455 0.775  13.372 5.452  1.751  1.708  O1B    U6F 34 
U6F O1G    O21 O 0 1 N N N N N N 43.388 1.815  10.717 7.111  -1.799 -1.186 O1G    U6F 35 
U6F O2B    O22 O 0 1 N N N N N N 43.263 -0.705 14.602 4.763  -0.424 2.787  O2B    U6F 36 
U6F O2G    O23 O 0 1 N N N N N N 42.517 1.777  14.761 3.227  0.777  1.023  O2G    U6F 37 
U6F O3G    O24 O 0 1 N N N N N N 41.469 0.255  10.047 7.728  -1.082 1.154  O3G    U6F 38 
U6F P08    P4  P 0 1 N N N N N N 42.839 3.057  9.774  8.258  -2.830 -1.648 P08    U6F 39 
U6F PB     P5  P 0 1 N N N N N N 43.090 0.531  13.832 4.749  0.475  1.451  PB     U6F 40 
U6F PG     P6  P 0 1 N N N N N N 42.579 0.405  10.973 7.035  -0.636 -0.075 PG     U6F 41 
U6F "H1'"  H1  H 0 1 N N N N N N 35.594 6.880  20.869 -6.378 -2.663 -1.677 "H1'"  U6F 42 
U6F H8     H2  H 0 1 N N N N N N 38.495 6.425  20.083 -8.233 -0.458 -0.616 H8     U6F 43 
U6F H9     H3  H 0 1 N N N N N N 38.368 8.623  19.042 -7.532 0.954  -2.360 H9     U6F 44 
U6F "H4'"  H4  H 0 1 N N N N N N 36.400 7.881  17.414 -5.037 -0.468 -2.888 "H4'"  U6F 45 
U6F H7     H5  H 0 1 N N N N N N 37.923 2.071  19.904 -7.315 -5.355 1.885  H7     U6F 46 
U6F "H5'1" H6  H 0 0 N N N N N N 38.298 5.618  17.855 -5.373 2.011  -2.562 "H5'1" U6F 47 
U6F "H5'2" H7  H 0 0 N N N N N N 39.003 7.228  17.484 -5.700 1.701  -0.840 "H5'2" U6F 48 
U6F H6     H8  H 0 1 N N N N N N 37.804 4.363  19.228 -6.867 -4.432 -0.329 H6     U6F 49 
U6F H3     H9  H 0 1 N N N N N N 35.183 2.816  23.209 -7.311 -1.471 3.402  H3     U6F 50 
U6F H1     H10 H 0 1 N N N N N N 38.106 3.645  11.498 0.758  3.886  -1.611 H1     U6F 51 
U6F H2     H11 H 0 1 N N N N N N 37.088 3.274  15.973 -2.547 3.334  -3.109 H2     U6F 52 
U6F "H2'"  H12 H 0 1 N N N N N N 37.997 6.945  22.285 -9.545 -1.338 -2.407 "H2'"  U6F 53 
U6F "H3'"  H13 H 0 1 N N N N N N 36.714 9.545  20.436 -8.218 -0.597 -4.071 "H3'"  U6F 54 
U6F H4     H14 H 0 1 N N N N N N 42.711 5.015  14.652 1.105  0.481  2.922  H4     U6F 55 
U6F H5     H15 H 0 1 N N N N N N 42.945 -1.237 9.917  7.342  1.042  -1.446 H5     U6F 56 
U6F H10    H16 H 0 1 N N N N N N 43.979 4.264  8.671  7.491  -4.565 -0.555 H10    U6F 57 
U6F H11    H17 H 0 1 N N N N N N 40.967 3.737  9.625  8.574  -4.007 -3.467 H11    U6F 58 
U6F H12    H18 H 0 1 N N N N N N 44.175 -0.971 14.575 4.318  -1.277 2.691  H12    U6F 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 
U6F O08   P08    DOUB N N 1  
U6F O07   P08    SING N N 2  
U6F P08   O09    SING N N 3  
U6F P08   O1G    SING N N 4  
U6F O3G   PG     DOUB N N 5  
U6F O02   PG     SING N N 6  
U6F O1G   PG     SING N N 7  
U6F PG    O06    SING N N 8  
U6F O04   P02    DOUB N N 9  
U6F O05   P02    SING N N 10 
U6F O06   PB     SING N N 11 
U6F P02   O3B    SING N N 12 
U6F P02   O3A    SING N N 13 
U6F O3B   P01    SING N N 14 
U6F O03   P01    DOUB N N 15 
U6F O1B   PB     DOUB N N 16 
U6F PB    O2B    SING N N 17 
U6F PB    O2G    SING N N 18 
U6F P01   O2G    SING N N 19 
U6F P01   O01    SING N N 20 
U6F O3A   PA     SING N N 21 
U6F O2A   PA     DOUB N N 22 
U6F PA    "O5'"  SING N N 23 
U6F PA    O1A    SING N N 24 
U6F "O5'" "C5'"  SING N N 25 
U6F "C5'" "C4'"  SING N N 26 
U6F "C4'" "O4'"  SING N N 27 
U6F "C4'" "C3'"  SING N N 28 
U6F "O4'" "C1'"  SING N N 29 
U6F "C3'" "O3'"  SING N N 30 
U6F "C3'" "C2'"  SING N N 31 
U6F C6    C5     DOUB N N 32 
U6F C6    N1     SING N N 33 
U6F "C1'" "C2'"  SING N N 34 
U6F "C1'" N1     SING N N 35 
U6F "C2'" "O2'"  SING N N 36 
U6F C5    C4     SING N N 37 
U6F N1    C2     SING N N 38 
U6F C4    O4     DOUB N N 39 
U6F C4    N3     SING N N 40 
U6F C2    N3     SING N N 41 
U6F C2    O2     DOUB N N 42 
U6F "C1'" "H1'"  SING N N 43 
U6F "C2'" H8     SING N N 44 
U6F "C3'" H9     SING N N 45 
U6F "C4'" "H4'"  SING N N 46 
U6F C5    H7     SING N N 47 
U6F "C5'" "H5'1" SING N N 48 
U6F "C5'" "H5'2" SING N N 49 
U6F C6    H6     SING N N 50 
U6F N3    H3     SING N N 51 
U6F O05   H1     SING N N 52 
U6F O1A   H2     SING N N 53 
U6F "O2'" "H2'"  SING N N 54 
U6F "O3'" "H3'"  SING N N 55 
U6F O01   H4     SING N N 56 
U6F O02   H5     SING N N 57 
U6F O07   H10    SING N N 58 
U6F O09   H11    SING N N 59 
U6F O2B   H12    SING N N 60 
# 
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 
U6F SMILES           ACDLabs              12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(N2C=CC(=O)NC2=O)C(O)C1O"                                                                                                                                                                         
U6F InChI            InChI                1.06  "InChI=1S/C9H18N2O24P6/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(30-8)3-29-37(19,20)32-39(23,24)34-41(27,28)35-40(25,26)33-38(21,22)31-36(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,23,24)(H,25,26)(H,27,28)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" 
U6F InChIKey         InChI                1.06  NJANLGXPTVMCFP-XVFCMESISA-N                                                                                                                                                                                                                                    
U6F SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                                          
U6F SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                                                 
U6F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                                   
U6F SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=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 
U6F "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine"                                                                      
U6F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] 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 
U6F "Create component" 2022-12-15 RCSB 
U6F "Initial release"  2023-12-20 RCSB 
# 
