data_LR6
# 
_chem_comp.id                                    LR6 
_chem_comp.name                                  
;[(1R,3R,4R,7S)-5-(N'-tert-butyl-N-methyl-carbamimidoyl)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C17 H28 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-07 
_chem_comp.pdbx_modified_date                    2023-08-04 
_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                        461.407 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LR6 
_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        8HIS 
_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 
LR6 C2     C1  C 0 1 N N N -0.777 -5.311  4.549  1.579  3.202  -0.695 C2     LR6 1  
LR6 C4     C2  C 0 1 N N N -0.425 -4.025  6.465  0.457  5.203  -0.252 C4     LR6 2  
LR6 C5     C3  C 0 1 N N N 0.741  -4.877  6.804  -0.731 4.471  -0.012 C5     LR6 3  
LR6 C6     C4  C 0 1 N N N 1.058  -5.923  5.950  -0.708 3.126  -0.126 C6     LR6 4  
LR6 N1     N1  N 0 1 N N N 0.326  -6.139  4.843  0.457  2.495  -0.469 N1     LR6 5  
LR6 N3     N2  N 0 1 N N N -1.120 -4.290  5.353  1.584  4.544  -0.588 N3     LR6 6  
LR6 CD     C5  C 0 1 N N N 1.135  -8.037  0.743  2.497  -1.703 0.189  CD     LR6 7  
LR6 "C1'"  C6  C 0 1 N N R 0.646  -7.247  3.927  0.482  1.035  -0.592 "C1'"  LR6 8  
LR6 "C2'"  C7  C 0 1 N N R 1.566  -6.825  2.790  1.102  0.395  0.689  "C2'"  LR6 9  
LR6 "C3'"  C8  C 0 1 N N S 2.913  -6.893  3.443  -0.199 0.295  1.566  "C3'"  LR6 10 
LR6 "C4'"  C9  C 0 1 N N R 2.685  -8.284  3.972  -1.027 -0.416 0.436  "C4'"  LR6 11 
LR6 "C5'"  C10 C 0 1 N N N 3.767  -8.779  4.915  -2.468 -0.794 0.785  "C5'"  LR6 12 
LR6 C5M    C11 C 0 1 N N N 1.560  -4.618  8.045  -2.004 5.183  0.366  C5M    LR6 13 
LR6 "C6'"  C12 C 0 1 N N N 2.442  -9.043  2.682  -0.055 -1.588 0.096  "C6'"  LR6 14 
LR6 "C7'"  C13 C 0 1 N N N -1.003 -7.688  -0.439 3.658  0.335  0.930  "C7'"  LR6 15 
LR6 "C8'"  C14 C 0 1 N N N 2.183  -9.385  -1.144 3.787  -3.623 -0.444 "C8'"  LR6 16 
LR6 "C9'"  C15 C 0 1 N N N 2.703  -8.912  -2.495 3.523  -5.033 -0.976 "C9'"  LR6 17 
LR6 "N2'"  N3  N 0 1 N N N 1.678  -8.024  1.958  1.301  -1.036 0.312  "N2'"  LR6 18 
LR6 "N3'"  N4  N 0 1 N N N -0.101 -7.782  0.692  3.677  -1.056 0.469  "N3'"  LR6 19 
LR6 "N4'"  N5  N 0 1 N N N 1.877  -8.189  -0.360 2.511  -2.950 -0.192 "N4'"  LR6 20 
LR6 O2     O1  O 0 1 N N N -1.446 -5.541  3.517  2.604  2.621  -0.993 O2     LR6 21 
LR6 "O3'"  O2  O 0 1 N N N 3.947  -6.873  2.465  -0.020 -0.535 2.716  "O3'"  LR6 22 
LR6 O4     O3  O 0 1 N N N -0.751 -3.073  7.206  0.461  6.417  -0.155 O4     LR6 23 
LR6 "O4'"  O4  O 0 1 N N N 1.425  -8.206  4.640  -0.860 0.517  -0.668 "O4'"  LR6 24 
LR6 "O5'"  O5  O 0 1 N N N 3.880  -7.768  5.912  -3.043 -1.529 -0.298 "O5'"  LR6 25 
LR6 OP1    O6  O 0 1 N N N 5.866  -8.799  7.115  -4.749 -2.926 0.930  OP1    LR6 26 
LR6 OP2    O7  O 0 1 N N N 4.724  -6.789  8.105  -5.582 -0.852 -0.243 OP2    LR6 27 
LR6 P      P1  P 0 1 N N N 4.558  -8.077  7.333  -4.552 -2.089 -0.274 P      LR6 28 
LR6 "C10'" C16 C 0 0 N N N 3.261  -10.225 -0.482 4.584  -3.711 0.859  "C10'" LR6 29 
LR6 "C11'" C17 C 0 0 N N N 0.969  -10.272 -1.386 4.588  -2.829 -1.479 "C11'" LR6 30 
LR6 H1     H1  H 0 1 N N N 1.896  -6.566  6.175  -1.604 2.551  0.052  H1     LR6 31 
LR6 H2     H2  H 0 1 N N N -1.907 -3.720  5.116  2.402  5.039  -0.754 H2     LR6 32 
LR6 H3     H3  H 0 1 N N N -0.273 -7.696  3.522  1.051  0.741  -1.475 H3     LR6 33 
LR6 H4     H4  H 0 1 N N N 1.311  -5.882  2.284  1.953  0.914  1.131  H4     LR6 34 
LR6 H5     H5  H 0 1 N N N 3.037  -6.149  4.244  -0.603 1.273  1.826  H5     LR6 35 
LR6 H6     H6  H 0 1 N N N 3.475  -9.738  5.368  -2.475 -1.408 1.685  H6     LR6 36 
LR6 H7     H7  H 0 1 N N N 4.720  -8.902  4.379  -3.050 0.111  0.958  H7     LR6 37 
LR6 H8     H8  H 0 1 N N N 1.148  -3.751  8.582  -1.821 6.257  0.406  H8     LR6 38 
LR6 H9     H9  H 0 1 N N N 1.527  -5.503  8.697  -2.772 4.974  -0.378 H9     LR6 39 
LR6 H10    H10 H 0 1 N N N 2.602  -4.412  7.760  -2.339 4.835  1.342  H10    LR6 40 
LR6 H11    H11 H 0 1 N N N 1.856  -9.959  2.846  -0.231 -2.431 0.763  H11    LR6 41 
LR6 H12    H12 H 0 1 N N N 3.382  -9.296  2.169  -0.180 -1.894 -0.942 H12    LR6 42 
LR6 H13    H13 H 0 1 N N N -2.015 -7.446  -0.082 4.681  0.690  1.055  H13    LR6 43 
LR6 H14    H14 H 0 1 N N N -0.655 -6.897  -1.120 3.145  0.954  0.194  H14    LR6 44 
LR6 H15    H15 H 0 1 N N N -1.023 -8.650  -0.973 3.134  0.394  1.883  H15    LR6 45 
LR6 H16    H16 H 0 1 N N N 3.582  -8.268  -2.345 2.954  -5.599 -0.239 H16    LR6 46 
LR6 H17    H17 H 0 1 N N N 2.986  -9.783  -3.104 2.956  -4.971 -1.905 H17    LR6 47 
LR6 H18    H18 H 0 1 N N N 1.916  -8.343  -3.012 4.473  -5.535 -1.164 H18    LR6 48 
LR6 H19    H19 H 0 1 N N N -0.529 -7.617  1.581  4.522  -1.520 0.361  H19    LR6 49 
LR6 "HO3'" H20 H 0 1 N Y N 4.792  -6.917  2.896  0.659  -0.218 3.328  H20    LR6 50 
LR6 HOP2   H22 H 0 1 N N N 5.641  -6.663  8.318  -5.509 -0.260 -1.004 H22    LR6 51 
LR6 H23    H23 H 0 1 N N N 2.903  -10.576 0.497  4.058  -4.354 1.564  H23    LR6 52 
LR6 H24    H24 H 0 1 N N N 3.494  -11.091 -1.119 5.571  -4.127 0.654  H24    LR6 53 
LR6 H25    H25 H 0 1 N N N 4.167  -9.616  -0.344 4.692  -2.714 1.287  H25    LR6 54 
LR6 H26    H26 H 0 1 N N N 0.575  -10.626 -0.422 5.496  -3.375 -1.733 H26    LR6 55 
LR6 H27    H27 H 0 1 N N N 0.192  -9.695  -1.910 3.984  -2.691 -2.376 H27    LR6 56 
LR6 H28    H28 H 0 1 N N N 1.263  -11.135 -2.002 4.852  -1.856 -1.065 H28    LR6 57 
LR6 OP3    OP3 O 0 1 N Y N 3.517  -9.055  8.067  -4.816 -2.975 -1.592 OP3    LR6 58 
LR6 HOP3   H30 H 0 1 N N N 3.928  -9.898  8.221  -5.708 -3.345 -1.645 H30    LR6 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 
LR6 "C9'"  "C8'"  SING N N 1  
LR6 "C11'" "C8'"  SING N N 2  
LR6 "C8'"  "C10'" SING N N 3  
LR6 "C8'"  "N4'"  SING N N 4  
LR6 "C7'"  "N3'"  SING N N 5  
LR6 "N4'"  CD     DOUB N N 6  
LR6 "N3'"  CD     SING N N 7  
LR6 CD     "N2'"  SING N N 8  
LR6 "N2'"  "C6'"  SING N N 9  
LR6 "N2'"  "C2'"  SING N N 10 
LR6 "O3'"  "C3'"  SING N N 11 
LR6 "C6'"  "C4'"  SING N N 12 
LR6 "C2'"  "C3'"  SING N N 13 
LR6 "C2'"  "C1'"  SING N N 14 
LR6 "C3'"  "C4'"  SING N N 15 
LR6 O2     C2     DOUB N N 16 
LR6 "C1'"  "O4'"  SING N N 17 
LR6 "C1'"  N1     SING N N 18 
LR6 "C4'"  "O4'"  SING N N 19 
LR6 "C4'"  "C5'"  SING N N 20 
LR6 C2     N1     SING N N 21 
LR6 C2     N3     SING N N 22 
LR6 N1     C6     SING N N 23 
LR6 "C5'"  "O5'"  SING N N 24 
LR6 N3     C4     SING N N 25 
LR6 "O5'"  P      SING N N 26 
LR6 C6     C5     DOUB N N 27 
LR6 C4     C5     SING N N 28 
LR6 C4     O4     DOUB N N 29 
LR6 C5     C5M    SING N N 30 
LR6 OP1    P      DOUB N N 31 
LR6 P      OP2    SING N N 32 
LR6 C6     H1     SING N N 33 
LR6 N3     H2     SING N N 34 
LR6 "C1'"  H3     SING N N 35 
LR6 "C2'"  H4     SING N N 36 
LR6 "C3'"  H5     SING N N 37 
LR6 "C5'"  H6     SING N N 38 
LR6 "C5'"  H7     SING N N 39 
LR6 C5M    H8     SING N N 40 
LR6 C5M    H9     SING N N 41 
LR6 C5M    H10    SING N N 42 
LR6 "C6'"  H11    SING N N 43 
LR6 "C6'"  H12    SING N N 44 
LR6 "C7'"  H13    SING N N 45 
LR6 "C7'"  H14    SING N N 46 
LR6 "C7'"  H15    SING N N 47 
LR6 "C9'"  H16    SING N N 48 
LR6 "C9'"  H17    SING N N 49 
LR6 "C9'"  H18    SING N N 50 
LR6 "N3'"  H19    SING N N 51 
LR6 "O3'"  "HO3'" SING N N 52 
LR6 OP2    HOP2   SING N N 53 
LR6 "C10'" H23    SING N N 54 
LR6 "C10'" H24    SING N N 55 
LR6 "C10'" H25    SING N N 56 
LR6 "C11'" H26    SING N N 57 
LR6 "C11'" H27    SING N N 58 
LR6 "C11'" H28    SING N N 59 
LR6 P      OP3    SING N N 60 
LR6 OP3    HOP3   SING N N 61 
# 
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 
LR6 InChI            InChI                1.06  "InChI=1S/C17H28N5O8P/c1-9-6-21(15(25)19-12(9)24)13-10-11(23)17(30-13,8-29-31(26,27)28)7-22(10)14(18-5)20-16(2,3)4/h6,10-11,13,23H,7-8H2,1-5H3,(H,18,20)(H,19,24,25)(H2,26,27,28)/t10-,11+,13-,17-/m1/s1" 
LR6 InChIKey         InChI                1.06  VZAHOKWRQQERGL-WYFUGZQLSA-N                                                                                                                                                                               
LR6 SMILES_CANONICAL CACTVS               3.385 "CNC(=NC(C)(C)C)N1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=C(C)C(=O)NC3=O"                                                                                                                          
LR6 SMILES           CACTVS               3.385 "CNC(=NC(C)(C)C)N1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=C(C)C(=O)NC3=O"                                                                                                                               
LR6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CN3C(=NC(C)(C)C)NC)COP(=O)(O)O)O"                                                                                                                         
LR6 SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CN3C(=NC(C)(C)C)NC)COP(=O)(O)O)O"                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           LR6 
_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        
;[(1~{R},3~{R},4~{R},7~{S})-5-(~{N}'-~{tert}-butyl-~{N}-methyl-carbamimidoyl)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[2.2.1]heptan-1-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 
LR6 "Create component" 2022-12-07 PDBJ 
LR6 "Initial release"  2023-08-09 RCSB 
# 
