data_SJO
# 
_chem_comp.id                                    SJO 
_chem_comp.name                                  "[(2R,3R,4R,5R)-5-(2-azanyl-8-methyl-6-oxidanylidene-1H-purin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H18 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-12 
_chem_comp.pdbx_modified_date                    2023-04-21 
_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                        391.274 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     SJO 
_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        8HMW 
_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 
SJO P      P1  P 0 1 N N N 1.552  -6.216 5.858  5.087  -1.096 -0.408 P      SJO 1  
SJO O1P    O1  O 0 1 N Y N 2.792  -6.697 5.209  4.994  -2.010 0.914  O1P    SJO 2  
SJO O2P    O2  O 0 1 N N N 0.283  -6.951 5.659  5.454  -2.019 -1.674 O2P    SJO 3  
SJO "O5'"  O3  O 0 1 N N N 1.826  -6.104 7.446  3.671  -0.374 -0.662 "O5'"  SJO 4  
SJO C2A    C1  C 0 0 N N N 1.942  -7.837 13.712 -1.444 4.026  1.001  "C2'A" SJO 5  
SJO "C2'"  C2  C 0 1 N N R 2.480  -7.068 11.535 -0.311 1.951  0.608  "C2'"  SJO 6  
SJO "O2'"  O4  O 0 1 N N N 2.569  -8.155 12.464 -1.019 3.056  0.042  "O2'"  SJO 7  
SJO "C5'"  C3  C 0 1 N N N 0.847  -6.546 8.397  3.118  0.593  0.233  "C5'"  SJO 8  
SJO "C4'"  C4  C 0 1 N N R 1.442  -7.564 9.392  1.770  1.075  -0.306 "C4'"  SJO 9  
SJO "O4'"  O5  O 0 1 N N N 2.867  -7.605 9.235  0.783  0.019  -0.216 "O4'"  SJO 10 
SJO "C1'"  C5  C 0 1 N N R 3.538  -7.233 10.452 -0.496 0.688  -0.261 "C1'"  SJO 11 
SJO N9     N1  N 0 1 Y N N 4.272  -5.975 10.274 -1.541 -0.171 0.302  N9     SJO 12 
SJO C4     C6  C 0 1 Y N N 3.691  -4.759 10.044 -2.790 -0.374 -0.219 C4     SJO 13 
SJO N3     N2  N 0 1 N N N 2.360  -4.533 9.929  -3.436 0.083  -1.298 N3     SJO 14 
SJO C2     C7  C 0 1 N N N 2.089  -3.250 9.705  -4.668 -0.292 -1.561 C2     SJO 15 
SJO N2     N3  N 0 1 N N N 0.825  -2.848 9.566  -5.291 0.203  -2.679 N2     SJO 16 
SJO N1     N4  N 0 1 N N N 3.048  -2.272 9.603  -5.345 -1.160 -0.756 N1     SJO 17 
SJO C6     C8  C 0 1 N N N 4.416  -2.481 9.717  -4.756 -1.663 0.352  C6     SJO 18 
SJO O6     O6  O 0 1 N N N 5.199  -1.542 9.610  -5.353 -2.440 1.078  O6     SJO 19 
SJO C5     C9  C 0 1 Y N N 4.717  -3.850 9.957  -3.431 -1.267 0.647  C5     SJO 20 
SJO N7     N5  N 0 1 Y N N 5.946  -4.487 10.131 -2.557 -1.562 1.640  N7     SJO 21 
SJO C8     C10 C 0 1 Y N N 5.622  -5.738 10.314 -1.444 -0.919 1.440  C8     SJO 22 
SJO C8A    C11 C 0 1 N N N 6.668  -6.831 10.555 -0.229 -0.993 2.328  C8A    SJO 23 
SJO "C3'"  C12 C 0 1 N N R 1.140  -7.117 10.826 1.212  2.211  0.579  "C3'"  SJO 24 
SJO "O3'"  O7  O 0 1 N N N 0.300  -8.085 11.459 1.492  3.485  -0.005 "O3'"  SJO 25 
SJO H2     H1  H 0 1 N N N 3.168  -5.998 4.686  4.324  -2.706 0.865  H2     SJO 26 
SJO H3     H2  H 0 1 N N N -0.378 -6.357 5.322  6.297  -2.486 -1.590 H3     SJO 27 
SJO H31    H3  H 0 0 N N N 2.031  -8.694 14.396 -1.973 4.832  0.492  "2H2'" SJO 28 
SJO H32    H4  H 0 0 N N N 2.435  -6.960 14.157 -2.110 3.555  1.724  "3H2'" SJO 29 
SJO H33    H5  H 0 0 N N N 0.879  -7.613 13.541 -0.575 4.432  1.518  "1H2'" SJO 30 
SJO "H2''" H6  H 0 0 N N N 2.606  -6.099 12.040 -0.647 1.766  1.628  "H2''" SJO 31 
SJO "H5'"  H7  H 0 1 N N N 0.474  -5.675 8.957  2.976  0.140  1.214  "H5'"  SJO 32 
SJO "H5''" H8  H 0 0 N N N 0.013  -7.019 7.858  3.799  1.440  0.319  "H5''" SJO 33 
SJO "H4'"  H9  H 0 1 N N N 0.997  -8.554 9.213  1.873  1.413  -1.337 "H4'"  SJO 34 
SJO "H1'"  H10 H 0 1 N N N 4.236  -8.028 10.755 -0.743 0.965  -1.286 "H1'"  SJO 35 
SJO H21    H11 H 0 1 N N N 0.079  -3.511 9.630  -4.822 0.821  -3.261 H21    SJO 36 
SJO H22    H12 H 0 1 N N N 0.623  -1.883 9.398  -6.200 -0.064 -2.886 H22    SJO 37 
SJO H1     H13 H 0 1 N N N 2.737  -1.337 9.433  -6.253 -1.416 -0.979 H1     SJO 38 
SJO H81    H14 H 0 1 N N N 7.674  -6.386 10.544 -0.289 -0.218 3.092  H81    SJO 39 
SJO H82    H15 H 0 1 N N N 6.487  -7.303 11.532 -0.186 -1.972 2.805  H82    SJO 40 
SJO H83    H16 H 0 1 N N N 6.595  -7.590 9.762  0.669  -0.842 1.728  H83    SJO 41 
SJO "H3'"  H17 H 0 1 N N N 0.675  -6.120 10.820 1.630  2.153  1.584  "H3'"  SJO 42 
SJO H4     H18 H 0 1 N Y N 0.112  -7.809 12.348 2.435  3.674  -0.103 H4     SJO 43 
SJO O1     O8  O 0 1 N N N 1.319  -4.679 5.422  6.138  -0.069 -0.225 O1     SJO 44 
# 
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 
SJO O1P   P      SING N N 1  
SJO O2P   P      SING N N 2  
SJO P     "O5'"  SING N N 3  
SJO "O5'" "C5'"  SING N N 4  
SJO "C5'" "C4'"  SING N N 5  
SJO "O4'" "C4'"  SING N N 6  
SJO "O4'" "C1'"  SING N N 7  
SJO "C4'" "C3'"  SING N N 8  
SJO N2    C2     SING N N 9  
SJO N1    C2     SING N N 10 
SJO N1    C6     SING N N 11 
SJO O6    C6     DOUB N N 12 
SJO C2    N3     DOUB N N 13 
SJO C6    C5     SING N N 14 
SJO N3    C4     SING N N 15 
SJO C5    C4     DOUB Y N 16 
SJO C5    N7     SING Y N 17 
SJO C4    N9     SING Y N 18 
SJO N7    C8     DOUB Y N 19 
SJO N9    C8     SING Y N 20 
SJO N9    "C1'"  SING N N 21 
SJO C8    C8A    SING N N 22 
SJO "C1'" "C2'"  SING N N 23 
SJO "C3'" "O3'"  SING N N 24 
SJO "C3'" "C2'"  SING N N 25 
SJO "C2'" "O2'"  SING N N 26 
SJO "O2'" C2A    SING N N 27 
SJO O1P   H2     SING N N 28 
SJO O2P   H3     SING N N 29 
SJO C2A   H31    SING N N 30 
SJO C2A   H32    SING N N 31 
SJO C2A   H33    SING N N 32 
SJO "C2'" "H2''" SING N N 33 
SJO "C5'" "H5'"  SING N N 34 
SJO "C5'" "H5''" SING N N 35 
SJO "C4'" "H4'"  SING N N 36 
SJO "C1'" "H1'"  SING N N 37 
SJO N2    H21    SING N N 38 
SJO N2    H22    SING N N 39 
SJO N1    H1     SING N N 40 
SJO C8A   H81    SING N N 41 
SJO C8A   H82    SING N N 42 
SJO C8A   H83    SING N N 43 
SJO "C3'" "H3'"  SING N N 44 
SJO "O3'" H4     SING N N 45 
SJO P     O1     DOUB N N 46 
# 
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 
SJO InChI            InChI                1.06  "InChI=1S/C12H18N5O8P/c1-4-14-6-9(15-12(13)16-10(6)19)17(4)11-8(23-2)7(18)5(25-11)3-24-26(20,21)22/h5,7-8,11,18H,3H2,1-2H3,(H2,20,21,22)(H3,13,15,16,19)/t5-,7-,8-,11-/m1/s1" 
SJO InChIKey         InChI                1.06  WTQBWOMAWHYVTP-IOSLPCCCSA-N                                                                                                                                                   
SJO SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2c(C)nc3C(=O)NC(=Nc23)N"                                                                                                       
SJO SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1n2c(C)nc3C(=O)NC(=Nc23)N"                                                                                                             
SJO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)OC)N=C(NC2=O)N"                                                                                                         
SJO SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)OC)N=C(NC2=O)N"                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           SJO 
_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-8-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-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 
SJO "Create component" 2023-04-12 PDBJ 
SJO "Initial release"  2023-04-26 RCSB 
# 
