data_A1CWA
# 
_chem_comp.id                                    A1CWA 
_chem_comp.name                                  "(2-azanylimidazol-1-yl)-[[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy]phosphinic acid" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H17 N8 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-09-29 
_chem_comp.pdbx_modified_date                    2025-10-17 
_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                        412.298 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CWA 
_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        9YD4 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1CWA "C2'"  C1  C 0 1 N N N N N N -17.304 14.748 -1.313 1.773  2.385  -0.408 "C2'"  A1CWA 1  
A1CWA "C1'"  C2  C 0 1 N N R N N N -17.365 13.875 -0.019 1.597  1.009  0.273  "C1'"  A1CWA 2  
A1CWA C2     C3  C 0 1 N N N N N N -13.415 15.062 1.008  5.814  -0.118 1.273  C2     A1CWA 3  
A1CWA C4     C4  C 0 1 Y N N N N N -15.002 13.572 0.431  3.811  -0.201 0.124  C4     A1CWA 4  
A1CWA "C5'"  C5  C 0 1 N N N N N N -20.024 12.511 -1.912 -1.867 1.713  -0.620 "C5'"  A1CWA 5  
A1CWA "O5'"  O1  O 0 1 N N N N N N -18.830 11.812 -2.309 -2.706 0.771  0.052  "O5'"  A1CWA 6  
A1CWA C6     C6  C 0 1 N N N N N N -12.848 12.756 0.744  5.636  -1.663 -0.495 C6     A1CWA 7  
A1CWA C11    C7  C 0 1 Y N N N N N -20.558 8.602  -2.584 -5.531 -0.659 1.625  C11    A1CWA 8  
A1CWA O6     O2  O 0 1 N N N N N N -11.927 11.910 0.784  6.115  -2.539 -1.195 O6     A1CWA 9  
A1CWA N1     N1  N 0 1 N N N N N N -12.531 14.032 1.031  6.359  -1.096 0.496  N1     A1CWA 10 
A1CWA N2     N2  N 0 1 N N N N N N -13.001 16.262 1.266  6.572  0.440  2.272  N2     A1CWA 11 
A1CWA N3     N3  N 0 1 N N N N N N -14.694 14.860 0.719  4.585  0.310  1.089  N3     A1CWA 12 
A1CWA C5     C8  C 0 1 Y N N N N N -14.123 12.545 0.457  4.314  -1.208 -0.707 C5     A1CWA 13 
A1CWA N7     N4  N 0 1 Y N N N N N -14.817 11.453 0.132  3.332  -1.535 -1.582 N7     A1CWA 14 
A1CWA C8     C9  C 0 1 Y N N N N N -16.049 11.790 -0.074 2.282  -0.805 -1.342 C8     A1CWA 15 
A1CWA N9     N5  N 0 1 Y N N N N N -16.180 13.074 0.109  2.530  0.035  -0.296 N9     A1CWA 16 
A1CWA "O4'"  O3  O 0 1 N N N N N N -18.514 12.969 -0.093 0.234  0.627  -0.014 "O4'"  A1CWA 17 
A1CWA "C3'"  C10 C 0 1 N N S N N N -18.758 14.653 -1.810 0.337  2.945  -0.508 "C3'"  A1CWA 18 
A1CWA "O3'"  O4  O 0 1 N N N N N N -19.402 15.893 -1.566 0.222  4.163  0.230  "O3'"  A1CWA 19 
A1CWA "C4'"  C11 C 0 1 N N R N N N -19.485 13.599 -0.981 -0.539 1.839  0.130  "C4'"  A1CWA 20 
A1CWA P1     P1  P 0 1 N N N N N N -18.823 10.589 -3.353 -4.183 0.390  -0.462 P1     A1CWA 21 
A1CWA O1     O5  O 0 1 N N N N N N -17.406 10.499 -3.750 -4.114 -0.064 -1.868 O1     A1CWA 22 
A1CWA O2     O6  O 0 1 N N N N N N -19.764 11.087 -4.373 -5.137 1.684  -0.362 O2     A1CWA 23 
A1CWA N10    N6  N 0 1 Y N N N N N -19.380 9.213  -2.412 -4.794 -0.812 0.472  N10    A1CWA 24 
A1CWA C12    C12 C 0 1 Y N N N N N -20.641 7.587  -1.719 -5.826 -1.893 2.067  C12    A1CWA 25 
A1CWA N13    N7  N 0 1 Y N N N N N -19.517 7.559  -0.997 -5.294 -2.786 1.215  N13    A1CWA 26 
A1CWA C14    C13 C 0 1 Y N N N N N -18.755 8.550  -1.438 -4.667 -2.149 0.255  C14    A1CWA 27 
A1CWA N14    N8  N 0 1 N N N N N N -17.551 8.819  -0.961 -3.994 -2.737 -0.803 N14    A1CWA 28 
A1CWA "H2'"  H1  H 0 1 N N N N N N -17.023 15.787 -1.085 2.396  3.037  0.204  "H2'"  A1CWA 29 
A1CWA "H2''" H2  H 0 0 N N N N N N -16.599 14.331 -2.047 2.207  2.266  -1.401 "H2''" A1CWA 30 
A1CWA "H1'"  H3  H 0 1 N N N N N N -17.470 14.542 0.849  1.750  1.097  1.349  "H1'"  A1CWA 31 
A1CWA "H5'"  H4  H 0 1 N N N N N N -20.717 11.842 -1.381 -1.679 1.370  -1.638 "H5'"  A1CWA 32 
A1CWA "H5''" H5  H 0 0 N N N N N N -20.534 12.951 -2.782 -2.361 2.684  -0.649 "H5''" A1CWA 33 
A1CWA H11    H6  H 0 1 N N N N N N -21.315 8.882  -3.302 -5.814 0.275  2.088  H11    A1CWA 34 
A1CWA H1     H7  H 0 1 N N N N N N -11.583 14.234 1.277  7.271  -1.386 0.655  H1     A1CWA 35 
A1CWA HN21   H8  H 0 0 N N N N N N -13.644 17.028 1.246  7.482  0.137  2.417  HN21   A1CWA 36 
A1CWA HN22   H9  H 0 0 N N N N N N -12.039 16.423 1.485  6.198  1.137  2.833  HN22   A1CWA 37 
A1CWA H8     H10 H 0 1 N N N N N N -16.844 11.114 -0.354 1.352  -0.857 -1.890 H8     A1CWA 38 
A1CWA "H3'"  H11 H 0 1 N N N N N N -18.777 14.382 -2.876 0.060  3.103  -1.550 "H3'"  A1CWA 39 
A1CWA "HO3'" H12 H 0 0 N N N N N N -20.301 15.848 -1.868 0.798  4.872  -0.089 "HO3'" A1CWA 40 
A1CWA "H4'"  H13 H 0 1 N N N N N N -20.308 14.058 -0.414 -0.716 2.055  1.183  "H4'"  A1CWA 41 
A1CWA H2     H14 H 0 1 N N N N N N -19.290 11.284 -5.172 -5.228 2.037  0.534  H2     A1CWA 42 
A1CWA H12    H15 H 0 1 N N N N N N -21.474 6.906  -1.620 -6.393 -2.128 2.956  H12    A1CWA 43 
A1CWA H141   H16 H 0 0 N N N N N N -17.326 8.168  -0.237 -3.562 -2.183 -1.471 H141   A1CWA 44 
A1CWA H142   H17 H 0 0 N N N N N N -16.877 8.746  -1.696 -3.956 -3.704 -0.876 H142   A1CWA 45 
# 
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 
A1CWA C6    O6     DOUB N N 1  
A1CWA C6    N1     SING N N 2  
A1CWA C6    C5     SING N N 3  
A1CWA C2    N1     SING N N 4  
A1CWA C2    N2     SING N N 5  
A1CWA C2    N3     DOUB N N 6  
A1CWA C4    N3     SING N N 7  
A1CWA C4    C5     DOUB Y N 8  
A1CWA C4    N9     SING Y N 9  
A1CWA C5    N7     SING Y N 10 
A1CWA C8    N7     DOUB Y N 11 
A1CWA N9    C8     SING Y N 12 
A1CWA "C1'" N9     SING N N 13 
A1CWA "C1'" "O4'"  SING N N 14 
A1CWA "C1'" "C2'"  SING N N 15 
A1CWA "C4'" "O4'"  SING N N 16 
A1CWA "C3'" "C2'"  SING N N 17 
A1CWA "C3'" "O3'"  SING N N 18 
A1CWA "C3'" "C4'"  SING N N 19 
A1CWA "C4'" "C5'"  SING N N 20 
A1CWA "C5'" "O5'"  SING N N 21 
A1CWA P1    "O5'"  SING N N 22 
A1CWA P1    O1     DOUB N N 23 
A1CWA P1    O2     SING N N 24 
A1CWA N10   P1     SING N N 25 
A1CWA N10   C11    SING Y N 26 
A1CWA N10   C14    SING Y N 27 
A1CWA C11   C12    DOUB Y N 28 
A1CWA C12   N13    SING Y N 29 
A1CWA C14   N13    DOUB Y N 30 
A1CWA C14   N14    SING N N 31 
A1CWA "C2'" "H2'"  SING N N 32 
A1CWA "C2'" "H2''" SING N N 33 
A1CWA "C1'" "H1'"  SING N N 34 
A1CWA "C5'" "H5'"  SING N N 35 
A1CWA "C5'" "H5''" SING N N 36 
A1CWA C11   H11    SING N N 37 
A1CWA N1    H1     SING N N 38 
A1CWA N2    HN21   SING N N 39 
A1CWA N2    HN22   SING N N 40 
A1CWA C8    H8     SING N N 41 
A1CWA "C3'" "H3'"  SING N N 42 
A1CWA "O3'" "HO3'" SING N N 43 
A1CWA "C4'" "H4'"  SING N N 44 
A1CWA O2    H2     SING N N 45 
A1CWA C12   H12    SING N N 46 
A1CWA N14   H141   SING N N 47 
A1CWA N14   H142   SING N N 48 
# 
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 
A1CWA SMILES           ACDLabs              14.52   "Nc1nccn1P(=O)(O)OCC1OC(CC1O)n1cnc2c1N=C(N)NC2=O"                                                                                                                                    
A1CWA InChI            InChI                1.06    "InChI=1S/C13H17N8O6P/c14-12-18-10-9(11(23)19-12)17-5-20(10)8-3-6(22)7(27-8)4-26-28(24,25)21-2-1-16-13(21)15/h1-2,5-8,22H,3-4H2,(H2,15,16)(H,24,25)(H3,14,18,19,23)/t6-,7+,8+/m0/s1" 
A1CWA InChIKey         InChI                1.06    UDDIXTSYRLRNQW-XLPZGREQSA-N                                                                                                                                                          
A1CWA SMILES_CANONICAL CACTVS               3.385   "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)n4ccnc4N)O3"                                                                                                                 
A1CWA SMILES           CACTVS               3.385   "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)n4ccnc4N)O3"                                                                                                                     
A1CWA SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1cn(c(n1)N)P(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)n3cnc4c3N=C(NC4=O)N)O"                                                                                                                
A1CWA SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1cn(c(n1)N)P(=O)(O)OCC2C(CC(O2)n3cnc4c3N=C(NC4=O)N)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 
A1CWA "SYSTEMATIC NAME" ACDLabs              14.52   "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine"                                                                 
A1CWA "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2-azanylimidazol-1-yl)-[[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy]phosphinic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1CWA 
_pdbx_chem_comp_synonyms.name         "5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         "systematic name from ACDLabs" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1CWA "Create component" 2025-09-29 RCSB 
A1CWA "Initial release"  2025-10-22 RCSB 
# 
