data_A1MA9
# 
_chem_comp.id                                    A1MA9 
_chem_comp.name                                  
;8-CF3-2'F-riboguanosine monophosphate
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H12 F4 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         "[(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-8-(trifluoromethyl)-1~{H}-purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-07-25 
_chem_comp.pdbx_modified_date                    2026-02-13 
_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                        433.210 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     A1MA9 
_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        9VZW 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
A1MA9 P      P1   P 0 1 N N N N N N -0.112 5.497 -4.119 4.977  0.505  1.072  P      A1MA9 1  
A1MA9 OP2    O1   O 0 1 N N N N N N 0.645  4.572 -5.094 4.894  1.898  0.270  OP2    A1MA9 2  
A1MA9 "O5'"  O2   O 0 1 N N N N N N 0.956  6.283 -3.312 3.576  -0.276 0.938  "O5'"  A1MA9 3  
A1MA9 "C2'"  C1   C 0 1 N N R N N N 0.809  6.244 1.446  -0.337 -1.805 -1.322 "C2'"  A1MA9 4  
A1MA9 "C5'"  C2   C 0 1 N N N N N N 1.552  5.645 -2.180 3.076  -0.770 -0.306 "C5'"  A1MA9 5  
A1MA9 "C4'"  C3   C 0 1 N N R N N N 1.131  6.398 -0.922 1.728  -1.457 -0.077 "C4'"  A1MA9 6  
A1MA9 "O4'"  O3   O 0 1 N N N N N N -0.236 6.212 -0.657 0.732  -0.488 0.332  "O4'"  A1MA9 7  
A1MA9 "C1'"  C4   C 0 1 N N R N N N -0.477 6.551 0.690  -0.541 -1.105 0.040  "C1'"  A1MA9 8  
A1MA9 "C3'"  C5   C 0 1 N N R N N N 1.812  5.960 0.362  1.188  -2.041 -1.402 "C3'"  A1MA9 9  
A1MA9 "O3'"  O4   O 0 1 N N N N N N 2.985  6.736 0.540  1.476  -3.438 -1.487 "O3'"  A1MA9 10 
A1MA9 OP1    O5   O 0 1 N N N N N N -0.928 6.578 -4.867 6.062  -0.327 0.505  OP1    A1MA9 11 
A1MA9 N9     N1   N 0 1 Y N N N N N -1.670 5.800 1.144  -1.589 -0.087 -0.062 N9     A1MA9 12 
A1MA9 C4     C6   C 0 1 Y N N N N N -1.733 4.416 1.160  -2.846 -0.163 0.474  C4     A1MA9 13 
A1MA9 N3     N2   N 0 1 N N N N N N -0.824 3.465 0.874  -3.498 -1.080 1.197  N3     A1MA9 14 
A1MA9 C2     C7   C 0 1 N N N N N N -1.105 2.145 0.996  -4.737 -0.883 1.588  C2     A1MA9 15 
A1MA9 N2     N3   N 0 1 N N N N N N -0.161 1.245 0.745  -5.365 -1.853 2.329  N2     A1MA9 16 
A1MA9 N1     N4   N 0 1 N N N N N N -2.366 1.783 1.378  -5.417 0.257  1.279  N1     A1MA9 17 
A1MA9 C6     C8   C 0 1 N N N N N N -3.377 2.655 1.659  -4.824 1.229  0.550  C6     A1MA9 18 
A1MA9 O6     O6   O 0 1 N N N N N N -4.489 2.233 1.976  -5.424 2.252  0.268  O6     A1MA9 19 
A1MA9 C5     C9   C 0 1 Y N N N N N -3.041 4.046 1.566  -3.490 1.030  0.124  C5     A1MA9 20 
A1MA9 N7     N5   N 0 1 Y N N N N N -3.764 5.200 1.809  -2.610 1.765  -0.598 N7     A1MA9 21 
A1MA9 C8     C10  C 0 1 Y N N N N N -2.889 6.204 1.584  -1.489 1.113  -0.705 C8     A1MA9 22 
A1MA9 C      C11  C 0 1 N N N N N N -3.264 7.652 1.798  -0.265 1.608  -1.431 C      A1MA9 23 
A1MA9 "F2'"  F1   F 0 1 N N N N N N 1.195  7.338 2.217  -1.023 -3.023 -1.355 "F2'"  A1MA9 24 
A1MA9 F11    F2   F 0 1 N N N N N N -3.539 8.163 0.609  -0.141 0.933  -2.650 F11    A1MA9 25 
A1MA9 F12    F3   F 0 1 N N N N N N -2.240 8.268 2.359  -0.387 2.981  -1.669 F12    A1MA9 26 
A1MA9 F13    F4   F 0 1 N N N N N N -4.321 7.712 2.590  0.870  1.369  -0.648 F13    A1MA9 27 
A1MA9 HOP2   H1   H 0 0 N N N N N N 0.468  4.841 -5.988 4.203  2.495  0.589  HOP2   A1MA9 28 
A1MA9 "H2'"  H2   H 0 1 N N N N N N 0.666  5.346 2.065  -0.667 -1.160 -2.136 "H2'"  A1MA9 29 
A1MA9 "H5'"  H3   H 0 1 N N N N N N 1.210  4.601 -2.120 2.948  0.059  -1.001 "H5'"  A1MA9 30 
A1MA9 "H5''" H4   H 0 0 N N N N N N 2.648  5.667 -2.276 3.783  -1.487 -0.722 "H5''" A1MA9 31 
A1MA9 "H4'"  H5   H 0 1 N N N N N N 1.339  7.467 -1.076 1.825  -2.241 0.673  "H4'"  A1MA9 32 
A1MA9 "H1'"  H6   H 0 1 N N N N N N -0.680 7.629 0.775  -0.794 -1.836 0.808  "H1'"  A1MA9 33 
A1MA9 "H3'"  H7   H 0 1 N N N N N N 2.039  4.884 0.323  1.614  -1.511 -2.254 "H3'"  A1MA9 34 
A1MA9 H3     H8   H 0 1 N N N N N N 3.422  6.472 1.341  1.159  -3.856 -2.299 H3     A1MA9 35 
A1MA9 H21    H10  H 0 1 N N N N N N 0.752  1.543 0.467  -4.894 -2.670 2.557  H21    A1MA9 36 
A1MA9 H22    H11  H 0 1 N N N N N N -0.364 0.270 0.834  -6.280 -1.721 2.624  H22    A1MA9 37 
A1MA9 H1     H12  H 0 1 N N N N N N -2.563 0.806 1.458  -6.331 0.372  1.583  H1     A1MA9 38 
A1MA9 OP3    OP3  O 0 1 N Y N N N N -1.018 4.633 -3.188 5.282  0.798  2.626  OP3    A1MA9 39 
A1MA9 HOP3   HOP3 H 0 0 N Y N N N N -1.917 4.934 -3.252 6.113  1.267  2.782  HOP3   A1MA9 40 
# 
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 
A1MA9 OP2   P      SING N N 1  
A1MA9 OP1   P      DOUB N N 2  
A1MA9 P     "O5'"  SING N N 3  
A1MA9 "O5'" "C5'"  SING N N 4  
A1MA9 "C5'" "C4'"  SING N N 5  
A1MA9 "C4'" "O4'"  SING N N 6  
A1MA9 "C4'" "C3'"  SING N N 7  
A1MA9 "O4'" "C1'"  SING N N 8  
A1MA9 "C3'" "O3'"  SING N N 9  
A1MA9 "C3'" "C2'"  SING N N 10 
A1MA9 F11   C      SING N N 11 
A1MA9 "C1'" N9     SING N N 12 
A1MA9 "C1'" "C2'"  SING N N 13 
A1MA9 N2    C2     SING N N 14 
A1MA9 N3    C2     DOUB N N 15 
A1MA9 N3    C4     SING N N 16 
A1MA9 C2    N1     SING N N 17 
A1MA9 N9    C4     SING Y N 18 
A1MA9 N9    C8     SING Y N 19 
A1MA9 C4    C5     DOUB Y N 20 
A1MA9 N1    C6     SING N N 21 
A1MA9 "C2'" "F2'"  SING N N 22 
A1MA9 C5    C6     SING N N 23 
A1MA9 C5    N7     SING Y N 24 
A1MA9 C8    C      SING N N 25 
A1MA9 C8    N7     DOUB Y N 26 
A1MA9 C6    O6     DOUB N N 27 
A1MA9 C     F12    SING N N 28 
A1MA9 C     F13    SING N N 29 
A1MA9 OP2   HOP2   SING N N 30 
A1MA9 "C2'" "H2'"  SING N N 31 
A1MA9 "C5'" "H5'"  SING N N 32 
A1MA9 "C5'" "H5''" SING N N 33 
A1MA9 "C4'" "H4'"  SING N N 34 
A1MA9 "C1'" "H1'"  SING N N 35 
A1MA9 "C3'" "H3'"  SING N N 36 
A1MA9 "O3'" H3     SING N N 37 
A1MA9 N2    H21    SING N N 38 
A1MA9 N2    H22    SING N N 39 
A1MA9 N1    H1     SING N N 40 
A1MA9 P     OP3    SING N N 41 
A1MA9 OP3   HOP3   SING N N 42 
# 
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 
A1MA9 InChI            InChI                1.06  "InChI=1S/C11H12F4N5O7P/c12-3-5(21)2(1-26-28(23,24)25)27-8(3)20-6-4(7(22)19-10(16)18-6)17-9(20)11(13,14)15/h2-3,5,8,21H,1H2,(H2,23,24,25)(H3,16,18,19,22)/t2-,3-,5-,8-/m1/s1" 
A1MA9 InChIKey         InChI                1.06  UZSABTRADQLKAX-YOUMAJLPSA-N                                                                                                                                                   
A1MA9 SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2n([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3F)c(nc2C(=O)N1)C(F)(F)F"                                                                                                 
A1MA9 SMILES           CACTVS               3.385 "NC1=Nc2n([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3F)c(nc2C(=O)N1)C(F)(F)F"                                                                                                       
A1MA9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1[C@H]([C@H]([C@@H](O1)n2c3c(nc2C(F)(F)F)C(=O)NC(=N3)N)F)O)OP(=O)(O)O"                                                                                               
A1MA9 SMILES           "OpenEye OEToolkits" 2.0.7 "C(C1C(C(C(O1)n2c3c(nc2C(F)(F)F)C(=O)NC(=N3)N)F)O)OP(=O)(O)O"                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           A1MA9 
_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-6-oxidanylidene-8-(trifluoromethyl)-1~{H}-purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1MA9 
_pdbx_chem_comp_synonyms.name         "[(2~{R},3~{R},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-8-(trifluoromethyl)-1~{H}-purin-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1MA9 "Create component" 2025-07-25 PDBJ 
A1MA9 "Initial release"  2025-08-06 RCSB 
A1MA9 "Modify atom id"   2026-02-13 PDBJ 
# 
