data_A1BBC
# 
_chem_comp.id                                    A1BBC 
_chem_comp.name                                  "1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H14 F N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-09-29 
_chem_comp.pdbx_modified_date                    2025-01-31 
_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                        356.198 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BBC 
_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        9DA2 
_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 
A1BBC "C3'"  C1  C 0 1 N N R N N N -24.140 -13.214 -9.245  0.819  2.440  0.243  "C3'"  A1BBC 1  
A1BBC "C4'"  C2  C 0 1 N N R N N N -24.006 -14.612 -9.749  1.401  1.230  -0.521 "C4'"  A1BBC 2  
A1BBC "C5'"  C3  C 0 1 N N N N N N -23.282 -15.505 -8.784  2.675  0.730  0.163  "C5'"  A1BBC 3  
A1BBC "C1'"  C4  C 0 1 N N R N N N -26.367 -14.243 -9.459  -0.872 0.936  -0.659 "C1'"  A1BBC 4  
A1BBC C2     C5  C 0 1 N N N N N N -28.097 -14.156 -7.591  -1.947 -0.352 1.101  C2     A1BBC 5  
A1BBC C4     C6  C 0 1 N N N N N N -28.055 -15.757 -5.953  -4.065 -1.304 0.850  C4     A1BBC 6  
A1BBC C5     C7  C 0 1 N N N N N N -27.004 -16.546 -6.654  -4.133 -0.778 -0.463 C5     A1BBC 7  
A1BBC C7     C8  C 0 1 N N N N N N -26.532 -17.841 -5.958  -5.349 -1.021 -1.320 C7     A1BBC 8  
A1BBC C6     C9  C 0 1 N N N N N N -26.508 -16.138 -7.624  -3.095 -0.057 -0.937 C6     A1BBC 9  
A1BBC "C2'"  C10 C 0 1 N N S N N N -25.585 -13.024 -9.056  -0.711 2.242  0.150  "C2'"  A1BBC 10 
A1BBC F01    F1  F 0 1 N N N N N N -25.765 -12.790 -7.676  -1.264 2.099  1.427  F01    A1BBC 11 
A1BBC N1     N1  N 0 1 N N N N N N -26.921 -14.898 -8.359  -1.999 0.153  -0.145 N1     A1BBC 12 
A1BBC N3     N2  N 0 1 N N N N N N -28.550 -14.723 -6.304  -2.968 -1.074 1.599  N3     A1BBC 13 
A1BBC "O3'"  O1  O 0 1 N N N N N N -23.553 -12.228 -10.109 1.204  3.664  -0.385 "O3'"  A1BBC 14 
A1BBC "O5'"  O2  O 0 1 N N N N N N -23.236 -16.829 -9.294  3.260  -0.311 -0.621 "O5'"  A1BBC 15 
A1BBC OP1    O3  O 0 1 N N N N N N -22.706 -19.195 -9.233  5.691  -0.076 0.017  OP1    A1BBC 16 
A1BBC OP3    O4  O 0 1 N N N N N N -23.564 -18.085 -7.120  4.368  -1.896 1.160  OP3    A1BBC 17 
A1BBC OP2    O5  O 0 1 N N N N N N -21.267 -17.624 -7.924  5.050  -2.085 -1.372 OP2    A1BBC 18 
A1BBC "O4'"  O6  O 0 1 N N N N N N -25.374 -15.120 -10.005 0.368  0.222  -0.459 "O4'"  A1BBC 19 
A1BBC O07    O7  O 0 1 N N N N N N -26.036 -18.752 -6.895  -5.169 -0.390 -2.590 O07    A1BBC 20 
A1BBC O4     O8  O 0 1 N N N N N N -28.518 -16.147 -4.905  -4.990 -1.957 1.299  O4     A1BBC 21 
A1BBC O2     O9  O 0 1 N N N N N N -28.466 -13.146 -8.107  -0.961 -0.156 1.786  O2     A1BBC 22 
A1BBC P      P1  P 0 1 N N N N N N -22.665 -18.014 -8.334  4.616  -1.070 -0.199 P      A1BBC 23 
A1BBC "H3'"  H1  H 0 1 N N N N N N -23.652 -13.158 -8.261  1.144  2.426  1.283  "H3'"  A1BBC 24 
A1BBC "H4'"  H2  H 0 1 N N N N N N -23.449 -14.594 -10.697 1.608  1.499  -1.557 "H4'"  A1BBC 25 
A1BBC "H5'"  H3  H 0 1 N N N N N N -22.257 -15.133 -8.641  3.382  1.553  0.260  "H5'"  A1BBC 26 
A1BBC "H5''" H4  H 0 0 N N N N N N -23.810 -15.504 -7.819  2.428  0.345  1.153  "H5''" A1BBC 27 
A1BBC "H1'"  H5  H 0 1 N N N N N N -27.127 -13.980 -10.209 -1.017 1.159  -1.715 "H1'"  A1BBC 28 
A1BBC H71    H6  H 0 1 N N N N N N -27.381 -18.296 -5.427  -5.484 -2.093 -1.463 H71    A1BBC 29 
A1BBC H72    H7  H 0 1 N N N N N N -25.738 -17.595 -5.238  -6.229 -0.606 -0.829 H72    A1BBC 30 
A1BBC H6     H8  H 0 1 N N N N N N -25.680 -16.700 -8.030  -3.129 0.351  -1.936 H6     A1BBC 31 
A1BBC "H2'"  H9  H 0 1 N N N N N N -25.928 -12.160 -9.644  -1.173 3.077  -0.376 "H2'"  A1BBC 32 
A1BBC H3     H10 H 0 1 N N N N N N -29.242 -14.263 -5.748  -2.914 -1.431 2.499  H3     A1BBC 33 
A1BBC "HO3'" H11 H 0 0 N N N N N N -23.673 -11.364 -9.732  0.817  4.452  0.020  "HO3'" A1BBC 34 
A1BBC HOP3   H12 H 0 0 N N N N N N -24.035 -18.910 -7.122  3.675  -2.567 1.092  HOP3   A1BBC 35 
A1BBC HOP2   H13 H 0 0 N N N N N N -20.642 -18.218 -8.323  5.861  -2.577 -1.185 HOP2   A1BBC 36 
A1BBC HO7    H14 H 0 1 N N N N N N -25.751 -19.541 -6.450  -5.915 -0.505 -3.195 HO7    A1BBC 37 
# 
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 
A1BBC "O3'" "C3'"  SING N N 1  
A1BBC "O4'" "C4'"  SING N N 2  
A1BBC "O4'" "C1'"  SING N N 3  
A1BBC "C4'" "C3'"  SING N N 4  
A1BBC "C4'" "C5'"  SING N N 5  
A1BBC "C1'" "C2'"  SING N N 6  
A1BBC "C1'" N1     SING N N 7  
A1BBC "O5'" "C5'"  SING N N 8  
A1BBC "O5'" P      SING N N 9  
A1BBC "C3'" "C2'"  SING N N 10 
A1BBC OP1   P      DOUB N N 11 
A1BBC "C2'" F01    SING N N 12 
A1BBC N1    C6     SING N N 13 
A1BBC N1    C2     SING N N 14 
A1BBC P     OP2    SING N N 15 
A1BBC P     OP3    SING N N 16 
A1BBC O2    C2     DOUB N N 17 
A1BBC C6    C5     DOUB N N 18 
A1BBC C2    N3     SING N N 19 
A1BBC O07   C7     SING N N 20 
A1BBC C5    C7     SING N N 21 
A1BBC C5    C4     SING N N 22 
A1BBC N3    C4     SING N N 23 
A1BBC C4    O4     DOUB N N 24 
A1BBC "C3'" "H3'"  SING N N 25 
A1BBC "C4'" "H4'"  SING N N 26 
A1BBC "C5'" "H5'"  SING N N 27 
A1BBC "C5'" "H5''" SING N N 28 
A1BBC "C1'" "H1'"  SING N N 29 
A1BBC C7    H71    SING N N 30 
A1BBC C7    H72    SING N N 31 
A1BBC C6    H6     SING N N 32 
A1BBC "C2'" "H2'"  SING N N 33 
A1BBC N3    H3     SING N N 34 
A1BBC "O3'" "HO3'" SING N N 35 
A1BBC OP3   HOP3   SING N N 36 
A1BBC OP2   HOP2   SING N N 37 
A1BBC O07   HO7    SING N N 38 
# 
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 
A1BBC SMILES           ACDLabs              14.52 "O=P(O)(O)OCC1OC(N2C=C(CO)C(=O)NC2=O)C(F)C1O"                                                                                                                
A1BBC InChI            InChI                1.06  "InChI=1S/C10H14FN2O9P/c11-6-7(15)5(3-21-23(18,19)20)22-9(6)13-1-4(2-14)8(16)12-10(13)17/h1,5-7,9,14-15H,2-3H2,(H,12,16,17)(H2,18,19,20)/t5-,6+,7-,9-/m1/s1" 
A1BBC InChIKey         InChI                1.06  MCTFWHKMGAFQIE-JVZYCSMKSA-N                                                                                                                                  
A1BBC SMILES_CANONICAL CACTVS               3.385 "OCC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]2F)C(=O)NC1=O"                                                                                           
A1BBC SMILES           CACTVS               3.385 "OCC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2F)C(=O)NC1=O"                                                                                                  
A1BBC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F)CO"                                                                                           
A1BBC SMILES           "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)F)CO"                                                                                                            
# 
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 
A1BBC "SYSTEMATIC NAME" ACDLabs              14.52 "1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione"                                              
A1BBC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-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 
A1BBC "Create component" 2024-09-29 RCSB 
A1BBC "Initial release"  2025-02-05 RCSB 
# 
