data_A1A0L
# 
_chem_comp.id                                    A1A0L 
_chem_comp.name                                  "1-{(2R,3R,4S)-3-hydroxy-4-[(trihydroxy-lambda~5~-phosphanyl)oxy]oxolan-2-yl}-4-methoxy-5-methylpyrimidin-2(1H)-one" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-30 
_chem_comp.pdbx_modified_date                    2024-09-13 
_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                        322.208 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A0L 
_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        9CIH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
A1A0L P     P1   P 0 1 N N N N N N -62.615 -9.655  -3.544 -4.035 0.673  0.198  P     A1A0L 1  
A1A0L OP1   O1   O 0 1 N N N N N N -62.605 -11.169 -3.286 -5.009 -0.212 -0.478 OP1   A1A0L 2  
A1A0L OP2   O2   O 0 1 N N N N N N -64.008 -9.074  -3.827 -4.137 0.465  1.791  OP2   A1A0L 3  
A1A0L N1    N1   N 0 1 N N N N N N -59.224 -6.164  -2.528 1.645  -0.770 -0.232 N1    A1A0L 4  
A1A0L C6    C1   C 0 1 N N N N N N -60.438 -5.711  -2.797 2.767  -1.455 0.120  C6    A1A0L 5  
A1A0L C2    C2   C 0 1 N N N N N N -58.157 -5.372  -2.580 1.692  0.564  -0.410 C2    A1A0L 6  
A1A0L O2    O3   O 0 1 N N N N N N -57.130 -5.823  -2.344 0.678  1.162  -0.730 O2    A1A0L 7  
A1A0L N3    N2   N 0 1 N N N N N N -58.291 -4.081  -2.898 2.828  1.240  -0.243 N3    A1A0L 8  
A1A0L C4    C3   C 0 1 N N N N N N -59.466 -3.530  -3.172 3.943  0.615  0.104  C4    A1A0L 9  
A1A0L O4    O4   O 0 1 N N N N N N -59.573 -2.345  -3.466 5.088  1.312  0.270  O4    A1A0L 10 
A1A0L C5    C4   C 0 1 N N N N N N -60.592 -4.361  -3.119 3.929  -0.780 0.293  C5    A1A0L 11 
A1A0L "C4'" C5   C 0 1 N N N N N N -59.596 -9.657  -2.885 -1.581 -1.508 -1.613 "C4'" A1A0L 12 
A1A0L "O4'" O5   O 0 1 N N N N N N -59.038 -8.278  -3.308 -0.177 -1.185 -1.719 "O4'" A1A0L 13 
A1A0L "C3'" C6   C 0 1 N N S N N N -60.630 -9.235  -1.734 -1.997 -1.005 -0.213 "C3'" A1A0L 14 
A1A0L "O3'" O6   O 0 1 N N N N N N -61.836 -8.742  -2.366 -2.546 0.311  -0.297 "O3'" A1A0L 15 
A1A0L "C2'" C7   C 0 1 N N R N N N -60.080 -8.248  -1.134 -0.676 -0.991 0.588  "C2'" A1A0L 16 
A1A0L "O2'" O7   O 0 1 N N N N N N -59.286 -8.717  -0.039 -0.758 -1.880 1.704  "O2'" A1A0L 17 
A1A0L "C1'" C8   C 0 1 N N R N N N -59.003 -7.545  -2.212 0.382  -1.487 -0.422 "C1'" A1A0L 18 
A1A0L C1    C9   C 0 1 N N N N N N -58.458 -1.446  -3.529 5.025  2.724  0.060  C1    A1A0L 19 
A1A0L C3    C10  C 0 1 N N N N N N -61.994 -3.820  -3.430 5.187  -1.510 0.688  C3    A1A0L 20 
A1A0L H2    H2   H 0 1 N N N N N N -64.654 -9.770  -3.795 -3.525 1.016  2.300  H2    A1A0L 21 
A1A0L H3    H3   H 0 1 N N N N N N -61.292 -6.372  -2.768 2.732  -2.526 0.260  H3    A1A0L 22 
A1A0L H4    H4   H 0 1 N N N N N N -60.106 -10.159 -3.720 -2.149 -0.990 -2.387 H4    A1A0L 23 
A1A0L H5    H5   H 0 1 N N N N N N -58.802 -10.310 -2.494 -1.731 -2.585 -1.690 H5    A1A0L 24 
A1A0L H6    H6   H 0 1 N N N N N N -60.836 -10.104 -1.092 -2.713 -1.690 0.241  H6    A1A0L 25 
A1A0L H7    H7   H 0 1 N N N N N N -60.789 -7.473  -0.808 -0.443 0.020  0.923  H7    A1A0L 26 
A1A0L H8    H8   H 0 1 N Y N N N N -59.848 -9.128  0.607  -1.448 -1.650 2.341  H8    A1A0L 27 
A1A0L H9    H9   H 0 1 N N N N N N -58.015 -7.633  -1.737 0.536  -2.560 -0.317 H9    A1A0L 28 
A1A0L H10   H10  H 0 1 N N N N N N -58.810 -0.443  -3.813 4.705  2.926  -0.962 H10   A1A0L 29 
A1A0L H11   H11  H 0 1 N N N N N N -57.970 -1.398  -2.544 4.311  3.163  0.757  H11   A1A0L 30 
A1A0L H12   H12  H 0 1 N N N N N N -57.738 -1.807  -4.278 6.010  3.161  0.226  H12   A1A0L 31 
A1A0L H13   H13  H 0 1 N N N N N N -62.731 -4.631  -3.331 6.007  -0.797 0.782  H13   A1A0L 32 
A1A0L H14   H14  H 0 1 N N N N N N -62.240 -3.013  -2.724 5.031  -2.011 1.643  H14   A1A0L 33 
A1A0L H15   H15  H 0 1 N N N N N N -62.016 -3.428  -4.457 5.433  -2.249 -0.075 H15   A1A0L 34 
A1A0L OP3   OP3  O 0 1 N Y N N N N -62.241 -9.423  -5.080 -4.363 2.207  -0.165 OP3   A1A0L 35 
A1A0L HOP3  HOP3 H 0 0 N Y N N N N -62.094 -10.262 -5.501 -5.246 2.495  0.105  HOP3  A1A0L 36 
# 
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 
A1A0L OP2   P     SING N N 1  
A1A0L P     OP1   DOUB N N 2  
A1A0L P     "O3'" SING N N 3  
A1A0L C1    O4    SING N N 4  
A1A0L O4    C4    SING N N 5  
A1A0L C3    C5    SING N N 6  
A1A0L "O4'" "C4'" SING N N 7  
A1A0L "O4'" "C1'" SING N N 8  
A1A0L C4    C5    SING N N 9  
A1A0L C4    N3    DOUB N N 10 
A1A0L C5    C6    DOUB N N 11 
A1A0L N3    C2    SING N N 12 
A1A0L "C4'" "C3'" SING N N 13 
A1A0L C6    N1    SING N N 14 
A1A0L C2    N1    SING N N 15 
A1A0L C2    O2    DOUB N N 16 
A1A0L N1    "C1'" SING N N 17 
A1A0L "O3'" "C3'" SING N N 18 
A1A0L "C1'" "C2'" SING N N 19 
A1A0L "C3'" "C2'" SING N N 20 
A1A0L "C2'" "O2'" SING N N 21 
A1A0L OP2   H2    SING N N 22 
A1A0L C6    H3    SING N N 23 
A1A0L "C4'" H4    SING N N 24 
A1A0L "C4'" H5    SING N N 25 
A1A0L "C3'" H6    SING N N 26 
A1A0L "C2'" H7    SING N N 27 
A1A0L "O2'" H8    SING N N 28 
A1A0L "C1'" H9    SING N N 29 
A1A0L C1    H10   SING N N 30 
A1A0L C1    H11   SING N N 31 
A1A0L C1    H12   SING N N 32 
A1A0L C3    H13   SING N N 33 
A1A0L C3    H14   SING N N 34 
A1A0L C3    H15   SING N N 35 
A1A0L P     OP3   SING N N 36 
A1A0L OP3   HOP3  SING N N 37 
# 
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 
A1A0L SMILES           ACDLabs              12.01 "O=P(O)(O)OC1COC(N2C=C(C)C(=NC2=O)OC)C1O"                                                                                              
A1A0L InChI            InChI                1.06  "InChI=1S/C10H15N2O8P/c1-5-3-12(10(14)11-8(5)18-2)9-7(13)6(4-19-9)20-21(15,16)17/h3,6-7,9,13H,4H2,1-2H3,(H2,15,16,17)/t6-,7+,9+/m0/s1" 
A1A0L InChIKey         InChI                1.06  OJDLFCPBILBUDP-LKEWCRSYSA-N                                                                                                            
A1A0L SMILES_CANONICAL CACTVS               3.385 "COC1=NC(=O)N(C=C1C)[C@@H]2OC[C@H](O[P](O)(O)=O)[C@H]2O"                                                                               
A1A0L SMILES           CACTVS               3.385 "COC1=NC(=O)N(C=C1C)[CH]2OC[CH](O[P](O)(O)=O)[CH]2O"                                                                                   
A1A0L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1OC)[C@H]2[C@@H]([C@H](CO2)OP(=O)(O)O)O"                                                                               
A1A0L SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N=C1OC)C2C(C(CO2)OP(=O)(O)O)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 
A1A0L "SYSTEMATIC NAME" ACDLabs              12.01 "(3S,4R,5R)-4-hydroxy-5-(4-methoxy-5-methyl-2-oxopyrimidin-1(2H)-yl)oxolan-3-yl dihydrogen phosphate"                     
A1A0L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{S},4~{R},5~{R})-5-(4-methoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-4-oxidanyl-oxolan-3-yl] 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 
A1A0L "Create component" 2024-07-30 RCSB 
A1A0L "Initial release"  2024-09-18 RCSB 
# 
