data_A1CAL
# 
_chem_comp.id                                    A1CAL 
_chem_comp.name                                  "1-(5-O-{(R)-hydroxy[(3-phenylprop-2-yn-1-yl)oxy]phosphoryl}-2-O-methyl-beta-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C19 H21 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-04-23 
_chem_comp.pdbx_modified_date                    2026-04-24 
_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                        452.352 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CAL 
_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        9OBD 
_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 
A1CAL C2     C1  C 0 1 N N N N N N -23.689 29.479 22.718 4.072   -1.448 -1.041 C2    A1CAL 1  
A1CAL C4     C2  C 0 1 N N N N N N -22.664 27.105 22.350 4.867   -3.645 -1.026 C4    A1CAL 2  
A1CAL C5     C3  C 0 1 N N N N N N -22.235 27.044 23.731 4.662   -3.697 0.374  C5    A1CAL 3  
A1CAL O2     O1  O 0 1 N N N N N N -24.252 30.420 22.322 3.804   -0.436 -1.660 O2    A1CAL 4  
A1CAL O4     O2  O 0 1 N N N N N N -22.440 26.188 21.618 5.322   -4.608 -1.617 O4    A1CAL 5  
A1CAL "C1'"  C4  C 0 1 N N R N N N -23.467 30.456 25.086 3.329   -0.309 0.974  "C1'" A1CAL 6  
A1CAL "C2'"  C5  C 0 1 N N R N N N -24.057 29.997 26.200 4.294   0.888  0.830  "C2'" A1CAL 7  
A1CAL "C3'"  C6  C 0 1 N N R N N N -23.557 31.053 27.404 3.359   2.108  0.674  "C3'" A1CAL 8  
A1CAL "C4'"  C7  C 0 1 N N R N N N -22.335 31.252 27.181 1.939   1.503  0.742  "C4'" A1CAL 9  
A1CAL "C5'"  C8  C 0 1 N N N N N N -21.477 30.203 27.937 1.003   2.231  -0.225 "C5'" A1CAL 10 
A1CAL C6     C9  C 0 1 N N N N N N -22.507 28.162 24.625 4.156   -2.616 1.005  C6    A1CAL 11 
A1CAL "CB'"  C10 C 0 1 N N N N N N -21.063 28.763 31.595 -4.135  1.582  -1.247 "CB'" A1CAL 12 
A1CAL "CC'"  C11 C 0 1 N N N N N N -21.643 27.837 30.479 -5.123  0.642  -0.692 "CC'" A1CAL 13 
A1CAL "CD'"  C12 C 0 1 N N N N N N -22.078 27.136 29.590 -5.912  -0.107 -0.250 "CD'" A1CAL 14 
A1CAL "CE'"  C13 C 0 1 Y N N N N N -22.613 26.243 28.441 -6.873  -1.021 0.289  "CE'" A1CAL 15 
A1CAL "CF'"  C14 C 0 1 Y N N N N N -23.973 25.965 28.342 -6.514  -1.888 1.321  "CF'" A1CAL 16 
A1CAL "CG'"  C15 C 0 1 Y N N N N N -24.440 25.165 27.315 -7.446  -2.766 1.837  "CG'" A1CAL 17 
A1CAL "CH'"  C16 C 0 1 Y N N N N N -23.554 24.642 26.384 -8.733  -2.788 1.332  "CH'" A1CAL 18 
A1CAL "CI'"  C17 C 0 1 Y N N N N N -22.196 24.921 26.482 -9.096  -1.931 0.307  "CI'" A1CAL 19 
A1CAL "CJ'"  C18 C 0 1 Y N N N N N -21.727 25.721 27.511 -8.175  -1.045 -0.213 "CJ'" A1CAL 20 
A1CAL CM2    C19 C 0 1 N N N N N N -26.144 29.102 26.866 6.395   1.580  1.753  CM2   A1CAL 21 
A1CAL N1     N1  N 0 1 N N N N N N -23.209 29.347 24.149 3.867   -1.487 0.288  N1    A1CAL 22 
A1CAL N3     N2  N 0 1 N N N N N N -23.367 28.270 21.845 4.565   -2.515 -1.697 N3    A1CAL 23 
A1CAL "O2'"  O3  O 0 1 N N N N N N -25.451 30.038 26.060 5.103   1.023  2.000  "O2'" A1CAL 24 
A1CAL "O3'"  O4  O 0 1 N N N N N N -24.294 32.311 27.301 3.563   3.035  1.741  "O3'" A1CAL 25 
A1CAL "O4'"  O5  O 0 1 N N N N N N -22.158 31.064 25.558 2.105   0.125  0.342  "O4'" A1CAL 26 
A1CAL "O5'"  O6  O 0 1 N N N N N N -20.337 30.880 28.494 -0.328  1.737  -0.062 "O5'" A1CAL 27 
A1CAL OP1    O7  O 0 1 N N N N N N -18.944 29.029 29.695 -1.843  3.826  -0.561 OP1   A1CAL 28 
A1CAL OP2    O8  O 0 1 N N N N N N -18.751 31.360 30.493 -1.273  2.155  -2.365 OP2   A1CAL 29 
A1CAL O1     O9  O 0 1 N N N N N N -20.937 30.053 31.036 -2.887  1.413  -0.571 OP3   A1CAL 30 
A1CAL P      P1  P 0 1 N N N N N N -19.694 30.324 29.937 -1.576  2.280  -0.922 P     A1CAL 31 
A1CAL "H3'"  H1  H 0 1 N N N N N N -21.714 26.172 24.098 4.906   -4.590 0.930  H20   A1CAL 32 
A1CAL "H1'"  H2  H 0 1 N N N N N N -24.070 31.231 24.591 3.155   -0.531 2.027  H18   A1CAL 33 
A1CAL "H2'"  H3  H 0 1 N N N N N N -23.711 28.989 26.473 4.921   0.769  -0.054 H4    A1CAL 34 
A1CAL H4     H4  H 0 1 N N N N N N -23.758 30.572 28.372 3.522   2.593  -0.289 H5    A1CAL 35 
A1CAL "H4'"  H5  H 0 1 N N N N N N -21.991 32.262 27.448 1.551   1.559  1.759  H7    A1CAL 36 
A1CAL "H5''" H6  H 0 1 N N N N N N -21.143 29.421 27.239 1.021   3.300  -0.012 H9    A1CAL 37 
A1CAL "H5'"  H7  H 0 1 N N N N N N -22.070 29.746 28.743 1.332   2.059  -1.249 H8    A1CAL 38 
A1CAL "HO3'" H8  H 0 1 N N N N N N -22.184 28.112 25.654 3.992   -2.638 2.072  H19   A1CAL 39 
A1CAL H12    H9  H 0 1 N N N N N N -20.079 28.394 31.919 -4.002  1.384  -2.310 H12   A1CAL 40 
A1CAL H11    H10 H 0 1 N N N N N N -21.746 28.790 32.457 -4.488  2.604  -1.108 H11   A1CAL 41 
A1CAL H13    H11 H 0 1 N N N N N N -24.663 26.373 29.066 -5.509  -1.872 1.717  H13   A1CAL 42 
A1CAL H14    H12 H 0 1 N N N N N N -25.495 24.947 27.238 -7.169  -3.437 2.636  H14   A1CAL 43 
A1CAL H15    H13 H 0 1 N N N N N N -23.920 24.018 25.582 -9.458  -3.477 1.738  H15   A1CAL 44 
A1CAL H16    H14 H 0 1 N N N N N N -21.507 24.514 25.757 -10.103 -1.953 -0.083 H16   A1CAL 45 
A1CAL H17    H15 H 0 1 N N N N N N -20.672 25.938 27.589 -8.461  -0.373 -1.009 H17   A1CAL 46 
A1CAL H2     H16 H 0 1 N N N N N N -27.226 29.201 26.696 6.940   0.941  1.059  H2    A1CAL 47 
A1CAL H5     H17 H 0 1 N N N N N N -25.823 28.083 26.603 6.286   2.575  1.321  H3    A1CAL 48 
A1CAL H1     H18 H 0 1 N N N N N N -25.921 29.294 27.926 6.946   1.650  2.691  H1    A1CAL 49 
A1CAL H3     H19 H 0 1 N N N N N N -23.652 28.281 20.886 4.703   -2.471 -2.656 H21   A1CAL 50 
A1CAL H7     H20 H 0 1 N N N N N N -24.006 32.904 27.985 3.001   3.821  1.693  H6    A1CAL 51 
A1CAL HOP3   H21 H 0 1 N N N N N N -18.034 29.138 29.944 -2.049  3.983  0.370  H10   A1CAL 52 
# 
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 
A1CAL "O2'" CM2    SING N N 1  
A1CAL "C2'" "O2'"  SING N N 2  
A1CAL "C3'" "C2'"  SING N N 3  
A1CAL "O3'" "C3'"  SING N N 4  
A1CAL "C4'" "C3'"  SING N N 5  
A1CAL "O5'" "C5'"  SING N N 6  
A1CAL P     "O5'"  SING N N 7  
A1CAL OP1   P      SING N N 8  
A1CAL "CB'" O1     SING N N 9  
A1CAL "CC'" "CB'"  SING N N 10 
A1CAL "CD'" "CC'"  TRIP N N 11 
A1CAL "CE'" "CD'"  SING N N 12 
A1CAL "CF'" "CE'"  DOUB Y N 13 
A1CAL "CG'" "CF'"  SING Y N 14 
A1CAL "CH'" "CG'"  DOUB Y N 15 
A1CAL "CI'" "CH'"  SING Y N 16 
A1CAL "CJ'" "CI'"  DOUB Y N 17 
A1CAL O1    P      SING N N 18 
A1CAL OP2   P      DOUB N N 19 
A1CAL "C5'" "C4'"  SING N N 20 
A1CAL "O4'" "C4'"  SING N N 21 
A1CAL "C1'" "O4'"  SING N N 22 
A1CAL N1    "C1'"  SING N N 23 
A1CAL C6    N1     SING N N 24 
A1CAL C5    C6     DOUB N N 25 
A1CAL C4    C5     SING N N 26 
A1CAL C2    N3     SING N N 27 
A1CAL O2    C2     DOUB N N 28 
A1CAL N3    C4     SING N N 29 
A1CAL O4    C4     DOUB N N 30 
A1CAL "C2'" "C1'"  SING N N 31 
A1CAL "CE'" "CJ'"  SING Y N 32 
A1CAL N1    C2     SING N N 33 
A1CAL C5    "H3'"  SING N N 34 
A1CAL "C1'" "H1'"  SING N N 35 
A1CAL "C2'" "H2'"  SING N N 36 
A1CAL "C3'" H4     SING N N 37 
A1CAL "C4'" "H4'"  SING N N 38 
A1CAL "C5'" "H5''" SING N N 39 
A1CAL "C5'" "H5'"  SING N N 40 
A1CAL C6    "HO3'" SING N N 41 
A1CAL "CB'" H12    SING N N 42 
A1CAL "CB'" H11    SING N N 43 
A1CAL "CF'" H13    SING N N 44 
A1CAL "CG'" H14    SING N N 45 
A1CAL "CH'" H15    SING N N 46 
A1CAL "CI'" H16    SING N N 47 
A1CAL "CJ'" H17    SING N N 48 
A1CAL CM2   H2     SING N N 49 
A1CAL CM2   H5     SING N N 50 
A1CAL CM2   H1     SING N N 51 
A1CAL N3    H3     SING N N 52 
A1CAL "O3'" H7     SING N N 53 
A1CAL OP1   HOP3   SING N N 54 
# 
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 
A1CAL SMILES           ACDLabs              14.52   "O=P(O)(OCC#Cc1ccccc1)OCC1OC(N2C=CC(=O)NC2=O)C(OC)C1O"                                                                                                                            
A1CAL InChI            InChI                1.06    "InChI=1S/C19H21N2O9P/c1-27-17-16(23)14(30-18(17)21-10-9-15(22)20-19(21)24)12-29-31(25,26)28-11-5-8-13-6-3-2-4-7-13/h2-4,6-7,9-10,14,16-18,23H,11-12H2,1H3,(H,25,26)(H,20,22,24)" 
A1CAL InChIKey         InChI                1.06    LBXKGBOFNAUGOH-UHFFFAOYSA-N                                                                                                                                                       
A1CAL SMILES_CANONICAL CACTVS               3.385   "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(=O)OCC#Cc2ccccc2)O[C@H]1N3C=CC(=O)NC3=O"                                                                                                        
A1CAL SMILES           CACTVS               3.385   "CO[CH]1[CH](O)[CH](CO[P](O)(=O)OCC#Cc2ccccc2)O[CH]1N3C=CC(=O)NC3=O"                                                                                                              
A1CAL SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)OCC#Cc3ccccc3)O"                                                                                                          
A1CAL SMILES           "OpenEye OEToolkits" 3.1.0.0 "COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)OCC#Cc3ccccc3)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 
A1CAL "SYSTEMATIC NAME" ACDLabs              14.52   "1-(5-O-{(R)-hydroxy[(3-phenylprop-2-yn-1-yl)oxy]phosphoryl}-2-O-methyl-beta-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione"                         
A1CAL "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl 3-phenylprop-2-ynyl hydrogen 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 
A1CAL "Create component" 2025-04-23 RCSB 
A1CAL "Initial release"  2026-04-29 RCSB 
# 
