data_A1EEE
# 
_chem_comp.id                                    A1EEE 
_chem_comp.name                                  "(6~{S},9~{a}~{S})-6-(3-azidopropyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H30 F3 N7 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-10-20 
_chem_comp.pdbx_modified_date                    2025-02-14 
_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                        545.557 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EEE 
_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        9K2A 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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 
A1EEE C10 C1  C 0  1 N N N N N N -92.302 -60.604 165.962 -0.540 4.207  0.817  C10 A1EEE 1  
A1EEE C17 C2  C 0  1 N N S N N N -90.785 -59.551 169.512 0.072  0.684  -0.710 C17 A1EEE 2  
A1EEE C20 C3  C 0  1 N N N N N N -89.596 -55.848 169.048 2.252  -1.064 1.851  C20 A1EEE 3  
A1EEE C21 C4  C 0  1 Y N N N N N -90.594 -55.147 170.012 3.719  -1.226 1.545  C21 A1EEE 4  
A1EEE C22 C5  C 0  1 Y N N N N N -91.946 -54.790 169.617 4.129  -1.984 0.436  C22 A1EEE 5  
A1EEE C24 C6  C 0  1 Y N N N N N -93.760 -54.702 167.959 3.629  -3.331 -1.476 C24 A1EEE 6  
A1EEE C26 C7  C 0  1 Y N N N N N -94.115 -53.803 170.176 5.924  -2.884 -0.946 C26 A1EEE 7  
A1EEE C28 C8  C 0  1 Y N N N N N -92.300 -53.878 171.856 6.448  -1.504 1.010  C28 A1EEE 8  
A1EEE O01 O1  O 0  1 N N N N N N -92.872 -60.638 171.161 -1.895 -0.505 -3.411 O01 A1EEE 9  
A1EEE C02 C9  C 0  1 N N N N N N -91.827 -61.194 171.280 -1.480 -0.338 -2.280 C02 A1EEE 10 
A1EEE N03 N1  N 0  1 N N N N N N -90.660 -60.671 170.509 -0.364 0.389  -2.071 N03 A1EEE 11 
A1EEE C04 C10 C 0  1 N N N N N N -89.342 -61.287 170.517 0.414  0.886  -3.213 C04 A1EEE 12 
A1EEE C05 C11 C 0  1 N N N N N N -89.282 -62.106 169.270 0.516  2.410  -3.082 C05 A1EEE 13 
A1EEE C06 C12 C 0  1 N N N N N N -89.498 -61.279 167.991 0.997  2.750  -1.699 C06 A1EEE 14 
A1EEE N07 N2  N 0  1 N N N N N N -90.254 -59.982 168.110 0.761  1.974  -0.636 N07 A1EEE 15 
A1EEE C08 C13 C 0  1 N N S N N N -90.477 -59.223 167.256 1.204  2.421  0.698  C08 A1EEE 16 
A1EEE C09 C14 C 0  1 N N N N N N -92.004 -59.288 166.810 0.003  2.944  1.489  C09 A1EEE 17 
A1EEE C11 C15 C 0  1 N N N N N N -93.554 -61.301 166.665 -1.741 4.730  1.607  C11 A1EEE 18 
A1EEE C18 C16 C 0  1 N N N N N N -89.959 -58.166 169.916 1.036  -0.407 -0.233 C18 A1EEE 19 
A1EEE N19 N3  N 0  1 N N N N N N -89.919 -57.282 168.826 1.691  -0.008 1.005  N19 A1EEE 20 
A1EEE C23 C17 C 0  1 Y N N N N N -92.453 -55.062 168.303 3.194  -2.605 -0.410 C23 A1EEE 21 
A1EEE C25 C18 C 0  1 Y N N N N N -94.596 -54.070 168.892 4.990  -3.470 -1.743 C25 A1EEE 22 
A1EEE C27 C19 C 0  1 Y N N N N N -92.773 -54.169 170.531 5.513  -2.125 0.164  C27 A1EEE 23 
A1EEE C29 C20 C 0  1 Y N N N N N -90.997 -54.223 172.230 6.013  -0.772 2.072  C29 A1EEE 24 
A1EEE C30 C21 C 0  1 Y N N N N N -90.148 -54.856 171.309 4.653  -0.634 2.339  C30 A1EEE 25 
A1EEE C31 C22 C 0  1 N N N N N N -90.151 -57.798 167.501 1.814  1.253  1.423  C31 A1EEE 26 
A1EEE O32 O2  O 0  1 N N N N N N -90.112 -57.091 166.549 2.449  1.468  2.433  O32 A1EEE 27 
A1EEE O33 O3  O 0  1 N N N N N N -89.064 -61.682 166.964 1.628  3.774  -1.540 O33 A1EEE 28 
A1EEE N34 N4  N 0  1 N N N N N N -91.686 -62.340 172.188 -2.135 -0.881 -1.235 N34 A1EEE 29 
A1EEE C35 C23 C 0  1 N N N N N N -92.824 -62.864 172.978 -3.284 -1.761 -1.467 C35 A1EEE 30 
A1EEE C36 C24 C 0  1 N N N N N N -92.720 -62.506 174.474 -3.841 -2.238 -0.125 C36 A1EEE 31 
A1EEE C37 C25 C 0  1 N N N N N N -93.225 -61.234 174.708 -5.040 -3.157 -0.368 C37 A1EEE 32 
A1EEE C38 C26 C 0  1 N N N N N N -93.211 -60.946 176.065 -5.597 -3.634 0.975  C38 A1EEE 33 
A1EEE F40 F1  F 0  1 N N N N N N -91.923 -61.051 176.563 -4.606 -4.335 1.669  F40 A1EEE 34 
A1EEE F41 F2  F 0  1 N N N N N N -93.666 -59.651 176.226 -6.002 -2.528 1.731  F41 A1EEE 35 
A1EEE F42 F3  F 0  1 N N N N N N -94.028 -61.820 176.766 -6.694 -4.473 0.753  F42 A1EEE 36 
A1EEE N51 N5  N 0  1 N N N N N N -93.105 -62.387 167.602 -2.260 5.939  0.964  N51 A1EEE 37 
A1EEE N52 N6  N 1  1 N N N N N N -92.624 -63.432 168.573 -3.319 5.965  0.588  N52 A1EEE 38 
A1EEE N53 N7  N -1 1 N N N N N N -92.163 -64.511 169.513 -4.378 5.991  0.213  N53 A1EEE 39 
A1EEE H1  H1  H 0  1 N N N N N N -91.431 -61.275 165.978 0.239  4.969  0.793  H1  A1EEE 40 
A1EEE H2  H2  H 0  1 N N N N N N -92.544 -60.342 164.921 -0.850 3.972  -0.202 H2  A1EEE 41 
A1EEE H3  H3  H 0  1 N N N N N N -91.846 -59.278 169.411 -0.796 0.711  -0.051 H3  A1EEE 42 
A1EEE H4  H4  H 0  1 N N N N N N -88.585 -55.778 169.477 1.734  -2.002 1.653  H4  A1EEE 43 
A1EEE H5  H5  H 0  1 N N N N N N -89.620 -55.328 168.079 2.127  -0.795 2.900  H5  A1EEE 44 
A1EEE H6  H6  H 0  1 N N N N N N -94.129 -54.912 166.966 2.908  -3.808 -2.124 H6  A1EEE 45 
A1EEE H7  H7  H 0  1 N N N N N N -94.753 -53.321 170.902 6.975  -3.000 -1.165 H7  A1EEE 46 
A1EEE H8  H8  H 0  1 N N N N N N -92.953 -53.391 172.566 7.506  -1.603 0.815  H8  A1EEE 47 
A1EEE H9  H9  H 0  1 N N N N N N -89.221 -61.926 171.404 1.411  0.446  -3.200 H9  A1EEE 48 
A1EEE H10 H10 H 0  1 N N N N N N -88.557 -60.517 170.510 -0.091 0.628  -4.144 H10 A1EEE 49 
A1EEE H11 H11 H 0  1 N N N N N N -90.062 -62.880 169.322 1.223  2.793  -3.818 H11 A1EEE 50 
A1EEE H12 H12 H 0  1 N N N N N N -88.293 -62.585 169.214 -0.463 2.858  -3.249 H12 A1EEE 51 
A1EEE H13 H13 H 0  1 N N N N N N -89.916 -59.502 166.352 1.946  3.213  0.591  H13 A1EEE 52 
A1EEE H14 H14 H 0  1 N N N N N N -92.236 -58.405 166.196 0.312  3.179  2.507  H14 A1EEE 53 
A1EEE H15 H15 H 0  1 N N N N N N -92.640 -59.288 167.707 -0.776 2.182  1.513  H15 A1EEE 54 
A1EEE H16 H16 H 0  1 N N N N N N -94.116 -60.545 167.233 -2.520 3.968  1.631  H16 A1EEE 55 
A1EEE H17 H17 H 0  1 N N N N N N -94.204 -61.737 165.893 -1.431 4.965  2.626  H17 A1EEE 56 
A1EEE H18 H18 H 0  1 N N N N N N -88.931 -58.429 170.207 0.479  -1.329 -0.065 H18 A1EEE 57 
A1EEE H19 H19 H 0  1 N N N N N N -90.465 -57.676 170.761 1.791  -0.578 -1.000 H19 A1EEE 58 
A1EEE H20 H20 H 0  1 N N N N N N -91.821 -55.548 167.574 2.137  -2.507 -0.216 H20 A1EEE 59 
A1EEE H21 H21 H 0  1 N N N N N N -95.603 -53.792 168.620 5.308  -4.052 -2.595 H21 A1EEE 60 
A1EEE H22 H22 H 0  1 N N N N N N -90.645 -54.002 173.227 6.734  -0.292 2.717  H22 A1EEE 61 
A1EEE H23 H23 H 0  1 N N N N N N -89.143 -55.121 171.602 4.334  -0.048 3.189  H23 A1EEE 62 
A1EEE H24 H24 H 0  1 N N N N N N -90.793 -62.781 172.276 -1.847 -0.690 -0.329 H24 A1EEE 63 
A1EEE H25 H25 H 0  1 N N N N N N -93.756 -62.439 172.578 -4.056 -1.214 -2.008 H25 A1EEE 64 
A1EEE H26 H26 H 0  1 N N N N N N -92.848 -63.959 172.878 -2.968 -2.622 -2.056 H26 A1EEE 65 
A1EEE H27 H27 H 0  1 N N N N N N -93.295 -63.237 175.062 -3.068 -2.784 0.416  H27 A1EEE 66 
A1EEE H28 H28 H 0  1 N N N N N N -91.664 -62.538 174.781 -4.156 -1.377 0.464  H28 A1EEE 67 
A1EEE H29 H29 H 0  1 N N N N N N -92.607 -60.496 174.175 -5.813 -2.610 -0.908 H29 A1EEE 68 
A1EEE H30 H30 H 0  1 N N N N N N -94.260 -61.182 174.338 -4.725 -4.018 -0.956 H30 A1EEE 69 
# 
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 
A1EEE C10 C11 SING N N 1  
A1EEE C10 C09 SING N N 2  
A1EEE O32 C31 DOUB N N 3  
A1EEE C11 N51 SING N N 4  
A1EEE C09 C08 SING N N 5  
A1EEE O33 C06 DOUB N N 6  
A1EEE C08 C31 SING N N 7  
A1EEE C08 N07 SING N N 8  
A1EEE C31 N19 SING N N 9  
A1EEE N51 N52 DOUB N N 10 
A1EEE C24 C23 DOUB Y N 11 
A1EEE C24 C25 SING Y N 12 
A1EEE C06 N07 SING N N 13 
A1EEE C06 C05 SING N N 14 
A1EEE N07 C17 SING N N 15 
A1EEE C23 C22 SING Y N 16 
A1EEE N52 N53 DOUB N N 17 
A1EEE N19 C20 SING N N 18 
A1EEE N19 C18 SING N N 19 
A1EEE C25 C26 DOUB Y N 20 
A1EEE C20 C21 SING N N 21 
A1EEE C05 C04 SING N N 22 
A1EEE C17 C18 SING N N 23 
A1EEE C17 N03 SING N N 24 
A1EEE C22 C21 DOUB Y N 25 
A1EEE C22 C27 SING Y N 26 
A1EEE C21 C30 SING Y N 27 
A1EEE C26 C27 SING Y N 28 
A1EEE N03 C04 SING N N 29 
A1EEE N03 C02 SING N N 30 
A1EEE C27 C28 DOUB Y N 31 
A1EEE O01 C02 DOUB N N 32 
A1EEE C02 N34 SING N N 33 
A1EEE C30 C29 DOUB Y N 34 
A1EEE C28 C29 SING Y N 35 
A1EEE N34 C35 SING N N 36 
A1EEE C35 C36 SING N N 37 
A1EEE C36 C37 SING N N 38 
A1EEE C37 C38 SING N N 39 
A1EEE C38 F41 SING N N 40 
A1EEE C38 F40 SING N N 41 
A1EEE C38 F42 SING N N 42 
A1EEE C10 H1  SING N N 43 
A1EEE C10 H2  SING N N 44 
A1EEE C17 H3  SING N N 45 
A1EEE C20 H4  SING N N 46 
A1EEE C20 H5  SING N N 47 
A1EEE C24 H6  SING N N 48 
A1EEE C26 H7  SING N N 49 
A1EEE C28 H8  SING N N 50 
A1EEE C04 H9  SING N N 51 
A1EEE C04 H10 SING N N 52 
A1EEE C05 H11 SING N N 53 
A1EEE C05 H12 SING N N 54 
A1EEE C08 H13 SING N N 55 
A1EEE C09 H14 SING N N 56 
A1EEE C09 H15 SING N N 57 
A1EEE C11 H16 SING N N 58 
A1EEE C11 H17 SING N N 59 
A1EEE C18 H18 SING N N 60 
A1EEE C18 H19 SING N N 61 
A1EEE C23 H20 SING N N 62 
A1EEE C25 H21 SING N N 63 
A1EEE C29 H22 SING N N 64 
A1EEE C30 H23 SING N N 65 
A1EEE N34 H24 SING N N 66 
A1EEE C35 H25 SING N N 67 
A1EEE C35 H26 SING N N 68 
A1EEE C36 H27 SING N N 69 
A1EEE C36 H28 SING N N 70 
A1EEE C37 H29 SING N N 71 
A1EEE C37 H30 SING N N 72 
# 
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 
A1EEE InChI            InChI                1.06  "InChI=1S/C26H30F3N7O3/c27-26(28,29)12-5-13-31-25(39)35-15-11-23(37)36-21(10-4-14-32-33-30)24(38)34(17-22(35)36)16-19-8-3-7-18-6-1-2-9-20(18)19/h1-3,6-9,21-22H,4-5,10-17H2,(H,31,39)/t21-,22+/m0/s1" 
A1EEE InChIKey         InChI                1.06  JEFJDQXONGAAEJ-FCHUYYIVSA-N                                                                                                                                                                           
A1EEE SMILES_CANONICAL CACTVS               3.385 "FC(F)(F)CCCNC(=O)N1CCC(=O)N2[C@@H]1CN(Cc3cccc4ccccc34)C(=O)[C@@H]2CCCN=[N+]=[N-]"                                                                                                                    
A1EEE SMILES           CACTVS               3.385 "FC(F)(F)CCCNC(=O)N1CCC(=O)N2[CH]1CN(Cc3cccc4ccccc34)C(=O)[CH]2CCCN=[N+]=[N-]"                                                                                                                        
A1EEE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)cccc2CN3C[C@@H]4N(CCC(=O)N4[C@H](C3=O)CCCN=[N+]=[N-])C(=O)NCCCC(F)(F)F"                                                                                                                   
A1EEE SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)cccc2CN3CC4N(CCC(=O)N4C(C3=O)CCCN=[N+]=[N-])C(=O)NCCCC(F)(F)F"                                                                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           A1EEE 
_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        "(6~{S},9~{a}~{S})-6-(3-azidopropyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1EEE "Create component" 2024-10-20 PDBC 
A1EEE "Initial release"  2025-02-19 RCSB 
# 
