data_N9O
# 
_chem_comp.id                                    N9O 
_chem_comp.name                                  "5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[2-[6-(dimethylamino)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]ethyl]pentanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H31 N5 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-08-15 
_chem_comp.pdbx_modified_date                    2023-09-23 
_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                        509.620 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     N9O 
_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        8AQJ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.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 
N9O N1  N1  N 0 1 N N N 16.227 29.621 -7.310  -10.123 -1.535 -0.401 N1  N9O 1  
N9O C7  C1  C 0 1 N N N 17.290 25.562 -12.913 -3.775  0.613  -0.203 C7  N9O 2  
N9O C8  C2  C 0 1 N N N 18.049 24.439 -13.598 -2.693  1.309  0.625  C8  N9O 3  
N9O N2  N2  N 0 1 N N N 20.348 24.188 -14.273 -0.223  1.324  0.762  N2  N9O 4  
N9O C9  C3  C 0 1 N N N 19.260 24.960 -14.306 -1.334  0.841  0.171  C9  N9O 5  
N9O O1  O1  O 0 1 N N N 24.005 24.149 -17.228 3.436   -0.548 2.178  O1  N9O 6  
N9O C1  C4  C 0 1 N N S 17.197 29.355 -9.460  -8.724  0.278  -1.004 C1  N9O 7  
N9O C5  C5  C 0 1 N N N 17.245 27.330 -11.115 -6.237  0.391  -0.569 C5  N9O 8  
N9O C6  C6  C 0 1 N N N 17.980 26.089 -11.610 -5.155  1.088  0.258  C6  N9O 9  
N9O N3  N3  N 0 1 N N N 24.038 24.287 -14.961 3.500   1.111  0.707  N3  N9O 10 
N9O C4  C7  C 0 1 N N S 17.890 28.065 -9.946  -7.616  0.866  -0.108 C4  N9O 11 
N9O C3  C8  C 0 1 N N N 18.311 28.247 -7.487  -9.842  0.222  1.292  C3  N9O 12 
N9O O3  O2  O 0 1 N N N 19.237 26.071 -14.845 -1.241  0.031  -0.726 O3  N9O 13 
N9O C2  C9  C 0 1 N N R 17.538 29.482 -7.930  -9.986  -0.082 -0.212 C2  N9O 14 
N9O N4  N4  N 0 1 N N N 30.314 25.233 -16.320 9.140   -1.794 -0.345 N4  N9O 15 
N9O N   N5  N 0 1 N N N 15.739 29.315 -9.464  -8.272  -1.007 -1.559 N   N9O 16 
N9O S   S1  S 0 1 N N N 17.942 26.856 -8.558  -8.024  0.175  1.546  S   N9O 17 
N9O C   C10 C 0 1 N N N 15.202 29.467 -8.209  -9.116  -1.973 -1.168 C   N9O 18 
N9O O   O3  O 0 1 N N N 13.998 29.383 -7.933  -8.980  -3.139 -1.484 O   N9O 19 
N9O C10 C11 C 0 1 N N N 21.655 24.709 -14.657 1.097   0.869  0.321  C10 N9O 20 
N9O C11 C12 C 0 1 N N N 22.699 23.654 -14.895 2.179   1.566  1.148  C11 N9O 21 
N9O C20 C13 C 0 1 N N N 24.650 24.356 -16.220 4.044   0.030  1.296  C20 N9O 22 
N9O C19 C14 C 0 1 Y N N 26.085 24.710 -16.253 5.364   -0.457 0.883  C19 N9O 23 
N9O C18 C15 C 0 1 Y N N 26.765 25.031 -15.047 6.051   0.231  -0.143 C18 N9O 24 
N9O C13 C16 C 0 1 Y N N 26.090 24.985 -13.799 5.452   1.363  -0.742 C13 N9O 25 
N9O C12 C17 C 0 1 N N N 24.661 24.609 -13.744 4.123   1.787  -0.277 C12 N9O 26 
N9O O2  O4  O 0 1 N N N 24.048 24.516 -12.697 3.586   2.755  -0.780 O2  N9O 27 
N9O C21 C18 C 0 1 Y N N 26.783 24.627 -17.442 5.956   -1.572 1.471  C21 N9O 28 
N9O C22 C19 C 0 1 Y N N 28.148 24.855 -17.485 7.202   -2.002 1.056  C22 N9O 29 
N9O C23 C20 C 0 1 Y N N 28.856 25.172 -16.331 7.895   -1.343 0.051  C23 N9O 30 
N9O C25 C21 C 0 1 N N N 30.983 24.144 -15.617 10.089  -1.773 0.776  C25 N9O 31 
N9O C24 C22 C 0 1 N N N 31.039 26.140 -17.206 9.051   -3.137 -0.933 C24 N9O 32 
N9O C17 C23 C 0 1 Y N N 28.162 25.294 -15.077 7.322   -0.206 -0.567 C17 N9O 33 
N9O C16 C24 C 0 1 Y N N 28.814 25.561 -13.838 7.979   0.496  -1.587 C16 N9O 34 
N9O C15 C25 C 0 1 Y N N 28.148 25.461 -12.659 7.382   1.597  -2.159 C15 N9O 35 
N9O C14 C26 C 0 1 Y N N 26.793 25.169 -12.628 6.130   2.036  -1.749 C14 N9O 36 
N9O H1  H1  H 0 1 N N N 16.089 29.808 -6.337  -10.828 -2.087 -0.028 H1  N9O 37 
N9O H2  H2  H 0 1 N N N 17.198 26.400 -13.620 -3.640  0.857  -1.256 H2  N9O 38 
N9O H3  H3  H 0 1 N N N 16.288 25.193 -12.650 -3.698  -0.466 -0.067 H3  N9O 39 
N9O H4  H4  H 0 1 N N N 17.387 23.952 -14.329 -2.770  2.388  0.489  H4  N9O 40 
N9O H5  H5  H 0 1 N N N 18.363 23.704 -12.842 -2.828  1.065  1.679  H5  N9O 41 
N9O H6  H6  H 0 1 N N N 20.266 23.235 -13.980 -0.298  1.972  1.480  H6  N9O 42 
N9O H7  H7  H 0 1 N N N 17.582 30.228 -10.007 -8.968  0.974  -1.808 H7  N9O 43 
N9O H8  H8  H 0 1 N N N 17.170 28.035 -11.956 -6.102  0.636  -1.623 H8  N9O 44 
N9O H9  H9  H 0 1 N N N 16.236 27.022 -10.804 -6.160  -0.688 -0.434 H9  N9O 45 
N9O H10 H10 H 0 1 N N N 17.946 25.309 -10.835 -5.290  0.843  1.312  H10 N9O 46 
N9O H11 H11 H 0 1 N N N 19.028 26.345 -11.827 -5.232  2.167  0.123  H11 N9O 47 
N9O H12 H12 H 0 1 N N N 18.939 28.289 -10.190 -7.665  1.955  -0.098 H12 N9O 48 
N9O H13 H13 H 0 1 N N N 18.028 27.994 -6.455  -10.231 1.213  1.525  H13 N9O 49 
N9O H14 H14 H 0 1 N N N 19.389 28.460 -7.530  -10.344 -0.539 1.890  H14 N9O 50 
N9O H15 H15 H 0 1 N N N 18.146 30.384 -7.767  -10.852 0.436  -0.625 H15 N9O 51 
N9O H16 H16 H 0 1 N N N 15.190 29.190 -10.291 -7.489  -1.136 -2.117 H16 N9O 52 
N9O H17 H17 H 0 1 N N N 22.011 25.370 -13.853 1.174   -0.210 0.456  H17 N9O 53 
N9O H18 H18 H 0 1 N N N 21.535 25.290 -15.584 1.232   1.113  -0.733 H18 N9O 54 
N9O H19 H19 H 0 1 N N N 22.490 23.139 -15.844 2.044   1.321  2.202  H19 N9O 55 
N9O H20 H20 H 0 1 N N N 22.678 22.926 -14.071 2.102   2.644  1.013  H20 N9O 56 
N9O H21 H21 H 0 1 N N N 26.256 24.381 -18.352 5.438   -2.104 2.256  H21 N9O 57 
N9O H22 H22 H 0 1 N N N 28.670 24.786 -18.428 7.646   -2.868 1.524  H22 N9O 58 
N9O H23 H23 H 0 1 N N N 30.249 23.593 -15.010 9.721   -2.417 1.575  H23 N9O 59 
N9O H24 H24 H 0 1 N N N 31.440 23.461 -16.349 11.060  -2.132 0.438  H24 N9O 60 
N9O H25 H25 H 0 1 N N N 31.765 24.556 -14.962 10.189  -0.753 1.148  H25 N9O 61 
N9O H26 H26 H 0 1 N N N 32.121 26.029 -17.039 8.646   -3.830 -0.196 H26 N9O 62 
N9O H27 H27 H 0 1 N N N 30.803 25.897 -18.252 8.396   -3.109 -1.804 H27 N9O 63 
N9O H28 H28 H 0 1 N N N 30.740 27.177 -16.994 10.044  -3.468 -1.236 H28 N9O 64 
N9O H29 H29 H 0 1 N N N 29.855 25.848 -13.837 8.953   0.174  -1.924 H29 N9O 65 
N9O H30 H30 H 0 1 N N N 28.681 25.611 -11.732 7.897   2.130  -2.945 H30 N9O 66 
N9O H31 H31 H 0 1 N N N 26.285 25.085 -11.679 5.683   2.901  -2.214 H31 N9O 67 
# 
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 
N9O C22 C21 DOUB Y N 1  
N9O C22 C23 SING Y N 2  
N9O C21 C19 SING Y N 3  
N9O O1  C20 DOUB N N 4  
N9O C24 N4  SING N N 5  
N9O C23 N4  SING N N 6  
N9O C23 C17 DOUB Y N 7  
N9O N4  C25 SING N N 8  
N9O C19 C20 SING N N 9  
N9O C19 C18 DOUB Y N 10 
N9O C20 N3  SING N N 11 
N9O C17 C18 SING Y N 12 
N9O C17 C16 SING Y N 13 
N9O C18 C13 SING Y N 14 
N9O N3  C11 SING N N 15 
N9O N3  C12 SING N N 16 
N9O C11 C10 SING N N 17 
N9O O3  C9  DOUB N N 18 
N9O C10 N2  SING N N 19 
N9O C9  N2  SING N N 20 
N9O C9  C8  SING N N 21 
N9O C16 C15 DOUB Y N 22 
N9O C13 C12 SING N N 23 
N9O C13 C14 DOUB Y N 24 
N9O C12 O2  DOUB N N 25 
N9O C8  C7  SING N N 26 
N9O C7  C6  SING N N 27 
N9O C15 C14 SING Y N 28 
N9O C6  C5  SING N N 29 
N9O C5  C4  SING N N 30 
N9O C4  C1  SING N N 31 
N9O C4  S   SING N N 32 
N9O N   C1  SING N N 33 
N9O N   C   SING N N 34 
N9O C1  C2  SING N N 35 
N9O S   C3  SING N N 36 
N9O C   O   DOUB N N 37 
N9O C   N1  SING N N 38 
N9O C2  C3  SING N N 39 
N9O C2  N1  SING N N 40 
N9O N1  H1  SING N N 41 
N9O C7  H2  SING N N 42 
N9O C7  H3  SING N N 43 
N9O C8  H4  SING N N 44 
N9O C8  H5  SING N N 45 
N9O N2  H6  SING N N 46 
N9O C1  H7  SING N N 47 
N9O C5  H8  SING N N 48 
N9O C5  H9  SING N N 49 
N9O C6  H10 SING N N 50 
N9O C6  H11 SING N N 51 
N9O C4  H12 SING N N 52 
N9O C3  H13 SING N N 53 
N9O C3  H14 SING N N 54 
N9O C2  H15 SING N N 55 
N9O N   H16 SING N N 56 
N9O C10 H17 SING N N 57 
N9O C10 H18 SING N N 58 
N9O C11 H19 SING N N 59 
N9O C11 H20 SING N N 60 
N9O C21 H21 SING N N 61 
N9O C22 H22 SING N N 62 
N9O C25 H23 SING N N 63 
N9O C25 H24 SING N N 64 
N9O C25 H25 SING N N 65 
N9O C24 H26 SING N N 66 
N9O C24 H27 SING N N 67 
N9O C24 H28 SING N N 68 
N9O C16 H29 SING N N 69 
N9O C15 H30 SING N N 70 
N9O C14 H31 SING N N 71 
# 
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 
N9O InChI            InChI                1.06  "InChI=1S/C26H31N5O4S/c1-30(2)19-11-10-17-22-15(19)6-5-7-16(22)24(33)31(25(17)34)13-12-27-21(32)9-4-3-8-20-23-18(14-36-20)28-26(35)29-23/h5-7,10-11,18,20,23H,3-4,8-9,12-14H2,1-2H3,(H,27,32)(H2,28,29,35)/t18-,20-,23-/m0/s1" 
N9O InChIKey         InChI                1.06  WAGQBAHKYBJEAZ-LEDOBFOHSA-N                                                                                                                                                                                                    
N9O SMILES_CANONICAL CACTVS               3.385 "CN(C)c1ccc2C(=O)N(CCNC(=O)CCCC[C@@H]3SC[C@@H]4NC(=O)N[C@H]34)C(=O)c5cccc1c25"                                                                                                                                                 
N9O SMILES           CACTVS               3.385 "CN(C)c1ccc2C(=O)N(CCNC(=O)CCCC[CH]3SC[CH]4NC(=O)N[CH]34)C(=O)c5cccc1c25"                                                                                                                                                      
N9O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)c1ccc2c3c1cccc3C(=O)N(C2=O)CCNC(=O)CCCC[C@H]4[C@@H]5[C@H](CS4)NC(=O)N5"                                                                                                                                                  
N9O SMILES           "OpenEye OEToolkits" 2.0.7 "CN(C)c1ccc2c3c1cccc3C(=O)N(C2=O)CCNC(=O)CCCCC4C5C(CS4)NC(=O)N5"                                                                                                                                                               
# 
_pdbx_chem_comp_identifier.comp_id           N9O 
_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        "5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[2-[6-(dimethylamino)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]ethyl]pentanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
N9O "Create component"  2022-08-15 PDBE 
N9O "Initial release"   2022-08-31 RCSB 
N9O "Modify descriptor" 2023-09-23 RCSB 
# 
