data_Y2O
# 
_chem_comp.id                                    Y2O 
_chem_comp.name                                  "benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H29 Cl F N7 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-27 
_chem_comp.pdbx_modified_date                    2023-03-31 
_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                        582.026 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y2O 
_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        8FM7 
_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.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 
Y2O C10  C1  C  0 1 Y N N -33.771 -2.645 -78.307 6.769  -1.333 -2.352 C10  Y2O 1  
Y2O C13  C2  C  0 1 N N N -28.059 -2.500 -77.627 1.484  3.207  0.401  C13  Y2O 2  
Y2O C15  C3  C  0 1 N N N -25.697 -2.826 -78.600 0.399  5.388  0.739  C15  Y2O 3  
Y2O C20  C4  C  0 1 N N N -25.844 0.681  -75.910 -2.170 0.551  1.010  C20  Y2O 4  
Y2O C21  C5  C  0 1 N N N -25.648 2.191  -75.646 -3.459 0.165  0.363  C21  Y2O 5  
Y2O C24  C6  C  0 1 Y N N -24.709 4.991  -75.364 -6.070 -0.081 -0.772 C24  Y2O 6  
Y2O C02  C7  C  0 1 N N N -30.740 -1.395 -76.391 3.375  1.239  -1.001 C02  Y2O 7  
Y2O C04  C8  C  0 1 N N N -32.125 -0.676 -78.195 5.578  0.800  -1.808 C04  Y2O 8  
Y2O C05  C9  C  0 1 Y N N -32.660 -1.996 -78.840 6.705  -0.177 -1.596 C05  Y2O 9  
Y2O C06  C10 C  0 1 Y N N -31.999 -2.554 -79.961 7.675  0.082  -0.646 C06  Y2O 10 
Y2O C07  C11 C  0 1 Y N N -32.441 -3.730 -80.546 8.709  -0.815 -0.452 C07  Y2O 11 
Y2O C08  C12 C  0 1 Y N N -33.554 -4.368 -80.007 8.773  -1.970 -1.208 C08  Y2O 12 
Y2O C09  C13 C  0 1 Y N N -34.219 -3.836 -78.897 7.800  -2.232 -2.154 C09  Y2O 13 
Y2O C12  C14 C  0 1 N N R -28.225 -1.400 -76.532 1.114  1.815  -0.115 C12  Y2O 14 
Y2O C18  C15 C  0 1 N N S -27.177 -1.401 -75.496 0.202  1.097  0.893  C18  Y2O 15 
Y2O C23  C16 C  0 1 Y N N -24.198 4.191  -76.336 -5.748 -0.460 0.524  C23  Y2O 16 
Y2O C25  C17 C  0 1 Y N N -24.450 6.339  -75.473 -7.243 -0.532 -1.351 C25  Y2O 17 
Y2O C27  C18 C  0 1 Y N N -23.766 6.908  -76.522 -8.092 -1.365 -0.639 C27  Y2O 18 
Y2O C29  C19 C  0 1 Y N N -23.314 6.099  -77.542 -7.768 -1.747 0.651  C29  Y2O 19 
Y2O C30  C20 C  0 1 Y N N -23.563 4.733  -77.454 -6.601 -1.295 1.235  C30  Y2O 20 
Y2O C33  C21 C  0 1 Y N N -29.257 -2.049 -74.397 2.186  -0.140 0.618  C33  Y2O 21 
Y2O C34  C22 C  0 1 Y N N -27.898 -1.933 -74.150 0.979  -0.135 1.299  C34  Y2O 22 
Y2O C35  C23 C  0 1 Y N N -27.367 -2.239 -72.888 0.666  -1.156 2.176  C35  Y2O 23 
Y2O C36  C24 C  0 1 Y N N -28.243 -2.698 -71.856 1.557  -2.193 2.382  C36  Y2O 24 
Y2O C37  C25 C  0 1 Y N N -29.627 -2.824 -72.070 2.764  -2.206 1.708  C37  Y2O 25 
Y2O C38  C26 C  0 1 N N N -30.465 -3.355 -70.829 3.737  -3.335 1.931  C38  Y2O 26 
Y2O C40  C27 C  0 1 N N N -32.647 -3.623 -69.685 4.398  -5.532 1.158  C40  Y2O 27 
Y2O C41  C28 C  0 1 Y N N -30.157 -2.500 -73.357 3.081  -1.190 0.832  C41  Y2O 28 
Y2O F26  F1  F  0 1 N N N -24.887 7.136  -74.480 -7.561 -0.160 -2.610 F26  Y2O 29 
Y2O N11  N1  N  0 1 N N N -29.417 -1.645 -75.769 2.310  0.975  -0.217 N11  Y2O 30 
Y2O N14  N2  N  0 1 N N N -26.983 -2.111 -78.562 0.292  4.058  0.408  N14  Y2O 31 
Y2O N16  N3  N  0 1 N N N -24.669 -2.336 -79.510 1.562  5.892  1.047  N16  Y2O 32 
Y2O N17  N4  N  0 1 N N N -25.438 -3.820 -77.858 -0.719 6.188  0.745  N17  Y2O 33 
Y2O N19  N5  N  0 1 N N N -26.978 -0.036 -75.275 -1.063 0.718  0.259  N19  Y2O 34 
Y2O N22  N6  N  0 1 N N N -24.476 2.751  -76.372 -4.566 -0.002 1.114  N22  Y2O 35 
Y2O N39  N7  N  0 1 N N N -31.879 -2.900 -70.776 3.467  -4.412 0.969  N39  Y2O 36 
Y2O O01  O1  O  0 1 N N N -31.757 -1.507 -75.781 3.346  2.181  -1.767 O01  Y2O 37 
Y2O O03  O2  O  0 1 N N N -30.779 -0.980 -77.755 4.469  0.458  -0.934 O03  Y2O 38 
Y2O O31  O3  O  0 1 N N N -26.373 2.793  -74.911 -3.510 0.001  -0.838 O31  Y2O 39 
Y2O O32  O4  O  0 1 N N N -25.083 0.131  -76.607 -2.118 0.715  2.211  O32  Y2O 40 
Y2O CL28 CL1 CL 0 0 N N N -23.522 8.685  -76.511 -9.563 -1.930 -1.367 CL28 Y2O 41 
Y2O H1   H1  H  0 1 N N N -34.282 -2.235 -77.448 6.011  -1.535 -3.094 H1   Y2O 42 
Y2O H2   H2  H  0 1 N N N -29.003 -2.610 -78.181 1.878  3.125  1.415  H2   Y2O 43 
Y2O H3   H3  H  0 1 N N N -27.800 -3.456 -77.149 2.241  3.646  -0.248 H3   Y2O 44 
Y2O H4   H4  H  0 1 N N N -25.289 4.590  -74.546 -5.409 0.568  -1.327 H4   Y2O 45 
Y2O H5   H5  H  0 1 N N N -32.113 0.137  -78.936 5.923  1.808  -1.578 H5   Y2O 46 
Y2O H6   H6  H  0 1 N N N -32.752 -0.384 -77.340 5.249  0.757  -2.846 H6   Y2O 47 
Y2O H7   H7  H  0 1 N N N -31.133 -2.053 -80.368 7.625  0.984  -0.055 H7   Y2O 48 
Y2O H8   H8  H  0 1 N N N -31.931 -4.143 -81.404 9.470  -0.610 0.287  H8   Y2O 49 
Y2O H9   H9  H  0 1 N N N -33.909 -5.286 -80.451 9.581  -2.671 -1.057 H9   Y2O 50 
Y2O H10  H10 H  0 1 N N N -35.081 -4.345 -78.492 7.850  -3.135 -2.744 H10  Y2O 51 
Y2O H11  H11 H  0 1 N N N -28.273 -0.415 -77.020 0.622  1.891  -1.085 H11  Y2O 52 
Y2O H12  H12 H  0 1 N N N -26.281 -1.986 -75.750 0.017  1.733  1.759  H12  Y2O 53 
Y2O H13  H13 H  0 1 N N N -22.782 6.513  -78.385 -8.431 -2.396 1.204  H13  Y2O 54 
Y2O H14  H14 H  0 1 N N N -23.261 4.083  -78.262 -6.350 -1.594 2.242  H14  Y2O 55 
Y2O H15  H15 H  0 1 N N N -26.309 -2.129 -72.699 -0.278 -1.144 2.702  H15  Y2O 56 
Y2O H16  H16 H  0 1 N N N -27.833 -2.954 -70.890 1.311  -2.990 3.068  H16  Y2O 57 
Y2O H17  H17 H  0 1 N N N -30.463 -4.454 -70.863 4.755  -2.970 1.793  H17  Y2O 58 
Y2O H18  H18 H  0 1 N N N -29.964 -3.015 -69.910 3.623  -3.717 2.946  H18  Y2O 59 
Y2O H19  H19 H  0 1 N N N -33.687 -3.266 -69.670 5.421  -5.183 1.014  H19  Y2O 60 
Y2O H20  H20 H  0 1 N N N -32.633 -4.705 -69.883 4.289  -5.930 2.167  H20  Y2O 61 
Y2O H21  H21 H  0 1 N N N -32.177 -3.422 -68.711 4.176  -6.315 0.433  H21  Y2O 62 
Y2O H22  H22 H  0 1 N N N -31.216 -2.591 -73.551 4.025  -1.206 0.308  H22  Y2O 63 
Y2O H23  H23 H  0 1 N N N -27.132 -1.343 -79.185 -0.573 3.684  0.179  H23  Y2O 64 
Y2O H24  H24 H  0 1 N N N -23.825 -2.869 -79.444 1.637  6.830  1.281  H24  Y2O 65 
Y2O H25  H25 H  0 1 N N N -26.123 -4.152 -77.209 -1.584 5.813  0.516  H25  Y2O 66 
Y2O H26  H26 H  0 1 N N N -24.549 -4.273 -77.921 -0.643 7.126  0.978  H26  Y2O 67 
Y2O H27  H27 H  0 1 N N N -27.608 0.465  -74.681 -1.104 0.587  -0.701 H27  Y2O 68 
Y2O H28  H28 H  0 1 N N N -23.874 2.142  -76.888 -4.543 0.197  2.063  H28  Y2O 69 
Y2O H29  H29 H  0 1 N N N -31.899 -1.917 -70.592 2.510  -4.723 1.034  H29  Y2O 70 
# 
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 
Y2O C07 C08  DOUB Y N 1  
Y2O C07 C06  SING Y N 2  
Y2O C08 C09  SING Y N 3  
Y2O C06 C05  DOUB Y N 4  
Y2O N16 C15  DOUB N N 5  
Y2O C09 C10  DOUB Y N 6  
Y2O C05 C10  SING Y N 7  
Y2O C05 C04  SING N N 8  
Y2O C15 N14  SING N N 9  
Y2O C15 N17  SING N N 10 
Y2O N14 C13  SING N N 11 
Y2O C04 O03  SING N N 12 
Y2O O03 C02  SING N N 13 
Y2O C13 C12  SING N N 14 
Y2O C29 C30  DOUB Y N 15 
Y2O C29 C27  SING Y N 16 
Y2O C30 C23  SING Y N 17 
Y2O O32 C20  DOUB N N 18 
Y2O C12 N11  SING N N 19 
Y2O C12 C18  SING N N 20 
Y2O C27 CL28 SING N N 21 
Y2O C27 C25  DOUB Y N 22 
Y2O C02 O01  DOUB N N 23 
Y2O C02 N11  SING N N 24 
Y2O N22 C23  SING N N 25 
Y2O N22 C21  SING N N 26 
Y2O C23 C24  DOUB Y N 27 
Y2O C20 C21  SING N N 28 
Y2O C20 N19  SING N N 29 
Y2O N11 C33  SING N N 30 
Y2O C21 O31  DOUB N N 31 
Y2O C18 N19  SING N N 32 
Y2O C18 C34  SING N N 33 
Y2O C25 C24  SING Y N 34 
Y2O C25 F26  SING N N 35 
Y2O C33 C34  DOUB Y N 36 
Y2O C33 C41  SING Y N 37 
Y2O C34 C35  SING Y N 38 
Y2O C41 C37  DOUB Y N 39 
Y2O C35 C36  DOUB Y N 40 
Y2O C37 C36  SING Y N 41 
Y2O C37 C38  SING N N 42 
Y2O C38 N39  SING N N 43 
Y2O N39 C40  SING N N 44 
Y2O C10 H1   SING N N 45 
Y2O C13 H2   SING N N 46 
Y2O C13 H3   SING N N 47 
Y2O C24 H4   SING N N 48 
Y2O C04 H5   SING N N 49 
Y2O C04 H6   SING N N 50 
Y2O C06 H7   SING N N 51 
Y2O C07 H8   SING N N 52 
Y2O C08 H9   SING N N 53 
Y2O C09 H10  SING N N 54 
Y2O C12 H11  SING N N 55 
Y2O C18 H12  SING N N 56 
Y2O C29 H13  SING N N 57 
Y2O C30 H14  SING N N 58 
Y2O C35 H15  SING N N 59 
Y2O C36 H16  SING N N 60 
Y2O C38 H17  SING N N 61 
Y2O C38 H18  SING N N 62 
Y2O C40 H19  SING N N 63 
Y2O C40 H20  SING N N 64 
Y2O C40 H21  SING N N 65 
Y2O C41 H22  SING N N 66 
Y2O N14 H23  SING N N 67 
Y2O N16 H24  SING N N 68 
Y2O N17 H25  SING N N 69 
Y2O N17 H26  SING N N 70 
Y2O N19 H27  SING N N 71 
Y2O N22 H28  SING N N 72 
Y2O N39 H29  SING N N 73 
# 
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 
Y2O SMILES           ACDLabs              12.01 "Clc1ccc(cc1F)NC(=O)C(=O)NC1c2ccc(cc2N(C1CNC(=N)N)C(=O)OCc1ccccc1)CNC"                                                                                                                                                             
Y2O InChI            InChI                1.06  "InChI=1S/C28H29ClFN7O4/c1-33-13-17-7-9-19-22(11-17)37(28(40)41-15-16-5-3-2-4-6-16)23(14-34-27(31)32)24(19)36-26(39)25(38)35-18-8-10-20(29)21(30)12-18/h2-12,23-24,33H,13-15H2,1H3,(H,35,38)(H,36,39)(H4,31,32,34)/t23-,24+/m1/s1" 
Y2O InChIKey         InChI                1.06  JMHDRQIIOQZAQE-RPWUZVMVSA-N                                                                                                                                                                                                        
Y2O SMILES_CANONICAL CACTVS               3.385 "CNCc1ccc2[C@H](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[C@@H](CNC(N)=N)N(C(=O)OCc4ccccc4)c2c1"                                                                                                                                                
Y2O SMILES           CACTVS               3.385 "CNCc1ccc2[CH](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[CH](CNC(N)=N)N(C(=O)OCc4ccccc4)c2c1"                                                                                                                                                   
Y2O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NC[C@@H]1[C@H](c2ccc(cc2N1C(=O)OCc3ccccc3)CNC)NC(=O)C(=O)Nc4ccc(c(c4)F)Cl"                                                                                                                                            
Y2O SMILES           "OpenEye OEToolkits" 2.0.7 "CNCc1ccc2c(c1)N(C(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC(=N)N)C(=O)OCc4ccccc4"                                                                                                                                                         
# 
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 
Y2O "SYSTEMATIC NAME" ACDLabs              12.01 "benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate"                                        
Y2O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(phenylmethyl) (2~{R},3~{S})-2-(carbamimidamidomethyl)-3-[[2-[(4-chloranyl-3-fluoranyl-phenyl)amino]-2-oxidanylidene-ethanoyl]amino]-6-(methylaminomethyl)-2,3-dihydroindole-1-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y2O "Create component" 2022-12-27 RCSB 
Y2O "Initial release"  2023-04-05 RCSB 
# 
