data_RDO
# 
_chem_comp.id                                    RDO 
_chem_comp.name                                  "ethyl 4-oxidanylidene-4-[4-(trifluoromethyl)-2,3-dihydroindol-1-yl]butanoate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H16 F3 N O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA
N-3,4-DIOL; NEOMYCIN A; NEAMINE; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl
2,6-diamino-2,6-dideoxy-alpha-D-glucoside; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl
2,6-diamino-2,6-dideoxy-D-glucoside; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl
2,6-diamino-2,6-dideoxy-glucoside
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-11-29 
_chem_comp.pdbx_modified_date                    2022-12-09 
_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                        315.288 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     RDO 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8BSQ 
_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 
RDO C07 C1  C 0 1 N N N 23.262 -4.553 -6.063 2.383  -0.312 0.000  C07 RDO 1  
RDO C08 C2  C 0 1 N N N 24.694 -4.243 -5.640 1.150  0.554  -0.001 C08 RDO 2  
RDO C11 C3  C 0 1 N N N 25.623 -6.495 -6.502 -0.329 -1.455 0.001  C11 RDO 3  
RDO C12 C4  C 0 1 N N N 27.008 -7.063 -6.634 -1.861 -1.592 0.001  C12 RDO 4  
RDO C13 C5  C 0 1 Y N N 27.941 -6.090 -5.905 -2.370 -0.169 0.000  C13 RDO 5  
RDO C14 C6  C 0 1 Y N N 27.189 -4.990 -5.488 -1.282 0.689  -0.001 C14 RDO 6  
RDO C15 C7  C 0 1 Y N N 27.801 -3.944 -4.770 -1.505 2.067  -0.002 C15 RDO 7  
RDO C16 C8  C 0 1 Y N N 29.164 -3.987 -4.494 -2.792 2.563  -0.002 C16 RDO 8  
RDO C17 C9  C 0 1 Y N N 29.920 -5.083 -4.919 -3.871 1.699  -0.001 C17 RDO 9  
RDO C18 C10 C 0 1 Y N N 29.317 -6.129 -5.613 -3.658 0.333  0.000  C18 RDO 10 
RDO C19 C11 C 0 1 N N N 30.234 -7.259 -6.040 -4.832 -0.611 0.001  C19 RDO 11 
RDO F20 F1  F 0 1 N N N 30.856 -6.810 -7.158 -4.783 -1.418 -1.141 F20 RDO 12 
RDO F21 F2  F 0 1 N N N 29.608 -8.431 -6.353 -4.782 -1.417 1.143  F21 RDO 13 
RDO F22 F3  F 0 1 N N N 31.149 -7.443 -5.048 -6.022 0.124  0.001  F22 RDO 14 
RDO N10 N1  N 0 1 N N N 25.765 -5.192 -5.879 -0.073 -0.013 -0.000 N10 RDO 15 
RDO O09 O1  O 0 1 N N N 24.934 -3.212 -5.122 1.258  1.763  -0.001 O09 RDO 16 
RDO H1  H1  H 0 1 N N N 23.275 -4.210 -7.108 2.384  -0.941 0.890  H1  RDO 17 
RDO H2  H2  H 0 1 N N N 23.272 -5.653 -6.038 2.384  -0.942 -0.890 H2  RDO 18 
RDO H4  H4  H 0 1 N N N 25.159 -6.392 -7.494 0.091  -1.913 0.896  H4  RDO 19 
RDO H5  H5  H 0 1 N N N 27.057 -8.059 -6.170 -2.196 -2.117 -0.894 H5  RDO 20 
RDO H6  H6  H 0 1 N N N 27.210 -3.105 -4.432 -0.667 2.748  -0.002 H6  RDO 21 
RDO H7  H7  H 0 1 N N N 29.635 -3.178 -3.955 -2.957 3.631  -0.003 H7  RDO 22 
RDO H8  H8  H 0 1 N N N 30.979 -5.119 -4.708 -4.878 2.090  -0.001 H8  RDO 23 
RDO C06 C12 C 0 1 N N N ?      ?      ?      3.630  0.574  -0.000 C06 RDO 24 
RDO C04 C13 C 0 1 N N N ?      ?      ?      4.862  -0.293 0.000  C04 RDO 25 
RDO O03 O2  O 0 1 N N N ?      ?      ?      6.080  0.272  -0.000 O03 RDO 26 
RDO C02 C14 C 0 1 N N N ?      ?      ?      7.222  -0.624 0.001  C02 RDO 27 
RDO O05 O3  O 0 1 N N N ?      ?      ?      4.755  -1.496 0.001  O05 RDO 28 
RDO C01 C15 C 0 1 N N N ?      ?      ?      8.514  0.196  0.000  C01 RDO 29 
RDO H3  H3  H 0 1 N N N ?      ?      ?      3.628  1.203  -0.891 H3  RDO 30 
RDO H9  H9  H 0 1 N N N ?      ?      ?      3.628  1.204  0.889  H9  RDO 31 
RDO H10 H10 H 0 1 N N N ?      ?      ?      7.191  -1.252 0.891  H10 RDO 32 
RDO H11 H11 H 0 1 N N N ?      ?      ?      7.191  -1.253 -0.889 H11 RDO 33 
RDO H12 H12 H 0 1 N N N ?      ?      ?      9.372  -0.477 0.001  H12 RDO 34 
RDO H13 H13 H 0 1 N N N ?      ?      ?      8.545  0.824  -0.890 H13 RDO 35 
RDO H14 H14 H 0 1 N N N ?      ?      ?      8.545  0.825  0.890  H14 RDO 36 
RDO H15 H15 H 0 1 N N N 25.003 -7.150 -5.873 0.093  -1.915 -0.893 H15 RDO 37 
RDO H16 H16 H 0 1 N N N 27.290 -7.139 -7.695 -2.195 -2.115 0.897  H16 RDO 38 
# 
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 
RDO F20 C19 SING N N 1  
RDO C12 C11 SING N N 2  
RDO C12 C13 SING N N 3  
RDO C11 N10 SING N N 4  
RDO F21 C19 SING N N 5  
RDO C07 C08 SING N N 6  
RDO C19 C18 SING N N 7  
RDO C19 F22 SING N N 8  
RDO C13 C18 DOUB Y N 9  
RDO C13 C14 SING Y N 10 
RDO N10 C08 SING N N 11 
RDO N10 C14 SING N N 12 
RDO C08 O09 DOUB N N 13 
RDO C18 C17 SING Y N 14 
RDO C14 C15 DOUB Y N 15 
RDO C17 C16 DOUB Y N 16 
RDO C15 C16 SING Y N 17 
RDO C07 H1  SING N N 18 
RDO C07 H2  SING N N 19 
RDO C11 H4  SING N N 20 
RDO C12 H5  SING N N 21 
RDO C15 H6  SING N N 22 
RDO C16 H7  SING N N 23 
RDO C17 H8  SING N N 24 
RDO C07 C06 SING N N 25 
RDO C06 C04 SING N N 26 
RDO C04 O03 SING N N 27 
RDO O03 C02 SING N N 28 
RDO C04 O05 DOUB N N 29 
RDO C02 C01 SING N N 30 
RDO C06 H3  SING N N 31 
RDO C06 H9  SING N N 32 
RDO C02 H10 SING N N 33 
RDO C02 H11 SING N N 34 
RDO C01 H12 SING N N 35 
RDO C01 H13 SING N N 36 
RDO C01 H14 SING N N 37 
RDO C11 H15 SING N N 38 
RDO C12 H16 SING N N 39 
# 
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 
RDO InChI            InChI                1.06    "InChI=1S/C15H16F3NO3/c1-2-22-14(21)7-6-13(20)19-9-8-10-11(15(16,17)18)4-3-5-12(10)19/h3-5H,2,6-9H2,1H3" 
RDO InChIKey         InChI                1.06    ZUBJCDWADSBMLA-UHFFFAOYSA-N                                                                              
RDO SMILES_CANONICAL CACTVS               3.385   "CCOC(=O)CCC(=O)N1CCc2c1cccc2C(F)(F)F"                                                                   
RDO SMILES           CACTVS               3.385   "CCOC(=O)CCC(=O)N1CCc2c1cccc2C(F)(F)F"                                                                   
RDO SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CCOC(=O)CCC(=O)N1CCc2c1cccc2C(F)(F)F"                                                                   
RDO SMILES           "OpenEye OEToolkits" 3.1.0.0 "CCOC(=O)CCC(=O)N1CCc2c1cccc2C(F)(F)F"                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           RDO 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   3.1.0.0 
_pdbx_chem_comp_identifier.identifier        "ethyl 4-oxidanylidene-4-[4-(trifluoromethyl)-2,3-dihydroindol-1-yl]butanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
RDO "Create component" 2022-11-29 PDBE 
RDO "Initial release"  2022-12-14 RCSB 
# 
