# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:59:31 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: ethyl 3-{[1-(hydroxyamino)-2H-inden-5-yl]amino}thieno[2,3-c]pyridine-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1sc2cnccc2c1NC3=CC4=CCC(=C4C=C3)NO
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 SM6  SM6  'ethyl 3-{[1-(hydroxyamino)-2H-inden-5-yl]amino}thieno[2,3-c]pyridine-2-carboxylate'  ligand  43  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SM6
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 SM6  C1    C  CR56  0   0.021  -3.9170   0.1567   0.1866
 SM6  C2    C  CR56  0   0.158  -3.5684   0.0212  -1.2357
 SM6  C3    C  CR16  0  -0.419  -2.1908  -0.1742  -1.5931
 SM6  C4    C  CR6   0   0.303  -1.2506  -0.2584  -0.6200
 SM6  C5    C  CR16  0  -0.315  -1.6048  -0.1680   0.7842
 SM6  C6    C  CR16  0  -0.260  -2.8838   0.0379   1.1704
 SM6  C7    C  CR5   0   0.211  -5.2694   0.3589   0.2669
 SM6  C8    C  CH2   0  -0.534  -5.8507   0.3713  -1.1164
 SM6  C9    C  CR15  0  -0.422  -4.6737   0.1353  -2.0076
 SM6  N10   N  NH1   0  -0.773   0.0816  -0.5176  -0.9691
 SM6  C11   C  CR5   0   0.446   1.1838  -0.0940  -0.2951
 SM6  N12   N  NH1   0  -0.394  -6.0924   0.4722   1.3443
 SM6  C13   C  CR56  0   0.253   1.2833   1.1794   0.3861
 SM6  C14   C  CR56  0  -0.307   2.5466   1.3624   0.9612
 SM6  S15   S  S2    0   0.257   3.6239   0.0533   0.6557
 SM6  C16   C  CR5   0  -0.491   2.3786  -0.7782  -0.2348
 SM6  C17   C  C     0   0.632   2.6474  -2.0793  -0.8216
 SM6  O18   O  O     0  -0.465   1.8605  -2.6944  -1.5118
 SM6  C19   C  CR16  0  -0.352   0.3659   2.2300   0.4933
 SM6  C20   C  CR16  0  -0.075   0.7507   3.3561   1.1876
 SM6  N21   N  N     0  -0.400   1.9496   3.5073   1.7673
 SM6  C22   C  CR16  0  -0.075   2.8335   2.5396   1.6535
 SM6  O23   O  OH1   0  -0.550  -5.4928   0.8603   2.5250
 SM6  O24   O  O2    0  -0.469   3.8601  -2.5098  -0.5119
 SM6  C25   C  CH3   0  -0.687   5.7063  -4.0112  -0.5754
 SM6  C26   C  CH2   0  -0.180   4.2834  -3.7853  -1.0228
 SM6  H3    H  HCR6  0   0.251  -1.9085  -0.2516  -2.6366
 SM6  H5    H  HCR6  0   0.268  -0.8319  -0.2959   1.5305
 SM6  H6    H  HCR6  0   0.248  -3.1158   0.0904   2.2242
 SM6  H8    H  HCH2  0   0.284  -6.6319  -0.3884  -1.2292
 SM6  H9    H  HCR5  0   0.239  -4.7312   0.0849  -3.0844
 SM6  HN10  H  HNH1  0   0.410   0.2326  -1.2621  -1.6336
 SM6  HN12  H  HNH1  0   0.395  -6.9422   1.0005   1.1893
 SM6  H19   H  HCR6  0   0.284  -0.6169   2.1864   0.0473
 SM6  H20   H  HCR6  0   0.272   0.0626   4.1866   1.2882
 SM6  H22   H  HCR6  0   0.280   3.8033   2.6871   2.1164
 SM6  HO23  H  HOH1  0   0.477  -5.6410   0.1283   3.1351
 SM6  H25   H  HCH3  0   0.241   6.0471  -4.9753  -0.9513
 SM6  H25A  H  HCH3  0   0.238   6.3761  -3.2447  -0.9651
 SM6  H25B  H  HCH3  0   0.238   5.7889  -4.0280   0.5112
 SM6  H26   H  HCH2  0   0.240   3.6241  -4.5668  -0.6401
 SM6  H26A  H  HCH2  0   0.240   4.2109  -3.7847  -2.1120
 SM6  H8A   H  HCH2  0   0.282  -6.3379   1.3336  -1.3152

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 SM6  C2   C1    single    1.471  0.020  1.471
 SM6  C1   C7    double    1.370  0.020  1.370
 SM6  C1   C6    single    1.432  0.020  1.432
 SM6  C9   C2    double    1.353  0.020  1.353
 SM6  C3   C2    single    1.437  0.020  1.437
 SM6  C3   C4    double    1.356  0.020  1.356
 SM6  C3   H3    single    0.930  0.020  1.080
 SM6  N10  C4    single    1.401  0.020  1.401
 SM6  C4   C5    single    1.451  0.020  1.451
 SM6  C5   C6    double    1.352  0.020  1.352
 SM6  C5   H5    single    0.930  0.020  1.080
 SM6  C6   H6    single    0.930  0.020  1.080
 SM6  C8   C7    single    1.501  0.020  1.501
 SM6  C7   N12   single    1.361  0.020  1.361
 SM6  C9   C8    single    1.495  0.020  1.495
 SM6  C8   H8    single    0.970  0.020  1.090
 SM6  C9   H9    single    0.930  0.020  1.080
 SM6  C11  N10   single    1.360  0.020  1.360
 SM6  N10  HN10  single    0.860  0.020  1.020
 SM6  C16  C11   aromatic  1.378  0.020  1.378
 SM6  C13  C11   aromatic  1.448  0.020  1.448
 SM6  N12  O23   single    1.380  0.020  1.380
 SM6  N12  HN12  single    0.890  0.020  1.040
 SM6  C14  C13   aromatic  1.400  0.020  1.400
 SM6  C13  C19   aromatic  1.399  0.020  1.399
 SM6  C22  C14   aromatic  1.396  0.020  1.396
 SM6  S15  C14   aromatic  1.723  0.020  1.723
 SM6  S15  C16   aromatic  1.742  0.020  1.742
 SM6  C16  C17   single    1.452  0.020  1.452
 SM6  C17  O24   single    1.324  0.020  1.324
 SM6  C17  O18   double    1.214  0.020  1.214
 SM6  C20  C19   aromatic  1.378  0.020  1.378
 SM6  C19  H19   single    0.930  0.020  1.080
 SM6  N21  C20   aromatic  1.340  0.020  1.340
 SM6  C20  H20   single    0.930  0.020  1.080
 SM6  C22  N21   aromatic  1.316  0.020  1.316
 SM6  C22  H22   single    0.930  0.020  1.080
 SM6  O23  HO23  single    0.850  0.020  0.980
 SM6  C26  O24   single    1.438  0.020  1.438
 SM6  C25  C26   single    1.509  0.020  1.509
 SM6  C25  H25   single    0.970  0.020  1.090
 SM6  C25  H25A  single    0.970  0.020  1.090
 SM6  C25  H25B  single    0.970  0.020  1.090
 SM6  C26  H26   single    0.970  0.020  1.090
 SM6  C26  H26A  single    0.970  0.020  1.090
 SM6  C8   H8A   single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 SM6  C7    C1   C6    133.19  3.000
 SM6  C6    C1   C2    119.07  3.000
 SM6  C7    C1   C2    107.72  3.000
 SM6  C9    C2   C3    130.77  3.000
 SM6  C3    C2   C1    118.71  3.000
 SM6  C9    C2   C1    110.51  3.000
 SM6  H3    C3   C4    120.39  3.000
 SM6  H3    C3   C2    119.94  3.000
 SM6  C4    C3   C2    119.67  3.000
 SM6  N10   C4   C5    118.99  3.000
 SM6  C5    C4   C3    121.43  3.000
 SM6  N10   C4   C3    119.47  3.000
 SM6  H5    C5   C6    119.79  3.000
 SM6  H5    C5   C4    119.06  3.000
 SM6  C6    C5   C4    121.13  3.000
 SM6  H6    C6   C5    119.29  3.000
 SM6  H6    C6   C1    120.75  3.000
 SM6  C5    C6   C1    119.94  3.000
 SM6  N12   C7   C8    119.67  3.000
 SM6  N12   C7   C1    131.00  3.000
 SM6  C8    C7   C1    109.25  3.000
 SM6  H8A   C8   H8    105.85  3.000
 SM6  H8A   C8   C9    112.35  3.000
 SM6  H8    C8   C9    112.99  3.000
 SM6  H8A   C8   C7    110.27  3.000
 SM6  H8    C8   C7    111.43  3.000
 SM6  C9    C8   C7    104.07  3.000
 SM6  H9    C9   C8    124.05  3.000
 SM6  H9    C9   C2    127.50  3.000
 SM6  C8    C9   C2    108.45  3.000
 SM6  HN10  N10  C11   115.77  3.000
 SM6  HN10  N10  C4    116.28  3.000
 SM6  C11   N10  C4    126.13  3.000
 SM6  C16   C11  C13   110.89  3.000
 SM6  C13   C11  N10   124.26  3.000
 SM6  C16   C11  N10   124.74  3.000
 SM6  HN12  N12  O23   110.42  3.000
 SM6  HN12  N12  C7    115.46  3.000
 SM6  O23   N12  C7    115.99  3.000
 SM6  C19   C13  C14   117.52  3.000
 SM6  C19   C13  C11   130.67  3.000
 SM6  C14   C13  C11   111.73  3.000
 SM6  C22   C14  S15   126.90  3.000
 SM6  S15   C14  C13   113.09  3.000
 SM6  C22   C14  C13   119.97  3.000
 SM6  C16   S15  C14    90.36  3.000
 SM6  C17   C16  S15   120.12  3.000
 SM6  C17   C16  C11   125.98  3.000
 SM6  S15   C16  C11   113.90  3.000
 SM6  O24   C17  O18   124.20  3.000
 SM6  O18   C17  C16   124.31  3.000
 SM6  O24   C17  C16   111.49  3.000
 SM6  H19   C19  C20   119.68  3.000
 SM6  H19   C19  C13   122.32  3.000
 SM6  C20   C19  C13   117.99  3.000
 SM6  H20   C20  N21   116.21  3.000
 SM6  H20   C20  C19   119.74  3.000
 SM6  N21   C20  C19   124.05  3.000
 SM6  C22   N21  C20   118.73  3.000
 SM6  H22   C22  N21   117.63  3.000
 SM6  H22   C22  C14   120.68  3.000
 SM6  N21   C22  C14   121.69  3.000
 SM6  HO23  O23  N12   105.13  3.000
 SM6  C26   O24  C17   118.37  3.000
 SM6  H25B  C25  H25A  108.71  3.000
 SM6  H25B  C25  H25   107.86  3.000
 SM6  H25A  C25  H25   107.86  3.000
 SM6  H25B  C25  C26   111.68  3.000
 SM6  H25A  C25  C26   111.61  3.000
 SM6  H25   C25  C26   108.97  3.000
 SM6  H26A  C26  H26   108.06  3.000
 SM6  H26A  C26  C25   111.02  3.000
 SM6  H26   C26  C25   111.01  3.000
 SM6  H26A  C26  O24   109.54  3.000
 SM6  H26   C26  O24   109.43  3.000
 SM6  C25   C26  O24   107.77  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 SM6  CONST_01  C14  S15  C16  C11     0.00   0.0  0
 SM6  CONST_02  C22  C14  C13  C11   180.00   0.0  0
 SM6  CONST_03  S15  C14  C13  C11     0.00   0.0  0
 SM6  CONST_04  C20  C19  C13  C11   180.00   0.0  0
 SM6  CONST_05  S15  C16  C11  C13     0.00   0.0  0
 SM6  CONST_06  N21  C22  C14  C13     0.00   0.0  0
 SM6  CONST_07  C16  S15  C14  C13     0.00   0.0  0
 SM6  CONST_08  N21  C20  C19  C13     0.00   0.0  0
 SM6  CONST_09  C16  C11  C13  C14     0.00   0.0  0
 SM6  CONST_10  C20  C19  C13  C14     0.00   0.0  0
 SM6  CONST_11  C20  N21  C22  C14     0.00   0.0  0
 SM6  CONST_12  C19  C13  C14  S15   180.00   0.0  0
 SM6  CONST_13  N21  C22  C14  S15   180.00   0.0  0
 SM6  CONST_14  C19  C13  C11  C16   180.00   0.0  0
 SM6  CONST_15  C22  C14  S15  C16   180.00   0.0  0
 SM6  CONST_16  C22  C14  C13  C19     0.00   0.0  0
 SM6  CONST_17  C22  N21  C20  C19     0.00   0.0  0
 SM6  CONST_18  S15  C16  C11  N10   180.00   0.0  0
 SM6  CONST_19  C14  C13  C11  N10   180.00   0.0  0
 SM6  CONST_20  C19  C13  C11  N10     0.00   0.0  0
 SM6  CONST_21  C17  C16  C11  C13   180.00   0.0  0
 SM6  CONST_22  C17  C16  S15  C14   180.00   0.0  0
 SM6  CONST_27  H19  C19  C13  C11     0.00   0.0  0
 SM6  CONST_28  H22  C22  C14  C13   180.00   0.0  0
 SM6  CONST_29  H20  C20  C19  C13   180.00   0.0  0
 SM6  Var_01    C8   C9   C2   C1      0.49  30.0  1
 SM6  Var_02    C9   C8   C7   C1      0.66  30.0  1
 SM6  Var_03    C8   C7   C1   C2     -0.39  30.0  1
 SM6  Var_04    C7   C8   C9   C2     -0.69  30.0  1
 SM6  Var_05    O23  N12  C7   C1     22.96  30.0  2
 SM6  Var_06    O24  C17  C16  C11  -175.64  30.0  2
 SM6  Var_07    C25  C26  O24  C17   177.73  30.0  1
 SM6  Var_08    H25  C25  C26  O24   179.91  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SM6  plan-1  N10   0.020
 SM6  plan-1  C11   0.020
 SM6  plan-1  C13   0.020
 SM6  plan-1  C14   0.020
 SM6  plan-1  S15   0.020
 SM6  plan-1  C16   0.020
 SM6  plan-1  C17   0.020
 SM6  plan-1  C19   0.020
 SM6  plan-1  C20   0.020
 SM6  plan-1  N21   0.020
 SM6  plan-1  C22   0.020
 SM6  plan-1  H19   0.020
 SM6  plan-1  H20   0.020
 SM6  plan-1  H22   0.020
 SM6  plan-2  C1    0.020
 SM6  plan-2  C2    0.020
 SM6  plan-2  C3    0.020
 SM6  plan-2  C4    0.020
 SM6  plan-2  C5    0.020
 SM6  plan-2  C6    0.020
 SM6  plan-2  C7    0.020
 SM6  plan-2  C9    0.020
 SM6  plan-2  N10   0.020
 SM6  plan-2  H3    0.020
 SM6  plan-2  H5    0.020
 SM6  plan-2  H6    0.020
 SM6  plan-3  C4    0.020
 SM6  plan-3  N10   0.020
 SM6  plan-3  C11   0.020
 SM6  plan-3  HN10  0.020
 SM6  plan-4  C16   0.020
 SM6  plan-4  C17   0.020
 SM6  plan-4  O18   0.020
 SM6  plan-4  O24   0.020

