# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:04:03 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-{5-[(piperidin-4-yl)oxy]-2H-isoindol-2-yl}-4-(trifluoromethyl)pyridazin-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)C1=C(C=NNC1=O)n2cc3ccc(OC4CCNCC4)cc3c2
#
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
 T9D  T9D  5-{5-[(piperidin-4-yl)oxy]-2H-isoindol-2-yl}-4-(trifluoromethyl)pyridazin-3(2H)-one  ligand  44  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T9D
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
 T9D  C5   C  CR6   0  -0.362  -107.7728  167.5055  22.0387
 T9D  C6   C  CR6   0   0.339  -106.5660  167.7287  22.6234
 T9D  C7   C  CR16  0  -0.099  -106.5129  168.4628  23.8478
 T9D  C10  C  CR6   0   0.554  -108.9819  167.9040  22.7496
 T9D  N12  N  NR5   0  -0.543  -105.3453  167.2585  22.1279
 T9D  C13  C  CR15  0  -0.093  -105.0407  165.9392  21.9557
 T9D  C15  C  CR16  0  -0.306  -102.8535  164.8020  21.2459
 T9D  C17  C  CR6   0   0.382  -101.0820  166.4251  20.8007
 T9D  C20  C  CR15  0  -0.121  -104.2590  168.0587  21.8723
 T9D  C22  C  CR16  0   0.040   -99.1369  167.7521  20.3007
 T9D  C24  C  C     0  -0.322   -98.6327  169.7084  18.8249
 T9D  C26  C  C     0  -0.326   -96.8731  168.8050  20.1926
 T9D  F1   F  F     0  -0.306  -108.4992  165.6552  20.7871
 T9D  C2   C  CT    0   1.086  -107.9910  166.8872  20.6856
 T9D  F3   F  F     0  -0.297  -108.8444  167.6198  19.9680
 T9D  F4   F  F     0  -0.290  -106.8754  166.8005  19.9634
 T9D  N8   N  N     0  -0.163  -107.5718  168.8835  24.4472
 T9D  N9   N  NR16  0  -0.480  -108.7365  168.6015  23.9085
 T9D  O11  O  O     0  -0.454  -110.1214  167.6653  22.3918
 T9D  C14  C  CR56  0  -0.014  -103.7206  165.8807  21.5643
 T9D  C16  C  CR16  0  -0.354  -101.5772  165.0767  20.8762
 T9D  C18  C  CR16  0  -0.484  -101.8836  167.4897  21.1014
 T9D  C19  C  CR56  0   0.053  -103.2239  167.2272  21.5015
 T9D  O21  O  O2    0  -0.496   -99.7878  166.4921  20.4285
 T9D  C23  C  C     0  -0.479   -99.4681  168.4352  18.9797
 T9D  N25  N  NR16  0  -0.573   -97.2021  169.4999  18.9603
 T9D  C27  C  C     0  -0.459   -97.6420  167.4990  20.3995
 T9D  H1   H  HCR6  0   0.318  -105.5621  168.6732  24.3176
 T9D  H2   H  HCR5  0   0.302  -105.7596  165.1615  22.1553
 T9D  H3   H  HCR6  0   0.253  -103.2026  163.7785  21.2956
 T9D  H4   H  HCR5  0   0.301  -104.3260  169.1322  21.9394
 T9D  H5   H  HCR6  0   0.219   -99.4319  168.4024  21.1359
 T9D  H6   H  H     0   0.221   -98.9454  170.4396  19.5785
 T9D  H7   H  H     0   0.242   -98.8331  170.1624  17.8529
 T9D  H8   H  H     0   0.243   -95.7999  168.6086  20.2123
 T9D  H9   H  H     0   0.220   -97.0789  169.4819  21.0289
 T9D  H10  H  HNR6  0   0.443  -109.5388  168.9183  24.4397
 T9D  H11  H  HCR6  0   0.261  -100.8956  164.2721  20.6291
 T9D  H12  H  HCR6  0   0.266  -101.5387  168.5132  21.0458
 T9D  H13  H  H     0   0.243  -100.5299  168.6844  18.9123
 T9D  H14  H  H     0   0.229   -99.2477  167.7455  18.1582
 T9D  H15  H  HNR6  0   0.341   -96.8703  168.9559  18.1723
 T9D  H17  H  H     0   0.227   -97.3423  166.7717  19.6378
 T9D  H18  H  H     0   0.239   -97.3934  167.0739  21.3753

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
 T9D  C24  N25  single    1.452  0.020  1.452
 T9D  C24  C23  single    1.531  0.020  1.531
 T9D  N25  C26  single    1.452  0.020  1.452
 T9D  C23  C22  single    1.524  0.020  1.524
 T9D  F4   C2   single    1.332  0.020  1.332
 T9D  C26  C27  single    1.530  0.020  1.530
 T9D  C22  C27  single    1.519  0.020  1.519
 T9D  C22  O21  single    1.424  0.020  1.424
 T9D  C16  C15  aromatic  1.357  0.020  1.357
 T9D  C16  C17  aromatic  1.438  0.020  1.438
 T9D  C15  C14  aromatic  1.420  0.020  1.420
 T9D  F3   C2   single    1.334  0.020  1.334
 T9D  O21  C17  single    1.348  0.020  1.348
 T9D  C17  C18  aromatic  1.366  0.020  1.366
 T9D  F1   C2   single    1.337  0.020  1.337
 T9D  C2   C5   single    1.504  0.020  1.504
 T9D  C14  C13  aromatic  1.378  0.020  1.378
 T9D  C14  C19  aromatic  1.437  0.020  1.437
 T9D  C13  N12  aromatic  1.365  0.020  1.365
 T9D  C18  C19  aromatic  1.423  0.020  1.423
 T9D  C19  C20  aromatic  1.379  0.020  1.379
 T9D  N12  C20  aromatic  1.373  0.020  1.373
 T9D  N12  C6   single    1.399  0.020  1.399
 T9D  C5   C6   double    1.359  0.020  1.359
 T9D  C5   C10  single    1.458  0.020  1.458
 T9D  C6   C7   single    1.429  0.020  1.429
 T9D  O11  C10  double    1.218  0.020  1.218
 T9D  C10  N9   single    1.375  0.020  1.375
 T9D  C7   N8   double    1.287  0.020  1.287
 T9D  N9   N8   single    1.314  0.020  1.314
 T9D  C7   H1   single    0.930  0.020  1.080
 T9D  C13  H2   single    0.930  0.020  1.080
 T9D  C15  H3   single    0.930  0.020  1.080
 T9D  C20  H4   single    0.930  0.020  1.080
 T9D  C22  H5   single    0.970  0.020  1.090
 T9D  C24  H6   single    0.970  0.020  1.090
 T9D  C24  H7   single    0.970  0.020  1.090
 T9D  C26  H8   single    0.970  0.020  1.090
 T9D  C26  H9   single    0.970  0.020  1.090
 T9D  N9   H10  single    0.860  0.020  1.020
 T9D  C16  H11  single    0.930  0.020  1.080
 T9D  C18  H12  single    0.930  0.020  1.080
 T9D  C23  H13  single    0.970  0.020  1.090
 T9D  C23  H14  single    0.970  0.020  1.090
 T9D  N25  H15  single    0.890  0.020  1.040
 T9D  C27  H17  single    0.970  0.020  1.090
 T9D  C27  H18  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
 T9D  C2   C5   C10  115.52  3.000
 T9D  C10  C5   C6   118.79  3.000
 T9D  C2   C5   C6   125.69  3.000
 T9D  N12  C6   C7   116.35  3.000
 T9D  C7   C6   C5   119.08  3.000
 T9D  N12  C6   C5   124.55  3.000
 T9D  H1   C7   N8   117.22  3.000
 T9D  H1   C7   C6   120.34  3.000
 T9D  N8   C7   C6   122.43  3.000
 T9D  O11  C10  N9   120.94  3.000
 T9D  N9   C10  C5   113.68  3.000
 T9D  O11  C10  C5   125.38  3.000
 T9D  C20  N12  C13  111.30  3.000
 T9D  C20  N12  C6   124.08  3.000
 T9D  C13  N12  C6   124.35  3.000
 T9D  H2   C13  C14  131.37  3.000
 T9D  H2   C13  N12  121.69  3.000
 T9D  C14  C13  N12  106.90  3.000
 T9D  H3   C15  C16  120.48  3.000
 T9D  H3   C15  C14  120.73  3.000
 T9D  C16  C15  C14  118.79  3.000
 T9D  O21  C17  C18  125.82  3.000
 T9D  C18  C17  C16  121.13  3.000
 T9D  O21  C17  C16  113.05  3.000
 T9D  H4   C20  C19  131.63  3.000
 T9D  H4   C20  N12  121.31  3.000
 T9D  C19  C20  N12  107.01  3.000
 T9D  H5   C22  C27  108.25  3.000
 T9D  H5   C22  C23  109.60  3.000
 T9D  C27  C22  C23  110.18  3.000
 T9D  H5   C22  O21  109.44  3.000
 T9D  C27  C22  O21  107.25  3.000
 T9D  C23  C22  O21  112.03  3.000
 T9D  H7   C24  H6   106.42  3.000
 T9D  H7   C24  N25  108.89  3.000
 T9D  H6   C24  N25  108.23  3.000
 T9D  H7   C24  C23  109.62  3.000
 T9D  H6   C24  C23  109.25  3.000
 T9D  N25  C24  C23  114.13  3.000
 T9D  H9   C26  H8   106.39  3.000
 T9D  H9   C26  C27  109.26  3.000
 T9D  H8   C26  C27  109.77  3.000
 T9D  H9   C26  N25  108.04  3.000
 T9D  H8   C26  N25  108.92  3.000
 T9D  C27  C26  N25  114.17  3.000
 T9D  F4   C2   F3   106.25  3.000
 T9D  F3   C2   F1   107.69  3.000
 T9D  F4   C2   F1   107.44  3.000
 T9D  F1   C2   C5   111.46  3.000
 T9D  F3   C2   C5   110.56  3.000
 T9D  F4   C2   C5   113.15  3.000
 T9D  N9   N8   C7   117.91  3.000
 T9D  H10  N9   N8   114.84  3.000
 T9D  H10  N9   C10  117.34  3.000
 T9D  N8   N9   C10  127.79  3.000
 T9D  C19  C14  C15  119.41  3.000
 T9D  C19  C14  C13  107.68  3.000
 T9D  C15  C14  C13  132.91  3.000
 T9D  H11  C16  C17  117.89  3.000
 T9D  H11  C16  C15  120.25  3.000
 T9D  C17  C16  C15  121.86  3.000
 T9D  H12  C18  C19  119.30  3.000
 T9D  H12  C18  C17  122.62  3.000
 T9D  C19  C18  C17  118.08  3.000
 T9D  C18  C19  C14  120.72  3.000
 T9D  C18  C19  C20  132.18  3.000
 T9D  C14  C19  C20  107.10  3.000
 T9D  C22  O21  C17  120.50  3.000
 T9D  H14  C23  H13  107.04  3.000
 T9D  H14  C23  C24  109.77  3.000
 T9D  H13  C23  C24  109.53  3.000
 T9D  H14  C23  C22  108.92  3.000
 T9D  H13  C23  C22  111.52  3.000
 T9D  C24  C23  C22  110.00  3.000
 T9D  H15  N25  C26  109.19  3.000
 T9D  H15  N25  C24  109.10  3.000
 T9D  C26  N25  C24  111.78  3.000
 T9D  H18  C27  H17  107.49  3.000
 T9D  H18  C27  C26  109.79  3.000
 T9D  H17  C27  C26  109.60  3.000
 T9D  H18  C27  C22  110.28  3.000
 T9D  H17  C27  C22  109.55  3.000
 T9D  C26  C27  C22  110.09  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
 T9D  CONST_01  C15  C14  C13  N12  180.00   0.0  0
 T9D  CONST_02  C19  C14  C13  N12    0.00   0.0  0
 T9D  CONST_03  C14  C19  C20  N12    0.00   0.0  0
 T9D  CONST_04  C18  C19  C20  N12  180.00   0.0  0
 T9D  CONST_05  C16  C15  C14  C13  180.00   0.0  0
 T9D  CONST_06  C18  C19  C14  C13  180.00   0.0  0
 T9D  CONST_07  C20  C19  C14  C13    0.00   0.0  0
 T9D  CONST_08  C19  C20  N12  C13    0.00   0.0  0
 T9D  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 T9D  CONST_10  C18  C19  C14  C15    0.00   0.0  0
 T9D  CONST_11  C20  C19  C14  C15  180.00   0.0  0
 T9D  CONST_12  C14  C15  C16  C17    0.00   0.0  0
 T9D  CONST_13  C14  C19  C18  C17    0.00   0.0  0
 T9D  CONST_14  C20  C19  C18  C17  180.00   0.0  0
 T9D  CONST_15  C14  C13  N12  C20    0.00   0.0  0
 T9D  CONST_16  C19  C14  C15  C16    0.00   0.0  0
 T9D  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 T9D  CONST_18  C14  C13  N12  C6   180.00   0.0  0
 T9D  CONST_19  C19  C20  N12  C6   180.00   0.0  0
 T9D  CONST_20  N8   N9   C10  C5     0.00   0.0  0
 T9D  CONST_21  O21  C17  C16  C15  180.00   0.0  0
 T9D  CONST_22  O21  C17  C18  C19  180.00   0.0  0
 T9D  CONST_23  O11  C10  N9   N8   180.00   0.0  0
 T9D  CONST_24  H2   C13  N12  C6     0.00   0.0  0
 T9D  CONST_25  H4   C20  N12  C6     0.00   0.0  0
 T9D  CONST_26  H3   C15  C14  C13    0.00   0.0  0
 T9D  CONST_27  H12  C18  C19  C20    0.00   0.0  0
 T9D  CONST_28  H11  C16  C15  C14  180.00   0.0  0
 T9D  CONST_29  H10  N9   C10  C5   180.00   0.0  0
 T9D  Var_01    C13  N12  C6   C5   -60.49  30.0  3
 T9D  Var_02    N25  C24  C23  C22   54.40  30.0  1
 T9D  Var_03    N25  C26  C27  C22  -54.43  30.0  1
 T9D  Var_04    C27  C26  N25  C24   52.83  30.0  1
 T9D  Var_05    C23  C24  N25  C26  -52.85  30.0  1
 T9D  Var_06    C16  C17  O21  C22  179.88  30.0  2
 T9D  Var_07    F4   C2   C5   C6   -12.49  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 T9D  chir_01  C22  C23  C27  O21  positiv

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
 T9D  plan-1  C5   0.020
 T9D  plan-1  C6   0.020
 T9D  plan-1  C7   0.020
 T9D  plan-1  C10  0.020
 T9D  plan-1  N12  0.020
 T9D  plan-1  C2   0.020
 T9D  plan-1  N8   0.020
 T9D  plan-1  N9   0.020
 T9D  plan-1  O11  0.020
 T9D  plan-1  H1   0.020
 T9D  plan-1  H10  0.020
 T9D  plan-2  C6   0.020
 T9D  plan-2  N12  0.020
 T9D  plan-2  C13  0.020
 T9D  plan-2  C15  0.020
 T9D  plan-2  C17  0.020
 T9D  plan-2  C20  0.020
 T9D  plan-2  C14  0.020
 T9D  plan-2  C16  0.020
 T9D  plan-2  C18  0.020
 T9D  plan-2  C19  0.020
 T9D  plan-2  O21  0.020
 T9D  plan-2  H2   0.020
 T9D  plan-2  H3   0.020
 T9D  plan-2  H4   0.020
 T9D  plan-2  H11  0.020
 T9D  plan-2  H12  0.020

