# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:32:47 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: (5~{S})-5-[3-[(3~{S})-4-[3,5-bis(fluoranyl)phenyl]-3-methyl-piperazin-1-yl]-3-oxidanylidene-propyl]-5-cyclopropyl-imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(CCN1c2cc(F)cc(F)c2)C(=O)CC[C@]3(NC(=O)NC3=O)C4CC4
#
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
 OU5  OU5  (5~{S})-5-[3-[(3~{S})-4-[3,5-bis(fluoranyl)phenyl]-3-methyl-piperazin-1-yl]-3-oxidanylidene-propyl]-5-cyclopropyl-imidazolidine-2,4-dione  ligand  53  29  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OU5
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
 OU5  C14  C  C     0   0.554  19.5313  -6.5973   1.5774
 OU5  C2   C  CH2   0  -0.411  19.1966  -8.1261   3.5672
 OU5  C6   C  CR5   0   0.664  16.4489  -6.1363   3.0319
 OU5  C19  C  CH1   0  -0.122  18.2409  -6.9206  -1.6737
 OU5  C13  C  CH2   0  -0.483  16.9551  -6.9993   6.5479
 OU5  C11  C  CH1   0  -0.214  17.8878  -7.7713   5.6709
 OU5  C16  C  CH2   0  -0.320  19.0676  -4.7722   0.0329
 OU5  C1   C  CH2   0  -0.599  19.2959  -8.0217   2.0475
 OU5  C12  C  CH2   0  -0.485  18.4261  -6.7080   6.5730
 OU5  C17  C  CH2   0  -0.313  19.5531  -4.8611  -1.4048
 OU5  C20  C  CH2   0  -0.325  17.7817  -6.7625  -0.2282
 OU5  C22  C  CR6   0   0.423  18.6485  -5.4582  -3.5882
 OU5  C23  C  CR16  0  -0.544  19.6867  -4.7624  -4.2243
 OU5  C24  C  CR6   0   0.574  19.6540  -4.6033  -5.5957
 OU5  C25  C  CR16  0  -0.598  18.6521  -5.1011  -6.4025
 OU5  C26  C  CR6   0   0.563  17.6468  -5.7883  -5.7450
 OU5  C27  C  CR16  0  -0.513  17.6155  -5.9814  -4.3841
 OU5  C3   C  CR5   0  -0.021  17.8882  -7.5950   4.1621
 OU5  C30  C  CH3   0  -0.663  19.3664  -7.9417  -1.8101
 OU5  C4   C  CR5   0   0.576  16.6847  -8.3465   3.5924
 OU5  F28  F  F     0  -0.313  16.6350  -6.2787  -6.4749
 OU5  F29  F  F     0  -0.313  20.6674  -3.9467  -6.1789
 OU5  N15  N  NT    0  -0.458  18.7927  -6.0935   0.5627
 OU5  N18  N  NT    0  -0.524  18.6067  -5.6074  -2.2139
 OU5  N5   N  NR15  0  -0.696  15.9066  -7.4196   2.9732
 OU5  N7   N  NR15  0  -0.674  17.5885  -6.2453   3.7460
 OU5  O21  O  O     0  -0.497  20.4078  -5.9370   2.1229
 OU5  O8   O  O     0  -0.420  16.4732  -9.5305   3.6878
 OU5  O9   O  O     0  -0.464  15.9646  -5.1499   2.5265
 OU5  H1   H  HCH2  0   0.259  19.2930  -9.1736   3.8585
 OU5  H2   H  HCH2  0   0.262  20.0275  -7.5970   4.0363
 OU5  H3   H  HCH1  0   0.271  17.3723  -7.2868  -2.2198
 OU5  H4   H  HCH2  0   0.252  16.3067  -6.2608   6.0922
 OU5  H5   H  HCH2  0   0.257  16.5170  -7.5163   7.3913
 OU5  H6   H  HCH1  0   0.270  18.0872  -8.7953   5.9674
 OU5  H7   H  HCH2  0   0.274  19.8133  -4.2708   0.6421
 OU5  H8   H  HCH2  0   0.249  18.1465  -4.1830   0.0714
 OU5  H9   H  HCH2  0   0.263  18.4488  -8.5177   1.5784
 OU5  H10  H  HCH2  0   0.293  20.1739  -8.5884   1.7249
 OU5  H11  H  HCH2  0   0.260  19.0019  -7.0237   7.4331
 OU5  H12  H  HCH2  0   0.249  18.7617  -5.7750   6.1374
 OU5  H13  H  HCH2  0   0.232  20.5621  -5.2940  -1.4291
 OU5  H14  H  HCH2  0   0.266  19.6278  -3.8438  -1.7906
 OU5  H15  H  HCH2  0   0.264  16.8703  -6.1579  -0.2057
 OU5  H16  H  HCH2  0   0.272  17.5296  -7.7374   0.1758
 OU5  H17  H  HCR6  0   0.290  20.5296  -4.3674  -3.6756
 OU5  H18  H  HCR6  0   0.293  18.6521  -4.9639  -7.4751
 OU5  H19  H  HCR6  0   0.286  16.7710  -6.4984  -3.9503
 OU5  H20  H  HCH3  0   0.238  19.0395  -8.9142  -1.4402
 OU5  H21  H  HCH3  0   0.242  19.6563  -8.0635  -2.8544
 OU5  H22  H  HCH3  0   0.233  20.2549  -7.6529  -1.2476
 OU5  H23  H  HNR5  0   0.425  15.0342  -7.6224   2.5048
 OU5  H24  H  HNR5  0   0.413  18.2157  -5.4657   3.8663

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
 OU5  F28  C26  single    1.341  0.020  1.341
 OU5  C25  C26  aromatic  1.384  0.020  1.384
 OU5  C25  C24  aromatic  1.379  0.020  1.379
 OU5  F29  C24  single    1.341  0.020  1.341
 OU5  C26  C27  aromatic  1.375  0.020  1.375
 OU5  C24  C23  aromatic  1.381  0.020  1.381
 OU5  C27  C22  aromatic  1.405  0.020  1.405
 OU5  C23  C22  aromatic  1.402  0.020  1.402
 OU5  C22  N18  single    1.383  0.020  1.383
 OU5  N18  C19  single    1.466  0.020  1.466
 OU5  N18  C17  single    1.452  0.020  1.452
 OU5  C30  C19  single    1.526  0.020  1.526
 OU5  C19  C20  single    1.525  0.020  1.525
 OU5  C17  C16  single    1.520  0.020  1.520
 OU5  C20  N15  single    1.448  0.020  1.448
 OU5  C16  N15  single    1.450  0.020  1.450
 OU5  N15  C14  single    1.352  0.020  1.352
 OU5  C14  C1   single    1.518  0.020  1.518
 OU5  C14  O21  double    1.225  0.020  1.225
 OU5  C1   C2   single    1.527  0.020  1.527
 OU5  N5   C6   single    1.394  0.020  1.394
 OU5  N5   C4   single    1.359  0.020  1.359
 OU5  O9   C6   double    1.210  0.020  1.210
 OU5  C6   N7   single    1.349  0.020  1.349
 OU5  O8   C4   double    1.207  0.020  1.207
 OU5  C2   C3   single    1.532  0.020  1.532
 OU5  C4   C3   single    1.529  0.020  1.529
 OU5  N7   C3   single    1.444  0.020  1.444
 OU5  C3   C11  single    1.519  0.020  1.519
 OU5  C11  C13  single    1.495  0.020  1.495
 OU5  C11  C12  single    1.495  0.020  1.495
 OU5  C13  C12  single    1.500  0.020  1.500
 OU5  C2   H1   single    0.970  0.020  1.090
 OU5  C2   H2   single    0.970  0.020  1.090
 OU5  C19  H3   single    0.970  0.020  1.090
 OU5  C13  H4   single    0.970  0.020  1.090
 OU5  C13  H5   single    0.970  0.020  1.090
 OU5  C11  H6   single    0.970  0.020  1.090
 OU5  C16  H7   single    0.970  0.020  1.090
 OU5  C16  H8   single    0.970  0.020  1.090
 OU5  C1   H9   single    0.970  0.020  1.090
 OU5  C1   H10  single    0.970  0.020  1.090
 OU5  C12  H11  single    0.970  0.020  1.090
 OU5  C12  H12  single    0.970  0.020  1.090
 OU5  C17  H13  single    0.970  0.020  1.090
 OU5  C17  H14  single    0.970  0.020  1.090
 OU5  C20  H15  single    0.970  0.020  1.090
 OU5  C20  H16  single    0.970  0.020  1.090
 OU5  C23  H17  single    0.930  0.020  1.080
 OU5  C25  H18  single    0.930  0.020  1.080
 OU5  C27  H19  single    0.930  0.020  1.080
 OU5  C30  H20  single    0.970  0.020  1.090
 OU5  C30  H21  single    0.970  0.020  1.090
 OU5  C30  H22  single    0.970  0.020  1.090
 OU5  N5   H23  single    0.860  0.020  1.020
 OU5  N7   H24  single    0.860  0.020  1.020

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
 OU5  O21  C14  N15  121.59  3.000
 OU5  O21  C14  C1   118.59  3.000
 OU5  N15  C14  C1   119.81  3.000
 OU5  H2   C2   H1   106.47  3.000
 OU5  H2   C2   C3   108.38  3.000
 OU5  H1   C2   C3   107.73  3.000
 OU5  H2   C2   C1   110.20  3.000
 OU5  H1   C2   C1   109.00  3.000
 OU5  C3   C2   C1   114.73  3.000
 OU5  O9   C6   N7   128.70  3.000
 OU5  N7   C6   N5   106.05  3.000
 OU5  O9   C6   N5   125.25  3.000
 OU5  H3   C19  N18  108.38  3.000
 OU5  H3   C19  C30  108.57  3.000
 OU5  N18  C19  C30  112.48  3.000
 OU5  H3   C19  C20  105.66  3.000
 OU5  C30  C19  C20  112.10  3.000
 OU5  N18  C19  C20  109.36  3.000
 OU5  H5   C13  H4   114.29  3.000
 OU5  H5   C13  C12  118.48  3.000
 OU5  H4   C13  C12  117.50  3.000
 OU5  H5   C13  C11  117.59  3.000
 OU5  H4   C13  C11  118.60  3.000
 OU5  C12  C13  C11   59.88  3.000
 OU5  H6   C11  C3   112.40  3.000
 OU5  H6   C11  C12  116.13  3.000
 OU5  C3   C11  C12  121.12  3.000
 OU5  H6   C11  C13  116.23  3.000
 OU5  C12  C11  C13   60.22  3.000
 OU5  C3   C11  C13  121.53  3.000
 OU5  H8   C16  H7   108.04  3.000
 OU5  H8   C16  N15  108.56  3.000
 OU5  H7   C16  N15  110.24  3.000
 OU5  H8   C16  C17  109.49  3.000
 OU5  H7   C16  C17  109.78  3.000
 OU5  N15  C16  C17  110.66  3.000
 OU5  H10  C1   H9   105.17  3.000
 OU5  H10  C1   C2   108.08  3.000
 OU5  H9   C1   C2   110.33  3.000
 OU5  H10  C1   C14  105.68  3.000
 OU5  H9   C1   C14  114.52  3.000
 OU5  C2   C1   C14  112.49  3.000
 OU5  H12  C12  H11  113.97  3.000
 OU5  H12  C12  C11  118.79  3.000
 OU5  H11  C12  C11  117.63  3.000
 OU5  H12  C12  C13  117.68  3.000
 OU5  H11  C12  C13  118.59  3.000
 OU5  C11  C12  C13   59.90  3.000
 OU5  H14  C17  H13  107.27  3.000
 OU5  H14  C17  N18  109.09  3.000
 OU5  H13  C17  N18  112.59  3.000
 OU5  H14  C17  C16  107.57  3.000
 OU5  H13  C17  C16  109.72  3.000
 OU5  N18  C17  C16  110.43  3.000
 OU5  H16  C20  H15  107.18  3.000
 OU5  H16  C20  N15  111.97  3.000
 OU5  H15  C20  N15  108.38  3.000
 OU5  H16  C20  C19  109.26  3.000
 OU5  H15  C20  C19  109.12  3.000
 OU5  N15  C20  C19  110.83  3.000
 OU5  N18  C22  C27  120.03  3.000
 OU5  N18  C22  C23  121.78  3.000
 OU5  C27  C22  C23  118.17  3.000
 OU5  H17  C23  C24  118.73  3.000
 OU5  H17  C23  C22  121.91  3.000
 OU5  C24  C23  C22  119.35  3.000
 OU5  F29  C24  C25  118.11  3.000
 OU5  F29  C24  C23  118.06  3.000
 OU5  C25  C24  C23  123.81  3.000
 OU5  H18  C25  C26  122.30  3.000
 OU5  H18  C25  C24  122.30  3.000
 OU5  C26  C25  C24  115.40  3.000
 OU5  F28  C26  C27  118.05  3.000
 OU5  C27  C26  C25  123.82  3.000
 OU5  F28  C26  C25  118.12  3.000
 OU5  H19  C27  C26  118.83  3.000
 OU5  H19  C27  C22  121.68  3.000
 OU5  C26  C27  C22  119.44  3.000
 OU5  N7   C3   C4   100.88  3.000
 OU5  N7   C3   C11  113.24  3.000
 OU5  C4   C3   C11  108.23  3.000
 OU5  C11  C3   C2   110.22  3.000
 OU5  N7   C3   C2   112.92  3.000
 OU5  C4   C3   C2   110.93  3.000
 OU5  H22  C30  H21  107.87  3.000
 OU5  H22  C30  H20  107.78  3.000
 OU5  H21  C30  H20  107.75  3.000
 OU5  H22  C30  C19  112.19  3.000
 OU5  H21  C30  C19  110.88  3.000
 OU5  H20  C30  C19  110.20  3.000
 OU5  O8   C4   N5   127.21  3.000
 OU5  O8   C4   C3   126.22  3.000
 OU5  N5   C4   C3   106.57  3.000
 OU5  C20  N15  C16  110.73  3.000
 OU5  C16  N15  C14  120.67  3.000
 OU5  C20  N15  C14  128.26  3.000
 OU5  C22  N18  C17  118.60  3.000
 OU5  C17  N18  C19  114.69  3.000
 OU5  C22  N18  C19  118.05  3.000
 OU5  H23  N5   C4   124.64  3.000
 OU5  H23  N5   C6   122.67  3.000
 OU5  C4   N5   C6   112.68  3.000
 OU5  H24  N7   C3   124.03  3.000
 OU5  H24  N7   C6   121.76  3.000
 OU5  C3   N7   C6   113.78  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
 OU5  CONST_01  C25  C26  C27  C22     0.00   0.0  0
 OU5  CONST_02  C25  C24  C23  C22     0.00   0.0  0
 OU5  CONST_03  C26  C25  C24  C23     0.00   0.0  0
 OU5  CONST_04  C26  C27  C22  C23     0.00   0.0  0
 OU5  CONST_05  C27  C26  C25  C24     0.00   0.0  0
 OU5  CONST_06  C27  C22  C23  C24     0.00   0.0  0
 OU5  CONST_07  N18  C22  C23  C24   180.00   0.0  0
 OU5  CONST_08  N18  C22  C27  C26   180.00   0.0  0
 OU5  CONST_09  C3   C4   N5   C6      0.00   0.0  0
 OU5  CONST_10  N5   C6   N7   C3      0.00   0.0  0
 OU5  CONST_11  N7   C6   N5   C4      0.00   0.0  0
 OU5  CONST_12  F28  C26  C27  C22   180.00   0.0  0
 OU5  CONST_13  F29  C24  C23  C22   180.00   0.0  0
 OU5  CONST_14  F28  C26  C25  C24   180.00   0.0  0
 OU5  CONST_15  F29  C24  C25  C26   180.00   0.0  0
 OU5  CONST_16  O9   C6   N7   C3    180.00   0.0  0
 OU5  CONST_17  O9   C6   N5   C4    180.00   0.0  0
 OU5  CONST_18  H18  C25  C24  C23   180.00   0.0  0
 OU5  CONST_19  H19  C27  C22  C23   180.00   0.0  0
 OU5  CONST_20  H17  C23  C24  C25   180.00   0.0  0
 OU5  CONST_21  H23  N5   C4   C3    180.00   0.0  0
 OU5  CONST_22  H24  N7   C6   N5    180.00   0.0  0
 OU5  CONST_23  C1   C14  N15  C16   180.00   0.0  0
 OU5  CONST_24  O21  C14  N15  C16     0.00   0.0  0
 OU5  CONST_25  C20  N15  C14  C1      0.00   0.0  0
 OU5  CONST_26  O21  C14  N15  C20   180.00   0.0  0
 OU5  Var_01    C27  C22  N18  C19    44.65  30.0  2
 OU5  Var_02    C16  C17  N18  C19   -52.23  30.0  1
 OU5  Var_03    C16  N15  C20  C19    60.16  30.0  1
 OU5  Var_04    C3   C11  C12  C13   110.99  30.0  1
 OU5  Var_05    C20  N15  C16  C17   -59.38  30.0  1
 OU5  Var_06    N18  C17  C16  N15    54.31  30.0  1
 OU5  Var_07    C3   C2   C1   C14    73.91  30.0  3
 OU5  Var_08    N15  C14  C1   C2   -133.00  30.0  1

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
 OU5  chir_01  C19  N18  C30  C20  negativ
 OU5  chir_03  C3   C4   N7   C11  negativ
 OU5  chir_04  C11  C3   C13  C12  both

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
 OU5  plan-1  C14  0.020
 OU5  plan-1  C16  0.020
 OU5  plan-1  C1   0.020
 OU5  plan-1  C20  0.020
 OU5  plan-1  N15  0.020
 OU5  plan-1  O21  0.020
 OU5  plan-2  C22  0.020
 OU5  plan-2  C23  0.020
 OU5  plan-2  C24  0.020
 OU5  plan-2  C25  0.020
 OU5  plan-2  C26  0.020
 OU5  plan-2  C27  0.020
 OU5  plan-2  F28  0.020
 OU5  plan-2  F29  0.020
 OU5  plan-2  N18  0.020
 OU5  plan-2  H17  0.020
 OU5  plan-2  H18  0.020
 OU5  plan-2  H19  0.020
 OU5  plan-3  C6   0.020
 OU5  plan-3  C3   0.020
 OU5  plan-3  C4   0.020
 OU5  plan-3  N5   0.020
 OU5  plan-3  N7   0.020
 OU5  plan-3  O8   0.020
 OU5  plan-3  O9   0.020
 OU5  plan-3  H23  0.020
 OU5  plan-3  H24  0.020

