# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:02:57 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 1-{1-[4-(4-fluorophenyl)-4-oxobutyl]-1,2,3,6-tetrahydropyridin-4-yl}-1,3-dihydro-2H-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)C(=O)CCCN2CCC(=CC2)N3C(=O)Nc4ccccc34
#
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
 USS  USS  1-{1-[4-(4-fluorophenyl)-4-oxobutyl]-1,2,3,6-tetrahydropyridin-4-yl}-1,3-dihydro-2H-benzimidazol-2-one  ligand  50  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_USS
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
 USS  F01  F  F     0  -0.305  23.1868  -15.7643  33.5410
 USS  C02  C  CR6   0   0.537  22.5385  -14.7435  34.1130
 USS  C03  C  CR16  0  -0.394  22.9550  -14.2925  35.3510
 USS  C04  C  CR16  0  -0.275  22.2730  -13.2354  35.9339
 USS  C05  C  CR6   0  -0.020  21.1909  -12.6364  35.2887
 USS  C06  C  C     0   0.382  20.4296  -11.4994  35.8814
 USS  C07  C  CH2   0  -0.590  20.8399  -10.9799  37.2374
 USS  C08  C  CH2   0  -0.434  19.9672   -9.8408  37.7401
 USS  C09  C  CH2   0  -0.255  20.4137   -9.3531  39.1117
 USS  N10  N  NT    0  -0.433  19.5902   -8.2619  39.6024
 USS  C11  C  CH2   0  -0.301  19.8798   -6.9910  38.9643
 USS  C12  C  CH2   0  -0.490  18.7826   -5.9848  39.2737
 USS  C13  C  C     0   0.282  18.4705   -5.9994  40.7373
 USS  N14  N  NR5   0  -0.664  17.6897   -4.9267  41.2401
 USS  C15  C  CR56  0   0.319  16.3112   -4.8342  41.1623
 USS  C16  C  CR16  0  -0.313  15.3562   -5.7339  40.7320
 USS  C17  C  CR16  0  -0.272  14.0247   -5.3272  40.7878
 USS  C18  C  CR16  0  -0.274  13.6743   -4.0675  41.2643
 USS  C19  C  CR16  0  -0.310  14.6414   -3.1639  41.7006
 USS  C20  C  CR56  0   0.327  15.9609   -3.5673  41.6388
 USS  N21  N  NR15  0  -0.748  17.1394   -2.9364  41.9737
 USS  C22  C  CR5   0   0.633  18.2187   -3.7439  41.7206
 USS  O23  O  O     0  -0.485  19.3956   -3.4872  41.8804
 USS  C24  C  C1    0  -0.278  18.8925   -6.9630  41.5456
 USS  C25  C  CH2   0  -0.302  19.6650   -8.1385  41.0428
 USS  O26  O  O     0  -0.393  19.4995  -11.0109  35.2751
 USS  C27  C  CR16  0  -0.242  20.8030  -13.1213  34.0377
 USS  C28  C  CR16  0  -0.397  21.4702  -14.1752  33.4419
 USS  H1   H  HCR6  0   0.287  23.7943  -14.7561  35.8522
 USS  H2   H  HCR6  0   0.276  22.6024  -12.8873  36.9038
 USS  H3   H  HCH2  0   0.271  20.8296  -11.8147  37.9471
 USS  H4   H  HCH2  0   0.273  21.8880  -10.6634  37.1853
 USS  H5   H  HCH2  0   0.233  19.9940   -9.0225  37.0180
 USS  H6   H  HCH2  0   0.230  18.9266  -10.1647  37.8079
 USS  H7   H  HCH2  0   0.232  20.3281  -10.1828  39.8193
 USS  H8   H  HCH2  0   0.196  21.4823   -9.0794  39.0899
 USS  H10  H  HCH2  0   0.247  19.9468   -7.1276  37.8854
 USS  H11  H  HCH2  0   0.205  20.8522   -6.5860  39.2928
 USS  H12  H  HCH2  0   0.250  19.1053   -4.9839  38.9752
 USS  H13  H  HCH2  0   0.251  17.8817   -6.2081  38.6933
 USS  H15  H  HCR6  0   0.268  15.6298   -6.7146  40.3650
 USS  H16  H  HCR6  0   0.254  13.2510   -6.0062  40.4550
 USS  H17  H  HCR6  0   0.254  12.6317   -3.7805  41.2974
 USS  H18  H  HCR6  0   0.267  14.3684   -2.1844  42.0707
 USS  H19  H  HNR5  0   0.417  17.2256   -2.0030  42.3435
 USS  H20  H  H     0   0.265  18.6766   -6.9234  42.6068
 USS  H22  H  HCH2  0   0.253  19.2602   -9.0462  41.5004
 USS  H24  H  HCR6  0   0.271  19.9665  -12.6706  33.5212
 USS  H25  H  HCR6  0   0.285  21.1676  -14.5513  32.4735
 USS  H9   H  HCH2  0   0.214  20.7049   -8.0548  41.4085

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
 USS  F01  C02  single    1.338  0.020  1.338
 USS  C28  C02  aromatic  1.384  0.020  1.384
 USS  C28  C27  aromatic  1.382  0.020  1.382
 USS  C02  C03  aromatic  1.382  0.020  1.382
 USS  C27  C05  aromatic  1.397  0.020  1.397
 USS  C03  C04  aromatic  1.386  0.020  1.386
 USS  C05  C04  aromatic  1.395  0.020  1.395
 USS  C05  C06  single    1.491  0.020  1.491
 USS  C06  O26  double    1.213  0.020  1.213
 USS  C06  C07  single    1.509  0.020  1.509
 USS  C07  C08  single    1.521  0.020  1.521
 USS  C08  C09  single    1.523  0.020  1.523
 USS  C11  C12  single    1.520  0.020  1.520
 USS  C11  N10  single    1.451  0.020  1.451
 USS  C12  C13  single    1.497  0.020  1.497
 USS  C17  C16  aromatic  1.393  0.020  1.393
 USS  C17  C18  aromatic  1.392  0.020  1.392
 USS  C09  N10  single    1.452  0.020  1.452
 USS  C16  C15  aromatic  1.381  0.020  1.381
 USS  N10  C25  single    1.448  0.020  1.448
 USS  C18  C19  aromatic  1.394  0.020  1.394
 USS  C13  N14  single    1.419  0.020  1.419
 USS  C13  C24  double    1.327  0.020  1.327
 USS  C15  N14  single    1.384  0.020  1.384
 USS  C15  C20  aromatic  1.398  0.020  1.398
 USS  N14  C22  single    1.382  0.020  1.382
 USS  C25  C24  single    1.494  0.020  1.494
 USS  C19  C20  aromatic  1.381  0.020  1.381
 USS  C20  N21  single    1.378  0.020  1.378
 USS  C22  N21  single    1.371  0.020  1.371
 USS  C22  O23  double    1.215  0.020  1.215
 USS  C03  H1   single    0.930  0.020  1.080
 USS  C04  H2   single    0.930  0.020  1.080
 USS  C07  H3   single    0.970  0.020  1.090
 USS  C07  H4   single    0.970  0.020  1.090
 USS  C08  H5   single    0.970  0.020  1.090
 USS  C08  H6   single    0.970  0.020  1.090
 USS  C09  H7   single    0.970  0.020  1.090
 USS  C09  H8   single    0.970  0.020  1.090
 USS  C11  H10  single    0.970  0.020  1.090
 USS  C11  H11  single    0.970  0.020  1.090
 USS  C12  H12  single    0.970  0.020  1.090
 USS  C12  H13  single    0.970  0.020  1.090
 USS  C16  H15  single    0.930  0.020  1.080
 USS  C17  H16  single    0.930  0.020  1.080
 USS  C18  H17  single    0.930  0.020  1.080
 USS  C19  H18  single    0.930  0.020  1.080
 USS  N21  H19  single    0.860  0.020  1.020
 USS  C24  H20  single    0.930  0.020  1.080
 USS  C25  H22  single    0.970  0.020  1.090
 USS  C27  H24  single    0.930  0.020  1.080
 USS  C28  H25  single    0.930  0.020  1.080
 USS  C25  H9   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
 USS  C28  C02  C03  122.22  3.000
 USS  C03  C02  F01  119.09  3.000
 USS  C28  C02  F01  118.70  3.000
 USS  H1   C03  C04  120.90  3.000
 USS  H1   C03  C02  120.59  3.000
 USS  C04  C03  C02  118.51  3.000
 USS  H2   C04  C05  120.84  3.000
 USS  H2   C04  C03  118.20  3.000
 USS  C05  C04  C03  120.96  3.000
 USS  C27  C05  C06  118.62  3.000
 USS  C06  C05  C04  122.65  3.000
 USS  C27  C05  C04  118.73  3.000
 USS  O26  C06  C07  121.27  3.000
 USS  C07  C06  C05  118.74  3.000
 USS  O26  C06  C05  119.99  3.000
 USS  H4   C07  H3   105.06  3.000
 USS  H4   C07  C08  110.38  3.000
 USS  H3   C07  C08  110.56  3.000
 USS  H4   C07  C06  108.46  3.000
 USS  H3   C07  C06  108.49  3.000
 USS  C08  C07  C06  113.51  3.000
 USS  H6   C08  H5   106.67  3.000
 USS  H6   C08  C09  108.57  3.000
 USS  H5   C08  C09  110.40  3.000
 USS  H6   C08  C07  110.20  3.000
 USS  H5   C08  C07  109.19  3.000
 USS  C09  C08  C07  111.68  3.000
 USS  H8   C09  H7   106.07  3.000
 USS  H8   C09  N10  111.68  3.000
 USS  H7   C09  N10  107.87  3.000
 USS  H8   C09  C08  110.22  3.000
 USS  H7   C09  C08  108.47  3.000
 USS  N10  C09  C08  112.25  3.000
 USS  C25  N10  C11  110.64  3.000
 USS  C25  N10  C09  111.77  3.000
 USS  C11  N10  C09  113.34  3.000
 USS  H11  C11  H10  106.66  3.000
 USS  H11  C11  C12  109.42  3.000
 USS  H10  C11  C12  109.20  3.000
 USS  H11  C11  N10  111.49  3.000
 USS  H10  C11  N10  109.74  3.000
 USS  C12  C11  N10  110.24  3.000
 USS  H13  C12  H12  106.55  3.000
 USS  H13  C12  C13  110.17  3.000
 USS  H12  C12  C13  109.72  3.000
 USS  H13  C12  C11  110.55  3.000
 USS  H12  C12  C11  109.71  3.000
 USS  C13  C12  C11  110.06  3.000
 USS  C24  C13  N14  120.55  3.000
 USS  C24  C13  C12  122.45  3.000
 USS  N14  C13  C12  117.00  3.000
 USS  C22  N14  C15  110.10  3.000
 USS  C22  N14  C13  124.03  3.000
 USS  C15  N14  C13  125.37  3.000
 USS  C20  C15  C16  121.56  3.000
 USS  C20  C15  N14  106.92  3.000
 USS  C16  C15  N14  131.53  3.000
 USS  H15  C16  C17  121.31  3.000
 USS  H15  C16  C15  121.42  3.000
 USS  C17  C16  C15  117.28  3.000
 USS  H16  C17  C18  119.56  3.000
 USS  H16  C17  C16  119.21  3.000
 USS  C18  C17  C16  121.23  3.000
 USS  H17  C18  C19  119.16  3.000
 USS  H17  C18  C17  119.55  3.000
 USS  C19  C18  C17  121.29  3.000
 USS  H18  C19  C20  121.38  3.000
 USS  H18  C19  C18  121.26  3.000
 USS  C20  C19  C18  117.36  3.000
 USS  N21  C20  C19  132.25  3.000
 USS  N21  C20  C15  106.46  3.000
 USS  C19  C20  C15  121.29  3.000
 USS  H19  N21  C22  123.08  3.000
 USS  H19  N21  C20  125.90  3.000
 USS  C22  N21  C20  111.02  3.000
 USS  O23  C22  N21  127.85  3.000
 USS  O23  C22  N14  126.67  3.000
 USS  N21  C22  N14  105.48  3.000
 USS  H20  C24  C25  117.48  3.000
 USS  H20  C24  C13  120.45  3.000
 USS  C25  C24  C13  122.07  3.000
 USS  H9   C25  H22  105.81  3.000
 USS  H9   C25  C24  108.39  3.000
 USS  H22  C25  C24  108.71  3.000
 USS  H9   C25  N10  112.60  3.000
 USS  H22  C25  N10  109.04  3.000
 USS  C24  C25  N10  112.04  3.000
 USS  H24  C27  C28  119.02  3.000
 USS  H24  C27  C05  119.86  3.000
 USS  C28  C27  C05  121.12  3.000
 USS  H25  C28  C27  121.05  3.000
 USS  H25  C28  C02  120.48  3.000
 USS  C27  C28  C02  118.47  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
 USS  CONST_01  C05  C27  C28  C02     0.00   0.0  0
 USS  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 USS  CONST_03  C27  C28  C02  C03     0.00   0.0  0
 USS  CONST_04  C27  C05  C04  C03     0.00   0.0  0
 USS  CONST_05  C28  C02  C03  C04     0.00   0.0  0
 USS  CONST_06  C28  C27  C05  C04     0.00   0.0  0
 USS  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 USS  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 USS  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 USS  CONST_10  C19  C20  C15  C16     0.00   0.0  0
 USS  CONST_11  C20  C15  C16  C17     0.00   0.0  0
 USS  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 USS  CONST_13  C20  C15  N14  C13   180.00   0.0  0
 USS  CONST_14  N21  C22  N14  C13   180.00   0.0  0
 USS  CONST_15  N21  C20  C15  N14     0.00   0.0  0
 USS  CONST_16  C20  N21  C22  N14     0.00   0.0  0
 USS  CONST_17  N21  C22  N14  C15     0.00   0.0  0
 USS  CONST_18  C22  N21  C20  C15     0.00   0.0  0
 USS  CONST_19  C22  N14  C15  C20     0.00   0.0  0
 USS  CONST_20  C27  C28  C02  F01   180.00   0.0  0
 USS  CONST_21  C04  C03  C02  F01   180.00   0.0  0
 USS  CONST_22  C06  C05  C04  C03   180.00   0.0  0
 USS  CONST_23  C28  C27  C05  C06   180.00   0.0  0
 USS  CONST_24  O23  C22  N14  C13     0.00   0.0  0
 USS  CONST_25  O23  C22  N14  C15   180.00   0.0  0
 USS  CONST_26  O23  C22  N21  C20   180.00   0.0  0
 USS  CONST_27  H24  C27  C28  C02   180.00   0.0  0
 USS  CONST_28  H2   C04  C03  C02   180.00   0.0  0
 USS  CONST_29  H25  C28  C02  C03   180.00   0.0  0
 USS  CONST_30  H1   C03  C04  C05   180.00   0.0  0
 USS  CONST_31  H15  C16  C15  N14     0.00   0.0  0
 USS  CONST_32  H16  C17  C16  C15   180.00   0.0  0
 USS  CONST_33  H18  C19  C20  C15   180.00   0.0  0
 USS  CONST_34  H17  C18  C17  C16   180.00   0.0  0
 USS  CONST_35  H19  N21  C22  N14   180.00   0.0  0
 USS  Var_01    C13  C12  C11  N10    47.20  30.0  1
 USS  Var_02    C13  C24  C25  N10   -14.61  30.0  1
 USS  Var_03    N14  C13  C12  C11   166.48  30.0  1
 USS  Var_04    C24  C25  N10  C11    48.90  30.0  1
 USS  Var_05    C25  N10  C11  C12   -66.97  30.0  1
 USS  Var_06    C15  N14  C13  C12    81.23  30.0  2
 USS  Var_07    C25  C24  C13  C12    -2.61  30.0  1
 USS  Var_08    O26  C06  C05  C04   179.68  30.0  2
 USS  Var_09    C11  N10  C09  C08   -75.89  30.0  3
 USS  Var_10    C08  C07  C06  C05  -178.81  30.0  3
 USS  Var_11    N10  C09  C08  C07   179.84  30.0  3
 USS  Var_12    C09  C08  C07  C06   179.77  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
 USS  plan-1  F01  0.020
 USS  plan-1  C02  0.020
 USS  plan-1  C03  0.020
 USS  plan-1  C04  0.020
 USS  plan-1  C05  0.020
 USS  plan-1  C06  0.020
 USS  plan-1  C27  0.020
 USS  plan-1  C28  0.020
 USS  plan-1  H1   0.020
 USS  plan-1  H2   0.020
 USS  plan-1  H24  0.020
 USS  plan-1  H25  0.020
 USS  plan-2  C13  0.020
 USS  plan-2  N14  0.020
 USS  plan-2  C15  0.020
 USS  plan-2  C16  0.020
 USS  plan-2  C17  0.020
 USS  plan-2  C18  0.020
 USS  plan-2  C19  0.020
 USS  plan-2  C20  0.020
 USS  plan-2  N21  0.020
 USS  plan-2  C22  0.020
 USS  plan-2  O23  0.020
 USS  plan-2  H15  0.020
 USS  plan-2  H16  0.020
 USS  plan-2  H17  0.020
 USS  plan-2  H18  0.020
 USS  plan-2  H19  0.020
 USS  plan-3  C05  0.020
 USS  plan-3  C06  0.020
 USS  plan-3  C07  0.020
 USS  plan-3  O26  0.020

