# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 11:51:06 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (5S)-5-[([1,1'-biphenyl]-4-yl)methyl]-4-methoxy-1,5-dihydro-2H-pyrrol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=CC(=O)N[C@H]1Cc2ccc(cc2)c3ccccc3
#
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
 84H  84H  "(5S)-5-[([1,1'-biphenyl]-4-yl)methyl]-4-methoxy-1,5-dihydro-2H-pyrrol-2-one"
  ligand  38  21  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_84H
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
 84H  C1   C  CR5   0   0.376  36.8652  109.2900  19.0165
 84H  C2   C  CR15  0  -0.508  35.6991  109.2949  19.6805
 84H  C3   C  CR5   0   0.520  34.6427  109.6715  18.7301
 84H  C4   C  CR15  0  -0.104  36.6770  109.6918  17.5806
 84H  C6   C  CR6   0   0.118  37.1231  112.1345  18.1082
 84H  C7   C  CR16  0  -0.286  36.0090  112.9357  17.8733
 84H  C9   C  CR6   0   0.073  36.4717  114.2647  19.8433
 84H  C10  C  CR16  0  -0.294  37.5943  113.4684  20.0718
 84H  C11  C  CR16  0  -0.284  37.9123  112.4228  19.2192
 84H  C13  C  CR16  0  -0.310  35.6290  116.5821  20.2605
 84H  C14  C  CR16  0  -0.238  35.3090  117.6243  21.1186
 84H  C15  C  CR16  0  -0.265  35.4854  117.4823  22.4885
 84H  N    N  NR15  0  -0.662  35.2491  109.8404  17.5245
 84H  O1   O  O     0  -0.491  33.4488  109.8001  18.9513
 84H  O    O  O2    0  -0.435  38.0949  109.0212  19.4090
 84H  C    C  CH3   0  -0.433  38.2671  108.7055  20.7844
 84H  C5   C  CH2   0  -0.531  37.4452  110.9744  17.2119
 84H  C8   C  CR16  0  -0.295  35.6867  113.9810  18.7252
 84H  C12  C  CR6   0   0.088  36.1307  115.3765  20.7546
 84H  C17  C  CR16  0  -0.310  36.3032  115.2465  22.1343
 84H  C16  C  CR16  0  -0.238  35.9835  116.2882  22.9929
 84H  H1   H  HCR5  0   0.280  35.5133  109.0676  20.7188
 84H  H2   H  HCR5  0   0.288  37.0178  108.8877  16.9179
 84H  H3   H  HCR6  0   0.248  35.3785  112.7435  17.0134
 84H  H4   H  HCR6  0   0.251  38.2434  113.6777  20.9131
 84H  H5   H  HCR6  0   0.250  38.7974  111.8302  19.4171
 84H  H7   H  HCR6  0   0.255  34.9280  118.5532  20.7140
 84H  H8   H  HCR6  0   0.255  35.2363  118.2955  23.1578
 84H  H61  H  HCH3  0   0.263  39.3270  108.5216  20.9345
 84H  H62  H  HCH3  0   0.238  37.9485  109.5365  21.4169
 84H  H63  H  HCH3  0   0.240  37.7019  107.8115  21.0555
 84H  H64  H  HCH2  0   0.265  38.5132  110.7516  17.2415
 84H  H65  H  HCH2  0   0.271  37.2065  111.2153  16.1736
 84H  H66  H  HCR6  0   0.250  34.8010  114.5708  18.5226
 84H  H67  H  HCR6  0   0.252  36.6727  114.3148  22.5449
 84H  H68  H  HCR6  0   0.255  36.1194  116.1640  24.0596
 84H  H9   H  HNR5  0   0.396  34.7653  110.1794  16.7088
 84H  H6   H  HCR6  0   0.252  35.5051  116.7165  19.1930

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
 84H  C5   C4   single    1.540  0.020  1.540
 84H  C5   C6   single    1.501  0.020  1.501
 84H  N    C4   single    1.437  0.020  1.437
 84H  N    C3   single    1.360  0.020  1.360
 84H  C4   C1   single    1.503  0.020  1.503
 84H  C7   C6   aromatic  1.392  0.020  1.392
 84H  C7   C8   aromatic  1.386  0.020  1.386
 84H  C6   C11  aromatic  1.393  0.020  1.393
 84H  C3   O1   double    1.221  0.020  1.221
 84H  C3   C2   single    1.470  0.020  1.470
 84H  C8   C9   aromatic  1.395  0.020  1.395
 84H  C1   O    single    1.318  0.020  1.318
 84H  C1   C2   double    1.342  0.020  1.342
 84H  C11  C10  aromatic  1.386  0.020  1.386
 84H  O    C    single    1.422  0.020  1.422
 84H  C9   C10  aromatic  1.395  0.020  1.395
 84H  C9   C12  single    1.477  0.020  1.477
 84H  C13  C12  aromatic  1.396  0.020  1.396
 84H  C13  C14  aromatic  1.387  0.020  1.387
 84H  C12  C17  aromatic  1.397  0.020  1.397
 84H  C14  C15  aromatic  1.389  0.020  1.389
 84H  C17  C16  aromatic  1.387  0.020  1.387
 84H  C15  C16  aromatic  1.389  0.020  1.389
 84H  C2   H1   single    0.930  0.020  1.080
 84H  C4   H2   single    0.970  0.020  1.090
 84H  C7   H3   single    0.930  0.020  1.080
 84H  C10  H4   single    0.930  0.020  1.080
 84H  C11  H5   single    0.930  0.020  1.080
 84H  C13  H6   single    0.930  0.020  1.080
 84H  C14  H7   single    0.930  0.020  1.080
 84H  C15  H8   single    0.930  0.020  1.080
 84H  C    H61  single    0.970  0.020  1.090
 84H  C    H62  single    0.970  0.020  1.090
 84H  C    H63  single    0.970  0.020  1.090
 84H  C5   H64  single    0.970  0.020  1.090
 84H  C5   H65  single    0.970  0.020  1.090
 84H  C8   H66  single    0.930  0.020  1.080
 84H  C17  H67  single    0.930  0.020  1.080
 84H  C16  H68  single    0.930  0.020  1.080
 84H  N    H9   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
 84H  O    C1   C4   117.12  3.000
 84H  O    C1   C2   131.60  3.000
 84H  C4   C1   C2   111.28  3.000
 84H  H1   C2   C3   123.53  3.000
 84H  H1   C2   C1   128.68  3.000
 84H  C3   C2   C1   107.79  3.000
 84H  O1   C3   N    125.70  3.000
 84H  O1   C3   C2   127.78  3.000
 84H  N    C3   C2   106.52  3.000
 84H  H2   C4   C5   108.13  3.000
 84H  H2   C4   N    111.18  3.000
 84H  C5   C4   N    113.60  3.000
 84H  H2   C4   C1   110.03  3.000
 84H  N    C4   C1   100.92  3.000
 84H  C5   C4   C1   112.89  3.000
 84H  C5   C6   C11  120.98  3.000
 84H  C11  C6   C7   117.96  3.000
 84H  C5   C6   C7   121.05  3.000
 84H  H3   C7   C8   119.09  3.000
 84H  H3   C7   C6   119.83  3.000
 84H  C8   C7   C6   121.08  3.000
 84H  C12  C9   C8   121.16  3.000
 84H  C12  C9   C10  120.94  3.000
 84H  C8   C9   C10  117.89  3.000
 84H  H4   C10  C11  119.08  3.000
 84H  H4   C10  C9   119.94  3.000
 84H  C11  C10  C9   120.96  3.000
 84H  H5   C11  C10  119.19  3.000
 84H  H5   C11  C6   119.69  3.000
 84H  C10  C11  C6   121.11  3.000
 84H  H6   C13  C12  119.81  3.000
 84H  H6   C13  C14  119.34  3.000
 84H  C12  C13  C14  120.84  3.000
 84H  H7   C14  C15  120.08  3.000
 84H  H7   C14  C13  119.65  3.000
 84H  C15  C14  C13  120.27  3.000
 84H  H8   C15  C16  120.27  3.000
 84H  H8   C15  C14  120.27  3.000
 84H  C16  C15  C14  119.46  3.000
 84H  H9   N    C4   122.95  3.000
 84H  H9   N    C3   123.06  3.000
 84H  C4   N    C3   113.31  3.000
 84H  C    O    C1   116.51  3.000
 84H  H63  C    H62  109.16  3.000
 84H  H63  C    H61  109.40  3.000
 84H  H62  C    H61  109.49  3.000
 84H  H63  C    O    111.06  3.000
 84H  H62  C    O    110.86  3.000
 84H  H61  C    O    106.83  3.000
 84H  H65  C5   H64  106.54  3.000
 84H  H65  C5   C6   110.51  3.000
 84H  H64  C5   C6   110.58  3.000
 84H  H65  C5   C4   107.59  3.000
 84H  H64  C5   C4   108.16  3.000
 84H  C6   C5   C4   113.19  3.000
 84H  H66  C8   C9   119.95  3.000
 84H  H66  C8   C7   119.05  3.000
 84H  C9   C8   C7   120.99  3.000
 84H  C17  C12  C13  118.32  3.000
 84H  C17  C12  C9   120.72  3.000
 84H  C13  C12  C9   120.96  3.000
 84H  H67  C17  C16  119.34  3.000
 84H  H67  C17  C12  119.78  3.000
 84H  C16  C17  C12  120.87  3.000
 84H  H68  C16  C17  119.66  3.000
 84H  H68  C16  C15  120.10  3.000
 84H  C17  C16  C15  120.24  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
 84H  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 84H  CONST_02  C9   C10  C11  C6      0.00   0.0  0
 84H  CONST_03  C10  C11  C6   C7      0.00   0.0  0
 84H  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 84H  CONST_05  C12  C9   C8   C7    180.00   0.0  0
 84H  CONST_06  C14  C13  C12  C9    180.00   0.0  0
 84H  CONST_07  C16  C17  C12  C9    180.00   0.0  0
 84H  CONST_10  C8   C7   C6   C11     0.00   0.0  0
 84H  CONST_11  C8   C9   C10  C11     0.00   0.0  0
 84H  CONST_12  C12  C9   C10  C11   180.00   0.0  0
 84H  CONST_14  C16  C17  C12  C13     0.00   0.0  0
 84H  CONST_15  C16  C15  C14  C13     0.00   0.0  0
 84H  CONST_16  C17  C12  C13  C14     0.00   0.0  0
 84H  CONST_17  C17  C16  C15  C14     0.00   0.0  0
 84H  CONST_18  C12  C13  C14  C15     0.00   0.0  0
 84H  CONST_19  C12  C17  C16  C15     0.00   0.0  0
 84H  CONST_21  C4   N    C3   C2      0.00   0.0  0
 84H  CONST_22  C5   C6   C11  C10   180.00   0.0  0
 84H  CONST_23  C8   C7   C6   C5    180.00   0.0  0
 84H  CONST_24  O1   C3   N    C4    180.00   0.0  0
 84H  CONST_25  H66  C8   C7   C6    180.00   0.0  0
 84H  CONST_26  H4   C10  C11  C6    180.00   0.0  0
 84H  CONST_27  H5   C11  C6   C7    180.00   0.0  0
 84H  CONST_28  H3   C7   C8   C9    180.00   0.0  0
 84H  CONST_29  H5   C11  C10  C9    180.00   0.0  0
 84H  CONST_30  H6   C13  C12  C9      0.00   0.0  0
 84H  CONST_31  H67  C17  C12  C9      0.00   0.0  0
 84H  CONST_32  H66  C8   C9   C10   180.00   0.0  0
 84H  CONST_33  H3   C7   C6   C11   180.00   0.0  0
 84H  CONST_34  H67  C17  C12  C13   180.00   0.0  0
 84H  CONST_35  H8   C15  C14  C13   180.00   0.0  0
 84H  CONST_36  H68  C16  C15  C14   180.00   0.0  0
 84H  CONST_37  H6   C13  C14  C15   180.00   0.0  0
 84H  CONST_38  H67  C17  C16  C15   180.00   0.0  0
 84H  CONST_39  H4   C10  C9   C8    180.00   0.0  0
 84H  CONST_40  H66  C8   C9   C12     0.00   0.0  0
 84H  CONST_41  H4   C10  C9   C12     0.00   0.0  0
 84H  CONST_42  H7   C14  C13  C12   180.00   0.0  0
 84H  CONST_43  H68  C16  C17  C12   180.00   0.0  0
 84H  CONST_44  H6   C13  C12  C17   180.00   0.0  0
 84H  CONST_45  H8   C15  C16  C17   180.00   0.0  0
 84H  CONST_46  H7   C14  C15  C16   180.00   0.0  0
 84H  CONST_47  H9   N    C3   C2    180.00   0.0  0
 84H  CONST_48  H9   N    C3   O1      0.00   0.0  0
 84H  Var_01    N    C3   C2   C1      1.47  30.0  1
 84H  Var_02    C4   C1   C2   C3      1.22  30.0  1
 84H  Var_03    O1   C3   C2   C1   -179.22  30.0  1
 84H  Var_04    O    C1   C2   C3   -179.91  30.0  1
 84H  Var_05    C7   C6   C5   C4    -83.98  30.0  2
 84H  Var_06    C11  C6   C5   C4     94.47  30.0  2
 84H  Var_07    H1   C2   C1   C4   -179.07  30.0  1
 84H  Var_08    H1   C2   C3   N    -178.25  30.0  1
 84H  Var_09    C    O    C1   C2     -1.75  30.0  3
 84H  Var_10    C    O    C1   C4    177.06  30.0  3
 84H  Var_11    H64  C5   C6   C7    154.48  30.0  2
 84H  Var_12    H65  C5   C6   C7     36.77  30.0  2
 84H  Var_13    H64  C5   C6   C11   -27.07  30.0  2
 84H  Var_14    H65  C5   C6   C11  -144.78  30.0  2
 84H  Var_15    H1   C2   C3   O1      1.06  30.0  1
 84H  Var_16    H1   C2   C1   O      -0.21  30.0  1
 84H  Var_17    H61  C    O    C1   -179.57  30.0  3
 84H  Var_18    H62  C    O    C1    -60.35  30.0  3
 84H  Var_19    H63  C    O    C1     61.20  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
 84H  chir_01  C4  C5  N  C1  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
 84H  plan-1  C6   0.020
 84H  plan-1  C7   0.020
 84H  plan-1  C9   0.020
 84H  plan-1  C10  0.020
 84H  plan-1  C11  0.020
 84H  plan-1  C5   0.020
 84H  plan-1  C8   0.020
 84H  plan-1  C12  0.020
 84H  plan-1  H3   0.020
 84H  plan-1  H4   0.020
 84H  plan-1  H5   0.020
 84H  plan-1  H66  0.020
 84H  plan-2  C9   0.020
 84H  plan-2  C13  0.020
 84H  plan-2  C14  0.020
 84H  plan-2  C15  0.020
 84H  plan-2  C12  0.020
 84H  plan-2  C17  0.020
 84H  plan-2  C16  0.020
 84H  plan-2  H7   0.020
 84H  plan-2  H8   0.020
 84H  plan-2  H67  0.020
 84H  plan-2  H68  0.020
 84H  plan-2  H6   0.020
 84H  plan-3  C2   0.020
 84H  plan-3  C3   0.020
 84H  plan-3  C4   0.020
 84H  plan-3  N    0.020
 84H  plan-3  O1   0.020
 84H  plan-3  H9   0.020

