# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:34:03 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-(4'-methoxy[1,1'-biphenyl]-2-yl)pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2ccccc2N3CCCC3=O
#
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
 H4Y  H4Y  1-(4'-methoxy[1,1'-biphenyl]-2-yl)pyrrolidin-2-one  ligand  37  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H4Y
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
 H4Y  N1   N  NR5   0  -0.582   1.5738   1.0492  -0.3447
 H4Y  C4   C  CR16  0  -0.279  -1.3970  -1.5438  -0.7347
 H4Y  C5   C  CR6   0   0.035  -0.4715  -0.9279   0.0993
 H4Y  C6   C  CR6   0   0.075   0.9622  -1.2780   0.0222
 H4Y  C7   C  CR16  0  -0.320   1.3649  -2.6094   0.1247
 H4Y  C8   C  CR16  0  -0.237   2.7051  -2.9611   0.0724
 H4Y  C10  C  CR16  0  -0.263   3.2899  -0.6530  -0.2160
 H4Y  C13  C  CH2   0  -0.480   0.4789   2.9196  -1.2009
 H4Y  C15  C  CR5   0   0.522   1.8508   2.0291   0.5469
 H4Y  C17  C  CR16  0  -0.326  -2.2870   0.3272   1.0916
 H4Y  C1   C  CH3   0  -0.437  -5.4612  -0.5147  -0.4622
 H4Y  C2   C  CR6   0   0.373  -3.2049  -0.2900   0.2377
 H4Y  C3   C  CR16  0  -0.371  -2.7512  -1.2364  -0.6766
 H4Y  C9   C  CR16  0  -0.276   3.6730  -1.9796  -0.0906
 H4Y  C11  C  CR6   0   0.287   1.9464  -0.3008  -0.1652
 H4Y  C12  C  CH2   0  -0.275   0.9936   1.5338  -1.5886
 H4Y  C14  C  CH2   0  -0.586   1.4017   3.3392  -0.0613
 H4Y  O2   O  O     0  -0.488   2.3770   1.8621   1.6328
 H4Y  C16  C  CR16  0  -0.272  -0.9450   0.0114   1.0195
 H4Y  H1   H  HCR6  0   0.257  -1.0618  -2.2737  -1.4616
 H4Y  H2   H  HCR6  0   0.256   0.6145  -3.3766   0.2698
 H4Y  H3   H  HCR6  0   0.260   2.9919  -4.0003   0.1655
 H4Y  H4   H  HCR6  0   0.264   4.0350   0.1168  -0.3713
 H4Y  H5   H  HCH2  0   0.258   0.4877   3.6099  -2.0416
 H4Y  H6   H  HCH2  0   0.250  -0.5474   2.8405  -0.8397
 H4Y  H7   H  HCR6  0   0.263  -2.6375   1.0514   1.8171
 H4Y  H8   H  HCH3  0   0.229  -5.2660  -0.3258  -1.5210
 H4Y  H9   H  HCH3  0   0.229  -5.5256  -1.5942  -0.3033
 H4Y  H10  H  HCH3  0   0.260  -6.4152  -0.0655  -0.1975
 H4Y  H11  H  HCR6  0   0.279  -3.4276  -1.7399  -1.3533
 H4Y  H12  H  HCR6  0   0.261   4.7215  -2.2437  -0.1288
 H4Y  H13  H  HCH2  0   0.248   1.7585   1.5816  -2.3696
 H4Y  H14  H  HCH2  0   0.257   0.1993   0.8719  -1.9336
 H4Y  H15  H  HCH2  0   0.275   2.2888   3.8647  -0.4285
 H4Y  H16  H  HCH2  0   0.275   0.9297   3.9783   0.6837
 H4Y  H17  H  HCR6  0   0.251  -0.2614   0.4865   1.7117
 H4Y  O1   O  O2    0  -0.470  -4.4901   0.0854   0.3717

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
 H4Y  C8   C7   aromatic  1.387  0.020  1.387
 H4Y  C8   C9   aromatic  1.388  0.020  1.388
 H4Y  C7   C6   aromatic  1.395  0.020  1.395
 H4Y  C9   C10  aromatic  1.386  0.020  1.386
 H4Y  C16  C17  aromatic  1.381  0.020  1.381
 H4Y  C16  C5   aromatic  1.398  0.020  1.398
 H4Y  C6   C5   single    1.478  0.020  1.478
 H4Y  C6   C11  aromatic  1.400  0.020  1.400
 H4Y  C17  C2   aromatic  1.397  0.020  1.397
 H4Y  C5   C4   aromatic  1.390  0.020  1.390
 H4Y  C2   O1   single    1.346  0.020  1.346
 H4Y  C2   C3   aromatic  1.392  0.020  1.392
 H4Y  C4   C3   aromatic  1.390  0.020  1.390
 H4Y  O1   C1   single    1.414  0.020  1.414
 H4Y  C10  C11  aromatic  1.390  0.020  1.390
 H4Y  C11  N1   single    1.412  0.020  1.412
 H4Y  O2   C15  double    1.218  0.020  1.218
 H4Y  N1   C15  single    1.353  0.020  1.353
 H4Y  N1   C12  single    1.456  0.020  1.456
 H4Y  C15  C14  single    1.513  0.020  1.513
 H4Y  C12  C13  single    1.528  0.020  1.528
 H4Y  C14  C13  single    1.525  0.020  1.525
 H4Y  C4   H1   single    0.930  0.020  1.080
 H4Y  C7   H2   single    0.930  0.020  1.080
 H4Y  C8   H3   single    0.930  0.020  1.080
 H4Y  C10  H4   single    0.930  0.020  1.080
 H4Y  C13  H5   single    0.970  0.020  1.090
 H4Y  C13  H6   single    0.970  0.020  1.090
 H4Y  C17  H7   single    0.930  0.020  1.080
 H4Y  C1   H8   single    0.970  0.020  1.090
 H4Y  C1   H9   single    0.970  0.020  1.090
 H4Y  C1   H10  single    0.970  0.020  1.090
 H4Y  C3   H11  single    0.930  0.020  1.080
 H4Y  C9   H12  single    0.930  0.020  1.080
 H4Y  C12  H13  single    0.970  0.020  1.090
 H4Y  C12  H14  single    0.970  0.020  1.090
 H4Y  C14  H15  single    0.970  0.020  1.090
 H4Y  C14  H16  single    0.970  0.020  1.090
 H4Y  C16  H17  single    0.930  0.020  1.080

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
 H4Y  C12  N1   C11  122.15  3.000
 H4Y  C12  N1   C15  113.80  3.000
 H4Y  C11  N1   C15  123.67  3.000
 H4Y  H1   C4   C3   118.59  3.000
 H4Y  H1   C4   C5   119.68  3.000
 H4Y  C3   C4   C5   121.72  3.000
 H4Y  C16  C5   C6   121.48  3.000
 H4Y  C6   C5   C4   120.65  3.000
 H4Y  C16  C5   C4   117.86  3.000
 H4Y  C11  C6   C7   118.25  3.000
 H4Y  C11  C6   C5   121.59  3.000
 H4Y  C7   C6   C5   120.16  3.000
 H4Y  H2   C7   C8   119.68  3.000
 H4Y  H2   C7   C6   119.08  3.000
 H4Y  C8   C7   C6   121.23  3.000
 H4Y  H3   C8   C9   120.29  3.000
 H4Y  H3   C8   C7   119.77  3.000
 H4Y  C9   C8   C7   119.93  3.000
 H4Y  H4   C10  C11  119.37  3.000
 H4Y  H4   C10  C9   120.21  3.000
 H4Y  C11  C10  C9   120.42  3.000
 H4Y  H6   C13  H5   108.03  3.000
 H4Y  H6   C13  C14  109.98  3.000
 H4Y  H5   C13  C14  113.45  3.000
 H4Y  H6   C13  C12  109.58  3.000
 H4Y  H5   C13  C12  112.13  3.000
 H4Y  C14  C13  C12  103.61  3.000
 H4Y  O2   C15  C14  127.26  3.000
 H4Y  C14  C15  N1   107.54  3.000
 H4Y  O2   C15  N1   125.20  3.000
 H4Y  H7   C17  C16  120.16  3.000
 H4Y  H7   C17  C2   119.47  3.000
 H4Y  C16  C17  C2   120.37  3.000
 H4Y  H10  C1   H9   108.72  3.000
 H4Y  H10  C1   H8   108.73  3.000
 H4Y  H9   C1   H8   108.78  3.000
 H4Y  H10  C1   O1   106.49  3.000
 H4Y  H9   C1   O1   111.96  3.000
 H4Y  H8   C1   O1   112.04  3.000
 H4Y  C3   C2   O1   124.50  3.000
 H4Y  C3   C2   C17  119.18  3.000
 H4Y  O1   C2   C17  116.31  3.000
 H4Y  H11  C3   C2   121.59  3.000
 H4Y  H11  C3   C4   118.72  3.000
 H4Y  C2   C3   C4   119.69  3.000
 H4Y  H12  C9   C10  119.88  3.000
 H4Y  H12  C9   C8   120.48  3.000
 H4Y  C10  C9   C8   119.64  3.000
 H4Y  C10  C11  C6   120.52  3.000
 H4Y  C10  C11  N1   119.52  3.000
 H4Y  C6   C11  N1   119.93  3.000
 H4Y  H14  C12  H13  108.06  3.000
 H4Y  H14  C12  C13  112.68  3.000
 H4Y  H13  C12  C13  112.14  3.000
 H4Y  H14  C12  N1   111.03  3.000
 H4Y  H13  C12  N1   110.23  3.000
 H4Y  C13  C12  N1   102.67  3.000
 H4Y  H16  C14  H15  107.39  3.000
 H4Y  H16  C14  C15  111.22  3.000
 H4Y  H15  C14  C15  108.07  3.000
 H4Y  H16  C14  C13  114.23  3.000
 H4Y  H15  C14  C13  111.82  3.000
 H4Y  C15  C14  C13  103.99  3.000
 H4Y  H17  C16  C17  118.69  3.000
 H4Y  H17  C16  C5   120.13  3.000
 H4Y  C17  C16  C5   121.16  3.000
 H4Y  C2   O1   C1   118.62  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
 H4Y  CONST_01  C17  C16  C5   C4     0.00   0.0  0
 H4Y  CONST_04  C17  C2   C3   C4     0.00   0.0  0
 H4Y  CONST_05  C2   C17  C16  C5     0.00   0.0  0
 H4Y  CONST_06  C8   C7   C6   C5   180.00   0.0  0
 H4Y  CONST_07  C10  C11  C6   C5   180.00   0.0  0
 H4Y  CONST_08  C2   C3   C4   C5     0.00   0.0  0
 H4Y  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 H4Y  CONST_10  C17  C16  C5   C6   180.00   0.0  0
 H4Y  CONST_11  C3   C4   C5   C6   180.00   0.0  0
 H4Y  CONST_12  C9   C10  C11  C6     0.00   0.0  0
 H4Y  CONST_13  C10  C9   C8   C7     0.00   0.0  0
 H4Y  CONST_15  C10  C11  C6   C7     0.00   0.0  0
 H4Y  CONST_16  C11  C6   C7   C8     0.00   0.0  0
 H4Y  CONST_17  C11  C10  C9   C8     0.00   0.0  0
 H4Y  CONST_18  C16  C17  C2   C3     0.00   0.0  0
 H4Y  CONST_19  C16  C5   C4   C3     0.00   0.0  0
 H4Y  CONST_21  C7   C6   C11  N1   180.00   0.0  0
 H4Y  CONST_22  C5   C6   C11  N1     0.00   0.0  0
 H4Y  CONST_23  C9   C10  C11  N1   180.00   0.0  0
 H4Y  CONST_24  C14  C15  N1   C11  180.00   0.0  0
 H4Y  CONST_25  C14  C15  N1   C12    0.00   0.0  0
 H4Y  CONST_26  O1   C2   C3   C4   180.00   0.0  0
 H4Y  CONST_27  C16  C17  C2   O1   180.00   0.0  0
 H4Y  CONST_28  O2   C15  N1   C11    0.00   0.0  0
 H4Y  CONST_29  O2   C15  N1   C12  180.00   0.0  0
 H4Y  CONST_30  H4   C10  C11  N1     0.00   0.0  0
 H4Y  CONST_31  H17  C16  C5   C4   180.00   0.0  0
 H4Y  CONST_32  H7   C17  C16  C5   180.00   0.0  0
 H4Y  CONST_33  H2   C7   C6   C5     0.00   0.0  0
 H4Y  CONST_34  H11  C3   C4   C5   180.00   0.0  0
 H4Y  CONST_35  H3   C8   C7   C6   180.00   0.0  0
 H4Y  CONST_36  H1   C4   C5   C6     0.00   0.0  0
 H4Y  CONST_37  H12  C9   C8   C7   180.00   0.0  0
 H4Y  Var_01    C13  C14  C15  N1    16.28  30.0  1
 H4Y  Var_02    C14  C13  C12  N1    27.68  30.0  1
 H4Y  Var_03    C15  N1   C11  C6   113.24  30.0  2
 H4Y  Var_04    C11  N1   C12  C13  167.65  30.0  1
 H4Y  Var_05    C12  C13  C14  C15  -27.00  30.0  1
 H4Y  Var_06    C3   C2   O1   C1     0.19  30.0  3
 H4Y  Var_07    H8   C1   O1   C2   -60.67  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
 H4Y  plan-1  N1   0.020
 H4Y  plan-1  C5   0.020
 H4Y  plan-1  C6   0.020
 H4Y  plan-1  C7   0.020
 H4Y  plan-1  C8   0.020
 H4Y  plan-1  C10  0.020
 H4Y  plan-1  C9   0.020
 H4Y  plan-1  C11  0.020
 H4Y  plan-1  H2   0.020
 H4Y  plan-1  H3   0.020
 H4Y  plan-1  H4   0.020
 H4Y  plan-1  H12  0.020
 H4Y  plan-2  C4   0.020
 H4Y  plan-2  C5   0.020
 H4Y  plan-2  C6   0.020
 H4Y  plan-2  C17  0.020
 H4Y  plan-2  C2   0.020
 H4Y  plan-2  C3   0.020
 H4Y  plan-2  C16  0.020
 H4Y  plan-2  H1   0.020
 H4Y  plan-2  H7   0.020
 H4Y  plan-2  H11  0.020
 H4Y  plan-2  H17  0.020
 H4Y  plan-2  O1   0.020
 H4Y  plan-3  N1   0.020
 H4Y  plan-3  C15  0.020
 H4Y  plan-3  C11  0.020
 H4Y  plan-3  C12  0.020
 H4Y  plan-3  C14  0.020
 H4Y  plan-3  O2   0.020

