# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 05:40:30 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-methyl-1-oxidanyl-2-[4-[[4-(trifluoromethyloxy)phenyl]methyl]phenyl]quinolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N(O)c2ccccc2C1=O)c3ccc(Cc4ccc(OC(F)(F)F)cc4)cc3
#
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
 JHE  JHE  3-methyl-1-oxidanyl-2-[4-[[4-(trifluoromethyloxy)phenyl]methyl]phenyl]quinolin-4-one  ligand  49  31  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JHE
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
 JHE  C1   C  CR66  0  -0.130  -69.8900  -62.5542  32.5421
 JHE  C2   C  CR66  0   0.374  -68.8234  -61.9633  31.8495
 JHE  C3   C  CR6   0   0.319  -68.3210  -64.0825  30.8242
 JHE  C5   C  CR16  0  -0.293  -70.6632  -61.7544  33.3949
 JHE  C6   C  CR16  0  -0.252  -70.3914  -60.4161  33.5516
 JHE  C7   C  CR16  0  -0.248  -69.3253  -59.8428  32.8493
 JHE  C8   C  CR16  0  -0.313  -68.5426  -60.5970  32.0060
 JHE  C10  C  CR6   0  -0.007  -67.4165  -64.7806  29.8798
 JHE  C11  C  CR16  0  -0.244  -66.3541  -65.5397  30.3605
 JHE  C12  C  CR16  0  -0.278  -65.5221  -66.2111  29.4789
 JHE  C13  C  CR6   0   0.141  -65.7309  -66.1384  28.1037
 JHE  C14  C  CR16  0  -0.311  -66.7976  -65.3795  27.6333
 JHE  C15  C  CR16  0  -0.242  -67.6340  -64.7038  28.5102
 JHE  C16  C  CH2   0  -0.603  -64.8269  -66.8824  27.1536
 JHE  C17  C  CR6   0   0.148  -65.0285  -68.3755  27.2234
 JHE  C19  C  CR16  0  -0.281  -64.2142  -70.5887  27.7722
 JHE  C21  C  CR16  0  -0.281  -66.4234  -70.3161  26.8421
 JHE  C22  C  CR16  0  -0.284  -66.2246  -68.9462  26.7921
 JHE  C23  C  CT    0   1.070  -66.1256  -73.0864  28.3864
 JHE  F2   F  F     0  -0.300  -65.4111  -72.9049  29.4993
 JHE  F    F  F     0  -0.278  -66.1999  -74.3865  28.1480
 JHE  F1   F  F     0  -0.300  -67.3566  -72.6369  28.6418
 JHE  C20  C  CR6   0   0.297  -65.4105  -71.1237  27.3339
 JHE  C18  C  CR16  0  -0.322  -64.0321  -69.2130  27.7118
 JHE  C4   C  CR6   0  -0.219  -69.3446  -64.7132  31.4698
 JHE  C    C  CR6   0   0.433  -70.1943  -63.9776  32.3811
 JHE  O    O  O     0  -0.459  -71.1257  -64.5137  32.9829
 JHE  N    N  NR6   0  -0.314  -68.0712  -62.7588  31.0258
 JHE  O1   O  OH1   0  -0.515  -67.0712  -62.1729  30.3176
 JHE  H1   H  HCR6  0   0.261  -71.4834  -62.2115  33.9319
 JHE  H2   H  HCR6  0   0.260  -70.9950  -59.8084  34.2120
 JHE  H3   H  HCR6  0   0.268  -69.1076  -58.7892  32.9663
 JHE  H4   H  HCR6  0   0.279  -67.7255  -60.1357  31.4717
 JHE  H5   H  HCH3  0   0.241  -70.6887  -66.3104  30.9867
 JHE  H6   H  HCH3  0   0.245  -69.0219  -66.6238  30.5159
 JHE  H7   H  HCH3  0   0.241  -69.4997  -66.7226  32.2063
 JHE  H8   H  HCR6  0   0.258  -66.1794  -65.6091  31.4270
 JHE  H9   H  HCR6  0   0.255  -64.6989  -66.7988  29.8681
 JHE  H10  H  HCR6  0   0.255  -66.9779  -65.3115  26.5672
 JHE  H11  H  HCR6  0   0.257  -68.4610  -64.1210  28.1242
 JHE  H12  H  HCH2  0   0.274  -63.7846  -66.6481  27.3798
 JHE  H13  H  HCH2  0   0.274  -65.0110  -66.5368  26.1339
 JHE  H14  H  HCR6  0   0.277  -63.4233  -71.2305  28.1380
 JHE  H15  H  HCR6  0   0.277  -67.3477  -70.7492  26.4828
 JHE  H16  H  HCR6  0   0.261  -67.0145  -68.3148  26.4029
 JHE  H17  H  HCR6  0   0.261  -63.0925  -68.7914  28.0471
 JHE  H18  H  HOH1  0   0.489  -66.2639  -62.2632  30.8476
 JHE  C9   C  CH3   0  -0.721  -69.6472  -66.1668  31.2782
 JHE  O2   O  O2    0  -0.521  -65.5725  -72.5062  27.3170

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
 JHE  C16  C17  single    1.508  0.020  1.508
 JHE  C16  C13  single    1.508  0.020  1.508
 JHE  C22  C17  aromatic  1.394  0.020  1.394
 JHE  C22  C21  aromatic  1.385  0.020  1.385
 JHE  C17  C18  aromatic  1.390  0.020  1.390
 JHE  C21  C20  aromatic  1.386  0.020  1.386
 JHE  C14  C13  aromatic  1.391  0.020  1.391
 JHE  C14  C15  aromatic  1.388  0.020  1.388
 JHE  C18  C19  aromatic  1.389  0.020  1.389
 JHE  C20  C19  aromatic  1.382  0.020  1.382
 JHE  C20  O2   single    1.392  0.020  1.392
 JHE  F1   C23  single    1.335  0.020  1.335
 JHE  C13  C12  aromatic  1.393  0.020  1.393
 JHE  O2   C23  single    1.337  0.020  1.337
 JHE  C15  C10  aromatic  1.389  0.020  1.389
 JHE  C23  F    single    1.324  0.020  1.324
 JHE  C23  F2   single    1.335  0.020  1.335
 JHE  C12  C11  aromatic  1.386  0.020  1.386
 JHE  C10  C11  aromatic  1.391  0.020  1.391
 JHE  C10  C3   single    1.482  0.020  1.482
 JHE  C9   C4   single    1.497  0.020  1.497
 JHE  C3   C4   double    1.365  0.020  1.365
 JHE  C3   N    single    1.362  0.020  1.362
 JHE  O1   N    single    1.358  0.020  1.358
 JHE  C4   C    single    1.447  0.020  1.447
 JHE  N    C2   single    1.370  0.020  1.370
 JHE  C    O    double    1.232  0.020  1.232
 JHE  C    C1   single    1.464  0.020  1.464
 JHE  C2   C8   aromatic  1.404  0.020  1.404
 JHE  C2   C1   aromatic  1.402  0.020  1.402
 JHE  C8   C7   aromatic  1.376  0.020  1.376
 JHE  C1   C5   aromatic  1.402  0.020  1.402
 JHE  C7   C6   aromatic  1.399  0.020  1.399
 JHE  C5   C6   aromatic  1.375  0.020  1.375
 JHE  C5   H1   single    0.930  0.020  1.080
 JHE  C6   H2   single    0.930  0.020  1.080
 JHE  C7   H3   single    0.930  0.020  1.080
 JHE  C8   H4   single    0.930  0.020  1.080
 JHE  C9   H5   single    0.970  0.020  1.090
 JHE  C9   H6   single    0.970  0.020  1.090
 JHE  C9   H7   single    0.970  0.020  1.090
 JHE  C11  H8   single    0.930  0.020  1.080
 JHE  C12  H9   single    0.930  0.020  1.080
 JHE  C14  H10  single    0.930  0.020  1.080
 JHE  C15  H11  single    0.930  0.020  1.080
 JHE  C16  H12  single    0.970  0.020  1.090
 JHE  C16  H13  single    0.970  0.020  1.090
 JHE  C19  H14  single    0.930  0.020  1.080
 JHE  C21  H15  single    0.930  0.020  1.080
 JHE  C22  H16  single    0.930  0.020  1.080
 JHE  C18  H17  single    0.930  0.020  1.080
 JHE  O1   H18  single    0.850  0.020  0.980

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
 JHE  C    C1   C5   120.45  3.000
 JHE  C5   C1   C2   118.66  3.000
 JHE  C    C1   C2   120.89  3.000
 JHE  N    C2   C8   121.50  3.000
 JHE  C8   C2   C1   120.48  3.000
 JHE  N    C2   C1   118.02  3.000
 JHE  N    C3   C4   121.11  3.000
 JHE  N    C3   C10  116.11  3.000
 JHE  C4   C3   C10  122.78  3.000
 JHE  H1   C5   C6   120.31  3.000
 JHE  H1   C5   C1   118.63  3.000
 JHE  C6   C5   C1   121.06  3.000
 JHE  H2   C6   C7   120.09  3.000
 JHE  H2   C6   C5   120.42  3.000
 JHE  C7   C6   C5   119.49  3.000
 JHE  H3   C7   C8   119.05  3.000
 JHE  H3   C7   C6   119.85  3.000
 JHE  C8   C7   C6   121.09  3.000
 JHE  H4   C8   C7   119.98  3.000
 JHE  H4   C8   C2   120.80  3.000
 JHE  C7   C8   C2   119.22  3.000
 JHE  C15  C10  C11  119.37  3.000
 JHE  C11  C10  C3   120.18  3.000
 JHE  C15  C10  C3   120.44  3.000
 JHE  H8   C11  C12  119.91  3.000
 JHE  H8   C11  C10  119.89  3.000
 JHE  C12  C11  C10  120.19  3.000
 JHE  H9   C12  C13  119.78  3.000
 JHE  H9   C12  C11  119.36  3.000
 JHE  C13  C12  C11  120.86  3.000
 JHE  C16  C13  C14  121.06  3.000
 JHE  C14  C13  C12  118.50  3.000
 JHE  C16  C13  C12  120.44  3.000
 JHE  H10  C14  C15  119.41  3.000
 JHE  H10  C14  C13  119.65  3.000
 JHE  C15  C14  C13  120.95  3.000
 JHE  H11  C15  C14  119.81  3.000
 JHE  H11  C15  C10  120.06  3.000
 JHE  C14  C15  C10  120.13  3.000
 JHE  H13  C16  H12  106.64  3.000
 JHE  H13  C16  C17  109.51  3.000
 JHE  H12  C16  C17  109.29  3.000
 JHE  H13  C16  C13  109.33  3.000
 JHE  H12  C16  C13  109.62  3.000
 JHE  C17  C16  C13  112.29  3.000
 JHE  C18  C17  C22  118.50  3.000
 JHE  C18  C17  C16  121.12  3.000
 JHE  C22  C17  C16  120.38  3.000
 JHE  H14  C19  C18  120.41  3.000
 JHE  H14  C19  C20  120.68  3.000
 JHE  C18  C19  C20  118.89  3.000
 JHE  H15  C21  C20  120.59  3.000
 JHE  H15  C21  C22  120.43  3.000
 JHE  C20  C21  C22  118.97  3.000
 JHE  H16  C22  C21  118.98  3.000
 JHE  H16  C22  C17  119.88  3.000
 JHE  C21  C22  C17  121.13  3.000
 JHE  O2   C23  F1   112.86  3.000
 JHE  O2   C23  F    107.78  3.000
 JHE  F1   C23  F    108.26  3.000
 JHE  F    C23  F2   108.29  3.000
 JHE  O2   C23  F2   112.73  3.000
 JHE  F1   C23  F2   106.76  3.000
 JHE  O2   C20  C21  119.31  3.000
 JHE  O2   C20  C19  119.28  3.000
 JHE  C21  C20  C19  121.31  3.000
 JHE  H17  C18  C19  119.07  3.000
 JHE  H17  C18  C17  119.74  3.000
 JHE  C19  C18  C17  121.19  3.000
 JHE  C    C4   C9   117.10  3.000
 JHE  C    C4   C3   120.23  3.000
 JHE  C9   C4   C3   122.67  3.000
 JHE  O    C    C4   122.04  3.000
 JHE  O    C    C1   121.77  3.000
 JHE  C4   C    C1   116.19  3.000
 JHE  O1   N    C3   118.50  3.000
 JHE  O1   N    C2   117.85  3.000
 JHE  C3   N    C2   123.54  3.000
 JHE  H18  O1   N    106.72  3.000
 JHE  H7   C9   H6   107.73  3.000
 JHE  H7   C9   H5   106.81  3.000
 JHE  H6   C9   H5   107.85  3.000
 JHE  H7   C9   C4   110.99  3.000
 JHE  H6   C9   C4   112.44  3.000
 JHE  H5   C9   C4   110.79  3.000
 JHE  C20  O2   C23  118.01  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
 JHE  CONST_01  C7   C8   C2   C1      0.00   0.0  0
 JHE  CONST_02  C7   C6   C5   C1      0.00   0.0  0
 JHE  CONST_03  C6   C7   C8   C2      0.00   0.0  0
 JHE  CONST_04  C6   C5   C1   C2      0.00   0.0  0
 JHE  CONST_05  C8   C2   C1   C5      0.00   0.0  0
 JHE  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 JHE  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 JHE  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 JHE  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 JHE  CONST_10  C14  C15  C10  C11     0.00   0.0  0
 JHE  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 JHE  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 JHE  CONST_13  C20  C21  C22  C17     0.00   0.0  0
 JHE  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 JHE  CONST_15  C22  C17  C18  C19     0.00   0.0  0
 JHE  CONST_16  C22  C21  C20  C19     0.00   0.0  0
 JHE  CONST_17  C18  C17  C22  C21     0.00   0.0  0
 JHE  CONST_18  C18  C19  C20  C21     0.00   0.0  0
 JHE  CONST_19  C14  C15  C10  C3    180.00   0.0  0
 JHE  CONST_20  C12  C11  C10  C3    180.00   0.0  0
 JHE  CONST_21  C16  C13  C12  C11   180.00   0.0  0
 JHE  CONST_22  C16  C13  C14  C15   180.00   0.0  0
 JHE  CONST_23  C21  C22  C17  C16   180.00   0.0  0
 JHE  CONST_24  C19  C18  C17  C16   180.00   0.0  0
 JHE  CONST_25  O2   C20  C21  C22   180.00   0.0  0
 JHE  CONST_26  C18  C19  C20  O2    180.00   0.0  0
 JHE  CONST_27  H4   C8   C2   C1    180.00   0.0  0
 JHE  CONST_28  H2   C6   C5   C1    180.00   0.0  0
 JHE  CONST_29  H3   C7   C8   C2    180.00   0.0  0
 JHE  CONST_30  H1   C5   C1   C2    180.00   0.0  0
 JHE  CONST_31  H11  C15  C10  C3      0.00   0.0  0
 JHE  CONST_32  H8   C11  C10  C3      0.00   0.0  0
 JHE  CONST_33  H10  C14  C15  C10   180.00   0.0  0
 JHE  CONST_34  H9   C12  C11  C10   180.00   0.0  0
 JHE  CONST_35  H15  C21  C22  C17   180.00   0.0  0
 JHE  CONST_36  H14  C19  C18  C17   180.00   0.0  0
 JHE  CONST_37  H17  C18  C17  C22   180.00   0.0  0
 JHE  CONST_38  H16  C22  C21  C20   180.00   0.0  0
 JHE  Var_01    C4   C3   C10  C11   -80.89  30.0  2
 JHE  Var_02    C17  C16  C13  C12    70.26  30.0  3
 JHE  Var_03    C22  C17  C16  C13    67.21  30.0  2
 JHE  Var_04    H5   C9   C4   C3   -125.66  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
 JHE  plan-1  C3   0.020
 JHE  plan-1  C10  0.020
 JHE  plan-1  C11  0.020
 JHE  plan-1  C12  0.020
 JHE  plan-1  C13  0.020
 JHE  plan-1  C14  0.020
 JHE  plan-1  C15  0.020
 JHE  plan-1  C16  0.020
 JHE  plan-1  H8   0.020
 JHE  plan-1  H9   0.020
 JHE  plan-1  H10  0.020
 JHE  plan-1  H11  0.020
 JHE  plan-2  C16  0.020
 JHE  plan-2  C17  0.020
 JHE  plan-2  C19  0.020
 JHE  plan-2  C21  0.020
 JHE  plan-2  C22  0.020
 JHE  plan-2  C20  0.020
 JHE  plan-2  C18  0.020
 JHE  plan-2  H14  0.020
 JHE  plan-2  H15  0.020
 JHE  plan-2  H16  0.020
 JHE  plan-2  H17  0.020
 JHE  plan-2  O2   0.020
 JHE  plan-3  C1   0.020
 JHE  plan-3  C2   0.020
 JHE  plan-3  C3   0.020
 JHE  plan-3  C5   0.020
 JHE  plan-3  C6   0.020
 JHE  plan-3  C7   0.020
 JHE  plan-3  C8   0.020
 JHE  plan-3  C10  0.020
 JHE  plan-3  C4   0.020
 JHE  plan-3  C    0.020
 JHE  plan-3  O    0.020
 JHE  plan-3  N    0.020
 JHE  plan-3  O1   0.020
 JHE  plan-3  H1   0.020
 JHE  plan-3  H2   0.020
 JHE  plan-3  H3   0.020
 JHE  plan-3  H4   0.020
 JHE  plan-3  C9   0.020

