# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:12:36 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(NC(=C(C)C2=O)c3cncc(c3)c4ccc(OC(F)(F)F)cc4)c1
#
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
 9XE  9XE  7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one  ligand  48  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9XE
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
 9XE  C12  C  CR16  0  -0.080  -1.0755   2.3315  -1.2327
 9XE  C15  C  CR16  0  -0.207   0.1334   0.4487  -0.4108
 9XE  C16  C  CR6   0   0.079   2.5884   0.6819   0.0002
 9XE  C20  C  CR16  0  -0.309   3.8909  -0.7176   1.4798
 9XE  C19  C  CR6   0   0.344   5.0512  -0.3399   0.8191
 9XE  C18  C  CR16  0  -0.325   5.0004   0.5436  -0.2486
 9XE  C11  C  CH3   0  -0.441  -8.8170   0.1239   2.2427
 9XE  C6   C  CR6   0   0.433  -3.7732  -1.6423  -1.3921
 9XE  C5   C  CR66  0  -0.128  -4.7769  -1.0476  -0.5144
 9XE  C3   C  CR16  0  -0.439  -5.4586   0.7171   1.0217
 9XE  C2   C  CR6   0   0.399  -6.6899   0.1053   1.1850
 9XE  N1   N  N     0  -0.390   0.0163   3.0822  -1.2569
 9XE  C8   C  CR6   0  -0.190  -2.5153  -0.9273  -1.5101
 9XE  C9   C  CH3   0  -0.732  -1.4977  -1.4900  -2.4541
 9XE  C10  C  CR6   0  -0.086  -1.0723   1.0035  -0.8173
 9XE  F2   F  F     0  -0.302   7.8631   0.4390   0.7117
 9XE  F    F  F     0  -0.301   7.3877  -1.2609  -0.5147
 9XE  F1   F  F     0  -0.272   8.2396  -1.5479   1.4416
 9XE  O2   O  O2    0  -0.504   6.2007  -0.9044   1.3335
 9XE  C17  C  CR16  0  -0.297   3.7674   1.0415  -0.6464
 9XE  C21  C  CR16  0  -0.297   2.6731  -0.2065   1.0727
 9XE  C14  C  CR6   0   0.011   1.2883   1.2224  -0.4302
 9XE  C13  C  CR16  0  -0.092   1.1595   2.5429  -0.8635
 9XE  C7   C  CR6   0   0.326  -2.3228   0.2175  -0.7924
 9XE  C    C  CR16  0  -0.283  -6.0321  -1.6392  -0.3320
 9XE  N    N  NR16  0  -0.759  -3.2900   0.7329   0.0102
 9XE  C4   C  CR66  0   0.407  -4.5097   0.1433   0.1752
 9XE  C1   C  CR16  0  -0.379  -6.9811  -1.0870   0.4949
 9XE  O1   O  O2    0  -0.466  -7.5479   0.7114   2.0161
 9XE  H1   H  HCR6  0   0.277  -1.9954   2.7984  -1.5694
 9XE  H2   H  HCR6  0   0.282   0.1686  -0.5855  -0.0901
 9XE  H3   H  HCR6  0   0.286   3.9433  -1.4020   2.3161
 9XE  H4   H  HCR6  0   0.293   5.8769   0.8643  -0.7922
 9XE  H5   H  HCH3  0   0.264  -9.3259   0.7644   2.9580
 9XE  H6   H  HCH3  0   0.234  -9.4121   0.0744   1.3280
 9XE  H7   H  HCH3  0   0.234  -8.7308  -0.8793   2.6658
 9XE  H8   H  HCR6  0   0.281  -5.2352   1.6373   1.5483
 9XE  H10  H  HCH3  0   0.246  -1.9474  -1.6830  -3.4288
 9XE  H11  H  HCH3  0   0.243  -0.6566  -0.8184  -2.6073
 9XE  H12  H  HCH3  0   0.243  -1.1008  -2.4420  -2.0959
 9XE  H13  H  HCR6  0   0.271   3.7417   1.7124  -1.4955
 9XE  H14  H  HCR6  0   0.270   1.7817  -0.4958   1.6147
 9XE  H15  H  HCR6  0   0.270   2.0259   3.1957  -0.8741
 9XE  H16  H  HCR6  0   0.265  -6.2585  -2.5583  -0.8560
 9XE  H17  H  HCR6  0   0.285  -7.9385  -1.5773   0.6020
 9XE  H9   H  HNR6  0   0.424  -3.0813   1.5636   0.5438
 9XE  O    O  O     0  -0.471  -3.9843  -2.6904  -2.0065
 9XE  C22  C  CT    0   1.082   7.3952  -0.8102   0.7394

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
 9XE  F    C22  single    1.333  0.020  1.333
 9XE  O2   C22  single    1.337  0.020  1.337
 9XE  O2   C19  single    1.380  0.020  1.380
 9XE  C22  F2   single    1.334  0.020  1.334
 9XE  C22  F1   single    1.323  0.020  1.323
 9XE  C19  C20  aromatic  1.388  0.020  1.388
 9XE  C19  C18  aromatic  1.387  0.020  1.387
 9XE  C20  C21  aromatic  1.382  0.020  1.382
 9XE  C18  C17  aromatic  1.388  0.020  1.388
 9XE  C21  C16  aromatic  1.395  0.020  1.395
 9XE  C17  C16  aromatic  1.392  0.020  1.392
 9XE  C16  C14  single    1.472  0.020  1.472
 9XE  C14  C13  aromatic  1.396  0.020  1.396
 9XE  C14  C15  aromatic  1.390  0.020  1.390
 9XE  C13  N1   aromatic  1.324  0.020  1.324
 9XE  C15  C10  aromatic  1.388  0.020  1.388
 9XE  N1   C12  aromatic  1.325  0.020  1.325
 9XE  C10  C12  aromatic  1.392  0.020  1.392
 9XE  C10  C7   single    1.477  0.020  1.477
 9XE  C9   C8   single    1.498  0.020  1.498
 9XE  C7   C8   double    1.365  0.020  1.365
 9XE  C7   N    single    1.358  0.020  1.358
 9XE  C8   C6   single    1.452  0.020  1.452
 9XE  N    C4   single    1.365  0.020  1.365
 9XE  C6   O    double    1.233  0.020  1.233
 9XE  C6   C5   single    1.460  0.020  1.460
 9XE  C4   C5   aromatic  1.402  0.020  1.402
 9XE  C4   C3   aromatic  1.395  0.020  1.395
 9XE  C5   C    aromatic  1.400  0.020  1.400
 9XE  C3   C2   aromatic  1.385  0.020  1.385
 9XE  C    C1   aromatic  1.375  0.020  1.375
 9XE  C2   C1   aromatic  1.408  0.020  1.408
 9XE  C2   O1   single    1.339  0.020  1.339
 9XE  O1   C11  single    1.417  0.020  1.417
 9XE  C12  H1   single    0.930  0.020  1.080
 9XE  C15  H2   single    0.930  0.020  1.080
 9XE  C20  H3   single    0.930  0.020  1.080
 9XE  C18  H4   single    0.930  0.020  1.080
 9XE  C11  H5   single    0.970  0.020  1.090
 9XE  C11  H6   single    0.970  0.020  1.090
 9XE  C11  H7   single    0.970  0.020  1.090
 9XE  C3   H8   single    0.930  0.020  1.080
 9XE  C9   H10  single    0.970  0.020  1.090
 9XE  C9   H11  single    0.970  0.020  1.090
 9XE  C9   H12  single    0.970  0.020  1.090
 9XE  C17  H13  single    0.930  0.020  1.080
 9XE  C21  H14  single    0.930  0.020  1.080
 9XE  C13  H15  single    0.930  0.020  1.080
 9XE  C    H16  single    0.930  0.020  1.080
 9XE  C1   H17  single    0.930  0.020  1.080
 9XE  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
 9XE  H1   C12  C10  120.34  3.000
 9XE  H1   C12  N1   116.69  3.000
 9XE  C10  C12  N1   122.97  3.000
 9XE  H2   C15  C14  120.56  3.000
 9XE  H2   C15  C10  119.76  3.000
 9XE  C14  C15  C10  119.67  3.000
 9XE  C14  C16  C21  120.80  3.000
 9XE  C14  C16  C17  121.15  3.000
 9XE  C21  C16  C17  118.05  3.000
 9XE  H3   C20  C21  120.29  3.000
 9XE  H3   C20  C19  119.98  3.000
 9XE  C21  C20  C19  119.73  3.000
 9XE  O2   C19  C18  125.32  3.000
 9XE  C18  C19  C20  120.62  3.000
 9XE  O2   C19  C20  114.06  3.000
 9XE  H4   C18  C17  118.04  3.000
 9XE  H4   C18  C19  123.15  3.000
 9XE  C17  C18  C19  118.80  3.000
 9XE  H7   C11  H6   109.01  3.000
 9XE  H7   C11  H5   108.86  3.000
 9XE  H6   C11  H5   108.84  3.000
 9XE  H7   C11  O1   111.85  3.000
 9XE  H6   C11  O1   111.89  3.000
 9XE  H5   C11  O1   106.28  3.000
 9XE  O    C6   C8   121.77  3.000
 9XE  O    C6   C5   121.88  3.000
 9XE  C8   C6   C5   116.36  3.000
 9XE  C4   C5   C    117.77  3.000
 9XE  C    C5   C6   121.51  3.000
 9XE  C4   C5   C6   120.71  3.000
 9XE  H8   C3   C4   120.26  3.000
 9XE  H8   C3   C2   120.09  3.000
 9XE  C4   C3   C2   119.65  3.000
 9XE  O1   C2   C1   123.69  3.000
 9XE  O1   C2   C3   116.29  3.000
 9XE  C1   C2   C3   120.02  3.000
 9XE  C13  N1   C12  118.38  3.000
 9XE  C7   C8   C9   123.42  3.000
 9XE  C7   C8   C6   119.51  3.000
 9XE  C9   C8   C6   117.06  3.000
 9XE  H12  C9   H11  107.67  3.000
 9XE  H12  C9   H10  106.78  3.000
 9XE  H11  C9   H10  107.60  3.000
 9XE  H12  C9   C8   111.58  3.000
 9XE  H11  C9   C8   112.48  3.000
 9XE  H10  C9   C8   110.47  3.000
 9XE  C7   C10  C15  121.18  3.000
 9XE  C7   C10  C12  120.73  3.000
 9XE  C15  C10  C12  118.09  3.000
 9XE  C22  O2   C19  123.34  3.000
 9XE  H13  C17  C18  117.92  3.000
 9XE  H13  C17  C16  120.29  3.000
 9XE  C18  C17  C16  121.78  3.000
 9XE  H14  C21  C20  118.63  3.000
 9XE  H14  C21  C16  120.33  3.000
 9XE  C20  C21  C16  121.03  3.000
 9XE  C13  C14  C16  121.30  3.000
 9XE  C13  C14  C15  117.02  3.000
 9XE  C16  C14  C15  121.68  3.000
 9XE  H15  C13  C14  119.91  3.000
 9XE  H15  C13  N1   116.21  3.000
 9XE  C14  C13  N1   123.87  3.000
 9XE  N    C7   C10  114.26  3.000
 9XE  N    C7   C8   121.91  3.000
 9XE  C10  C7   C8   123.84  3.000
 9XE  H16  C    C1   119.22  3.000
 9XE  H16  C    C5   118.93  3.000
 9XE  C1   C    C5   121.85  3.000
 9XE  H9   N    C4   118.46  3.000
 9XE  H9   N    C7   118.52  3.000
 9XE  C4   N    C7   122.95  3.000
 9XE  N    C4   C3   120.24  3.000
 9XE  C3   C4   C5   121.22  3.000
 9XE  N    C4   C5   118.54  3.000
 9XE  H17  C1   C    119.27  3.000
 9XE  H17  C1   C2   121.25  3.000
 9XE  C    C1   C2   119.49  3.000
 9XE  C2   O1   C11  119.04  3.000
 9XE  O2   C22  F1   107.16  3.000
 9XE  F1   C22  F    108.33  3.000
 9XE  O2   C22  F    112.90  3.000
 9XE  F1   C22  F2   108.02  3.000
 9XE  O2   C22  F2   112.85  3.000
 9XE  F    C22  F2   107.40  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
 9XE  CONST_01  C14  C13  N1   C12     0.00   0.0  0
 9XE  CONST_02  C14  C15  C10  C12     0.00   0.0  0
 9XE  CONST_05  N1   C13  C14  C15     0.00   0.0  0
 9XE  CONST_06  N1   C12  C10  C15     0.00   0.0  0
 9XE  CONST_07  C19  C20  C21  C16     0.00   0.0  0
 9XE  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 9XE  CONST_09  N1   C13  C14  C16   180.00   0.0  0
 9XE  CONST_10  C10  C15  C14  C16   180.00   0.0  0
 9XE  CONST_11  C17  C18  C19  C20     0.00   0.0  0
 9XE  CONST_12  C17  C16  C21  C20     0.00   0.0  0
 9XE  CONST_13  C14  C16  C21  C20   180.00   0.0  0
 9XE  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 9XE  CONST_15  C21  C16  C17  C18     0.00   0.0  0
 9XE  CONST_16  C14  C16  C17  C18   180.00   0.0  0
 9XE  CONST_17  C2   C3   C4   C5      0.00   0.0  0
 9XE  CONST_18  C2   C1   C    C5      0.00   0.0  0
 9XE  CONST_19  C    C5   C4   C3      0.00   0.0  0
 9XE  CONST_20  C    C1   C2   C3      0.00   0.0  0
 9XE  CONST_21  C13  C14  C15  C10     0.00   0.0  0
 9XE  CONST_22  C13  N1   C12  C10     0.00   0.0  0
 9XE  CONST_25  C1   C    C5   C4      0.00   0.0  0
 9XE  CONST_26  C1   C2   C3   C4      0.00   0.0  0
 9XE  CONST_27  C7   C10  C12  N1    180.00   0.0  0
 9XE  CONST_28  C7   C10  C15  C14   180.00   0.0  0
 9XE  CONST_29  C21  C20  C19  O2    180.00   0.0  0
 9XE  CONST_30  C17  C18  C19  O2    180.00   0.0  0
 9XE  CONST_31  O1   C2   C1   C     180.00   0.0  0
 9XE  CONST_32  O1   C2   C3   C4    180.00   0.0  0
 9XE  CONST_33  H15  C13  N1   C12   180.00   0.0  0
 9XE  CONST_34  H2   C15  C10  C12   180.00   0.0  0
 9XE  CONST_35  H1   C12  C10  C15   180.00   0.0  0
 9XE  CONST_36  H3   C20  C21  C16   180.00   0.0  0
 9XE  CONST_37  H4   C18  C17  C16   180.00   0.0  0
 9XE  CONST_38  H14  C21  C20  C19   180.00   0.0  0
 9XE  CONST_39  H13  C17  C18  C19   180.00   0.0  0
 9XE  CONST_40  H16  C    C5   C6      0.00   0.0  0
 9XE  CONST_41  H8   C3   C4   C5    180.00   0.0  0
 9XE  CONST_42  H17  C1   C    C5    180.00   0.0  0
 9XE  Var_01    C8   C7   C10  C12   120.16  30.0  2
 9XE  Var_02    C3   C2   O1   C11  -179.00  30.0  2
 9XE  Var_03    H10  C9   C8   C6     50.49  30.0  3
 9XE  Var_04    F    C22  O2   C19   -55.94  30.0  3
 9XE  Var_05    H5   C11  O1   C2    178.63  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
 9XE  plan-1  C16  0.020
 9XE  plan-1  C20  0.020
 9XE  plan-1  C19  0.020
 9XE  plan-1  C18  0.020
 9XE  plan-1  O2   0.020
 9XE  plan-1  C17  0.020
 9XE  plan-1  C21  0.020
 9XE  plan-1  C14  0.020
 9XE  plan-1  H3   0.020
 9XE  plan-1  H4   0.020
 9XE  plan-1  H13  0.020
 9XE  plan-1  H14  0.020
 9XE  plan-2  C12  0.020
 9XE  plan-2  C15  0.020
 9XE  plan-2  C16  0.020
 9XE  plan-2  N1   0.020
 9XE  plan-2  C10  0.020
 9XE  plan-2  C14  0.020
 9XE  plan-2  C13  0.020
 9XE  plan-2  C7   0.020
 9XE  plan-2  H1   0.020
 9XE  plan-2  H2   0.020
 9XE  plan-2  H15  0.020
 9XE  plan-3  C6   0.020
 9XE  plan-3  C5   0.020
 9XE  plan-3  C3   0.020
 9XE  plan-3  C2   0.020
 9XE  plan-3  C8   0.020
 9XE  plan-3  C9   0.020
 9XE  plan-3  C10  0.020
 9XE  plan-3  C7   0.020
 9XE  plan-3  C    0.020
 9XE  plan-3  N    0.020
 9XE  plan-3  C4   0.020
 9XE  plan-3  C1   0.020
 9XE  plan-3  O1   0.020
 9XE  plan-3  H8   0.020
 9XE  plan-3  H16  0.020
 9XE  plan-3  H17  0.020
 9XE  plan-3  H9   0.020
 9XE  plan-3  O    0.020

