# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:56:52 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]quinolin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(O)c(C)c(nc2c1)c3cncc(c3)c4ccc(OC(F)(F)F)cc4
#
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
 DY2  DY2  7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]quinolin-4-ol  ligand  48  31  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DY2
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
 DY2  C12  C  CR16  0  -0.084   1.0276   3.2758  -0.8016
 DY2  C15  C  CR16  0  -0.225  -0.1072   1.3259  -0.0502
 DY2  C16  C  CR6   0   0.088  -2.6039   1.2608  -0.1782
 DY2  C20  C  CR16  0  -0.283  -4.8621   0.7799  -0.9050
 DY2  C19  C  CR6   0   0.305  -5.0334  -0.0269   0.2061
 DY2  C18  C  CR16  0  -0.281  -4.0211  -0.1982   1.1343
 DY2  C11  C  CH3   0  -0.441   6.0390  -4.6593  -0.8885
 DY2  C6   C  CR6   0   0.411   4.5921   1.3250   0.9446
 DY2  C5   C  CR66  0  -0.031   4.7426   0.0094   0.4415
 DY2  C3   C  CR16  0  -0.423   3.7207  -1.8811  -0.7046
 DY2  C2   C  CR6   0   0.396   4.8775  -2.6108  -0.5471
 DY2  N1   N  N     0  -0.392  -0.1095   3.8729  -1.1296
 DY2  C8   C  CR6   0  -0.092   3.3978   2.0046   0.7892
 DY2  C9   C  CH3   0  -0.794   3.2164   3.3536   1.4276
 DY2  C10  C  CR6   0  -0.040   1.0903   2.0025  -0.2422
 DY2  N    N  N     0  -0.483   2.4789   0.1158  -0.4066
 DY2  C    C  CR16  0  -0.276   5.9195  -0.7514   0.5840
 DY2  O    O  OH1   0  -0.598   5.6466   1.8381   1.5811
 DY2  C1   C  CR16  0  -0.373   5.9923  -2.0320   0.1046
 DY2  C13  C  CR16  0  -0.100  -1.2441   3.2258  -0.9131
 DY2  C14  C  CR6   0   0.013  -1.3111   1.9379  -0.3811
 DY2  C17  C  CR16  0  -0.307  -2.8123   0.4490   0.9370
 DY2  C21  C  CR16  0  -0.306  -3.6464   1.4184  -1.0916
 DY2  C22  C  CT    0   1.073  -6.4613  -1.8526  -0.0847
 DY2  C4   C  CR66  0   0.217   3.6305  -0.5646  -0.2170
 DY2  C7   C  CR6   0   0.147   2.3820   1.3393   0.0569
 DY2  F    F  F     0  -0.276  -7.6815  -2.2384   0.2502
 DY2  F1   F  F     0  -0.299  -5.5927  -2.7517   0.3822
 DY2  F2   F  F     0  -0.299  -6.3621  -1.8778  -1.4152
 DY2  O2   O  O2    0  -0.522  -6.2663  -0.6306   0.4260
 DY2  H1   H  HCR6  0   0.270   1.9380   3.8275  -1.0108
 DY2  H2   H  HCR6  0   0.268  -0.0925   0.3191   0.3488
 DY2  H3   H  HCR6  0   0.284  -5.6643   0.9184  -1.6178
 DY2  H4   H  HCR6  0   0.284  -4.1759  -0.8094   2.0135
 DY2  H5   H  HCH3  0   0.232   6.2982  -4.8151   0.1612
 DY2  H6   H  HCH3  0   0.262   5.8066  -5.6216  -1.3371
 DY2  H7   H  HCH3  0   0.232   6.8998  -4.2305  -1.4071
 DY2  H8   H  HCR6  0   0.262   2.8636  -2.3119  -1.2070
 DY2  H9   H  HCH3  0   0.265   3.7152   4.1512   0.8724
 DY2  H10  H  HCH3  0   0.275   2.1671   3.6241   1.5102
 DY2  H11  H  HCH3  0   0.258   3.6074   3.3686   2.4479
 DY2  H12  H  HCR6  0   0.269   6.7832  -0.3305   1.0800
 DY2  H13  H  HOH1  0   0.493   5.4827   2.7427   1.8731
 DY2  H14  H  HCR6  0   0.286   6.9113  -2.5870   0.2339
 DY2  H15  H  HCR6  0   0.267  -2.1559   3.7588  -1.1622
 DY2  H16  H  HCR6  0   0.270  -2.0307   0.3286   1.6759
 DY2  H17  H  HCR6  0   0.269  -3.5107   2.0304  -1.9738
 DY2  O1   O  O2    0  -0.470   4.8788  -3.8620  -1.0365

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
 DY2  C11  O1   single    1.416  0.020  1.416
 DY2  C1   C    aromatic  1.369  0.020  1.369
 DY2  C1   C2   aromatic  1.415  0.020  1.415
 DY2  O1   C2   single    1.343  0.020  1.343
 DY2  C    C5   aromatic  1.409  0.020  1.409
 DY2  C2   C3   aromatic  1.377  0.020  1.377
 DY2  O    C6   single    1.334  0.020  1.334
 DY2  C5   C6   aromatic  1.417  0.020  1.417
 DY2  C5   C4   aromatic  1.414  0.020  1.414
 DY2  C3   C4   aromatic  1.407  0.020  1.407
 DY2  C6   C8   aromatic  1.383  0.020  1.383
 DY2  C4   N    aromatic  1.351  0.020  1.351
 DY2  C8   C9   single    1.503  0.020  1.503
 DY2  C8   C7   aromatic  1.418  0.020  1.418
 DY2  N    C7   aromatic  1.312  0.020  1.312
 DY2  C7   C10  single    1.482  0.020  1.482
 DY2  C10  C15  aromatic  1.389  0.020  1.389
 DY2  C10  C12  aromatic  1.392  0.020  1.392
 DY2  C15  C14  aromatic  1.390  0.020  1.390
 DY2  C17  C18  aromatic  1.385  0.020  1.385
 DY2  C17  C16  aromatic  1.395  0.020  1.395
 DY2  C12  N1   aromatic  1.326  0.020  1.326
 DY2  C18  C19  aromatic  1.384  0.020  1.384
 DY2  C14  C16  single    1.473  0.020  1.473
 DY2  C14  C13  aromatic  1.395  0.020  1.395
 DY2  C16  C21  aromatic  1.395  0.020  1.395
 DY2  N1   C13  aromatic  1.324  0.020  1.324
 DY2  C19  O2   single    1.390  0.020  1.390
 DY2  C19  C20  aromatic  1.384  0.020  1.384
 DY2  O2   C22  single    1.339  0.020  1.339
 DY2  C21  C20  aromatic  1.386  0.020  1.386
 DY2  F2   C22  single    1.334  0.020  1.334
 DY2  C22  F1   single    1.334  0.020  1.334
 DY2  C22  F    single    1.323  0.020  1.323
 DY2  C12  H1   single    0.930  0.020  1.080
 DY2  C15  H2   single    0.930  0.020  1.080
 DY2  C20  H3   single    0.930  0.020  1.080
 DY2  C18  H4   single    0.930  0.020  1.080
 DY2  C11  H5   single    0.970  0.020  1.090
 DY2  C11  H6   single    0.970  0.020  1.090
 DY2  C11  H7   single    0.970  0.020  1.090
 DY2  C3   H8   single    0.930  0.020  1.080
 DY2  C9   H9   single    0.970  0.020  1.090
 DY2  C9   H10  single    0.970  0.020  1.090
 DY2  C9   H11  single    0.970  0.020  1.090
 DY2  C    H12  single    0.930  0.020  1.080
 DY2  O    H13  single    0.850  0.020  0.980
 DY2  C1   H14  single    0.930  0.020  1.080
 DY2  C13  H15  single    0.930  0.020  1.080
 DY2  C17  H16  single    0.930  0.020  1.080
 DY2  C21  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
 DY2  H1   C12  C10  120.32  3.000
 DY2  H1   C12  N1   116.30  3.000
 DY2  C10  C12  N1   123.37  3.000
 DY2  H2   C15  C14  120.57  3.000
 DY2  H2   C15  C10  119.48  3.000
 DY2  C14  C15  C10  119.95  3.000
 DY2  C21  C16  C17  118.53  3.000
 DY2  C21  C16  C14  120.91  3.000
 DY2  C17  C16  C14  120.57  3.000
 DY2  H3   C20  C21  120.18  3.000
 DY2  H3   C20  C19  120.78  3.000
 DY2  C21  C20  C19  119.03  3.000
 DY2  O2   C19  C18  119.26  3.000
 DY2  O2   C19  C20  119.34  3.000
 DY2  C18  C19  C20  121.34  3.000
 DY2  H4   C18  C17  120.30  3.000
 DY2  H4   C18  C19  120.68  3.000
 DY2  C17  C18  C19  119.00  3.000
 DY2  H7   C11  H6   108.67  3.000
 DY2  H7   C11  H5   108.97  3.000
 DY2  H6   C11  H5   108.72  3.000
 DY2  H7   C11  O1   112.03  3.000
 DY2  H6   C11  O1   106.28  3.000
 DY2  H5   C11  O1   112.04  3.000
 DY2  O    C6   C8   123.17  3.000
 DY2  C8   C6   C5   120.55  3.000
 DY2  O    C6   C5   116.27  3.000
 DY2  C4   C5   C    119.01  3.000
 DY2  C4   C5   C6   117.31  3.000
 DY2  C    C5   C6   123.68  3.000
 DY2  H8   C3   C4   118.84  3.000
 DY2  H8   C3   C2   120.48  3.000
 DY2  C4   C3   C2   120.68  3.000
 DY2  O1   C2   C1   123.23  3.000
 DY2  O1   C2   C3   116.92  3.000
 DY2  C1   C2   C3   119.86  3.000
 DY2  C13  N1   C12  118.33  3.000
 DY2  C7   C8   C9   123.63  3.000
 DY2  C7   C8   C6   116.50  3.000
 DY2  C9   C8   C6   119.83  3.000
 DY2  H11  C9   H10  105.74  3.000
 DY2  H11  C9   H9   107.52  3.000
 DY2  H10  C9   H9   107.32  3.000
 DY2  H11  C9   C8   111.45  3.000
 DY2  H10  C9   C8   111.85  3.000
 DY2  H9   C9   C8   112.60  3.000
 DY2  C7   C10  C15  120.36  3.000
 DY2  C15  C10  C12  117.54  3.000
 DY2  C7   C10  C12  121.97  3.000
 DY2  C7   N    C4   118.89  3.000
 DY2  H12  C    C1   118.83  3.000
 DY2  H12  C    C5   120.23  3.000
 DY2  C1   C    C5   120.94  3.000
 DY2  H13  O    C6   111.76  3.000
 DY2  H14  C1   C    118.90  3.000
 DY2  H14  C1   C2   120.98  3.000
 DY2  C    C1   C2   120.13  3.000
 DY2  H15  C13  C14  120.05  3.000
 DY2  H15  C13  N1   116.26  3.000
 DY2  C14  C13  N1   123.69  3.000
 DY2  C13  C14  C16  121.25  3.000
 DY2  C13  C14  C15  117.10  3.000
 DY2  C16  C14  C15  121.65  3.000
 DY2  H16  C17  C18  118.75  3.000
 DY2  H16  C17  C16  120.17  3.000
 DY2  C18  C17  C16  121.07  3.000
 DY2  H17  C21  C20  118.70  3.000
 DY2  H17  C21  C16  120.26  3.000
 DY2  C20  C21  C16  121.02  3.000
 DY2  O2   C22  F2   112.75  3.000
 DY2  F2   C22  F1   106.72  3.000
 DY2  O2   C22  F1   112.75  3.000
 DY2  F1   C22  F    108.38  3.000
 DY2  F2   C22  F    108.39  3.000
 DY2  O2   C22  F    107.70  3.000
 DY2  N    C4   C3   118.51  3.000
 DY2  N    C4   C5   122.09  3.000
 DY2  C3   C4   C5   119.39  3.000
 DY2  N    C7   C10  114.23  3.000
 DY2  C10  C7   C8   121.23  3.000
 DY2  N    C7   C8   124.55  3.000
 DY2  C22  O2   C19  117.73  3.000
 DY2  C2   O1   C11  119.16  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
 DY2  CONST_03  C14  C15  C10  C12    0.00   0.0  0
 DY2  CONST_04  C14  C13  N1   C12    0.00   0.0  0
 DY2  CONST_07  N1   C12  C10  C15    0.00   0.0  0
 DY2  CONST_10  N1   C13  C14  C15    0.00   0.0  0
 DY2  CONST_11  C19  C18  C17  C16    0.00   0.0  0
 DY2  CONST_12  C10  C15  C14  C16  180.00   0.0  0
 DY2  CONST_13  N1   C13  C14  C16  180.00   0.0  0
 DY2  CONST_14  C19  C20  C21  C16    0.00   0.0  0
 DY2  CONST_15  C17  C18  C19  C20    0.00   0.0  0
 DY2  CONST_16  C17  C16  C21  C20    0.00   0.0  0
 DY2  CONST_17  C14  C16  C21  C20  180.00   0.0  0
 DY2  CONST_18  C14  C16  C17  C18  180.00   0.0  0
 DY2  CONST_19  C21  C16  C17  C18    0.00   0.0  0
 DY2  CONST_20  C21  C20  C19  C18    0.00   0.0  0
 DY2  CONST_21  C1   C    C5   C6   180.00   0.0  0
 DY2  CONST_22  C3   C4   C5   C6   180.00   0.0  0
 DY2  CONST_23  N    C4   C5   C6     0.00   0.0  0
 DY2  CONST_24  N    C7   C8   C6     0.00   0.0  0
 DY2  CONST_25  C10  C7   C8   C6   180.00   0.0  0
 DY2  CONST_26  C2   C1   C    C5     0.00   0.0  0
 DY2  CONST_27  C7   C8   C6   C5     0.00   0.0  0
 DY2  CONST_28  C2   C3   C4   C5     0.00   0.0  0
 DY2  CONST_29  C7   N    C4   C5     0.00   0.0  0
 DY2  CONST_30  C    C1   C2   C3     0.00   0.0  0
 DY2  CONST_31  C    C5   C4   C3     0.00   0.0  0
 DY2  CONST_32  C7   N    C4   C3   180.00   0.0  0
 DY2  CONST_33  N    C4   C3   C2   180.00   0.0  0
 DY2  CONST_34  C7   C10  C12  N1   180.00   0.0  0
 DY2  CONST_35  C    C5   C6   C8   180.00   0.0  0
 DY2  CONST_36  C4   C5   C6   C8     0.00   0.0  0
 DY2  CONST_37  C4   N    C7   C8     0.00   0.0  0
 DY2  CONST_38  C4   N    C7   C10  180.00   0.0  0
 DY2  CONST_39  C13  C14  C15  C10    0.00   0.0  0
 DY2  CONST_40  C13  N1   C12  C10    0.00   0.0  0
 DY2  CONST_41  C    C5   C4   N    180.00   0.0  0
 DY2  CONST_42  C4   C5   C    C1     0.00   0.0  0
 DY2  CONST_43  C4   C3   C2   C1     0.00   0.0  0
 DY2  CONST_46  C7   C10  C15  C14  180.00   0.0  0
 DY2  CONST_47  C9   C8   C6   C5   180.00   0.0  0
 DY2  CONST_48  N    C7   C8   C9   180.00   0.0  0
 DY2  CONST_49  C10  C7   C8   C9     0.00   0.0  0
 DY2  CONST_50  O1   C2   C1   C    180.00   0.0  0
 DY2  CONST_51  O    C6   C5   C      0.00   0.0  0
 DY2  CONST_52  C4   C5   C6   O    180.00   0.0  0
 DY2  CONST_53  C7   C8   C6   O    180.00   0.0  0
 DY2  CONST_54  O2   C19  C18  C17  180.00   0.0  0
 DY2  CONST_55  O2   C19  C20  C21  180.00   0.0  0
 DY2  CONST_56  O1   C2   C3   C4   180.00   0.0  0
 DY2  CONST_57  H2   C15  C10  C12  180.00   0.0  0
 DY2  CONST_58  H15  C13  N1   C12  180.00   0.0  0
 DY2  CONST_59  H1   C12  C10  C15  180.00   0.0  0
 DY2  CONST_60  H4   C18  C17  C16  180.00   0.0  0
 DY2  CONST_61  H3   C20  C21  C16  180.00   0.0  0
 DY2  CONST_62  H16  C17  C18  C19  180.00   0.0  0
 DY2  CONST_63  H17  C21  C20  C19  180.00   0.0  0
 DY2  CONST_64  H12  C    C5   C6     0.00   0.0  0
 DY2  CONST_65  H14  C1   C    C5   180.00   0.0  0
 DY2  CONST_66  H8   C3   C4   C5   180.00   0.0  0
 DY2  Var_01    C1   C2   O1   C11    0.72  30.0  2
 DY2  Var_02    H9   C9   C8   C6    77.77  30.0  2
 DY2  Var_03    F2   C22  O2   C19  -61.03  30.0  3
 DY2  Var_04    H5   C11  O1   C2    60.40  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
 DY2  plan-1  C12  0.020
 DY2  plan-1  C15  0.020
 DY2  plan-1  C16  0.020
 DY2  plan-1  N1   0.020
 DY2  plan-1  C10  0.020
 DY2  plan-1  C13  0.020
 DY2  plan-1  C14  0.020
 DY2  plan-1  C7   0.020
 DY2  plan-1  H1   0.020
 DY2  plan-1  H2   0.020
 DY2  plan-1  H15  0.020
 DY2  plan-2  C16  0.020
 DY2  plan-2  C20  0.020
 DY2  plan-2  C19  0.020
 DY2  plan-2  C18  0.020
 DY2  plan-2  C14  0.020
 DY2  plan-2  C17  0.020
 DY2  plan-2  C21  0.020
 DY2  plan-2  O2   0.020
 DY2  plan-2  H3   0.020
 DY2  plan-2  H4   0.020
 DY2  plan-2  H16  0.020
 DY2  plan-2  H17  0.020
 DY2  plan-3  C6   0.020
 DY2  plan-3  C5   0.020
 DY2  plan-3  C3   0.020
 DY2  plan-3  C2   0.020
 DY2  plan-3  C8   0.020
 DY2  plan-3  C9   0.020
 DY2  plan-3  C10  0.020
 DY2  plan-3  N    0.020
 DY2  plan-3  C    0.020
 DY2  plan-3  O    0.020
 DY2  plan-3  C1   0.020
 DY2  plan-3  C4   0.020
 DY2  plan-3  C7   0.020
 DY2  plan-3  H8   0.020
 DY2  plan-3  H12  0.020
 DY2  plan-3  H14  0.020
 DY2  plan-3  O1   0.020

