# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 01:19:29 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-(1-methylpyrazol-4-yl)-7-[[(2~{S})-2-(trifluoromethyl)morpholin-4-yl]methyl]quinoline-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cc(nc3cc(CN4CCO[C@@H](C4)C(F)(F)F)ccc23)C(N)=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
 J9R  J9R  4-(1-methylpyrazol-4-yl)-7-[[(2~{S})-2-(trifluoromethyl)morpholin-4-yl]methyl]quinoline-2-carboxamide  ligand  50  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J9R
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
 J9R  N1   N  NH2   0  -0.808  17.3850  -48.0079  39.7130
 J9R  N3   N  NT    0  -0.421  16.3122  -53.0143  46.0053
 J9R  C4   C  CR16  0  -0.408  14.6276  -47.2071  41.9987
 J9R  C5   C  CR6   0   0.113  15.6799  -47.9062  41.3889
 J9R  C6   C  C     0   0.490  16.4016  -47.2679  40.2296
 J9R  C7   C  CR66  0   0.230  15.4434  -49.6815  42.8034
 J9R  C8   C  CR16  0  -0.358  15.8749  -50.9714  43.1930
 J9R  C13  C  CH1   0  -0.188  18.3642  -52.6970  47.2906
 J9R  C15  C  CH2   0  -0.284  17.5330  -52.2224  46.0892
 J9R  C17  C  CR16  0  -0.348  13.8682  -49.7079  44.6521
 J9R  N    N  NR5   0  -0.266  11.5522  -45.4294  44.3799
 J9R  C    C  CH3   0  -0.506  11.0110  -44.1469  44.7630
 J9R  O    O  O     0  -0.463  16.0832  -46.1584  39.8285
 J9R  C1   C  CR15  0   0.038  12.7612  -45.6812  43.8641
 J9R  C11  C  CH2   0  -0.362  16.5209  -54.3590  46.5016
 J9R  C12  C  CH2   0  -0.158  16.8067  -54.2860  47.9986
 J9R  C14  C  CT    0   1.016  19.2497  -51.5995  47.8480
 J9R  C16  C  CR16  0  -0.264  14.3206  -50.9445  45.0158
 J9R  C18  C  CR66  0   0.041  14.3954  -49.0449  43.5182
 J9R  C19  C  CR15  0  -0.093  11.5886  -47.5194  44.1102
 J9R  C2   C  CR5   0  -0.189  12.8441  -47.0488  43.6708
 J9R  C3   C  CR6   0   0.224  13.9588  -47.7680  43.0633
 J9R  C9   C  CR6   0   0.096  15.3205  -51.6092  44.2673
 J9R  F    F  F     0  -0.306  18.5533  -50.6202  48.4328
 J9R  F1   F  F     0  -0.311  19.9773  -51.0407  46.8720
 J9R  F2   F  F     0  -0.308  20.1032  -52.0713  48.7634
 J9R  N2   N  N     0  -0.476  16.0644  -49.1003  41.7574
 J9R  N4   N  N     0  -0.272  10.8234  -46.5324  44.5287
 J9R  O1   O  O2    0  -0.494  17.5405  -53.1181  48.3358
 J9R  H1   H  HNH2  0   0.404  17.9278  -47.6705  38.9355
 J9R  H2   H  HNH2  0   0.409  17.5906  -48.9171  40.0929
 J9R  H4   H  HCR6  0   0.266  14.3315  -46.2446  41.6061
 J9R  H5   H  HCR6  0   0.258  16.6640  -51.4385  42.6152
 J9R  H6   H  HCH2  0   0.261  14.8820  -53.6510  44.6578
 J9R  H7   H  HCH2  0   0.226  16.4608  -53.3845  43.9203
 J9R  H8   H  HCH1  0   0.269  19.0411  -53.5016  46.9661
 J9R  H9   H  HCH2  0   0.224  18.1494  -52.3230  45.1835
 J9R  H10  H  HCH2  0   0.252  17.2646  -51.1661  46.1770
 J9R  H11  H  HCR6  0   0.264  13.1100  -49.2272  45.2542
 J9R  H12  H  HCH3  0   0.263  10.1164  -43.9272  44.1839
 J9R  H13  H  HCH3  0   0.263  10.7623  -44.1435  45.8222
 J9R  H14  H  HCH3  0   0.262  11.7545  -43.3790  44.5705
 J9R  H15  H  HCR5  0   0.298  13.4817  -44.8984  43.6856
 J9R  H16  H  HCH2  0   0.266  15.6149  -54.9482  46.3491
 J9R  H17  H  HCH2  0   0.220  17.3272  -54.8858  45.9666
 J9R  H18  H  HCH2  0   0.234  15.8734  -54.2298  48.5602
 J9R  H19  H  HCH2  0   0.218  17.3438  -55.1853  48.3209
 J9R  H20  H  HCR6  0   0.256  13.9104  -51.4295  45.8928
 J9R  H21  H  HCR5  0   0.267  11.2134  -48.5318  44.1038
 J9R  C10  C  CH2   0  -0.344  15.7546  -52.9914  44.6692

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
 J9R  N1   C6   single    1.335  0.020  1.335
 J9R  C6   O    double    1.222  0.020  1.222
 J9R  C6   C5   single    1.507  0.020  1.507
 J9R  C5   N2   aromatic  1.307  0.020  1.307
 J9R  C5   C4   aromatic  1.403  0.020  1.403
 J9R  N2   C7   aromatic  1.348  0.020  1.348
 J9R  C4   C3   aromatic  1.377  0.020  1.377
 J9R  C7   C8   aromatic  1.415  0.020  1.415
 J9R  C7   C18  aromatic  1.419  0.020  1.419
 J9R  C3   C18  aromatic  1.424  0.020  1.424
 J9R  C3   C2   single    1.459  0.020  1.459
 J9R  C8   C9   aromatic  1.367  0.020  1.367
 J9R  C18  C17  aromatic  1.415  0.020  1.415
 J9R  C2   C19  aromatic  1.411  0.020  1.411
 J9R  C2   C1   aromatic  1.384  0.020  1.384
 J9R  C19  N4   aromatic  1.317  0.020  1.317
 J9R  C1   N    aromatic  1.338  0.020  1.338
 J9R  C9   C10  single    1.503  0.020  1.503
 J9R  C9   C16  aromatic  1.415  0.020  1.415
 J9R  C17  C16  aromatic  1.366  0.020  1.366
 J9R  N4   N    aromatic  1.330  0.020  1.330
 J9R  C10  N3   single    1.448  0.020  1.448
 J9R  N    C    single    1.444  0.020  1.444
 J9R  N3   C15  single    1.458  0.020  1.458
 J9R  N3   C11  single    1.448  0.020  1.448
 J9R  C15  C13  single    1.536  0.020  1.536
 J9R  C11  C12  single    1.526  0.020  1.526
 J9R  C13  C14  single    1.516  0.020  1.516
 J9R  C13  O1   single    1.396  0.020  1.396
 J9R  C12  O1   single    1.420  0.020  1.420
 J9R  F    C14  single    1.336  0.020  1.336
 J9R  F1   C14  single    1.340  0.020  1.340
 J9R  C14  F2   single    1.338  0.020  1.338
 J9R  N1   H1   single    0.860  0.020  1.020
 J9R  N1   H2   single    0.860  0.020  1.020
 J9R  C4   H4   single    0.930  0.020  1.080
 J9R  C8   H5   single    0.930  0.020  1.080
 J9R  C10  H6   single    0.970  0.020  1.090
 J9R  C10  H7   single    0.970  0.020  1.090
 J9R  C13  H8   single    0.970  0.020  1.090
 J9R  C15  H9   single    0.970  0.020  1.090
 J9R  C15  H10  single    0.970  0.020  1.090
 J9R  C17  H11  single    0.930  0.020  1.080
 J9R  C    H12  single    0.970  0.020  1.090
 J9R  C    H13  single    0.970  0.020  1.090
 J9R  C    H14  single    0.970  0.020  1.090
 J9R  C1   H15  single    0.930  0.020  1.080
 J9R  C11  H16  single    0.970  0.020  1.090
 J9R  C11  H17  single    0.970  0.020  1.090
 J9R  C12  H18  single    0.970  0.020  1.090
 J9R  C12  H19  single    0.970  0.020  1.090
 J9R  C16  H20  single    0.930  0.020  1.080
 J9R  C19  H21  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
 J9R  H2   N1   H1   118.96  3.000
 J9R  H2   N1   C6   120.34  3.000
 J9R  H1   N1   C6   120.70  3.000
 J9R  C11  N3   C15  111.34  3.000
 J9R  C11  N3   C10  112.72  3.000
 J9R  C15  N3   C10  111.53  3.000
 J9R  H4   C4   C3   120.70  3.000
 J9R  H4   C4   C5   119.44  3.000
 J9R  C3   C4   C5   119.84  3.000
 J9R  N2   C5   C6   117.56  3.000
 J9R  N2   C5   C4   123.59  3.000
 J9R  C6   C5   C4   118.85  3.000
 J9R  O    C6   C5   120.80  3.000
 J9R  C5   C6   N1   114.57  3.000
 J9R  O    C6   N1   124.63  3.000
 J9R  N2   C7   C18  122.51  3.000
 J9R  C18  C7   C8   119.70  3.000
 J9R  N2   C7   C8   117.79  3.000
 J9R  H5   C8   C9   120.88  3.000
 J9R  H5   C8   C7   117.91  3.000
 J9R  C9   C8   C7   121.21  3.000
 J9R  H8   C13  O1   111.30  3.000
 J9R  H8   C13  C14  106.16  3.000
 J9R  O1   C13  C14  106.72  3.000
 J9R  H8   C13  C15  109.16  3.000
 J9R  O1   C13  C15  111.07  3.000
 J9R  C14  C13  C15  112.33  3.000
 J9R  H10  C15  H9   106.98  3.000
 J9R  H10  C15  C13  111.62  3.000
 J9R  H9   C15  C13  108.21  3.000
 J9R  H10  C15  N3   108.90  3.000
 J9R  H9   C15  N3   111.85  3.000
 J9R  C13  C15  N3   109.29  3.000
 J9R  H11  C17  C18  119.94  3.000
 J9R  H11  C17  C16  119.12  3.000
 J9R  C18  C17  C16  120.93  3.000
 J9R  N4   N    C1   112.45  3.000
 J9R  N4   N    C    120.10  3.000
 J9R  C1   N    C    127.45  3.000
 J9R  H14  C    H13  109.07  3.000
 J9R  H14  C    H12  109.01  3.000
 J9R  H13  C    H12  109.25  3.000
 J9R  H14  C    N    108.93  3.000
 J9R  H13  C    N    110.28  3.000
 J9R  H12  C    N    110.26  3.000
 J9R  H15  C1   C2   130.85  3.000
 J9R  H15  C1   N    122.04  3.000
 J9R  C2   C1   N    107.09  3.000
 J9R  H17  C11  H16  106.35  3.000
 J9R  H17  C11  C12  111.23  3.000
 J9R  H16  C11  C12  108.56  3.000
 J9R  H17  C11  N3   112.52  3.000
 J9R  H16  C11  N3   109.50  3.000
 J9R  C12  C11  N3   108.59  3.000
 J9R  H19  C12  H18  108.07  3.000
 J9R  H19  C12  O1   110.60  3.000
 J9R  H18  C12  O1   106.11  3.000
 J9R  H19  C12  C11  109.95  3.000
 J9R  H18  C12  C11  110.32  3.000
 J9R  O1   C12  C11  111.66  3.000
 J9R  F2   C14  F1   107.41  3.000
 J9R  F2   C14  F    106.95  3.000
 J9R  F1   C14  F    107.23  3.000
 J9R  F2   C14  C13  111.65  3.000
 J9R  F1   C14  C13  110.57  3.000
 J9R  F    C14  C13  112.76  3.000
 J9R  H20  C16  C9   119.06  3.000
 J9R  H20  C16  C17  119.71  3.000
 J9R  C9   C16  C17  121.23  3.000
 J9R  C3   C18  C17  124.18  3.000
 J9R  C17  C18  C7   117.93  3.000
 J9R  C3   C18  C7   117.89  3.000
 J9R  H21  C19  N4   120.18  3.000
 J9R  H21  C19  C2   128.32  3.000
 J9R  N4   C19  C2   111.46  3.000
 J9R  C3   C2   C19  130.17  3.000
 J9R  C19  C2   C1   103.47  3.000
 J9R  C3   C2   C1   126.23  3.000
 J9R  C2   C3   C18  122.90  3.000
 J9R  C2   C3   C4   119.49  3.000
 J9R  C18  C3   C4   117.60  3.000
 J9R  C16  C9   C10  119.64  3.000
 J9R  C16  C9   C8   118.89  3.000
 J9R  C10  C9   C8   121.47  3.000
 J9R  C7   N2   C5   118.48  3.000
 J9R  C19  N4   N    105.52  3.000
 J9R  C12  O1   C13  112.04  3.000
 J9R  H7   C10  H6   106.81  3.000
 J9R  H7   C10  C9   109.35  3.000
 J9R  H6   C10  C9   108.73  3.000
 J9R  H7   C10  N3   112.01  3.000
 J9R  H6   C10  N3   107.90  3.000
 J9R  C9   C10  N3   111.86  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
 J9R  CONST_01  C7   N2   C5   C4     0.00   0.0  0
 J9R  CONST_02  C7   C18  C3   C4     0.00   0.0  0
 J9R  CONST_03  C17  C18  C3   C4   180.00   0.0  0
 J9R  CONST_06  C8   C7   N2   C5   180.00   0.0  0
 J9R  CONST_07  C18  C7   N2   C5     0.00   0.0  0
 J9R  CONST_08  C18  C3   C4   C5     0.00   0.0  0
 J9R  CONST_09  C2   C3   C4   C5   180.00   0.0  0
 J9R  CONST_10  C16  C9   C8   C7     0.00   0.0  0
 J9R  CONST_11  C2   C3   C18  C7   180.00   0.0  0
 J9R  CONST_12  C16  C17  C18  C7     0.00   0.0  0
 J9R  CONST_13  C3   C18  C7   C8   180.00   0.0  0
 J9R  CONST_14  C17  C18  C7   C8     0.00   0.0  0
 J9R  CONST_15  C17  C16  C9   C8     0.00   0.0  0
 J9R  CONST_16  N2   C7   C18  C17  180.00   0.0  0
 J9R  CONST_17  C2   C3   C18  C17    0.00   0.0  0
 J9R  CONST_18  C3   C2   C1   N    180.00   0.0  0
 J9R  CONST_19  C19  C2   C1   N      0.00   0.0  0
 J9R  CONST_20  C2   C19  N4   N      0.00   0.0  0
 J9R  CONST_22  N4   C19  C2   C1     0.00   0.0  0
 J9R  CONST_23  C19  N4   N    C1     0.00   0.0  0
 J9R  CONST_24  C3   C18  C17  C16  180.00   0.0  0
 J9R  CONST_25  C9   C8   C7   C18    0.00   0.0  0
 J9R  CONST_27  C9   C16  C17  C18    0.00   0.0  0
 J9R  CONST_28  N4   N    C1   C2     0.00   0.0  0
 J9R  CONST_29  N2   C5   C4   C3     0.00   0.0  0
 J9R  CONST_30  N2   C7   C18  C3     0.00   0.0  0
 J9R  CONST_31  N4   C19  C2   C3   180.00   0.0  0
 J9R  CONST_32  N2   C7   C8   C9   180.00   0.0  0
 J9R  CONST_33  C7   N2   C5   C6   180.00   0.0  0
 J9R  CONST_34  C3   C4   C5   C6   180.00   0.0  0
 J9R  CONST_35  C10  C9   C8   C7   180.00   0.0  0
 J9R  CONST_36  C17  C16  C9   C10  180.00   0.0  0
 J9R  CONST_37  C2   C1   N    C    180.00   0.0  0
 J9R  CONST_38  C19  N4   N    C    180.00   0.0  0
 J9R  CONST_39  H11  C17  C18  C7   180.00   0.0  0
 J9R  CONST_40  H20  C16  C9   C8   180.00   0.0  0
 J9R  CONST_41  H21  C19  N4   N    180.00   0.0  0
 J9R  CONST_42  H5   C8   C9   C16  180.00   0.0  0
 J9R  CONST_43  H4   C4   C3   C18  180.00   0.0  0
 J9R  CONST_44  H15  C1   C2   C19  180.00   0.0  0
 J9R  CONST_45  H1   N1   C6   C5   180.00   0.0  0
 J9R  CONST_46  H2   N1   C6   C5     0.00   0.0  0
 J9R  Var_01    O1   C12  C11  N3   -34.57  30.0  1
 J9R  Var_02    C11  N3   C15  C13  -31.07  30.0  1
 J9R  Var_03    C11  C12  O1   C13  -29.70  30.0  1
 J9R  Var_04    C12  C11  N3   C15   66.27  30.0  1
 J9R  Var_05    C8   C9   C10  N3   118.86  30.0  1
 J9R  Var_06    C9   C10  N3   C15  -63.97  30.0  3
 J9R  Var_07    N2   C5   C6   N1    -0.85  30.0  2
 J9R  Var_08    H12  C    N    C1   119.35  30.0  2

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
 J9R  chir_01  C13  C15  C14  O1  negativ

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
 J9R  plan-1  N    0.020
 J9R  plan-1  C    0.020
 J9R  plan-1  C1   0.020
 J9R  plan-1  C19  0.020
 J9R  plan-1  C2   0.020
 J9R  plan-1  C3   0.020
 J9R  plan-1  N4   0.020
 J9R  plan-1  H15  0.020
 J9R  plan-1  H21  0.020
 J9R  plan-2  C4   0.020
 J9R  plan-2  C5   0.020
 J9R  plan-2  C6   0.020
 J9R  plan-2  C7   0.020
 J9R  plan-2  C8   0.020
 J9R  plan-2  C17  0.020
 J9R  plan-2  C16  0.020
 J9R  plan-2  C18  0.020
 J9R  plan-2  C2   0.020
 J9R  plan-2  C3   0.020
 J9R  plan-2  C9   0.020
 J9R  plan-2  N2   0.020
 J9R  plan-2  H4   0.020
 J9R  plan-2  H5   0.020
 J9R  plan-2  H11  0.020
 J9R  plan-2  H20  0.020
 J9R  plan-2  C10  0.020
 J9R  plan-3  N1   0.020
 J9R  plan-3  C5   0.020
 J9R  plan-3  C6   0.020
 J9R  plan-3  O    0.020
 J9R  plan-3  H1   0.020
 J9R  plan-3  H2   0.020

