# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:16:28 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-(3-methyl-4-{[3-(pyrimidin-4-yl)pyridin-2-yl]oxy}phenyl)-3-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(NC(=O)c2cccc(c2)C(F)(F)F)ccc1Oc3ncccc3c4ccncn4
#
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
 LJE  LJE  N-(3-methyl-4-{[3-(pyrimidin-4-yl)pyridin-2-yl]oxy}phenyl)-3-(trifluoromethyl)benzamide  ligand  50  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LJE
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
 LJE  C1    C  CR16  0  -0.224  -5.7738  -2.3000  -1.1446
 LJE  F1    F  F     0  -0.303  -9.0488  -0.0567  -0.0181
 LJE  N1    N  N     0  -0.394   5.9195  -1.4231  -0.1170
 LJE  O1    O  O2    0  -0.503   3.5200   0.0516   0.3451
 LJE  C2    C  CR16  0  -0.276  -6.8786  -1.5060  -0.8797
 LJE  F2    F  F     0  -0.309  -7.8263   1.1340   1.2924
 LJE  N2    N  N     0  -0.395   7.6900  -2.3837   1.1267
 LJE  O2    O  O     0  -0.457  -2.9294   0.5178   1.3963
 LJE  C3    C  CR6   0  -0.175  -6.7123  -0.3076  -0.1963
 LJE  F3    F  F     0  -0.313  -7.9309   1.6052  -0.8017
 LJE  N3    N  N     0  -0.436   3.5011   2.0280  -0.8049
 LJE  C4    C  CR16  0  -0.295  -5.4499   0.0944   0.2156
 LJE  N4    N  NH1   0  -0.764  -1.9457  -0.6397  -0.2967
 LJE  C5    C  CR6   0  -0.025  -4.3388  -0.6916  -0.0683
 LJE  C6    C  CR16  0  -0.286  -4.5097  -1.8976  -0.7446
 LJE  C7    C  CT    0   1.057  -7.8823   0.5882   0.0716
 LJE  C8    C  C     0   0.539  -3.0091  -0.2121   0.4239
 LJE  C9    C  CR6   0   0.258   6.3235  -0.2021   0.2309
 LJE  C10   C  CR16  0   0.045   6.6195  -2.4434   0.3474
 LJE  C11   C  CR16  0  -0.022   8.0911  -1.1659   1.4710
 LJE  C12   C  CR16  0  -0.340   7.4346  -0.0243   1.0474
 LJE  C13   C  CR16  0  -0.340   5.5467   3.0877  -1.4189
 LJE  C14   C  CR16  0  -0.168   6.2573   2.0265  -0.8726
 LJE  C15   C  CR6   0  -0.105   5.5844   0.9554  -0.3054
 LJE  C16   C  CR6   0   0.503   4.1830   1.0356  -0.2863
 LJE  C17   C  CR16  0  -0.052   4.1681   3.0313  -1.3708
 LJE  C18   C  CR6   0   0.311   2.1586  -0.0617   0.1685
 LJE  C19   C  CR6   0   0.073   1.6623  -0.6567  -0.9894
 LJE  C20   C  CR16  0  -0.425   0.2884  -0.8162  -1.0867
 LJE  C21   C  CR6   0   0.406  -0.5836  -0.4025  -0.0768
 LJE  C22   C  CR16  0  -0.333  -0.0588   0.1826   1.0733
 LJE  C23   C  CR16  0  -0.304   1.3148   0.3490   1.1806
 LJE  H1    H  HCR6  0   0.280  -5.9014  -3.2416  -1.6604
 LJE  H2    H  HCR6  0   0.282  -7.8567  -1.8360  -1.2011
 LJE  H4    H  HCR6  0   0.280  -5.3148   1.0225   0.7558
 LJE  HN4   H  HNH1  0   0.426  -2.1473  -1.1322  -1.1531
 LJE  H6    H  HCR6  0   0.275  -3.6710  -2.5526  -0.9443
 LJE  H10   H  HCR6  0   0.264   6.2828  -3.4325   0.0568
 LJE  H11   H  HCR6  0   0.284   8.9629  -1.0955   2.1110
 LJE  H12   H  HCR6  0   0.287   7.7691   0.9572   1.3514
 LJE  H13   H  HCR6  0   0.276   6.0511   3.9248  -1.8788
 LJE  H14   H  HCR6  0   0.280   7.3394   2.0192  -0.9141
 LJE  H17   H  HCR6  0   0.275   3.5669   3.8253  -1.7979
 LJE  H20   H  HCR6  0   0.271  -0.1167  -1.2791  -1.9802
 LJE  H22   H  HCR6  0   0.283  -0.6906   0.5102   1.8813
 LJE  H23   H  HCR6  0   0.270   1.7278   0.8002   2.0738
 LJE  H24   H  HCH3  0   0.258   3.4323  -1.6584  -1.7054
 LJE  H24A  H  HCH3  0   0.255   2.0435  -1.7446  -2.7955
 LJE  H24B  H  HCH3  0   0.250   2.9646  -0.2556  -2.6512
 LJE  C24   C  CH3   0  -0.742   2.5739  -1.1072  -2.0903

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
 LJE  C1   C2    aromatic  1.386  0.020  1.386
 LJE  C1   C6    aromatic  1.386  0.020  1.386
 LJE  F1   C7    single    1.336  0.020  1.336
 LJE  N1   C9    aromatic  1.332  0.020  1.332
 LJE  N1   C10   aromatic  1.322  0.020  1.322
 LJE  O1   C16   single    1.344  0.020  1.344
 LJE  O1   C18   single    1.377  0.020  1.377
 LJE  C2   C3    aromatic  1.389  0.020  1.389
 LJE  F2   C7    single    1.338  0.020  1.338
 LJE  N2   C10   aromatic  1.325  0.020  1.325
 LJE  N2   C11   aromatic  1.328  0.020  1.328
 LJE  O2   C8    double    1.218  0.020  1.218
 LJE  C3   C4    aromatic  1.387  0.020  1.387
 LJE  C3   C7    single    1.498  0.020  1.498
 LJE  F3   C7    single    1.341  0.020  1.341
 LJE  N3   C16   aromatic  1.311  0.020  1.311
 LJE  N3   C17   aromatic  1.331  0.020  1.331
 LJE  C4   C5    aromatic  1.390  0.020  1.390
 LJE  N4   C8    single    1.354  0.020  1.354
 LJE  N4   C21   single    1.400  0.020  1.400
 LJE  C5   C6    aromatic  1.393  0.020  1.393
 LJE  C5   C8    single    1.497  0.020  1.497
 LJE  C9   C12   aromatic  1.390  0.020  1.390
 LJE  C9   C15   single    1.474  0.020  1.474
 LJE  C11  C12   aromatic  1.383  0.020  1.383
 LJE  C13  C14   aromatic  1.389  0.020  1.389
 LJE  C13  C17   aromatic  1.381  0.020  1.381
 LJE  C14  C15   aromatic  1.386  0.020  1.386
 LJE  C15  C16   aromatic  1.404  0.020  1.404
 LJE  C18  C19   aromatic  1.393  0.020  1.393
 LJE  C18  C23   aromatic  1.380  0.020  1.380
 LJE  C19  C20   aromatic  1.387  0.020  1.387
 LJE  C19  C24   single    1.499  0.020  1.499
 LJE  C20  C21   aromatic  1.397  0.020  1.397
 LJE  C21  C22   aromatic  1.393  0.020  1.393
 LJE  C22  C23   aromatic  1.388  0.020  1.388
 LJE  C1   H1    single    0.930  0.020  1.080
 LJE  C2   H2    single    0.930  0.020  1.080
 LJE  C4   H4    single    0.930  0.020  1.080
 LJE  N4   HN4   single    0.860  0.020  1.020
 LJE  C6   H6    single    0.930  0.020  1.080
 LJE  C10  H10   single    0.930  0.020  1.080
 LJE  C11  H11   single    0.930  0.020  1.080
 LJE  C12  H12   single    0.930  0.020  1.080
 LJE  C13  H13   single    0.930  0.020  1.080
 LJE  C14  H14   single    0.930  0.020  1.080
 LJE  C17  H17   single    0.930  0.020  1.080
 LJE  C20  H20   single    0.930  0.020  1.080
 LJE  C22  H22   single    0.930  0.020  1.080
 LJE  C23  H23   single    0.930  0.020  1.080
 LJE  C24  H24   single    0.970  0.020  1.090
 LJE  C24  H24A  single    0.970  0.020  1.090
 LJE  C24  H24B  single    0.970  0.020  1.090

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
 LJE  H1    C1   C6    119.89  3.000
 LJE  H1    C1   C2    119.74  3.000
 LJE  C6    C1   C2    120.38  3.000
 LJE  C10   N1   C9    117.07  3.000
 LJE  C18   O1   C16   119.18  3.000
 LJE  H2    C2   C3    121.18  3.000
 LJE  H2    C2   C1    119.30  3.000
 LJE  C3    C2   C1    119.51  3.000
 LJE  C11   N2   C10   115.96  3.000
 LJE  C7    C3   C4    118.97  3.000
 LJE  C7    C3   C2    120.68  3.000
 LJE  C4    C3   C2    120.32  3.000
 LJE  C17   N3   C16   118.57  3.000
 LJE  H4    C4   C5    119.14  3.000
 LJE  H4    C4   C3    120.68  3.000
 LJE  C5    C4   C3    120.18  3.000
 LJE  HN4   N4   C21   114.25  3.000
 LJE  HN4   N4   C8    116.70  3.000
 LJE  C21   N4   C8    128.84  3.000
 LJE  C8    C5   C6    123.09  3.000
 LJE  C8    C5   C4    117.49  3.000
 LJE  C6    C5   C4    119.37  3.000
 LJE  H6    C6   C5    121.21  3.000
 LJE  H6    C6   C1    118.54  3.000
 LJE  C5    C6   C1    120.23  3.000
 LJE  F3    C7   C3    111.43  3.000
 LJE  F3    C7   F2    106.63  3.000
 LJE  C3    C7   F2    111.98  3.000
 LJE  F3    C7   F1    106.90  3.000
 LJE  C3    C7   F1    112.42  3.000
 LJE  F2    C7   F1    107.14  3.000
 LJE  C5    C8   N4    114.93  3.000
 LJE  C5    C8   O2    120.83  3.000
 LJE  N4    C8   O2    124.23  3.000
 LJE  C15   C9   C12   120.92  3.000
 LJE  C15   C9   N1    118.20  3.000
 LJE  C12   C9   N1    120.86  3.000
 LJE  H10   C10  N2    116.70  3.000
 LJE  H10   C10  N1    116.46  3.000
 LJE  N2    C10  N1    126.84  3.000
 LJE  H11   C11  C12   120.59  3.000
 LJE  H11   C11  N2    117.12  3.000
 LJE  C12   C11  N2    122.29  3.000
 LJE  H12   C12  C11   121.10  3.000
 LJE  H12   C12  C9    121.92  3.000
 LJE  C11   C12  C9    116.97  3.000
 LJE  H13   C13  C17   120.85  3.000
 LJE  H13   C13  C14   121.38  3.000
 LJE  C17   C13  C14   117.77  3.000
 LJE  H14   C14  C15   119.71  3.000
 LJE  H14   C14  C13   120.08  3.000
 LJE  C15   C14  C13   120.19  3.000
 LJE  C16   C15  C14   116.49  3.000
 LJE  C16   C15  C9    122.71  3.000
 LJE  C14   C15  C9    120.80  3.000
 LJE  C15   C16  N3    123.85  3.000
 LJE  C15   C16  O1    117.20  3.000
 LJE  N3    C16  O1    118.91  3.000
 LJE  H17   C17  C13   120.69  3.000
 LJE  H17   C17  N3    116.22  3.000
 LJE  C13   C17  N3    123.09  3.000
 LJE  C23   C18  C19   121.25  3.000
 LJE  C23   C18  O1    119.06  3.000
 LJE  C19   C18  O1    119.59  3.000
 LJE  C24   C19  C20   121.10  3.000
 LJE  C24   C19  C18   121.48  3.000
 LJE  C20   C19  C18   117.41  3.000
 LJE  H20   C20  C21   119.26  3.000
 LJE  H20   C20  C19   118.48  3.000
 LJE  C21   C20  C19   122.26  3.000
 LJE  C22   C21  C20   119.09  3.000
 LJE  C22   C21  N4    124.57  3.000
 LJE  C20   C21  N4    116.33  3.000
 LJE  H22   C22  C23   119.09  3.000
 LJE  H22   C22  C21   121.76  3.000
 LJE  C23   C22  C21   119.15  3.000
 LJE  H23   C23  C22   119.43  3.000
 LJE  H23   C23  C18   119.72  3.000
 LJE  C22   C23  C18   120.84  3.000
 LJE  H24B  C24  H24A  107.35  3.000
 LJE  H24B  C24  H24   107.09  3.000
 LJE  H24A  C24  H24   108.44  3.000
 LJE  H24B  C24  C19   111.13  3.000
 LJE  H24A  C24  C19   110.83  3.000
 LJE  H24   C24  C19   111.81  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
 LJE  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 LJE  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 LJE  CONST_03  C11  C12  C9   N1     0.00   0.0  0
 LJE  CONST_06  C11  N2   C10  N1     0.00   0.0  0
 LJE  CONST_07  C5   C6   C1   C2     0.00   0.0  0
 LJE  CONST_08  C5   C4   C3   C2     0.00   0.0  0
 LJE  CONST_09  C9   N1   C10  N2     0.00   0.0  0
 LJE  CONST_10  C9   C12  C11  N2     0.00   0.0  0
 LJE  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 LJE  CONST_12  C6   C5   C4   C3     0.00   0.0  0
 LJE  CONST_13  C9   C15  C16  N3   180.00   0.0  0
 LJE  CONST_14  C14  C15  C16  N3     0.00   0.0  0
 LJE  CONST_15  C14  C13  C17  N3     0.00   0.0  0
 LJE  CONST_16  C13  C14  C15  C9   180.00   0.0  0
 LJE  CONST_17  C12  C9   N1   C10    0.00   0.0  0
 LJE  CONST_18  C15  C9   N1   C10  180.00   0.0  0
 LJE  CONST_19  C12  C11  N2   C10    0.00   0.0  0
 LJE  CONST_20  C15  C9   C12  C11  180.00   0.0  0
 LJE  CONST_23  C16  C15  C14  C13    0.00   0.0  0
 LJE  CONST_24  C16  N3   C17  C13    0.00   0.0  0
 LJE  CONST_25  C17  C13  C14  C15    0.00   0.0  0
 LJE  CONST_26  C17  N3   C16  C15    0.00   0.0  0
 LJE  CONST_27  C21  C20  C19  C18    0.00   0.0  0
 LJE  CONST_28  C21  C22  C23  C18    0.00   0.0  0
 LJE  CONST_29  C22  C23  C18  C19    0.00   0.0  0
 LJE  CONST_30  C22  C21  C20  C19    0.00   0.0  0
 LJE  CONST_31  C23  C18  C19  C20    0.00   0.0  0
 LJE  CONST_32  C23  C22  C21  C20    0.00   0.0  0
 LJE  CONST_33  C7   C3   C2   C1   180.00   0.0  0
 LJE  CONST_34  C8   C5   C6   C1   180.00   0.0  0
 LJE  CONST_35  C17  N3   C16  O1   180.00   0.0  0
 LJE  CONST_36  C9   C15  C16  O1     0.00   0.0  0
 LJE  CONST_37  C14  C15  C16  O1   180.00   0.0  0
 LJE  CONST_38  C20  C19  C18  O1   180.00   0.0  0
 LJE  CONST_39  C22  C23  C18  O1   180.00   0.0  0
 LJE  CONST_40  C8   C5   C4   C3   180.00   0.0  0
 LJE  CONST_41  C19  C20  C21  N4   180.00   0.0  0
 LJE  CONST_42  C23  C22  C21  N4   180.00   0.0  0
 LJE  CONST_43  C7   C3   C4   C5   180.00   0.0  0
 LJE  CONST_44  C24  C19  C20  C21  180.00   0.0  0
 LJE  CONST_45  C24  C19  C18  C23  180.00   0.0  0
 LJE  CONST_46  H12  C12  C9   N1   180.00   0.0  0
 LJE  CONST_47  H6   C6   C1   C2   180.00   0.0  0
 LJE  CONST_48  H4   C4   C3   C2   180.00   0.0  0
 LJE  CONST_49  H1   C1   C2   C3   180.00   0.0  0
 LJE  CONST_50  H13  C13  C17  N3   180.00   0.0  0
 LJE  CONST_51  H2   C2   C3   C4   180.00   0.0  0
 LJE  CONST_52  H10  C10  N1   C9   180.00   0.0  0
 LJE  CONST_53  H11  C11  C12  C9   180.00   0.0  0
 LJE  CONST_54  H14  C14  C15  C9     0.00   0.0  0
 LJE  CONST_55  H17  C17  C13  C14  180.00   0.0  0
 LJE  CONST_56  H20  C20  C19  C18  180.00   0.0  0
 LJE  CONST_57  H22  C22  C23  C18  180.00   0.0  0
 LJE  CONST_58  H23  C23  C18  C19  180.00   0.0  0
 LJE  CONST_59  C21  N4   C8   C5   180.00   0.0  0
 LJE  CONST_60  C20  C21  N4   C8   180.00   0.0  0
 LJE  CONST_61  C22  C21  N4   C8     0.00   0.0  0
 LJE  CONST_62  HN4  N4   C21  C20    0.00   0.0  0
 LJE  CONST_63  C21  N4   C8   O2     0.00   0.0  0
 LJE  Var_01    C19  C18  O1   C16   79.16  30.0  2
 LJE  Var_02    C2   C3   C7   F1    19.70  30.0  2
 LJE  Var_03    C4   C5   C8   O2    25.78  30.0  2
 LJE  Var_04    H24  C24  C19  C18   45.80  30.0  2

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
 LJE  plan-1  C1   0.020
 LJE  plan-1  C2   0.020
 LJE  plan-1  C3   0.020
 LJE  plan-1  C4   0.020
 LJE  plan-1  C5   0.020
 LJE  plan-1  C6   0.020
 LJE  plan-1  C7   0.020
 LJE  plan-1  C8   0.020
 LJE  plan-1  H1   0.020
 LJE  plan-1  H2   0.020
 LJE  plan-1  H4   0.020
 LJE  plan-1  H6   0.020
 LJE  plan-2  N1   0.020
 LJE  plan-2  N2   0.020
 LJE  plan-2  C9   0.020
 LJE  plan-2  C10  0.020
 LJE  plan-2  C11  0.020
 LJE  plan-2  C12  0.020
 LJE  plan-2  C15  0.020
 LJE  plan-2  H10  0.020
 LJE  plan-2  H11  0.020
 LJE  plan-2  H12  0.020
 LJE  plan-3  O1   0.020
 LJE  plan-3  N3   0.020
 LJE  plan-3  C9   0.020
 LJE  plan-3  C13  0.020
 LJE  plan-3  C14  0.020
 LJE  plan-3  C15  0.020
 LJE  plan-3  C16  0.020
 LJE  plan-3  C17  0.020
 LJE  plan-3  H13  0.020
 LJE  plan-3  H14  0.020
 LJE  plan-3  H17  0.020
 LJE  plan-4  O1   0.020
 LJE  plan-4  N4   0.020
 LJE  plan-4  C18  0.020
 LJE  plan-4  C19  0.020
 LJE  plan-4  C20  0.020
 LJE  plan-4  C21  0.020
 LJE  plan-4  C22  0.020
 LJE  plan-4  C23  0.020
 LJE  plan-4  H20  0.020
 LJE  plan-4  H22  0.020
 LJE  plan-4  H23  0.020
 LJE  plan-4  C24  0.020
 LJE  plan-5  O2   0.020
 LJE  plan-5  N4   0.020
 LJE  plan-5  C5   0.020
 LJE  plan-5  C8   0.020
 LJE  plan-5  C21  0.020
 LJE  plan-5  HN4  0.020

