# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:11:46 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 1-{(1S,2S)-1-(2,4-difluorophenyl)-2-[2-(3-methyl-1H-pyrazol-5-yl)-4-(trifluoromethyl)phenoxy]cyclopropyl}methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc([nH]n1)c2cc(ccc2O[C@H]3C[C@@]3(CN)c4ccc(F)cc4F)C(F)(F)F
#
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
 W47  W47  1-{(1S,2S)-1-(2,4-difluorophenyl)-2-[2-(3-methyl-1H-pyrazol-5-yl)-4-(trifluoromethyl)phenoxy]cyclopropyl}methanamine  ligand  48  30  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W47
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
 W47  C1   C  CH3   0  -0.741  -1.6577  -6.6790  35.9963
 W47  C10  C  CR6   0  -0.206  -7.0921  -1.8091  35.1141
 W47  C11  C  CR16  0  -0.279  -7.6232  -1.5840  36.3732
 W47  C12  C  CR16  0  -0.350  -7.0061  -2.1142  37.4953
 W47  C13  C  CR6   0   0.370  -5.8465  -2.8713  37.3696
 W47  C15  C  CH1   0   0.021  -5.7325  -3.2428  39.6856
 W47  C17  C  CH2   0  -0.516  -6.7834  -4.2224  40.0925
 W47  C18  C  CT    0  -0.119  -5.3913  -4.3133  40.6659
 W47  C19  C  CH2   0  -0.279  -5.2261  -3.8952  42.1142
 W47  C2   C  CR5   0   0.243  -2.5192  -5.4797  35.7993
 W47  C21  C  CR6   0  -0.085  -4.5052  -5.4257  40.2263
 W47  C22  C  CR16  0  -0.270  -4.9536  -6.7338  40.0906
 W47  C23  C  CR16  0  -0.422  -4.1064  -7.7681  39.7163
 W47  C24  C  CR6   0   0.537  -2.7773  -7.4715  39.4887
 W47  C26  C  CR16  0  -0.561  -2.2736  -6.1917  39.6166
 W47  C27  C  CR6   0   0.569  -3.1592  -5.1972  39.9796
 W47  C29  C  CT    0   1.054  -7.7295  -1.2594  33.8817
 W47  C3   C  CR15  0  -0.525  -3.7052  -5.1414  36.4777
 W47  C4   C  CR5   0   0.432  -4.1128  -3.9488  35.9159
 W47  C8   C  CR6   0  -0.043  -5.3083  -3.1242  36.0948
 W47  C9   C  CR16  0  -0.314  -5.9441  -2.5836  34.9858
 W47  F25  F  F     0  -0.312  -1.9388  -8.4529  39.1267
 W47  F28  F  F     0  -0.303  -2.6862  -3.9494  40.0983
 W47  F30  F  F     0  -0.316  -8.0895  -2.2310  33.0280
 W47  F31  F  F     0  -0.303  -8.8278  -0.5457  34.1447
 W47  F32  F  F     0  -0.316  -6.8952  -0.4572  33.2015
 W47  N20  N  NH2   0  -0.788  -5.6154  -4.9807  42.9935
 W47  N5   N  NR15  0  -0.502  -3.1843  -3.6533  34.9818
 W47  N6   N  N     0  -0.288  -2.2164  -4.5574  34.8995
 W47  H1   H  HCH3  0   0.248  -0.9579  -6.7934  35.1697
 W47  H2   H  HCH3  0   0.244  -1.0752  -6.6075  36.9158
 W47  H3   H  HCH3  0   0.243  -2.2557  -7.5873  36.0645
 W47  H4   H  HCR6  0   0.278  -8.5205  -0.9966  36.5080
 W47  H5   H  HCR6  0   0.295  -7.4407  -1.9221  38.4656
 W47  H6   H  HCH1  0   0.274  -5.7890  -2.2175  40.0445
 W47  H7   H  HCH2  0   0.270  -7.5846  -3.8791  40.7358
 W47  H8   H  HCH2  0   0.277  -7.0848  -4.9581  39.3564
 W47  H9   H  HCH2  0   0.236  -4.1785  -3.6530  42.3061
 W47  H10  H  HCH2  0   0.206  -5.7904  -2.9657  42.2780
 W47  H11  H  HCR6  0   0.270  -5.9966  -6.9493  40.2817
 W47  H12  H  HCR6  0   0.282  -4.4722  -8.7808  39.6129
 W47  H13  H  HCR6  0   0.298  -1.2308  -5.9720  39.4282
 W47  H14  H  HCR5  0   0.254  -4.2063  -5.7084  37.2442
 W47  H15  H  HCR6  0   0.277  -5.5421  -2.7960  34.0024
 W47  H16  H  HNH2  0   0.351  -5.4262  -4.7210  43.9529
 W47  H17  H  HNH2  0   0.341  -6.6165  -5.1213  42.9362
 W47  H19  H  HNR5  0   0.417  -3.1409  -2.8249  34.4092
 W47  O14  O  O2    0  -0.452  -5.1747  -3.3781  38.4140

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
 W47  F30  C29  single    1.343  0.020  1.343
 W47  F32  C29  single    1.342  0.020  1.342
 W47  C29  F31  single    1.336  0.020  1.336
 W47  C29  C10  single    1.492  0.020  1.492
 W47  N6   N5   aromatic  1.327  0.020  1.327
 W47  N6   C2   aromatic  1.324  0.020  1.324
 W47  N5   C4   aromatic  1.350  0.020  1.350
 W47  C9   C10  aromatic  1.391  0.020  1.391
 W47  C9   C8   aromatic  1.388  0.020  1.388
 W47  C10  C11  aromatic  1.385  0.020  1.385
 W47  C2   C1   single    1.490  0.020  1.490
 W47  C2   C3   aromatic  1.408  0.020  1.408
 W47  C4   C8   single    1.463  0.020  1.463
 W47  C4   C3   aromatic  1.380  0.020  1.380
 W47  C8   C13  aromatic  1.407  0.020  1.407
 W47  C11  C12  aromatic  1.386  0.020  1.386
 W47  C13  C12  aromatic  1.391  0.020  1.391
 W47  C13  O14  single    1.341  0.020  1.341
 W47  O14  C15  single    1.395  0.020  1.395
 W47  F25  C24  single    1.341  0.020  1.341
 W47  C26  C24  aromatic  1.381  0.020  1.381
 W47  C26  C27  aromatic  1.380  0.020  1.380
 W47  C15  C17  single    1.493  0.020  1.493
 W47  C15  C18  single    1.491  0.020  1.491
 W47  C24  C23  aromatic  1.381  0.020  1.381
 W47  F28  C27  single    1.340  0.020  1.340
 W47  C27  C21  aromatic  1.387  0.020  1.387
 W47  C17  C18  single    1.508  0.020  1.508
 W47  C23  C22  aromatic  1.388  0.020  1.388
 W47  C21  C22  aromatic  1.389  0.020  1.389
 W47  C21  C18  single    1.489  0.020  1.489
 W47  C18  C19  single    1.516  0.020  1.516
 W47  C19  N20  single    1.450  0.020  1.450
 W47  C1   H1   single    0.970  0.020  1.090
 W47  C1   H2   single    0.970  0.020  1.090
 W47  C1   H3   single    0.970  0.020  1.090
 W47  C11  H4   single    0.930  0.020  1.080
 W47  C12  H5   single    0.930  0.020  1.080
 W47  C15  H6   single    0.970  0.020  1.090
 W47  C17  H7   single    0.970  0.020  1.090
 W47  C17  H8   single    0.970  0.020  1.090
 W47  C19  H9   single    0.970  0.020  1.090
 W47  C19  H10  single    0.970  0.020  1.090
 W47  C22  H11  single    0.930  0.020  1.080
 W47  C23  H12  single    0.930  0.020  1.080
 W47  C26  H13  single    0.930  0.020  1.080
 W47  C3   H14  single    0.930  0.020  1.080
 W47  C9   H15  single    0.930  0.020  1.080
 W47  N20  H16  single    0.890  0.020  1.040
 W47  N20  H17  single    0.890  0.020  1.040
 W47  N5   H19  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
 W47  H3   C1   H2   107.16  3.000
 W47  H3   C1   H1   108.21  3.000
 W47  H2   C1   H1   107.68  3.000
 W47  H3   C1   C2   111.22  3.000
 W47  H2   C1   C2   111.56  3.000
 W47  H1   C1   C2   110.84  3.000
 W47  C9   C10  C29  118.78  3.000
 W47  C9   C10  C11  119.40  3.000
 W47  C29  C10  C11  121.81  3.000
 W47  H4   C11  C12  118.46  3.000
 W47  H4   C11  C10  121.33  3.000
 W47  C12  C11  C10  120.21  3.000
 W47  H5   C12  C13  120.90  3.000
 W47  H5   C12  C11  118.68  3.000
 W47  C13  C12  C11  120.42  3.000
 W47  O14  C13  C8   116.50  3.000
 W47  O14  C13  C12  123.57  3.000
 W47  C8   C13  C12  119.92  3.000
 W47  H6   C15  O14  114.38  3.000
 W47  H6   C15  C18  118.15  3.000
 W47  O14  C15  C18  115.99  3.000
 W47  H6   C15  C17  119.47  3.000
 W47  C18  C15  C17   60.72  3.000
 W47  O14  C15  C17  117.78  3.000
 W47  H8   C17  H7   114.39  3.000
 W47  H8   C17  C18  118.30  3.000
 W47  H7   C17  C18  118.42  3.000
 W47  H8   C17  C15  117.14  3.000
 W47  H7   C17  C15  118.32  3.000
 W47  C18  C17  C15   59.57  3.000
 W47  C21  C18  C19  115.04  3.000
 W47  C19  C18  C17  116.55  3.000
 W47  C21  C18  C17  118.83  3.000
 W47  C19  C18  C15  117.06  3.000
 W47  C21  C18  C15  118.59  3.000
 W47  C17  C18  C15   59.71  3.000
 W47  H10  C19  H9   106.17  3.000
 W47  H10  C19  N20  113.87  3.000
 W47  H9   C19  N20  108.48  3.000
 W47  H10  C19  C18  108.62  3.000
 W47  H9   C19  C18  109.48  3.000
 W47  N20  C19  C18  110.09  3.000
 W47  N6   C2   C3   110.67  3.000
 W47  C3   C2   C1   128.09  3.000
 W47  N6   C2   C1   121.24  3.000
 W47  C27  C21  C22  116.80  3.000
 W47  C22  C21  C18  122.70  3.000
 W47  C27  C21  C18  120.46  3.000
 W47  H11  C22  C23  119.17  3.000
 W47  H11  C22  C21  118.78  3.000
 W47  C23  C22  C21  122.05  3.000
 W47  H12  C23  C24  120.72  3.000
 W47  H12  C23  C22  121.12  3.000
 W47  C24  C23  C22  118.16  3.000
 W47  F25  C24  C26  118.37  3.000
 W47  C26  C24  C23  122.33  3.000
 W47  F25  C24  C23  119.30  3.000
 W47  H13  C26  C27  121.18  3.000
 W47  H13  C26  C24  121.56  3.000
 W47  C27  C26  C24  117.25  3.000
 W47  F28  C27  C26  117.90  3.000
 W47  F28  C27  C21  118.70  3.000
 W47  C26  C27  C21  123.41  3.000
 W47  F32  C29  F31  106.94  3.000
 W47  F31  C29  F30  106.94  3.000
 W47  F32  C29  F30  106.07  3.000
 W47  F31  C29  C10  112.66  3.000
 W47  F32  C29  C10  111.90  3.000
 W47  F30  C29  C10  111.91  3.000
 W47  H14  C3   C4   127.39  3.000
 W47  H14  C3   C2   127.48  3.000
 W47  C4   C3   C2   105.09  3.000
 W47  N5   C4   C8   121.55  3.000
 W47  C8   C4   C3   132.73  3.000
 W47  N5   C4   C3   105.53  3.000
 W47  C9   C8   C4   119.74  3.000
 W47  C4   C8   C13  121.64  3.000
 W47  C9   C8   C13  118.61  3.000
 W47  H15  C9   C8   118.62  3.000
 W47  H15  C9   C10  119.95  3.000
 W47  C8   C9   C10  121.42  3.000
 W47  H17  N20  H16  105.92  3.000
 W47  H17  N20  C19  109.57  3.000
 W47  H16  N20  C19  109.43  3.000
 W47  H19  N5   N6   119.56  3.000
 W47  H19  N5   C4   127.06  3.000
 W47  N6   N5   C4   113.30  3.000
 W47  N5   N6   C2   105.41  3.000
 W47  C15  O14  C13  118.22  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
 W47  CONST_01  C4   C8   C9   C10   180.00   0.0  0
 W47  CONST_02  C13  C8   C9   C10     0.00   0.0  0
 W47  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 W47  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 W47  CONST_05  C8   C13  C12  C11     0.00   0.0  0
 W47  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 W47  CONST_07  C9   C8   C13  C12     0.00   0.0  0
 W47  CONST_08  C4   C8   C13  C12   180.00   0.0  0
 W47  CONST_11  C4   N5   N6   C2      0.00   0.0  0
 W47  CONST_12  N5   C4   C3   C2      0.00   0.0  0
 W47  CONST_13  C8   C4   C3   C2    180.00   0.0  0
 W47  CONST_14  C24  C26  C27  C21     0.00   0.0  0
 W47  CONST_15  C24  C23  C22  C21     0.00   0.0  0
 W47  CONST_16  C26  C24  C23  C22     0.00   0.0  0
 W47  CONST_17  C26  C27  C21  C22     0.00   0.0  0
 W47  CONST_18  C27  C26  C24  C23     0.00   0.0  0
 W47  CONST_19  C27  C21  C22  C23     0.00   0.0  0
 W47  CONST_20  N5   N6   C2   C3      0.00   0.0  0
 W47  CONST_21  N6   N5   C4   C3      0.00   0.0  0
 W47  CONST_23  N6   C2   C3   C4      0.00   0.0  0
 W47  CONST_24  N6   N5   C4   C8    180.00   0.0  0
 W47  CONST_26  C26  C27  C21  C18   180.00   0.0  0
 W47  CONST_27  C23  C22  C21  C18   180.00   0.0  0
 W47  CONST_28  N5   N6   C2   C1    180.00   0.0  0
 W47  CONST_29  C4   C3   C2   C1    180.00   0.0  0
 W47  CONST_30  O14  C13  C12  C11   180.00   0.0  0
 W47  CONST_31  C29  C10  C11  C12   180.00   0.0  0
 W47  CONST_32  F28  C27  C21  C18     0.00   0.0  0
 W47  CONST_33  F25  C24  C23  C22   180.00   0.0  0
 W47  CONST_34  F28  C27  C21  C22   180.00   0.0  0
 W47  CONST_35  F28  C27  C26  C24   180.00   0.0  0
 W47  CONST_36  F25  C24  C26  C27   180.00   0.0  0
 W47  CONST_37  C8   C9   C10  C29   180.00   0.0  0
 W47  CONST_38  O14  C13  C8   C4      0.00   0.0  0
 W47  CONST_39  O14  C13  C8   C9    180.00   0.0  0
 W47  CONST_40  H5   C12  C11  C10   180.00   0.0  0
 W47  CONST_41  H15  C9   C10  C11   180.00   0.0  0
 W47  CONST_42  H4   C11  C12  C13   180.00   0.0  0
 W47  CONST_43  H11  C22  C21  C18     0.00   0.0  0
 W47  CONST_44  H19  N5   N6   C2    180.00   0.0  0
 W47  CONST_45  H13  C26  C27  C21   180.00   0.0  0
 W47  CONST_46  H12  C23  C22  C21   180.00   0.0  0
 W47  CONST_47  H14  C3   C4   C8      0.00   0.0  0
 W47  Var_01    C21  C18  C17  C15  -108.12  30.0  1
 W47  Var_02    C27  C21  C18  C15    70.25  30.0  2
 W47  Var_03    C17  C15  O14  C13    81.67  30.0  3
 W47  Var_04    C8   C13  O14  C15  -174.88  30.0  2
 W47  Var_05    F30  C29  C10  C11  -120.17  30.0  3
 W47  Var_06    N20  C19  C18  C15   149.19  30.0  3
 W47  Var_07    H1   C1   C2   C3    165.79  30.0  2
 W47  Var_08    H16  N20  C19  C18   175.14  30.0  3

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
 W47  chir_01  C15  O14  C17  C18  both
 W47  chir_02  C18  C21  C17  C15  both

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
 W47  plan-1  C1   0.020
 W47  plan-1  C2   0.020
 W47  plan-1  C3   0.020
 W47  plan-1  C4   0.020
 W47  plan-1  C8   0.020
 W47  plan-1  N5   0.020
 W47  plan-1  N6   0.020
 W47  plan-1  H14  0.020
 W47  plan-1  H19  0.020
 W47  plan-2  C18  0.020
 W47  plan-2  C21  0.020
 W47  plan-2  C22  0.020
 W47  plan-2  C23  0.020
 W47  plan-2  C24  0.020
 W47  plan-2  C26  0.020
 W47  plan-2  C27  0.020
 W47  plan-2  F25  0.020
 W47  plan-2  F28  0.020
 W47  plan-2  H11  0.020
 W47  plan-2  H12  0.020
 W47  plan-2  H13  0.020
 W47  plan-3  C10  0.020
 W47  plan-3  C11  0.020
 W47  plan-3  C12  0.020
 W47  plan-3  C13  0.020
 W47  plan-3  C29  0.020
 W47  plan-3  C4   0.020
 W47  plan-3  C8   0.020
 W47  plan-3  C9   0.020
 W47  plan-3  H4   0.020
 W47  plan-3  H5   0.020
 W47  plan-3  H15  0.020
 W47  plan-3  O14  0.020

