# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 04:42:35 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-[(1~{R})-1-[5-bromanyl-4-[4-(trifluoromethyl)phenyl]-1,3-oxazol-2-yl]ethoxy]-2,6-bis(fluoranyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(F)c(C(N)=O)c1F)c2oc(Br)c(n2)c3ccc(cc3)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
 ZI1  ZI1  3-[(1~{R})-1-[5-bromanyl-4-[4-(trifluoromethyl)phenyl]-1,3-oxazol-2-yl]ethoxy]-2,6-bis(fluoranyl)benzamide  ligand  42  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZI1
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
 ZI1  F5   F   F     0  -0.314   6.7204  -2.6293  -1.8121
 ZI1  C19  C   CT    0   1.053   6.8174  -1.7003  -0.8478
 ZI1  F3   F   F     0  -0.309   7.4260  -2.2901   0.1888
 ZI1  F4   F   F     0  -0.303   7.6451  -0.7553  -1.3036
 ZI1  C16  C   CR6   0  -0.205   5.4758  -1.1561  -0.4718
 ZI1  C15  C   CR16  0  -0.256   4.6548  -1.8899   0.3781
 ZI1  C14  C   CR16  0  -0.278   3.3984  -1.4161   0.7055
 ZI1  C17  C   CR16  0  -0.260   5.0216   0.0444  -1.0008
 ZI1  C18  C   CR16  0  -0.310   3.7609   0.5162  -0.6720
 ZI1  C13  C   CR6   0   0.046   2.9383  -0.2010   0.1941
 ZI1  C11  C   CR5   0   0.193   1.6068   0.2620   0.5752
 ZI1  N2   N   N     0  -0.422   0.6169  -0.6333   0.9307
 ZI1  C12  C   CR5   0   0.103   1.0805   1.5073   0.7003
 ZI1  BR1  BR  BR    0   0.051   1.7407   3.2090   0.5023
 ZI1  O3   O   O     0  -0.391  -0.1966   1.3944   1.1167
 ZI1  C10  C   CR5   0   0.529  -0.4083   0.0755   1.2322
 ZI1  C8   C   CH1   0  -0.115  -1.7408  -0.4045   1.6935
 ZI1  C9   C   CH3   0  -0.685  -2.1121   0.1389   3.0639
 ZI1  O2   O   O2    0  -0.482  -2.6654   0.0090   0.6940
 ZI1  C4   C   CR6   0   0.260  -3.8446  -0.6325   0.5819
 ZI1  C5   C   CR16  0  -0.357  -4.2355  -1.7712   1.2731
 ZI1  C3   C   CR6   0   0.522  -4.7423  -0.0936  -0.3398
 ZI1  F1   F   F     0  -0.293  -4.3820   1.0011  -1.0169
 ZI1  C2   C   CR6   0  -0.454  -5.9771  -0.6503  -0.5887
 ZI1  C7   C   CR6   0   0.550  -6.3216  -1.7926   0.1170
 ZI1  F2   F   F     0  -0.302  -7.5228  -2.3386  -0.1175
 ZI1  C6   C   CR16  0  -0.413  -5.4774  -2.3548   1.0439
 ZI1  C1   C   C     0   0.479  -6.8879  -0.0890  -1.6477
 ZI1  O1   O   O     0  -0.456  -6.9659  -0.6170  -2.7422
 ZI1  N1   N   NH2   0  -0.770  -7.5674   0.9936  -1.2690
 ZI1  H1   H   HCR6  0   0.279   4.9839  -2.8317   0.7970
 ZI1  H2   H   HCR6  0   0.270   2.7714  -1.9918   1.3723
 ZI1  H3   H   HCR6  0   0.278   5.6331   0.6238  -1.6784
 ZI1  H4   H   HCR6  0   0.263   3.4246   1.4384  -1.1239
 ZI1  H5   H   HCH1  0   0.288  -1.6597  -1.4950   1.7245
 ZI1  H6   H   HCH3  0   0.252  -2.1730   1.2265   3.0568
 ZI1  H7   H   HCH3  0   0.261  -3.0727  -0.2558   3.3925
 ZI1  H8   H   HCH3  0   0.261  -1.3633  -0.1636   3.7953
 ZI1  H9   H   HCR6  0   0.310  -3.5882  -2.2345   2.0042
 ZI1  H10  H   HCR6  0   0.295  -5.7712  -3.2406   1.5905
 ZI1  H11  H   HNH2  0   0.421  -7.4952   1.3673  -0.3379
 ZI1  H12  H   HNH2  0   0.414  -8.2111   1.4417  -1.9023

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
 ZI1  C9   C8   single    1.520  0.020  1.520
 ZI1  C8   O2   single    1.423  0.020  1.423
 ZI1  C8   C10  single    1.490  0.020  1.490
 ZI1  O3   C10  aromatic  1.341  0.020  1.341
 ZI1  O3   C12  aromatic  1.348  0.020  1.348
 ZI1  BR1  C12  single    1.836  0.020  1.836
 ZI1  O2   C4   single    1.347  0.020  1.347
 ZI1  C5   C4   aromatic  1.388  0.020  1.388
 ZI1  C5   C6   aromatic  1.391  0.020  1.391
 ZI1  C10  N2   aromatic  1.282  0.020  1.282
 ZI1  C12  C11  aromatic  1.358  0.020  1.358
 ZI1  C4   C3   aromatic  1.395  0.020  1.395
 ZI1  C6   C7   aromatic  1.374  0.020  1.374
 ZI1  N1   C1   single    1.333  0.020  1.333
 ZI1  C3   F1   single    1.337  0.020  1.337
 ZI1  C3   C2   aromatic  1.377  0.020  1.377
 ZI1  C7   C2   aromatic  1.386  0.020  1.386
 ZI1  C7   F2   single    1.340  0.020  1.340
 ZI1  C2   C1   single    1.505  0.020  1.505
 ZI1  N2   C11  aromatic  1.381  0.020  1.381
 ZI1  C11  C13  single    1.460  0.020  1.460
 ZI1  C1   O1   double    1.218  0.020  1.218
 ZI1  C13  C18  aromatic  1.393  0.020  1.393
 ZI1  C13  C14  aromatic  1.396  0.020  1.396
 ZI1  C18  C17  aromatic  1.386  0.020  1.386
 ZI1  C17  C16  aromatic  1.388  0.020  1.388
 ZI1  C14  C15  aromatic  1.382  0.020  1.382
 ZI1  C15  C16  aromatic  1.391  0.020  1.391
 ZI1  C16  C19  single    1.496  0.020  1.496
 ZI1  F5   C19  single    1.342  0.020  1.342
 ZI1  F3   C19  single    1.339  0.020  1.339
 ZI1  C19  F4   single    1.336  0.020  1.336
 ZI1  C15  H1   single    0.930  0.020  1.080
 ZI1  C14  H2   single    0.930  0.020  1.080
 ZI1  C17  H3   single    0.930  0.020  1.080
 ZI1  C18  H4   single    0.930  0.020  1.080
 ZI1  C8   H5   single    0.970  0.020  1.090
 ZI1  C9   H6   single    0.970  0.020  1.090
 ZI1  C9   H7   single    0.970  0.020  1.090
 ZI1  C9   H8   single    0.970  0.020  1.090
 ZI1  C5   H9   single    0.930  0.020  1.080
 ZI1  C6   H10  single    0.930  0.020  1.080
 ZI1  N1   H11  single    0.860  0.020  1.020
 ZI1  N1   H12  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
 ZI1  C16  C19  F4   112.58  3.000
 ZI1  F4   C19  F3   107.10  3.000
 ZI1  C16  C19  F3   111.92  3.000
 ZI1  F4   C19  F5   106.80  3.000
 ZI1  F3   C19  F5   106.51  3.000
 ZI1  C16  C19  F5   111.57  3.000
 ZI1  C17  C16  C15  119.73  3.000
 ZI1  C15  C16  C19  119.40  3.000
 ZI1  C17  C16  C19  120.82  3.000
 ZI1  H1   C15  C14  118.89  3.000
 ZI1  H1   C15  C16  121.08  3.000
 ZI1  C14  C15  C16  120.03  3.000
 ZI1  H2   C14  C13  119.87  3.000
 ZI1  H2   C14  C15  119.39  3.000
 ZI1  C13  C14  C15  120.74  3.000
 ZI1  H3   C17  C18  118.74  3.000
 ZI1  H3   C17  C16  121.15  3.000
 ZI1  C18  C17  C16  120.11  3.000
 ZI1  H4   C18  C13  121.03  3.000
 ZI1  H4   C18  C17  118.33  3.000
 ZI1  C13  C18  C17  120.62  3.000
 ZI1  C11  C13  C18  122.50  3.000
 ZI1  C18  C13  C14  118.76  3.000
 ZI1  C11  C13  C14  118.74  3.000
 ZI1  C12  C11  N2   107.04  3.000
 ZI1  N2   C11  C13  121.00  3.000
 ZI1  C12  C11  C13  131.94  3.000
 ZI1  C10  N2   C11  105.97  3.000
 ZI1  O3   C12  BR1  116.85  3.000
 ZI1  BR1  C12  C11  134.49  3.000
 ZI1  O3   C12  C11  108.59  3.000
 ZI1  C10  O3   C12  104.99  3.000
 ZI1  C8   C10  O3   119.00  3.000
 ZI1  O3   C10  N2   113.41  3.000
 ZI1  C8   C10  N2   127.58  3.000
 ZI1  H5   C8   O2   110.96  3.000
 ZI1  H5   C8   C9   110.42  3.000
 ZI1  O2   C8   C9   111.75  3.000
 ZI1  H5   C8   C10  105.28  3.000
 ZI1  O2   C8   C10  105.67  3.000
 ZI1  C9   C8   C10  112.49  3.000
 ZI1  H8   C9   H7   107.63  3.000
 ZI1  H8   C9   H6   108.66  3.000
 ZI1  H7   C9   H6   108.33  3.000
 ZI1  H8   C9   C8   109.75  3.000
 ZI1  H7   C9   C8   110.96  3.000
 ZI1  H6   C9   C8   111.39  3.000
 ZI1  C4   O2   C8   119.27  3.000
 ZI1  C3   C4   C5   117.69  3.000
 ZI1  C3   C4   O2   115.75  3.000
 ZI1  C5   C4   O2   126.56  3.000
 ZI1  H9   C5   C6   117.79  3.000
 ZI1  H9   C5   C4   121.32  3.000
 ZI1  C6   C5   C4   120.89  3.000
 ZI1  C2   C3   F1   118.77  3.000
 ZI1  C2   C3   C4   122.70  3.000
 ZI1  F1   C3   C4   118.53  3.000
 ZI1  C1   C2   C7   121.00  3.000
 ZI1  C1   C2   C3   121.25  3.000
 ZI1  C7   C2   C3   117.64  3.000
 ZI1  C6   C7   F2   120.13  3.000
 ZI1  F2   C7   C2   117.99  3.000
 ZI1  C6   C7   C2   121.87  3.000
 ZI1  H10  C6   C7   120.61  3.000
 ZI1  H10  C6   C5   120.19  3.000
 ZI1  C7   C6   C5   119.20  3.000
 ZI1  N1   C1   O1   125.08  3.000
 ZI1  O1   C1   C2   120.63  3.000
 ZI1  N1   C1   C2   114.29  3.000
 ZI1  H12  N1   H11  117.53  3.000
 ZI1  H12  N1   C1   120.53  3.000
 ZI1  H11  N1   C1   121.87  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
 ZI1  CONST_01  C13  C18  C17  C16    0.00   0.0  0
 ZI1  CONST_02  C13  C14  C15  C16    0.00   0.0  0
 ZI1  CONST_03  C11  C13  C14  C15  180.00   0.0  0
 ZI1  CONST_04  C18  C13  C14  C15    0.00   0.0  0
 ZI1  CONST_05  C18  C17  C16  C15    0.00   0.0  0
 ZI1  CONST_08  C17  C18  C13  C14    0.00   0.0  0
 ZI1  CONST_09  C17  C16  C15  C14    0.00   0.0  0
 ZI1  CONST_10  C11  C13  C18  C17  180.00   0.0  0
 ZI1  CONST_13  O3   C12  C11  C13  180.00   0.0  0
 ZI1  CONST_14  C10  N2   C11  C13  180.00   0.0  0
 ZI1  CONST_15  C10  O3   C12  C11    0.00   0.0  0
 ZI1  CONST_16  O3   C10  N2   C11    0.00   0.0  0
 ZI1  CONST_17  C12  O3   C10  N2     0.00   0.0  0
 ZI1  CONST_18  O3   C12  C11  N2     0.00   0.0  0
 ZI1  CONST_19  C10  N2   C11  C12    0.00   0.0  0
 ZI1  CONST_20  C7   C6   C5   C4     0.00   0.0  0
 ZI1  CONST_21  C7   C2   C3   C4     0.00   0.0  0
 ZI1  CONST_22  C2   C3   C4   C5     0.00   0.0  0
 ZI1  CONST_23  C2   C7   C6   C5     0.00   0.0  0
 ZI1  CONST_24  C6   C5   C4   C3     0.00   0.0  0
 ZI1  CONST_25  C6   C7   C2   C3     0.00   0.0  0
 ZI1  CONST_26  C18  C17  C16  C19  180.00   0.0  0
 ZI1  CONST_27  C14  C15  C16  C19  180.00   0.0  0
 ZI1  CONST_28  BR1  C12  C11  C13    0.00   0.0  0
 ZI1  CONST_29  C8   C10  N2   C11  180.00   0.0  0
 ZI1  CONST_30  BR1  C12  C11  N2   180.00   0.0  0
 ZI1  CONST_31  C8   C10  O3   C12  180.00   0.0  0
 ZI1  CONST_32  C10  O3   C12  BR1  180.00   0.0  0
 ZI1  CONST_33  C6   C5   C4   O2   180.00   0.0  0
 ZI1  CONST_34  C2   C3   C4   O2   180.00   0.0  0
 ZI1  CONST_35  C1   C2   C3   C4   180.00   0.0  0
 ZI1  CONST_36  F1   C3   C4   C5   180.00   0.0  0
 ZI1  CONST_37  F2   C7   C6   C5   180.00   0.0  0
 ZI1  CONST_38  F2   C7   C2   C3   180.00   0.0  0
 ZI1  CONST_39  C7   C2   C3   F1   180.00   0.0  0
 ZI1  CONST_40  C1   C2   C7   C6   180.00   0.0  0
 ZI1  CONST_41  H4   C18  C17  C16  180.00   0.0  0
 ZI1  CONST_42  H2   C14  C15  C16  180.00   0.0  0
 ZI1  CONST_43  H3   C17  C16  C15  180.00   0.0  0
 ZI1  CONST_44  H1   C15  C16  C17  180.00   0.0  0
 ZI1  CONST_45  H10  C6   C5   C4   180.00   0.0  0
 ZI1  CONST_46  H9   C5   C4   C3   180.00   0.0  0
 ZI1  CONST_47  H11  N1   C1   C2     0.00   0.0  0
 ZI1  CONST_48  H12  N1   C1   C2   180.00   0.0  0
 ZI1  Var_01    C17  C16  C19  F5   -98.11  30.0  3
 ZI1  Var_02    C5   C4   O2   C8    -6.41  30.0  2
 ZI1  Var_03    N1   C1   C2   C3   -79.94  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
 ZI1  chir_01  C8  C9  O2  C10  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
 ZI1  plan-1  C13  0.020
 ZI1  plan-1  C11  0.020
 ZI1  plan-1  N2   0.020
 ZI1  plan-1  C12  0.020
 ZI1  plan-1  BR1  0.020
 ZI1  plan-1  O3   0.020
 ZI1  plan-1  C10  0.020
 ZI1  plan-1  C8   0.020
 ZI1  plan-2  C19  0.020
 ZI1  plan-2  C16  0.020
 ZI1  plan-2  C15  0.020
 ZI1  plan-2  C14  0.020
 ZI1  plan-2  C17  0.020
 ZI1  plan-2  C18  0.020
 ZI1  plan-2  C13  0.020
 ZI1  plan-2  C11  0.020
 ZI1  plan-2  H1   0.020
 ZI1  plan-2  H2   0.020
 ZI1  plan-2  H3   0.020
 ZI1  plan-2  H4   0.020
 ZI1  plan-3  O2   0.020
 ZI1  plan-3  C4   0.020
 ZI1  plan-3  C5   0.020
 ZI1  plan-3  C3   0.020
 ZI1  plan-3  F1   0.020
 ZI1  plan-3  C2   0.020
 ZI1  plan-3  C7   0.020
 ZI1  plan-3  F2   0.020
 ZI1  plan-3  C6   0.020
 ZI1  plan-3  C1   0.020
 ZI1  plan-3  H9   0.020
 ZI1  plan-3  H10  0.020
 ZI1  plan-4  C2   0.020
 ZI1  plan-4  C1   0.020
 ZI1  plan-4  O1   0.020
 ZI1  plan-4  N1   0.020
 ZI1  plan-4  H11  0.020
 ZI1  plan-4  H12  0.020

