# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 13:02:40 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cc(ccc1Oc2cc(F)cc(Br)c2)[S](=O)(=O)C(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
 UKJ  UKJ  1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene  ligand  31  24  .  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_UKJ
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
 UKJ  O5   O   O     -1  -0.354  25.0574   0.8050  -13.4638
 UKJ  N1   N   N      1   0.334  25.8247   0.0167  -12.9728
 UKJ  O4   O   O      0  -0.364  26.7169  -0.5410  -13.5658
 UKJ  C3   C   CR6    0   0.191  25.6948  -0.2679  -11.5530
 UKJ  C2   C   CR16   0  -0.235  26.8560  -0.5069  -10.8449
 UKJ  C4   C   CR6    0   0.426  24.4396  -0.3045  -10.9275
 UKJ  O3   O   O2     0  -0.474  23.3516  -0.1153  -11.6786
 UKJ  C11  C   CR6    0   0.320  22.1050  -0.3964  -11.1714
 UKJ  C10  C   CR16   0  -0.282  21.2732   0.6683  -10.8730
 UKJ  C9   C   CR6    0  -0.097  19.9930   0.3814  -10.4206
 UKJ  BR1  BR  BR     0  -0.004  18.8305   1.8006  -10.0083
 UKJ  C12  C   CR16   0  -0.442  21.7075  -1.7160  -11.0321
 UKJ  C13  C   CR6    0   0.552  20.4255  -1.9427  -10.5730
 UKJ  F3   F   F      0  -0.299  20.0115  -3.2038  -10.4296
 UKJ  C8   C   CR16   0  -0.382  19.5474  -0.9213  -10.2601
 UKJ  C5   C   CR16   0  -0.339  24.3855  -0.5607   -9.5582
 UKJ  C6   C   CR16   0  -0.188  25.5426  -0.7710   -8.8383
 UKJ  C1   C   CR6    0  -0.248  26.7718  -0.7498   -9.4862
 UKJ  S1   S   S      0   1.163  28.2507  -1.0646   -8.5839
 UKJ  O1   O   OS     0  -0.625  29.2699  -1.5494   -9.4993
 UKJ  O2   O   OS     0  -0.626  27.9280  -1.7881   -7.3657
 UKJ  C7   C   CH1    0   0.402  28.7725   0.6190   -8.0578
 UKJ  F1   F   F      0  -0.302  27.7434   1.1788   -7.4055
 UKJ  F2   F   F      0  -0.300  29.0259   1.3374   -9.1608
 UKJ  H1   H   HCR6   0   0.328  27.8089  -0.5005  -11.3565
 UKJ  H2   H   HCR6   0   0.306  21.6222   1.6844  -10.9989
 UKJ  H3   H   HCR6   0   0.316  22.3694  -2.5368  -11.2780
 UKJ  H4   H   HCR6   0   0.309  18.5499  -1.1483   -9.9081
 UKJ  H5   H   HCR6   0   0.323  23.4350  -0.5948   -9.0448
 UKJ  H6   H   HCR6   0   0.312  25.4720  -0.9649   -7.7766
 UKJ  H7   H   HCH1   0   0.279  29.6564   0.5463   -7.4188

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
 UKJ  O4   N1   double    1.208  0.020  1.208
 UKJ  O5   N1   single    1.205  0.020  1.205
 UKJ  N1   C3   single    1.454  0.020  1.454
 UKJ  O3   C11  single    1.375  0.020  1.375
 UKJ  O3   C4   single    1.336  0.020  1.336
 UKJ  C3   C4   aromatic  1.403  0.020  1.403
 UKJ  C3   C2   aromatic  1.381  0.020  1.381
 UKJ  C12  C11  aromatic  1.385  0.020  1.385
 UKJ  C12  C13  aromatic  1.380  0.020  1.380
 UKJ  C11  C10  aromatic  1.384  0.020  1.384
 UKJ  F3   C13  single    1.335  0.020  1.335
 UKJ  C4   C5   aromatic  1.394  0.020  1.394
 UKJ  C13  C8   aromatic  1.383  0.020  1.383
 UKJ  C2   C1   aromatic  1.383  0.020  1.383
 UKJ  C10  C9   aromatic  1.388  0.020  1.388
 UKJ  C8   C9   aromatic  1.386  0.020  1.386
 UKJ  C9   BR1  single    1.880  0.020  1.880
 UKJ  C5   C6   aromatic  1.379  0.020  1.379
 UKJ  C1   C6   aromatic  1.390  0.020  1.390
 UKJ  C1   S1   single    1.761  0.020  1.761
 UKJ  F2   C7   single    1.341  0.020  1.341
 UKJ  O1   S1   double    1.453  0.020  1.453
 UKJ  S1   C7   single    1.839  0.020  1.839
 UKJ  S1   O2   double    1.453  0.020  1.453
 UKJ  C7   F1   single    1.341  0.020  1.341
 UKJ  C2   H1   single    0.930  0.020  1.080
 UKJ  C10  H2   single    0.930  0.020  1.080
 UKJ  C12  H3   single    0.930  0.020  1.080
 UKJ  C8   H4   single    0.930  0.020  1.080
 UKJ  C5   H5   single    0.930  0.020  1.080
 UKJ  C6   H6   single    0.930  0.020  1.080
 UKJ  C7   H7   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
 UKJ  C3   N1   O4   117.08  3.000
 UKJ  C3   N1   O5   117.98  3.000
 UKJ  O4   N1   O5   124.92  3.000
 UKJ  C4   C3   C2   121.28  3.000
 UKJ  C2   C3   N1   117.36  3.000
 UKJ  C4   C3   N1   121.36  3.000
 UKJ  H1   C2   C1   121.30  3.000
 UKJ  H1   C2   C3   119.82  3.000
 UKJ  C1   C2   C3   118.88  3.000
 UKJ  C5   C4   O3   123.15  3.000
 UKJ  C5   C4   C3   118.52  3.000
 UKJ  O3   C4   C3   118.32  3.000
 UKJ  C11  O3   C4   120.15  3.000
 UKJ  C12  C11  C10  122.61  3.000
 UKJ  C10  C11  O3   117.86  3.000
 UKJ  C12  C11  O3   119.47  3.000
 UKJ  H2   C10  C9   121.99  3.000
 UKJ  H2   C10  C11  120.25  3.000
 UKJ  C9   C10  C11  117.76  3.000
 UKJ  C8   C9   BR1  119.02  3.000
 UKJ  BR1  C9   C10  119.06  3.000
 UKJ  C8   C9   C10  121.91  3.000
 UKJ  H3   C12  C13  121.25  3.000
 UKJ  H3   C12  C11  121.59  3.000
 UKJ  C13  C12  C11  117.15  3.000
 UKJ  C8   C13  F3   118.45  3.000
 UKJ  C8   C13  C12  122.93  3.000
 UKJ  F3   C13  C12  118.61  3.000
 UKJ  H4   C8   C13  120.27  3.000
 UKJ  H4   C8   C9   122.10  3.000
 UKJ  C13  C8   C9   117.63  3.000
 UKJ  H5   C5   C6   119.02  3.000
 UKJ  H5   C5   C4   120.43  3.000
 UKJ  C6   C5   C4   120.55  3.000
 UKJ  H6   C6   C1   121.21  3.000
 UKJ  H6   C6   C5   119.02  3.000
 UKJ  C1   C6   C5   119.77  3.000
 UKJ  S1   C1   C6   120.08  3.000
 UKJ  S1   C1   C2   118.93  3.000
 UKJ  C6   C1   C2   120.98  3.000
 UKJ  C7   S1   O2   106.20  3.000
 UKJ  O2   S1   O1   121.18  3.000
 UKJ  C7   S1   O1   106.65  3.000
 UKJ  O2   S1   C1   109.40  3.000
 UKJ  C7   S1   C1   102.78  3.000
 UKJ  O1   S1   C1   109.02  3.000
 UKJ  H7   C7   F2   111.34  3.000
 UKJ  H7   C7   F1   111.35  3.000
 UKJ  F2   C7   F1   108.76  3.000
 UKJ  H7   C7   S1   109.61  3.000
 UKJ  F1   C7   S1   107.67  3.000
 UKJ  F2   C7   S1   107.99  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
 UKJ  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 UKJ  CONST_02  C6   C1   C2   C3     0.00   0.0  0
 UKJ  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 UKJ  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 UKJ  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 UKJ  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 UKJ  CONST_07  C8   C13  C12  C11    0.00   0.0  0
 UKJ  CONST_08  C8   C9   C10  C11    0.00   0.0  0
 UKJ  CONST_09  C13  C12  C11  C10    0.00   0.0  0
 UKJ  CONST_10  C13  C8   C9   C10    0.00   0.0  0
 UKJ  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 UKJ  CONST_12  C12  C13  C8   C9     0.00   0.0  0
 UKJ  CONST_13  C5   C4   C3   N1   180.00   0.0  0
 UKJ  CONST_14  C1   C2   C3   N1   180.00   0.0  0
 UKJ  CONST_15  S1   C1   C2   C3   180.00   0.0  0
 UKJ  CONST_16  O3   C4   C3   C2   180.00   0.0  0
 UKJ  CONST_17  C13  C12  C11  O3   180.00   0.0  0
 UKJ  CONST_18  C9   C10  C11  O3   180.00   0.0  0
 UKJ  CONST_19  C6   C5   C4   O3   180.00   0.0  0
 UKJ  CONST_20  F3   C13  C12  C11  180.00   0.0  0
 UKJ  CONST_21  BR1  C9   C10  C11  180.00   0.0  0
 UKJ  CONST_22  F3   C13  C8   C9   180.00   0.0  0
 UKJ  CONST_23  C13  C8   C9   BR1  180.00   0.0  0
 UKJ  CONST_24  S1   C1   C6   C5   180.00   0.0  0
 UKJ  CONST_25  H5   C5   C4   C3   180.00   0.0  0
 UKJ  CONST_26  H6   C6   C1   C2   180.00   0.0  0
 UKJ  CONST_27  H1   C2   C3   C4   180.00   0.0  0
 UKJ  CONST_28  H3   C12  C11  C10  180.00   0.0  0
 UKJ  CONST_29  H4   C8   C9   C10  180.00   0.0  0
 UKJ  CONST_30  H2   C10  C11  C12  180.00   0.0  0
 UKJ  Var_01    C12  C11  O3   C4   -74.21  30.0  2
 UKJ  Var_02    C5   C4   O3   C11  -11.41  30.0  2
 UKJ  Var_03    O1   S1   C1   C2   -23.16  30.0  2
 UKJ  Var_04    F2   C7   S1   C1   -62.58  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
 UKJ  plan-1  N1   0.020
 UKJ  plan-1  C3   0.020
 UKJ  plan-1  C2   0.020
 UKJ  plan-1  C4   0.020
 UKJ  plan-1  O3   0.020
 UKJ  plan-1  C5   0.020
 UKJ  plan-1  C6   0.020
 UKJ  plan-1  C1   0.020
 UKJ  plan-1  S1   0.020
 UKJ  plan-1  H1   0.020
 UKJ  plan-1  H5   0.020
 UKJ  plan-1  H6   0.020
 UKJ  plan-2  O3   0.020
 UKJ  plan-2  C11  0.020
 UKJ  plan-2  C10  0.020
 UKJ  plan-2  C9   0.020
 UKJ  plan-2  BR1  0.020
 UKJ  plan-2  C12  0.020
 UKJ  plan-2  C13  0.020
 UKJ  plan-2  F3   0.020
 UKJ  plan-2  C8   0.020
 UKJ  plan-2  H2   0.020
 UKJ  plan-2  H3   0.020
 UKJ  plan-2  H4   0.020
 UKJ  plan-3  O5   0.020
 UKJ  plan-3  N1   0.020
 UKJ  plan-3  O4   0.020
 UKJ  plan-3  C3   0.020

