# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 10:09:22 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: N-hydroxy-4-({[(pyridin-3-yl)methyl][(2,3,4,5-tetrafluorophenyl)sulfonyl]amino}methyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(CN(Cc2cccnc2)[S](=O)(=O)c3cc(F)c(F)c(F)c3F)cc1
#
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
 TO3  TO3  N-hydroxy-4-({[(pyridin-3-yl)methyl][(2,3,4,5-tetrafluorophenyl)sulfonyl]amino}methyl)benzamide  ligand  47  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TO3
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
 TO3  C02  C  C     0   0.444  -27.9758   2.4023  -28.8613
 TO3  C05  C  CR6   0  -0.077  -29.0936   3.2094  -29.4376
 TO3  C06  C  CR16  0  -0.236  -30.4165   2.9796  -29.0672
 TO3  C07  C  CR16  0  -0.250  -31.4400   3.6837  -29.6767
 TO3  C08  C  CR6   0   0.077  -31.1586   4.5960  -30.6892
 TO3  C09  C  CH2   0  -0.363  -32.2666   5.2363  -31.4790
 TO3  C11  C  CH2   0  -0.412  -32.2225   3.2617  -33.0219
 TO3  C12  C  CR6   0   0.050  -31.9112   2.0082  -32.2439
 TO3  C13  C  CR16  0  -0.066  -30.6022   1.5882  -32.0492
 TO3  C15  C  CR16  0  -0.051  -31.2414  -0.1794  -30.7606
 TO3  C16  C  CR16  0  -0.314  -32.5831   0.1336  -30.9153
 TO3  C17  C  CR16  0  -0.168  -32.9198   1.2498  -31.6603
 TO3  C20  C  CR6   0  -0.402  -34.4454   5.6106  -34.1229
 TO3  C21  C  CR16  0  -0.410  -34.6277   5.0572  -35.3861
 TO3  C22  C  CR6   0   0.434  -34.5560   5.8640  -36.4978
 TO3  C24  C  CR6   0   0.298  -34.3178   7.2228  -36.3764
 TO3  C26  C  CR6   0   0.309  -34.1374   7.7716  -35.1214
 TO3  C28  C  CR6   0   0.493  -34.2061   6.9684  -33.9963
 TO3  C31  C  CR16  0  -0.280  -29.8344   4.8606  -31.0140
 TO3  C32  C  CR16  0  -0.255  -28.8020   4.1868  -30.3790
 TO3  F23  F  F     0  -0.289  -34.7226   5.3555  -37.7143
 TO3  F25  F  F     0  -0.277  -34.2597   7.9957  -37.4474
 TO3  F27  F  F     0  -0.281  -33.9047   9.0694  -34.9955
 TO3  F29  F  F     0  -0.277  -34.0231   7.5425  -32.8160
 TO3  N03  N  NH1   0  -0.374  -28.1308   1.0897  -29.1139
 TO3  N10  N  N     0  -0.566  -33.0114   4.2092  -32.2233
 TO3  N14  N  N     0  -0.430  -30.2668   0.5306  -31.3169
 TO3  O01  O  O     0  -0.456  -27.0374   2.8908  -28.2580
 TO3  O04  O  OH1   0  -0.546  -27.2182   0.1875  -28.6567
 TO3  O19  O  OS    0  -0.620  -35.2033   5.2626  -31.6304
 TO3  O30  O  OS    0  -0.623  -35.1236   3.2972  -33.1876
 TO3  S18  S  S     0   1.395  -34.5478   4.5357  -32.6969
 TO3  H1   H  HCR6  0   0.266  -30.6493   2.2375  -28.3141
 TO3  H2   H  HCR6  0   0.262  -32.4678   3.4852  -29.3990
 TO3  H3   H  HCH2  0   0.268  -31.8365   5.9727  -32.1641
 TO3  H4   H  HCH2  0   0.294  -32.9539   5.7503  -30.8099
 TO3  H5   H  HCH2  0   0.291  -31.3030   3.7521  -33.3477
 TO3  H6   H  HCH2  0   0.302  -32.7598   2.9990  -33.9333
 TO3  H7   H  HCR6  0   0.265  -29.7824   2.1529  -32.4807
 TO3  H8   H  HCR6  0   0.269  -30.9411  -1.0300  -30.1596
 TO3  H9   H  HCR6  0   0.272  -33.3434  -0.4765  -30.4474
 TO3  H10  H  HCR6  0   0.269  -33.9579   1.5339  -31.7717
 TO3  H11  H  HCR6  0   0.331  -34.8299   4.0020  -35.5098
 TO3  H12  H  HCR6  0   0.262  -29.6049   5.5782  -31.7925
 TO3  H13  H  HCR6  0   0.265  -27.7754   4.3877  -30.6584
 TO3  H14  H  HNH1  0   0.434  -28.7681   0.7553  -29.8382
 TO3  H15  H  HOH1  0   0.471  -26.4592   0.2214  -29.2564

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
 TO3  F23  C22  single    1.329  0.020  1.329
 TO3  F25  C24  single    1.322  0.020  1.322
 TO3  C22  C24  aromatic  1.385  0.020  1.385
 TO3  C22  C21  aromatic  1.375  0.020  1.375
 TO3  C24  C26  aromatic  1.382  0.020  1.382
 TO3  C21  C20  aromatic  1.391  0.020  1.391
 TO3  C26  F27  single    1.325  0.020  1.325
 TO3  C26  C28  aromatic  1.384  0.020  1.384
 TO3  C17  C16  aromatic  1.384  0.020  1.384
 TO3  C17  C12  aromatic  1.390  0.020  1.390
 TO3  C28  C20  aromatic  1.385  0.020  1.385
 TO3  C28  F29  single    1.325  0.020  1.325
 TO3  C20  S18  single    1.789  0.020  1.789
 TO3  C11  C12  single    1.508  0.020  1.508
 TO3  C11  N10  single    1.469  0.020  1.469
 TO3  C16  C15  aromatic  1.386  0.020  1.386
 TO3  C12  C13  aromatic  1.388  0.020  1.388
 TO3  C15  N14  aromatic  1.328  0.020  1.328
 TO3  N10  S18  single    1.641  0.020  1.641
 TO3  N10  C09  single    1.471  0.020  1.471
 TO3  C13  N14  aromatic  1.329  0.020  1.329
 TO3  O30  S18  double    1.451  0.020  1.451
 TO3  S18  O19  double    1.448  0.020  1.448
 TO3  C09  C08  single    1.504  0.020  1.504
 TO3  C31  C08  aromatic  1.389  0.020  1.389
 TO3  C31  C32  aromatic  1.387  0.020  1.387
 TO3  C08  C07  aromatic  1.392  0.020  1.392
 TO3  C32  C05  aromatic  1.388  0.020  1.388
 TO3  C07  C06  aromatic  1.384  0.020  1.384
 TO3  C05  C06  aromatic  1.393  0.020  1.393
 TO3  C05  C02  single    1.494  0.020  1.494
 TO3  C02  O01  double    1.218  0.020  1.218
 TO3  C02  N03  single    1.346  0.020  1.346
 TO3  N03  O04  single    1.362  0.020  1.362
 TO3  C06  H1   single    0.930  0.020  1.080
 TO3  C07  H2   single    0.930  0.020  1.080
 TO3  C09  H3   single    0.970  0.020  1.090
 TO3  C09  H4   single    0.970  0.020  1.090
 TO3  C11  H5   single    0.970  0.020  1.090
 TO3  C11  H6   single    0.970  0.020  1.090
 TO3  C13  H7   single    0.930  0.020  1.080
 TO3  C15  H8   single    0.930  0.020  1.080
 TO3  C16  H9   single    0.930  0.020  1.080
 TO3  C17  H10  single    0.930  0.020  1.080
 TO3  C21  H11  single    0.930  0.020  1.080
 TO3  C31  H12  single    0.930  0.020  1.080
 TO3  C32  H13  single    0.930  0.020  1.080
 TO3  N03  H14  single    0.860  0.020  1.020
 TO3  O04  H15  single    0.850  0.020  0.980

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
 TO3  O01  C02  N03  124.96  3.000
 TO3  N03  C02  C05  111.61  3.000
 TO3  O01  C02  C05  123.43  3.000
 TO3  C32  C05  C06  119.74  3.000
 TO3  C06  C05  C02  121.25  3.000
 TO3  C32  C05  C02  118.99  3.000
 TO3  H1   C06  C07  119.74  3.000
 TO3  H1   C06  C05  120.16  3.000
 TO3  C07  C06  C05  120.09  3.000
 TO3  H2   C07  C08  119.91  3.000
 TO3  H2   C07  C06  119.72  3.000
 TO3  C08  C07  C06  120.30  3.000
 TO3  C31  C08  C09  119.91  3.000
 TO3  C31  C08  C07  119.19  3.000
 TO3  C09  C08  C07  120.82  3.000
 TO3  H4   C09  H3   108.38  3.000
 TO3  H4   C09  N10  108.73  3.000
 TO3  H3   C09  N10  110.63  3.000
 TO3  H4   C09  C08  110.09  3.000
 TO3  H3   C09  C08  109.02  3.000
 TO3  N10  C09  C08  109.97  3.000
 TO3  H6   C11  H5   105.89  3.000
 TO3  H6   C11  N10  110.20  3.000
 TO3  H5   C11  N10  108.95  3.000
 TO3  H6   C11  C12  109.44  3.000
 TO3  H5   C11  C12  110.70  3.000
 TO3  N10  C11  C12  111.51  3.000
 TO3  C17  C12  C13  117.39  3.000
 TO3  C13  C12  C11  121.23  3.000
 TO3  C17  C12  C11  121.35  3.000
 TO3  H7   C13  N14  116.26  3.000
 TO3  H7   C13  C12  119.94  3.000
 TO3  N14  C13  C12  123.77  3.000
 TO3  H8   C15  N14  116.65  3.000
 TO3  H8   C15  C16  120.47  3.000
 TO3  N14  C15  C16  122.88  3.000
 TO3  H9   C16  C17  121.14  3.000
 TO3  H9   C16  C15  120.32  3.000
 TO3  C17  C16  C15  118.54  3.000
 TO3  H10  C17  C16  120.05  3.000
 TO3  H10  C17  C12  120.64  3.000
 TO3  C16  C17  C12  119.31  3.000
 TO3  S18  C20  C28  121.76  3.000
 TO3  S18  C20  C21  118.51  3.000
 TO3  C28  C20  C21  119.72  3.000
 TO3  H11  C21  C22  119.32  3.000
 TO3  H11  C21  C20  121.09  3.000
 TO3  C22  C21  C20  119.59  3.000
 TO3  F23  C22  C24  118.51  3.000
 TO3  C24  C22  C21  120.90  3.000
 TO3  F23  C22  C21  120.59  3.000
 TO3  F25  C24  C26  119.86  3.000
 TO3  C26  C24  C22  119.46  3.000
 TO3  F25  C24  C22  120.67  3.000
 TO3  F27  C26  C28  120.00  3.000
 TO3  C28  C26  C24  120.10  3.000
 TO3  F27  C26  C24  119.90  3.000
 TO3  F29  C28  C26  117.76  3.000
 TO3  F29  C28  C20  122.01  3.000
 TO3  C26  C28  C20  120.22  3.000
 TO3  H12  C31  C32  119.55  3.000
 TO3  H12  C31  C08  119.74  3.000
 TO3  C32  C31  C08  120.68  3.000
 TO3  H13  C32  C31  119.84  3.000
 TO3  H13  C32  C05  120.32  3.000
 TO3  C31  C32  C05  119.75  3.000
 TO3  H14  N03  O04  116.06  3.000
 TO3  H14  N03  C02  121.64  3.000
 TO3  O04  N03  C02  120.39  3.000
 TO3  S18  N10  C11  118.32  3.000
 TO3  S18  N10  C09  118.77  3.000
 TO3  C11  N10  C09  116.97  3.000
 TO3  C15  N14  C13  118.09  3.000
 TO3  H15  O04  N03  107.11  3.000
 TO3  O30  S18  O19  119.86  3.000
 TO3  O19  S18  N10  108.14  3.000
 TO3  O30  S18  N10  107.42  3.000
 TO3  O19  S18  C20  108.15  3.000
 TO3  O30  S18  C20  105.43  3.000
 TO3  N10  S18  C20  107.23  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
 TO3  CONST_01  C08  C31  C32  C05     0.00   0.0  0
 TO3  CONST_02  C08  C07  C06  C05     0.00   0.0  0
 TO3  CONST_03  C31  C08  C07  C06     0.00   0.0  0
 TO3  CONST_04  C31  C32  C05  C06     0.00   0.0  0
 TO3  CONST_05  C32  C31  C08  C07     0.00   0.0  0
 TO3  CONST_06  C32  C05  C06  C07     0.00   0.0  0
 TO3  CONST_07  C15  C16  C17  C12     0.00   0.0  0
 TO3  CONST_08  C15  N14  C13  C12     0.00   0.0  0
 TO3  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 TO3  CONST_10  C16  C15  N14  C13     0.00   0.0  0
 TO3  CONST_11  N14  C15  C16  C17     0.00   0.0  0
 TO3  CONST_12  N14  C13  C12  C17     0.00   0.0  0
 TO3  CONST_13  C24  C22  C21  C20     0.00   0.0  0
 TO3  CONST_14  C24  C26  C28  C20     0.00   0.0  0
 TO3  CONST_15  C26  C24  C22  C21     0.00   0.0  0
 TO3  CONST_16  C26  C28  C20  C21     0.00   0.0  0
 TO3  CONST_17  C28  C26  C24  C22     0.00   0.0  0
 TO3  CONST_18  C28  C20  C21  C22     0.00   0.0  0
 TO3  CONST_19  C31  C32  C05  C02   180.00   0.0  0
 TO3  CONST_20  C07  C06  C05  C02   180.00   0.0  0
 TO3  CONST_21  C09  C08  C07  C06   180.00   0.0  0
 TO3  CONST_22  C32  C31  C08  C09   180.00   0.0  0
 TO3  CONST_23  C16  C17  C12  C11   180.00   0.0  0
 TO3  CONST_24  N14  C13  C12  C11   180.00   0.0  0
 TO3  CONST_25  F23  C22  C21  C20   180.00   0.0  0
 TO3  CONST_26  F27  C26  C28  C20   180.00   0.0  0
 TO3  CONST_27  F25  C24  C22  C21   180.00   0.0  0
 TO3  CONST_28  F29  C28  C20  C21   180.00   0.0  0
 TO3  CONST_29  F27  C26  C24  C22   180.00   0.0  0
 TO3  CONST_30  S18  C20  C21  C22   180.00   0.0  0
 TO3  CONST_31  F29  C28  C26  C24   180.00   0.0  0
 TO3  CONST_32  F23  C22  C24  C26   180.00   0.0  0
 TO3  CONST_33  S18  C20  C28  C26   180.00   0.0  0
 TO3  CONST_34  F25  C24  C26  C28   180.00   0.0  0
 TO3  CONST_35  H12  C31  C32  C05   180.00   0.0  0
 TO3  CONST_36  H2   C07  C06  C05   180.00   0.0  0
 TO3  CONST_37  H13  C32  C05  C06   180.00   0.0  0
 TO3  CONST_38  H1   C06  C07  C08   180.00   0.0  0
 TO3  CONST_39  H9   C16  C17  C12   180.00   0.0  0
 TO3  CONST_40  H10  C17  C12  C13   180.00   0.0  0
 TO3  CONST_41  H8   C15  N14  C13   180.00   0.0  0
 TO3  CONST_42  H7   C13  N14  C15   180.00   0.0  0
 TO3  CONST_43  H11  C21  C22  C24   180.00   0.0  0
 TO3  CONST_44  O04  N03  C02  C05   180.00   0.0  0
 TO3  CONST_46  O04  N03  C02  O01     0.00   0.0  0
 TO3  Var_01    O01  C02  C05  C06  -122.23  30.0  2
 TO3  Var_02    N10  C09  C08  C07   -62.96  30.0  3
 TO3  Var_03    N10  C11  C12  C13  -123.16  30.0  2
 TO3  Var_04    N10  S18  C20  C21   101.29  30.0  2
 TO3  Var_05    C11  N10  C09  C08   -49.88  30.0  2
 TO3  Var_06    C12  C11  N10  C09    93.36  30.0  1
 TO3  Var_07    C20  S18  N10  C09    77.04  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
 TO3  plan-1  C11  0.020
 TO3  plan-1  C12  0.020
 TO3  plan-1  C13  0.020
 TO3  plan-1  C15  0.020
 TO3  plan-1  C16  0.020
 TO3  plan-1  C17  0.020
 TO3  plan-1  N14  0.020
 TO3  plan-1  H7   0.020
 TO3  plan-1  H8   0.020
 TO3  plan-1  H9   0.020
 TO3  plan-1  H10  0.020
 TO3  plan-2  C20  0.020
 TO3  plan-2  C21  0.020
 TO3  plan-2  C22  0.020
 TO3  plan-2  C24  0.020
 TO3  plan-2  C26  0.020
 TO3  plan-2  C28  0.020
 TO3  plan-2  F23  0.020
 TO3  plan-2  F25  0.020
 TO3  plan-2  F27  0.020
 TO3  plan-2  F29  0.020
 TO3  plan-2  S18  0.020
 TO3  plan-2  H11  0.020
 TO3  plan-3  C02  0.020
 TO3  plan-3  C05  0.020
 TO3  plan-3  C06  0.020
 TO3  plan-3  C07  0.020
 TO3  plan-3  C08  0.020
 TO3  plan-3  C09  0.020
 TO3  plan-3  C31  0.020
 TO3  plan-3  C32  0.020
 TO3  plan-3  H1   0.020
 TO3  plan-3  H2   0.020
 TO3  plan-3  H12  0.020
 TO3  plan-3  H13  0.020
 TO3  plan-4  C02  0.020
 TO3  plan-4  C05  0.020
 TO3  plan-4  N03  0.020
 TO3  plan-4  O01  0.020
 TO3  plan-4  O04  0.020
 TO3  plan-4  H14  0.020

