# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:20:45 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: [methyl-oxidanylidene-[1-[6-(trifluoromethyl)pyridin-3-yl]ethyl]-$l^{6}-sulfanylidene]cyanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](c1ccc(nc1)C(F)(F)F)[S@@](C)(=O)=NC#N
#
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
 7II  7II  "Sulfoxaflor"
  ligand  28  18  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7II
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
 7II  C1   C  CH3   0  -0.663  25.3832  11.9906   9.3504
 7II  C2   C  CH1   0  -0.513  25.6574  12.0501  10.8428
 7II  C3   C  CR6   0   0.067  27.0384  11.6589  11.2798
 7II  C4   C  CR16  0  -0.157  28.1716  11.9506  10.5361
 7II  C5   C  CR16  0  -0.297  29.4195  11.6060  11.0366
 7II  C6   C  CR6   0  -0.008  29.4698  10.9908  12.2730
 7II  N1   N  N     0  -0.413  28.3967  10.6894  12.9898
 7II  C7   C  CR16  0  -0.069  27.2141  11.0135  12.5036
 7II  C8   C  CT    0   1.050  30.7687  10.6263  12.9418
 7II  F1   F  F     0  -0.309  30.9453  11.3459  14.0552
 7II  F2   F  F     0  -0.297  31.8269  10.8411  12.1588
 7II  F3   F  F     0  -0.306  30.7870   9.3410  13.3002
 7II  S1   S  S     0   1.060  25.3937  13.7139  11.5287
 7II  O1   O  OS    0  -0.624  25.6625  13.7268  12.9648
 7II  N2   N  N     0  -0.618  26.2990  14.6074  10.5990
 7II  C9   C  CSP   0   0.231  26.5706  15.8306  10.9811
 7II  N3   N  NS    0  -0.372  26.8653  16.9200  11.2541
 7II  C10  C  CH3   0  -0.768  23.6795  14.1109  11.2622
 7II  H3   H  HCH3  0   0.275  24.3440  12.2253   9.1293
 7II  H1   H  HCH3  0   0.266  26.0190  12.6626   8.7795
 7II  H2   H  HCH3  0   0.281  25.5666  10.9713   9.0127
 7II  H4   H  HCH1  0   0.362  24.9170  11.4505  11.3827
 7II  H5   H  HCR6  0   0.289  28.1028  12.4405   9.5746
 7II  H6   H  HCR6  0   0.292  30.3122  11.8262  10.4695
 7II  H7   H  HCR6  0   0.284  26.3534  10.7467  13.1078
 7II  H10  H  HCH3  0   0.329  23.5194  15.0983  11.6953
 7II  H8   H  HCH3  0   0.311  23.4586  14.1297  10.1989
 7II  H9   H  HCH3  0   0.317  23.0714  13.3702  11.7784

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
 7II  C1   C2   single    1.519  0.020  1.519
 7II  C2   C3   single    1.500  0.020  1.500
 7II  C2   S1   single    1.819  0.020  1.819
 7II  C3   C4   aromatic  1.386  0.020  1.386
 7II  C3   C7   aromatic  1.395  0.020  1.395
 7II  C4   C5   aromatic  1.388  0.020  1.388
 7II  C5   C6   aromatic  1.382  0.020  1.382
 7II  C6   N1   aromatic  1.325  0.020  1.325
 7II  C6   C8   single    1.506  0.020  1.506
 7II  N1   C7   aromatic  1.319  0.020  1.319
 7II  C8   F1   single    1.337  0.020  1.337
 7II  C8   F2   single    1.334  0.020  1.334
 7II  C8   F3   single    1.334  0.020  1.334
 7II  S1   O1   double    1.461  0.020  1.461
 7II  S1   N2   double    1.576  0.020  1.576
 7II  S1   C10  single    1.780  0.020  1.780
 7II  N2   C9   single    1.310  0.020  1.310
 7II  C9   N3   triple    1.161  0.020  1.161
 7II  C1   H3   single    0.970  0.020  1.090
 7II  C1   H1   single    0.970  0.020  1.090
 7II  C1   H2   single    0.970  0.020  1.090
 7II  C2   H4   single    0.970  0.020  1.090
 7II  C4   H5   single    0.930  0.020  1.080
 7II  C5   H6   single    0.930  0.020  1.080
 7II  C7   H7   single    0.930  0.020  1.080
 7II  C10  H10  single    0.970  0.020  1.090
 7II  C10  H8   single    0.970  0.020  1.090
 7II  C10  H9   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
 7II  H2   C1   H1   108.49  3.000
 7II  H2   C1   H3   107.43  3.000
 7II  H1   C1   H3   108.58  3.000
 7II  H2   C1   C2   108.11  3.000
 7II  H1   C1   C2   112.73  3.000
 7II  H3   C1   C2   111.33  3.000
 7II  H4   C2   S1   102.52  3.000
 7II  H4   C2   C3   109.63  3.000
 7II  S1   C2   C3   105.19  3.000
 7II  H4   C2   C1   109.94  3.000
 7II  S1   C2   C1   112.35  3.000
 7II  C3   C2   C1   116.25  3.000
 7II  C7   C3   C4   117.72  3.000
 7II  C7   C3   C2   119.48  3.000
 7II  C4   C3   C2   122.76  3.000
 7II  H5   C4   C5   119.36  3.000
 7II  H5   C4   C3   121.35  3.000
 7II  C5   C4   C3   119.29  3.000
 7II  H6   C5   C6   122.03  3.000
 7II  H6   C5   C4   120.20  3.000
 7II  C6   C5   C4   117.77  3.000
 7II  C8   C6   N1   113.77  3.000
 7II  C8   C6   C5   122.46  3.000
 7II  N1   C6   C5   123.76  3.000
 7II  C7   N1   C6   118.08  3.000
 7II  H7   C7   N1   116.47  3.000
 7II  H7   C7   C3   120.16  3.000
 7II  N1   C7   C3   123.37  3.000
 7II  F3   C8   F2   107.57  3.000
 7II  F3   C8   F1   107.03  3.000
 7II  F2   C8   F1   107.30  3.000
 7II  F3   C8   C6   111.37  3.000
 7II  F2   C8   C6   112.62  3.000
 7II  F1   C8   C6   110.70  3.000
 7II  C10  S1   N2   109.79  3.000
 7II  C10  S1   O1   108.81  3.000
 7II  N2   S1   O1   117.99  3.000
 7II  C10  S1   C2   106.69  3.000
 7II  N2   S1   C2   102.29  3.000
 7II  O1   S1   C2   110.61  3.000
 7II  C9   N2   S1   118.46  3.000
 7II  N3   C9   N2   180.00  3.000
 7II  H9   C10  H8   111.25  3.000
 7II  H9   C10  H10  110.24  3.000
 7II  H8   C10  H10  110.08  3.000
 7II  H9   C10  S1   108.38  3.000
 7II  H8   C10  S1   110.27  3.000
 7II  H10  C10  S1   106.51  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
 7II  CONST_01  C6   C5   C4  C3     0.00   0.0  0
 7II  CONST_02  C6   N1   C7  C3     0.00   0.0  0
 7II  CONST_03  N1   C7   C3  C4     0.00   0.0  0
 7II  CONST_04  N1   C6   C5  C4     0.00   0.0  0
 7II  CONST_05  C7   C3   C4  C5     0.00   0.0  0
 7II  CONST_06  C7   N1   C6  C5     0.00   0.0  0
 7II  CONST_07  C5   C4   C3  C2   180.00   0.0  0
 7II  CONST_08  N1   C7   C3  C2   180.00   0.0  0
 7II  CONST_09  C8   C6   C5  C4   180.00   0.0  0
 7II  CONST_10  C8   C6   N1  C7   180.00   0.0  0
 7II  CONST_11  H6   C5   C4  C3   180.00   0.0  0
 7II  CONST_12  H7   C7   C3  C4   180.00   0.0  0
 7II  CONST_13  H5   C4   C5  C6   180.00   0.0  0
 7II  CONST_14  H7   C7   N1  C6   180.00   0.0  0
 7II  CONST_15  H6   C5   C6  N1   180.00   0.0  0
 7II  CONST_16  H5   C4   C3  C7   180.00   0.0  0
 7II  Var_01    F1   C8   C6  C5   113.95  30.0  2
 7II  Var_02    F2   C8   C6  C5    -6.16  30.0  2
 7II  Var_03    F3   C8   C6  C5  -127.10  30.0  2
 7II  Var_04    F1   C8   C6  N1   -64.88  30.0  2
 7II  Var_05    F2   C8   C6  N1   175.01  30.0  2
 7II  Var_06    F3   C8   C6  N1    54.07  30.0  2
 7II  Var_07    C9   N2   S1  C2  -165.77  30.0  2
 7II  Var_08    N3   C9   N2  S1   172.64  30.0  3
 7II  Var_09    C9   N2   S1  O1   -44.18  30.0  2
 7II  Var_10    C10  S1   N2  C9    81.22  30.0  2
 7II  Var_11    H10  C10  S1  C2   178.69  30.0  3
 7II  Var_12    H8   C10  S1  C2   -61.89  30.0  3
 7II  Var_13    H9   C10  S1  C2    60.10  30.0  3
 7II  Var_14    H10  C10  S1  O1    59.33  30.0  3
 7II  Var_15    H8   C10  S1  O1   178.74  30.0  3
 7II  Var_16    H9   C10  S1  O1   -59.27  30.0  3
 7II  Var_17    H10  C10  S1  N2   -71.18  30.0  3
 7II  Var_18    H8   C10  S1  N2    48.23  30.0  3
 7II  Var_19    H9   C10  S1  N2   170.23  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
 7II  chir_01  C2  C1  C3  S1   negativ
 7II  chir_02  S1  O1  N2  C10  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
 7II  plan-1  C2  0.020
 7II  plan-1  C3  0.020
 7II  plan-1  C4  0.020
 7II  plan-1  C5  0.020
 7II  plan-1  C6  0.020
 7II  plan-1  N1  0.020
 7II  plan-1  C7  0.020
 7II  plan-1  C8  0.020
 7II  plan-1  H5  0.020
 7II  plan-1  H6  0.020
 7II  plan-1  H7  0.020

