# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:06:48 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 2,4-dichloro-5-methylphenyl 2,6-dinitro-4-(trifluoromethyl)phenyl sulfone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(c(Cl)cc1Cl)[S](=O)(=O)c2c(cc(cc2[N+]([O-])=O)C(F)(F)F)[N+]([O-])=O
#
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
 D3F  D3F  '2,4-dichloro-5-methylphenyl 2,6-dinitro-4-(trifluoromethyl)phenyl sulfone'  ligand  35  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D3F
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
 D3F  C1   C   CR6    0  -0.113  -4.2862   0.9066  -0.7828
 D3F  C2   C   CR16   0  -0.129  -3.2507   0.7310  -1.6864
 D3F  C3   C   CR6    0  -0.041  -2.1511  -0.0204  -1.3166
 D3F  C4   C   CR6    0  -0.065  -2.0881  -0.5600  -0.0394
 D3F  C5   C   CR16   0  -0.310  -3.1366  -0.3706   0.8502
 D3F  C6   C   CR6    0   0.201  -4.2620   0.3624   0.5012
 D3F  C7   C   CH3    0  -0.720  -5.3832   0.5537   1.4719
 D3F  S1   S   S      0   1.222  -0.7802  -1.6355   0.4824
 D3F  O1   O   OS     0  -0.606  -0.7415  -2.7623  -0.4293
 D3F  O2   O   OS     0  -0.607  -0.9125  -1.8431   1.9138
 D3F  C8   C   CR6    0  -0.182   0.7852  -0.7493   0.2886
 D3F  C9   C   CR6    0   0.249   1.7813  -1.1971  -0.5672
 D3F  C10  C   CR16   0  -0.236   3.0002  -0.5539  -0.6839
 D3F  C11  C   CR6    0  -0.198   3.2710   0.5344   0.1221
 D3F  C12  C   CR16   0  -0.238   2.3384   0.9593   1.0539
 D3F  C13  C   CR6    0   0.334   1.1196   0.3208   1.1139
 D3F  N1   N   N      1   0.324   0.1790   0.8470   2.1024
 D3F  O3   O   O     -1  -0.331   0.5281   0.8077   3.2511
 D3F  O4   O   O      0  -0.333  -0.8486   1.3112   1.6831
 D3F  C14  C   CT     0   1.079   4.6025   1.2307   0.0451
 D3F  F1   F   F      0  -0.299   5.4044   0.8247   1.0313
 D3F  F2   F   F      0  -0.291   5.2215   0.9845  -1.1068
 D3F  F3   F   F      0  -0.297   4.4623   2.5508   0.1611
 D3F  N2   N   N      1   0.330   1.6723  -2.4139  -1.3819
 D3F  O5   O   O     -1  -0.334   1.9411  -3.4437  -0.8258
 D3F  O6   O   O      0  -0.332   1.4170  -2.2731  -2.5467
 D3F  CL1  CL  CL     0  -0.070  -0.8776  -0.2393  -2.4473
 D3F  CL2  CL  CL     0  -0.081  -5.6456   1.8385  -1.2817
 D3F  H2   H   HCR6   0   0.317  -3.3013   1.1687  -2.6733
 D3F  H5   H   HCR6   0   0.303  -3.0843  -0.7934   1.8443
 D3F  H71  H   HCH3   0   0.262  -5.5704   1.6116   1.6578
 D3F  H72  H   HCH3   0   0.264  -6.3105   0.1212   1.0946
 D3F  H73  H   HCH3   0   0.262  -5.1522   0.0803   2.4235
 D3F  H10  H   HCR6   0   0.332   3.7335  -0.9284  -1.3860
 D3F  H12  H   HCR6   0   0.337   2.5413   1.7885   1.7188

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
 D3F  C1   C2   aromatic  1.385  0.020  1.385
 D3F  C1   C6   aromatic  1.395  0.020  1.395
 D3F  C1   CL2  single    1.722  0.020  1.722
 D3F  C2   C3   aromatic  1.382  0.020  1.382
 D3F  C2   H2   single    0.930  0.020  1.080
 D3F  C3   C4   aromatic  1.388  0.020  1.388
 D3F  C3   CL1  single    1.717  0.020  1.717
 D3F  C4   C5   aromatic  1.388  0.020  1.388
 D3F  C4   S1   single    1.772  0.020  1.772
 D3F  C5   C6   aromatic  1.388  0.020  1.388
 D3F  C5   H5   single    0.930  0.020  1.080
 D3F  C6   C7   single    1.495  0.020  1.495
 D3F  C7   H71  single    0.970  0.020  1.090
 D3F  C7   H72  single    0.970  0.020  1.090
 D3F  C7   H73  single    0.970  0.020  1.090
 D3F  S1   O1   double    1.450  0.020  1.450
 D3F  S1   O2   double    1.452  0.020  1.452
 D3F  S1   C8   single    1.809  0.020  1.809
 D3F  C8   C9   aromatic  1.387  0.020  1.387
 D3F  C8   C13  aromatic  1.392  0.020  1.392
 D3F  C9   C10  aromatic  1.383  0.020  1.383
 D3F  C9   N2   single    1.468  0.020  1.468
 D3F  C10  C11  aromatic  1.381  0.020  1.381
 D3F  C10  H10  single    0.930  0.020  1.080
 D3F  C11  C12  aromatic  1.385  0.020  1.385
 D3F  C11  C14  single    1.505  0.020  1.505
 D3F  C12  C13  aromatic  1.377  0.020  1.377
 D3F  C12  H12  single    0.930  0.020  1.080
 D3F  C13  N1   single    1.462  0.020  1.462
 D3F  N1   O3   single    1.201  0.020  1.201
 D3F  N1   O4   double    1.203  0.020  1.203
 D3F  C14  F1   single    1.334  0.020  1.334
 D3F  C14  F2   single    1.331  0.020  1.331
 D3F  C14  F3   single    1.333  0.020  1.333
 D3F  N2   O5   single    1.201  0.020  1.201
 D3F  N2   O6   double    1.201  0.020  1.201

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
 D3F  CL2  C1   C6   119.45  3.000
 D3F  CL2  C1   C2   118.01  3.000
 D3F  C6   C1   C2   122.54  3.000
 D3F  H2   C2   C3   120.11  3.000
 D3F  H2   C2   C1   120.61  3.000
 D3F  C3   C2   C1   119.28  3.000
 D3F  CL1  C3   C4   121.52  3.000
 D3F  CL1  C3   C2   118.90  3.000
 D3F  C4   C3   C2   119.57  3.000
 D3F  S1   C4   C5   116.85  3.000
 D3F  S1   C4   C3   122.71  3.000
 D3F  C5   C4   C3   120.17  3.000
 D3F  H5   C5   C6   118.48  3.000
 D3F  H5   C5   C4   119.95  3.000
 D3F  C6   C5   C4   121.57  3.000
 D3F  C7   C6   C5   120.83  3.000
 D3F  C7   C6   C1   122.32  3.000
 D3F  C5   C6   C1   116.85  3.000
 D3F  H73  C7   H72  108.10  3.000
 D3F  H73  C7   H71  108.03  3.000
 D3F  H72  C7   H71  107.32  3.000
 D3F  H73  C7   C6   110.68  3.000
 D3F  H72  C7   C6   111.24  3.000
 D3F  H71  C7   C6   111.32  3.000
 D3F  C8   S1   O2   104.73  3.000
 D3F  C8   S1   O1   106.87  3.000
 D3F  O2   S1   O1   120.73  3.000
 D3F  C8   S1   C4   108.05  3.000
 D3F  O2   S1   C4   108.04  3.000
 D3F  O1   S1   C4   107.83  3.000
 D3F  C13  C8   C9   116.19  3.000
 D3F  C13  C8   S1   121.39  3.000
 D3F  C9   C8   S1   121.95  3.000
 D3F  N2   C9   C10  113.83  3.000
 D3F  N2   C9   C8   123.80  3.000
 D3F  C10  C9   C8   122.32  3.000
 D3F  H10  C10  C11  121.24  3.000
 D3F  H10  C10  C9   119.40  3.000
 D3F  C11  C10  C9   119.34  3.000
 D3F  C14  C11  C12  119.23  3.000
 D3F  C14  C11  C10  120.55  3.000
 D3F  C12  C11  C10  120.16  3.000
 D3F  H12  C12  C13  119.63  3.000
 D3F  H12  C12  C11  121.48  3.000
 D3F  C13  C12  C11  118.88  3.000
 D3F  N1   C13  C12  115.58  3.000
 D3F  N1   C13  C8   121.52  3.000
 D3F  C12  C13  C8   122.89  3.000
 D3F  O4   N1   O3   126.45  3.000
 D3F  O4   N1   C13  116.91  3.000
 D3F  O3   N1   C13  116.60  3.000
 D3F  F3   C14  F2   107.92  3.000
 D3F  F3   C14  F1   107.48  3.000
 D3F  F2   C14  F1   107.69  3.000
 D3F  F3   C14  C11  111.15  3.000
 D3F  F2   C14  C11  111.73  3.000
 D3F  F1   C14  C11  110.68  3.000
 D3F  O6   N2   O5   126.68  3.000
 D3F  O6   N2   C9   117.18  3.000
 D3F  O5   N2   C9   115.92  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
 D3F  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D3F  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 D3F  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 D3F  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 D3F  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 D3F  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 D3F  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 D3F  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 D3F  CONST_09  C12  C13  C8   C9      0.00   0.0  0
 D3F  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 D3F  CONST_11  C13  C8   C9   C10     0.00   0.0  0
 D3F  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 D3F  CONST_13  CL1  C3   C2   C1    180.00   0.0  0
 D3F  CONST_14  C7   C6   C1   C2    180.00   0.0  0
 D3F  CONST_15  S1   C4   C3   C2    180.00   0.0  0
 D3F  CONST_16  CL2  C1   C2   C3    180.00   0.0  0
 D3F  CONST_17  C7   C6   C5   C4    180.00   0.0  0
 D3F  CONST_18  CL1  C3   C4   C5    180.00   0.0  0
 D3F  CONST_19  CL2  C1   C6   C5    180.00   0.0  0
 D3F  CONST_20  S1   C4   C5   C6    180.00   0.0  0
 D3F  CONST_21  C10  C9   C8   S1    180.00   0.0  0
 D3F  CONST_22  C12  C13  C8   S1    180.00   0.0  0
 D3F  CONST_23  N1   C13  C8   C9    180.00   0.0  0
 D3F  CONST_24  C14  C11  C10  C9    180.00   0.0  0
 D3F  CONST_25  N2   C9   C10  C11   180.00   0.0  0
 D3F  CONST_26  N1   C13  C12  C11   180.00   0.0  0
 D3F  CONST_27  N2   C9   C8   C13   180.00   0.0  0
 D3F  CONST_28  C14  C11  C12  C13   180.00   0.0  0
 D3F  CONST_29  H5   C5   C6   C1    180.00   0.0  0
 D3F  CONST_30  H2   C2   C3   C4    180.00   0.0  0
 D3F  CONST_31  H10  C10  C9   C8    180.00   0.0  0
 D3F  CONST_32  H12  C12  C13  C8    180.00   0.0  0
 D3F  Var_01    C8   S1   C4   C3     58.57  30.0  2
 D3F  Var_02    C9   C8   S1   C4   -118.12  30.0  2
 D3F  Var_03    F1   C14  C11  C10   -99.27  30.0  2
 D3F  Var_04    H71  C7   C6   C1    -57.85  30.0  2

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
 D3F  plan-1  C1   0.020
 D3F  plan-1  C2   0.020
 D3F  plan-1  C3   0.020
 D3F  plan-1  C4   0.020
 D3F  plan-1  C5   0.020
 D3F  plan-1  C6   0.020
 D3F  plan-1  C7   0.020
 D3F  plan-1  S1   0.020
 D3F  plan-1  CL1  0.020
 D3F  plan-1  CL2  0.020
 D3F  plan-1  H2   0.020
 D3F  plan-1  H5   0.020
 D3F  plan-2  S1   0.020
 D3F  plan-2  C8   0.020
 D3F  plan-2  C9   0.020
 D3F  plan-2  C10  0.020
 D3F  plan-2  C11  0.020
 D3F  plan-2  C12  0.020
 D3F  plan-2  C13  0.020
 D3F  plan-2  N1   0.020
 D3F  plan-2  C14  0.020
 D3F  plan-2  N2   0.020
 D3F  plan-2  H10  0.020
 D3F  plan-2  H12  0.020
 D3F  plan-3  C13  0.020
 D3F  plan-3  N1   0.020
 D3F  plan-3  O3   0.020
 D3F  plan-3  O4   0.020
 D3F  plan-4  C9   0.020
 D3F  plan-4  N2   0.020
 D3F  plan-4  O5   0.020
 D3F  plan-4  O6   0.020

