# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:22:09 2021
#   Inital geometry file: a 59 line input string
#   Ligand name: 1,3-dichloro-2-[(methylsulfonyl)methyl]benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Cc1c(Cl)cccc1Cl
#
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
 PJD  PJD  1,3-dichloro-2-[(methylsulfonyl)methyl]benzene  ligand  21  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PJD
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
 PJD  C1   C   CR6   0   0.293   1.5672  18.7966  -14.0686
 PJD  C2   C   CH2   0  -0.734   2.4918  17.6352  -14.1984
 PJD  C3   C   CR6   0  -0.126   0.2864  18.6779  -13.5234
 PJD  C13  C   CR16  0  -0.281  -0.1519  21.0066  -13.8243
 PJD  C10  C   CH3   0  -0.798   2.7890  16.8674  -11.4626
 PJD  C4   C   CR6   0  -0.103   1.9387  20.0715  -14.5078
 PJD  C6   C   CR16  0  -0.182  -0.5696  19.7595  -13.3937
 PJD  C8   C   CR16  0  -0.185   1.1012  21.1677  -14.3914
 PJD  O11  O   OS    0  -0.677   4.6914  16.5422  -13.2558
 PJD  O12  O   OS    0  -0.662   4.1402  18.8721  -12.4883
 PJD  S5   S   S     0   1.202   3.6938  17.5285  -12.8432
 PJD  CL7  CL  CL    0  -0.099  -0.2955  17.1320  -12.9991
 PJD  CL9  CL  CL    0  -0.101   3.4747  20.3123  -15.2636
 PJD  H1   H   HCH2  0   0.336   1.9734  16.6778  -14.2346
 PJD  H2   H   HCH2  0   0.344   3.1100  17.7042  -15.0948
 PJD  H3   H   HCR6  0   0.285  -0.8107  21.8581  -13.7260
 PJD  H4   H   HCH3  0   0.317   3.5133  16.7392  -10.6586
 PJD  H5   H   HCH3  0   0.291   2.0182  17.5667  -11.1493
 PJD  H6   H   HCH3  0   0.295   2.3539  15.9084  -11.7299
 PJD  H7   H   HCR6  0   0.291  -1.5526  19.6270  -12.9642
 PJD  H8   H   HCR6  0   0.292   1.4249  22.1377  -14.7413

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
 PJD  CL9  C4   single    1.729  0.020  1.729
 PJD  C4   C8   aromatic  1.384  0.020  1.384
 PJD  C4   C1   aromatic  1.399  0.020  1.399
 PJD  C8   C13  aromatic  1.385  0.020  1.385
 PJD  C2   C1   single    1.490  0.020  1.490
 PJD  C2   S5   single    1.815  0.020  1.815
 PJD  C1   C3   aromatic  1.397  0.020  1.397
 PJD  C13  C6   aromatic  1.384  0.020  1.384
 PJD  C3   C6   aromatic  1.386  0.020  1.386
 PJD  C3   CL7  single    1.733  0.020  1.733
 PJD  O11  S5   double    1.462  0.020  1.462
 PJD  S5   O12  double    1.460  0.020  1.460
 PJD  S5   C10  single    1.778  0.020  1.778
 PJD  C2   H1   single    0.970  0.020  1.090
 PJD  C2   H2   single    0.970  0.020  1.090
 PJD  C13  H3   single    0.930  0.020  1.080
 PJD  C10  H4   single    0.970  0.020  1.090
 PJD  C10  H5   single    0.970  0.020  1.090
 PJD  C10  H6   single    0.970  0.020  1.090
 PJD  C6   H7   single    0.930  0.020  1.080
 PJD  C8   H8   single    0.930  0.020  1.080

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
 PJD  C4   C1   C3   116.33  3.000
 PJD  C3   C1   C2   122.45  3.000
 PJD  C4   C1   C2   121.22  3.000
 PJD  H2   C2   H1   107.33  3.000
 PJD  H2   C2   S5   104.00  3.000
 PJD  H1   C2   S5   106.76  3.000
 PJD  H2   C2   C1   111.95  3.000
 PJD  H1   C2   C1   113.12  3.000
 PJD  S5   C2   C1   113.07  3.000
 PJD  CL7  C3   C6   117.43  3.000
 PJD  CL7  C3   C1   120.11  3.000
 PJD  C6   C3   C1   122.45  3.000
 PJD  H3   C13  C8   119.80  3.000
 PJD  H3   C13  C6   119.83  3.000
 PJD  C8   C13  C6   120.36  3.000
 PJD  H6   C10  H5   110.78  3.000
 PJD  H6   C10  H4   110.12  3.000
 PJD  H5   C10  H4   109.54  3.000
 PJD  H6   C10  S5   109.93  3.000
 PJD  H5   C10  S5   110.21  3.000
 PJD  H4   C10  S5   106.16  3.000
 PJD  CL9  C4   C8   117.64  3.000
 PJD  C8   C4   C1   122.32  3.000
 PJD  CL9  C4   C1   120.02  3.000
 PJD  H7   C6   C13  120.57  3.000
 PJD  H7   C6   C3   120.22  3.000
 PJD  C13  C6   C3   119.20  3.000
 PJD  H8   C8   C4   120.15  3.000
 PJD  H8   C8   C13  120.53  3.000
 PJD  C4   C8   C13  119.32  3.000
 PJD  O12  S5   O11  118.74  3.000
 PJD  O12  S5   C10  108.01  3.000
 PJD  O11  S5   C10  108.39  3.000
 PJD  C10  S5   C2   105.34  3.000
 PJD  O12  S5   C2   109.27  3.000
 PJD  O11  S5   C2   106.31  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
 PJD  CONST_01  C13  C8   C4  C1      0.00   0.0  0
 PJD  CONST_02  C13  C6   C3  C1      0.00   0.0  0
 PJD  CONST_03  C8   C4   C1  C3      0.00   0.0  0
 PJD  CONST_04  C8   C13  C6  C3      0.00   0.0  0
 PJD  CONST_05  C6   C13  C8  C4      0.00   0.0  0
 PJD  CONST_06  C6   C3   C1  C4      0.00   0.0  0
 PJD  CONST_07  C8   C4   C1  C2    180.00   0.0  0
 PJD  CONST_08  C6   C3   C1  C2    180.00   0.0  0
 PJD  CONST_09  CL9  C4   C1  C3    180.00   0.0  0
 PJD  CONST_10  CL9  C4   C8  C13   180.00   0.0  0
 PJD  CONST_11  CL7  C3   C6  C13   180.00   0.0  0
 PJD  CONST_12  CL7  C3   C1  C4    180.00   0.0  0
 PJD  CONST_13  H8   C8   C4  C1    180.00   0.0  0
 PJD  CONST_14  H7   C6   C3  C1    180.00   0.0  0
 PJD  CONST_15  H3   C13  C6  C3    180.00   0.0  0
 PJD  Var_01    S5   C2   C1  C3    -97.44  30.0  2
 PJD  Var_02    O11  S5   C2  C1   -167.94  30.0  3
 PJD  Var_03    H4   C10  S5  C2    176.56  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
 PJD  plan-1  C1   0.020
 PJD  plan-1  C2   0.020
 PJD  plan-1  C3   0.020
 PJD  plan-1  C13  0.020
 PJD  plan-1  C4   0.020
 PJD  plan-1  C6   0.020
 PJD  plan-1  C8   0.020
 PJD  plan-1  CL7  0.020
 PJD  plan-1  CL9  0.020
 PJD  plan-1  H3   0.020
 PJD  plan-1  H7   0.020
 PJD  plan-1  H8   0.020

