# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:20:15 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: dibenzothiophene 5-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=[S]1c2ccccc2c3ccccc13
#
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
 83U  83U  'dibenzothiophene 5-oxide '  ligand  22  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_83U
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
 83U  C4   C  CR56  0  -0.292   1.2610  -0.4412  -0.1587
 83U  C7   C  CR16  0  -0.266  -2.6035  -0.7000  -0.1560
 83U  C1   C  CR56  0   0.247  -0.7261   0.8430  -0.0421
 83U  C10  C  CR16  0  -0.231   2.9751   1.6767   0.1229
 83U  S1   S  S3    0   0.847   0.0089  -1.6939  -0.4020
 83U  C2   C  CR56  0   0.247   0.7367   0.8443  -0.0367
 83U  C3   C  CR56  0  -0.292  -1.2473  -0.4435  -0.1675
 83U  C5   C  CR16  0  -0.337  -1.5989   1.9147   0.0820
 83U  C6   C  CR16  0  -0.337   1.6067   1.9175   0.0951
 83U  C8   C  CR16  0  -0.266   2.6175  -0.6954  -0.1369
 83U  C9   C  CR16  0  -0.231  -2.9671   1.6717   0.0994
 83U  C11  C  CR16  0  -0.263  -3.4687   0.3789  -0.0107
 83U  C12  C  CR16  0  -0.263   3.4797   0.3848   0.0156
 83U  H3   H  HCR6  0   0.282  -2.9862  -1.7076  -0.2568
 83U  H6   H  HCR6  0   0.274   3.6586   2.5080   0.2313
 83U  H1   H  HCR6  0   0.263  -1.2277   2.9277   0.1717
 83U  H2   H  HCR6  0   0.263   1.2332   2.9297   0.1827
 83U  H4   H  HCR6  0   0.282   3.0027  -1.7022  -0.2361
 83U  H5   H  HCR6  0   0.274  -3.6528   2.5020   0.2018
 83U  H7   H  HCR6  0   0.273  -4.5370   0.2117   0.0117
 83U  H8   H  HCR6  0   0.273   4.5481   0.2193   0.0455
 83U  O1   O  O     0  -0.748   0.0064  -2.6689   0.7448

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
 83U  C4   S1   single    1.788  0.020  1.788
 83U  C4   C2   aromatic  1.394  0.020  1.394
 83U  C4   C8   aromatic  1.380  0.020  1.380
 83U  C7   C3   aromatic  1.380  0.020  1.380
 83U  C7   C11  aromatic  1.391  0.020  1.391
 83U  C1   C2   aromatic  1.463  0.020  1.463
 83U  C1   C3   aromatic  1.394  0.020  1.394
 83U  C1   C5   aromatic  1.388  0.020  1.388
 83U  O1   S1   double    1.505  0.020  1.505
 83U  C10  C6   aromatic  1.390  0.020  1.390
 83U  C10  C12  aromatic  1.391  0.020  1.391
 83U  S1   C3   single    1.788  0.020  1.788
 83U  C2   C6   aromatic  1.388  0.020  1.388
 83U  C5   C9   aromatic  1.390  0.020  1.390
 83U  C8   C12  aromatic  1.390  0.020  1.390
 83U  C9   C11  aromatic  1.391  0.020  1.391
 83U  C7   H3   single    0.930  0.020  1.080
 83U  C10  H6   single    0.930  0.020  1.080
 83U  C5   H1   single    0.930  0.020  1.080
 83U  C6   H2   single    0.930  0.020  1.080
 83U  C8   H4   single    0.930  0.020  1.080
 83U  C9   H5   single    0.930  0.020  1.080
 83U  C11  H7   single    0.930  0.020  1.080
 83U  C12  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
 83U  C8   C4   C2   122.56  3.000
 83U  C8   C4   S1   124.15  3.000
 83U  C2   C4   S1   113.25  3.000
 83U  H3   C7   C11  120.79  3.000
 83U  H3   C7   C3   121.30  3.000
 83U  C11  C7   C3   117.90  3.000
 83U  C5   C1   C3   119.06  3.000
 83U  C5   C1   C2   128.90  3.000
 83U  C3   C1   C2   112.03  3.000
 83U  H6   C10  C12  119.49  3.000
 83U  H6   C10  C6   119.41  3.000
 83U  C12  C10  C6   121.10  3.000
 83U  C3   S1   O1   110.60  3.000
 83U  C3   S1   C4    89.10  3.000
 83U  O1   S1   C4   110.57  3.000
 83U  C6   C2   C1   128.90  3.000
 83U  C6   C2   C4   119.06  3.000
 83U  C1   C2   C4   112.03  3.000
 83U  S1   C3   C1   113.24  3.000
 83U  S1   C3   C7   124.16  3.000
 83U  C1   C3   C7   122.56  3.000
 83U  H1   C5   C9   120.02  3.000
 83U  H1   C5   C1   120.95  3.000
 83U  C9   C5   C1   119.03  3.000
 83U  H2   C6   C2   120.96  3.000
 83U  H2   C6   C10  120.01  3.000
 83U  C2   C6   C10  119.03  3.000
 83U  H4   C8   C12  120.80  3.000
 83U  H4   C8   C4   121.30  3.000
 83U  C12  C8   C4   117.91  3.000
 83U  H5   C9   C11  119.49  3.000
 83U  H5   C9   C5   119.41  3.000
 83U  C11  C9   C5   121.10  3.000
 83U  H7   C11  C9   119.88  3.000
 83U  H7   C11  C7   119.79  3.000
 83U  C9   C11  C7   120.33  3.000
 83U  H8   C12  C8   119.78  3.000
 83U  H8   C12  C10  119.89  3.000
 83U  C8   C12  C10  120.33  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
 83U  CONST_01  C3   C1   C2   C4     0.00  0.0  0
 83U  CONST_02  C5   C1   C2   C4   180.00  0.0  0
 83U  CONST_03  C10  C6   C2   C4     0.00  0.0  0
 83U  CONST_04  C10  C12  C8   C4     0.00  0.0  0
 83U  CONST_05  C2   C1   C3   C7   180.00  0.0  0
 83U  CONST_06  C5   C1   C3   C7     0.00  0.0  0
 83U  CONST_07  C5   C9   C11  C7     0.00  0.0  0
 83U  CONST_08  C8   C4   C2   C1   180.00  0.0  0
 83U  CONST_09  C10  C6   C2   C1   180.00  0.0  0
 83U  CONST_10  C11  C7   C3   C1     0.00  0.0  0
 83U  CONST_11  C11  C9   C5   C1     0.00  0.0  0
 83U  CONST_12  C12  C8   C4   C2     0.00  0.0  0
 83U  CONST_13  C9   C5   C1   C2   180.00  0.0  0
 83U  CONST_14  C12  C10  C6   C2     0.00  0.0  0
 83U  CONST_15  C9   C11  C7   C3     0.00  0.0  0
 83U  CONST_16  C6   C2   C1   C3   180.00  0.0  0
 83U  CONST_17  C9   C5   C1   C3     0.00  0.0  0
 83U  CONST_18  C6   C2   C1   C5     0.00  0.0  0
 83U  CONST_19  C8   C12  C10  C6     0.00  0.0  0
 83U  CONST_20  C8   C4   C2   C6     0.00  0.0  0
 83U  CONST_21  H2   C6   C2   C4   180.00  0.0  0
 83U  CONST_22  H8   C12  C8   C4   180.00  0.0  0
 83U  CONST_23  H5   C9   C11  C7   180.00  0.0  0
 83U  CONST_24  H3   C7   C3   C1   180.00  0.0  0
 83U  CONST_25  H4   C8   C12  C10  180.00  0.0  0
 83U  CONST_26  H1   C5   C1   C2     0.00  0.0  0
 83U  CONST_27  H6   C10  C6   C2   180.00  0.0  0
 83U  CONST_28  H7   C11  C7   C3   180.00  0.0  0

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
 83U  plan-1  C4   0.020
 83U  plan-1  C7   0.020
 83U  plan-1  C1   0.020
 83U  plan-1  C10  0.020
 83U  plan-1  S1   0.020
 83U  plan-1  C2   0.020
 83U  plan-1  C3   0.020
 83U  plan-1  C5   0.020
 83U  plan-1  C6   0.020
 83U  plan-1  C8   0.020
 83U  plan-1  C9   0.020
 83U  plan-1  C11  0.020
 83U  plan-1  C12  0.020
 83U  plan-1  H3   0.020
 83U  plan-1  H6   0.020
 83U  plan-1  H1   0.020
 83U  plan-1  H2   0.020
 83U  plan-1  H4   0.020
 83U  plan-1  H5   0.020
 83U  plan-1  H7   0.020
 83U  plan-1  H8   0.020
 83U  plan-1  O1   0.020

