# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:05:40 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: [5-(bromomethyl)-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[B-](O)(O)c1sc2ccc(CBr)cc2c1
#
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
 H9E  H9E  '[5-(bromomethyl)-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide'  ligand  24  15  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H9E
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
 H9E  C01  C   CR6    0   0.137   1.8290   0.5290   0.7746
 H9E  C02  C   CR16   0  -0.374   0.8221  -0.4144   0.8945
 H9E  C03  C   CR56   0   0.235  -0.4795  -0.1100   0.4831
 H9E  C04  C   CR15   0  -0.339  -1.6626  -0.9227   0.5113
 H9E  O08  O   OB     0  -0.731  -5.0445  -0.5460   1.1853
 H9E  O09  O   OB     0  -0.743  -5.0641   0.0260  -1.0533
 H9E  C11  C   CR56   0  -0.245  -0.7397   1.1672  -0.0508
 H9E  C12  C   CR16   0  -0.266   0.2681   2.1207  -0.1783
 H9E  C13  C   CR16   0  -0.309   1.5444   1.7943   0.2342
 H9E  C14  C   CH2    0  -0.594   3.2105   0.2054   1.2166
 H9E  C05  C   CR5    0  -0.339  -2.7785  -0.3167   0.0279
 H9E  B06  B   B     -1   0.463  -4.3468  -0.8019  -0.0782
 H9E  O07  O   OB     0  -0.742  -4.2904  -2.2237  -0.4398
 H9E  S10  S   S2     0   0.115  -2.4088   1.3070  -0.4888
 H9E  BR   BR  BR     0  -0.161   4.3041  -0.4605  -0.3132
 H9E  H1   H   HCR6   0   0.250   1.0419  -1.3916   1.3102
 H9E  H2   H   HCR5   0   0.235  -1.6614  -1.9404   0.8813
 H9E  H3   H   H      0   0.425  -4.5456  -0.9336   1.9077
 H9E  H4   H   H      0   0.426  -4.6744  -0.0844  -1.9233
 H9E  H5   H   HCR6   0   0.260   0.0584   3.1001  -0.5892
 H9E  H6   H   HCR6   0   0.254   2.3380   2.5258   0.1415
 H9E  H7   H   HCH2   0   0.306   3.7475   1.0734   1.5935
 H9E  H8   H   HCH2   0   0.306   3.2373  -0.5887   1.9593
 H9E  H9   H   H      0   0.430  -5.1881  -2.5609  -0.5168

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
 H9E  C13  C12  aromatic  1.380  0.020  1.380
 H9E  C13  C01  aromatic  1.405  0.020  1.405
 H9E  C14  C01  single    1.486  0.020  1.486
 H9E  C14  BR   single    1.995  0.020  1.995
 H9E  C12  C11  aromatic  1.393  0.020  1.393
 H9E  C01  C02  aromatic  1.385  0.020  1.385
 H9E  C11  C03  aromatic  1.409  0.020  1.409
 H9E  C11  S10  aromatic  1.731  0.020  1.731
 H9E  C02  C03  aromatic  1.399  0.020  1.399
 H9E  C03  C04  aromatic  1.436  0.020  1.436
 H9E  S10  C05  aromatic  1.744  0.020  1.744
 H9E  C04  C05  aromatic  1.359  0.020  1.359
 H9E  C05  B06  single    1.645  0.020  1.645
 H9E  O07  B06  single    1.468  0.020  1.468
 H9E  B06  O08  single    1.466  0.020  1.466
 H9E  B06  O09  single    1.467  0.020  1.467
 H9E  C02  H1   single    0.930  0.020  1.080
 H9E  C04  H2   single    0.930  0.020  1.080
 H9E  O08  H3   single    0.850  0.020  0.980
 H9E  O09  H4   single    0.850  0.020  0.980
 H9E  C12  H5   single    0.930  0.020  1.080
 H9E  C13  H6   single    0.930  0.020  1.080
 H9E  C14  H7   single    0.970  0.020  1.090
 H9E  C14  H8   single    0.970  0.020  1.090
 H9E  O07  H9   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
 H9E  C14  C01  C13  119.92  3.000
 H9E  C14  C01  C02  120.12  3.000
 H9E  C13  C01  C02  119.96  3.000
 H9E  H1   C02  C03  119.83  3.000
 H9E  H1   C02  C01  119.97  3.000
 H9E  C03  C02  C01  120.19  3.000
 H9E  C11  C03  C04  111.62  3.000
 H9E  C04  C03  C02  129.64  3.000
 H9E  C11  C03  C02  118.73  3.000
 H9E  H2   C04  C05  122.80  3.000
 H9E  H2   C04  C03  122.53  3.000
 H9E  C05  C04  C03  114.67  3.000
 H9E  H3   O08  B06  109.33  3.000
 H9E  H4   O09  B06  109.82  3.000
 H9E  S10  C11  C12  128.24  3.000
 H9E  S10  C11  C03  110.32  3.000
 H9E  C12  C11  C03  121.44  3.000
 H9E  H5   C12  C13  120.42  3.000
 H9E  H5   C12  C11  120.92  3.000
 H9E  C13  C12  C11  118.66  3.000
 H9E  H6   C13  C12  119.48  3.000
 H9E  H6   C13  C01  119.51  3.000
 H9E  C12  C13  C01  121.01  3.000
 H9E  H8   C14  H7   109.49  3.000
 H9E  H8   C14  BR   105.45  3.000
 H9E  H7   C14  BR   105.15  3.000
 H9E  H8   C14  C01  112.64  3.000
 H9E  H7   C14  C01  112.84  3.000
 H9E  BR   C14  C01  110.75  3.000
 H9E  S10  C05  B06  117.24  3.000
 H9E  B06  C05  C04  132.41  3.000
 H9E  S10  C05  C04  110.28  3.000
 H9E  O07  B06  C05  105.36  3.000
 H9E  O07  B06  O09  113.69  3.000
 H9E  C05  B06  O09  110.04  3.000
 H9E  O09  B06  O08  103.99  3.000
 H9E  O07  B06  O08  113.56  3.000
 H9E  C05  B06  O08  110.28  3.000
 H9E  H9   O07  B06  108.86  3.000
 H9E  C05  S10  C11   93.11  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
 H9E  CONST_01  C11  C12  C13  C01    0.00   0.0  0
 H9E  CONST_02  C11  C03  C02  C01    0.00   0.0  0
 H9E  CONST_03  C04  C03  C02  C01  180.00   0.0  0
 H9E  CONST_04  C12  C13  C01  C02    0.00   0.0  0
 H9E  CONST_05  C12  C11  C03  C02    0.00   0.0  0
 H9E  CONST_06  S10  C11  C03  C02  180.00   0.0  0
 H9E  CONST_07  C05  C04  C03  C02  180.00   0.0  0
 H9E  CONST_08  C13  C12  C11  C03    0.00   0.0  0
 H9E  CONST_09  C05  S10  C11  C03    0.00   0.0  0
 H9E  CONST_10  C13  C01  C02  C03    0.00   0.0  0
 H9E  CONST_11  S10  C05  C04  C03    0.00   0.0  0
 H9E  CONST_12  C12  C11  C03  C04  180.00   0.0  0
 H9E  CONST_13  S10  C11  C03  C04    0.00   0.0  0
 H9E  CONST_14  C11  S10  C05  C04    0.00   0.0  0
 H9E  CONST_15  C05  C04  C03  C11    0.00   0.0  0
 H9E  CONST_16  C05  S10  C11  C12  180.00   0.0  0
 H9E  CONST_17  S10  C11  C12  C13  180.00   0.0  0
 H9E  CONST_18  C14  C01  C02  C03  180.00   0.0  0
 H9E  CONST_19  B06  C05  C04  C03  180.00   0.0  0
 H9E  CONST_20  B06  C05  S10  C11  180.00   0.0  0
 H9E  CONST_21  C14  C01  C13  C12  180.00   0.0  0
 H9E  CONST_22  H5   C12  C13  C01  180.00   0.0  0
 H9E  CONST_23  H6   C13  C01  C02  180.00   0.0  0
 H9E  CONST_24  H2   C04  C03  C02    0.00   0.0  0
 H9E  CONST_25  H1   C02  C03  C04    0.00   0.0  0
 H9E  Var_01    BR   C14  C01  C02   94.24  30.0  2
 H9E  Var_02    O07  B06  C05  C04  -38.85  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
 H9E  plan-1  C01  0.020
 H9E  plan-1  C02  0.020
 H9E  plan-1  C03  0.020
 H9E  plan-1  C04  0.020
 H9E  plan-1  C11  0.020
 H9E  plan-1  C12  0.020
 H9E  plan-1  C13  0.020
 H9E  plan-1  C14  0.020
 H9E  plan-1  C05  0.020
 H9E  plan-1  B06  0.020
 H9E  plan-1  S10  0.020
 H9E  plan-1  H1   0.020
 H9E  plan-1  H2   0.020
 H9E  plan-1  H5   0.020
 H9E  plan-1  H6   0.020

