# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:02:52 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (3-bromo-4-methylphenyl)boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1Br)B(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
 7NJ  7NJ  '(3-bromo-4-methylphenyl)boronic acid'  ligand  19  11  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7NJ
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
 7NJ  BR   BR  BR    0  -0.058  -2.1788  -0.8826   0.1594
 7NJ  C02  C   CR6   0  -0.145  -0.5832   0.1387   0.0794
 7NJ  C03  C   CR16  0  -0.288   0.6246  -0.5410   0.0652
 7NJ  C04  C   CR6   0  -0.092   1.8326   0.1554   0.0020
 7NJ  B05  B   B     0   0.514   3.2037  -0.6101  -0.0165
 7NJ  O07  O   OH1   0  -0.635   3.1711  -1.9629   0.1210
 7NJ  O08  O   OH1   0  -0.634   4.3337   0.1309  -0.1704
 7NJ  C09  C   CR16  0  -0.305   1.7720   1.5484  -0.0443
 7NJ  C10  C   CR16  0  -0.279   0.5575   2.2145  -0.0241
 7NJ  C11  C   CR6   0   0.128  -0.6566   1.5313   0.0375
 7NJ  C12  C   CH3   0  -0.726  -1.9496   2.2856   0.0571
 7NJ  H1   H   HCR6  0   0.271   0.6281  -1.6231   0.1017
 7NJ  H2   H   HOH1  0   0.485   4.0244  -2.4077   0.1066
 7NJ  H3   H   HOH1  0   0.485   5.1609  -0.3609  -0.1744
 7NJ  H4   H   HCR6  0   0.257   2.6822   2.1322  -0.0947
 7NJ  H5   H   HCR6  0   0.257   0.5411   3.2971  -0.0576
 7NJ  H6   H   HCH3  0   0.254  -2.5276   2.0730   0.9578
 7NJ  H7   H   HCH3  0   0.255  -1.7662   3.3581   0.0246
 7NJ  H8   H   HCH3  0   0.254  -2.5791   2.0295  -0.7965

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
 7NJ  O08  B05  single    1.360  0.020  1.360
 7NJ  B05  O07  single    1.360  0.020  1.360
 7NJ  B05  C04  single    1.570  0.020  1.570
 7NJ  C04  C03  aromatic  1.396  0.020  1.396
 7NJ  C04  C09  aromatic  1.395  0.020  1.395
 7NJ  C03  C02  aromatic  1.386  0.020  1.386
 7NJ  C09  C10  aromatic  1.385  0.020  1.385
 7NJ  C02  BR   single    1.896  0.020  1.896
 7NJ  C02  C11  aromatic  1.395  0.020  1.395
 7NJ  C10  C11  aromatic  1.394  0.020  1.394
 7NJ  C11  C12  single    1.497  0.020  1.497
 7NJ  C03  H1   single    0.930  0.020  1.080
 7NJ  O07  H2   single    0.850  0.020  0.980
 7NJ  O08  H3   single    0.850  0.020  0.980
 7NJ  C09  H4   single    0.930  0.020  1.080
 7NJ  C10  H5   single    0.930  0.020  1.080
 7NJ  C12  H6   single    0.970  0.020  1.090
 7NJ  C12  H7   single    0.970  0.020  1.090
 7NJ  C12  H8   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
 7NJ  C11  C02  C03  122.34  3.000
 7NJ  C11  C02  BR   119.65  3.000
 7NJ  C03  C02  BR   118.01  3.000
 7NJ  H1   C03  C04  119.83  3.000
 7NJ  H1   C03  C02  119.51  3.000
 7NJ  C04  C03  C02  120.66  3.000
 7NJ  C09  C04  B05  121.62  3.000
 7NJ  C09  C04  C03  117.52  3.000
 7NJ  B05  C04  C03  120.86  3.000
 7NJ  O08  B05  O07  124.98  3.000
 7NJ  O07  B05  C04  117.56  3.000
 7NJ  O08  B05  C04  117.46  3.000
 7NJ  H2   O07  B05  115.91  3.000
 7NJ  H3   O08  B05  115.86  3.000
 7NJ  H4   C09  C10  118.59  3.000
 7NJ  H4   C09  C04  120.23  3.000
 7NJ  C10  C09  C04  121.18  3.000
 7NJ  H5   C10  C11  118.54  3.000
 7NJ  H5   C10  C09  119.56  3.000
 7NJ  C11  C10  C09  121.90  3.000
 7NJ  C12  C11  C10  120.38  3.000
 7NJ  C12  C11  C02  123.23  3.000
 7NJ  C10  C11  C02  116.39  3.000
 7NJ  H8   C12  H7   107.77  3.000
 7NJ  H8   C12  H6   107.12  3.000
 7NJ  H7   C12  H6   107.81  3.000
 7NJ  H8   C12  C11  111.70  3.000
 7NJ  H7   C12  C11  110.52  3.000
 7NJ  H6   C12  C11  111.72  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
 7NJ  CONST_01  C09  C04  C03  C02    0.00   0.0  0
 7NJ  CONST_02  C09  C10  C11  C02    0.00   0.0  0
 7NJ  CONST_03  C10  C09  C04  C03    0.00   0.0  0
 7NJ  CONST_04  C10  C11  C02  C03    0.00   0.0  0
 7NJ  CONST_05  C11  C02  C03  C04    0.00   0.0  0
 7NJ  CONST_06  C11  C10  C09  C04    0.00   0.0  0
 7NJ  CONST_07  C04  C03  C02  BR   180.00   0.0  0
 7NJ  CONST_08  C10  C11  C02  BR   180.00   0.0  0
 7NJ  CONST_09  B05  C04  C03  C02  180.00   0.0  0
 7NJ  CONST_10  C12  C11  C02  C03  180.00   0.0  0
 7NJ  CONST_11  C10  C09  C04  B05  180.00   0.0  0
 7NJ  CONST_12  C12  C11  C10  C09  180.00   0.0  0
 7NJ  CONST_13  H5   C10  C11  C02  180.00   0.0  0
 7NJ  CONST_14  H4   C09  C04  C03  180.00   0.0  0
 7NJ  CONST_15  H1   C03  C04  C09  180.00   0.0  0
 7NJ  Var_01    O08  B05  C04  C03  175.65  30.0  3
 7NJ  Var_02    H6   C12  C11  C02   59.51  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
 7NJ  plan-1  BR   0.020
 7NJ  plan-1  C02  0.020
 7NJ  plan-1  C03  0.020
 7NJ  plan-1  C04  0.020
 7NJ  plan-1  B05  0.020
 7NJ  plan-1  C09  0.020
 7NJ  plan-1  C10  0.020
 7NJ  plan-1  C11  0.020
 7NJ  plan-1  C12  0.020
 7NJ  plan-1  H1   0.020
 7NJ  plan-1  H4   0.020
 7NJ  plan-1  H5   0.020

