# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:39:49 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (3-bromo-5-phenoxyphenyl)boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1cc(Br)cc(Oc2ccccc2)c1
#
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
 7ND  7ND  '(3-bromo-5-phenoxyphenyl)boronic acid'  ligand  27  17  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7ND
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
 7ND  BR   BR  BR    0  -0.039   3.6750   1.1903  -0.8454
 7ND  C02  C   CR6   0  -0.079   1.9848   0.4025  -0.5437
 7ND  C03  C   CR16  0  -0.331   1.8887  -0.9761  -0.4225
 7ND  C04  C   CR6   0  -0.072   0.6429  -1.5574  -0.1925
 7ND  B05  B   B     0   0.531   0.4935  -3.1198  -0.0521
 7ND  O06  O   OH1   0  -0.626   1.4259  -3.9972  -0.5099
 7ND  O07  O   OH1   0  -0.626  -0.6219  -3.5911   0.5584
 7ND  C09  C   CR16  0  -0.419  -0.4844  -0.7403  -0.0877
 7ND  C10  C   CR6   0   0.404  -0.3671   0.6367  -0.2187
 7ND  O11  O   O2    0  -0.512  -1.4127   1.4993  -0.1444
 7ND  C12  C   CR6   0   0.298  -2.6641   1.0146   0.1590
 7ND  C13  C   CR16  0  -0.298  -3.0304   0.8424   1.4856
 7ND  C14  C   CR16  0  -0.254  -4.3115   0.3962   1.7797
 7ND  C15  C   CR16  0  -0.255  -5.2124   0.1242   0.7578
 7ND  C16  C   CR16  0  -0.253  -4.8308   0.3029  -0.5653
 7ND  C17  C   CR16  0  -0.303  -3.5509   0.7463  -0.8719
 7ND  C18  C   CR16  0  -0.324   0.8758   1.2220  -0.4484
 7ND  H1   H   HCR6  0   0.264   2.7834  -1.5820  -0.4927
 7ND  H2   H   HOH1  0   0.485   2.1544  -3.6008  -0.9952
 7ND  H3   H   HOH1  0   0.489  -0.6770  -4.5522   0.5891
 7ND  H4   H   HCR6  0   0.283  -1.4523  -1.1891   0.0927
 7ND  H5   H   HCR6  0   0.276  -2.3252   1.0588   2.2784
 7ND  H6   H   HCR6  0   0.266  -4.6052   0.2622   2.8124
 7ND  H7   H   HCR6  0   0.262  -6.2097  -0.2223   0.9939
 7ND  H8   H   HCR6  0   0.265  -5.5290   0.0956  -1.3655
 7ND  H9   H   HCR6  0   0.275  -3.2460   0.8879  -1.9010
 7ND  H10  H   HCR6  0   0.294   0.9531   2.2972  -0.5456

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
 7ND  O06  B05  single    1.360  0.020  1.360
 7ND  B05  O07  single    1.356  0.020  1.356
 7ND  B05  C04  single    1.576  0.020  1.576
 7ND  C04  C09  aromatic  1.396  0.020  1.396
 7ND  C04  C03  aromatic  1.394  0.020  1.394
 7ND  C09  C10  aromatic  1.388  0.020  1.388
 7ND  C03  C02  aromatic  1.387  0.020  1.387
 7ND  O11  C10  single    1.358  0.020  1.358
 7ND  O11  C12  single    1.376  0.020  1.376
 7ND  C10  C18  aromatic  1.393  0.020  1.393
 7ND  C02  C18  aromatic  1.382  0.020  1.382
 7ND  C02  BR   single    1.889  0.020  1.889
 7ND  C12  C13  aromatic  1.387  0.020  1.387
 7ND  C12  C17  aromatic  1.386  0.020  1.386
 7ND  C13  C14  aromatic  1.388  0.020  1.388
 7ND  C17  C16  aromatic  1.389  0.020  1.389
 7ND  C14  C15  aromatic  1.389  0.020  1.389
 7ND  C16  C15  aromatic  1.389  0.020  1.389
 7ND  C03  H1   single    0.930  0.020  1.080
 7ND  O06  H2   single    0.850  0.020  0.980
 7ND  O07  H3   single    0.850  0.020  0.980
 7ND  C09  H4   single    0.930  0.020  1.080
 7ND  C13  H5   single    0.930  0.020  1.080
 7ND  C14  H6   single    0.930  0.020  1.080
 7ND  C15  H7   single    0.930  0.020  1.080
 7ND  C16  H8   single    0.930  0.020  1.080
 7ND  C17  H9   single    0.930  0.020  1.080
 7ND  C18  H10  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
 7ND  C18  C02  C03  121.85  3.000
 7ND  C18  C02  BR   118.79  3.000
 7ND  C03  C02  BR   119.36  3.000
 7ND  H1   C03  C04  121.05  3.000
 7ND  H1   C03  C02  119.56  3.000
 7ND  C04  C03  C02  119.39  3.000
 7ND  C09  C04  B05  119.80  3.000
 7ND  C09  C04  C03  119.34  3.000
 7ND  B05  C04  C03  120.86  3.000
 7ND  O07  B05  O06  119.43  3.000
 7ND  O07  B05  C04  117.56  3.000
 7ND  O06  B05  C04  123.01  3.000
 7ND  H2   O06  B05  115.07  3.000
 7ND  H3   O07  B05  114.09  3.000
 7ND  H4   C09  C10  120.18  3.000
 7ND  H4   C09  C04  119.47  3.000
 7ND  C10  C09  C04  120.35  3.000
 7ND  C18  C10  O11  115.42  3.000
 7ND  C18  C10  C09  120.52  3.000
 7ND  O11  C10  C09  124.06  3.000
 7ND  C12  O11  C10  119.26  3.000
 7ND  C17  C12  C13  121.23  3.000
 7ND  C17  C12  O11  119.09  3.000
 7ND  C13  C12  O11  119.66  3.000
 7ND  H5   C13  C14  120.67  3.000
 7ND  H5   C13  C12  120.23  3.000
 7ND  C14  C13  C12  119.10  3.000
 7ND  H6   C14  C15  120.12  3.000
 7ND  H6   C14  C13  119.51  3.000
 7ND  C15  C14  C13  120.37  3.000
 7ND  H7   C15  C16  120.16  3.000
 7ND  H7   C15  C14  120.00  3.000
 7ND  C16  C15  C14  119.84  3.000
 7ND  H8   C16  C17  119.51  3.000
 7ND  H8   C16  C15  120.18  3.000
 7ND  C17  C16  C15  120.31  3.000
 7ND  H9   C17  C16  120.75  3.000
 7ND  H9   C17  C12  120.10  3.000
 7ND  C16  C17  C12  119.16  3.000
 7ND  H10  C18  C10  119.74  3.000
 7ND  H10  C18  C02  121.70  3.000
 7ND  C10  C18  C02  118.56  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
 7ND  CONST_01  C09  C04  C03  C02     0.00   0.0  0
 7ND  CONST_02  C09  C10  C18  C02     0.00   0.0  0
 7ND  CONST_03  C10  C09  C04  C03     0.00   0.0  0
 7ND  CONST_04  C10  C18  C02  C03     0.00   0.0  0
 7ND  CONST_05  C18  C10  C09  C04     0.00   0.0  0
 7ND  CONST_06  C18  C02  C03  C04     0.00   0.0  0
 7ND  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 7ND  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 7ND  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 7ND  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 7ND  CONST_11  C17  C12  C13  C14     0.00   0.0  0
 7ND  CONST_12  C17  C16  C15  C14     0.00   0.0  0
 7ND  CONST_13  C04  C03  C02  BR    180.00   0.0  0
 7ND  CONST_14  C10  C18  C02  BR    180.00   0.0  0
 7ND  CONST_15  B05  C04  C03  C02   180.00   0.0  0
 7ND  CONST_16  O11  C10  C18  C02   180.00   0.0  0
 7ND  CONST_17  O11  C10  C09  C04   180.00   0.0  0
 7ND  CONST_18  C10  C09  C04  B05   180.00   0.0  0
 7ND  CONST_19  C14  C13  C12  O11   180.00   0.0  0
 7ND  CONST_20  C16  C17  C12  O11   180.00   0.0  0
 7ND  CONST_21  H4   C09  C04  C03   180.00   0.0  0
 7ND  CONST_22  H10  C18  C02  C03   180.00   0.0  0
 7ND  CONST_23  H1   C03  C04  C09   180.00   0.0  0
 7ND  CONST_24  H6   C14  C13  C12   180.00   0.0  0
 7ND  CONST_25  H8   C16  C17  C12   180.00   0.0  0
 7ND  CONST_26  H9   C17  C12  C13   180.00   0.0  0
 7ND  CONST_27  H7   C15  C14  C13   180.00   0.0  0
 7ND  CONST_28  H5   C13  C14  C15   180.00   0.0  0
 7ND  Var_01    C13  C12  O11  C10    85.08  30.0  2
 7ND  Var_02    C18  C10  O11  C12  -176.17  30.0  2
 7ND  Var_03    O06  B05  C04  C03   -19.44  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
 7ND  plan-1  BR   0.020
 7ND  plan-1  C02  0.020
 7ND  plan-1  C03  0.020
 7ND  plan-1  C04  0.020
 7ND  plan-1  B05  0.020
 7ND  plan-1  C09  0.020
 7ND  plan-1  C10  0.020
 7ND  plan-1  O11  0.020
 7ND  plan-1  C18  0.020
 7ND  plan-1  H1   0.020
 7ND  plan-1  H4   0.020
 7ND  plan-1  H10  0.020
 7ND  plan-2  O11  0.020
 7ND  plan-2  C12  0.020
 7ND  plan-2  C13  0.020
 7ND  plan-2  C14  0.020
 7ND  plan-2  C15  0.020
 7ND  plan-2  C16  0.020
 7ND  plan-2  C17  0.020
 7ND  plan-2  H5   0.020
 7ND  plan-2  H6   0.020
 7ND  plan-2  H7   0.020
 7ND  plan-2  H8   0.020
 7ND  plan-2  H9   0.020

