# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:51:13 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2,5-dibromo-3-methyl-6-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C1=C(Br)C(=O)C(=C(Br)C1=O)C
#
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
 BNT  BNT  2,5-dibromo-3-methyl-6-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione  ligand  24  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 PERFECT
;

data_comp_BNT
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
 BNT  CAA   C   CH3   0  -0.652   1.4051  -2.9552   1.2567
 BNT  CAD   C   CH1   0  -0.320   1.6310  -2.1009   0.0061
 BNT  CAC   C   CH3   0  -0.650   1.5086  -2.9165  -1.2846
 BNT  CAE   C   CR6   0   0.107   0.7711  -0.8612  -0.0128
 BNT  CAF   C   CR6   0   0.449  -0.7120  -1.0415  -0.0316
 BNT  OAB   O   O     0  -0.330  -1.2008  -2.1432  -0.0881
 BNT  CAG   C   CR6   0  -0.274  -1.5896   0.1590   0.0207
 BNT  BRAH  BR  BR    0   0.030  -3.4196  -0.2295   0.0351
 BNT  CAL   C   CR6   0   0.019  -1.1220   1.4115   0.0436
 BNT  CAM   C   CH3   0  -0.711  -1.9420   2.6549   0.0865
 BNT  CAK   C   CR6   0   0.460   0.3530   1.5970  -0.0423
 BNT  OAN   O   O     0  -0.334   0.8200   2.7070  -0.1219
 BNT  CAJ   C   CR6   0  -0.332   1.2337   0.3970  -0.0301
 BNT  BRAI  BR  BR    0   0.029   3.0592   0.8304  -0.0518
 BNT  HAA1  H   HCH3  0   0.237   1.4633  -2.3553   2.1656
 BNT  HAA2  H   HCH3  0   0.238   0.4474  -3.4706   1.2462
 BNT  HAA3  H   HCH3  0   0.241   2.1886  -3.7118   1.3120
 BNT  HAD   H   HCH1  0   0.264   2.6654  -1.7642   0.0559
 BNT  HAC1  H   HCH3  0   0.238   0.5470  -3.4178  -1.3695
 BNT  HAC2  H   HCH3  0   0.237   1.6506  -2.2901  -2.1659
 BNT  HAC3  H   HCH3  0   0.240   2.2856  -3.6816  -1.2942
 BNT  HAM1  H   HCH3  0   0.278  -2.1116   3.0238  -0.9276
 BNT  HAM2  H   HCH3  0   0.265  -2.9121   2.4884   0.5467
 BNT  HAM3  H   HCH3  0   0.271  -1.4324   3.4415   0.6370

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
 BNT  CAA  CAD   single  1.531  0.020  1.531
 BNT  CAA  HAA1  single  0.970  0.020  1.090
 BNT  CAA  HAA2  single  0.970  0.020  1.090
 BNT  CAA  HAA3  single  0.970  0.020  1.090
 BNT  CAD  CAC   single  1.532  0.020  1.532
 BNT  CAD  CAE   single  1.509  0.020  1.509
 BNT  CAD  HAD   single  0.970  0.020  1.090
 BNT  CAC  HAC1  single  0.970  0.020  1.090
 BNT  CAC  HAC2  single  0.970  0.020  1.090
 BNT  CAC  HAC3  single  0.970  0.020  1.090
 BNT  CAE  CAF   single  1.494  0.020  1.494
 BNT  CAE  CAJ   double  1.341  0.020  1.341
 BNT  CAF  OAB   double  1.207  0.020  1.207
 BNT  CAF  CAG   single  1.488  0.020  1.488
 BNT  CAG  BRAH  single  1.871  0.020  1.871
 BNT  CAG  CAL   double  1.337  0.020  1.337
 BNT  CAL  CAM   single  1.490  0.020  1.490
 BNT  CAL  CAK   single  1.489  0.020  1.489
 BNT  CAM  HAM1  single  0.970  0.020  1.090
 BNT  CAM  HAM2  single  0.970  0.020  1.090
 BNT  CAM  HAM3  single  0.970  0.020  1.090
 BNT  CAK  OAN   double  1.207  0.020  1.207
 BNT  CAK  CAJ   single  1.489  0.020  1.489
 BNT  CAJ  BRAI  single  1.876  0.020  1.876

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
 BNT  HAA3  CAA  HAA2  107.72  3.000
 BNT  HAA3  CAA  HAA1  107.52  3.000
 BNT  HAA2  CAA  HAA1  108.41  3.000
 BNT  HAA3  CAA  CAD   108.81  3.000
 BNT  HAA2  CAA  CAD   112.73  3.000
 BNT  HAA1  CAA  CAD   111.46  3.000
 BNT  HAD   CAD  CAE   106.73  3.000
 BNT  HAD   CAD  CAC   106.20  3.000
 BNT  CAE   CAD  CAC   112.42  3.000
 BNT  HAD   CAD  CAA   105.98  3.000
 BNT  CAE   CAD  CAA   112.62  3.000
 BNT  CAC   CAD  CAA   112.29  3.000
 BNT  HAC3  CAC  HAC2  107.64  3.000
 BNT  HAC3  CAC  HAC1  107.81  3.000
 BNT  HAC2  CAC  HAC1  108.46  3.000
 BNT  HAC3  CAC  CAD   108.91  3.000
 BNT  HAC2  CAC  CAD   111.39  3.000
 BNT  HAC1  CAC  CAD   112.45  3.000
 BNT  CAJ   CAE  CAF   117.10  3.000
 BNT  CAJ   CAE  CAD   125.07  3.000
 BNT  CAF   CAE  CAD   117.82  3.000
 BNT  CAG   CAF  OAB   119.96  3.000
 BNT  CAG   CAF  CAE   119.19  3.000
 BNT  OAB   CAF  CAE   120.85  3.000
 BNT  CAL   CAG  BRAH  122.45  3.000
 BNT  CAL   CAG  CAF   123.37  3.000
 BNT  BRAH  CAG  CAF   114.18  3.000
 BNT  CAK   CAL  CAM   116.29  3.000
 BNT  CAK   CAL  CAG   117.53  3.000
 BNT  CAM   CAL  CAG   126.13  3.000
 BNT  HAM3  CAM  HAM2  108.36  3.000
 BNT  HAM3  CAM  HAM1  107.37  3.000
 BNT  HAM2  CAM  HAM1  107.84  3.000
 BNT  HAM3  CAM  CAL   111.13  3.000
 BNT  HAM2  CAM  CAL   112.07  3.000
 BNT  HAM1  CAM  CAL   109.91  3.000
 BNT  CAJ   CAK  OAN   120.87  3.000
 BNT  CAJ   CAK  CAL   119.02  3.000
 BNT  OAN   CAK  CAL   120.11  3.000
 BNT  BRAI  CAJ  CAK   112.91  3.000
 BNT  BRAI  CAJ  CAE   123.55  3.000
 BNT  CAK   CAJ  CAE   123.54  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
 BNT  Var_01  CAF   CAE  CAD  CAA  -62.03  30.0  3
 BNT  Var_02  HAM1  CAM  CAL  CAG  -93.43  30.0  3
 BNT  Var_03  HAA1  CAA  CAD  CAE  -50.04  30.0  3
 BNT  Var_04  HAC1  CAC  CAD  CAE  -71.45  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
 BNT  plan-1  CAD   0.020
 BNT  plan-1  CAE   0.020
 BNT  plan-1  CAF   0.020
 BNT  plan-1  OAB   0.020
 BNT  plan-1  CAG   0.020
 BNT  plan-1  BRAH  0.020
 BNT  plan-1  CAL   0.020
 BNT  plan-1  CAM   0.020
 BNT  plan-1  CAK   0.020
 BNT  plan-1  OAN   0.020
 BNT  plan-1  CAJ   0.020
 BNT  plan-1  BRAI  0.020

