# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 14:38:38 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 2,6-dibromo-3-(2,4-dibromophenoxy)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(Br)ccc(Oc2ccc(Br)cc2Br)c1Br
#
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
 YUG  YUG  2,6-dibromo-3-(2,4-dibromophenoxy)phenol  ligand  24  18  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YUG
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
 YUG  O    O   O2    0  -0.486   0.2161  -0.9970  -0.9382
 YUG  C1   C   CR6   0   0.443  -0.8278  -0.2057  -0.5889
 YUG  C2   C   CR6   0  -0.330  -2.0654  -0.8292  -0.4682
 YUG  C3   C   CR6   0   0.472  -3.2108  -0.1025  -0.1336
 YUG  O3   O   OH1   0  -0.587  -4.3557  -0.7744  -0.0369
 YUG  C4   C   CR6   0  -0.256  -3.0722   1.2724   0.0835
 YUG  BR3  BR  BR    0  -0.017   5.8707   0.9636  -0.4156
 YUG  C5   C   CR16  0  -0.223  -1.8393   1.8890  -0.0349
 YUG  C6   C   CR16  0  -0.358  -0.7126   1.1599  -0.3714
 YUG  C1'  C   CR6   0   0.357   1.4862  -0.5177  -0.8050
 YUG  C2'  C   CR6   0  -0.167   2.1174  -0.5183   0.4352
 YUG  BR2  BR  BR    0   0.013  -2.2079  -2.6749  -0.7525
 YUG  C3'  C   CR16  0  -0.212   3.4260  -0.0760   0.5584
 YUG  C4'  C   CR6   0  -0.110   4.0923   0.3647  -0.5760
 YUG  BR1  BR  BR    0   0.018   1.1977  -1.1428   1.9458
 YUG  C5'  C   CR16  0  -0.227   3.4786   0.3655  -1.8195
 YUG  C6'  C   CR16  0  -0.294   2.1690  -0.0748  -1.9252
 YUG  H1   H   HOH1  0   0.483  -5.1013  -0.1970   0.1729
 YUG  H2   H   HCR6  0   0.296  -1.7442   2.9531   0.1317
 YUG  H3   H   HCR6  0   0.297   0.2370   1.6678  -0.4677
 YUG  H4   H   HCR6  0   0.307   3.9144  -0.0788   1.5234
 YUG  H5   H   HCR6  0   0.296   4.0002   0.7054  -2.7032
 YUG  H6   H   HCR6  0   0.299   1.6751  -0.0814  -2.8882
 YUG  BR4  BR  BR    0  -0.017  -4.5857   2.3007   0.5423

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
 YUG  BR3  C4'  single    1.883  0.020  1.883
 YUG  C4'  C5'  aromatic  1.387  0.020  1.387
 YUG  C4'  C3'  aromatic  1.387  0.020  1.387
 YUG  C5'  C6'  aromatic  1.386  0.020  1.386
 YUG  C3'  C2'  aromatic  1.387  0.020  1.387
 YUG  C6'  C1'  aromatic  1.385  0.020  1.385
 YUG  C2'  C1'  aromatic  1.392  0.020  1.392
 YUG  C2'  BR1  single    1.876  0.020  1.876
 YUG  C1'  O    single    1.364  0.020  1.364
 YUG  C6   C5   aromatic  1.384  0.020  1.384
 YUG  C6   C1   aromatic  1.388  0.020  1.388
 YUG  C5   C4   aromatic  1.384  0.020  1.384
 YUG  O    C1   single    1.356  0.020  1.356
 YUG  C1   C2   aromatic  1.391  0.020  1.391
 YUG  C4   BR4  single    1.886  0.020  1.886
 YUG  C4   C3   aromatic  1.399  0.020  1.399
 YUG  C2   C3   aromatic  1.397  0.020  1.397
 YUG  C2   BR2  single    1.873  0.020  1.873
 YUG  C3   O3   single    1.331  0.020  1.331
 YUG  O3   H1   single    0.850  0.020  0.980
 YUG  C5   H2   single    0.930  0.020  1.080
 YUG  C6   H3   single    0.930  0.020  1.080
 YUG  C3'  H4   single    0.930  0.020  1.080
 YUG  C5'  H5   single    0.930  0.020  1.080
 YUG  C6'  H6   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
 YUG  C1'  O    C1   119.13  3.000
 YUG  C6   C1   C2   120.09  3.000
 YUG  C2   C1   O    116.47  3.000
 YUG  C6   C1   O    123.43  3.000
 YUG  BR2  C2   C3   119.11  3.000
 YUG  BR2  C2   C1   119.75  3.000
 YUG  C3   C2   C1   121.13  3.000
 YUG  C4   C3   O3   124.76  3.000
 YUG  O3   C3   C2   117.39  3.000
 YUG  C4   C3   C2   117.85  3.000
 YUG  H1   O3   C3   112.21  3.000
 YUG  C5   C4   C3   120.86  3.000
 YUG  C3   C4   BR4  119.61  3.000
 YUG  C5   C4   BR4  119.53  3.000
 YUG  H2   C5   C6   118.98  3.000
 YUG  H2   C5   C4   120.25  3.000
 YUG  C6   C5   C4   120.77  3.000
 YUG  H3   C6   C5   119.30  3.000
 YUG  H3   C6   C1   121.42  3.000
 YUG  C5   C6   C1   119.28  3.000
 YUG  C6'  C1'  C2'  119.83  3.000
 YUG  C2'  C1'  O    120.61  3.000
 YUG  C6'  C1'  O    119.51  3.000
 YUG  BR1  C2'  C3'  119.83  3.000
 YUG  BR1  C2'  C1'  119.70  3.000
 YUG  C3'  C2'  C1'  120.47  3.000
 YUG  H4   C3'  C4'  120.90  3.000
 YUG  H4   C3'  C2'  120.30  3.000
 YUG  C4'  C3'  C2'  118.80  3.000
 YUG  C5'  C4'  C3'  121.39  3.000
 YUG  C3'  C4'  BR3  119.00  3.000
 YUG  C5'  C4'  BR3  119.61  3.000
 YUG  H5   C5'  C6'  119.57  3.000
 YUG  H5   C5'  C4'  121.31  3.000
 YUG  C6'  C5'  C4'  119.11  3.000
 YUG  H6   C6'  C5'  120.08  3.000
 YUG  H6   C6'  C1'  119.53  3.000
 YUG  C5'  C6'  C1'  120.39  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
 YUG  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 YUG  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 YUG  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 YUG  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 YUG  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 YUG  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 YUG  CONST_07  C4'  C5'  C6'  C1'     0.00   0.0  0
 YUG  CONST_08  C4'  C3'  C2'  C1'     0.00   0.0  0
 YUG  CONST_09  C5'  C4'  C3'  C2'     0.00   0.0  0
 YUG  CONST_10  C5'  C6'  C1'  C2'     0.00   0.0  0
 YUG  CONST_11  C6'  C5'  C4'  C3'     0.00   0.0  0
 YUG  CONST_12  C6'  C1'  C2'  C3'     0.00   0.0  0
 YUG  CONST_13  C5'  C6'  C1'  O     180.00   0.0  0
 YUG  CONST_14  C3'  C2'  C1'  O     180.00   0.0  0
 YUG  CONST_15  C5   C6   C1   O     180.00   0.0  0
 YUG  CONST_16  C3   C2   C1   O     180.00   0.0  0
 YUG  CONST_17  O3   C3   C2   C1    180.00   0.0  0
 YUG  CONST_18  BR4  C4   C3   C2    180.00   0.0  0
 YUG  CONST_19  C6   C5   C4   BR4   180.00   0.0  0
 YUG  CONST_20  C5   C4   C3   O3    180.00   0.0  0
 YUG  CONST_21  BR2  C2   C3   C4    180.00   0.0  0
 YUG  CONST_22  C6'  C5'  C4'  BR3   180.00   0.0  0
 YUG  CONST_23  C2'  C3'  C4'  BR3   180.00   0.0  0
 YUG  CONST_24  BR2  C2   C1   C6    180.00   0.0  0
 YUG  CONST_25  BR1  C2'  C3'  C4'   180.00   0.0  0
 YUG  CONST_26  C6'  C1'  C2'  BR1   180.00   0.0  0
 YUG  CONST_27  H2   C5   C6   C1    180.00   0.0  0
 YUG  CONST_28  H3   C6   C1   C2    180.00   0.0  0
 YUG  CONST_29  H5   C5'  C6'  C1'   180.00   0.0  0
 YUG  CONST_30  H4   C3'  C2'  C1'   180.00   0.0  0
 YUG  CONST_31  H6   C6'  C1'  C2'   180.00   0.0  0
 YUG  Var_01    C6'  C1'  O    C1   -102.28  30.0  1

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
 YUG  plan-1  O    0.020
 YUG  plan-1  C1   0.020
 YUG  plan-1  C2   0.020
 YUG  plan-1  C3   0.020
 YUG  plan-1  O3   0.020
 YUG  plan-1  C4   0.020
 YUG  plan-1  C5   0.020
 YUG  plan-1  C6   0.020
 YUG  plan-1  BR2  0.020
 YUG  plan-1  H2   0.020
 YUG  plan-1  H3   0.020
 YUG  plan-1  BR4  0.020
 YUG  plan-2  O    0.020
 YUG  plan-2  BR3  0.020
 YUG  plan-2  C1'  0.020
 YUG  plan-2  C2'  0.020
 YUG  plan-2  C3'  0.020
 YUG  plan-2  C4'  0.020
 YUG  plan-2  BR1  0.020
 YUG  plan-2  C5'  0.020
 YUG  plan-2  C6'  0.020
 YUG  plan-2  H4   0.020
 YUG  plan-2  H5   0.020
 YUG  plan-2  H6   0.020

