# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 04:35:10 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: biphenyl-4,4'-diyldiboronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1ccc(cc1)c2ccc(cc2)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
 BDB  BDB  'biphenyl-4,4'-diyldiboronic acid'  ligand  30  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BDB
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
 BDB  B1    B  B     0   0.507  -0.0121  -0.0355   5.1588
 BDB  OB1   O  OH1   0  -0.635   1.1693  -0.2811   5.7886
 BDB  OB2   O  OH1   0  -0.635  -1.1913   0.2083   5.7936
 BDB  CP1   C  CR6   0  -0.091  -0.0131  -0.0313   3.5897
 BDB  CP2   C  CR16  0  -0.307  -1.1526   0.3227   2.8623
 BDB  CP3   C  CR16  0  -0.284  -1.1550   0.3315   1.4766
 BDB  CP4   C  CR6   0   0.064  -0.0091  -0.0153   0.7591
 BDB  CP5   C  CR16  0  -0.283   1.1340  -0.3722   1.4761
 BDB  CP6   C  CR16  0  -0.307   1.1279  -0.3789   2.8616
 BDB  CB1   C  CR6   0   0.066  -0.0037  -0.0035  -0.7161
 BDB  CB2   C  CR16  0  -0.283   1.1255   0.4104  -1.4235
 BDB  CB3   C  CR16  0  -0.315   1.1294   0.4162  -2.8087
 BDB  CB4   C  CR6   0  -0.104   0.0147   0.0128  -3.5481
 BDB  CB5   C  CR16  0  -0.310  -1.1128  -0.3945  -2.8294
 BDB  CB6   C  CR16  0  -0.282  -1.1252  -0.4050  -1.4442
 BDB  B2    B  B     0   0.512   0.0180   0.0149  -5.1183
 BDB  OH1   O  OH1   0  -0.630  -1.1731  -0.1121  -5.7593
 BDB  OH2   O  OH1   0  -0.631   1.1542   0.1427  -5.8589
 BDB  HO11  H  HOH1  0   0.484   1.1405  -0.2770   6.7502
 BDB  HO21  H  HOH1  0   0.484  -1.1583   0.2037   6.7551
 BDB  HC21  H  HCR6  0   0.252  -2.0591   0.6093   3.3807
 BDB  HC31  H  HCR6  0   0.252  -2.0516   0.6336   0.9495
 BDB  HC51  H  HCR6  0   0.252   2.0318  -0.6691   0.9479
 BDB  HC61  H  HCR6  0   0.252   2.0331  -0.6709   3.3792
 BDB  HB21  H  HCR6  0   0.256   2.0032   0.7527  -0.8898
 BDB  HB31  H  HCR6  0   0.240   2.0279   0.7645  -3.3058
 BDB  HB51  H  HCR6  0   0.254  -2.0002  -0.7235  -3.3552
 BDB  HB61  H  HCR6  0   0.254  -2.0099  -0.7511  -0.9245
 BDB  HH11  H  HOH1  0   0.486  -1.0997  -0.1202  -6.7194
 BDB  HH21  H  HOH1  0   0.484   1.9664   0.1686  -5.3464

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
 BDB  B1   OB1   single    1.361  0.020  1.361
 BDB  B1   OB2   single    1.361  0.020  1.361
 BDB  B1   CP1   single    1.569  0.020  1.569
 BDB  OB1  HO11  single    0.850  0.020  0.980
 BDB  OB2  HO21  single    0.850  0.020  0.980
 BDB  CP1  CP2   aromatic  1.397  0.020  1.397
 BDB  CP1  CP6   aromatic  1.397  0.020  1.397
 BDB  CP2  CP3   aromatic  1.386  0.020  1.386
 BDB  CP2  HC21  single    0.930  0.020  1.080
 BDB  CP3  CP4   aromatic  1.396  0.020  1.396
 BDB  CP3  HC31  single    0.930  0.020  1.080
 BDB  CP4  CP5   aromatic  1.396  0.020  1.396
 BDB  CP4  CB1   single    1.475  0.020  1.475
 BDB  CP5  CP6   aromatic  1.385  0.020  1.385
 BDB  CP5  HC51  single    0.930  0.020  1.080
 BDB  CP6  HC61  single    0.930  0.020  1.080
 BDB  CB1  CB2   aromatic  1.395  0.020  1.395
 BDB  CB1  CB6   aromatic  1.396  0.020  1.396
 BDB  CB2  CB3   aromatic  1.385  0.020  1.385
 BDB  CB2  HB21  single    0.930  0.020  1.080
 BDB  CB3  CB4   aromatic  1.397  0.020  1.397
 BDB  CB3  HB31  single    0.930  0.020  1.080
 BDB  CB4  CB5   aromatic  1.398  0.020  1.398
 BDB  CB4  B2    single    1.570  0.020  1.570
 BDB  CB5  CB6   aromatic  1.385  0.020  1.385
 BDB  CB5  HB51  single    0.930  0.020  1.080
 BDB  CB6  HB61  single    0.930  0.020  1.080
 BDB  B2   OH1   single    1.359  0.020  1.359
 BDB  B2   OH2   single    1.362  0.020  1.362
 BDB  OH1  HH11  single    0.850  0.020  0.980
 BDB  OH2  HH21  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
 BDB  CP1   B1   OB2  117.74  3.000
 BDB  CP1   B1   OB1  117.63  3.000
 BDB  OB2   B1   OB1  124.64  3.000
 BDB  HO11  OB1  B1   115.83  3.000
 BDB  HO21  OB2  B1   115.82  3.000
 BDB  CP6   CP1  CP2  117.23  3.000
 BDB  CP6   CP1  B1   121.32  3.000
 BDB  CP2   CP1  B1   121.44  3.000
 BDB  HC21  CP2  CP3  118.40  3.000
 BDB  HC21  CP2  CP1  120.03  3.000
 BDB  CP3   CP2  CP1  121.57  3.000
 BDB  HC31  CP3  CP4  119.92  3.000
 BDB  HC31  CP3  CP2  119.33  3.000
 BDB  CP4   CP3  CP2  120.73  3.000
 BDB  CB1   CP4  CP5  120.84  3.000
 BDB  CB1   CP4  CP3  121.01  3.000
 BDB  CP5   CP4  CP3  118.15  3.000
 BDB  HC51  CP5  CP6  119.34  3.000
 BDB  HC51  CP5  CP4  119.90  3.000
 BDB  CP6   CP5  CP4  120.75  3.000
 BDB  HC61  CP6  CP5  118.40  3.000
 BDB  HC61  CP6  CP1  120.04  3.000
 BDB  CP5   CP6  CP1  121.56  3.000
 BDB  CB6   CB1  CB2  118.10  3.000
 BDB  CB6   CB1  CP4  121.08  3.000
 BDB  CB2   CB1  CP4  120.82  3.000
 BDB  HB21  CB2  CB3  119.30  3.000
 BDB  HB21  CB2  CB1  119.99  3.000
 BDB  CB3   CB2  CB1  120.70  3.000
 BDB  HB31  CB3  CB4  120.75  3.000
 BDB  HB31  CB3  CB2  117.52  3.000
 BDB  CB4   CB3  CB2  121.72  3.000
 BDB  B2    CB4  CB5  121.08  3.000
 BDB  B2    CB4  CB3  121.82  3.000
 BDB  CB5   CB4  CB3  117.10  3.000
 BDB  HB51  CB5  CB6  118.43  3.000
 BDB  HB51  CB5  CB4  120.00  3.000
 BDB  CB6   CB5  CB4  121.57  3.000
 BDB  HB61  CB6  CB5  119.31  3.000
 BDB  HB61  CB6  CB1  119.87  3.000
 BDB  CB5   CB6  CB1  120.81  3.000
 BDB  OH2   B2   OH1  118.92  3.000
 BDB  OH2   B2   CB4  123.06  3.000
 BDB  OH1   B2   CB4  118.02  3.000
 BDB  HH11  OH1  B2   113.85  3.000
 BDB  HH21  OH2  B2   114.69  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
 BDB  CONST_01  CP4   CP3  CP2  CP1     0.00   0.0  0
 BDB  CONST_02  CP4   CP5  CP6  CP1     0.00   0.0  0
 BDB  CONST_03  CP5   CP6  CP1  CP2     0.00   0.0  0
 BDB  CONST_04  CP5   CP4  CP3  CP2     0.00   0.0  0
 BDB  CONST_05  CB1   CP4  CP3  CP2   180.00   0.0  0
 BDB  CONST_06  CP6   CP1  CP2  CP3     0.00   0.0  0
 BDB  CONST_07  CP6   CP5  CP4  CP3     0.00   0.0  0
 BDB  CONST_10  CB3   CB2  CB1  CP4   180.00   0.0  0
 BDB  CONST_11  CB5   CB6  CB1  CP4   180.00   0.0  0
 BDB  CONST_14  CB1   CP4  CP5  CP6   180.00   0.0  0
 BDB  CONST_15  CB4   CB3  CB2  CB1     0.00   0.0  0
 BDB  CONST_16  CB4   CB5  CB6  CB1     0.00   0.0  0
 BDB  CONST_17  CB5   CB6  CB1  CB2     0.00   0.0  0
 BDB  CONST_18  CB5   CB4  CB3  CB2     0.00   0.0  0
 BDB  CONST_19  CB6   CB1  CB2  CB3     0.00   0.0  0
 BDB  CONST_20  CB6   CB5  CB4  CB3     0.00   0.0  0
 BDB  CONST_21  CP3   CP2  CP1  B1    180.00   0.0  0
 BDB  CONST_22  CP5   CP6  CP1  B1    180.00   0.0  0
 BDB  CONST_23  B2    CB4  CB3  CB2   180.00   0.0  0
 BDB  CONST_24  B2    CB4  CB5  CB6   180.00   0.0  0
 BDB  CONST_25  HC31  CP3  CP2  CP1   180.00   0.0  0
 BDB  CONST_26  HC51  CP5  CP6  CP1   180.00   0.0  0
 BDB  CONST_27  HC61  CP6  CP1  CP2   180.00   0.0  0
 BDB  CONST_28  HC21  CP2  CP3  CP4   180.00   0.0  0
 BDB  CONST_29  HB21  CB2  CB1  CP4     0.00   0.0  0
 BDB  CONST_30  HB61  CB6  CB1  CP4     0.00   0.0  0
 BDB  CONST_31  HB31  CB3  CB2  CB1   180.00   0.0  0
 BDB  CONST_32  HB51  CB5  CB6  CB1   180.00   0.0  0
 BDB  Var_01    CP2   CP1  B1   OB1  -174.50  30.0  2
 BDB  Var_02    OH1   B2   CB4  CB3  -166.20  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
 BDB  plan-1  B1    0.020
 BDB  plan-1  CP1   0.020
 BDB  plan-1  CP2   0.020
 BDB  plan-1  CP3   0.020
 BDB  plan-1  CP4   0.020
 BDB  plan-1  CP5   0.020
 BDB  plan-1  CP6   0.020
 BDB  plan-1  CB1   0.020
 BDB  plan-1  HC21  0.020
 BDB  plan-1  HC31  0.020
 BDB  plan-1  HC51  0.020
 BDB  plan-1  HC61  0.020
 BDB  plan-2  CP4   0.020
 BDB  plan-2  CB1   0.020
 BDB  plan-2  CB2   0.020
 BDB  plan-2  CB3   0.020
 BDB  plan-2  CB4   0.020
 BDB  plan-2  CB5   0.020
 BDB  plan-2  CB6   0.020
 BDB  plan-2  B2    0.020
 BDB  plan-2  HB21  0.020
 BDB  plan-2  HB31  0.020
 BDB  plan-2  HB51  0.020
 BDB  plan-2  HB61  0.020

