# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:54:59 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: biphenyl
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc(cc1)c2ccccc2
#
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
 BNL  BNL  'biphenyl                 '  ligand  22  12  .  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_BNL
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
 BNL  C1   C  CR16  0  -0.310   1.4495   1.1296  -0.4111
 BNL  C2   C  CR6   0   0.087   0.7356  -0.0019  -0.0123
 BNL  C3   C  CR16  0  -0.310   1.4524  -1.1316   0.3865
 BNL  C4   C  CR16  0  -0.240   2.8397  -1.1306   0.3862
 BNL  C5   C  CR16  0  -0.267   3.5383   0.0013  -0.0132
 BNL  C6   C  CR16  0  -0.240   2.8368   1.1316  -0.4119
 BNL  C12  C  CR16  0  -0.240  -2.8456   1.1313   0.3687
 BNL  C13  C  CR16  0  -0.267  -3.5444  -0.0071  -0.0115
 BNL  C14  C  CR16  0  -0.240  -2.8430  -1.1438  -0.3919
 BNL  C15  C  CR16  0  -0.310  -1.4557  -1.1417  -0.3920
 BNL  C16  C  CR6   0   0.087  -0.7417  -0.0036  -0.0122
 BNL  C17  C  CR16  0  -0.310  -1.4583   1.1327   0.3679
 BNL  H1   H  HCR6  0   0.254   0.9181   2.0123  -0.7447
 BNL  H3   H  HCR6  0   0.254   0.9227  -2.0156   0.7196
 BNL  H4   H  HCR6  0   0.258   3.3750  -2.0148   0.7073
 BNL  H5   H  HCR6  0   0.257   4.6205   0.0024  -0.0143
 BNL  H6   H  HCR6  0   0.257   3.3698   2.0171  -0.7333
 BNL  H13  H  HCR6  0   0.257  -4.6265  -0.0084  -0.0111
 BNL  H14  H  HCR6  0   0.258  -3.3760  -2.0345  -0.6986
 BNL  H15  H  HCR6  0   0.254  -0.9243  -2.0297  -0.7111
 BNL  H17  H  HCR6  0   0.254  -0.9289   2.0219   0.6872
 BNL  H12  H  HCR6  0   0.257  -3.3807   2.0208   0.6752

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
 BNL  C1   C2   aromatic  1.396  0.020  1.396
 BNL  C1   C6   aromatic  1.387  0.020  1.387
 BNL  C2   C3   aromatic  1.396  0.020  1.396
 BNL  C2   C16  single    1.477  0.020  1.477
 BNL  C3   C4   aromatic  1.387  0.020  1.387
 BNL  C4   C5   aromatic  1.389  0.020  1.389
 BNL  C5   C6   aromatic  1.389  0.020  1.389
 BNL  C12  C13  aromatic  1.389  0.020  1.389
 BNL  C12  C17  aromatic  1.387  0.020  1.387
 BNL  C13  C14  aromatic  1.389  0.020  1.389
 BNL  C14  C15  aromatic  1.387  0.020  1.387
 BNL  C15  C16  aromatic  1.396  0.020  1.396
 BNL  C16  C17  aromatic  1.396  0.020  1.396
 BNL  C1   H1   single    0.930  0.020  1.080
 BNL  C3   H3   single    0.930  0.020  1.080
 BNL  C4   H4   single    0.930  0.020  1.080
 BNL  C5   H5   single    0.930  0.020  1.080
 BNL  C6   H6   single    0.930  0.020  1.080
 BNL  C12  H12  single    0.930  0.020  1.080
 BNL  C13  H13  single    0.930  0.020  1.080
 BNL  C14  H14  single    0.930  0.020  1.080
 BNL  C15  H15  single    0.930  0.020  1.080
 BNL  C17  H17  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
 BNL  H1   C1   C6   119.30  3.000
 BNL  H1   C1   C2   119.84  3.000
 BNL  C6   C1   C2   120.84  3.000
 BNL  C16  C2   C3   120.83  3.000
 BNL  C16  C2   C1   120.82  3.000
 BNL  C3   C2   C1   118.35  3.000
 BNL  H3   C3   C4   119.33  3.000
 BNL  H3   C3   C2   119.82  3.000
 BNL  C4   C3   C2   120.85  3.000
 BNL  H4   C4   C5   120.16  3.000
 BNL  H4   C4   C3   119.59  3.000
 BNL  C5   C4   C3   120.25  3.000
 BNL  H5   C5   C6   120.26  3.000
 BNL  H5   C5   C4   120.28  3.000
 BNL  C6   C5   C4   119.46  3.000
 BNL  H6   C6   C5   120.15  3.000
 BNL  H6   C6   C1   119.59  3.000
 BNL  C5   C6   C1   120.26  3.000
 BNL  H12  C12  C17  119.59  3.000
 BNL  H12  C12  C13  120.16  3.000
 BNL  C17  C12  C13  120.25  3.000
 BNL  H13  C13  C14  120.27  3.000
 BNL  H13  C13  C12  120.27  3.000
 BNL  C14  C13  C12  119.46  3.000
 BNL  H14  C14  C15  119.58  3.000
 BNL  H14  C14  C13  120.16  3.000
 BNL  C15  C14  C13  120.25  3.000
 BNL  H15  C15  C16  119.84  3.000
 BNL  H15  C15  C14  119.30  3.000
 BNL  C16  C15  C14  120.84  3.000
 BNL  C17  C16  C15  118.36  3.000
 BNL  C17  C16  C2   120.82  3.000
 BNL  C15  C16  C2   120.82  3.000
 BNL  H17  C17  C16  119.84  3.000
 BNL  H17  C17  C12  119.31  3.000
 BNL  C16  C17  C12  120.84  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
 BNL  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 BNL  CONST_04  C4   C5   C6   C1     0.00  0.0  0
 BNL  CONST_05  C5   C6   C1   C2     0.00  0.0  0
 BNL  CONST_06  C5   C4   C3   C2     0.00  0.0  0
 BNL  CONST_07  C14  C15  C16  C2   180.00  0.0  0
 BNL  CONST_08  C12  C17  C16  C2   180.00  0.0  0
 BNL  CONST_09  C6   C1   C2   C3     0.00  0.0  0
 BNL  CONST_12  C6   C5   C4   C3     0.00  0.0  0
 BNL  CONST_13  C16  C2   C3   C4   180.00  0.0  0
 BNL  CONST_14  C16  C2   C1   C6   180.00  0.0  0
 BNL  CONST_15  C15  C14  C13  C12    0.00  0.0  0
 BNL  CONST_16  C15  C16  C17  C12    0.00  0.0  0
 BNL  CONST_17  C16  C17  C12  C13    0.00  0.0  0
 BNL  CONST_18  C16  C15  C14  C13    0.00  0.0  0
 BNL  CONST_19  C17  C12  C13  C14    0.00  0.0  0
 BNL  CONST_20  C17  C16  C15  C14    0.00  0.0  0
 BNL  CONST_21  H3   C3   C2   C1   180.00  0.0  0
 BNL  CONST_22  H5   C5   C6   C1   180.00  0.0  0
 BNL  CONST_23  H6   C6   C1   C2   180.00  0.0  0
 BNL  CONST_24  H4   C4   C3   C2   180.00  0.0  0
 BNL  CONST_25  H15  C15  C16  C2     0.00  0.0  0
 BNL  CONST_26  H17  C17  C16  C2     0.00  0.0  0
 BNL  CONST_27  H1   C1   C2   C3   180.00  0.0  0
 BNL  CONST_28  H14  C14  C13  C12  180.00  0.0  0
 BNL  CONST_29  H12  C12  C13  C14  180.00  0.0  0
 BNL  CONST_30  H13  C13  C14  C15  180.00  0.0  0

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
 BNL  plan-1  C1   0.020
 BNL  plan-1  C2   0.020
 BNL  plan-1  C3   0.020
 BNL  plan-1  C4   0.020
 BNL  plan-1  C5   0.020
 BNL  plan-1  C6   0.020
 BNL  plan-1  C16  0.020
 BNL  plan-1  H1   0.020
 BNL  plan-1  H3   0.020
 BNL  plan-1  H4   0.020
 BNL  plan-1  H5   0.020
 BNL  plan-1  H6   0.020
 BNL  plan-2  C2   0.020
 BNL  plan-2  C12  0.020
 BNL  plan-2  C13  0.020
 BNL  plan-2  C14  0.020
 BNL  plan-2  C15  0.020
 BNL  plan-2  C16  0.020
 BNL  plan-2  C17  0.020
 BNL  plan-2  H13  0.020
 BNL  plan-2  H14  0.020
 BNL  plan-2  H15  0.020
 BNL  plan-2  H17  0.020
 BNL  plan-2  H12  0.020

