# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:44:19 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-benzylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1Cc2ccccc2
#
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
 17D  17D  '2-benzylbenzoic acid     '  ligand  28  16  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_17D
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
 17D  OAA   O  O     0  -0.435  -2.2663  -2.2191  -0.5225
 17D  OAB   O  OH1   0  -0.592  -3.7977  -1.2358   0.7571
 17D  CAC   C  CR16  0  -0.269   4.4433   0.0038   0.2790
 17D  CAD   C  CR16  0  -0.243   3.5872  -0.1201   1.3673
 17D  CAE   C  CR16  0  -0.242   3.9508  -0.1852  -1.0045
 17D  CAF   C  CR16  0  -0.230  -0.9412   2.6541  -0.1669
 17D  CAG   C  CR16  0  -0.259  -2.3033   2.5073   0.0394
 17D  CAH   C  CR16  0  -0.285   2.2499  -0.4294   1.1687
 17D  CAI   C  CR16  0  -0.301   2.6097  -0.4953  -1.1978
 17D  CAJ   C  CR16  0  -0.288  -0.1294   1.5345  -0.2718
 17D  CAK   C  CR16  0  -0.249  -2.8371   1.2340   0.1322
 17D  CAM   C  C     0   0.498  -2.6790  -1.2338   0.0410
 17D  CAN   C  CR6   0   0.088   1.7440  -0.6199  -0.1160
 17D  CAO   C  CR6   0   0.118  -0.6426   0.2419  -0.1947
 17D  CAP   C  CR6   0  -0.097  -2.0285   0.1023   0.0057
 17D  HOAB  H  HOH1  0   0.486  -4.2105  -2.1114   0.7163
 17D  HAD   H  HCR6  0   0.254   3.9634   0.0223   2.3724
 17D  HAE   H  HCR6  0   0.255   4.6102  -0.0931  -1.8579
 17D  HAF   H  HCR6  0   0.264  -0.5032   3.6409  -0.2434
 17D  HAG   H  HCR6  0   0.264  -2.9466   3.3722   0.1285
 17D  HAH   H  HCR6  0   0.249   1.5878  -0.5232   2.0219
 17D  HAI   H  HCR6  0   0.250   2.2329  -0.6427  -2.2034
 17D  HAJ   H  HCR6  0   0.259   0.9333   1.6767  -0.4146
 17D  HAK   H  HCR6  0   0.269  -3.9014   1.1241   0.2870
 17D  CAL   C  CH2   0  -0.553   0.2899  -0.9480  -0.3179
 17D  HAC   H  HCR6  0   0.255   5.4880   0.2415   0.4328
 17D  HAL   H  HCH2  0   0.272   0.1539  -1.4009  -1.3024
 17D  HALA  H  HCH2  0   0.263   0.0020  -1.7140   0.4034

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
 17D  OAA  CAM   double    1.208  0.020  1.208
 17D  CAM  OAB   single    1.328  0.020  1.328
 17D  OAB  HOAB  single    0.850  0.020  0.980
 17D  CAD  CAC   aromatic  1.390  0.020  1.390
 17D  CAC  CAE   aromatic  1.388  0.020  1.388
 17D  CAC  HAC   single    0.930  0.020  1.080
 17D  CAH  CAD   aromatic  1.387  0.020  1.387
 17D  CAD  HAD   single    0.930  0.020  1.080
 17D  CAI  CAE   aromatic  1.390  0.020  1.390
 17D  CAE  HAE   single    0.930  0.020  1.080
 17D  CAF  CAG   aromatic  1.385  0.020  1.385
 17D  CAF  CAJ   aromatic  1.387  0.020  1.387
 17D  CAF  HAF   single    0.930  0.020  1.080
 17D  CAG  CAK   aromatic  1.384  0.020  1.384
 17D  CAG  HAG   single    0.930  0.020  1.080
 17D  CAH  CAN   aromatic  1.394  0.020  1.394
 17D  CAH  HAH   single    0.930  0.020  1.080
 17D  CAN  CAI   aromatic  1.391  0.020  1.391
 17D  CAI  HAI   single    0.930  0.020  1.080
 17D  CAJ  CAO   aromatic  1.393  0.020  1.393
 17D  CAJ  HAJ   single    0.930  0.020  1.080
 17D  CAK  CAP   aromatic  1.397  0.020  1.397
 17D  CAK  HAK   single    0.930  0.020  1.080
 17D  CAO  CAL   single    1.517  0.020  1.517
 17D  CAL  CAN   single    1.504  0.020  1.504
 17D  CAL  HAL   single    0.970  0.020  1.090
 17D  CAL  HALA  single    0.970  0.020  1.090
 17D  CAP  CAM   single    1.486  0.020  1.486
 17D  CAO  CAP   aromatic  1.407  0.020  1.407

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
 17D  HOAB  OAB  CAM  109.73  3.000
 17D  HAC   CAC  CAE  120.26  3.000
 17D  HAC   CAC  CAD  120.18  3.000
 17D  CAE   CAC  CAD  119.56  3.000
 17D  HAD   CAD  CAH  119.82  3.000
 17D  HAD   CAD  CAC  120.07  3.000
 17D  CAH   CAD  CAC  120.10  3.000
 17D  HAE   CAE  CAI  119.81  3.000
 17D  HAE   CAE  CAC  120.09  3.000
 17D  CAI   CAE  CAC  120.10  3.000
 17D  HAF   CAF  CAJ  119.59  3.000
 17D  HAF   CAF  CAG  120.33  3.000
 17D  CAJ   CAF  CAG  120.08  3.000
 17D  HAG   CAG  CAK  120.06  3.000
 17D  HAG   CAG  CAF  120.82  3.000
 17D  CAK   CAG  CAF  119.13  3.000
 17D  HAH   CAH  CAN  119.47  3.000
 17D  HAH   CAH  CAD  119.71  3.000
 17D  CAN   CAH  CAD  120.83  3.000
 17D  HAI   CAI  CAN  119.53  3.000
 17D  HAI   CAI  CAE  119.66  3.000
 17D  CAN   CAI  CAE  120.81  3.000
 17D  HAJ   CAJ  CAO  119.43  3.000
 17D  HAJ   CAJ  CAF  118.62  3.000
 17D  CAO   CAJ  CAF  121.96  3.000
 17D  HAK   CAK  CAP  120.04  3.000
 17D  HAK   CAK  CAG  118.88  3.000
 17D  CAP   CAK  CAG  121.08  3.000
 17D  CAP   CAM  OAB  112.50  3.000
 17D  CAP   CAM  OAA  124.93  3.000
 17D  OAB   CAM  OAA  122.56  3.000
 17D  CAL   CAN  CAI  121.11  3.000
 17D  CAL   CAN  CAH  120.29  3.000
 17D  CAI   CAN  CAH  118.60  3.000
 17D  CAP   CAO  CAL  122.63  3.000
 17D  CAP   CAO  CAJ  117.57  3.000
 17D  CAL   CAO  CAJ  119.80  3.000
 17D  CAO   CAP  CAM  121.57  3.000
 17D  CAO   CAP  CAK  120.18  3.000
 17D  CAM   CAP  CAK  118.22  3.000
 17D  HALA  CAL  HAL  105.78  3.000
 17D  HALA  CAL  CAO  109.57  3.000
 17D  HAL   CAL  CAO  108.78  3.000
 17D  HALA  CAL  CAN  108.63  3.000
 17D  HAL   CAL  CAN  109.38  3.000
 17D  CAO   CAL  CAN  114.35  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
 17D  CONST_01  CAN   CAH  CAD  CAC    0.00   0.0  0
 17D  CONST_02  CAN   CAI  CAE  CAC    0.00   0.0  0
 17D  CONST_03  CAI   CAE  CAC  CAD    0.00   0.0  0
 17D  CONST_04  CAI   CAN  CAH  CAD    0.00   0.0  0
 17D  CONST_05  CAH   CAD  CAC  CAE    0.00   0.0  0
 17D  CONST_06  CAH   CAN  CAI  CAE    0.00   0.0  0
 17D  CONST_07  CAP   CAK  CAG  CAF    0.00   0.0  0
 17D  CONST_08  CAP   CAO  CAJ  CAF    0.00   0.0  0
 17D  CONST_09  CAO   CAJ  CAF  CAG    0.00   0.0  0
 17D  CONST_10  CAO   CAP  CAK  CAG    0.00   0.0  0
 17D  CONST_11  CAK   CAG  CAF  CAJ    0.00   0.0  0
 17D  CONST_12  CAK   CAP  CAO  CAJ    0.00   0.0  0
 17D  CONST_13  CAL   CAN  CAH  CAD  180.00   0.0  0
 17D  CONST_14  CAL   CAN  CAI  CAE  180.00   0.0  0
 17D  CONST_15  CAL   CAO  CAJ  CAF  180.00   0.0  0
 17D  CONST_16  CAM   CAP  CAK  CAG  180.00   0.0  0
 17D  CONST_17  CAM   CAP  CAO  CAJ  180.00   0.0  0
 17D  CONST_18  CAL   CAO  CAP  CAK  180.00   0.0  0
 17D  CONST_19  HAH   CAH  CAD  CAC  180.00   0.0  0
 17D  CONST_20  HAI   CAI  CAE  CAC  180.00   0.0  0
 17D  CONST_21  HAE   CAE  CAC  CAD  180.00   0.0  0
 17D  CONST_22  HAD   CAD  CAC  CAE  180.00   0.0  0
 17D  CONST_23  HAK   CAK  CAG  CAF  180.00   0.0  0
 17D  CONST_24  HAJ   CAJ  CAF  CAG  180.00   0.0  0
 17D  CONST_25  HAC   CAC  CAD  CAH  180.00   0.0  0
 17D  CONST_26  HAG   CAG  CAF  CAJ  180.00   0.0  0
 17D  CONST_27  HAF   CAF  CAG  CAK  180.00   0.0  0
 17D  CONST_28  HOAB  OAB  CAM  CAP  180.00   0.0  0
 17D  Var_01    CAO   CAL  CAN  CAH   77.76  30.0  1
 17D  Var_02    CAN   CAL  CAO  CAJ   17.00  30.0  2
 17D  Var_03    CAK   CAP  CAM  OAA  150.77  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
 17D  plan-1  CAC   0.020
 17D  plan-1  CAD   0.020
 17D  plan-1  CAE   0.020
 17D  plan-1  CAH   0.020
 17D  plan-1  CAI   0.020
 17D  plan-1  CAN   0.020
 17D  plan-1  HAD   0.020
 17D  plan-1  HAE   0.020
 17D  plan-1  HAH   0.020
 17D  plan-1  HAI   0.020
 17D  plan-1  CAL   0.020
 17D  plan-1  HAC   0.020
 17D  plan-2  CAF   0.020
 17D  plan-2  CAG   0.020
 17D  plan-2  CAJ   0.020
 17D  plan-2  CAK   0.020
 17D  plan-2  CAM   0.020
 17D  plan-2  CAO   0.020
 17D  plan-2  CAP   0.020
 17D  plan-2  HAF   0.020
 17D  plan-2  HAG   0.020
 17D  plan-2  HAJ   0.020
 17D  plan-2  HAK   0.020
 17D  plan-2  CAL   0.020
 17D  plan-3  OAA   0.020
 17D  plan-3  OAB   0.020
 17D  plan-3  CAM   0.020
 17D  plan-3  CAP   0.020
 17D  plan-3  HOAB  0.020

