# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 10:48:51 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  27  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  -0.590  -2.3520  -2.1100   0.4549
 17D  OAB   O  OC    -1  -0.596  -3.5121  -1.2869  -1.2594
 17D  CAC   C  CR16   0  -0.273   4.4412  -0.0629  -0.2646
 17D  CAD   C  CR16   0  -0.242   3.9836  -0.2547   1.0309
 17D  CAE   C  CR16   0  -0.243   3.5454  -0.1399  -1.3258
 17D  CAF   C  CR16   0  -0.254  -0.9259   2.7074   0.1902
 17D  CAG   C  CR16   0  -0.265  -2.2455   2.5571  -0.2083
 17D  CAH   C  CR16   0  -0.312   2.6388  -0.5222   1.2633
 17D  CAI   C  CR16   0  -0.288   2.2057  -0.4062  -1.0873
 17D  CAJ   C  CR16   0  -0.285  -0.1359   1.5836   0.3811
 17D  CAK   C  CR16   0  -0.281  -2.7504   1.2815  -0.4044
 17D  CAM   C  C      0   0.364  -2.6661  -1.2101  -0.3480
 17D  CAN   C  CR6    0   0.103   1.7332  -0.6017   0.2103
 17D  CAO   C  CR6    0   0.083  -0.6383   0.2926   0.2116
 17D  CAP   C  CR6    0  -0.114  -1.9790   0.1406  -0.1783
 17D  HAE   H  HCR6   0   0.252   3.8933   0.0064  -2.3405
 17D  HAF   H  HCR6   0   0.248  -0.5067   3.6936   0.3445
 17D  HAG   H  HCR6   0   0.245  -2.8730   3.4240  -0.3726
 17D  HAH   H  HCR6   0   0.247   2.2899  -0.6719   2.2786
 17D  HAI   H  HCR6   0   0.245   1.5126  -0.4612  -1.9191
 17D  HAJ   H  HCR6   0   0.243   0.9007   1.7197   0.6643
 17D  HAK   H  HCR6   0   0.242  -3.7755   1.1609  -0.7301
 17D  HAC   H  HCR6   0   0.252   5.4879   0.1416  -0.4494
 17D  CAL   C  CH2    0  -0.541   0.2770  -0.8937   0.4507
 17D  HAD   H  HCR6   0   0.252   4.6726  -0.1973   1.8638
 17D  HAL   H  HCH2   0   0.253  -0.0288  -1.7245  -0.1838
 17D  HALA  H  HCH2   0   0.255   0.1424  -1.2459   1.4765

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   deloc     1.246  0.020  1.246
 17D  CAM  OAB   deloc     1.246  0.020  1.246
 17D  CAD  CAC   aromatic  1.387  0.020  1.387
 17D  CAC  CAE   aromatic  1.391  0.020  1.391
 17D  CAC  HAC   single    0.930  0.020  1.080
 17D  CAH  CAD   aromatic  1.391  0.020  1.391
 17D  CAD  HAD   single    0.930  0.020  1.080
 17D  CAI  CAE   aromatic  1.387  0.020  1.387
 17D  CAE  HAE   single    0.930  0.020  1.080
 17D  CAF  CAG   aromatic  1.387  0.020  1.387
 17D  CAF  CAJ   aromatic  1.387  0.020  1.387
 17D  CAF  HAF   single    0.930  0.020  1.080
 17D  CAG  CAK   aromatic  1.386  0.020  1.386
 17D  CAG  HAG   single    0.930  0.020  1.080
 17D  CAH  CAN   aromatic  1.391  0.020  1.391
 17D  CAH  HAH   single    0.930  0.020  1.080
 17D  CAN  CAI   aromatic  1.395  0.020  1.395
 17D  CAI  HAI   single    0.930  0.020  1.080
 17D  CAJ  CAO   aromatic  1.396  0.020  1.396
 17D  CAJ  HAJ   single    0.930  0.020  1.080
 17D  CAK  CAP   aromatic  1.396  0.020  1.396
 17D  CAK  HAK   single    0.930  0.020  1.080
 17D  CAO  CAL   single    1.517  0.020  1.517
 17D  CAL  CAN   single    1.505  0.020  1.505
 17D  CAL  HAL   single    0.970  0.020  1.090
 17D  CAL  HALA  single    0.970  0.020  1.090
 17D  CAP  CAM   single    1.525  0.020  1.525
 17D  CAO  CAP   aromatic  1.404  0.020  1.404

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  HAC   CAC  CAE  120.21  3.000
 17D  HAC   CAC  CAD  120.30  3.000
 17D  CAE   CAC  CAD  119.49  3.000
 17D  HAD   CAD  CAH  119.81  3.000
 17D  HAD   CAD  CAC  120.08  3.000
 17D  CAH   CAD  CAC  120.11  3.000
 17D  HAE   CAE  CAI  119.84  3.000
 17D  HAE   CAE  CAC  120.04  3.000
 17D  CAI   CAE  CAC  120.12  3.000
 17D  HAF   CAF  CAJ  119.86  3.000
 17D  HAF   CAF  CAG  120.55  3.000
 17D  CAJ   CAF  CAG  119.59  3.000
 17D  HAG   CAG  CAK  120.29  3.000
 17D  HAG   CAG  CAF  120.55  3.000
 17D  CAK   CAG  CAF  119.16  3.000
 17D  HAH   CAH  CAN  119.44  3.000
 17D  HAH   CAH  CAD  119.63  3.000
 17D  CAN   CAH  CAD  120.93  3.000
 17D  HAI   CAI  CAN  119.35  3.000
 17D  HAI   CAI  CAE  119.70  3.000
 17D  CAN   CAI  CAE  120.95  3.000
 17D  HAJ   CAJ  CAO  119.50  3.000
 17D  HAJ   CAJ  CAF  118.64  3.000
 17D  CAO   CAJ  CAF  121.86  3.000
 17D  HAK   CAK  CAP  118.76  3.000
 17D  HAK   CAK  CAG  119.35  3.000
 17D  CAP   CAK  CAG  121.88  3.000
 17D  CAP   CAM  OAB  116.23  3.000
 17D  CAP   CAM  OAA  117.02  3.000
 17D  OAB   CAM  OAA  126.73  3.000
 17D  CAL   CAN  CAI  120.25  3.000
 17D  CAL   CAN  CAH  121.35  3.000
 17D  CAI   CAN  CAH  118.40  3.000
 17D  CAP   CAO  CAL  122.34  3.000
 17D  CAP   CAO  CAJ  118.52  3.000
 17D  CAL   CAO  CAJ  119.14  3.000
 17D  CAO   CAP  CAM  123.84  3.000
 17D  CAO   CAP  CAK  118.96  3.000
 17D  CAM   CAP  CAK  117.19  3.000
 17D  HALA  CAL  HAL  105.45  3.000
 17D  HALA  CAL  CAO  109.00  3.000
 17D  HAL   CAL  CAO  109.59  3.000
 17D  HALA  CAL  CAN  109.37  3.000
 17D  HAL   CAL  CAN  109.07  3.000
 17D  CAO   CAL  CAN  114.01  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  Var_01    CAO  CAL  CAN  CAH   109.13  30.0  3
 17D  Var_02    CAN  CAL  CAO  CAJ   -27.66  30.0  2
 17D  Var_03    CAK  CAP  CAM  OAA  -142.23  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  HAE  0.020
 17D  plan-1  HAH  0.020
 17D  plan-1  HAI  0.020
 17D  plan-1  HAC  0.020
 17D  plan-1  CAL  0.020
 17D  plan-1  HAD  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

