# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 12:46:10 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2R)-2-(3-phenoxyphenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C(O)=O)c1cccc(Oc2ccccc2)c1
#
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
 PFN  PFN  '(2R)-2-(3-phenoxyphenyl)propanoic acid'  ligand  32  18  .  2021-08-19  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PFN
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
 PFN  CAL   C  CR16  0  -0.314   3.1425   0.7801   0.4947
 PFN  CAJ   C  CR16  0  -0.247   4.4728   1.1644   0.4075
 PFN  CAP   C  CR16  0  -0.265   5.4586   0.2377   0.0914
 PFN  CAI   C  CR16  0  -0.249   5.1048  -1.0848  -0.1389
 PFN  CAK   C  CR16  0  -0.330   3.7761  -1.4810  -0.0652
 PFN  CAR   C  CR6   0   0.334   2.8014  -0.5462   0.2536
 PFN  OAN   O  O2    0  -0.512   1.5153  -0.9953   0.3812
 PFN  CAO   C  C     0   0.576  -4.1610  -0.5911   0.0698
 PFN  OAB   O  O     0  -0.431  -4.0441  -1.0848  -1.0224
 PFN  OAA   O  OH1   0  -0.593  -5.2327  -0.7655   0.8345
 PFN  CAM   C  CH3   0  -0.648  -3.7121   1.7004   0.9880
 PFN  CAH   C  CR16  0  -0.338   0.6007   0.3736  -1.3883
 PFN  CAF   C  CR16  0  -0.236  -0.5153   1.0198  -1.9033
 PFN  C2    C  CR6   0   0.366   0.4854  -0.2934  -0.1767
 PFN  CAD   C  CR16  0  -0.312  -1.7275   0.9988  -1.2321
 PFN  C13   C  CH1   0  -0.500  -3.1375   0.2964   0.7490
 PFN  CAE   C  CR6   0   0.194  -1.8418   0.3234  -0.0191
 PFN  CAG   C  CR16  0  -0.401  -0.7262  -0.3175   0.5039
 PFN  HAK   H  HCR6  0   0.269   3.4958  -2.5104  -0.2491
 PFN  HAI   H  HCR6  0   0.262   5.8641  -1.8158  -0.3849
 PFN  HAP   H  HCR6  0   0.258   6.4945   0.5436   0.0291
 PFN  HAJ   H  HCR6  0   0.263   4.7380   2.1963   0.5971
 PFN  HAL   H  HCR6  0   0.279   2.3829   1.5080   0.7514
 PFN  HAA   H  HOH1  0   0.482  -5.8803  -1.3216   0.3761
 PFN  H13   H  HCH1  0   0.301  -2.9435  -0.1473   1.7310
 PFN  HAM1  H  HCH3  0   0.252  -4.5731   1.6655   1.6529
 PFN  HAM2  H  HCH3  0   0.250  -2.9544   2.3292   1.4528
 PFN  HAM3  H  HCH3  0   0.236  -4.0234   2.1775   0.0590
 PFN  HAG   H  HCR6  0   0.266  -0.7935  -0.8459   1.4481
 PFN  HAD   H  HCR6  0   0.251  -2.5793   1.5117  -1.6589
 PFN  HAF   H  HCR6  0   0.262  -0.4322   1.5426  -2.8471
 PFN  HAH   H  HCR6  0   0.278   1.5376   0.3959  -1.9299

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
 PFN  CAK  CAI   aromatic  1.389  0.020  1.389
 PFN  CAK  CAR   aromatic  1.388  0.020  1.388
 PFN  CAI  CAP   aromatic  1.388  0.020  1.388
 PFN  CAP  CAJ   aromatic  1.389  0.020  1.389
 PFN  CAJ  CAL   aromatic  1.387  0.020  1.387
 PFN  CAL  CAR   aromatic  1.391  0.020  1.391
 PFN  CAR  OAN   single    1.368  0.020  1.368
 PFN  OAN  C2    single    1.366  0.020  1.366
 PFN  CAO  OAB   double    1.204  0.020  1.204
 PFN  CAO  OAA   single    1.328  0.020  1.328
 PFN  CAO  C13   single    1.515  0.020  1.515
 PFN  CAM  C13   single    1.536  0.020  1.536
 PFN  CAG  CAE   aromatic  1.389  0.020  1.389
 PFN  CAG  C2    aromatic  1.390  0.020  1.390
 PFN  CAE  CAD   aromatic  1.393  0.020  1.393
 PFN  CAE  C13   single    1.506  0.020  1.506
 PFN  CAD  CAF   aromatic  1.386  0.020  1.386
 PFN  CAF  CAH   aromatic  1.389  0.020  1.389
 PFN  CAH  C2    aromatic  1.388  0.020  1.388
 PFN  CAK  HAK   single    0.930  0.020  1.080
 PFN  CAI  HAI   single    0.930  0.020  1.080
 PFN  CAP  HAP   single    0.930  0.020  1.080
 PFN  CAJ  HAJ   single    0.930  0.020  1.080
 PFN  CAL  HAL   single    0.930  0.020  1.080
 PFN  OAA  HAA   single    0.850  0.020  0.980
 PFN  C13  H13   single    0.970  0.020  1.090
 PFN  CAM  HAM1  single    0.970  0.020  1.090
 PFN  CAM  HAM2  single    0.970  0.020  1.090
 PFN  CAM  HAM3  single    0.970  0.020  1.090
 PFN  CAG  HAG   single    0.930  0.020  1.080
 PFN  CAD  HAD   single    0.930  0.020  1.080
 PFN  CAF  HAF   single    0.930  0.020  1.080
 PFN  CAH  HAH   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
 PFN  HAL   CAL  CAR   120.67  3.000
 PFN  HAL   CAL  CAJ   120.09  3.000
 PFN  CAR   CAL  CAJ   119.24  3.000
 PFN  HAJ   CAJ  CAP   120.13  3.000
 PFN  HAJ   CAJ  CAL   119.21  3.000
 PFN  CAP   CAJ  CAL   120.65  3.000
 PFN  HAP   CAP  CAI   120.25  3.000
 PFN  HAP   CAP  CAJ   120.25  3.000
 PFN  CAI   CAP  CAJ   119.49  3.000
 PFN  HAI   CAI  CAK   119.39  3.000
 PFN  HAI   CAI  CAP   120.15  3.000
 PFN  CAK   CAI  CAP   120.46  3.000
 PFN  HAK   CAK  CAR   119.85  3.000
 PFN  HAK   CAK  CAI   120.67  3.000
 PFN  CAR   CAK  CAI   119.48  3.000
 PFN  OAN   CAR  CAK   117.42  3.000
 PFN  OAN   CAR  CAL   121.84  3.000
 PFN  CAK   CAR  CAL   120.67  3.000
 PFN  C2    OAN  CAR   120.14  3.000
 PFN  C13   CAO  OAA   111.34  3.000
 PFN  C13   CAO  OAB   125.52  3.000
 PFN  OAA   CAO  OAB   123.15  3.000
 PFN  HAA   OAA  CAO   110.01  3.000
 PFN  HAM3  CAM  HAM2  108.05  3.000
 PFN  HAM3  CAM  HAM1  107.99  3.000
 PFN  HAM2  CAM  HAM1  107.95  3.000
 PFN  HAM3  CAM  C13   111.99  3.000
 PFN  HAM2  CAM  C13   109.51  3.000
 PFN  HAM1  CAM  C13   111.21  3.000
 PFN  HAH   CAH  C2    121.24  3.000
 PFN  HAH   CAH  CAF   120.03  3.000
 PFN  C2    CAH  CAF   118.73  3.000
 PFN  HAF   CAF  CAD   119.80  3.000
 PFN  HAF   CAF  CAH   119.11  3.000
 PFN  CAD   CAF  CAH   121.09  3.000
 PFN  CAG   C2   CAH   120.55  3.000
 PFN  CAH   C2   OAN   122.75  3.000
 PFN  CAG   C2   OAN   116.65  3.000
 PFN  HAD   CAD  CAE   120.58  3.000
 PFN  HAD   CAD  CAF   119.37  3.000
 PFN  CAE   CAD  CAF   120.06  3.000
 PFN  H13   C13  CAE   108.19  3.000
 PFN  H13   C13  CAM   107.29  3.000
 PFN  CAE   C13  CAM   112.64  3.000
 PFN  H13   C13  CAO   106.51  3.000
 PFN  CAE   C13  CAO   111.27  3.000
 PFN  CAM   C13  CAO   110.64  3.000
 PFN  CAG   CAE  C13   119.39  3.000
 PFN  C13   CAE  CAD   121.55  3.000
 PFN  CAG   CAE  CAD   119.06  3.000
 PFN  HAG   CAG  CAE   120.20  3.000
 PFN  HAG   CAG  C2    119.28  3.000
 PFN  CAE   CAG  C2    120.53  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
 PFN  CONST_01  CAI  CAP  CAJ  CAL     0.00   0.0  0
 PFN  CONST_02  CAI  CAK  CAR  CAL     0.00   0.0  0
 PFN  CONST_03  CAK  CAI  CAP  CAJ     0.00   0.0  0
 PFN  CONST_04  CAK  CAR  CAL  CAJ     0.00   0.0  0
 PFN  CONST_05  CAR  CAK  CAI  CAP     0.00   0.0  0
 PFN  CONST_06  CAR  CAL  CAJ  CAP     0.00   0.0  0
 PFN  CONST_07  CAE  CAD  CAF  CAH     0.00   0.0  0
 PFN  CONST_08  CAE  CAG  C2   CAH     0.00   0.0  0
 PFN  CONST_09  CAG  CAE  CAD  CAF     0.00   0.0  0
 PFN  CONST_10  CAG  C2   CAH  CAF     0.00   0.0  0
 PFN  CONST_11  CAD  CAE  CAG  C2      0.00   0.0  0
 PFN  CONST_12  CAD  CAF  CAH  C2      0.00   0.0  0
 PFN  CONST_13  OAN  CAR  CAL  CAJ   180.00   0.0  0
 PFN  CONST_14  OAN  CAR  CAK  CAI   180.00   0.0  0
 PFN  CONST_15  CAE  CAG  C2   OAN   180.00   0.0  0
 PFN  CONST_16  CAF  CAH  C2   OAN   180.00   0.0  0
 PFN  CONST_17  C13  CAE  CAD  CAF   180.00   0.0  0
 PFN  CONST_18  C13  CAE  CAG  C2    180.00   0.0  0
 PFN  CONST_19  HAP  CAP  CAJ  CAL   180.00   0.0  0
 PFN  CONST_20  HAK  CAK  CAR  CAL   180.00   0.0  0
 PFN  CONST_21  HAI  CAI  CAP  CAJ   180.00   0.0  0
 PFN  CONST_22  HAL  CAL  CAJ  CAP   180.00   0.0  0
 PFN  CONST_23  HAJ  CAJ  CAP  CAI   180.00   0.0  0
 PFN  CONST_24  HAD  CAD  CAF  CAH   180.00   0.0  0
 PFN  CONST_25  HAG  CAG  C2   CAH   180.00   0.0  0
 PFN  CONST_26  HAF  CAF  CAH  C2    180.00   0.0  0
 PFN  CONST_27  HAH  CAH  CAF  CAD   180.00   0.0  0
 PFN  CONST_28  HAA  OAA  CAO  OAB     0.00   0.0  0
 PFN  Var_01    CAG  C2   OAN  CAR  -146.63  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PFN  chir_01  C13  CAO  CAM  CAE  positiv

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
 PFN  plan-1  CAL  0.020
 PFN  plan-1  CAJ  0.020
 PFN  plan-1  CAP  0.020
 PFN  plan-1  CAI  0.020
 PFN  plan-1  CAK  0.020
 PFN  plan-1  CAR  0.020
 PFN  plan-1  OAN  0.020
 PFN  plan-1  HAK  0.020
 PFN  plan-1  HAI  0.020
 PFN  plan-1  HAP  0.020
 PFN  plan-1  HAJ  0.020
 PFN  plan-1  HAL  0.020
 PFN  plan-2  OAN  0.020
 PFN  plan-2  CAH  0.020
 PFN  plan-2  CAF  0.020
 PFN  plan-2  C2   0.020
 PFN  plan-2  CAD  0.020
 PFN  plan-2  C13  0.020
 PFN  plan-2  CAE  0.020
 PFN  plan-2  CAG  0.020
 PFN  plan-2  HAG  0.020
 PFN  plan-2  HAD  0.020
 PFN  plan-2  HAF  0.020
 PFN  plan-2  HAH  0.020
 PFN  plan-3  CAO  0.020
 PFN  plan-3  OAB  0.020
 PFN  plan-3  OAA  0.020
 PFN  plan-3  C13  0.020
 PFN  plan-3  HAA  0.020

