# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 21:33:04 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-methoxy-4-phenoxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1Oc2ccccc2)C(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
 HKA  HKA  '3-methoxy-4-phenoxybenzoic acid'  ligand  29  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HKA
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
 HKA  CAL   C  CR6    0   0.335  -0.9946  -1.2148  -0.0045
 HKA  CAJ   C  CR16   0  -0.432  -2.2440  -0.6187  -0.0273
 HKA  CAP   C  CR6    0  -0.100  -2.3854   0.7713  -0.0458
 HKA  CAI   C  CR16   0  -0.317  -1.2436   1.5551  -0.0418
 HKA  CAK   C  CR16   0  -0.330   0.0216   0.9741  -0.0203
 HKA  CAR   C  CR6    0   0.286   0.1524  -0.4024  -0.0016
 HKA  CAO   C  C      0   0.398  -3.7729   1.3957  -0.0697
 HKA  OAN   O  O2     0  -0.506   1.3404  -1.0675   0.0197
 HKA  OAB   O  OC    -1  -0.596  -3.8259   2.6407  -0.0766
 HKA  OAA   O  O      0  -0.595  -4.7403   0.6089  -0.0792
 HKA  CAM   C  CH3    0  -0.435  -1.8841  -3.4086   0.0060
 HKA  CAG   C  C1     0  -0.303   3.0903   0.0140   1.2236
 HKA  CAE   C  C1     0  -0.254   4.2957   0.7031   1.2160
 HKA  C2    C  C      0   0.303   2.5049  -0.3417   0.0175
 HKA  CAD   C  C1     0  -0.257   4.9051   1.0387   0.0139
 HKA  CAF   C  C1     0  -0.254   4.3066   0.6776  -1.1864
 HKA  OAL   O  O2     0  -0.468  -0.7680  -2.5438   0.0158
 HKA  CAH   C  C1     0  -0.303   3.1020  -0.0122  -1.1905
 HKA  HAJ   H  HCR6   0   0.271  -3.1398  -1.2245  -0.0320
 HKA  HAI   H  HCR6   0   0.243  -1.3287   2.6330  -0.0553
 HKA  HAK   H  HCR6   0   0.272   0.8971   1.6102  -0.0177
 HKA  HAM1  H  HCH3   0   0.226  -2.4921  -3.2845  -0.8943
 HKA  HAM2  H  HCH3   0   0.258  -1.4898  -4.4216   0.0246
 HKA  HAM3  H  HCH3   0   0.226  -2.5240  -3.2639   0.8808
 HKA  HAH   H  H      0   0.273   2.6327  -0.2961  -2.1240
 HKA  HAF   H  H      0   0.264   4.7787   0.9297  -2.1269
 HKA  HAD   H  H      0   0.260   5.8442   1.5762   0.0123
 HKA  HAG   H  H      0   0.272   2.6128  -0.2505   2.1585
 HKA  HAE   H  H      0   0.264   4.7583   0.9760   2.1554

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
 HKA  CAL  CAJ   aromatic  1.385  0.020  1.385
 HKA  CAL  CAR   aromatic  1.406  0.020  1.406
 HKA  CAL  OAL   single    1.348  0.020  1.348
 HKA  CAJ  CAP   aromatic  1.397  0.020  1.397
 HKA  CAI  CAK   aromatic  1.392  0.020  1.392
 HKA  CAI  CAP   aromatic  1.385  0.020  1.385
 HKA  CAK  CAR   aromatic  1.383  0.020  1.383
 HKA  CAR  OAN   single    1.362  0.020  1.362
 HKA  OAN  C2    single    1.372  0.020  1.372
 HKA  CAO  OAB   deloc     1.246  0.020  1.246
 HKA  CAO  OAA   deloc     1.247  0.020  1.247
 HKA  CAO  CAP   single    1.522  0.020  1.522
 HKA  CAM  OAL   single    1.412  0.020  1.412
 HKA  CAH  CAF   aromatic  1.388  0.020  1.388
 HKA  CAH  C2    aromatic  1.387  0.020  1.387
 HKA  CAF  CAD   aromatic  1.389  0.020  1.389
 HKA  C2   CAG   aromatic  1.387  0.020  1.387
 HKA  CAD  CAE   aromatic  1.389  0.020  1.389
 HKA  CAE  CAG   aromatic  1.389  0.020  1.389
 HKA  CAJ  HAJ   single    0.930  0.020  1.080
 HKA  CAI  HAI   single    0.930  0.020  1.080
 HKA  CAK  HAK   single    0.930  0.020  1.080
 HKA  CAM  HAM1  single    0.970  0.020  1.090
 HKA  CAM  HAM2  single    0.970  0.020  1.090
 HKA  CAM  HAM3  single    0.970  0.020  1.090
 HKA  CAH  HAH   single    0.930  0.020  1.080
 HKA  CAF  HAF   single    0.930  0.020  1.080
 HKA  CAD  HAD   single    0.930  0.020  1.080
 HKA  CAG  HAG   single    0.930  0.020  1.080
 HKA  CAE  HAE   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
 HKA  OAL   CAL  CAR   115.63  3.000
 HKA  OAL   CAL  CAJ   125.19  3.000
 HKA  CAR   CAL  CAJ   119.18  3.000
 HKA  HAJ   CAJ  CAP   118.26  3.000
 HKA  HAJ   CAJ  CAL   120.42  3.000
 HKA  CAP   CAJ  CAL   121.32  3.000
 HKA  CAO   CAP  CAI   121.31  3.000
 HKA  CAO   CAP  CAJ   120.04  3.000
 HKA  CAI   CAP  CAJ   118.65  3.000
 HKA  HAI   CAI  CAK   119.18  3.000
 HKA  HAI   CAI  CAP   119.94  3.000
 HKA  CAK   CAI  CAP   120.87  3.000
 HKA  HAK   CAK  CAR   120.57  3.000
 HKA  HAK   CAK  CAI   119.33  3.000
 HKA  CAR   CAK  CAI   120.10  3.000
 HKA  OAN   CAR  CAK   124.68  3.000
 HKA  OAN   CAR  CAL   115.45  3.000
 HKA  CAK   CAR  CAL   119.87  3.000
 HKA  OAA   CAO  OAB   126.68  3.000
 HKA  OAA   CAO  CAP   116.65  3.000
 HKA  OAB   CAO  CAP   116.67  3.000
 HKA  C2    OAN  CAR   118.82  3.000
 HKA  HAM3  CAM  HAM2  108.77  3.000
 HKA  HAM3  CAM  HAM1  108.57  3.000
 HKA  HAM2  CAM  HAM1  108.75  3.000
 HKA  HAM3  CAM  OAL   112.09  3.000
 HKA  HAM2  CAM  OAL   106.49  3.000
 HKA  HAM1  CAM  OAL   112.06  3.000
 HKA  HAG   CAG  C2    120.14  3.000
 HKA  HAG   CAG  CAE   120.58  3.000
 HKA  C2    CAG  CAE   119.27  3.000
 HKA  HAE   CAE  CAD   120.19  3.000
 HKA  HAE   CAE  CAG   119.45  3.000
 HKA  CAD   CAE  CAG   120.36  3.000
 HKA  CAH   C2   CAG   120.98  3.000
 HKA  CAG   C2   OAN   119.50  3.000
 HKA  CAH   C2   OAN   119.49  3.000
 HKA  HAD   CAD  CAF   120.11  3.000
 HKA  HAD   CAD  CAE   120.14  3.000
 HKA  CAF   CAD  CAE   119.74  3.000
 HKA  HAF   CAF  CAH   119.46  3.000
 HKA  HAF   CAF  CAD   120.17  3.000
 HKA  CAH   CAF  CAD   120.37  3.000
 HKA  CAM   OAL  CAL   118.08  3.000
 HKA  HAH   CAH  CAF   120.59  3.000
 HKA  HAH   CAH  C2    120.14  3.000
 HKA  CAF   CAH  C2    119.27  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
 HKA  CONST_01  CAI   CAP  CAJ  CAL    0.00   0.0  0
 HKA  CONST_02  CAI   CAK  CAR  CAL    0.00   0.0  0
 HKA  CONST_03  CAK   CAR  CAL  CAJ    0.00   0.0  0
 HKA  CONST_04  CAK   CAI  CAP  CAJ    0.00   0.0  0
 HKA  CONST_05  CAR   CAL  CAJ  CAP    0.00   0.0  0
 HKA  CONST_06  CAR   CAK  CAI  CAP    0.00   0.0  0
 HKA  CONST_07  CAF   CAH  C2   CAG    0.00   0.0  0
 HKA  CONST_08  CAF   CAD  CAE  CAG    0.00   0.0  0
 HKA  CONST_09  CAH   CAF  CAD  CAE    0.00   0.0  0
 HKA  CONST_10  CAH   C2   CAG  CAE    0.00   0.0  0
 HKA  CONST_11  CAD   CAF  CAH  C2     0.00   0.0  0
 HKA  CONST_12  CAD   CAE  CAG  C2     0.00   0.0  0
 HKA  CONST_13  CAO   CAP  CAJ  CAL  180.00   0.0  0
 HKA  CONST_14  OAN   CAR  CAL  CAJ  180.00   0.0  0
 HKA  CONST_15  OAL   CAL  CAJ  CAP  180.00   0.0  0
 HKA  CONST_16  OAN   CAR  CAK  CAI  180.00   0.0  0
 HKA  CONST_17  CAO   CAP  CAI  CAK  180.00   0.0  0
 HKA  CONST_18  OAL   CAL  CAR  CAK  180.00   0.0  0
 HKA  CONST_19  CAF   CAH  C2   OAN  180.00   0.0  0
 HKA  CONST_20  CAE   CAG  C2   OAN  180.00   0.0  0
 HKA  CONST_21  HAK   CAK  CAR  CAL  180.00   0.0  0
 HKA  CONST_22  HAI   CAI  CAP  CAJ  180.00   0.0  0
 HKA  CONST_23  HAJ   CAJ  CAP  CAI  180.00   0.0  0
 HKA  CONST_24  HAH   CAH  C2   CAG  180.00   0.0  0
 HKA  CONST_25  HAD   CAD  CAE  CAG  180.00   0.0  0
 HKA  CONST_26  HAF   CAF  CAD  CAE  180.00   0.0  0
 HKA  CONST_27  HAE   CAE  CAG  C2   180.00   0.0  0
 HKA  CONST_28  HAG   CAG  CAE  CAD  180.00   0.0  0
 HKA  Var_01    CAH   C2   OAN  CAR  -90.64  30.0  2
 HKA  Var_02    OAB   CAO  CAP  CAJ  179.55  30.0  2
 HKA  Var_03    HAM1  CAM  OAL  CAL   61.15  30.0  3

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
 HKA  plan-1  CAL  0.020
 HKA  plan-1  CAJ  0.020
 HKA  plan-1  CAP  0.020
 HKA  plan-1  CAI  0.020
 HKA  plan-1  CAK  0.020
 HKA  plan-1  CAR  0.020
 HKA  plan-1  CAO  0.020
 HKA  plan-1  OAN  0.020
 HKA  plan-1  OAL  0.020
 HKA  plan-1  HAJ  0.020
 HKA  plan-1  HAI  0.020
 HKA  plan-1  HAK  0.020
 HKA  plan-2  OAN  0.020
 HKA  plan-2  CAG  0.020
 HKA  plan-2  CAE  0.020
 HKA  plan-2  C2   0.020
 HKA  plan-2  CAD  0.020
 HKA  plan-2  CAF  0.020
 HKA  plan-2  CAH  0.020
 HKA  plan-2  HAH  0.020
 HKA  plan-2  HAF  0.020
 HKA  plan-2  HAD  0.020
 HKA  plan-2  HAG  0.020
 HKA  plan-2  HAE  0.020
 HKA  plan-3  CAP  0.020
 HKA  plan-3  CAO  0.020
 HKA  plan-3  OAB  0.020
 HKA  plan-3  OAA  0.020

