# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:18:35 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)c2C(=O)C[C@H](Oc2c1)c3ccc(O)cc3
#
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
 SAK  SAK  (2S)-5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-2,3-dihydro-4H-chromen-4-one  ligand  35  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SAK
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
 SAK  CAG   C  CR16  0  -0.308  -3.2867  -0.1625  -1.3585
 SAK  CAE   C  CR16  0  -0.323  -4.6143   0.2128  -1.2288
 SAK  CAO   C  CR6   0   0.349  -5.0923   0.6487   0.0039
 SAK  OAC   O  OH1   0  -0.628  -6.3864   1.0090   0.0856
 SAK  CAF   C  CR16  0  -0.370  -4.2273   0.6986   1.0969
 SAK  CAH   C  CR16  0  -0.280  -2.9052   0.3142   0.9520
 SAK  CAR   C  CR6   0   0.096  -2.4156  -0.1228  -0.2760
 SAK  CAU   C  CH1   0  -0.058  -0.9879  -0.5525  -0.4306
 SAK  OAM   O  O2    0  -0.476  -0.1606   0.5675  -0.0929
 SAK  CAK   C  CH2   0  -0.594  -0.6316  -1.7541   0.4285
 SAK  CAN   C  C     0   0.454   0.8359  -2.0618   0.3404
 SAK  OAB   O  O     0  -0.468   1.2660  -3.2036   0.5071
 SAK  CAT   C  CR6   0  -0.348   1.7014  -0.9334   0.0988
 SAK  CAS   C  CR6   0   0.443   1.1638   0.3616  -0.0676
 SAK  CAJ   C  CR16  0  -0.491   1.9804   1.4628  -0.1993
 SAK  CAP   C  CR6   0   0.431   3.3701   1.2886  -0.1696
 SAK  OAL   O  O2    0  -0.459   4.0858   2.4051  -0.3053
 SAK  CAA   C  CH3   0  -0.442   5.5021   2.3294  -0.3031
 SAK  CAI   C  CR16  0  -0.508   3.9402   0.0258  -0.0229
 SAK  CAQ   C  CR6   0   0.418   3.1080  -1.0775   0.1127
 SAK  OAD   O  OH1   0  -0.622   3.6659  -2.2714   0.2691
 SAK  HAG   H  HCR6  0   0.259  -2.9264  -0.4925  -2.3256
 SAK  HAE   H  HCR6  0   0.266  -5.2801   0.1750  -2.0817
 SAK  HOAC  H  HOH1  0   0.476  -6.6045   1.2883   0.9818
 SAK  HAF   H  HCR6  0   0.274  -4.5858   1.0380   2.0619
 SAK  HAH   H  HCR6  0   0.262  -2.2536   0.3626   1.8164
 SAK  HAU   H  HCH1  0   0.270  -0.8009  -0.8067  -1.4814
 SAK  HAK   H  HCH2  0   0.296  -0.8719  -1.5639   1.4809
 SAK  HAKA  H  HCH2  0   0.295  -1.2146  -2.6210   0.1157
 SAK  HAJ   H  HCR6  0   0.276   1.5579   2.4498  -0.3352
 SAK  HAA   H  HCH3  0   0.238   5.8757   1.7185  -1.1274
 SAK  HAAA  H  HCH3  0   0.267   5.8603   3.3474  -0.4286
 SAK  HAAB  H  HCH3  0   0.237   5.8843   1.9325   0.6396
 SAK  HAI   H  HCR6  0   0.290   5.0107  -0.1241  -0.0066
 SAK  HOAD  H  HOH1  0   0.477   2.9415  -2.9304   0.3832

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
 SAK  CAG  CAE   aromatic  1.386  0.020  1.386
 SAK  CAG  CAR   aromatic  1.390  0.020  1.390
 SAK  CAE  CAO   aromatic  1.392  0.020  1.392
 SAK  CAO  OAC   single    1.346  0.020  1.346
 SAK  CAO  CAF   aromatic  1.395  0.020  1.395
 SAK  CAF  CAH   aromatic  1.384  0.020  1.384
 SAK  CAH  CAR   aromatic  1.392  0.020  1.392
 SAK  CAR  CAU   single    1.499  0.020  1.499
 SAK  CAU  OAM   single    1.433  0.020  1.433
 SAK  CAU  CAK   single    1.520  0.020  1.520
 SAK  OAM  CAS   single    1.341  0.020  1.341
 SAK  CAK  CAN   single    1.502  0.020  1.502
 SAK  CAN  OAB   double    1.231  0.020  1.231
 SAK  CAN  CAT   single    1.442  0.020  1.442
 SAK  CAT  CAS   aromatic  1.412  0.020  1.412
 SAK  CAT  CAQ   aromatic  1.414  0.020  1.414
 SAK  CAS  CAJ   aromatic  1.377  0.020  1.377
 SAK  CAJ  CAP   aromatic  1.401  0.020  1.401
 SAK  CAP  OAL   single    1.333  0.020  1.333
 SAK  CAP  CAI   aromatic  1.393  0.020  1.393
 SAK  OAL  CAA   single    1.418  0.020  1.418
 SAK  CAI  CAQ   aromatic  1.389  0.020  1.389
 SAK  CAQ  OAD   single    1.327  0.020  1.327
 SAK  CAG  HAG   single    0.930  0.020  1.080
 SAK  CAE  HAE   single    0.930  0.020  1.080
 SAK  OAC  HOAC  single    0.850  0.020  0.980
 SAK  CAF  HAF   single    0.930  0.020  1.080
 SAK  CAH  HAH   single    0.930  0.020  1.080
 SAK  CAU  HAU   single    0.970  0.020  1.090
 SAK  CAK  HAK   single    0.970  0.020  1.090
 SAK  CAK  HAKA  single    0.970  0.020  1.090
 SAK  CAJ  HAJ   single    0.930  0.020  1.080
 SAK  CAA  HAA   single    0.970  0.020  1.090
 SAK  CAA  HAAA  single    0.970  0.020  1.090
 SAK  CAA  HAAB  single    0.970  0.020  1.090
 SAK  CAI  HAI   single    0.930  0.020  1.080
 SAK  OAD  HOAD  single    0.850  0.020  0.980

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
 SAK  HAG   CAG  CAR   119.70  3.000
 SAK  HAG   CAG  CAE   118.99  3.000
 SAK  CAR   CAG  CAE   121.31  3.000
 SAK  HAE   CAE  CAO   119.83  3.000
 SAK  HAE   CAE  CAG   120.39  3.000
 SAK  CAO   CAE  CAG   119.78  3.000
 SAK  CAF   CAO  OAC   122.64  3.000
 SAK  CAF   CAO  CAE   119.48  3.000
 SAK  OAC   CAO  CAE   117.89  3.000
 SAK  HOAC  OAC  CAO   110.59  3.000
 SAK  HAF   CAF  CAH   119.73  3.000
 SAK  HAF   CAF  CAO   120.24  3.000
 SAK  CAH   CAF  CAO   120.02  3.000
 SAK  HAH   CAH  CAR   120.41  3.000
 SAK  HAH   CAH  CAF   118.58  3.000
 SAK  CAR   CAH  CAF   121.01  3.000
 SAK  CAU   CAR  CAH   121.05  3.000
 SAK  CAU   CAR  CAG   120.55  3.000
 SAK  CAH   CAR  CAG   118.39  3.000
 SAK  HAU   CAU  CAK   108.56  3.000
 SAK  HAU   CAU  OAM   107.97  3.000
 SAK  CAK   CAU  OAM   110.45  3.000
 SAK  HAU   CAU  CAR   109.12  3.000
 SAK  CAK   CAU  CAR   113.06  3.000
 SAK  OAM   CAU  CAR   107.55  3.000
 SAK  CAS   OAM  CAU   117.05  3.000
 SAK  HAKA  CAK  HAK   107.23  3.000
 SAK  HAKA  CAK  CAN   110.04  3.000
 SAK  HAK   CAK  CAN   107.82  3.000
 SAK  HAKA  CAK  CAU   109.94  3.000
 SAK  HAK   CAK  CAU   110.75  3.000
 SAK  CAN   CAK  CAU   110.97  3.000
 SAK  CAT   CAN  OAB   122.58  3.000
 SAK  CAT   CAN  CAK   115.84  3.000
 SAK  OAB   CAN  CAK   121.55  3.000
 SAK  CAQ   CAT  CAS   118.25  3.000
 SAK  CAQ   CAT  CAN   121.03  3.000
 SAK  CAS   CAT  CAN   120.58  3.000
 SAK  CAJ   CAS  CAT   121.26  3.000
 SAK  CAJ   CAS  OAM   117.46  3.000
 SAK  CAT   CAS  OAM   121.28  3.000
 SAK  HAJ   CAJ  CAP   120.22  3.000
 SAK  HAJ   CAJ  CAS   120.65  3.000
 SAK  CAP   CAJ  CAS   119.12  3.000
 SAK  CAI   CAP  OAL   123.37  3.000
 SAK  CAI   CAP  CAJ   121.39  3.000
 SAK  OAL   CAP  CAJ   115.23  3.000
 SAK  CAA   OAL  CAP   119.42  3.000
 SAK  HAAB  CAA  HAAA  108.96  3.000
 SAK  HAAB  CAA  HAA   109.18  3.000
 SAK  HAAA  CAA  HAA   108.92  3.000
 SAK  HAAB  CAA  OAL   111.74  3.000
 SAK  HAAA  CAA  OAL   106.21  3.000
 SAK  HAA   CAA  OAL   111.74  3.000
 SAK  HAI   CAI  CAQ   118.81  3.000
 SAK  HAI   CAI  CAP   122.17  3.000
 SAK  CAQ   CAI  CAP   119.02  3.000
 SAK  OAD   CAQ  CAI   118.31  3.000
 SAK  OAD   CAQ  CAT   120.73  3.000
 SAK  CAI   CAQ  CAT   120.95  3.000
 SAK  HOAD  OAD  CAQ   107.82  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
 SAK  CONST_01  CAF  CAO  CAE  CAG    0.00   0.0  0
 SAK  CONST_02  CAF  CAH  CAR  CAG    0.00   0.0  0
 SAK  CONST_03  CAH  CAR  CAG  CAE    0.00   0.0  0
 SAK  CONST_04  CAH  CAF  CAO  CAE    0.00   0.0  0
 SAK  CONST_05  CAR  CAG  CAE  CAO    0.00   0.0  0
 SAK  CONST_06  CAR  CAH  CAF  CAO    0.00   0.0  0
 SAK  CONST_07  CAP  CAJ  CAS  CAT    0.00   0.0  0
 SAK  CONST_08  CAP  CAI  CAQ  CAT    0.00   0.0  0
 SAK  CONST_09  CAI  CAQ  CAT  CAS    0.00   0.0  0
 SAK  CONST_10  CAI  CAP  CAJ  CAS    0.00   0.0  0
 SAK  CONST_11  CAQ  CAT  CAS  CAJ    0.00   0.0  0
 SAK  CONST_12  CAQ  CAI  CAP  CAJ    0.00   0.0  0
 SAK  CONST_13  CAU  CAR  CAG  CAE  180.00   0.0  0
 SAK  CONST_14  CAU  CAR  CAH  CAF  180.00   0.0  0
 SAK  CONST_15  OAC  CAO  CAE  CAG  180.00   0.0  0
 SAK  CONST_16  CAH  CAF  CAO  OAC  180.00   0.0  0
 SAK  CONST_17  OAD  CAQ  CAT  CAN    0.00   0.0  0
 SAK  CONST_18  OAD  CAQ  CAT  CAS  180.00   0.0  0
 SAK  CONST_19  OAL  CAP  CAJ  CAS  180.00   0.0  0
 SAK  CONST_20  OAD  CAQ  CAI  CAP  180.00   0.0  0
 SAK  CONST_21  CAQ  CAI  CAP  OAL  180.00   0.0  0
 SAK  CONST_22  HAH  CAH  CAR  CAG  180.00   0.0  0
 SAK  CONST_23  HAF  CAF  CAO  CAE  180.00   0.0  0
 SAK  CONST_24  HAG  CAG  CAE  CAO  180.00   0.0  0
 SAK  CONST_25  HAE  CAE  CAO  CAF  180.00   0.0  0
 SAK  CONST_26  HAJ  CAJ  CAS  OAM    0.00   0.0  0
 SAK  CONST_27  HAI  CAI  CAQ  CAT  180.00   0.0  0
 SAK  Var_01    CAT  CAS  OAM  CAU  -22.04  30.0  1
 SAK  Var_02    CAT  CAN  CAK  CAU   29.89  30.0  1
 SAK  Var_03    CAS  CAT  CAN  CAK   -1.28  30.0  1
 SAK  Var_04    CAI  CAP  OAL  CAA   -0.02  30.0  3
 SAK  Var_05    HAA  CAA  OAL  CAP   61.19  30.0  3

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
 SAK  chir_01  CAU  CAR  OAM  CAK  negativ

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
 SAK  plan-1  CAG  0.020
 SAK  plan-1  CAE  0.020
 SAK  plan-1  CAO  0.020
 SAK  plan-1  OAC  0.020
 SAK  plan-1  CAF  0.020
 SAK  plan-1  CAH  0.020
 SAK  plan-1  CAR  0.020
 SAK  plan-1  CAU  0.020
 SAK  plan-1  HAG  0.020
 SAK  plan-1  HAE  0.020
 SAK  plan-1  HAF  0.020
 SAK  plan-1  HAH  0.020
 SAK  plan-2  OAM  0.020
 SAK  plan-2  CAN  0.020
 SAK  plan-2  CAT  0.020
 SAK  plan-2  CAS  0.020
 SAK  plan-2  CAJ  0.020
 SAK  plan-2  CAP  0.020
 SAK  plan-2  OAL  0.020
 SAK  plan-2  CAI  0.020
 SAK  plan-2  CAQ  0.020
 SAK  plan-2  OAD  0.020
 SAK  plan-2  HAJ  0.020
 SAK  plan-2  HAI  0.020
 SAK  plan-3  CAK  0.020
 SAK  plan-3  CAN  0.020
 SAK  plan-3  OAB  0.020
 SAK  plan-3  CAT  0.020

