# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 18:15:52 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C2=CC(=O)c3c(O)cc(O)cc3O2
#
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
 AGI  AGI  5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one  ligand  30  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AGI
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
 AGI  CAG   C  CR16  0  -0.258  -2.5553  -1.2183  -0.2802
 AGI  CAE   C  CR16  0  -0.323  -3.9000  -1.5304  -0.2890
 AGI  CAM   C  CR6   0   0.366  -4.8481  -0.5529   0.0125
 AGI  OAB   O  OH1   0  -0.617  -6.1395  -0.9063  -0.0065
 AGI  CAF   C  CR16  0  -0.364  -4.4239   0.7397   0.3222
 AGI  CAH   C  CR16  0  -0.294  -3.0772   1.0424   0.3265
 AGI  CAP   C  CR6   0  -0.005  -2.1159   0.0754   0.0222
 AGI  CAQ   C  CR6   0   0.423  -0.6944   0.4128   0.0190
 AGI  OAL   O  O     0  -0.471   0.0927  -0.6725   0.0362
 AGI  CAJ   C  CR16  0  -0.525  -0.1758   1.6637  -0.0068
 AGI  CAR   C  CR6   0   0.535   1.2442   1.8802   0.0027
 AGI  OAA   O  O     0  -0.512   1.7544   3.0131  -0.0068
 AGI  CAT   C  CR66  0  -0.353   2.0513   0.6805   0.0123
 AGI  CAS   C  CR66  0   0.421   1.4384  -0.5719   0.0205
 AGI  CAK   C  CR16  0  -0.514   2.1528  -1.7553   0.0191
 AGI  CAN   C  CR6   0   0.397   3.5432  -1.6731   0.0085
 AGI  OAC   O  OH1   0  -0.616   4.3139  -2.7650   0.0035
 AGI  CAI   C  CR16  0  -0.454   4.2017  -0.4408   0.0016
 AGI  CAO   C  CR6   0   0.402   3.4657   0.7296   0.0030
 AGI  OAD   O  OH1   0  -0.630   4.0945   1.9003  -0.0060
 AGI  HAG   H  HCR6  0   0.268  -1.8485  -1.9992  -0.5241
 AGI  HAE   H  HCR6  0   0.275  -4.2224  -2.5343  -0.5331
 AGI  HOAB  H  HOH1  0   0.481  -6.7031  -0.1584   0.2237
 AGI  HAF   H  HCR6  0   0.283  -5.1463   1.5093   0.5673
 AGI  HAH   H  HCR6  0   0.269  -2.7819   2.0482   0.5928
 AGI  HAJ   H  HCR6  0   0.282  -0.8305   2.5217  -0.0482
 AGI  HAK   H  HCR6  0   0.294   1.6386  -2.7084   0.0266
 AGI  HOAC  H  HOH1  0   0.484   3.7776  -3.5666   0.0028
 AGI  HAI   H  HCR6  0   0.280   5.2836  -0.4039  -0.0067
 AGI  HOAD  H  HOH1  0   0.476   3.4030   2.6069  -0.0051

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
 AGI  CAG  CAE   aromatic  1.380  0.020  1.380
 AGI  CAG  CAP   aromatic  1.399  0.020  1.399
 AGI  CAE  CAM   aromatic  1.395  0.020  1.395
 AGI  CAM  OAB   single    1.339  0.020  1.339
 AGI  CAM  CAF   aromatic  1.395  0.020  1.395
 AGI  CAF  CAH   aromatic  1.380  0.020  1.380
 AGI  CAH  CAP   aromatic  1.397  0.020  1.397
 AGI  CAP  CAQ   single    1.461  0.020  1.461
 AGI  CAQ  OAL   single    1.341  0.020  1.341
 AGI  CAQ  CAJ   double    1.354  0.020  1.354
 AGI  OAL  CAS   single    1.350  0.020  1.350
 AGI  CAJ  CAR   single    1.436  0.020  1.436
 AGI  CAR  OAA   double    1.243  0.020  1.243
 AGI  CAR  CAT   single    1.446  0.020  1.446
 AGI  CAT  CAS   aromatic  1.394  0.020  1.394
 AGI  CAT  CAO   aromatic  1.415  0.020  1.415
 AGI  CAS  CAK   aromatic  1.382  0.020  1.382
 AGI  CAK  CAN   aromatic  1.393  0.020  1.393
 AGI  CAN  OAC   single    1.336  0.020  1.336
 AGI  CAN  CAI   aromatic  1.397  0.020  1.397
 AGI  CAI  CAO   aromatic  1.383  0.020  1.383
 AGI  CAO  OAD   single    1.329  0.020  1.329
 AGI  CAG  HAG   single    0.930  0.020  1.080
 AGI  CAE  HAE   single    0.930  0.020  1.080
 AGI  OAB  HOAB  single    0.850  0.020  0.980
 AGI  CAF  HAF   single    0.930  0.020  1.080
 AGI  CAH  HAH   single    0.930  0.020  1.080
 AGI  CAJ  HAJ   single    0.930  0.020  1.080
 AGI  CAK  HAK   single    0.930  0.020  1.080
 AGI  OAC  HOAC  single    0.850  0.020  0.980
 AGI  CAI  HAI   single    0.930  0.020  1.080
 AGI  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
 AGI  HAG   CAG  CAP  120.74  3.000
 AGI  HAG   CAG  CAE  118.18  3.000
 AGI  CAP   CAG  CAE  121.08  3.000
 AGI  HAE   CAE  CAM  119.76  3.000
 AGI  HAE   CAE  CAG  120.08  3.000
 AGI  CAM   CAE  CAG  120.16  3.000
 AGI  CAF   CAM  OAB  122.74  3.000
 AGI  CAF   CAM  CAE  119.38  3.000
 AGI  OAB   CAM  CAE  117.88  3.000
 AGI  HOAB  OAB  CAM  110.83  3.000
 AGI  HAF   CAF  CAH  119.60  3.000
 AGI  HAF   CAF  CAM  120.37  3.000
 AGI  CAH   CAF  CAM  120.03  3.000
 AGI  HAH   CAH  CAP  120.63  3.000
 AGI  HAH   CAH  CAF  118.10  3.000
 AGI  CAP   CAH  CAF  121.25  3.000
 AGI  CAQ   CAP  CAH  120.67  3.000
 AGI  CAQ   CAP  CAG  121.23  3.000
 AGI  CAH   CAP  CAG  118.10  3.000
 AGI  CAJ   CAQ  OAL  121.54  3.000
 AGI  CAJ   CAQ  CAP  125.87  3.000
 AGI  OAL   CAQ  CAP  112.59  3.000
 AGI  CAS   OAL  CAQ  121.66  3.000
 AGI  HAJ   CAJ  CAR  118.66  3.000
 AGI  HAJ   CAJ  CAQ  120.16  3.000
 AGI  CAR   CAJ  CAQ  121.17  3.000
 AGI  CAT   CAR  OAA  121.83  3.000
 AGI  CAT   CAR  CAJ  115.26  3.000
 AGI  OAA   CAR  CAJ  122.91  3.000
 AGI  CAO   CAT  CAS  118.06  3.000
 AGI  CAO   CAT  CAR  121.94  3.000
 AGI  CAS   CAT  CAR  119.99  3.000
 AGI  CAK   CAS  CAT  122.80  3.000
 AGI  CAK   CAS  OAL  116.85  3.000
 AGI  CAT   CAS  OAL  120.35  3.000
 AGI  HAK   CAK  CAN  121.73  3.000
 AGI  HAK   CAK  CAS  120.53  3.000
 AGI  CAN   CAK  CAS  117.74  3.000
 AGI  CAI   CAN  OAC  116.66  3.000
 AGI  CAI   CAN  CAK  121.50  3.000
 AGI  OAC   CAN  CAK  121.84  3.000
 AGI  HOAC  OAC  CAN  111.00  3.000
 AGI  HAI   CAI  CAO  120.21  3.000
 AGI  HAI   CAI  CAN  120.07  3.000
 AGI  CAO   CAI  CAN  119.72  3.000
 AGI  OAD   CAO  CAI  119.59  3.000
 AGI  OAD   CAO  CAT  120.23  3.000
 AGI  CAI   CAO  CAT  120.18  3.000
 AGI  HOAD  OAD  CAO  107.38  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
 AGI  CONST_01  CAF  CAM  CAE  CAG    0.00   0.0  0
 AGI  CONST_02  CAF  CAH  CAP  CAG    0.00   0.0  0
 AGI  CONST_03  CAH  CAP  CAG  CAE    0.00   0.0  0
 AGI  CONST_04  CAH  CAF  CAM  CAE    0.00   0.0  0
 AGI  CONST_05  CAP  CAG  CAE  CAM    0.00   0.0  0
 AGI  CONST_06  CAP  CAH  CAF  CAM    0.00   0.0  0
 AGI  CONST_07  CAN  CAK  CAS  CAT    0.00   0.0  0
 AGI  CONST_08  CAN  CAI  CAO  CAT    0.00   0.0  0
 AGI  CONST_09  CAI  CAO  CAT  CAS    0.00   0.0  0
 AGI  CONST_10  CAI  CAN  CAK  CAS    0.00   0.0  0
 AGI  CONST_11  CAO  CAT  CAS  CAK    0.00   0.0  0
 AGI  CONST_12  CAO  CAI  CAN  CAK    0.00   0.0  0
 AGI  CONST_13  CAQ  CAP  CAG  CAE  180.00   0.0  0
 AGI  CONST_14  CAQ  CAP  CAH  CAF  180.00   0.0  0
 AGI  CONST_15  OAB  CAM  CAE  CAG  180.00   0.0  0
 AGI  CONST_16  CAH  CAF  CAM  OAB  180.00   0.0  0
 AGI  CONST_17  OAD  CAO  CAT  CAR    0.00   0.0  0
 AGI  CONST_18  OAD  CAO  CAT  CAS  180.00   0.0  0
 AGI  CONST_19  OAC  CAN  CAK  CAS  180.00   0.0  0
 AGI  CONST_20  OAD  CAO  CAI  CAN  180.00   0.0  0
 AGI  CONST_21  CAO  CAI  CAN  OAC  180.00   0.0  0
 AGI  CONST_22  HAH  CAH  CAP  CAG  180.00   0.0  0
 AGI  CONST_23  HAF  CAF  CAM  CAE  180.00   0.0  0
 AGI  CONST_24  HAG  CAG  CAE  CAM  180.00   0.0  0
 AGI  CONST_25  HAE  CAE  CAM  CAF  180.00   0.0  0
 AGI  CONST_26  HAK  CAK  CAS  OAL    0.00   0.0  0
 AGI  CONST_27  HAI  CAI  CAO  CAT  180.00   0.0  0
 AGI  Var_01    OAL  CAQ  CAP  CAG  -15.57  30.0  2
 AGI  Var_02    CAR  CAJ  CAQ  CAP  179.53  30.0  1
 AGI  Var_03    CAT  CAS  OAL  CAQ    1.27  30.0  1
 AGI  Var_04    CAT  CAR  CAJ  CAQ    1.26  30.0  1
 AGI  Var_05    CAS  CAT  CAR  CAJ   -0.41  30.0  1

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
 AGI  plan-1  CAG  0.020
 AGI  plan-1  CAE  0.020
 AGI  plan-1  CAM  0.020
 AGI  plan-1  OAB  0.020
 AGI  plan-1  CAF  0.020
 AGI  plan-1  CAH  0.020
 AGI  plan-1  CAP  0.020
 AGI  plan-1  CAQ  0.020
 AGI  plan-1  HAG  0.020
 AGI  plan-1  HAE  0.020
 AGI  plan-1  HAF  0.020
 AGI  plan-1  HAH  0.020
 AGI  plan-2  OAL  0.020
 AGI  plan-2  CAR  0.020
 AGI  plan-2  CAT  0.020
 AGI  plan-2  CAS  0.020
 AGI  plan-2  CAK  0.020
 AGI  plan-2  CAN  0.020
 AGI  plan-2  OAC  0.020
 AGI  plan-2  CAI  0.020
 AGI  plan-2  CAO  0.020
 AGI  plan-2  OAD  0.020
 AGI  plan-2  HAK  0.020
 AGI  plan-2  HAI  0.020
 AGI  plan-3  CAJ  0.020
 AGI  plan-3  CAR  0.020
 AGI  plan-3  OAA  0.020
 AGI  plan-3  CAT  0.020

