# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:12:49 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C2=COc3cc(O)cc(O)c3C2=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
 QSO  QSO  5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one  ligand  33  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QSO
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
 QSO  C2   C  CR16  0   0.038  -0.2761   1.7891  -0.0010
 QSO  C4   C  CR6   0   0.494  -0.6325  -0.5879   0.1214
 QSO  O4   O  OH1   0  -0.616  -6.0434   0.7363   0.1032
 QSO  C4A  C  CR66  0  -0.333  -2.0429  -0.2741   0.1121
 QSO  C8A  C  CR66  0   0.409  -2.4820   1.0520   0.0537
 QSO  C7   C  CR6   0   0.400  -4.7569   0.3777   0.1084
 QSO  C6   C  CR16  0  -0.499  -4.3700  -0.9632   0.1697
 QSO  C5   C  CR6   0   0.405  -3.0261  -1.2929   0.1727
 QSO  C8   C  CR16  0  -0.464  -3.8169   1.4035   0.0496
 QSO  C3   C  CR6   0  -0.199   0.2648   0.5565   0.0617
 QSO  O1   O  O     0  -0.427  -1.5823   2.0560  -0.0021
 QSO  C1'  C  CR6   0   0.068   1.7279   0.3930   0.1093
 QSO  O2   O  O     0  -0.487  -0.2240  -1.7552   0.1840
 QSO  C2'  C  CR16  0  -0.287   2.4936   1.1495   0.9995
 QSO  C3'  C  CR16  0  -0.328   3.8704   1.0406   1.0351
 QSO  C4'  C  CR6   0   0.376   4.5266   0.1546   0.1794
 QSO  C5'  C  CR16  0  -0.371   3.7761  -0.6133  -0.7099
 QSO  C6'  C  CR16  0  -0.274   2.3938  -0.4890  -0.7366
 QSO  O5   O  O2    0  -0.469   5.8664   0.1067   0.2829
 QSO  O3   O  OH1   0  -0.627  -2.6706  -2.5704   0.2323
 QSO  CM   C  CH3   0  -0.438   6.5809  -0.7776  -0.5581
 QSO  H2   H  HCR6  0   0.311   0.3141   2.6943  -0.0609
 QSO  HO4  H  HOH1  0   0.484  -6.6190  -0.0364   0.1483
 QSO  H6   H  HCR6  0   0.288  -5.1128  -1.7510   0.2146
 QSO  H8   H  HCR6  0   0.289  -4.1219   2.4405   0.0030
 QSO  H2'  H  HCR6  0   0.257   2.0035   1.8295   1.6858
 QSO  H3'  H  HCR6  0   0.265   4.4469   1.6325   1.7350
 QSO  H5'  H  HCR6  0   0.280   4.2468  -1.3088  -1.3917
 QSO  H6'  H  HCR6  0   0.255   1.8378  -1.0815  -1.4505
 QSO  HO3  H  HOH1  0   0.480  -1.6825  -2.6045   0.2280
 QSO  HM1  H  HCH3  0   0.230   6.2956  -1.8192  -0.3908
 QSO  HM2  H  HCH3  0   0.230   6.4409  -0.5396  -1.6155
 QSO  HM3  H  HCH3  0   0.261   7.6323  -0.6580  -0.3096

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
 QSO  O1   C2   single    1.333  0.020  1.333
 QSO  O1   C8A  single    1.349  0.020  1.349
 QSO  C8   C8A  aromatic  1.380  0.020  1.380
 QSO  C8   C7   aromatic  1.393  0.020  1.393
 QSO  C2   C3   double    1.347  0.020  1.347
 QSO  O4   C7   single    1.336  0.020  1.336
 QSO  C8A  C4A  aromatic  1.398  0.020  1.398
 QSO  C7   C6   aromatic  1.397  0.020  1.397
 QSO  C6'  C5'  aromatic  1.388  0.020  1.388
 QSO  C6'  C1'  aromatic  1.392  0.020  1.392
 QSO  C3   C1'  single    1.473  0.020  1.473
 QSO  C3   C4   single    1.456  0.020  1.456
 QSO  C5'  C4'  aromatic  1.394  0.020  1.394
 QSO  C1'  C2'  aromatic  1.397  0.020  1.397
 QSO  C4A  C4   single    1.445  0.020  1.445
 QSO  C4A  C5   aromatic  1.417  0.020  1.417
 QSO  CM   O5   single    1.414  0.020  1.414
 QSO  C6   C5   aromatic  1.384  0.020  1.384
 QSO  C4   O2   double    1.238  0.020  1.238
 QSO  C4'  O5   single    1.345  0.020  1.345
 QSO  C4'  C3'  aromatic  1.396  0.020  1.396
 QSO  C2'  C3'  aromatic  1.382  0.020  1.382
 QSO  C5   O3   single    1.327  0.020  1.327
 QSO  C2   H2   single    0.930  0.020  1.080
 QSO  O4   HO4  single    0.850  0.020  0.980
 QSO  C6   H6   single    0.930  0.020  1.080
 QSO  C8   H8   single    0.930  0.020  1.080
 QSO  C2'  H2'  single    0.930  0.020  1.080
 QSO  C3'  H3'  single    0.930  0.020  1.080
 QSO  C5'  H5'  single    0.930  0.020  1.080
 QSO  C6'  H6'  single    0.930  0.020  1.080
 QSO  O3   HO3  single    0.850  0.020  0.980
 QSO  CM   HM1  single    0.970  0.020  1.090
 QSO  CM   HM2  single    0.970  0.020  1.090
 QSO  CM   HM3  single    0.970  0.020  1.090

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
 QSO  H2   C2   O1   111.52  3.000
 QSO  H2   C2   C3   123.28  3.000
 QSO  O1   C2   C3   125.21  3.000
 QSO  O2   C4   C3   122.67  3.000
 QSO  O2   C4   C4A  121.81  3.000
 QSO  C3   C4   C4A  115.51  3.000
 QSO  HO4  O4   C7   111.08  3.000
 QSO  C5   C4A  C8A  117.76  3.000
 QSO  C5   C4A  C4   121.38  3.000
 QSO  C8A  C4A  C4   120.85  3.000
 QSO  O1   C8A  C8   117.08  3.000
 QSO  C8   C8A  C4A  123.05  3.000
 QSO  O1   C8A  C4A  119.87  3.000
 QSO  C8   C7   C6   121.46  3.000
 QSO  C6   C7   O4   121.65  3.000
 QSO  C8   C7   O4   116.89  3.000
 QSO  H6   C6   C5   119.50  3.000
 QSO  H6   C6   C7   120.65  3.000
 QSO  C5   C6   C7   119.85  3.000
 QSO  O3   C5   C6   119.31  3.000
 QSO  O3   C5   C4A  120.53  3.000
 QSO  C6   C5   C4A  120.16  3.000
 QSO  H8   C8   C7   121.17  3.000
 QSO  H8   C8   C8A  121.12  3.000
 QSO  C7   C8   C8A  117.71  3.000
 QSO  C1'  C3   C4   121.59  3.000
 QSO  C4   C3   C2   118.27  3.000
 QSO  C1'  C3   C2   120.12  3.000
 QSO  C8A  O1   C2   120.28  3.000
 QSO  C6'  C1'  C2'  117.93  3.000
 QSO  C2'  C1'  C3   120.33  3.000
 QSO  C6'  C1'  C3   121.73  3.000
 QSO  H2'  C2'  C3'  118.94  3.000
 QSO  H2'  C2'  C1'  119.72  3.000
 QSO  C3'  C2'  C1'  121.34  3.000
 QSO  H3'  C3'  C4'  119.54  3.000
 QSO  H3'  C3'  C2'  120.28  3.000
 QSO  C4'  C3'  C2'  120.18  3.000
 QSO  O5   C4'  C5'  124.46  3.000
 QSO  O5   C4'  C3'  116.35  3.000
 QSO  C5'  C4'  C3'  119.19  3.000
 QSO  H5'  C5'  C6'  118.61  3.000
 QSO  H5'  C5'  C4'  121.46  3.000
 QSO  C6'  C5'  C4'  119.93  3.000
 QSO  H6'  C6'  C5'  118.40  3.000
 QSO  H6'  C6'  C1'  120.16  3.000
 QSO  C5'  C6'  C1'  121.43  3.000
 QSO  CM   O5   C4'  118.68  3.000
 QSO  HO3  O3   C5   107.49  3.000
 QSO  HM3  CM   HM2  108.73  3.000
 QSO  HM3  CM   HM1  108.80  3.000
 QSO  HM2  CM   HM1  108.80  3.000
 QSO  HM3  CM   O5   106.50  3.000
 QSO  HM2  CM   O5   111.99  3.000
 QSO  HM1  CM   O5   111.91  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
 QSO  CONST_01  C7   C8   C8A  C4A     0.00   0.0  0
 QSO  CONST_02  C7   C6   C5   C4A     0.00   0.0  0
 QSO  CONST_03  C6   C7   C8   C8A     0.00   0.0  0
 QSO  CONST_04  C6   C5   C4A  C8A     0.00   0.0  0
 QSO  CONST_05  C8   C8A  C4A  C5      0.00   0.0  0
 QSO  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 QSO  CONST_07  C4'  C5'  C6'  C1'     0.00   0.0  0
 QSO  CONST_08  C4'  C3'  C2'  C1'     0.00   0.0  0
 QSO  CONST_09  C5'  C6'  C1'  C2'     0.00   0.0  0
 QSO  CONST_10  C5'  C4'  C3'  C2'     0.00   0.0  0
 QSO  CONST_11  C6'  C5'  C4'  C3'     0.00   0.0  0
 QSO  CONST_12  C6'  C1'  C2'  C3'     0.00   0.0  0
 QSO  CONST_13  C5'  C6'  C1'  C3    180.00   0.0  0
 QSO  CONST_14  C3'  C2'  C1'  C3    180.00   0.0  0
 QSO  CONST_15  O3   C5   C4A  C4      0.00   0.0  0
 QSO  CONST_16  C8A  C8   C7   O4    180.00   0.0  0
 QSO  CONST_17  C5   C6   C7   O4    180.00   0.0  0
 QSO  CONST_18  O3   C5   C4A  C8A   180.00   0.0  0
 QSO  CONST_19  O3   C5   C6   C7    180.00   0.0  0
 QSO  CONST_20  O5   C4'  C3'  C2'   180.00   0.0  0
 QSO  CONST_21  O5   C4'  C5'  C6'   180.00   0.0  0
 QSO  CONST_22  H8   C8   C8A  C4A   180.00   0.0  0
 QSO  CONST_23  H6   C6   C5   C4A   180.00   0.0  0
 QSO  CONST_24  H6'  C6'  C1'  C3      0.00   0.0  0
 QSO  CONST_25  H2'  C2'  C1'  C3      0.00   0.0  0
 QSO  CONST_26  H5'  C5'  C6'  C1'   180.00   0.0  0
 QSO  CONST_27  H3'  C3'  C2'  C1'   180.00   0.0  0
 QSO  Var_01    C8   C8A  O1   C2    179.97  30.0  1
 QSO  Var_02    C6'  C1'  C3   C2   -130.68  30.0  2
 QSO  Var_03    C4A  C4   C3   C2     -0.24  30.0  1
 QSO  Var_04    O1   C2   C3   C4      0.59  30.0  1
 QSO  Var_05    C3   C2   O1   C8A    -0.46  30.0  1
 QSO  Var_06    C3   C4   C4A  C8A    -0.21  30.0  1
 QSO  Var_07    HM1  CM   O5   C4'   -61.10  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
 QSO  plan-1  C3   0.020
 QSO  plan-1  C1'  0.020
 QSO  plan-1  C2'  0.020
 QSO  plan-1  C3'  0.020
 QSO  plan-1  C4'  0.020
 QSO  plan-1  C5'  0.020
 QSO  plan-1  C6'  0.020
 QSO  plan-1  O5   0.020
 QSO  plan-1  H2'  0.020
 QSO  plan-1  H3'  0.020
 QSO  plan-1  H5'  0.020
 QSO  plan-1  H6'  0.020
 QSO  plan-2  C4   0.020
 QSO  plan-2  O4   0.020
 QSO  plan-2  C4A  0.020
 QSO  plan-2  C8A  0.020
 QSO  plan-2  C7   0.020
 QSO  plan-2  C6   0.020
 QSO  plan-2  C5   0.020
 QSO  plan-2  C8   0.020
 QSO  plan-2  O1   0.020
 QSO  plan-2  O3   0.020
 QSO  plan-2  H6   0.020
 QSO  plan-2  H8   0.020
 QSO  plan-3  C4   0.020
 QSO  plan-3  C4A  0.020
 QSO  plan-3  C3   0.020
 QSO  plan-3  O2   0.020

