# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:17:20 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S,3R)-2,7-dihydroxy-3-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1Oc2cc(O)ccc2C(=O)[C@@H]1c3ccc(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
 2HI  2HI  (2S,3R)-2,7-dihydroxy-3-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one  ligand  32  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2HI
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
 2HI  C1   C  CR16  0  -0.391   3.5388   0.8350  -1.1813
 2HI  C2   C  CR16  0  -0.259   2.5108   0.0023  -1.5546
 2HI  C3   C  CR6   0  -0.154   1.5648  -0.4538  -0.6309
 2HI  C4   C  CR6   0   0.416   1.6965  -0.0544   0.7081
 2HI  C5   C  CR16  0  -0.450   2.7260   0.7845   1.1025
 2HI  C6   C  CR6   0   0.385   3.6410   1.2372   0.1579
 2HI  O1   O  O2    0  -0.482   0.8233  -0.4401   1.6574
 2HI  C7   C  C     0   0.418   0.4324  -1.2777  -1.0449
 2HI  O2   O  O     0  -0.397   0.2802  -1.6814  -2.1806
 2HI  C8   C  CH1   0  -0.555  -0.5992  -1.5539   0.0352
 2HI  C9   C  CH1   0   0.261   0.0833  -1.6271   1.3958
 2HI  O3   O  OH1   0  -0.642   0.9146  -2.7297   1.3873
 2HI  C10  C  CR6   0   0.139  -1.7147  -0.5320   0.0063
 2HI  C11  C  CR16  0  -0.297  -3.0306  -0.9664   0.1324
 2HI  C12  C  CR16  0  -0.369  -4.0937  -0.0763   0.1441
 2HI  C13  C  CR6   0   0.344  -3.8551   1.2892   0.0219
 2HI  C14  C  CR16  0  -0.321  -2.5444   1.7409  -0.1134
 2HI  C15  C  CR16  0  -0.284  -1.4936   0.8393  -0.1180
 2HI  O4   O  OH1   0  -0.630  -4.8406   2.2072   0.0242
 2HI  O5   O  OH1   0  -0.613   4.6095   2.0531   0.5841
 2HI  H1   H  HCR6  0   0.281   4.2562   1.1832  -1.9146
 2HI  H2   H  HCR6  0   0.273   2.4215  -0.3009  -2.5897
 2HI  H5   H  HCR6  0   0.282   2.8162   1.0852   2.1388
 2HI  H8   H  HCH1  0   0.309  -1.0362  -2.5356  -0.1631
 2HI  H9   H  HCH1  0   0.255  -0.6550  -1.6632   2.2010
 2HI  HO3  H  HOH1  0   0.470   1.2203  -2.9109   2.2836
 2HI  H11  H  HCR6  0   0.261  -3.2368  -2.0257   0.2289
 2HI  H12  H  HCR6  0   0.273  -5.1062  -0.4500   0.2474
 2HI  H14  H  HCR6  0   0.265  -2.3498   2.8012  -0.2150
 2HI  H15  H  HCR6  0   0.253  -0.4920   1.2330  -0.2345
 2HI  HO4  H  HOH1  0   0.475  -5.6995   1.7794   0.1140
 2HI  HO5  H  HOH1  0   0.483   5.1948   2.2999  -0.1417

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
 2HI  C1   C2   aromatic  1.375  0.020  1.375
 2HI  C1   C6   aromatic  1.402  0.020  1.402
 2HI  C1   H1   single    0.930  0.020  1.080
 2HI  C2   C3   aromatic  1.399  0.020  1.399
 2HI  C2   H2   single    0.930  0.020  1.080
 2HI  C3   C4   aromatic  1.403  0.020  1.403
 2HI  C3   C7   single    1.460  0.020  1.460
 2HI  C4   C5   aromatic  1.385  0.020  1.385
 2HI  C4   O1   single    1.346  0.020  1.346
 2HI  C5   C6   aromatic  1.391  0.020  1.391
 2HI  C5   H5   single    0.930  0.020  1.080
 2HI  C6   O5   single    1.336  0.020  1.336
 2HI  O1   C9   single    1.423  0.020  1.423
 2HI  C7   O2   double    1.215  0.020  1.215
 2HI  C7   C8   single    1.519  0.020  1.519
 2HI  C8   C9   single    1.524  0.020  1.524
 2HI  C8   C10  single    1.513  0.020  1.513
 2HI  C8   H8   single    0.970  0.020  1.090
 2HI  C9   O3   single    1.381  0.020  1.381
 2HI  C9   H9   single    0.970  0.020  1.090
 2HI  O3   HO3  single    0.850  0.020  0.980
 2HI  C10  C11  aromatic  1.391  0.020  1.391
 2HI  C10  C15  aromatic  1.395  0.020  1.395
 2HI  C11  C12  aromatic  1.387  0.020  1.387
 2HI  C11  H11  single    0.930  0.020  1.080
 2HI  C12  C13  aromatic  1.392  0.020  1.392
 2HI  C12  H12  single    0.930  0.020  1.080
 2HI  C13  C14  aromatic  1.393  0.020  1.393
 2HI  C13  O4   single    1.347  0.020  1.347
 2HI  C14  C15  aromatic  1.385  0.020  1.385
 2HI  C14  H14  single    0.930  0.020  1.080
 2HI  C15  H15  single    0.930  0.020  1.080
 2HI  O4   HO4  single    0.850  0.020  0.980
 2HI  O5   HO5  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
 2HI  H1   C1   C6   120.41  3.000
 2HI  H1   C1   C2   120.40  3.000
 2HI  C6   C1   C2   119.19  3.000
 2HI  H2   C2   C3   118.98  3.000
 2HI  H2   C2   C1   119.42  3.000
 2HI  C3   C2   C1   121.60  3.000
 2HI  C7   C3   C4   120.25  3.000
 2HI  C7   C3   C2   121.41  3.000
 2HI  C4   C3   C2   118.29  3.000
 2HI  O1   C4   C5   117.05  3.000
 2HI  O1   C4   C3   122.03  3.000
 2HI  C5   C4   C3   120.90  3.000
 2HI  H5   C5   C6   120.32  3.000
 2HI  H5   C5   C4   120.16  3.000
 2HI  C6   C5   C4   119.51  3.000
 2HI  O5   C6   C5   117.32  3.000
 2HI  O5   C6   C1   122.19  3.000
 2HI  C5   C6   C1   120.50  3.000
 2HI  C9   O1   C4   116.53  3.000
 2HI  C8   C7   O2   121.29  3.000
 2HI  C8   C7   C3   115.32  3.000
 2HI  O2   C7   C3   123.34  3.000
 2HI  H8   C8   C10  107.96  3.000
 2HI  H8   C8   C9   107.34  3.000
 2HI  C10  C8   C9   112.31  3.000
 2HI  H8   C8   C7   107.82  3.000
 2HI  C10  C8   C7   111.36  3.000
 2HI  C9   C8   C7   109.85  3.000
 2HI  H9   C9   O3   112.63  3.000
 2HI  H9   C9   C8   110.91  3.000
 2HI  O3   C9   C8   107.60  3.000
 2HI  H9   C9   O1   104.09  3.000
 2HI  O3   C9   O1   110.74  3.000
 2HI  C8   C9   O1   110.91  3.000
 2HI  HO3  O3   C9   109.59  3.000
 2HI  C15  C10  C11  117.71  3.000
 2HI  C15  C10  C8   123.29  3.000
 2HI  C11  C10  C8   118.99  3.000
 2HI  H11  C11  C12  118.74  3.000
 2HI  H11  C11  C10  119.56  3.000
 2HI  C12  C11  C10  121.70  3.000
 2HI  H12  C12  C13  120.44  3.000
 2HI  H12  C12  C11  119.71  3.000
 2HI  C13  C12  C11  119.85  3.000
 2HI  O4   C13  C14  117.89  3.000
 2HI  O4   C13  C12  122.90  3.000
 2HI  C14  C13  C12  119.21  3.000
 2HI  H14  C14  C15  120.06  3.000
 2HI  H14  C14  C13  119.72  3.000
 2HI  C15  C14  C13  120.22  3.000
 2HI  H15  C15  C14  117.76  3.000
 2HI  H15  C15  C10  120.93  3.000
 2HI  C14  C15  C10  121.31  3.000
 2HI  HO4  O4   C13  110.48  3.000
 2HI  HO5  O5   C6   110.86  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
 2HI  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 2HI  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 2HI  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 2HI  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 2HI  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 2HI  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 2HI  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 2HI  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 2HI  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 2HI  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 2HI  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 2HI  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 2HI  CONST_13  C12  C11  C10  C8    180.00   0.0  0
 2HI  CONST_14  C14  C15  C10  C8    180.00   0.0  0
 2HI  CONST_15  O5   C6   C1   C2    180.00   0.0  0
 2HI  CONST_16  O5   C6   C5   C4    180.00   0.0  0
 2HI  CONST_17  O4   C13  C12  C11   180.00   0.0  0
 2HI  CONST_18  O4   C13  C14  C15   180.00   0.0  0
 2HI  CONST_19  H5   C5   C6   C1    180.00   0.0  0
 2HI  CONST_20  H1   C1   C2   C3    180.00   0.0  0
 2HI  CONST_21  H2   C2   C3   C4    180.00   0.0  0
 2HI  CONST_22  H11  C11  C10  C8      0.00   0.0  0
 2HI  CONST_23  H15  C15  C10  C8      0.00   0.0  0
 2HI  CONST_24  H12  C12  C11  C10   180.00   0.0  0
 2HI  CONST_25  H14  C14  C15  C10   180.00   0.0  0
 2HI  Var_01    C8   C7   C3   C2   -172.83  30.0  1

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
 2HI  chir_01  C8  C7  C9  C10  negativ
 2HI  chir_02  C9  O1  O3  C8   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
 2HI  plan-1  C8   0.020
 2HI  plan-1  C10  0.020
 2HI  plan-1  C11  0.020
 2HI  plan-1  C12  0.020
 2HI  plan-1  C13  0.020
 2HI  plan-1  C14  0.020
 2HI  plan-1  C15  0.020
 2HI  plan-1  O4   0.020
 2HI  plan-1  H11  0.020
 2HI  plan-1  H12  0.020
 2HI  plan-1  H14  0.020
 2HI  plan-1  H15  0.020
 2HI  plan-2  C1   0.020
 2HI  plan-2  C2   0.020
 2HI  plan-2  C3   0.020
 2HI  plan-2  C4   0.020
 2HI  plan-2  C5   0.020
 2HI  plan-2  C6   0.020
 2HI  plan-2  O1   0.020
 2HI  plan-2  C7   0.020
 2HI  plan-2  O5   0.020
 2HI  plan-2  H1   0.020
 2HI  plan-2  H2   0.020
 2HI  plan-2  H5   0.020
 2HI  plan-3  C3   0.020
 2HI  plan-3  C7   0.020
 2HI  plan-3  O2   0.020
 2HI  plan-3  C8   0.020

