# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 07:35:50 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: (2~{S},3~{S})-7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]-2,3-dihydrochromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)c2C(=O)[C@@H](O)[C@@H](Oc2c1)c3cc(O)c(O)c(O)c3
#
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
 HF0  HF0  (2~{S},3~{S})-7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]-2,3-dihydrochromen-4-one  ligand  38  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HF0
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
 HF0  C4   C  CR16  0  -0.527  -24.3751  20.6480  -16.6055
 HF0  C5   C  CR66  0   0.456  -24.9845  19.6422  -15.8778
 HF0  C6   C  CR66  0  -0.335  -25.5887  18.5397  -16.5056
 HF0  C7   C  CR16  0  -0.074  -25.1874  18.5931  -13.7626
 HF0  C8   C  CR16  0  -0.047  -26.4420  17.8703  -14.2460
 HF0  C10  C  CR6   0   0.130  -25.2797  19.0114  -12.3234
 HF0  C13  C  CR6   0   0.076  -25.4649  19.7410   -9.6557
 HF0  C15  C  CR16  0  -0.421  -26.2303  19.9484  -11.9341
 HF0  C1   C  CR6   0   0.410  -25.5382  18.4563  -17.9214
 HF0  C11  C  CR16  0  -0.448  -24.4134  18.4511  -11.3976
 HF0  C12  C  CR6   0   0.348  -24.5041  18.8168  -10.0570
 HF0  C14  C  CR6   0   0.348  -26.3218  20.3132  -10.5975
 HF0  C16  C  CH3   0  -0.443  -23.1838  22.5995  -18.2124
 HF0  C2   C  CR16  0  -0.466  -24.9344  19.4559  -18.6572
 HF0  C3   C  CR6   0   0.430  -24.3646  20.5503  -17.9993
 HF0  C9   C  CR6   0   0.388  -26.2929  17.5616  -15.7228
 HF0  O1   O  O     0  -0.472  -24.9807  19.7689  -14.5430
 HF0  O2   O  O     0  -0.453  -26.8028  16.5483  -16.1943
 HF0  O3   O  OH1   0  -0.619  -26.0831  17.4276  -18.5628
 HF0  O4   O  O2    0  -0.454  -23.8103  21.4671  -18.7907
 HF0  O5   O  OH1   0  -0.648  -26.6159  16.7269  -13.4750
 HF0  O6   O  OH1   0  -0.625  -27.2413  21.2222  -10.2331
 HF0  O7   O  OH1   0  -0.657  -25.5331  20.1369   -8.3434
 HF0  O8   O  OH1   0  -0.625  -23.6479  18.2696   -9.1784
 HF0  H1   H  HCR6  0   0.294  -23.9162  21.4729  -16.0791
 HF0  H2   H  HCR6  0   0.278  -24.3279  17.9229  -13.8981
 HF0  H3   H  HCR6  0   0.262  -27.2996  18.5624  -14.1673
 HF0  H4   H  HCR6  0   0.262  -26.9025  20.4034  -12.6514
 HF0  H5   H  HCR6  0   0.264  -23.6622  17.7341  -11.7052
 HF0  H6   H  HCH3  0   0.267  -22.8025  23.1914  -19.0400
 HF0  H7   H  HCH3  0   0.238  -23.8900  23.2043  -17.6399
 HF0  H8   H  HCH3  0   0.237  -22.3501  22.3144  -17.5670
 HF0  H9   H  HCR6  0   0.275  -24.9014  19.3951  -19.7374
 HF0  H10  H  HOH1  0   0.477  -26.4659  16.8137  -17.9009
 HF0  H11  H  HOH1  0   0.459  -27.2129  16.1290  -13.9412
 HF0  H12  H  HOH1  0   0.468  -27.1457  21.4306   -9.2947
 HF0  H13  H  HOH1  0   0.481  -26.1504  19.5733   -7.8580
 HF0  H14  H  HOH1  0   0.469  -23.7799  18.6558   -8.3029

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
 HF0  O4   C16  single    1.418  0.020  1.418
 HF0  O4   C3   single    1.332  0.020  1.332
 HF0  C2   C3   aromatic  1.398  0.020  1.398
 HF0  C2   C1   aromatic  1.380  0.020  1.380
 HF0  O3   C1   single    1.329  0.020  1.329
 HF0  C3   C4   aromatic  1.397  0.020  1.397
 HF0  C1   C6   aromatic  1.419  0.020  1.419
 HF0  C4   C5   aromatic  1.383  0.020  1.383
 HF0  C6   C5   aromatic  1.405  0.020  1.405
 HF0  C6   C9   single    1.437  0.020  1.437
 HF0  O2   C9   double    1.228  0.020  1.228
 HF0  C5   O1   single    1.341  0.020  1.341
 HF0  C9   C8   single    1.516  0.020  1.516
 HF0  O1   C7   single    1.426  0.020  1.426
 HF0  C8   C7   single    1.527  0.020  1.527
 HF0  C8   O5   single    1.390  0.020  1.390
 HF0  C7   C10  single    1.502  0.020  1.502
 HF0  C10  C15  aromatic  1.390  0.020  1.390
 HF0  C10  C11  aromatic  1.386  0.020  1.386
 HF0  C15  C14  aromatic  1.389  0.020  1.389
 HF0  C11  C12  aromatic  1.393  0.020  1.393
 HF0  C14  O6   single    1.343  0.020  1.343
 HF0  C14  C13  aromatic  1.396  0.020  1.396
 HF0  C12  C13  aromatic  1.392  0.020  1.392
 HF0  C12  O8   single    1.343  0.020  1.343
 HF0  C13  O7   single    1.372  0.020  1.372
 HF0  C4   H1   single    0.930  0.020  1.080
 HF0  C7   H2   single    0.970  0.020  1.090
 HF0  C8   H3   single    0.970  0.020  1.090
 HF0  C15  H4   single    0.930  0.020  1.080
 HF0  C11  H5   single    0.930  0.020  1.080
 HF0  C16  H6   single    0.970  0.020  1.090
 HF0  C16  H7   single    0.970  0.020  1.090
 HF0  C16  H8   single    0.970  0.020  1.090
 HF0  C2   H9   single    0.930  0.020  1.080
 HF0  O3   H10  single    0.850  0.020  0.980
 HF0  O5   H11  single    0.850  0.020  0.980
 HF0  O6   H12  single    0.850  0.020  0.980
 HF0  O7   H13  single    0.850  0.020  0.980
 HF0  O8   H14  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
 HF0  H1   C4   C3   122.41  3.000
 HF0  H1   C4   C5   119.08  3.000
 HF0  C3   C4   C5   118.51  3.000
 HF0  O1   C5   C6   121.34  3.000
 HF0  O1   C5   C4   116.99  3.000
 HF0  C6   C5   C4   121.67  3.000
 HF0  C9   C6   C1   121.39  3.000
 HF0  C9   C6   C5   120.09  3.000
 HF0  C1   C6   C5   118.45  3.000
 HF0  H2   C7   O1   108.79  3.000
 HF0  H2   C7   C10  109.65  3.000
 HF0  O1   C7   C10  107.68  3.000
 HF0  H2   C7   C8   108.37  3.000
 HF0  C10  C7   C8   112.64  3.000
 HF0  O1   C7   C8   109.64  3.000
 HF0  H3   C8   O5   112.25  3.000
 HF0  H3   C8   C9   105.86  3.000
 HF0  O5   C8   C9   112.66  3.000
 HF0  H3   C8   C7   108.58  3.000
 HF0  O5   C8   C7   108.46  3.000
 HF0  C9   C8   C7   108.91  3.000
 HF0  C11  C10  C15  120.84  3.000
 HF0  C11  C10  C7   119.28  3.000
 HF0  C15  C10  C7   119.88  3.000
 HF0  O7   C13  C14  119.75  3.000
 HF0  O7   C13  C12  120.09  3.000
 HF0  C14  C13  C12  120.09  3.000
 HF0  H4   C15  C14  119.09  3.000
 HF0  H4   C15  C10  121.46  3.000
 HF0  C14  C15  C10  119.45  3.000
 HF0  O3   C1   C2   118.85  3.000
 HF0  O3   C1   C6   120.82  3.000
 HF0  C2   C1   C6   120.32  3.000
 HF0  H5   C11  C12  119.50  3.000
 HF0  H5   C11  C10  120.76  3.000
 HF0  C12  C11  C10  119.74  3.000
 HF0  O8   C12  C11  118.76  3.000
 HF0  O8   C12  C13  121.45  3.000
 HF0  C11  C12  C13  119.79  3.000
 HF0  O6   C14  C15  118.95  3.000
 HF0  O6   C14  C13  120.97  3.000
 HF0  C15  C14  C13  120.08  3.000
 HF0  H8   C16  H7   109.18  3.000
 HF0  H8   C16  H6   108.93  3.000
 HF0  H7   C16  H6   108.94  3.000
 HF0  H8   C16  O4   111.71  3.000
 HF0  H7   C16  O4   111.75  3.000
 HF0  H6   C16  O4   106.23  3.000
 HF0  H9   C2   C3   120.08  3.000
 HF0  H9   C2   C1   120.31  3.000
 HF0  C3   C2   C1   119.62  3.000
 HF0  O4   C3   C2   115.38  3.000
 HF0  C2   C3   C4   121.40  3.000
 HF0  O4   C3   C4   123.21  3.000
 HF0  O2   C9   C8   120.07  3.000
 HF0  C8   C9   C6   116.12  3.000
 HF0  O2   C9   C6   123.76  3.000
 HF0  C7   O1   C5   117.80  3.000
 HF0  H10  O3   C1   108.59  3.000
 HF0  C3   O4   C16  119.43  3.000
 HF0  H11  O5   C8   108.60  3.000
 HF0  H12  O6   C14  109.98  3.000
 HF0  H13  O7   C13  110.10  3.000
 HF0  H14  O8   C12  110.05  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
 HF0  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 HF0  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 HF0  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 HF0  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 HF0  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 HF0  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 HF0  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 HF0  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 HF0  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 HF0  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 HF0  CONST_11  C14  C15  C10  C11     0.00   0.0  0
 HF0  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 HF0  CONST_13  C14  C15  C10  C7    180.00   0.0  0
 HF0  CONST_14  C12  C11  C10  C7    180.00   0.0  0
 HF0  CONST_15  O4   C3   C4   C5    180.00   0.0  0
 HF0  CONST_16  O3   C1   C6   C5    180.00   0.0  0
 HF0  CONST_17  O6   C14  C15  C10   180.00   0.0  0
 HF0  CONST_18  O8   C12  C11  C10   180.00   0.0  0
 HF0  CONST_19  O7   C13  C14  C15   180.00   0.0  0
 HF0  CONST_20  O4   C3   C2   C1    180.00   0.0  0
 HF0  CONST_21  O7   C13  C12  C11   180.00   0.0  0
 HF0  CONST_22  O6   C14  C13  C12   180.00   0.0  0
 HF0  CONST_23  O8   C12  C13  C14   180.00   0.0  0
 HF0  CONST_24  O3   C1   C2   C3    180.00   0.0  0
 HF0  CONST_25  O3   C1   C6   C9      0.00   0.0  0
 HF0  CONST_26  H9   C2   C3   C4    180.00   0.0  0
 HF0  CONST_27  H1   C4   C5   C6    180.00   0.0  0
 HF0  CONST_28  H4   C15  C10  C7      0.00   0.0  0
 HF0  CONST_29  H5   C11  C10  C7      0.00   0.0  0
 HF0  Var_01    C8   C9   C6   C5      5.52  30.0  1
 HF0  Var_02    C2   C3   O4   C16  -178.74  30.0  2
 HF0  Var_03    H6   C16  O4   C3    179.45  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
 HF0  chir_01  C7  O1  C8  C10  positiv
 HF0  chir_02  C8  O5  C7  C9   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
 HF0  plan-1  C7   0.020
 HF0  plan-1  C10  0.020
 HF0  plan-1  C13  0.020
 HF0  plan-1  C15  0.020
 HF0  plan-1  C11  0.020
 HF0  plan-1  C12  0.020
 HF0  plan-1  C14  0.020
 HF0  plan-1  O6   0.020
 HF0  plan-1  O7   0.020
 HF0  plan-1  O8   0.020
 HF0  plan-1  H4   0.020
 HF0  plan-1  H5   0.020
 HF0  plan-2  C4   0.020
 HF0  plan-2  C5   0.020
 HF0  plan-2  C6   0.020
 HF0  plan-2  C1   0.020
 HF0  plan-2  C2   0.020
 HF0  plan-2  C3   0.020
 HF0  plan-2  C9   0.020
 HF0  plan-2  O1   0.020
 HF0  plan-2  O3   0.020
 HF0  plan-2  O4   0.020
 HF0  plan-2  H1   0.020
 HF0  plan-2  H9   0.020
 HF0  plan-3  C6   0.020
 HF0  plan-3  C8   0.020
 HF0  plan-3  C9   0.020
 HF0  plan-3  O2   0.020

