# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 05:14:03 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: 7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)c2C(=O)C(=C(Oc2c1)c3cc(O)c(O)c(O)c3)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
 HER  HER  7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one  ligand  36  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_HER
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
 HER  C4   C  CR6   0   0.316  13.6674  14.5642  39.0826
 HER  C5   C  CR16  0  -0.457  13.4477  13.5043  39.9505
 HER  C6   C  CR6   0   0.049  14.3411  13.2466  40.9906
 HER  C7   C  CR6   0   0.225  14.1117  12.1562  41.9374
 HER  C8   C  CR66  0   0.429  14.5571  11.5647  44.1831
 HER  C10  C  CR6   0   0.420  13.3424   9.9953  42.7587
 HER  C13  C  CR6   0   0.418  15.0722  11.0782  46.4517
 HER  C15  C  CR6   0   0.405  13.8537   9.4629  45.1423
 HER  C1   C  CR16  0  -0.441  15.4590  14.0662  41.1538
 HER  C11  C  CR6   0   0.183  13.4947  10.9715  41.6998
 HER  C12  C  CR16  0  -0.517  15.1444  11.9580  45.3770
 HER  C14  C  CR16  0  -0.460  14.4279   9.8357  46.3373
 HER  C16  C  CH3   0  -0.442  16.2962  12.5534  47.8503
 HER  C2   C  CR6   0   0.297  15.6773  15.1195  40.2815
 HER  C3   C  CR6   0   0.211  14.7877  15.3821  39.2382
 HER  C9   C  CR66  0  -0.329  13.9114  10.3394  44.0270
 HER  O1   O  O     0  -0.465  14.6214  12.4270  43.1606
 HER  O2   O  O     0  -0.504  12.7554   8.9240  42.5306
 HER  O3   O  OH1   0  -0.624  13.0173  10.6453  40.4884
 HER  O4   O  OH1   0  -0.623  13.2512   8.2810  45.0419
 HER  O5   O  O2    0  -0.456  15.5967  11.3372  47.6501
 HER  O6   O  OH1   0  -0.643  16.7340  15.9567  40.3656
 HER  O7   O  OH1   0  -0.616  14.9600  16.4019  38.3762
 HER  O8   O  OH1   0  -0.625  12.8365  14.8724  38.0678
 HER  H1   H  HCR6  0   0.275  12.5586  12.9022  39.8225
 HER  H2   H  HCR6  0   0.276  16.1730  13.8894  41.9485
 HER  H3   H  HCR6  0   0.299  15.6309  12.9211  45.4380
 HER  H4   H  HCR6  0   0.278  14.3891   9.1713  47.1910
 HER  H5   H  HCH3  0   0.267  16.6452  12.5391  48.8792
 HER  H6   H  HCH3  0   0.236  17.1578  12.6374  47.1845
 HER  H7   H  HCH3  0   0.237  15.6476  13.4205  47.7073
 HER  H8   H  HOH1  0   0.474  12.6372   9.7554  40.5496
 HER  H9   H  HOH1  0   0.477  12.9081   8.1859  44.1265
 HER  H10  H  HOH1  0   0.483  17.3142  15.7147  41.0963
 HER  H11  H  HOH1  0   0.473  15.7740  16.8773  38.5810
 HER  H12  H  HOH1  0   0.475  12.0969  14.2546  38.0397

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
 HER  O7   C3   single    1.346  0.020  1.346
 HER  O8   C4   single    1.347  0.020  1.347
 HER  C3   C4   aromatic  1.396  0.020  1.396
 HER  C3   C2   aromatic  1.396  0.020  1.396
 HER  C4   C5   aromatic  1.387  0.020  1.387
 HER  O6   C2   single    1.351  0.020  1.351
 HER  C2   C1   aromatic  1.385  0.020  1.385
 HER  C5   C6   aromatic  1.395  0.020  1.395
 HER  O3   C11  single    1.342  0.020  1.342
 HER  C1   C6   aromatic  1.396  0.020  1.396
 HER  C6   C7   single    1.462  0.020  1.462
 HER  C11  C7   double    1.357  0.020  1.357
 HER  C11  C10  single    1.448  0.020  1.448
 HER  C7   O1   single    1.353  0.020  1.353
 HER  O2   C10  double    1.243  0.020  1.243
 HER  C10  C9   single    1.432  0.020  1.432
 HER  O1   C8   single    1.339  0.020  1.339
 HER  C9   C8   aromatic  1.394  0.020  1.394
 HER  C9   C15  aromatic  1.420  0.020  1.420
 HER  C8   C12  aromatic  1.387  0.020  1.387
 HER  O4   C15  single    1.330  0.020  1.330
 HER  C15  C14  aromatic  1.377  0.020  1.377
 HER  C12  C13  aromatic  1.391  0.020  1.391
 HER  C14  C13  aromatic  1.404  0.020  1.404
 HER  C13  O5   single    1.334  0.020  1.334
 HER  O5   C16  single    1.417  0.020  1.417
 HER  C5   H1   single    0.930  0.020  1.080
 HER  C1   H2   single    0.930  0.020  1.080
 HER  C12  H3   single    0.930  0.020  1.080
 HER  C14  H4   single    0.930  0.020  1.080
 HER  C16  H5   single    0.970  0.020  1.090
 HER  C16  H6   single    0.970  0.020  1.090
 HER  C16  H7   single    0.970  0.020  1.090
 HER  O3   H8   single    0.850  0.020  0.980
 HER  O4   H9   single    0.850  0.020  0.980
 HER  O6   H10  single    0.850  0.020  0.980
 HER  O7   H11  single    0.850  0.020  0.980
 HER  O8   H12  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
 HER  O8   C4   C3   116.42  3.000
 HER  C3   C4   C5   120.34  3.000
 HER  O8   C4   C5   123.24  3.000
 HER  H1   C5   C6   120.79  3.000
 HER  H1   C5   C4   118.79  3.000
 HER  C6   C5   C4   120.40  3.000
 HER  C1   C6   C7   119.20  3.000
 HER  C7   C6   C5   121.33  3.000
 HER  C1   C6   C5   119.45  3.000
 HER  O1   C7   C11  120.30  3.000
 HER  O1   C7   C6   112.16  3.000
 HER  C11  C7   C6   127.53  3.000
 HER  O1   C8   C9   120.19  3.000
 HER  C9   C8   C12  122.80  3.000
 HER  O1   C8   C12  117.01  3.000
 HER  O2   C10  C9   123.88  3.000
 HER  C9   C10  C11  116.34  3.000
 HER  O2   C10  C11  119.77  3.000
 HER  O5   C13  C14  115.19  3.000
 HER  O5   C13  C12  123.44  3.000
 HER  C14  C13  C12  121.37  3.000
 HER  O4   C15  C9   120.51  3.000
 HER  O4   C15  C14  119.65  3.000
 HER  C9   C15  C14  119.84  3.000
 HER  H2   C1   C2   118.85  3.000
 HER  H2   C1   C6   121.20  3.000
 HER  C2   C1   C6   119.95  3.000
 HER  O3   C11  C10  117.30  3.000
 HER  C10  C11  C7   120.56  3.000
 HER  O3   C11  C7   122.14  3.000
 HER  H3   C12  C13  122.92  3.000
 HER  H3   C12  C8   119.46  3.000
 HER  C13  C12  C8   117.62  3.000
 HER  H4   C14  C15  120.21  3.000
 HER  H4   C14  C13  119.69  3.000
 HER  C15  C14  C13  120.10  3.000
 HER  H7   C16  H6   109.13  3.000
 HER  H7   C16  H5   108.97  3.000
 HER  H6   C16  H5   108.95  3.000
 HER  H7   C16  O5   111.70  3.000
 HER  H6   C16  O5   111.68  3.000
 HER  H5   C16  O5   106.32  3.000
 HER  O6   C2   C3   115.37  3.000
 HER  O6   C2   C1   123.74  3.000
 HER  C3   C2   C1   120.89  3.000
 HER  O7   C3   C2   122.65  3.000
 HER  C2   C3   C4   118.98  3.000
 HER  O7   C3   C4   118.37  3.000
 HER  C15  C9   C10  122.09  3.000
 HER  C15  C9   C8   118.27  3.000
 HER  C10  C9   C8   119.64  3.000
 HER  C8   O1   C7   122.93  3.000
 HER  H8   O3   C11  107.78  3.000
 HER  H9   O4   C15  108.33  3.000
 HER  C16  O5   C13  119.19  3.000
 HER  H10  O6   C2   111.25  3.000
 HER  H11  O7   C3   110.20  3.000
 HER  H12  O8   C4   110.39  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
 HER  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 HER  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 HER  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 HER  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 HER  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 HER  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 HER  CONST_07  C14  C15  C9   C8      0.00   0.0  0
 HER  CONST_08  C14  C13  C12  C8      0.00   0.0  0
 HER  CONST_09  C9   C8   C12  C13     0.00   0.0  0
 HER  CONST_10  C9   C15  C14  C13     0.00   0.0  0
 HER  CONST_11  C12  C8   C9   C15     0.00   0.0  0
 HER  CONST_12  C12  C13  C14  C15     0.00   0.0  0
 HER  CONST_13  C7   C6   C5   C4    180.00   0.0  0
 HER  CONST_14  C2   C1   C6   C7    180.00   0.0  0
 HER  CONST_15  O6   C2   C3   C4    180.00   0.0  0
 HER  CONST_16  O7   C3   C4   C5    180.00   0.0  0
 HER  CONST_17  O8   C4   C5   C6    180.00   0.0  0
 HER  CONST_18  O6   C2   C1   C6    180.00   0.0  0
 HER  CONST_19  O4   C15  C9   C8    180.00   0.0  0
 HER  CONST_20  O5   C13  C12  C8    180.00   0.0  0
 HER  CONST_21  O4   C15  C9   C10     0.00   0.0  0
 HER  CONST_22  O4   C15  C14  C13   180.00   0.0  0
 HER  CONST_23  O5   C13  C14  C15   180.00   0.0  0
 HER  CONST_24  O7   C3   C2   C1    180.00   0.0  0
 HER  CONST_25  O8   C4   C3   C2    180.00   0.0  0
 HER  CONST_26  H2   C1   C6   C5    180.00   0.0  0
 HER  CONST_27  H1   C5   C6   C7      0.00   0.0  0
 HER  CONST_28  H4   C14  C13  C12   180.00   0.0  0
 HER  CONST_29  H3   C12  C13  C14   180.00   0.0  0
 HER  Var_01    C11  C7   C6   C5     31.55  30.0  2
 HER  Var_02    C10  C11  C7   C6   -179.67  30.0  1
 HER  Var_03    C9   C10  C11  C7     -1.94  30.0  1
 HER  Var_04    C9   C8   O1   C7     -1.84  30.0  1
 HER  Var_05    C11  C10  C9   C8      0.48  30.0  1
 HER  Var_06    H5   C16  O5   C13  -178.96  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
 HER  plan-1  C4   0.020
 HER  plan-1  C5   0.020
 HER  plan-1  C6   0.020
 HER  plan-1  C7   0.020
 HER  plan-1  C1   0.020
 HER  plan-1  C2   0.020
 HER  plan-1  C3   0.020
 HER  plan-1  O6   0.020
 HER  plan-1  O7   0.020
 HER  plan-1  O8   0.020
 HER  plan-1  H1   0.020
 HER  plan-1  H2   0.020
 HER  plan-2  C8   0.020
 HER  plan-2  C10  0.020
 HER  plan-2  C13  0.020
 HER  plan-2  C15  0.020
 HER  plan-2  C12  0.020
 HER  plan-2  C14  0.020
 HER  plan-2  C9   0.020
 HER  plan-2  O1   0.020
 HER  plan-2  O4   0.020
 HER  plan-2  O5   0.020
 HER  plan-2  H3   0.020
 HER  plan-2  H4   0.020
 HER  plan-3  C10  0.020
 HER  plan-3  C11  0.020
 HER  plan-3  C9   0.020
 HER  plan-3  O2   0.020

