# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 11:32:25 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[[2-(4-hydroxyphenyl)-5,7-bis(oxidanyl)-2~{H}-chromen-3-yl]oxy]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](OC2=Cc3c(O)cc(O)cc3O[C@H]2c4ccc(O)cc4)[C@@H](O)[C@H](O)[C@H]1O
#
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
 PUQ  PUQ  (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[[2-(4-hydroxyphenyl)-5,7-bis(oxidanyl)-2~{H}-chromen-3-yl]oxy]oxane-3,4,5-triol  ligand  53  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PUQ
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
 PUQ  O10   O  OH1   0  -0.667  37.9434  -40.6197  -1.8663
 PUQ  C20   C  CH1   0   0.014  39.0177  -39.8276  -1.4403
 PUQ  C19   C  CH1   0  -0.009  40.2180  -39.8948  -2.3761
 PUQ  O9    O  OH1   0  -0.675  40.6786  -41.2259  -2.3668
 PUQ  C18   C  CH1   0  -0.005  41.2919  -38.9249  -1.8974
 PUQ  O8    O  OH1   0  -0.667  42.3388  -38.9458  -2.8422
 PUQ  C17   C  CH1   0  -0.029  40.7075  -37.5162  -1.7472
 PUQ  C21   C  CH2   0  -0.164  41.6970  -36.5668  -1.1096
 PUQ  O7    O  OH1   0  -0.663  41.1584  -35.2678  -1.1063
 PUQ  O6    O  O2    0  -0.491  39.5582  -37.5490  -0.9064
 PUQ  C16   C  CH1   0   0.221  38.5343  -38.3870  -1.3181
 PUQ  O2    O  O2    0  -0.473  38.0293  -38.0216  -2.5776
 PUQ  C8    C  C     0   0.348  37.3415  -36.8753  -2.7244
 PUQ  C7    C  C1    0  -0.354  36.9724  -36.0080  -1.7809
 PUQ  C5    C  CR6   0  -0.118  36.1441  -34.8731  -2.1589
 PUQ  C4    C  CR6   0   0.330  35.5276  -34.0238  -1.2374
 PUQ  O3    O  OH1   0  -0.626  35.7003  -34.3088   0.0673
 PUQ  C3    C  CR16  0  -0.541  34.7726  -32.9312  -1.6539
 PUQ  C2    C  CR6   0   0.372  34.6324  -32.6738  -3.0137
 PUQ  O4    O  OH1   0  -0.635  33.9131  -31.6318  -3.4734
 PUQ  C9    C  CH1   0  -0.079  36.9626  -36.6789  -4.1727
 PUQ  O1    O  O2    0  -0.496  36.5970  -35.3321  -4.4498
 PUQ  C6    C  CR6   0   0.380  35.9754  -34.5832  -3.5127
 PUQ  C1    C  CR16  0  -0.477  35.2316  -33.5025  -3.9577
 PUQ  C10   C  CR6   0   0.089  38.1165  -37.0225  -5.0769
 PUQ  C15   C  CR16  0  -0.266  39.2733  -36.2466  -5.0666
 PUQ  C14   C  CR16  0  -0.322  40.3612  -36.5807  -5.8505
 PUQ  C13   C  CR6   0   0.350  40.3096  -37.7093  -6.6689
 PUQ  O5    O  OH1   0  -0.632  41.3974  -37.9911  -7.4127
 PUQ  C12   C  CR16  0  -0.375  39.1575  -38.4884  -6.6902
 PUQ  C11   C  CR16  0  -0.300  38.0733  -38.1386  -5.8962
 PUQ  HO10  H  HOH1  0   0.455  38.2365  -41.5364  -1.8796
 PUQ  H20   H  HCH1  0   0.229  39.3531  -40.1240  -0.4346
 PUQ  H19   H  HCH1  0   0.228  39.9046  -39.5989  -3.3891
 PUQ  HO9   H  HOH1  0   0.454  41.3809  -41.3064  -3.0201
 PUQ  H18   H  HCH1  0   0.222  41.6463  -39.2656  -0.9130
 PUQ  HO8   H  HOH1  0   0.459  43.1759  -38.8287  -2.3854
 PUQ  H17   H  HCH1  0   0.250  40.4476  -37.1354  -2.7440
 PUQ  H211  H  HCH2  0   0.197  41.9288  -36.9185  -0.0940
 PUQ  H212  H  HCH2  0   0.201  42.6291  -36.6099  -1.6855
 PUQ  HO7   H  HOH1  0   0.455  41.8252  -34.6750  -0.7485
 PUQ  H16   H  HCH1  0   0.262  37.7486  -38.3105  -0.5573
 PUQ  H7    H  H     0   0.272  37.2569  -36.1268  -0.7452
 PUQ  HO3   H  HOH1  0   0.478  35.2789  -33.6393   0.6175
 PUQ  H3    H  HCR6  0   0.279  34.2986  -32.2871  -0.9200
 PUQ  HO4   H  HOH1  0   0.475  33.5308  -31.1373  -2.7401
 PUQ  H1    H  HCR6  0   0.266  35.1262  -33.3034  -5.0165
 PUQ  H15   H  HCR6  0   0.256  39.3388  -35.3762  -4.4243
 PUQ  H14   H  HCR6  0   0.262  41.2574  -35.9734  -5.8303
 PUQ  HO5   H  HOH1  0   0.474  41.2582  -38.7958  -7.9240
 PUQ  H12   H  HCR6  0   0.270  39.1004  -39.3657  -7.3244
 PUQ  H11   H  HCR6  0   0.255  37.1837  -38.7570  -5.9169
 PUQ  H2    H  HCH1  0   0.264  36.1138  -37.3387  -4.4106

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
 PUQ  O5   C13   single    1.348  0.020  1.348
 PUQ  C13  C14   aromatic  1.395  0.020  1.395
 PUQ  C13  C12   aromatic  1.391  0.020  1.391
 PUQ  C14  C15   aromatic  1.382  0.020  1.382
 PUQ  C12  C11   aromatic  1.389  0.020  1.389
 PUQ  C15  C10   aromatic  1.393  0.020  1.393
 PUQ  C11  C10   aromatic  1.385  0.020  1.385
 PUQ  C10  C9    single    1.506  0.020  1.506
 PUQ  O1   C9    single    1.423  0.020  1.423
 PUQ  O1   C6    single    1.351  0.020  1.351
 PUQ  C9   C8    single    1.510  0.020  1.510
 PUQ  C1   C6    aromatic  1.385  0.020  1.385
 PUQ  C1   C2    aromatic  1.392  0.020  1.392
 PUQ  C6   C5    aromatic  1.395  0.020  1.395
 PUQ  C8   O2    single    1.345  0.020  1.345
 PUQ  C8   C7    double    1.334  0.020  1.334
 PUQ  O2   C16   single    1.405  0.020  1.405
 PUQ  O10  C20   single    1.401  0.020  1.401
 PUQ  O4   C2    single    1.347  0.020  1.347
 PUQ  C2   C3    aromatic  1.391  0.020  1.391
 PUQ  C5   C7    single    1.455  0.020  1.455
 PUQ  C5   C4    aromatic  1.397  0.020  1.397
 PUQ  C16  C20   single    1.524  0.020  1.524
 PUQ  C16  O6    single    1.386  0.020  1.386
 PUQ  C19  C20   single    1.523  0.020  1.523
 PUQ  C19  O9    single    1.409  0.020  1.409
 PUQ  C19  C18   single    1.524  0.020  1.524
 PUQ  C3   C4    aromatic  1.392  0.020  1.392
 PUQ  C4   O3    single    1.347  0.020  1.347
 PUQ  O8   C18   single    1.410  0.020  1.410
 PUQ  C18  C17   single    1.532  0.020  1.532
 PUQ  O6   C17   single    1.424  0.020  1.424
 PUQ  C17  C21   single    1.512  0.020  1.512
 PUQ  C21  O7    single    1.406  0.020  1.406
 PUQ  O10  HO10  single    0.850  0.020  0.980
 PUQ  C20  H20   single    0.970  0.020  1.090
 PUQ  C19  H19   single    0.970  0.020  1.090
 PUQ  O9   HO9   single    0.850  0.020  0.980
 PUQ  C18  H18   single    0.970  0.020  1.090
 PUQ  O8   HO8   single    0.850  0.020  0.980
 PUQ  C17  H17   single    0.970  0.020  1.090
 PUQ  C21  H211  single    0.970  0.020  1.090
 PUQ  C21  H212  single    0.970  0.020  1.090
 PUQ  O7   HO7   single    0.850  0.020  0.980
 PUQ  C16  H16   single    0.970  0.020  1.090
 PUQ  C7   H7    single    0.930  0.020  1.080
 PUQ  O3   HO3   single    0.850  0.020  0.980
 PUQ  C3   H3    single    0.930  0.020  1.080
 PUQ  O4   HO4   single    0.850  0.020  0.980
 PUQ  C1   H1    single    0.930  0.020  1.080
 PUQ  C15  H15   single    0.930  0.020  1.080
 PUQ  C14  H14   single    0.930  0.020  1.080
 PUQ  O5   HO5   single    0.850  0.020  0.980
 PUQ  C12  H12   single    0.930  0.020  1.080
 PUQ  C11  H11   single    0.930  0.020  1.080
 PUQ  C9   H2    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
 PUQ  HO10  O10  C20   108.01  3.000
 PUQ  H20   C20  C16   106.13  3.000
 PUQ  H20   C20  C19   108.02  3.000
 PUQ  C16   C20  C19   109.92  3.000
 PUQ  H20   C20  O10   111.05  3.000
 PUQ  C19   C20  O10   113.11  3.000
 PUQ  C16   C20  O10   108.39  3.000
 PUQ  H19   C19  C18   108.58  3.000
 PUQ  H19   C19  O9    110.68  3.000
 PUQ  C18   C19  O9    111.65  3.000
 PUQ  H19   C19  C20   109.21  3.000
 PUQ  C18   C19  C20   109.52  3.000
 PUQ  O9    C19  C20   107.17  3.000
 PUQ  HO9   O9   C19   108.24  3.000
 PUQ  H18   C18  C17   108.65  3.000
 PUQ  H18   C18  O8    110.83  3.000
 PUQ  C17   C18  O8    111.25  3.000
 PUQ  H18   C18  C19   108.12  3.000
 PUQ  C17   C18  C19   110.30  3.000
 PUQ  O8    C18  C19   107.65  3.000
 PUQ  HO8   O8   C18   109.06  3.000
 PUQ  H17   C17  O6    110.66  3.000
 PUQ  H17   C17  C21   108.65  3.000
 PUQ  O6    C17  C21   107.07  3.000
 PUQ  H17   C17  C18   108.66  3.000
 PUQ  C21   C17  C18   111.65  3.000
 PUQ  O6    C17  C18   110.15  3.000
 PUQ  H212  C21  H211  107.06  3.000
 PUQ  H212  C21  O7    111.30  3.000
 PUQ  H211  C21  O7    111.97  3.000
 PUQ  H212  C21  C17   108.06  3.000
 PUQ  H211  C21  C17   109.06  3.000
 PUQ  O7    C21  C17   109.28  3.000
 PUQ  HO7   O7   C21   107.74  3.000
 PUQ  C16   O6   C17   115.77  3.000
 PUQ  H16   C16  O2    110.26  3.000
 PUQ  H16   C16  O6    106.33  3.000
 PUQ  O2    C16  O6    111.99  3.000
 PUQ  H16   C16  C20   110.42  3.000
 PUQ  O6    C16  C20   111.16  3.000
 PUQ  O2    C16  C20   106.73  3.000
 PUQ  C8    O2   C16   120.22  3.000
 PUQ  C9    C8   C7    121.64  3.000
 PUQ  C7    C8   O2    128.22  3.000
 PUQ  C9    C8   O2    110.11  3.000
 PUQ  H7    C7   C5    118.99  3.000
 PUQ  H7    C7   C8    122.26  3.000
 PUQ  C5    C7   C8    118.75  3.000
 PUQ  C6    C5   C4    117.43  3.000
 PUQ  C4    C5   C7    123.66  3.000
 PUQ  C6    C5   C7    118.89  3.000
 PUQ  C3    C4   O3    121.71  3.000
 PUQ  O3    C4   C5    117.00  3.000
 PUQ  C3    C4   C5    121.29  3.000
 PUQ  HO3   O3   C4    110.49  3.000
 PUQ  H3    C3   C2    120.47  3.000
 PUQ  H3    C3   C4    120.02  3.000
 PUQ  C2    C3   C4    119.51  3.000
 PUQ  C1    C2   O4    117.32  3.000
 PUQ  O4    C2   C3    122.05  3.000
 PUQ  C1    C2   C3    120.63  3.000
 PUQ  HO4   O4   C2    110.43  3.000
 PUQ  H2    C9   C10   108.92  3.000
 PUQ  H2    C9   O1    109.08  3.000
 PUQ  C10   C9   O1    107.21  3.000
 PUQ  H2    C9   C8    108.83  3.000
 PUQ  O1    C9   C8    111.99  3.000
 PUQ  C10   C9   C8    110.74  3.000
 PUQ  C6    O1   C9    120.52  3.000
 PUQ  C1    C6   O1    117.17  3.000
 PUQ  C1    C6   C5    122.60  3.000
 PUQ  O1    C6   C5    120.16  3.000
 PUQ  H1    C1   C6    120.66  3.000
 PUQ  H1    C1   C2    120.80  3.000
 PUQ  C6    C1   C2    118.55  3.000
 PUQ  C11   C10  C15   118.63  3.000
 PUQ  C11   C10  C9    121.01  3.000
 PUQ  C15   C10  C9    120.32  3.000
 PUQ  H15   C15  C14   118.87  3.000
 PUQ  H15   C15  C10   120.13  3.000
 PUQ  C14   C15  C10   120.99  3.000
 PUQ  H14   C14  C13   119.69  3.000
 PUQ  H14   C14  C15   120.36  3.000
 PUQ  C13   C14  C15   119.95  3.000
 PUQ  C12   C13  O5    122.89  3.000
 PUQ  C12   C13  C14   119.52  3.000
 PUQ  O5    C13  C14   117.59  3.000
 PUQ  HO5   O5   C13   110.54  3.000
 PUQ  H12   C12  C11   119.81  3.000
 PUQ  H12   C12  C13   120.39  3.000
 PUQ  C11   C12  C13   119.80  3.000
 PUQ  H11   C11  C12   119.10  3.000
 PUQ  H11   C11  C10   119.78  3.000
 PUQ  C12   C11  C10   121.11  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
 PUQ  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 PUQ  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 PUQ  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 PUQ  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 PUQ  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 PUQ  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 PUQ  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 PUQ  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 PUQ  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 PUQ  CONST_10  C12  C11  C10  C15     0.00   0.0  0
 PUQ  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 PUQ  CONST_12  C11  C10  C15  C14     0.00   0.0  0
 PUQ  CONST_13  C14  C15  C10  C9    180.00   0.0  0
 PUQ  CONST_14  C12  C11  C10  C9    180.00   0.0  0
 PUQ  CONST_15  O3   C4   C5   C7      0.00   0.0  0
 PUQ  CONST_16  O4   C2   C3   C4    180.00   0.0  0
 PUQ  CONST_17  C6   C5   C4   O3    180.00   0.0  0
 PUQ  CONST_18  C2   C3   C4   O3    180.00   0.0  0
 PUQ  CONST_19  C6   C1   C2   O4    180.00   0.0  0
 PUQ  CONST_20  O5   C13  C14  C15   180.00   0.0  0
 PUQ  CONST_21  C11  C12  C13  O5    180.00   0.0  0
 PUQ  CONST_22  H1   C1   C6   C5    180.00   0.0  0
 PUQ  CONST_23  H3   C3   C4   C5    180.00   0.0  0
 PUQ  CONST_24  H15  C15  C10  C9      0.00   0.0  0
 PUQ  CONST_25  H11  C11  C10  C9      0.00   0.0  0
 PUQ  CONST_26  H14  C14  C15  C10   180.00   0.0  0
 PUQ  CONST_27  H12  C12  C11  C10   180.00   0.0  0
 PUQ  Var_01    C6   C5   C7   C8    -12.13  30.0  1
 PUQ  Var_02    C9   C8   C7   C5      2.22  30.0  1
 PUQ  Var_03    C1   C6   O1   C9   -157.31  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
 PUQ  chir_01  C20  O10  C16  C19  positiv
 PUQ  chir_02  C19  O9   C20  C18  negativ
 PUQ  chir_03  C18  O8   C17  C19  negativ
 PUQ  chir_04  C17  O6   C18  C21  positiv
 PUQ  chir_05  C16  O6   O2   C20  negativ
 PUQ  chir_06  C9   O1   C8   C10  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
 PUQ  plan-1  C9   0.020
 PUQ  plan-1  C10  0.020
 PUQ  plan-1  C15  0.020
 PUQ  plan-1  C14  0.020
 PUQ  plan-1  C13  0.020
 PUQ  plan-1  O5   0.020
 PUQ  plan-1  C12  0.020
 PUQ  plan-1  C11  0.020
 PUQ  plan-1  H15  0.020
 PUQ  plan-1  H14  0.020
 PUQ  plan-1  H12  0.020
 PUQ  plan-1  H11  0.020
 PUQ  plan-2  C7   0.020
 PUQ  plan-2  C5   0.020
 PUQ  plan-2  C4   0.020
 PUQ  plan-2  O3   0.020
 PUQ  plan-2  C3   0.020
 PUQ  plan-2  C2   0.020
 PUQ  plan-2  O4   0.020
 PUQ  plan-2  O1   0.020
 PUQ  plan-2  C6   0.020
 PUQ  plan-2  C1   0.020
 PUQ  plan-2  H3   0.020
 PUQ  plan-2  H1   0.020

