# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 20 11:38:38 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4ccc(O)c(O)c4)[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
 QCT  QCT  '2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside'  ligand  52  32  .  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_QCT
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
 QCT  O10   O  OH1   0  -0.672   4.1149   3.0043   0.8791
 QCT  C23   C  CH1   0   0.005   3.0831   2.1404   0.4684
 QCT  C22   C  CH1   0  -0.045   1.7621   2.8722   0.2540
 QCT  O9    O  OH1   0  -0.666   1.9823   3.9239  -0.6505
 QCT  C24   C  CH1   0   0.043   3.5223   1.4690  -0.8277
 QCT  O11   O  OH1   0  -0.674   4.6835   0.6986  -0.6363
 QCT  C25   C  CH1   0   0.012   2.4249   0.5196  -1.3070
 QCT  C26   C  CH3   0  -0.682   2.7181  -0.0781  -2.6663
 QCT  O8    O  O2    0  -0.483   1.1788   1.2042  -1.4199
 QCT  C21   C  CH1   0   0.234   0.7244   1.9040  -0.3178
 QCT  O7    O  O2    0  -0.504   0.3385   1.0366   0.7438
 QCT  C3    C  CR6   0   0.136  -0.8388   0.3936   0.5478
 QCT  C4    C  CR6   0   0.473  -2.0687   1.1504   0.6783
 QCT  O2    O  O     0  -0.497  -2.0752   2.3489   0.9950
 QCT  C2    C  CR6   0   0.243  -0.8717  -0.9303   0.2640
 QCT  C11   C  CR6   0   0.001   0.2885  -1.8190   0.1849
 QCT  C12   C  CR16  0  -0.387   1.2493  -1.8172   1.1989
 QCT  C13   C  CR6   0   0.280   2.3431  -2.6579   1.1268
 QCT  O5    O  OH1   0  -0.642   3.3101  -2.7232   2.0675
 QCT  C14   C  CR6   0   0.300   2.4969  -3.5168   0.0274
 QCT  O6    O  OH1   0  -0.623   3.5502  -4.3439  -0.0776
 QCT  C15   C  CR16  0  -0.331   1.5374  -3.5166  -0.9736
 QCT  C16   C  CR16  0  -0.279   0.4335  -2.6824  -0.8950
 QCT  O1    O  O     0  -0.456  -2.0278  -1.5754   0.0329
 QCT  C9    C  CR66  0   0.410  -3.2150  -0.9384   0.0572
 QCT  C8    C  CR16  0  -0.471  -4.3362  -1.6864  -0.2437
 QCT  C7    C  CR6   0   0.400  -5.5720  -1.0460  -0.2014
 QCT  O4    O  OH1   0  -0.616  -6.6467  -1.7833  -0.4934
 QCT  C6    C  CR16  0  -0.497  -5.6828   0.3062   0.1349
 QCT  C5    C  CR6   0   0.405  -4.5470   1.0363   0.4331
 QCT  C10   C  CR66  0  -0.336  -3.2747   0.4161   0.3917
 QCT  O3    O  OH1   0  -0.625  -4.6608   2.3206   0.7516
 QCT  H101  H  HOH1  0   0.457   3.9907   3.2165   1.8092
 QCT  H23   H  HCH1  0   0.223   2.9152   1.3525   1.2168
 QCT  H22   H  HCH1  0   0.240   1.3869   3.2470   1.2162
 QCT  HO91  H  HOH1  0   0.457   1.1988   4.4821  -0.6706
 QCT  H24   H  HCH1  0   0.209   3.6841   2.2399  -1.5961
 QCT  HO11  H  HOH1  0   0.450   5.3681   1.2803  -0.2904
 QCT  H25   H  HCH1  0   0.238   2.3403  -0.2926  -0.5768
 QCT  H262  H  HCH3  0   0.236   3.6499  -0.6404  -2.6410
 QCT  H263  H  HCH3  0   0.239   1.9259  -0.7673  -2.9589
 QCT  H261  H  HCH3  0   0.224   2.8080   0.6966  -3.4300
 QCT  H21   H  HCH1  0   0.252  -0.1462   2.4657  -0.6714
 QCT  H12   H  HCR6  0   0.280   1.1401  -1.1621   2.0547
 QCT  HO51  H  HOH1  0   0.484   3.1203  -2.1303   2.8031
 QCT  HO61  H  HOH1  0   0.477   4.1188  -4.2767   0.6991
 QCT  H15   H  HCR6  0   0.273   1.6601  -4.1799  -1.8202
 QCT  H16   H  HCR6  0   0.264  -0.2956  -2.6976  -1.6939
 QCT  H8    H  HCR6  0   0.288  -4.2566  -2.7352  -0.4964
 QCT  HO4   H  HOH1  0   0.484  -7.4528  -1.2566  -0.4362
 QCT  H6    H  HCR6  0   0.288  -6.6526   0.7889   0.1695
 QCT  HO3   H  HOH1  0   0.478  -3.7538   2.6651   0.9320

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
 QCT  O9   C22   single    1.405  0.020  1.405
 QCT  O10  C23   single    1.407  0.020  1.407
 QCT  C22  C23   single    1.525  0.020  1.525
 QCT  C22  C21   single    1.530  0.020  1.530
 QCT  C23  C24   single    1.524  0.020  1.524
 QCT  C24  O11   single    1.407  0.020  1.407
 QCT  C24  C25   single    1.528  0.020  1.528
 QCT  C21  O8    single    1.382  0.020  1.382
 QCT  C21  O7    single    1.424  0.020  1.424
 QCT  O8   C25   single    1.426  0.020  1.426
 QCT  O7   C3    single    1.356  0.020  1.356
 QCT  C25  C26   single    1.514  0.020  1.514
 QCT  O2   C4    double    1.240  0.020  1.240
 QCT  O5   C13   single    1.351  0.020  1.351
 QCT  C4   C3    single    1.450  0.020  1.450
 QCT  C4   C10   single    1.441  0.020  1.441
 QCT  C3   C2    double    1.354  0.020  1.354
 QCT  O3   C5    single    1.328  0.020  1.328
 QCT  C12  C13   aromatic  1.381  0.020  1.381
 QCT  C12  C11   aromatic  1.397  0.020  1.397
 QCT  C13  C14   aromatic  1.404  0.020  1.404
 QCT  C2   C11   single    1.464  0.020  1.464
 QCT  C2   O1    single    1.344  0.020  1.344
 QCT  C10  C5    aromatic  1.416  0.020  1.416
 QCT  C10  C9    aromatic  1.397  0.020  1.397
 QCT  C11  C16   aromatic  1.390  0.020  1.390
 QCT  C5   C6    aromatic  1.383  0.020  1.383
 QCT  C14  O6    single    1.343  0.020  1.343
 QCT  C14  C15   aromatic  1.387  0.020  1.387
 QCT  O1   C9    single    1.348  0.020  1.348
 QCT  C9   C8    aromatic  1.381  0.020  1.381
 QCT  C16  C15   aromatic  1.386  0.020  1.386
 QCT  C6   C7    aromatic  1.398  0.020  1.398
 QCT  C8   C7    aromatic  1.392  0.020  1.392
 QCT  C7   O4    single    1.336  0.020  1.336
 QCT  O10  H101  single    0.850  0.020  0.980
 QCT  C23  H23   single    0.970  0.020  1.090
 QCT  C22  H22   single    0.970  0.020  1.090
 QCT  O9   HO91  single    0.850  0.020  0.980
 QCT  C24  H24   single    0.970  0.020  1.090
 QCT  O11  HO11  single    0.850  0.020  0.980
 QCT  C25  H25   single    0.970  0.020  1.090
 QCT  C26  H262  single    0.970  0.020  1.090
 QCT  C26  H263  single    0.970  0.020  1.090
 QCT  C26  H261  single    0.970  0.020  1.090
 QCT  C21  H21   single    0.970  0.020  1.090
 QCT  C12  H12   single    0.930  0.020  1.080
 QCT  O5   HO51  single    0.850  0.020  0.980
 QCT  O6   HO61  single    0.850  0.020  0.980
 QCT  C15  H15   single    0.930  0.020  1.080
 QCT  C16  H16   single    0.930  0.020  1.080
 QCT  C8   H8    single    0.930  0.020  1.080
 QCT  O4   HO4   single    0.850  0.020  0.980
 QCT  C6   H6    single    0.930  0.020  1.080
 QCT  O3   HO3   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
 QCT  H101  O10  C23   108.84  3.000
 QCT  H23   C23  C24   107.88  3.000
 QCT  H23   C23  C22   107.89  3.000
 QCT  C24   C23  C22   109.96  3.000
 QCT  H23   C23  O10   110.69  3.000
 QCT  C24   C23  O10   107.90  3.000
 QCT  C22   C23  O10   112.43  3.000
 QCT  H22   C22  C21   108.16  3.000
 QCT  H22   C22  O9    111.23  3.000
 QCT  C21   C22  O9    109.84  3.000
 QCT  H22   C22  C23   109.66  3.000
 QCT  C21   C22  C23   109.65  3.000
 QCT  O9    C22  C23   108.30  3.000
 QCT  HO91  O9   C22   108.67  3.000
 QCT  H24   C24  C25   108.77  3.000
 QCT  H24   C24  O11   110.93  3.000
 QCT  C25   C24  O11   107.17  3.000
 QCT  H24   C24  C23   109.12  3.000
 QCT  C25   C24  C23   109.48  3.000
 QCT  O11   C24  C23   111.31  3.000
 QCT  HO11  O11  C24   107.76  3.000
 QCT  H25   C25  O8    109.95  3.000
 QCT  H25   C25  C26   108.71  3.000
 QCT  O8    C25  C26   106.72  3.000
 QCT  H25   C25  C24   107.88  3.000
 QCT  C26   C25  C24   112.82  3.000
 QCT  O8    C25  C24   110.73  3.000
 QCT  H261  C26  H263  108.71  3.000
 QCT  H261  C26  H262  108.20  3.000
 QCT  H263  C26  H262  107.56  3.000
 QCT  H261  C26  C25   111.35  3.000
 QCT  H263  C26  C25   110.48  3.000
 QCT  H262  C26  C25   110.42  3.000
 QCT  C21   O8   C25   117.85  3.000
 QCT  H21   C21  O7    109.74  3.000
 QCT  H21   C21  O8    105.29  3.000
 QCT  O7    C21  O8    112.02  3.000
 QCT  H21   C21  C22   109.60  3.000
 QCT  O7    C21  C22   106.89  3.000
 QCT  O8    C21  C22   113.29  3.000
 QCT  C3    O7   C21   114.60  3.000
 QCT  C2    C3   C4    120.56  3.000
 QCT  C2    C3   O7    121.00  3.000
 QCT  C4    C3   O7    118.42  3.000
 QCT  C10   C4   O2    122.62  3.000
 QCT  C10   C4   C3    115.22  3.000
 QCT  O2    C4   C3    122.15  3.000
 QCT  O1    C2   C11   112.41  3.000
 QCT  O1    C2   C3    121.75  3.000
 QCT  C11   C2   C3    125.84  3.000
 QCT  C16   C11  C12   119.53  3.000
 QCT  C16   C11  C2    120.12  3.000
 QCT  C12   C11  C2    120.35  3.000
 QCT  H12   C12  C13   119.28  3.000
 QCT  H12   C12  C11   120.32  3.000
 QCT  C13   C12  C11   120.40  3.000
 QCT  C14   C13  O5    115.95  3.000
 QCT  C14   C13  C12   120.00  3.000
 QCT  O5    C13  C12   124.05  3.000
 QCT  HO51  O5   C13   111.15  3.000
 QCT  C15   C14  O6    119.09  3.000
 QCT  C15   C14  C13   119.31  3.000
 QCT  O6    C14  C13   121.59  3.000
 QCT  HO61  O6   C14   110.88  3.000
 QCT  H15   C15  C16   120.23  3.000
 QCT  H15   C15  C14   119.09  3.000
 QCT  C16   C15  C14   120.69  3.000
 QCT  H16   C16  C15   119.12  3.000
 QCT  H16   C16  C11   120.80  3.000
 QCT  C15   C16  C11   120.07  3.000
 QCT  C9    O1   C2    121.87  3.000
 QCT  C10   C9   C8    122.88  3.000
 QCT  C8    C9   O1    117.09  3.000
 QCT  C10   C9   O1    120.03  3.000
 QCT  H8    C8   C7    121.21  3.000
 QCT  H8    C8   C9    121.08  3.000
 QCT  C7    C8   C9    117.70  3.000
 QCT  C6    C7   O4    121.52  3.000
 QCT  O4    C7   C8    116.98  3.000
 QCT  C6    C7   C8    121.50  3.000
 QCT  HO4   O4   C7    110.98  3.000
 QCT  H6    C6   C5    119.53  3.000
 QCT  H6    C6   C7    120.63  3.000
 QCT  C5    C6   C7    119.83  3.000
 QCT  O3    C5   C10   120.50  3.000
 QCT  C10   C5   C6    120.03  3.000
 QCT  O3    C5   C6    119.46  3.000
 QCT  C5    C10  C9    118.05  3.000
 QCT  C9    C10  C4    120.41  3.000
 QCT  C5    C10  C4    121.54  3.000
 QCT  HO3   O3   C5    107.62  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
 QCT  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 QCT  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 QCT  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 QCT  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 QCT  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 QCT  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 QCT  CONST_07  C6   C5   C10  C9      0.00   0.0  0
 QCT  CONST_08  C6   C7   C8   C9      0.00   0.0  0
 QCT  CONST_09  C5   C10  C9   C8      0.00   0.0  0
 QCT  CONST_10  C5   C6   C7   C8      0.00   0.0  0
 QCT  CONST_11  C10  C5   C6   C7      0.00   0.0  0
 QCT  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 QCT  CONST_13  C13  C12  C11  C2    180.00   0.0  0
 QCT  CONST_14  C15  C16  C11  C2    180.00   0.0  0
 QCT  CONST_15  O3   C5   C10  C4      0.00   0.0  0
 QCT  CONST_16  O5   C13  C12  C11   180.00   0.0  0
 QCT  CONST_17  O6   C14  C13  C12   180.00   0.0  0
 QCT  CONST_18  C15  C14  C13  O5    180.00   0.0  0
 QCT  CONST_19  C16  C15  C14  O6    180.00   0.0  0
 QCT  CONST_20  O3   C5   C10  C9    180.00   0.0  0
 QCT  CONST_21  O4   C7   C8   C9    180.00   0.0  0
 QCT  CONST_22  O3   C5   C6   C7    180.00   0.0  0
 QCT  CONST_23  C5   C6   C7   O4    180.00   0.0  0
 QCT  CONST_24  H12  C12  C11  C2      0.00   0.0  0
 QCT  CONST_25  H16  C16  C11  C2      0.00   0.0  0
 QCT  CONST_26  H15  C15  C16  C11   180.00   0.0  0
 QCT  CONST_27  H8   C8   C9   O1      0.00   0.0  0
 QCT  CONST_28  H6   C6   C7   C8    180.00   0.0  0
 QCT  Var_01    C5   C10  C4   C3   -177.82  30.0  1
 QCT  Var_02    C12  C11  C2   C3     48.24  30.0  2
 QCT  Var_03    C11  C2   C3   C4   -176.16  30.0  1
 QCT  Var_04    C10  C4   C3   C2     -4.26  30.0  1
 QCT  Var_05    C10  C9   O1   C2     -3.10  30.0  1
 QCT  Var_06    C4   C3   O7   C21   -74.09  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
 QCT  chir_01  C23  O10  C22  C24  negativ
 QCT  chir_02  C22  O9   C21  C23  negativ
 QCT  chir_03  C24  O11  C23  C25  positiv
 QCT  chir_04  C25  O8   C24  C26  positiv
 QCT  chir_05  C21  O8   O7   C22  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
 QCT  plan-1  C2   0.020
 QCT  plan-1  C11  0.020
 QCT  plan-1  C12  0.020
 QCT  plan-1  C13  0.020
 QCT  plan-1  O5   0.020
 QCT  plan-1  C14  0.020
 QCT  plan-1  O6   0.020
 QCT  plan-1  C15  0.020
 QCT  plan-1  C16  0.020
 QCT  plan-1  H12  0.020
 QCT  plan-1  H15  0.020
 QCT  plan-1  H16  0.020
 QCT  plan-2  C4   0.020
 QCT  plan-2  O1   0.020
 QCT  plan-2  C9   0.020
 QCT  plan-2  C8   0.020
 QCT  plan-2  C7   0.020
 QCT  plan-2  O4   0.020
 QCT  plan-2  C6   0.020
 QCT  plan-2  C5   0.020
 QCT  plan-2  C10  0.020
 QCT  plan-2  O3   0.020
 QCT  plan-2  H8   0.020
 QCT  plan-2  H6   0.020
 QCT  plan-3  C3   0.020
 QCT  plan-3  C4   0.020
 QCT  plan-3  O2   0.020
 QCT  plan-3  C10  0.020

