# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 20 16:43:06 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 5,7-dihydroxy-2-(4-hydroxyphenyl)-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)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
 AFE  AFE  '5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside'  ligand  51  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFE
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
 AFE  O9    O  OH1   0  -0.666   4.3486   2.8554   0.9698
 AFE  C23   C  CH1   0   0.026   3.3154   1.9968   0.5644
 AFE  C22   C  CH1   0  -0.056   2.0251   2.7585   0.2655
 AFE  O22   O  OH1   0  -0.666   2.3136   3.7485  -0.6892
 AFE  C24   C  CH1   0   0.029   3.7591   1.2422  -0.6796
 AFE  O61   O  OH1   0  -0.668   4.9037   0.4925  -0.3520
 AFE  C25   C  CH1   0  -0.000   2.6260   0.3116  -1.1346
 AFE  C51   C  CH3   0  -0.698   2.9324  -0.3840  -2.4446
 AFE  O7    O  O2    0  -0.482   1.4102   1.0309  -1.3305
 AFE  C21   C  CH1   0   0.239   0.9591   1.8100  -0.2833
 AFE  O8    O  O2    0  -0.503   0.4999   1.0223   0.8116
 AFE  C3    C  CR6   0   0.137  -0.7064   0.4348   0.6164
 AFE  C4    C  CR6   0   0.472  -1.8937   1.2647   0.6585
 AFE  O2    O  O     0  -0.498  -1.8420   2.4785   0.9060
 AFE  C2    C  CR6   0   0.245  -0.8055  -0.9001   0.4087
 AFE  C11   C  CR6   0  -0.012   0.3051  -1.8512   0.4140
 AFE  C12   C  CR16  0  -0.249   1.2533  -1.8449   1.4356
 AFE  C13   C  CR16  0  -0.371   2.3026  -2.7463   1.4326
 AFE  C14   C  CR6   0   0.364   2.4269  -3.6686   0.3949
 AFE  O5    O  OH1   0  -0.621   3.4272  -4.5604   0.3331
 AFE  C15   C  CR16  0  -0.325   1.4797  -3.6855  -0.6290
 AFE  C16   C  CR16  0  -0.253   0.4268  -2.7923  -0.6097
 AFE  O1    O  O     0  -0.456  -1.9905  -1.4924   0.1785
 AFE  C9    C  CR66  0   0.414  -3.1368  -0.7882   0.1173
 AFE  C8    C  CR16  0  -0.516  -4.2913  -1.4880  -0.1824
 AFE  C7    C  CR6   0   0.400  -5.4864  -0.7762  -0.2330
 AFE  O4    O  OH1   0  -0.615  -6.6492  -1.3702  -0.5154
 AFE  C6    C  CR16  0  -0.456  -5.5289   0.5997   0.0122
 AFE  C5    C  CR6   0   0.403  -4.3647   1.2788   0.3133
 AFE  C10   C  CR66  0  -0.336  -3.1297   0.5847   0.3655
 AFE  O3    O  OH1   0  -0.627  -4.4118   2.5862   0.5464
 AFE  HO9   H  HOH1  0   0.452   4.1108   3.2340   1.8221
 AFE  H23   H  HCH1  0   0.219   3.0932   1.2560   1.3477
 AFE  H22   H  HCH1  0   0.244   1.6410   3.2034   1.1939
 AFE  HO22  H  HOH1  0   0.457   1.5557   4.3370  -0.7608
 AFE  H24   H  HCH1  0   0.217   3.9745   1.9625  -1.4815
 AFE  HO61  H  HOH1  0   0.454   5.3481   0.2388  -1.1658
 AFE  H25   H  HCH1  0   0.240   2.4898  -0.4487  -0.3579
 AFE  H512  H  HCH3  0   0.230   3.8079  -1.0254  -2.3463
 AFE  H513  H  HCH3  0   0.246   2.1018  -1.0246  -2.7401
 AFE  H511  H  HCH3  0   0.229   3.1178   0.3348  -3.2453
 AFE  H21   H  HCH1  0   0.252   0.1273   2.3919  -0.6922
 AFE  H12   H  HCR6  0   0.266   1.1758  -1.1374   2.2497
 AFE  H13   H  HCR6  0   0.280   3.0258  -2.7274   2.2396
 AFE  HO5   H  HOH1  0   0.479   4.0177  -4.4652   1.0892
 AFE  H15   H  HCR6  0   0.272   1.5739  -4.3999  -1.4366
 AFE  H16   H  HCR6  0   0.267  -0.2926  -2.8187  -1.4180
 AFE  H8    H  HCR6  0   0.296  -4.2566  -2.5551  -0.3646
 AFE  HO4   H  HOH1  0   0.484  -6.5279  -2.3156  -0.6630
 AFE  H6    H  HCR6  0   0.281  -6.4721   1.1294  -0.0306
 AFE  HO3   H  HOH1  0   0.478  -3.4935   2.8883   0.7444

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
 AFE  O22  C22   single    1.405  0.020  1.405
 AFE  O9   C23   single    1.403  0.020  1.403
 AFE  C22  C23   single    1.528  0.020  1.528
 AFE  C22  C21   single    1.529  0.020  1.529
 AFE  C23  C24   single    1.521  0.020  1.521
 AFE  C24  O61   single    1.407  0.020  1.407
 AFE  C24  C25   single    1.535  0.020  1.535
 AFE  C21  O7    single    1.381  0.020  1.381
 AFE  C21  O8    single    1.425  0.020  1.425
 AFE  O7   C25   single    1.426  0.020  1.426
 AFE  O8   C3    single    1.356  0.020  1.356
 AFE  O2   C4    double    1.240  0.020  1.240
 AFE  C25  C51   single    1.515  0.020  1.515
 AFE  C3   C4    single    1.449  0.020  1.449
 AFE  C3   C2    double    1.355  0.020  1.355
 AFE  C4   C10   single    1.441  0.020  1.441
 AFE  C12  C13   aromatic  1.383  0.020  1.383
 AFE  C12  C11   aromatic  1.394  0.020  1.394
 AFE  O3   C5    single    1.329  0.020  1.329
 AFE  C13  C14   aromatic  1.394  0.020  1.394
 AFE  C2   C11   single    1.462  0.020  1.462
 AFE  C2   O1    single    1.345  0.020  1.345
 AFE  C10  C5    aromatic  1.418  0.020  1.418
 AFE  C10  C9    aromatic  1.395  0.020  1.395
 AFE  C11  C16   aromatic  1.396  0.020  1.396
 AFE  C5   C6    aromatic  1.381  0.020  1.381
 AFE  C14  O5    single    1.342  0.020  1.342
 AFE  C14  C15   aromatic  1.395  0.020  1.395
 AFE  O1   C9    single    1.347  0.020  1.347
 AFE  C9   C8    aromatic  1.383  0.020  1.383
 AFE  C16  C15   aromatic  1.381  0.020  1.381
 AFE  C6   C7    aromatic  1.398  0.020  1.398
 AFE  C8   C7    aromatic  1.392  0.020  1.392
 AFE  C7   O4    single    1.336  0.020  1.336
 AFE  O9   HO9   single    0.850  0.020  0.980
 AFE  C23  H23   single    0.970  0.020  1.090
 AFE  C22  H22   single    0.970  0.020  1.090
 AFE  O22  HO22  single    0.850  0.020  0.980
 AFE  C24  H24   single    0.970  0.020  1.090
 AFE  O61  HO61  single    0.850  0.020  0.980
 AFE  C25  H25   single    0.970  0.020  1.090
 AFE  C51  H512  single    0.970  0.020  1.090
 AFE  C51  H513  single    0.970  0.020  1.090
 AFE  C51  H511  single    0.970  0.020  1.090
 AFE  C21  H21   single    0.970  0.020  1.090
 AFE  C12  H12   single    0.930  0.020  1.080
 AFE  C13  H13   single    0.930  0.020  1.080
 AFE  O5   HO5   single    0.850  0.020  0.980
 AFE  C15  H15   single    0.930  0.020  1.080
 AFE  C16  H16   single    0.930  0.020  1.080
 AFE  C8   H8    single    0.930  0.020  1.080
 AFE  O4   HO4   single    0.850  0.020  0.980
 AFE  C6   H6    single    0.930  0.020  1.080
 AFE  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
 AFE  HO9   O9   C23   108.33  3.000
 AFE  H23   C23  C24   107.88  3.000
 AFE  H23   C23  C22   107.72  3.000
 AFE  C24   C23  C22   109.49  3.000
 AFE  H23   C23  O9    110.79  3.000
 AFE  C24   C23  O9    108.97  3.000
 AFE  C22   C23  O9    111.91  3.000
 AFE  H22   C22  C21   108.10  3.000
 AFE  H22   C22  O22   111.13  3.000
 AFE  C21   C22  O22   109.65  3.000
 AFE  H22   C22  C23   109.37  3.000
 AFE  C21   C22  C23   110.47  3.000
 AFE  O22   C22  C23   108.11  3.000
 AFE  HO22  O22  C22   108.65  3.000
 AFE  H24   C24  C25   109.00  3.000
 AFE  H24   C24  O61   111.08  3.000
 AFE  C25   C24  O61   110.27  3.000
 AFE  H24   C24  C23   109.20  3.000
 AFE  C25   C24  C23   109.14  3.000
 AFE  O61   C24  C23   108.13  3.000
 AFE  HO61  O61  C24   108.64  3.000
 AFE  H25   C25  O7    109.97  3.000
 AFE  H25   C25  C51   108.64  3.000
 AFE  O7    C25  C51   106.58  3.000
 AFE  H25   C25  C24   107.60  3.000
 AFE  C51   C25  C24   112.67  3.000
 AFE  O7    C25  C24   111.36  3.000
 AFE  H511  C51  H513  108.51  3.000
 AFE  H511  C51  H512  108.49  3.000
 AFE  H513  C51  H512  106.91  3.000
 AFE  H511  C51  C25   111.49  3.000
 AFE  H513  C51  C25   110.51  3.000
 AFE  H512  C51  C25   110.79  3.000
 AFE  C21   O7   C25   117.31  3.000
 AFE  H21   C21  O8    109.64  3.000
 AFE  H21   C21  O7    105.36  3.000
 AFE  O8    C21  O7    112.09  3.000
 AFE  H21   C21  C22   109.52  3.000
 AFE  O8    C21  C22   106.97  3.000
 AFE  O7    C21  C22   113.23  3.000
 AFE  C3    O8   C21   114.56  3.000
 AFE  C2    C3   C4    120.59  3.000
 AFE  C2    C3   O8    120.94  3.000
 AFE  C4    C3   O8    118.46  3.000
 AFE  C10   C4   O2    122.57  3.000
 AFE  C10   C4   C3    115.25  3.000
 AFE  O2    C4   C3    122.16  3.000
 AFE  O1    C2   C11   112.55  3.000
 AFE  O1    C2   C3    121.66  3.000
 AFE  C11   C2   C3    125.80  3.000
 AFE  C16   C11  C12   118.77  3.000
 AFE  C16   C11  C2    120.14  3.000
 AFE  C12   C11  C2    121.09  3.000
 AFE  H12   C12  C13   118.83  3.000
 AFE  H12   C12  C11   120.40  3.000
 AFE  C13   C12  C11   120.76  3.000
 AFE  H13   C13  C14   120.42  3.000
 AFE  H13   C13  C12   119.55  3.000
 AFE  C14   C13  C12   120.02  3.000
 AFE  C15   C14  O5    117.68  3.000
 AFE  C15   C14  C13   119.60  3.000
 AFE  O5    C14  C13   122.73  3.000
 AFE  HO5   O5   C14   110.79  3.000
 AFE  H15   C15  C16   120.25  3.000
 AFE  H15   C15  C14   119.78  3.000
 AFE  C16   C15  C14   119.98  3.000
 AFE  H16   C16  C15   118.72  3.000
 AFE  H16   C16  C11   120.41  3.000
 AFE  C15   C16  C11   120.85  3.000
 AFE  C9    O1   C2    121.84  3.000
 AFE  C10   C9   C8    122.74  3.000
 AFE  C8    C9   O1    117.12  3.000
 AFE  C10   C9   O1    120.14  3.000
 AFE  H8    C8   C7    121.68  3.000
 AFE  H8    C8   C9    120.55  3.000
 AFE  C7    C8   C9    117.77  3.000
 AFE  C6    C7   O4    116.62  3.000
 AFE  O4    C7   C8    121.85  3.000
 AFE  C6    C7   C8    121.53  3.000
 AFE  HO4   O4   C7    111.02  3.000
 AFE  H6    C6   C5    120.16  3.000
 AFE  H6    C6   C7    120.06  3.000
 AFE  C5    C6   C7    119.77  3.000
 AFE  O3    C5   C10   120.41  3.000
 AFE  C10   C5   C6    120.11  3.000
 AFE  O3    C5   C6    119.49  3.000
 AFE  C5    C10  C9    118.09  3.000
 AFE  C9    C10  C4    120.33  3.000
 AFE  C5    C10  C4    121.58  3.000
 AFE  HO3   O3   C5    107.67  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
 AFE  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 AFE  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 AFE  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 AFE  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 AFE  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 AFE  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 AFE  CONST_07  C6   C5   C10  C9      0.00   0.0  0
 AFE  CONST_08  C6   C7   C8   C9      0.00   0.0  0
 AFE  CONST_09  C5   C10  C9   C8      0.00   0.0  0
 AFE  CONST_10  C5   C6   C7   C8      0.00   0.0  0
 AFE  CONST_11  C10  C5   C6   C7      0.00   0.0  0
 AFE  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 AFE  CONST_13  C13  C12  C11  C2    180.00   0.0  0
 AFE  CONST_14  C15  C16  C11  C2    180.00   0.0  0
 AFE  CONST_15  O3   C5   C10  C4      0.00   0.0  0
 AFE  CONST_16  O5   C14  C13  C12   180.00   0.0  0
 AFE  CONST_17  C16  C15  C14  O5    180.00   0.0  0
 AFE  CONST_18  O3   C5   C10  C9    180.00   0.0  0
 AFE  CONST_19  O4   C7   C8   C9    180.00   0.0  0
 AFE  CONST_20  O3   C5   C6   C7    180.00   0.0  0
 AFE  CONST_21  C5   C6   C7   O4    180.00   0.0  0
 AFE  CONST_22  H12  C12  C11  C2      0.00   0.0  0
 AFE  CONST_23  H16  C16  C11  C2      0.00   0.0  0
 AFE  CONST_24  H13  C13  C12  C11   180.00   0.0  0
 AFE  CONST_25  H15  C15  C16  C11   180.00   0.0  0
 AFE  CONST_26  H8   C8   C9   O1      0.00   0.0  0
 AFE  CONST_27  H6   C6   C7   C8    180.00   0.0  0
 AFE  Var_01    C5   C10  C4   C3   -177.28  30.0  1
 AFE  Var_02    C12  C11  C2   C3     47.57  30.0  2
 AFE  Var_03    C11  C2   C3   C4   -176.62  30.0  1
 AFE  Var_04    C10  C4   C3   C2     -4.54  30.0  1
 AFE  Var_05    C10  C9   O1   C2     -3.45  30.0  1
 AFE  Var_06    C4   C3   O8   C21   -73.41  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
 AFE  chir_01  C23  O9   C22  C24  negativ
 AFE  chir_02  C22  O22  C21  C23  negativ
 AFE  chir_03  C24  O61  C23  C25  positiv
 AFE  chir_04  C25  O7   C24  C51  positiv
 AFE  chir_05  C21  O7   O8   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
 AFE  plan-1  C2   0.020
 AFE  plan-1  C11  0.020
 AFE  plan-1  C12  0.020
 AFE  plan-1  C13  0.020
 AFE  plan-1  C14  0.020
 AFE  plan-1  O5   0.020
 AFE  plan-1  C15  0.020
 AFE  plan-1  C16  0.020
 AFE  plan-1  H12  0.020
 AFE  plan-1  H13  0.020
 AFE  plan-1  H15  0.020
 AFE  plan-1  H16  0.020
 AFE  plan-2  C4   0.020
 AFE  plan-2  O1   0.020
 AFE  plan-2  C9   0.020
 AFE  plan-2  C8   0.020
 AFE  plan-2  C7   0.020
 AFE  plan-2  O4   0.020
 AFE  plan-2  C6   0.020
 AFE  plan-2  C5   0.020
 AFE  plan-2  C10  0.020
 AFE  plan-2  O3   0.020
 AFE  plan-2  H8   0.020
 AFE  plan-2  H6   0.020
 AFE  plan-3  C3   0.020
 AFE  plan-3  C4   0.020
 AFE  plan-3  O2   0.020
 AFE  plan-3  C10  0.020

