# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:53:35 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2S,2'S,5S,5'S)-5,5'-bis(hydroxymethyl)octahydro-2H,2'H-2,2'-bipyran-5,5'-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(O)CC[C@H](OC1)[C@@H]2CC[C@](O)(CO)CO2
#
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
 88Q  88Q  (2S,2'S,5S,5'S)-5,5'-bis(hydroxymethyl)octahydro-2H,2'H-2,2'-bipyran-5,5'-diol  ligand  40  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_88Q
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
 88Q  O5    O  OH1   0  -0.679  -3.6460   2.3480   0.0936
 88Q  C11   C  CH2   0  -0.159  -3.2207   1.3094  -0.7653
 88Q  C10   C  CT    0   0.179  -3.3894  -0.0131  -0.0221
 88Q  C9    C  CH2   0  -0.474  -3.0557  -1.1905  -0.9331
 88Q  C8    C  CH2   0  -0.468  -1.5579  -1.2896  -1.2120
 88Q  O4    O  OH1   0  -0.683  -4.7347  -0.1617   0.3875
 88Q  C12   C  CH2   0  -0.201  -2.4744  -0.0889   1.2084
 88Q  O6    O  O2    0  -0.493  -1.1143  -0.1042   0.8504
 88Q  C7    C  CH1   0   0.050  -0.7671  -1.2421   0.0900
 88Q  C5    C  CH1   0   0.050   0.7380  -1.2512  -0.1176
 88Q  O3    O  O2    0  -0.493   1.0997  -0.1131  -0.8712
 88Q  C6    C  CH2   0  -0.202   2.4600  -0.1131  -1.2290
 88Q  C4    C  CH2   0  -0.468   1.5285  -1.3179   1.1836
 88Q  C3    C  CH2   0  -0.474   3.0275  -1.2350   0.9056
 88Q  C2    C  CT    0   0.179   3.3755  -0.0558   0.0022
 88Q  O2    O  OH1   0  -0.683   4.7190  -0.2170  -0.4078
 88Q  C1    C  CH2   0  -0.160   3.2216   1.2637   0.7539
 88Q  O1    O  OH1   0  -0.679   3.6554   2.3039  -0.0992
 88Q  H5    H  HOH1  0   0.462  -3.7111   3.1598  -0.4165
 88Q  H111  H  HCH2  0   0.211  -3.8294   1.2755  -1.6784
 88Q  H112  H  HCH2  0   0.206  -2.1787   1.4491  -1.0723
 88Q  H91C  H  HCH2  0   0.238  -3.3901  -2.1077  -0.4374
 88Q  H92C  H  HCH2  0   0.243  -3.6173  -1.1192  -1.8686
 88Q  H4    H  HOH1  0   0.442  -5.0231   0.6775   0.7653
 88Q  H121  H  HCH2  0   0.235  -2.6224   0.7712   1.8656
 88Q  H122  H  HCH2  0   0.208  -2.7379  -0.9912   1.7814
 88Q  H81C  H  HCH2  0   0.242  -1.3439  -2.2296  -1.7254
 88Q  H82C  H  HCH2  0   0.236  -1.2347  -0.4880  -1.8786
 88Q  H7    H  HCH1  0   0.206  -1.0088  -2.1534   0.6631
 88Q  HA    H  HCH1  0   0.206   0.9674  -2.1615  -0.6975
 88Q  H41C  H  HCH2  0   0.236   1.2154  -0.5172   1.8561
 88Q  H42C  H  HCH2  0   0.242   1.3027  -2.2593   1.6897
 88Q  H61C  H  HCH2  0   0.208   2.7119  -1.0155  -1.8068
 88Q  H62C  H  HCH2  0   0.235   2.6188   0.7484  -1.8820
 88Q  H31C  H  HCH2  0   0.243   3.5893  -1.1754   1.8418
 88Q  H32C  H  HCH2  0   0.238   3.3519  -2.1529   0.4044
 88Q  H2    H  HOH1  0   0.442   5.0165   0.6216  -0.7799
 88Q  H11C  H  HCH2  0   0.205   2.1817   1.4122   1.0639
 88Q  H12C  H  HCH2  0   0.212   3.8315   1.2184   1.6657
 88Q  H1    H  HOH1  0   0.462   3.7526   3.1057   0.4213

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
 88Q  O5   C11   single  1.413  0.020  1.413
 88Q  C11  C10   single  1.526  0.020  1.526
 88Q  C10  C9    single  1.526  0.020  1.526
 88Q  C10  O4    single  1.414  0.020  1.414
 88Q  C10  C12   single  1.535  0.020  1.535
 88Q  C9   C8    single  1.527  0.020  1.527
 88Q  C8   C7    single  1.524  0.020  1.524
 88Q  C12  O6    single  1.407  0.020  1.407
 88Q  O6   C7    single  1.412  0.020  1.412
 88Q  C7   C5    single  1.519  0.020  1.519
 88Q  C5   O3    single  1.412  0.020  1.412
 88Q  C5   C4    single  1.524  0.020  1.524
 88Q  O3   C6    single  1.407  0.020  1.407
 88Q  C6   C2    single  1.535  0.020  1.535
 88Q  C4   C3    single  1.527  0.020  1.527
 88Q  C3   C2    single  1.526  0.020  1.526
 88Q  C2   O2    single  1.414  0.020  1.414
 88Q  C2   C1    single  1.526  0.020  1.526
 88Q  C1   O1    single  1.413  0.020  1.413
 88Q  O5   H5    single  0.850  0.020  0.980
 88Q  C11  H111  single  0.970  0.020  1.090
 88Q  C11  H112  single  0.970  0.020  1.090
 88Q  C9   H91C  single  0.970  0.020  1.090
 88Q  C9   H92C  single  0.970  0.020  1.090
 88Q  O4   H4    single  0.850  0.020  0.980
 88Q  C12  H121  single  0.970  0.020  1.090
 88Q  C12  H122  single  0.970  0.020  1.090
 88Q  C8   H81C  single  0.970  0.020  1.090
 88Q  C8   H82C  single  0.970  0.020  1.090
 88Q  C7   H7    single  0.970  0.020  1.090
 88Q  C5   HA    single  0.970  0.020  1.090
 88Q  C4   H41C  single  0.970  0.020  1.090
 88Q  C4   H42C  single  0.970  0.020  1.090
 88Q  C6   H61C  single  0.970  0.020  1.090
 88Q  C6   H62C  single  0.970  0.020  1.090
 88Q  C3   H31C  single  0.970  0.020  1.090
 88Q  C3   H32C  single  0.970  0.020  1.090
 88Q  O2   H2    single  0.850  0.020  0.980
 88Q  C1   H11C  single  0.970  0.020  1.090
 88Q  C1   H12C  single  0.970  0.020  1.090
 88Q  O1   H1    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
 88Q  H5    O5   C11   108.58  3.000
 88Q  H112  C11  H111  107.35  3.000
 88Q  H112  C11  C10   110.62  3.000
 88Q  H111  C11  C10   108.47  3.000
 88Q  H112  C11  O5    111.28  3.000
 88Q  H111  C11  O5    111.18  3.000
 88Q  C10   C11  O5    107.91  3.000
 88Q  C12   C10  O4    109.25  3.000
 88Q  C12   C10  C9    108.06  3.000
 88Q  O4    C10  C9    107.46  3.000
 88Q  C12   C10  C11   111.54  3.000
 88Q  O4    C10  C11   109.71  3.000
 88Q  C9    C10  C11   110.71  3.000
 88Q  H92C  C9   H91C  106.56  3.000
 88Q  H92C  C9   C8    110.60  3.000
 88Q  H91C  C9   C8    109.15  3.000
 88Q  H92C  C9   C10   110.38  3.000
 88Q  H91C  C9   C10   108.02  3.000
 88Q  C8    C9   C10   111.95  3.000
 88Q  H82C  C8   H81C  106.68  3.000
 88Q  H82C  C8   C7    110.19  3.000
 88Q  H81C  C8   C7    109.07  3.000
 88Q  H82C  C8   C9    110.76  3.000
 88Q  H81C  C8   C9    109.51  3.000
 88Q  C7    C8   C9    110.54  3.000
 88Q  H4    O4   C10   107.85  3.000
 88Q  H122  C12  H121  107.44  3.000
 88Q  H122  C12  O6    110.80  3.000
 88Q  H121  C12  O6    107.02  3.000
 88Q  H122  C12  C10   108.36  3.000
 88Q  H121  C12  C10   111.25  3.000
 88Q  O6    C12  C10   111.89  3.000
 88Q  C7    O6   C12   112.56  3.000
 88Q  H7    C7   C5    106.44  3.000
 88Q  H7    C7   O6    109.39  3.000
 88Q  C5    C7   O6    108.78  3.000
 88Q  H7    C7   C8    107.72  3.000
 88Q  C5    C7   C8    113.40  3.000
 88Q  O6    C7   C8    110.95  3.000
 88Q  HA    C5   C4    107.75  3.000
 88Q  HA    C5   O3    109.34  3.000
 88Q  C4    C5   O3    110.98  3.000
 88Q  HA    C5   C7    106.42  3.000
 88Q  C4    C5   C7    113.42  3.000
 88Q  O3    C5   C7    108.77  3.000
 88Q  C6    O3   C5    112.55  3.000
 88Q  H62C  C6   H61C  107.42  3.000
 88Q  H62C  C6   C2    111.29  3.000
 88Q  H61C  C6   C2    108.36  3.000
 88Q  H62C  C6   O3    107.01  3.000
 88Q  H61C  C6   O3    110.78  3.000
 88Q  C2    C6   O3    111.88  3.000
 88Q  H42C  C4   H41C  106.71  3.000
 88Q  H42C  C4   C3    109.51  3.000
 88Q  H41C  C4   C3    110.73  3.000
 88Q  H42C  C4   C5    109.03  3.000
 88Q  H41C  C4   C5    110.19  3.000
 88Q  C3    C4   C5    110.58  3.000
 88Q  H32C  C3   H31C  106.58  3.000
 88Q  H32C  C3   C2    108.01  3.000
 88Q  H31C  C3   C2    110.34  3.000
 88Q  H32C  C3   C4    109.19  3.000
 88Q  H31C  C3   C4    110.58  3.000
 88Q  C2    C3   C4    111.94  3.000
 88Q  C1    C2   O2    109.70  3.000
 88Q  C1    C2   C3    110.70  3.000
 88Q  O2    C2   C3    107.48  3.000
 88Q  C1    C2   C6    111.53  3.000
 88Q  O2    C2   C6    109.26  3.000
 88Q  C3    C2   C6    108.06  3.000
 88Q  H2    O2   C2    107.80  3.000
 88Q  H12C  C1   H11C  107.33  3.000
 88Q  H12C  C1   O1    111.17  3.000
 88Q  H11C  C1   O1    111.25  3.000
 88Q  H12C  C1   C2    108.50  3.000
 88Q  H11C  C1   C2    110.63  3.000
 88Q  O1    C1   C2    107.94  3.000
 88Q  H1    O1   C1    108.56  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
 88Q  Var_01  C7  C8  C9  C10   50.55  30.0  1
 88Q  Var_02  C2  C6  O3  C5   -63.08  30.0  1
 88Q  Var_03  C2  C3  C4  C5    50.50  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
 88Q  chir_01  C10  C9  O4  C12  negativ
 88Q  chir_02  C7   O6  C5  C8   positiv
 88Q  chir_03  C5   O3  C4  C7   negativ
 88Q  chir_04  C2   C1  C3  C6   negativ

