# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:25:19 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-O-octanoyl-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)O[C@@H]1[C@@H](O)[C@@H](O)O[C@H](CO)[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
 TU4  TU4  3-O-octanoyl-alpha-D-glucopyranose  D-saccharide  47  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TU4
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
 TU4  C13  C  C     0   0.606  5.0819  44.3288   -6.4294
 TU4  C7   C  CH2   0  -0.591  5.1569  44.1178   -4.9422
 TU4  C8   C  CH2   0  -0.418  4.9255  45.3828   -4.1309
 TU4  C9   C  CH2   0  -0.412  5.0636  45.1320   -2.6350
 TU4  C10  C  CH2   0  -0.417  4.7898  46.3755   -1.7985
 TU4  C11  C  CH2   0  -0.418  4.9647  46.1326   -0.3042
 TU4  C12  C  CH2   0  -0.425  4.7397  47.3673    0.5651
 TU4  C1   C  CH1   0   0.251  3.9628  42.0075  -10.4872
 TU4  C2   C  CH1   0  -0.023  3.8443  42.2354   -8.9762
 TU4  C3   C  CH1   0  -0.024  4.9883  43.1166   -8.4951
 TU4  C4   C  CH1   0   0.021  6.3219  42.5198   -8.9085
 TU4  C5   C  CH1   0  -0.011  6.3208  42.3310  -10.4310
 TU4  O2   O  OH1   0  -0.670  2.5867  42.8174   -8.7448
 TU4  O3   O  O2    0  -0.482  4.9269  43.1668   -7.0682
 TU4  O4   O  OH1   0  -0.665  7.3431  43.3948   -8.5004
 TU4  O5   O  O2    0  -0.499  5.2183  41.5209  -10.8183
 TU4  C31  C  CH3   0  -0.667  3.3151  47.9057    0.5182
 TU4  O7   O  O     0  -0.445  5.1558  45.3964   -6.9800
 TU4  H13  H  HCH2  0   0.266  4.4486  43.3372   -4.6532
 TU4  H14  H  HCH2  0   0.277  6.1501  43.7067   -4.7264
 TU4  H15  H  HCH2  0   0.225  5.6345  46.1570   -4.4341
 TU4  H16  H  HCH2  0   0.224  3.9273  45.7759   -4.3437
 TU4  H17  H  HCH2  0   0.212  4.3779  44.3334   -2.3310
 TU4  H6   H  HCH2  0   0.212  6.0723  44.7620   -2.4213
 TU4  H7   H  HCH2  0   0.207  5.4600  47.1833   -2.1144
 TU4  H8   H  HCH2  0   0.215  3.7743  46.7258   -2.0070
 TU4  H9   H  HCH2  0   0.206  4.2824  45.3369    0.0158
 TU4  H10  H  HCH2  0   0.216  5.9757  45.7527   -0.1254
 TU4  H11  H  HCH2  0   0.220  4.9915  47.1188    1.5998
 TU4  H12  H  HCH2  0   0.209  5.4393  48.1541    0.2655
 TU4  H1   H  HCH1  0   0.236  3.2533  41.2230  -10.7821
 TU4  H2   H  HCH1  0   0.238  3.9237  41.2533   -8.4906
 TU4  H3   H  HCH1  0   0.257  4.8813  44.1219   -8.9110
 TU4  H4   H  HCH1  0   0.234  6.4271  41.5385   -8.4286
 TU4  H5   H  HCH1  0   0.238  6.2626  43.3197  -10.9048
 TU4  HO2  H  HOH1  0   0.463  2.3973  42.8050   -7.8017
 TU4  HO4  H  HOH1  0   0.461  8.1442  42.8851   -8.3505
 TU4  HO6  H  HOH1  0   0.460  8.6215  40.0809  -10.6050
 TU4  H34  H  HCH3  0   0.227  3.1834  48.7349    1.2142
 TU4  H35  H  HCH3  0   0.220  3.0468  48.2701   -0.4740
 TU4  H36  H  HCH3  0   0.214  2.5949  47.1307    0.7896
 TU4  O1   O  OH1   0  -0.667  3.7354  43.1832  -11.2101
 TU4  HO1  H  HOH1  0   0.458  2.9204  43.5918  -10.8958
 TU4  C6   C  CH2   0  -0.197  7.5791  41.6743  -10.9554
 TU4  O6   O  OH1   0  -0.672  7.7859  40.4458  -10.3010
 TU4  H61  H  HCH2  0   0.223  7.4781  41.5489  -12.0411
 TU4  H62  H  HCH2  0   0.210  8.4124  42.3699  -10.7993

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
 TU4  C6   C5   single  1.513  0.020  1.513
 TU4  C6   O6   single  1.407  0.020  1.407
 TU4  O5   C5   single  1.422  0.020  1.422
 TU4  O5   C1   single  1.387  0.020  1.387
 TU4  C5   C4   single  1.534  0.020  1.534
 TU4  C1   C2   single  1.533  0.020  1.533
 TU4  C4   O4   single  1.405  0.020  1.405
 TU4  C4   C3   single  1.518  0.020  1.518
 TU4  C2   C3   single  1.522  0.020  1.522
 TU4  C2   O2   single  1.405  0.020  1.405
 TU4  C3   O3   single  1.429  0.020  1.429
 TU4  O3   C13  single  1.335  0.020  1.335
 TU4  O7   C13  double  1.204  0.020  1.204
 TU4  C13  C7   single  1.504  0.020  1.504
 TU4  C7   C8   single  1.521  0.020  1.521
 TU4  C8   C9   single  1.523  0.020  1.523
 TU4  C9   C10  single  1.524  0.020  1.524
 TU4  C10  C11  single  1.524  0.020  1.524
 TU4  C11  C12  single  1.527  0.020  1.527
 TU4  C12  C31  single  1.524  0.020  1.524
 TU4  C7   H13  single  0.970  0.020  1.090
 TU4  C7   H14  single  0.970  0.020  1.090
 TU4  C8   H15  single  0.970  0.020  1.090
 TU4  C8   H16  single  0.970  0.020  1.090
 TU4  C9   H17  single  0.970  0.020  1.090
 TU4  C9   H6   single  0.970  0.020  1.090
 TU4  C10  H7   single  0.970  0.020  1.090
 TU4  C10  H8   single  0.970  0.020  1.090
 TU4  C11  H9   single  0.970  0.020  1.090
 TU4  C11  H10  single  0.970  0.020  1.090
 TU4  C12  H11  single  0.970  0.020  1.090
 TU4  C12  H12  single  0.970  0.020  1.090
 TU4  C1   H1   single  0.970  0.020  1.090
 TU4  C2   H2   single  0.970  0.020  1.090
 TU4  C3   H3   single  0.970  0.020  1.090
 TU4  C4   H4   single  0.970  0.020  1.090
 TU4  C5   H5   single  0.970  0.020  1.090
 TU4  O2   HO2  single  0.850  0.020  0.980
 TU4  O4   HO4  single  0.850  0.020  0.980
 TU4  C6   H61  single  0.970  0.020  1.090
 TU4  C6   H62  single  0.970  0.020  1.090
 TU4  O6   HO6  single  0.850  0.020  0.980
 TU4  C31  H34  single  0.970  0.020  1.090
 TU4  C31  H35  single  0.970  0.020  1.090
 TU4  C31  H36  single  0.970  0.020  1.090
 TU4  C1   O1   single  1.399  0.020  1.399
 TU4  O1   HO1  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
 TU4  O7   C13  O3   124.07  3.000
 TU4  O7   C13  C7   125.02  3.000
 TU4  O3   C13  C7   110.90  3.000
 TU4  H14  C7   H13  105.50  3.000
 TU4  H14  C7   C8   110.17  3.000
 TU4  H13  C7   C8   110.76  3.000
 TU4  H14  C7   C13  107.01  3.000
 TU4  H13  C7   C13  109.23  3.000
 TU4  C8   C7   C13  113.78  3.000
 TU4  H16  C8   H15  106.48  3.000
 TU4  H16  C8   C9   109.45  3.000
 TU4  H15  C8   C9   109.29  3.000
 TU4  H16  C8   C7   109.51  3.000
 TU4  H15  C8   C7   110.04  3.000
 TU4  C9   C8   C7   111.91  3.000
 TU4  H6   C9   H17  106.02  3.000
 TU4  H6   C9   C10  109.51  3.000
 TU4  H17  C9   C10  109.28  3.000
 TU4  H6   C9   C8   109.31  3.000
 TU4  H17  C9   C8   109.63  3.000
 TU4  C10  C9   C8   112.87  3.000
 TU4  H8   C10  H7   106.05  3.000
 TU4  H8   C10  C11  110.14  3.000
 TU4  H7   C10  C11  109.26  3.000
 TU4  H8   C10  C9   108.87  3.000
 TU4  H7   C10  C9   109.48  3.000
 TU4  C11  C10  C9   112.81  3.000
 TU4  H10  C11  H9   105.98  3.000
 TU4  H10  C11  C12  108.89  3.000
 TU4  H9   C11  C12  109.22  3.000
 TU4  H10  C11  C10  108.75  3.000
 TU4  H9   C11  C10  109.31  3.000
 TU4  C12  C11  C10  114.36  3.000
 TU4  H12  C12  H11  105.97  3.000
 TU4  H12  C12  C31  109.58  3.000
 TU4  H11  C12  C31  108.95  3.000
 TU4  H12  C12  C11  109.34  3.000
 TU4  H11  C12  C11  108.73  3.000
 TU4  C31  C12  C11  113.95  3.000
 TU4  O1   C1   H1   110.90  3.000
 TU4  O1   C1   O5   108.59  3.000
 TU4  H1   C1   O5   105.68  3.000
 TU4  O1   C1   C2   111.83  3.000
 TU4  H1   C1   C2   108.73  3.000
 TU4  O5   C1   C2   110.95  3.000
 TU4  H2   C2   O2   111.23  3.000
 TU4  H2   C2   C3   108.88  3.000
 TU4  O2   C2   C3   112.39  3.000
 TU4  H2   C2   C1   107.29  3.000
 TU4  O2   C2   C1   107.05  3.000
 TU4  C3   C2   C1   109.86  3.000
 TU4  H3   C3   O3   110.08  3.000
 TU4  H3   C3   C4   110.11  3.000
 TU4  O3   C3   C4   108.87  3.000
 TU4  H3   C3   C2   109.79  3.000
 TU4  O3   C3   C2   107.68  3.000
 TU4  C4   C3   C2   110.27  3.000
 TU4  H4   C4   O4   111.11  3.000
 TU4  H4   C4   C5   108.90  3.000
 TU4  O4   C4   C5   111.43  3.000
 TU4  H4   C4   C3   108.45  3.000
 TU4  O4   C4   C3   108.33  3.000
 TU4  C5   C4   C3   108.54  3.000
 TU4  H5   C5   C6   106.58  3.000
 TU4  H5   C5   O5   110.76  3.000
 TU4  C6   C5   O5   107.65  3.000
 TU4  H5   C5   C4   108.51  3.000
 TU4  O5   C5   C4   109.93  3.000
 TU4  C6   C5   C4   113.37  3.000
 TU4  HO2  O2   C2   109.42  3.000
 TU4  C3   O3   C13  120.22  3.000
 TU4  HO4  O4   C4   108.70  3.000
 TU4  C5   O5   C1   115.92  3.000
 TU4  H36  C31  H35  107.52  3.000
 TU4  H36  C31  H34  107.54  3.000
 TU4  H35  C31  H34  107.27  3.000
 TU4  H36  C31  C12  110.99  3.000
 TU4  H35  C31  C12  112.09  3.000
 TU4  H34  C31  C12  111.22  3.000
 TU4  HO1  O1   C1   108.97  3.000
 TU4  H62  C6   H61  106.45  3.000
 TU4  H62  C6   O6   112.08  3.000
 TU4  H61  C6   O6   111.95  3.000
 TU4  H62  C6   C5   107.90  3.000
 TU4  H61  C6   C5   108.41  3.000
 TU4  O6   C6   C5   109.88  3.000
 TU4  HO6  O6   C6   108.19  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
 TU4  Var_01  O7   C13  O3   C3      7.04  30.0  3
 TU4  Var_02  C9   C8   C7   C13  -177.82  30.0  3
 TU4  Var_03  C10  C9   C8   C7   -178.07  30.0  3
 TU4  Var_04  O3   C13  C7   C8   -163.09  30.0  2
 TU4  Var_05  C11  C10  C9   C8   -178.46  30.0  3
 TU4  Var_06  C12  C11  C10  C9    178.25  30.0  3
 TU4  Var_07  C31  C12  C11  C10    64.28  30.0  3
 TU4  Var_08  H34  C31  C12  C11   175.40  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
 TU4  chir_01  C1  O5  C2  O1  negativ
 TU4  chir_02  C2  O2  C1  C3  negativ
 TU4  chir_03  C3  O3  C4  C2  negativ
 TU4  chir_04  C4  O4  C5  C3  positiv
 TU4  chir_05  C5  O5  C4  C6  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
 TU4  plan-1  C13  0.020
 TU4  plan-1  C7   0.020
 TU4  plan-1  O3   0.020
 TU4  plan-1  O7   0.020

