# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:32:31 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-O-decanoyl-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)OC[C@H]1O[C@H](O)[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
 U2D  U2D  6-O-decanoyl-alpha-D-glucopyranose  D-saccharide  53  23  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U2D
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
 U2D  C1   C  CH1   0   0.261  -28.4154  11.2054  28.8602
 U2D  C2   C  CH1   0  -0.020  -29.0131   9.8227  28.5683
 U2D  C3   C  CH1   0   0.026  -30.5352   9.9364  28.4392
 U2D  C4   C  CH1   0  -0.026  -31.0491  11.1175  29.2546
 U2D  C5   C  CH1   0  -0.033  -30.4474  12.4032  28.6719
 U2D  C6   C  CH2   0  -0.197  -30.4686  13.5437  29.6791
 U2D  CAX  C  C     0   0.585  -30.8137  15.4624  28.3271
 U2D  CAY  C  CH2   0  -0.568  -30.1254  16.6221  27.6550
 U2D  CAZ  C  CH2   0  -0.440  -30.5549  16.8321  26.2009
 U2D  CBA  C  CH2   0  -0.415  -29.9099  15.8819  25.1928
 U2D  CBB  C  CH2   0  -0.440  -30.1844  14.4023  25.4341
 U2D  CBC  C  CH2   0  -0.407  -29.6748  13.4925  24.3227
 U2D  CBD  C  CH2   0  -0.447  -29.9627  12.0203  24.6027
 U2D  CBE  C  CH2   0  -0.420  -29.3850  11.0581  23.5676
 U2D  CBF  C  CH2   0  -0.433  -29.8940  11.2534  22.1412
 U2D  CBG  C  CH3   0  -0.665  -31.4012  11.0822  21.9991
 U2D  O11  O  O     0  -0.450  -31.9906  15.2193  28.2250
 U2D  O2   O  OH1   0  -0.666  -28.5329   9.2558  27.3767
 U2D  O3   O  OH1   0  -0.673  -31.2081   8.7834  28.8859
 U2D  O4   O  OH1   0  -0.664  -32.4438  11.2508  29.1821
 U2D  O5   O  O2    0  -0.500  -29.1385  12.2037  28.1750
 U2D  O6   O  O2    0  -0.459  -29.9803  14.7444  29.0783
 U2D  H1   H  HCH1  0   0.201  -28.4765  11.3890  29.9450
 U2D  H2   H  HCH1  0   0.218  -28.7868   9.1828  29.4343
 U2D  H3   H  HCH1  0   0.226  -30.7667  10.1356  27.3822
 U2D  H4   H  HCH1  0   0.221  -30.7324  10.9873  30.3029
 U2D  H5   H  HCH1  0   0.262  -31.0578  12.6736  27.8037
 U2D  H61  H  HCH2  0   0.257  -29.7898  13.3387  30.5080
 U2D  H62  H  HCH2  0   0.252  -31.4712  13.6799  30.0871
 U2D  H64  H  HCH2  0   0.257  -29.0415  16.5189  27.7287
 U2D  HAY  H  HCH2  0   0.286  -30.3923  17.5115  28.2351
 U2D  H65  H  HCH2  0   0.241  -30.2953  17.8557  25.9238
 U2D  HAZ  H  HCH2  0   0.228  -31.6436  16.7670  26.1313
 U2D  H66  H  HCH2  0   0.212  -28.8274  16.0483  25.1801
 U2D  HBA  H  HCH2  0   0.221  -30.2695  16.1550  24.1959
 U2D  HBB  H  HCH2  0   0.208  -31.2610  14.2436  25.5605
 U2D  H67  H  HCH2  0   0.221  -29.7121  14.0874  26.3686
 U2D  HBC  H  HCH2  0   0.204  -28.5951  13.6353  24.1962
 U2D  H68  H  HCH2  0   0.210  -30.1331  13.7941  23.3749
 U2D  H69  H  HCH2  0   0.204  -31.0457  11.8775  24.6844
 U2D  HBD  H  HCH2  0   0.238  -29.5561  11.7561  25.5836
 U2D  HBE  H  HCH2  0   0.212  -29.6019  10.0320  23.8832
 U2D  H7A  H  HCH2  0   0.211  -28.2938  11.1502  23.5721
 U2D  H7B  H  HCH2  0   0.220  -29.3900  10.5345  21.4894
 U2D  HBF  H  HCH2  0   0.213  -29.6048  12.2415  21.7717
 U2D  H7G  H  HCH3  0   0.225  -31.7098  11.1521  20.9552
 U2D  H7C  H  HCH3  0   0.214  -31.7236  10.1086  22.3742
 U2D  HBG  H  HCH3  0   0.219  -31.9519  11.8453  22.5511
 U2D  HO2  H  HOH1  0   0.450  -27.5725   9.2107  27.4259
 U2D  HO3  H  HOH1  0   0.459  -31.1060   8.0904  28.2269
 U2D  HO4  H  HOH1  0   0.454  -32.8374  10.4317  29.5013
 U2D  O1   O  OH1   0  -0.661  -27.1089  11.2307  28.4276
 U2D  HO1  H  HOH1  0   0.470  -26.6369  11.9489  28.8619

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
 U2D  CBG  CBF  single  1.523  0.020  1.523
 U2D  CBF  CBE  single  1.527  0.020  1.527
 U2D  CBE  CBD  single  1.527  0.020  1.527
 U2D  CBD  CBC  single  1.526  0.020  1.526
 U2D  CBC  CBB  single  1.524  0.020  1.524
 U2D  CBB  CBA  single  1.524  0.020  1.524
 U2D  CBA  CAZ  single  1.528  0.020  1.528
 U2D  CAZ  CAY  single  1.531  0.020  1.531
 U2D  CAY  CAX  single  1.507  0.020  1.507
 U2D  O11  CAX  double  1.206  0.020  1.206
 U2D  CAX  O6   single  1.332  0.020  1.332
 U2D  O6   C6   single  1.429  0.020  1.429
 U2D  C6   C5   single  1.522  0.020  1.522
 U2D  C5   O5   single  1.414  0.020  1.414
 U2D  C5   C4   single  1.534  0.020  1.534
 U2D  O4   C4   single  1.403  0.020  1.403
 U2D  O5   C1   single  1.410  0.020  1.410
 U2D  C4   C3   single  1.524  0.020  1.524
 U2D  C3   O3   single  1.408  0.020  1.408
 U2D  C3   C2   single  1.532  0.020  1.532
 U2D  C1   C2   single  1.534  0.020  1.534
 U2D  O2   C2   single  1.404  0.020  1.404
 U2D  C1   H1   single  0.970  0.020  1.090
 U2D  C2   H2   single  0.970  0.020  1.090
 U2D  C3   H3   single  0.970  0.020  1.090
 U2D  C4   H4   single  0.970  0.020  1.090
 U2D  C5   H5   single  0.970  0.020  1.090
 U2D  C6   H61  single  0.970  0.020  1.090
 U2D  C6   H62  single  0.970  0.020  1.090
 U2D  CAY  H64  single  0.970  0.020  1.090
 U2D  CAY  HAY  single  0.970  0.020  1.090
 U2D  CAZ  H65  single  0.970  0.020  1.090
 U2D  CAZ  HAZ  single  0.970  0.020  1.090
 U2D  CBA  H66  single  0.970  0.020  1.090
 U2D  CBA  HBA  single  0.970  0.020  1.090
 U2D  CBB  HBB  single  0.970  0.020  1.090
 U2D  CBB  H67  single  0.970  0.020  1.090
 U2D  CBC  HBC  single  0.970  0.020  1.090
 U2D  CBC  H68  single  0.970  0.020  1.090
 U2D  CBD  H69  single  0.970  0.020  1.090
 U2D  CBD  HBD  single  0.970  0.020  1.090
 U2D  CBE  HBE  single  0.970  0.020  1.090
 U2D  CBE  H7A  single  0.970  0.020  1.090
 U2D  CBF  H7B  single  0.970  0.020  1.090
 U2D  CBF  HBF  single  0.970  0.020  1.090
 U2D  CBG  H7G  single  0.970  0.020  1.090
 U2D  CBG  H7C  single  0.970  0.020  1.090
 U2D  CBG  HBG  single  0.970  0.020  1.090
 U2D  O2   HO2  single  0.850  0.020  0.980
 U2D  O3   HO3  single  0.850  0.020  0.980
 U2D  O4   HO4  single  0.850  0.020  0.980
 U2D  C1   O1   single  1.377  0.020  1.377
 U2D  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
 U2D  O1   C1   H1   111.03  3.000
 U2D  O1   C1   O5   108.72  3.000
 U2D  H1   C1   O5   109.39  3.000
 U2D  O1   C1   C2   109.06  3.000
 U2D  H1   C1   C2   108.41  3.000
 U2D  O5   C1   C2   110.23  3.000
 U2D  H2   C2   O2   111.27  3.000
 U2D  H2   C2   C3   108.29  3.000
 U2D  O2   C2   C3   107.35  3.000
 U2D  H2   C2   C1   107.12  3.000
 U2D  O2   C2   C1   113.08  3.000
 U2D  C3   C2   C1   109.65  3.000
 U2D  H3   C3   O3   110.64  3.000
 U2D  H3   C3   C4   107.62  3.000
 U2D  O3   C3   C4   107.68  3.000
 U2D  H3   C3   C2   107.67  3.000
 U2D  O3   C3   C2   112.79  3.000
 U2D  C4   C3   C2   110.33  3.000
 U2D  H4   C4   O4   110.24  3.000
 U2D  H4   C4   C5   110.32  3.000
 U2D  O4   C4   C5   106.89  3.000
 U2D  H4   C4   C3   108.67  3.000
 U2D  O4   C4   C3   112.40  3.000
 U2D  C5   C4   C3   108.29  3.000
 U2D  H5   C5   O5   105.79  3.000
 U2D  H5   C5   C6   109.39  3.000
 U2D  O5   C5   C6   110.56  3.000
 U2D  H5   C5   C4   106.82  3.000
 U2D  O5   C5   C4   112.22  3.000
 U2D  C6   C5   C4   111.79  3.000
 U2D  H62  C6   H61  108.13  3.000
 U2D  H62  C6   O6   111.49  3.000
 U2D  H61  C6   O6   105.35  3.000
 U2D  H62  C6   C5   110.73  3.000
 U2D  H61  C6   C5   110.70  3.000
 U2D  O6   C6   C5   110.29  3.000
 U2D  O6   CAX  O11  123.34  3.000
 U2D  O6   CAX  CAY  112.37  3.000
 U2D  O11  CAX  CAY  124.27  3.000
 U2D  HAY  CAY  H64  106.45  3.000
 U2D  HAY  CAY  CAZ  108.87  3.000
 U2D  H64  CAY  CAZ  110.85  3.000
 U2D  HAY  CAY  CAX  106.12  3.000
 U2D  H64  CAY  CAX  110.53  3.000
 U2D  CAZ  CAY  CAX  113.65  3.000
 U2D  HAZ  CAZ  H65  106.05  3.000
 U2D  HAZ  CAZ  CBA  109.97  3.000
 U2D  H65  CAZ  CBA  108.37  3.000
 U2D  HAZ  CAZ  CAY  109.38  3.000
 U2D  H65  CAZ  CAY  107.64  3.000
 U2D  CBA  CAZ  CAY  115.02  3.000
 U2D  HBA  CBA  H66  106.04  3.000
 U2D  HBA  CBA  CBB  109.10  3.000
 U2D  H66  CBA  CBB  109.11  3.000
 U2D  HBA  CBA  CAZ  107.88  3.000
 U2D  H66  CBA  CAZ  109.29  3.000
 U2D  CBB  CBA  CAZ  115.04  3.000
 U2D  H67  CBB  HBB  106.50  3.000
 U2D  H67  CBB  CBC  107.88  3.000
 U2D  HBB  CBB  CBC  109.04  3.000
 U2D  H67  CBB  CBA  109.70  3.000
 U2D  HBB  CBB  CBA  109.62  3.000
 U2D  CBC  CBB  CBA  113.83  3.000
 U2D  H68  CBC  HBC  106.04  3.000
 U2D  H68  CBC  CBD  110.21  3.000
 U2D  HBC  CBC  CBD  109.43  3.000
 U2D  H68  CBC  CBB  109.08  3.000
 U2D  HBC  CBC  CBB  109.61  3.000
 U2D  CBD  CBC  CBB  112.28  3.000
 U2D  HBD  CBD  H69  105.60  3.000
 U2D  HBD  CBD  CBE  108.36  3.000
 U2D  H69  CBD  CBE  110.03  3.000
 U2D  HBD  CBD  CBC  109.11  3.000
 U2D  H69  CBD  CBC  109.03  3.000
 U2D  CBE  CBD  CBC  114.35  3.000
 U2D  H7A  CBE  HBE  105.96  3.000
 U2D  H7A  CBE  CBF  108.98  3.000
 U2D  HBE  CBE  CBF  108.85  3.000
 U2D  H7A  CBE  CBD  108.74  3.000
 U2D  HBE  CBE  CBD  108.67  3.000
 U2D  CBF  CBE  CBD  115.24  3.000
 U2D  HBF  CBF  H7B  105.71  3.000
 U2D  HBF  CBF  CBG  109.37  3.000
 U2D  H7B  CBF  CBG  109.06  3.000
 U2D  HBF  CBF  CBE  110.06  3.000
 U2D  H7B  CBF  CBE  108.60  3.000
 U2D  CBG  CBF  CBE  113.73  3.000
 U2D  HBG  CBG  H7C  107.51  3.000
 U2D  HBG  CBG  H7G  107.25  3.000
 U2D  H7C  CBG  H7G  107.60  3.000
 U2D  HBG  CBG  CBF  111.93  3.000
 U2D  H7C  CBG  CBF  111.12  3.000
 U2D  H7G  CBG  CBF  111.22  3.000
 U2D  HO2  O2   C2   108.46  3.000
 U2D  HO3  O3   C3   108.79  3.000
 U2D  HO4  O4   C4   107.95  3.000
 U2D  C5   O5   C1   113.81  3.000
 U2D  CAX  O6   C6   118.45  3.000
 U2D  HO1  O1   C1   109.71  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
 U2D  Var_01  CAY  CAX  O6   C6   -174.44  30.0  1
 U2D  Var_02  CBA  CAZ  CAY  CAX   -78.80  30.0  1
 U2D  Var_03  CBB  CBA  CAZ  CAY    59.88  30.0  2
 U2D  Var_04  CBC  CBB  CBA  CAZ   172.90  30.0  1
 U2D  Var_05  CBD  CBC  CBB  CBA   179.76  30.0  1
 U2D  Var_06  CBE  CBD  CBC  CBB  -175.87  30.0  1
 U2D  Var_07  CBF  CBE  CBD  CBC   -60.34  30.0  2
 U2D  Var_08  CBG  CBF  CBE  CBD   -60.17  30.0  1
 U2D  Var_09  H61  C6   O6   CAX  -159.28  30.0  3
 U2D  Var_10  H7G  CBG  CBF  CBE  -175.52  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
 U2D  chir_01  C1  O5  C2  O1  negativ
 U2D  chir_02  C2  O2  C1  C3  negativ
 U2D  chir_03  C3  O3  C2  C4  positiv
 U2D  chir_04  C4  O4  C3  C5  negativ
 U2D  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
 U2D  plan-1  CAX  0.020
 U2D  plan-1  CAY  0.020
 U2D  plan-1  O11  0.020
 U2D  plan-1  O6   0.020

