# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:05:14 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCO[C@@H]1O[C@H](CO)[C@H](O)C[C@H]1O[C@@H]2O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]2O
#
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
 DA8  DA8  'octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside'  ligand  67  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DA8
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
 DA8  C16   C  CH2   0  -0.406   -7.1382   0.8036   0.2005
 DA8  C15   C  CH2   0  -0.411   -6.1217  -0.2542  -0.2110
 DA8  C14   C  CH2   0  -0.409   -4.7007   0.0903   0.2163
 DA8  C13   C  CH2   0  -0.420   -3.6661  -0.9410  -0.2168
 DA8  C12   C  CH2   0  -0.456   -2.2575  -0.5725   0.2328
 DA8  C11   C  CH2   0  -0.156   -1.2135  -1.5543  -0.2606
 DA8  O1    O  O2    0  -0.493    0.0497  -1.1618   0.2539
 DA8  C1    C  CH1   0   0.289    1.1467  -1.7204  -0.3603
 DA8  O5    O  O2    0  -0.503    1.2686  -3.0486   0.0995
 DA8  C5    C  CH1   0  -0.002    2.3499  -3.7614  -0.4575
 DA8  C6    C  CH2   0  -0.158    2.2793  -5.1936   0.0294
 DA8  O6    O  OH1   0  -0.663    1.1574  -5.8170  -0.5551
 DA8  C4    C  CH1   0   0.013    3.6762  -3.0973  -0.1063
 DA8  O4    O  OH1   0  -0.664    3.8924  -3.2428   1.2832
 DA8  C3    C  CH2   0  -0.516    3.6272  -1.6317  -0.5234
 DA8  C2    C  CH1   0   0.025    2.3925  -0.9337   0.0356
 DA8  O2    O  O2    0  -0.502    2.2947   0.3714  -0.5011
 DA8  C1F   C  CH1   0   0.255    2.7559   1.3924   0.3187
 DA8  O5F   O  O2    0  -0.495    1.8847   1.6730   1.3751
 DA8  C5F   C  CH1   0   0.006    0.5977   2.1381   0.9853
 DA8  C6F   C  CH3   0  -0.709   -0.2264   2.2883   2.2461
 DA8  C4F   C  CH1   0   0.001    0.7055   3.4319   0.1772
 DA8  O4F   O  OH1   0  -0.656    1.2254   4.5057   0.9251
 DA8  C3F   C  CH1   0   0.029    1.6183   3.1833  -1.0137
 DA8  O3F   O  OH1   0  -0.661    1.7683   4.3726  -1.7466
 DA8  C2F   C  CH1   0  -0.028    2.9625   2.6452  -0.5378
 DA8  O2F   O  OH1   0  -0.654    3.7565   2.3954  -1.6736
 DA8  H16   H  HCH2  0   0.207   -6.8482   1.7692  -0.2286
 DA8  C19   C  CH2   0  -0.412   -8.5640   0.4738  -0.2231
 DA8  H16A  H  HCH2  0   0.206   -7.1048   0.9350   1.2879
 DA8  H15   H  HCH2  0   0.207   -6.4084  -1.2208   0.2174
 DA8  H15A  H  HCH2  0   0.206   -6.1540  -0.3834  -1.2986
 DA8  H14   H  HCH2  0   0.208   -4.4259   1.0675  -0.1958
 DA8  H14A  H  HCH2  0   0.208   -4.6654   0.2022   1.3055
 DA8  H13   H  HCH2  0   0.212   -3.9377  -1.9228   0.1853
 DA8  H13A  H  HCH2  0   0.212   -3.6904  -1.0409  -1.3074
 DA8  H12   H  HCH2  0   0.211   -2.0114   0.4292  -0.1339
 DA8  H12A  H  HCH2  0   0.218   -2.2236  -0.5208   1.3257
 DA8  H11   H  HCH2  0   0.198   -1.4666  -2.5688   0.0708
 DA8  H11A  H  HCH2  0   0.244   -1.1928  -1.5634  -1.3563
 DA8  H1    H  HCH1  0   0.241    1.0389  -1.7126  -1.4575
 DA8  H5    H  HCH1  0   0.231    2.2863  -3.7782  -1.5533
 DA8  H6    H  HCH2  0   0.195    3.2119  -5.6950  -0.2612
 DA8  H6A   H  HCH2  0   0.208    2.2277  -5.2149   1.1235
 DA8  HO6   H  HOH1  0   0.439    1.1236  -6.7205  -0.2319
 DA8  H4    H  HCH1  0   0.228    4.4666  -3.6025  -0.6779
 DA8  HO4   H  HOH1  0   0.436    4.7643  -2.8943   1.4871
 DA8  H3    H  HCH2  0   0.233    4.5378  -1.1166  -0.1993
 DA8  H3A   H  HCH2  0   0.253    3.6111  -1.5698  -1.6155
 DA8  H2    H  HCH1  0   0.228    2.4378  -0.9067   1.1311
 DA8  H1F   H  HCH1  0   0.213    3.7033   1.1106   0.8011
 DA8  H5F   H  HCH1  0   0.241    0.1114   1.3949   0.3460
 DA8  H6F   H  HCH3  0   0.218    0.2390   2.9633   2.9669
 DA8  H6FA  H  HCH3  0   0.229   -1.2205   2.6691   2.0079
 DA8  H6FB  H  HCH3  0   0.257   -0.3548   1.3215   2.7319
 DA8  H4F   H  HCH1  0   0.218   -0.3001   3.6704  -0.2016
 DA8  HO4F  H  HOH1  0   0.434    0.5703   4.7580   1.5801
 DA8  H3F   H  HCH1  0   0.216    1.1313   2.4107  -1.6273
 DA8  HO3F  H  HOH1  0   0.430    2.3912   4.1890  -2.4561
 DA8  H2F   H  HCH1  0   0.228    3.4318   3.3994   0.1056
 DA8  HO2F  H  HOH1  0   0.435    4.6800   2.4806  -1.4293
 DA8  H34   H  HCH2  0   0.205   -8.8567  -0.4894   0.2061
 DA8  C20   C  CH3   0  -0.647   -9.5662   1.5415   0.1920
 DA8  H35   H  HCH2  0   0.205   -8.5987   0.3428  -1.3092
 DA8  H36   H  HCH3  0   0.210   -9.3077   2.5119  -0.2357
 DA8  H37   H  HCH3  0   0.219  -10.5764   1.2952  -0.1362
 DA8  H38   H  HCH3  0   0.211   -9.5910   1.6585   1.2768

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
 DA8  C16  C15   single  1.524  0.020  1.524
 DA8  C16  H16   single  0.970  0.020  1.090
 DA8  C16  C19   single  1.524  0.020  1.524
 DA8  C16  H16A  single  0.970  0.020  1.090
 DA8  C15  C14   single  1.523  0.020  1.523
 DA8  C15  H15   single  0.970  0.020  1.090
 DA8  C15  H15A  single  0.970  0.020  1.090
 DA8  C14  C13   single  1.524  0.020  1.524
 DA8  C14  H14   single  0.970  0.020  1.090
 DA8  C14  H14A  single  0.970  0.020  1.090
 DA8  C13  C12   single  1.524  0.020  1.524
 DA8  C13  H13   single  0.970  0.020  1.090
 DA8  C13  H13A  single  0.970  0.020  1.090
 DA8  C12  C11   single  1.516  0.020  1.516
 DA8  C12  H12   single  0.970  0.020  1.090
 DA8  C12  H12A  single  0.970  0.020  1.090
 DA8  C11  O1    single  1.419  0.020  1.419
 DA8  C11  H11   single  0.970  0.020  1.090
 DA8  C11  H11A  single  0.970  0.020  1.090
 DA8  O1   C1    single  1.376  0.020  1.376
 DA8  C1   O5    single  1.411  0.020  1.411
 DA8  C1   C2    single  1.526  0.020  1.526
 DA8  C1   H1    single  0.970  0.020  1.090
 DA8  O5   C5    single  1.410  0.020  1.410
 DA8  C5   C6    single  1.514  0.020  1.514
 DA8  C5   C4    single  1.524  0.020  1.524
 DA8  C5   H5    single  0.970  0.020  1.090
 DA8  C6   O6    single  1.410  0.020  1.410
 DA8  C6   H6    single  0.970  0.020  1.090
 DA8  C6   H6A   single  0.970  0.020  1.090
 DA8  O6   HO6   single  0.850  0.020  0.980
 DA8  C4   O4    single  1.414  0.020  1.414
 DA8  C4   C3    single  1.525  0.020  1.525
 DA8  C4   H4    single  0.970  0.020  1.090
 DA8  O4   HO4   single  0.850  0.020  0.980
 DA8  C3   C2    single  1.524  0.020  1.524
 DA8  C3   H3    single  0.970  0.020  1.090
 DA8  C3   H3A   single  0.970  0.020  1.090
 DA8  C2   O2    single  1.415  0.020  1.415
 DA8  C2   H2    single  0.970  0.020  1.090
 DA8  O2   C1F   single  1.388  0.020  1.388
 DA8  C1F  O5F   single  1.398  0.020  1.398
 DA8  C1F  C2F   single  1.532  0.020  1.532
 DA8  C1F  H1F   single  0.970  0.020  1.090
 DA8  O5F  C5F   single  1.423  0.020  1.423
 DA8  C5F  C6F   single  1.514  0.020  1.514
 DA8  C5F  C4F   single  1.529  0.020  1.529
 DA8  C5F  H5F   single  0.970  0.020  1.090
 DA8  C6F  H6F   single  0.970  0.020  1.090
 DA8  C6F  H6FA  single  0.970  0.020  1.090
 DA8  C6F  H6FB  single  0.970  0.020  1.090
 DA8  C4F  O4F   single  1.408  0.020  1.408
 DA8  C4F  C3F   single  1.521  0.020  1.521
 DA8  C4F  H4F   single  0.970  0.020  1.090
 DA8  O4F  HO4F  single  0.850  0.020  0.980
 DA8  C3F  O3F   single  1.405  0.020  1.405
 DA8  C3F  C2F   single  1.524  0.020  1.524
 DA8  C3F  H3F   single  0.970  0.020  1.090
 DA8  O3F  HO3F  single  0.850  0.020  0.980
 DA8  C2F  O2F   single  1.408  0.020  1.408
 DA8  C2F  H2F   single  0.970  0.020  1.090
 DA8  O2F  HO2F  single  0.850  0.020  0.980
 DA8  C19  H34   single  0.970  0.020  1.090
 DA8  C19  C20   single  1.522  0.020  1.522
 DA8  C19  H35   single  0.970  0.020  1.090
 DA8  C20  H36   single  0.970  0.020  1.090
 DA8  C20  H37   single  0.970  0.020  1.090
 DA8  C20  H38   single  0.970  0.020  1.090

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
 DA8  H16A  C16  C19   109.30  3.000
 DA8  H16A  C16  H16   105.95  3.000
 DA8  C19   C16  H16   109.24  3.000
 DA8  H16A  C16  C15   109.32  3.000
 DA8  C19   C16  C15   113.51  3.000
 DA8  H16   C16  C15   109.24  3.000
 DA8  H15A  C15  H15   106.05  3.000
 DA8  H15A  C15  C14   109.42  3.000
 DA8  H15   C15  C14   109.51  3.000
 DA8  H15A  C15  C16   109.29  3.000
 DA8  H15   C15  C16   109.42  3.000
 DA8  C14   C15  C16   112.93  3.000
 DA8  H14A  C14  H14   105.95  3.000
 DA8  H14A  C14  C13   109.26  3.000
 DA8  H14   C14  C13   109.06  3.000
 DA8  H14A  C14  C15   109.39  3.000
 DA8  H14   C14  C15   109.28  3.000
 DA8  C13   C14  C15   113.62  3.000
 DA8  H13A  C13  H13   106.16  3.000
 DA8  H13A  C13  C12   109.65  3.000
 DA8  H13   C13  C12   109.74  3.000
 DA8  H13A  C13  C14   109.25  3.000
 DA8  H13   C13  C14   109.51  3.000
 DA8  C12   C13  C14   112.34  3.000
 DA8  H12A  C12  H12   106.52  3.000
 DA8  H12A  C12  C11   109.53  3.000
 DA8  H12   C12  C11   109.20  3.000
 DA8  H12A  C12  C13   109.55  3.000
 DA8  H12   C12  C13   109.28  3.000
 DA8  C11   C12  C13   112.58  3.000
 DA8  H11A  C11  H11   107.39  3.000
 DA8  H11A  C11  O1    110.36  3.000
 DA8  H11   C11  O1    110.59  3.000
 DA8  H11A  C11  C12   110.11  3.000
 DA8  H11   C11  C12   109.99  3.000
 DA8  O1    C11  C12   108.41  3.000
 DA8  C1    O1   C11   115.82  3.000
 DA8  H1    C1   C2    109.54  3.000
 DA8  H1    C1   O5    109.84  3.000
 DA8  C2    C1   O5    109.29  3.000
 DA8  H1    C1   O1    111.31  3.000
 DA8  C2    C1   O1    109.03  3.000
 DA8  O5    C1   O1    107.80  3.000
 DA8  C5    O5   C1    114.43  3.000
 DA8  H5    C5   C4    106.69  3.000
 DA8  H5    C5   C6    107.68  3.000
 DA8  C4    C5   C6    112.24  3.000
 DA8  H5    C5   O5    110.95  3.000
 DA8  C4    C5   O5    110.86  3.000
 DA8  C6    C5   O5    108.38  3.000
 DA8  H6A   C6   H6    107.19  3.000
 DA8  H6A   C6   O6    111.59  3.000
 DA8  H6    C6   O6    111.35  3.000
 DA8  H6A   C6   C5    109.98  3.000
 DA8  H6    C6   C5    107.89  3.000
 DA8  O6    C6   C5    108.78  3.000
 DA8  HO6   O6   C6    107.72  3.000
 DA8  H4    C4   C3    108.84  3.000
 DA8  H4    C4   O4    110.74  3.000
 DA8  C3    C4   O4    111.89  3.000
 DA8  H4    C4   C5    107.80  3.000
 DA8  C3    C4   C5    109.14  3.000
 DA8  O4    C4   C5    108.34  3.000
 DA8  HO4   O4   C4    108.06  3.000
 DA8  H3A   C3   H3    106.32  3.000
 DA8  H3A   C3   C2    109.16  3.000
 DA8  H3    C3   C2    110.46  3.000
 DA8  H3A   C3   C4    109.14  3.000
 DA8  H3    C3   C4    110.14  3.000
 DA8  C2    C3   C4    111.46  3.000
 DA8  H2    C2   O2    111.04  3.000
 DA8  H2    C2   C3    110.12  3.000
 DA8  O2    C2   C3    109.83  3.000
 DA8  H2    C2   C1    107.80  3.000
 DA8  O2    C2   C1    108.72  3.000
 DA8  C3    C2   C1    109.28  3.000
 DA8  C1F   O2   C2    115.57  3.000
 DA8  H1F   C1F  C2F   109.80  3.000
 DA8  H1F   C1F  O5F   104.88  3.000
 DA8  C2F   C1F  O5F   110.03  3.000
 DA8  H1F   C1F  O2    110.90  3.000
 DA8  C2F   C1F  O2    108.43  3.000
 DA8  O5F   C1F  O2    112.76  3.000
 DA8  C5F   O5F  C1F   114.98  3.000
 DA8  H5F   C5F  C4F   107.29  3.000
 DA8  H5F   C5F  C6F   108.18  3.000
 DA8  C4F   C5F  C6F   113.24  3.000
 DA8  H5F   C5F  O5F   109.88  3.000
 DA8  C4F   C5F  O5F   110.95  3.000
 DA8  C6F   C5F  O5F   107.26  3.000
 DA8  H6FB  C6F  H6FA  107.44  3.000
 DA8  H6FB  C6F  H6F   107.73  3.000
 DA8  H6FA  C6F  H6F   108.47  3.000
 DA8  H6FB  C6F  C5F   110.33  3.000
 DA8  H6FA  C6F  C5F   110.42  3.000
 DA8  H6F   C6F  C5F   112.29  3.000
 DA8  H4F   C4F  C3F   108.32  3.000
 DA8  H4F   C4F  O4F   110.79  3.000
 DA8  C3F   C4F  O4F   108.60  3.000
 DA8  H4F   C4F  C5F   107.50  3.000
 DA8  C3F   C4F  C5F   108.53  3.000
 DA8  O4F   C4F  C5F   112.99  3.000
 DA8  HO4F  O4F  C4F   108.10  3.000
 DA8  H3F   C3F  C2F   108.46  3.000
 DA8  H3F   C3F  O3F   110.53  3.000
 DA8  C2F   C3F  O3F   111.57  3.000
 DA8  H3F   C3F  C4F   106.60  3.000
 DA8  C2F   C3F  C4F   110.03  3.000
 DA8  O3F   C3F  C4F   109.52  3.000
 DA8  HO3F  O3F  C3F   107.00  3.000
 DA8  H2F   C2F  O2F   110.73  3.000
 DA8  H2F   C2F  C3F   108.52  3.000
 DA8  O2F   C2F  C3F   107.94  3.000
 DA8  H2F   C2F  C1F   106.99  3.000
 DA8  O2F   C2F  C1F   112.47  3.000
 DA8  C3F   C2F  C1F   110.15  3.000
 DA8  HO2F  O2F  C2F   108.77  3.000
 DA8  H35   C19  C20   109.49  3.000
 DA8  H35   C19  H34   105.99  3.000
 DA8  C20   C19  H34   109.53  3.000
 DA8  H35   C19  C16   109.36  3.000
 DA8  C20   C19  C16   112.86  3.000
 DA8  H34   C19  C16   109.38  3.000
 DA8  H38   C20  H37   107.60  3.000
 DA8  H38   C20  H36   107.43  3.000
 DA8  H37   C20  H36   107.60  3.000
 DA8  H38   C20  C19   111.18  3.000
 DA8  H37   C20  C19   111.69  3.000
 DA8  H36   C20  C19   111.15  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
 DA8  Var_01  H11  C11  O1   C1     75.59  30.0  1
 DA8  Var_02  C13  C14  C15  C16  -178.61  30.0  3
 DA8  Var_03  C20  C19  C16  C15  -179.85  30.0  3
 DA8  Var_04  C12  C13  C14  C15  -179.64  30.0  3
 DA8  Var_05  C19  C16  C15  C14   179.87  30.0  1
 DA8  Var_06  C11  C12  C13  C14  -176.82  30.0  3
 DA8  Var_07  O1   C11  C12  C13  -177.51  30.0  3
 DA8  Var_08  H36  C20  C19  C16    58.78  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
 DA8  chir_01  C1   O1   O5   C2   positiv
 DA8  chir_02  C5   O5   C4   C6   negativ
 DA8  chir_03  C4   O4   C5   C3   negativ
 DA8  chir_04  C2   O2   C1   C3   negativ
 DA8  chir_05  C1F  O2   O5F  C2F  positiv
 DA8  chir_06  C5F  O5F  C6F  C4F  negativ
 DA8  chir_07  C4F  O4F  C5F  C3F  positiv
 DA8  chir_08  C3F  O3F  C2F  C4F  negativ
 DA8  chir_09  C2F  O2F  C3F  C1F  negativ

