# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:22:17 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: dodecyl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[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
 XKJ  XKJ  'dodecyl beta-D-glucopyranoside'  D-saccharide  60  24  .  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_XKJ
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
 XKJ  C6    C  CH2   0  -0.192  -26.6874  49.5953   -4.4157
 XKJ  C3    C  CH1   0  -0.015  -26.1385  45.9697   -5.6415
 XKJ  C24   C  CH2   0  -0.438  -28.6128  47.7721  -10.2853
 XKJ  C26   C  CH2   0  -0.423  -30.2744  45.8574  -10.6090
 XKJ  C28   C  CH2   0  -0.430  -30.2541  44.1229  -12.4938
 XKJ  C5    C  CH1   0  -0.017  -26.8347  48.3140   -5.2056
 XKJ  C4    C  CH1   0   0.013  -25.8873  47.1910   -4.7660
 XKJ  C1    C  CH1   0   0.311  -26.9348  47.5127   -7.4134
 XKJ  C2    C  CH1   0   0.004  -26.0138  46.3343   -7.1158
 XKJ  C25   C  CH2   0  -0.437  -29.4410  46.6749   -9.6243
 XKJ  C27   C  CH2   0  -0.434  -29.4387  44.9380  -11.4923
 XKJ  C29   C  CH2   0  -0.446  -31.3205  43.2160  -11.8801
 XKJ  C30   C  CH2   0  -0.446  -30.8077  42.2484  -10.8149
 XKJ  C31   C  CH2   0  -0.440  -29.6947  41.3105  -11.2780
 XKJ  C32   C  CH2   0  -0.430  -30.0415  40.4526  -12.4937
 XKJ  C33   C  CH2   0  -0.430  -31.2916  39.5898  -12.3413
 XKJ  C34   C  CH3   0  -0.664  -31.2169  38.5974  -11.1882
 XKJ  O6    O  OH1   0  -0.667  -25.3546  50.0420   -4.4747
 XKJ  O5    O  O2    0  -0.498  -26.6104  48.5940   -6.5733
 XKJ  O4    O  OH1   0  -0.671  -26.1153  46.8087   -3.4289
 XKJ  O2    O  OH1   0  -0.663  -26.3820  45.2688   -7.9513
 XKJ  O1    O  O2    0  -0.495  -26.7521  47.9078   -8.7162
 XKJ  O3    O  OH1   0  -0.669  -25.2235  44.9302   -5.3911
 XKJ  H61   H  HCH2  0   0.218  -27.3866  50.3361   -4.8254
 XKJ  H62   H  HCH2  0   0.207  -27.0108  49.3979   -3.3863
 XKJ  H3    H  HCH1  0   0.210  -27.1722  45.6290   -5.4613
 XKJ  H241  H  HCH2  0   0.225  -27.9266  47.3481  -11.0238
 XKJ  H242  H  HCH2  0   0.216  -29.2820  48.4385  -10.8392
 XKJ  H262  H  HCH2  0   0.205  -30.8690  46.5313  -11.2362
 XKJ  H261  H  HCH2  0   0.224  -30.9931  45.2581  -10.0430
 XKJ  H281  H  HCH2  0   0.216  -30.7403  44.8062  -13.1977
 XKJ  H282  H  HCH2  0   0.219  -29.5661  43.5203  -13.0946
 XKJ  H5    H  HCH1  0   0.222  -27.8714  47.9690   -5.0537
 XKJ  H4    H  HCH1  0   0.223  -24.8503  47.5189   -4.9143
 XKJ  H1    H  HCH1  0   0.186  -27.9812  47.2107   -7.2223
 XKJ  H2    H  HCH1  0   0.212  -24.9772  46.6555   -7.3086
 XKJ  H232  H  HCH2  0   0.232  -27.3725  49.4722   -9.8533
 XKJ  H231  H  HCH2  0   0.213  -28.4834  49.0581   -8.5564
 XKJ  H252  H  HCH2  0   0.217  -30.1047  47.1366   -8.8860
 XKJ  H251  H  HCH2  0   0.217  -28.7902  45.9942   -9.0685
 XKJ  H271  H  HCH2  0   0.211  -28.8574  44.2661  -10.8521
 XKJ  H272  H  HCH2  0   0.223  -28.7031  45.5268  -12.0477
 XKJ  H291  H  HCH2  0   0.221  -32.1147  43.8263  -11.4405
 XKJ  H292  H  HCH2  0   0.222  -31.8013  42.6527  -12.6858
 XKJ  H302  H  HCH2  0   0.221  -31.6525  41.6596  -10.4451
 XKJ  H301  H  HCH2  0   0.222  -30.4491  42.8144   -9.9496
 XKJ  H312  H  HCH2  0   0.220  -29.4113  40.6665  -10.4405
 XKJ  H311  H  HCH2  0   0.221  -28.7981  41.8935  -11.5094
 XKJ  H322  H  HCH2  0   0.218  -30.1597  41.0952  -13.3713
 XKJ  H321  H  HCH2  0   0.215  -29.1890  39.8023  -12.7152
 XKJ  H331  H  HCH2  0   0.214  -32.1724  40.2267  -12.2185
 XKJ  H332  H  HCH2  0   0.220  -31.4512  39.0431  -13.2747
 XKJ  H343  H  HCH3  0   0.225  -32.0980  37.9550  -11.1634
 XKJ  H342  H  HCH3  0   0.214  -30.3405  37.9526  -11.2799
 XKJ  H341  H  HCH3  0   0.220  -31.1548  39.1005  -10.2221
 XKJ  HO6   H  HOH1  0   0.457  -25.2720  50.8193   -3.9152
 XKJ  HO4   H  HOH1  0   0.459  -25.6117  47.3875   -2.8492
 XKJ  HO2   H  HOH1  0   0.451  -25.8819  44.4906   -7.6830
 XKJ  HO3   H  HOH1  0   0.453  -25.3817  44.5940   -4.5033
 XKJ  C23   C  CH2   0  -0.189  -27.8196  48.6316   -9.3172

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
 XKJ  C28  C27   single  1.527  0.020  1.527
 XKJ  C28  C29   single  1.529  0.020  1.529
 XKJ  C32  C31   single  1.528  0.020  1.528
 XKJ  C32  C33   single  1.527  0.020  1.527
 XKJ  C26  C27   single  1.524  0.020  1.524
 XKJ  C26  C25   single  1.527  0.020  1.527
 XKJ  C31  C30   single  1.527  0.020  1.527
 XKJ  C29  C30   single  1.528  0.020  1.528
 XKJ  C24  C25   single  1.525  0.020  1.525
 XKJ  C24  C23   single  1.518  0.020  1.518
 XKJ  C33  C34   single  1.523  0.020  1.523
 XKJ  C23  O1    single  1.423  0.020  1.423
 XKJ  O2   C2    single  1.403  0.020  1.403
 XKJ  O1   C1    single  1.374  0.020  1.374
 XKJ  C1   C2    single  1.525  0.020  1.525
 XKJ  C1   O5    single  1.407  0.020  1.407
 XKJ  C2   C3    single  1.524  0.020  1.524
 XKJ  C3   O3    single  1.407  0.020  1.407
 XKJ  C3   C4    single  1.524  0.020  1.524
 XKJ  O5   C5    single  1.414  0.020  1.414
 XKJ  C4   C5    single  1.534  0.020  1.534
 XKJ  C4   O4    single  1.409  0.020  1.409
 XKJ  C5   C6    single  1.512  0.020  1.512
 XKJ  C6   O6    single  1.407  0.020  1.407
 XKJ  C6   H61   single  0.970  0.020  1.090
 XKJ  C6   H62   single  0.970  0.020  1.090
 XKJ  C3   H3    single  0.970  0.020  1.090
 XKJ  C24  H241  single  0.970  0.020  1.090
 XKJ  C24  H242  single  0.970  0.020  1.090
 XKJ  C26  H262  single  0.970  0.020  1.090
 XKJ  C26  H261  single  0.970  0.020  1.090
 XKJ  C28  H281  single  0.970  0.020  1.090
 XKJ  C28  H282  single  0.970  0.020  1.090
 XKJ  C5   H5    single  0.970  0.020  1.090
 XKJ  C4   H4    single  0.970  0.020  1.090
 XKJ  C1   H1    single  0.970  0.020  1.090
 XKJ  C2   H2    single  0.970  0.020  1.090
 XKJ  C23  H232  single  0.970  0.020  1.090
 XKJ  C23  H231  single  0.970  0.020  1.090
 XKJ  C25  H252  single  0.970  0.020  1.090
 XKJ  C25  H251  single  0.970  0.020  1.090
 XKJ  C27  H271  single  0.970  0.020  1.090
 XKJ  C27  H272  single  0.970  0.020  1.090
 XKJ  C29  H291  single  0.970  0.020  1.090
 XKJ  C29  H292  single  0.970  0.020  1.090
 XKJ  C30  H302  single  0.970  0.020  1.090
 XKJ  C30  H301  single  0.970  0.020  1.090
 XKJ  C31  H312  single  0.970  0.020  1.090
 XKJ  C31  H311  single  0.970  0.020  1.090
 XKJ  C32  H322  single  0.970  0.020  1.090
 XKJ  C32  H321  single  0.970  0.020  1.090
 XKJ  C33  H331  single  0.970  0.020  1.090
 XKJ  C33  H332  single  0.970  0.020  1.090
 XKJ  C34  H343  single  0.970  0.020  1.090
 XKJ  C34  H342  single  0.970  0.020  1.090
 XKJ  C34  H341  single  0.970  0.020  1.090
 XKJ  O6   HO6   single  0.850  0.020  0.980
 XKJ  O4   HO4   single  0.850  0.020  0.980
 XKJ  O2   HO2   single  0.850  0.020  0.980
 XKJ  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
 XKJ  H62   C6   H61   106.48  3.000
 XKJ  H62   C6   O6    112.07  3.000
 XKJ  H61   C6   O6    111.93  3.000
 XKJ  H62   C6   C5    108.00  3.000
 XKJ  H61   C6   C5    108.34  3.000
 XKJ  O6    C6   C5    109.84  3.000
 XKJ  H3    C3   O3    110.62  3.000
 XKJ  H3    C3   C2    107.98  3.000
 XKJ  O3    C3   C2    107.20  3.000
 XKJ  H3    C3   C4    107.95  3.000
 XKJ  O3    C3   C4    112.50  3.000
 XKJ  C2    C3   C4    110.53  3.000
 XKJ  H242  C24  H241  106.14  3.000
 XKJ  H242  C24  C25   108.98  3.000
 XKJ  H241  C24  C25   110.76  3.000
 XKJ  H242  C24  C23   107.29  3.000
 XKJ  H241  C24  C23   108.80  3.000
 XKJ  C25   C24  C23   114.49  3.000
 XKJ  H261  C26  H262  106.06  3.000
 XKJ  H261  C26  C27   109.25  3.000
 XKJ  H262  C26  C27   109.67  3.000
 XKJ  H261  C26  C25   108.56  3.000
 XKJ  H262  C26  C25   109.63  3.000
 XKJ  C27   C26  C25   113.41  3.000
 XKJ  H282  C28  H281  105.66  3.000
 XKJ  H282  C28  C29   109.41  3.000
 XKJ  H281  C28  C29   108.58  3.000
 XKJ  H282  C28  C27   108.56  3.000
 XKJ  H281  C28  C27   109.00  3.000
 XKJ  C29   C28  C27   115.21  3.000
 XKJ  H5    C5   O5    110.13  3.000
 XKJ  H5    C5   C4    108.18  3.000
 XKJ  O5    C5   C4    108.92  3.000
 XKJ  H5    C5   C6    106.54  3.000
 XKJ  C4    C5   C6    114.24  3.000
 XKJ  O5    C5   C6    108.78  3.000
 XKJ  H4    C4   O4    111.23  3.000
 XKJ  H4    C4   C5    109.03  3.000
 XKJ  O4    C4   C5    111.76  3.000
 XKJ  H4    C4   C3    108.52  3.000
 XKJ  O4    C4   C3    107.53  3.000
 XKJ  C5    C4   C3    108.69  3.000
 XKJ  H1    C1   O1    111.62  3.000
 XKJ  H1    C1   O5    108.95  3.000
 XKJ  O1    C1   O5    108.34  3.000
 XKJ  H1    C1   C2    109.07  3.000
 XKJ  O5    C1   C2    109.76  3.000
 XKJ  O1    C1   C2    109.09  3.000
 XKJ  H2    C2   O2    111.34  3.000
 XKJ  H2    C2   C1    107.98  3.000
 XKJ  O2    C2   C1    108.19  3.000
 XKJ  H2    C2   C3    108.42  3.000
 XKJ  C1    C2   C3    108.92  3.000
 XKJ  O2    C2   C3    111.89  3.000
 XKJ  H251  C25  H252  106.29  3.000
 XKJ  H251  C25  C26   108.62  3.000
 XKJ  H252  C25  C26   109.25  3.000
 XKJ  H251  C25  C24   110.17  3.000
 XKJ  H252  C25  C24   108.55  3.000
 XKJ  C26   C25  C24   113.69  3.000
 XKJ  H272  C27  H271  105.67  3.000
 XKJ  H272  C27  C28   108.27  3.000
 XKJ  H271  C27  C28   109.83  3.000
 XKJ  H272  C27  C26   109.77  3.000
 XKJ  H271  C27  C26   108.80  3.000
 XKJ  C28   C27  C26   114.15  3.000
 XKJ  H292  C29  H291  105.32  3.000
 XKJ  H292  C29  C30   109.56  3.000
 XKJ  H291  C29  C30   108.47  3.000
 XKJ  H292  C29  C28   108.44  3.000
 XKJ  H291  C29  C28   109.69  3.000
 XKJ  C30   C29  C28   114.93  3.000
 XKJ  H301  C30  H302  105.31  3.000
 XKJ  H301  C30  C31   108.57  3.000
 XKJ  H302  C30  C31   109.56  3.000
 XKJ  H301  C30  C29   109.49  3.000
 XKJ  H302  C30  C29   108.50  3.000
 XKJ  C31   C30  C29   114.97  3.000
 XKJ  H311  C31  H312  105.27  3.000
 XKJ  H311  C31  C32   108.47  3.000
 XKJ  H312  C31  C32   109.72  3.000
 XKJ  H311  C31  C30   109.52  3.000
 XKJ  H312  C31  C30   108.55  3.000
 XKJ  C32   C31  C30   114.87  3.000
 XKJ  H321  C32  H322  105.71  3.000
 XKJ  H321  C32  C33   108.79  3.000
 XKJ  H322  C32  C33   108.88  3.000
 XKJ  H321  C32  C31   108.52  3.000
 XKJ  H322  C32  C31   109.45  3.000
 XKJ  C33   C32  C31   115.08  3.000
 XKJ  H332  C33  H331  105.63  3.000
 XKJ  H332  C33  C34   109.12  3.000
 XKJ  H331  C33  C34   109.50  3.000
 XKJ  H332  C33  C32   108.48  3.000
 XKJ  H331  C33  C32   109.97  3.000
 XKJ  C34   C33  C32   113.81  3.000
 XKJ  H341  C34  H342  107.51  3.000
 XKJ  H341  C34  H343  107.31  3.000
 XKJ  H342  C34  H343  107.61  3.000
 XKJ  H341  C34  C33   111.88  3.000
 XKJ  H342  C34  C33   111.13  3.000
 XKJ  H343  C34  C33   111.19  3.000
 XKJ  HO6   O6   C6    108.28  3.000
 XKJ  C1    O5   C5    112.88  3.000
 XKJ  HO4   O4   C4    108.90  3.000
 XKJ  HO2   O2   C2    108.15  3.000
 XKJ  C23   O1   C1    116.56  3.000
 XKJ  HO3   O3   C3    108.38  3.000
 XKJ  H231  C23  H232  106.80  3.000
 XKJ  H231  C23  O1    111.05  3.000
 XKJ  H232  C23  O1    106.96  3.000
 XKJ  H231  C23  C24   110.27  3.000
 XKJ  H232  C23  C24   109.66  3.000
 XKJ  O1    C23  C24   111.92  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
 XKJ  Var_01  H232  C23  O1   C1    135.54  30.0  2
 XKJ  Var_02  C27   C26  C25  C24    70.93  30.0  2
 XKJ  Var_03  C29   C28  C27  C26   -58.48  30.0  2
 XKJ  Var_04  C23   C24  C25  C26   177.69  30.0  1
 XKJ  Var_05  C25   C26  C27  C28  -179.40  30.0  2
 XKJ  Var_06  C31   C30  C29  C28   -57.33  30.0  3
 XKJ  Var_07  O1    C23  C24  C25    69.45  30.0  3
 XKJ  Var_08  C30   C29  C28  C27   -54.37  30.0  3
 XKJ  Var_09  C32   C31  C30  C29   -56.58  30.0  2
 XKJ  Var_10  C33   C32  C31  C30   -56.11  30.0  1
 XKJ  Var_11  C34   C33  C32  C31   -59.65  30.0  3
 XKJ  Var_12  H343  C34  C33  C32  -175.82  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
 XKJ  chir_01  C3  C2  O3  C4  negativ
 XKJ  chir_02  C5  O5  C4  C6  negativ
 XKJ  chir_03  C4  O4  C5  C3  positiv
 XKJ  chir_04  C1  O1  O5  C2  positiv
 XKJ  chir_05  C2  O2  C1  C3  negativ

