# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 26 23:28:49 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (5R)-5-[(2R)-2-hydroxynonyl]-beta-D-xylulofuranosyl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[C@@H](O)C[C@H]1O[C@@](CO)(O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[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
 SUM  SUM  '(5R)-5-[(2R)-2-hydroxynonyl]-beta-D-xylulofuranosyl alpha-D-glucopyranoside'  ligand  69  31  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SUM
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
 SUM  C1    C  CH1   0   0.188  -0.1543   0.1696  -3.2291
 SUM  C2    C  CH1   0   0.036  -0.1134  -1.3560  -3.3504
 SUM  C3    C  CH1   0  -0.017   0.8763  -1.9342  -2.3460
 SUM  C4    C  CH1   0   0.038   2.2376  -1.2673  -2.5120
 SUM  C5    C  CH1   0  -0.028   2.0798   0.2466  -2.3954
 SUM  C6    C  CH2   0  -0.157   3.3667   0.9946  -2.6672
 SUM  O1    O  O2    0  -0.511  -0.7228   0.5017  -2.0005
 SUM  O2    O  OH1   0  -0.689  -1.3697  -1.9527  -3.1549
 SUM  O3    O  OH1   0  -0.676   1.0631  -3.3196  -2.5335
 SUM  O4    O  OH1   0  -0.673   3.1439  -1.6865  -1.5227
 SUM  O5    O  O2    0  -0.507   1.1330   0.7033  -3.3523
 SUM  O6    O  OH1   0  -0.668   3.1285   2.3663  -2.4472
 SUM  C11   C  CH2   0  -0.214  -1.1725   2.8490  -2.6307
 SUM  C12   C  CT    0   0.438  -1.6121   1.5990  -1.8707
 SUM  C13   C  CH1   0  -0.010  -3.0412   1.1400  -2.1825
 SUM  C14   C  CH1   0  -0.021  -3.3655   0.3156  -0.9384
 SUM  C15   C  CH1   0   0.039  -2.6101   1.0683   0.1615
 SUM  O11   O  OH1   0  -0.674   0.0707   3.3483  -2.2262
 SUM  O13   O  OH1   0  -0.670  -3.1085   0.4397  -3.3989
 SUM  O14   O  OH1   0  -0.666  -4.7289   0.2334  -0.6153
 SUM  O15   O  O2    0  -0.498  -1.6511   1.8875  -0.5156
 SUM  C21   C  CH1   0   0.051  -1.3229   0.8128   2.3794
 SUM  C22   C  CH2   0  -0.431  -0.7483  -0.2307   3.3350
 SUM  C23   C  CH2   0  -0.412  -0.1418   0.3599   4.6007
 SUM  C24   C  CH2   0  -0.411   0.3349  -0.7046   5.5820
 SUM  C25   C  CH2   0  -0.410   1.0045  -0.1193   6.8189
 SUM  C26   C  CH2   0  -0.406   1.4491  -1.1755   7.8233
 SUM  C27   C  CH2   0  -0.417   2.1569  -0.5902   9.0393
 SUM  C28   C  CH3   0  -0.662   2.5818  -1.6507  10.0459
 SUM  O21   O  OH1   0  -0.672  -0.3570   1.7839   2.0219
 SUM  CM    C  CH2   0  -0.505  -1.9563   0.1381   1.1671
 SUM  H1    H  HCH1  0   0.263  -0.7137   0.5854  -4.0714
 SUM  H2    H  HCH1  0   0.213   0.2614  -1.5723  -4.3626
 SUM  H3    H  HCH1  0   0.221   0.5125  -1.7288  -1.3282
 SUM  H4    H  HCH1  0   0.211   2.6178  -1.5003  -3.5202
 SUM  H5    H  HCH1  0   0.234   1.7397   0.4884  -1.3788
 SUM  H61   H  HCH2  0   0.213   4.1468   0.6096  -2.0022
 SUM  H62   H  HCH2  0   0.204   3.6901   0.7964  -3.6975
 SUM  HO2   H  HOH1  0   0.452  -2.0673  -1.3113  -3.3528
 SUM  HO3   H  HOH1  0   0.458   0.2910  -3.7818  -2.1938
 SUM  HO4   H  HOH1  0   0.454   3.2117  -2.6460  -1.5690
 SUM  HO6   H  HOH1  0   0.461   3.8867   2.8631  -2.7670
 SUM  H111  H  HCH2  0   0.217  -1.2186   2.6645  -3.7111
 SUM  H112  H  HCH2  0   0.244  -1.9174   3.6221  -2.4265
 SUM  H13   H  HCH1  0   0.247  -3.6945   2.0234  -2.2032
 SUM  H14   H  HCH1  0   0.229  -2.9340  -0.6861  -1.0698
 SUM  H15   H  HCH1  0   0.235  -3.3092   1.7383   0.6773
 SUM  HO11  H  HOH1  0   0.451   0.7728   2.7805  -2.5657
 SUM  HO13  H  HOH1  0   0.473  -4.0314   0.3302  -3.6501
 SUM  HO14  H  HOH1  0   0.459  -5.1206  -0.4921  -1.1099
 SUM  H21   H  HCH1  0   0.209  -2.1100   1.3618   2.9128
 SUM  H221  H  HCH2  0   0.211   0.0050  -0.8304   2.8095
 SUM  H222  H  HCH2  0   0.213  -1.5526  -0.9226   3.6061
 SUM  H231  H  HCH2  0   0.205  -0.8820   0.9981   5.0971
 SUM  H232  H  HCH2  0   0.212   0.6960   1.0115   4.3377
 SUM  H241  H  HCH2  0   0.206   1.0355  -1.3791   5.0769
 SUM  H242  H  HCH2  0   0.206  -0.5158  -1.3241   5.8867
 SUM  H251  H  HCH2  0   0.205   0.3169   0.5787   7.3096
 SUM  H252  H  HCH2  0   0.205   1.8715   0.4756   6.5105
 SUM  H261  H  HCH2  0   0.205   2.1150  -1.8913   7.3283
 SUM  H262  H  HCH2  0   0.205   0.5771  -1.7509   8.1539
 SUM  H271  H  HCH2  0   0.209   1.4991   0.1351   9.5281
 SUM  H272  H  HCH2  0   0.209   3.0355  -0.0275   8.7083
 SUM  H281  H  HCH3  0   0.225   3.1072  -1.2113  10.8947
 SUM  H282  H  HCH3  0   0.215   1.7183  -2.1924  10.4366
 SUM  H283  H  HCH3  0   0.215   3.2499  -2.3833   9.5887
 SUM  HO21  H  HOH1  0   0.437   0.0949   1.4913   1.2249
 SUM  HCM1  H  HCH2  0   0.236  -1.2167  -0.4867   0.6506
 SUM  HCM2  H  HCH2  0   0.247  -2.7288  -0.5449   1.5333

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
 SUM  C1   C2    single  1.531  0.020  1.531
 SUM  C1   O1    single  1.394  0.020  1.394
 SUM  C1   O5    single  1.399  0.020  1.399
 SUM  C1   H1    single  0.970  0.020  1.090
 SUM  C2   C3    single  1.524  0.020  1.524
 SUM  C2   O2    single  1.404  0.020  1.404
 SUM  C2   H2    single  0.970  0.020  1.090
 SUM  C3   C4    single  1.525  0.020  1.525
 SUM  C3   O3    single  1.410  0.020  1.410
 SUM  C3   H3    single  0.970  0.020  1.090
 SUM  C4   C5    single  1.527  0.020  1.527
 SUM  C4   O4    single  1.406  0.020  1.406
 SUM  C4   H4    single  0.970  0.020  1.090
 SUM  C5   C6    single  1.513  0.020  1.513
 SUM  C5   O5    single  1.421  0.020  1.421
 SUM  C5   H5    single  0.970  0.020  1.090
 SUM  C6   O6    single  1.410  0.020  1.410
 SUM  C6   H61   single  0.970  0.020  1.090
 SUM  C6   H62   single  0.970  0.020  1.090
 SUM  O1   C12   single  1.418  0.020  1.418
 SUM  O2   HO2   single  0.850  0.020  0.980
 SUM  O3   HO3   single  0.850  0.020  0.980
 SUM  O4   HO4   single  0.850  0.020  0.980
 SUM  O6   HO6   single  0.850  0.020  0.980
 SUM  C11  C12   single  1.528  0.020  1.528
 SUM  C11  O11   single  1.399  0.020  1.399
 SUM  C11  H111  single  0.970  0.020  1.090
 SUM  C11  H112  single  0.970  0.020  1.090
 SUM  C12  C13   single  1.533  0.020  1.533
 SUM  C12  O15   single  1.386  0.020  1.386
 SUM  C13  C14   single  1.527  0.020  1.527
 SUM  C13  O13   single  1.405  0.020  1.405
 SUM  C13  H13   single  0.970  0.020  1.090
 SUM  C14  C15   single  1.532  0.020  1.532
 SUM  C14  O14   single  1.404  0.020  1.404
 SUM  C14  H14   single  0.970  0.020  1.090
 SUM  C15  O15   single  1.432  0.020  1.432
 SUM  C15  CM    single  1.518  0.020  1.518
 SUM  C15  H15   single  0.970  0.020  1.090
 SUM  O11  HO11  single  0.850  0.020  0.980
 SUM  O13  HO13  single  0.850  0.020  0.980
 SUM  O14  HO14  single  0.850  0.020  0.980
 SUM  C21  C22   single  1.527  0.020  1.527
 SUM  C21  O21   single  1.416  0.020  1.416
 SUM  C21  CM    single  1.525  0.020  1.525
 SUM  C21  H21   single  0.970  0.020  1.090
 SUM  C22  C23   single  1.523  0.020  1.523
 SUM  C22  H221  single  0.970  0.020  1.090
 SUM  C22  H222  single  0.970  0.020  1.090
 SUM  C23  C24   single  1.524  0.020  1.524
 SUM  C23  H231  single  0.970  0.020  1.090
 SUM  C23  H232  single  0.970  0.020  1.090
 SUM  C24  C25   single  1.524  0.020  1.524
 SUM  C24  H241  single  0.970  0.020  1.090
 SUM  C24  H242  single  0.970  0.020  1.090
 SUM  C25  C26   single  1.524  0.020  1.524
 SUM  C25  H251  single  0.970  0.020  1.090
 SUM  C25  H252  single  0.970  0.020  1.090
 SUM  C26  C27   single  1.524  0.020  1.524
 SUM  C26  H261  single  0.970  0.020  1.090
 SUM  C26  H262  single  0.970  0.020  1.090
 SUM  C27  C28   single  1.523  0.020  1.523
 SUM  C27  H271  single  0.970  0.020  1.090
 SUM  C27  H272  single  0.970  0.020  1.090
 SUM  C28  H281  single  0.970  0.020  1.090
 SUM  C28  H282  single  0.970  0.020  1.090
 SUM  C28  H283  single  0.970  0.020  1.090
 SUM  O21  HO21  single  0.850  0.020  0.980
 SUM  CM   HCM1  single  0.970  0.020  1.090
 SUM  CM   HCM2  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
 SUM  H1    C1   O5    104.95  3.000
 SUM  H1    C1   O1    112.32  3.000
 SUM  O5    C1   O1    111.23  3.000
 SUM  H1    C1   C2    109.37  3.000
 SUM  O5    C1   C2    110.40  3.000
 SUM  O1    C1   C2    108.55  3.000
 SUM  H2    C2   O2    110.43  3.000
 SUM  H2    C2   C3    108.08  3.000
 SUM  O2    C2   C3    109.15  3.000
 SUM  H2    C2   C1    106.13  3.000
 SUM  O2    C2   C1    112.86  3.000
 SUM  C3    C2   C1    110.07  3.000
 SUM  H3    C3   O3    110.50  3.000
 SUM  H3    C3   C4    108.32  3.000
 SUM  O3    C3   C4    107.26  3.000
 SUM  H3    C3   C2    108.91  3.000
 SUM  O3    C3   C2    111.78  3.000
 SUM  C4    C3   C2    110.00  3.000
 SUM  H4    C4   O4    111.00  3.000
 SUM  H4    C4   C5    108.37  3.000
 SUM  O4    C4   C5    107.98  3.000
 SUM  H4    C4   C3    108.36  3.000
 SUM  O4    C4   C3    111.62  3.000
 SUM  C5    C4   C3    109.45  3.000
 SUM  H5    C5   O5    110.24  3.000
 SUM  H5    C5   C6    108.70  3.000
 SUM  O5    C5   C6    106.67  3.000
 SUM  H5    C5   C4    108.71  3.000
 SUM  O5    C5   C4    109.64  3.000
 SUM  C6    C5   C4    112.86  3.000
 SUM  H62   C6   H61   107.25  3.000
 SUM  H62   C6   O6    111.84  3.000
 SUM  H61   C6   O6    111.58  3.000
 SUM  H62   C6   C5    109.26  3.000
 SUM  H61   C6   C5    108.85  3.000
 SUM  O6    C6   C5    108.02  3.000
 SUM  C12   O1   C1    121.38  3.000
 SUM  HO2   O2   C2    109.55  3.000
 SUM  HO3   O3   C3    108.58  3.000
 SUM  HO4   O4   C4    107.98  3.000
 SUM  C5    O5   C1    115.53  3.000
 SUM  HO6   O6   C6    108.53  3.000
 SUM  H112  C11  H111  105.93  3.000
 SUM  H112  C11  O11   107.41  3.000
 SUM  H111  C11  O11   112.46  3.000
 SUM  H112  C11  C12   106.84  3.000
 SUM  H111  C11  C12   109.89  3.000
 SUM  O11   C11  C12   113.82  3.000
 SUM  O15   C12  C13   103.59  3.000
 SUM  O15   C12  C11   108.91  3.000
 SUM  C13   C12  C11   114.34  3.000
 SUM  O15   C12  O1    105.55  3.000
 SUM  C13   C12  O1    109.53  3.000
 SUM  C11   C12  O1    114.02  3.000
 SUM  H13   C13  O13   110.85  3.000
 SUM  H13   C13  C14   108.85  3.000
 SUM  O13   C13  C14   115.21  3.000
 SUM  H13   C13  C12   108.50  3.000
 SUM  O13   C13  C12   111.71  3.000
 SUM  C14   C13  C12   101.18  3.000
 SUM  H14   C14  O14   110.83  3.000
 SUM  H14   C14  C15   109.89  3.000
 SUM  O14   C14  C15   110.03  3.000
 SUM  H14   C14  C13   108.13  3.000
 SUM  O14   C14  C13   115.18  3.000
 SUM  C15   C14  C13   102.41  3.000
 SUM  H15   C15  CM    109.71  3.000
 SUM  H15   C15  O15   107.44  3.000
 SUM  CM    C15  O15   112.05  3.000
 SUM  H15   C15  C14   108.87  3.000
 SUM  CM    C15  C14   112.76  3.000
 SUM  O15   C15  C14   105.78  3.000
 SUM  HO11  O11  C11   109.56  3.000
 SUM  HO13  O13  C13   109.17  3.000
 SUM  HO14  O14  C14   108.76  3.000
 SUM  C15   O15  C12   111.23  3.000
 SUM  H21   C21  CM    108.04  3.000
 SUM  H21   C21  O21   105.59  3.000
 SUM  CM    C21  O21   112.72  3.000
 SUM  H21   C21  C22   107.90  3.000
 SUM  CM    C21  C22   110.57  3.000
 SUM  O21   C21  C22   111.72  3.000
 SUM  H222  C22  H221  106.11  3.000
 SUM  H222  C22  C23   109.38  3.000
 SUM  H221  C22  C23   109.67  3.000
 SUM  H222  C22  C21   108.08  3.000
 SUM  H221  C22  C21   109.40  3.000
 SUM  C23   C22  C21   113.89  3.000
 SUM  H232  C23  H231  106.22  3.000
 SUM  H232  C23  C24   109.35  3.000
 SUM  H231  C23  C24   109.04  3.000
 SUM  H232  C23  C22   109.66  3.000
 SUM  H231  C23  C22   109.47  3.000
 SUM  C24   C23  C22   112.88  3.000
 SUM  H242  C24  H241  106.05  3.000
 SUM  H242  C24  C25   109.43  3.000
 SUM  H241  C24  C25   109.25  3.000
 SUM  H242  C24  C23   109.33  3.000
 SUM  H241  C24  C23   109.46  3.000
 SUM  C25   C24  C23   113.07  3.000
 SUM  H252  C25  H251  106.06  3.000
 SUM  H252  C25  C26   109.33  3.000
 SUM  H251  C25  C26   109.24  3.000
 SUM  H252  C25  C24   109.13  3.000
 SUM  H251  C25  C24   109.42  3.000
 SUM  C26   C25  C24   113.40  3.000
 SUM  H262  C26  H261  106.07  3.000
 SUM  H262  C26  C27   109.30  3.000
 SUM  H261  C26  C27   109.22  3.000
 SUM  H262  C26  C25   109.31  3.000
 SUM  H261  C26  C25   109.41  3.000
 SUM  C27   C26  C25   113.28  3.000
 SUM  H272  C27  H271  106.07  3.000
 SUM  H272  C27  C28   109.51  3.000
 SUM  H271  C27  C28   109.51  3.000
 SUM  H272  C27  C26   109.21  3.000
 SUM  H271  C27  C26   109.38  3.000
 SUM  C28   C27  C26   112.93  3.000
 SUM  H283  C28  H282  107.51  3.000
 SUM  H283  C28  H281  107.54  3.000
 SUM  H282  C28  H281  107.61  3.000
 SUM  H283  C28  C27   111.18  3.000
 SUM  H282  C28  C27   111.19  3.000
 SUM  H281  C28  C27   111.61  3.000
 SUM  HO21  O21  C21   108.73  3.000
 SUM  HCM2  CM   HCM1  106.14  3.000
 SUM  HCM2  CM   C21   107.65  3.000
 SUM  HCM1  CM   C21   110.25  3.000
 SUM  HCM2  CM   C15   107.47  3.000
 SUM  HCM1  CM   C15   109.11  3.000
 SUM  C21   CM   C15   115.74  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
 SUM  Var_01  C24   C23  C22  C21  175.92  30.0  3
 SUM  Var_02  C25   C24  C23  C22  177.17  30.0  3
 SUM  Var_03  C26   C25  C24  C23  178.39  30.0  3
 SUM  Var_04  C27   C26  C25  C24  178.22  30.0  3
 SUM  Var_05  C28   C27  C26  C25  179.26  30.0  3
 SUM  Var_06  H281  C28  C27  C26  178.60  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
 SUM  chir_01  C1   C2   O1   O5   negativ
 SUM  chir_02  C2   O2   C1   C3   negativ
 SUM  chir_03  C3   O3   C2   C4   positiv
 SUM  chir_04  C4   O4   C3   C5   negativ
 SUM  chir_05  C5   O5   C4   C6   negativ
 SUM  chir_06  C12  O15  C11  C13  positiv
 SUM  chir_07  C13  O13  C12  C14  positiv
 SUM  chir_08  C14  O14  C13  C15  negativ
 SUM  chir_09  C15  O15  CM   C14  positiv
 SUM  chir_10  C21  O21  CM   C22  negativ

