# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:34:49 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: (5R)-5-[(2R)-2-hydroxynonyl]-beta-D-xylulofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[C@@H](O)C[C@H]1O[C@](O)(CO)[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
 Z6W  Z6W  (5R)-5-[(2R)-2-hydroxynonyl]-beta-D-xylulofuranose  D-saccharide  48  20  .  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_Z6W
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
 Z6W  O2    O  OH1   0  -0.658  -37.6955  112.6156  35.8291
 Z6W  C1    C  CH2   0  -0.187  -36.5047  110.5895  35.6714
 Z6W  C2    C  CR5   0   0.490  -36.9591  111.7224  36.5776
 Z6W  C3    C  CR15  0  -0.072  -35.7925  112.3894  37.3555
 Z6W  C4    C  CR15  0  -0.001  -36.3167  112.4515  38.7835
 Z6W  C5    C  CR15  0   0.027  -37.1445  111.1744  38.8488
 Z6W  O1    O  OH1   0  -0.668  -35.6148  111.1097  34.7176
 Z6W  O3    O  OH1   0  -0.663  -35.4869  113.6299  36.7841
 Z6W  O4    O  OH1   0  -0.664  -35.2601  112.5203  39.7006
 Z6W  O5    O  O     0  -0.541  -37.7906  111.1505  37.5815
 Z6W  C7    C  CH1   0   0.054  -38.9870  109.8128  39.9501
 Z6W  C8    C  CH2   0  -0.445  -39.7475  109.5859  41.2500
 Z6W  C9    C  CH2   0  -0.425  -40.7945  110.6373  41.5997
 Z6W  C10   C  CH2   0  -0.410  -41.4883  110.3338  42.9225
 Z6W  C11   C  CH2   0  -0.411  -42.5728  111.3405  43.2834
 Z6W  C12   C  CH2   0  -0.406  -43.2460  111.0413  44.6170
 Z6W  C13   C  CH2   0  -0.419  -44.3489  112.0296  44.9747
 Z6W  C14   C  CH3   0  -0.662  -45.0072  111.7203  46.3123
 Z6W  O7    O  OH1   0  -0.689  -39.9156  109.7744  38.8838
 Z6W  C6    C  CH2   0  -0.500  -38.1710  111.1082  39.9599
 Z6W  HO2   H  HOH1  0   0.455  -37.5512  113.5139  36.1505
 Z6W  H11   H  HCH2  0   0.206  -36.0305  109.8217  36.2961
 Z6W  H12   H  HCH2  0   0.216  -37.3882  110.1293  35.2072
 Z6W  H3    H  HCR5  0   0.237  -34.9215  111.7179  37.3435
 Z6W  H4    H  HCR5  0   0.225  -36.9908  113.3159  38.8814
 Z6W  H5    H  HCR5  0   0.223  -36.4629  110.3138  38.9420
 Z6W  HO1   H  HOH1  0   0.460  -35.2505  110.3752  34.2164
 Z6W  HO3   H  HOH1  0   0.464  -34.8580  114.0847  37.3544
 Z6W  HO4   H  HOH1  0   0.460  -35.5966  112.8507  40.5387
 Z6W  H7    H  HCH1  0   0.197  -38.2674  108.9831  39.8531
 Z6W  H71   H  HCH2  0   0.226  -40.2295  108.6033  41.2028
 Z6W  H72   H  HCH2  0   0.219  -39.0116  109.5171  42.0574
 Z6W  H81   H  HCH2  0   0.215  -40.3318  111.6279  41.6603
 Z6W  H82   H  HCH2  0   0.214  -41.5416  110.6970  40.8033
 Z6W  H91   H  HCH2  0   0.207  -41.9273  109.3304  42.8809
 Z6W  H92   H  HCH2  0   0.207  -40.7412  110.3021  43.7234
 Z6W  H101  H  HCH2  0   0.206  -42.1420  112.3477  43.3122
 Z6W  H102  H  HCH2  0   0.206  -43.3292  111.3580  42.4909
 Z6W  H111  H  HCH2  0   0.205  -43.6631  110.0280  44.5938
 Z6W  H112  H  HCH2  0   0.206  -42.4911  111.0378  45.4114
 Z6W  H121  H  HCH2  0   0.209  -43.9349  113.0427  44.9941
 Z6W  H122  H  HCH2  0   0.210  -45.1063  112.0278  44.1847
 Z6W  H131  H  HCH3  0   0.226  -45.8016  112.4305  46.5446
 Z6W  H132  H  HCH3  0   0.215  -45.4474  110.7212  46.3118
 Z6W  H133  H  HCH3  0   0.216  -44.2816  111.7581  47.1270
 Z6W  HO7   H  HOH1  0   0.444  -39.4538  110.0371  38.0794
 Z6W  H61   H  HCH2  0   0.237  -37.6298  111.1704  40.9091
 Z6W  H62   H  HCH2  0   0.239  -38.8277  111.9822  39.9088

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
 Z6W  O2   C2    single  1.378  0.020  1.378
 Z6W  C1   C2    single  1.520  0.020  1.520
 Z6W  C1   O1    single  1.404  0.020  1.404
 Z6W  C1   H11   single  0.970  0.020  1.090
 Z6W  C1   H12   single  0.970  0.020  1.090
 Z6W  C2   C3    single  1.553  0.020  1.553
 Z6W  C2   O5    single  1.424  0.020  1.424
 Z6W  C3   C4    single  1.522  0.020  1.522
 Z6W  C3   O3    single  1.400  0.020  1.400
 Z6W  C3   H3    single  0.970  0.020  1.090
 Z6W  C4   C5    single  1.523  0.020  1.523
 Z6W  C4   O4    single  1.401  0.020  1.401
 Z6W  C4   H4    single  0.970  0.020  1.090
 Z6W  C5   O5    single  1.423  0.020  1.423
 Z6W  C5   C6    single  1.514  0.020  1.514
 Z6W  C5   H5    single  0.970  0.020  1.090
 Z6W  O1   HO1   single  0.850  0.020  0.980
 Z6W  O3   HO3   single  0.850  0.020  0.980
 Z6W  O4   HO4   single  0.850  0.020  0.980
 Z6W  C7   C8    single  1.523  0.020  1.523
 Z6W  C7   O7    single  1.414  0.020  1.414
 Z6W  C7   C6    single  1.531  0.020  1.531
 Z6W  C7   H7    single  0.970  0.020  1.090
 Z6W  C8   C9    single  1.524  0.020  1.524
 Z6W  C8   H71   single  0.970  0.020  1.090
 Z6W  C8   H72   single  0.970  0.020  1.090
 Z6W  C9   C10   single  1.524  0.020  1.524
 Z6W  C9   H81   single  0.970  0.020  1.090
 Z6W  C9   H82   single  0.970  0.020  1.090
 Z6W  C10  C11   single  1.523  0.020  1.523
 Z6W  C10  H91   single  0.970  0.020  1.090
 Z6W  C10  H92   single  0.970  0.020  1.090
 Z6W  C11  C12   single  1.524  0.020  1.524
 Z6W  C11  H101  single  0.970  0.020  1.090
 Z6W  C11  H102  single  0.970  0.020  1.090
 Z6W  C12  C13   single  1.524  0.020  1.524
 Z6W  C12  H111  single  0.970  0.020  1.090
 Z6W  C12  H112  single  0.970  0.020  1.090
 Z6W  C13  C14   single  1.523  0.020  1.523
 Z6W  C13  H121  single  0.970  0.020  1.090
 Z6W  C13  H122  single  0.970  0.020  1.090
 Z6W  C14  H131  single  0.970  0.020  1.090
 Z6W  C14  H132  single  0.970  0.020  1.090
 Z6W  C14  H133  single  0.970  0.020  1.090
 Z6W  O7   HO7   single  0.850  0.020  0.980
 Z6W  C6   H61   single  0.970  0.020  1.090
 Z6W  C6   H62   single  0.970  0.020  1.090
 Z6W  HO2  O2    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
 Z6W  HO2   O2   C2    110.03  3.000
 Z6W  H12   C1   H11   107.15  3.000
 Z6W  H12   C1   O1    112.19  3.000
 Z6W  H11   C1   O1    111.83  3.000
 Z6W  H12   C1   C2    108.88  3.000
 Z6W  H11   C1   C2    108.13  3.000
 Z6W  O1    C1   C2    108.55  3.000
 Z6W  O5    C2   C3    104.96  3.000
 Z6W  O5    C2   C1    107.19  3.000
 Z6W  C3    C2   C1    113.22  3.000
 Z6W  O5    C2   O2    109.34  3.000
 Z6W  C3    C2   O2    113.27  3.000
 Z6W  C1    C2   O2    108.59  3.000
 Z6W  H3    C3   O3    111.33  3.000
 Z6W  H3    C3   C4    107.93  3.000
 Z6W  O3    C3   C4    114.96  3.000
 Z6W  H3    C3   C2    109.11  3.000
 Z6W  O3    C3   C2    109.89  3.000
 Z6W  C4    C3   C2    103.22  3.000
 Z6W  H4    C4   O4    111.42  3.000
 Z6W  H4    C4   C5    108.77  3.000
 Z6W  O4    C4   C5    115.02  3.000
 Z6W  H4    C4   C3    109.06  3.000
 Z6W  O4    C4   C3    110.88  3.000
 Z6W  C5    C4   C3    101.13  3.000
 Z6W  H5    C5   C6    108.85  3.000
 Z6W  H5    C5   O5    110.07  3.000
 Z6W  C6    C5   O5    110.19  3.000
 Z6W  H5    C5   C4    108.80  3.000
 Z6W  C6    C5   C4    115.88  3.000
 Z6W  O5    C5   C4    102.87  3.000
 Z6W  HO1   O1   C1    108.13  3.000
 Z6W  HO3   O3   C3    108.62  3.000
 Z6W  HO4   O4   C4    108.88  3.000
 Z6W  C5    O5   C2    110.86  3.000
 Z6W  H7    C7   C6    106.82  3.000
 Z6W  H7    C7   O7    109.98  3.000
 Z6W  C6    C7   O7    112.19  3.000
 Z6W  H7    C7   C8    106.79  3.000
 Z6W  C6    C7   C8    112.75  3.000
 Z6W  O7    C7   C8    108.16  3.000
 Z6W  H72   C8   H71   105.73  3.000
 Z6W  H72   C8   C9    109.63  3.000
 Z6W  H71   C8   C9    109.05  3.000
 Z6W  H72   C8   C7    107.65  3.000
 Z6W  H71   C8   C7    108.45  3.000
 Z6W  C9    C8   C7    115.85  3.000
 Z6W  H82   C9   H81   106.24  3.000
 Z6W  H82   C9   C10   109.38  3.000
 Z6W  H81   C9   C10   108.93  3.000
 Z6W  H82   C9   C8    109.86  3.000
 Z6W  H81   C9   C8    110.27  3.000
 Z6W  C10   C9   C8    111.98  3.000
 Z6W  H92   C10  H91   105.92  3.000
 Z6W  H92   C10  C11   109.35  3.000
 Z6W  H91   C10  C11   109.20  3.000
 Z6W  H92   C10  C9    109.25  3.000
 Z6W  H91   C10  C9    109.37  3.000
 Z6W  C11   C10  C9    113.46  3.000
 Z6W  H102  C11  H101  106.00  3.000
 Z6W  H102  C11  C12   109.34  3.000
 Z6W  H101  C11  C12   109.34  3.000
 Z6W  H102  C11  C10   109.31  3.000
 Z6W  H101  C11  C10   109.50  3.000
 Z6W  C12   C11  C10   113.10  3.000
 Z6W  H112  C12  H111  105.94  3.000
 Z6W  H112  C12  C13   109.30  3.000
 Z6W  H111  C12  C13   109.22  3.000
 Z6W  H112  C12  C11   109.32  3.000
 Z6W  H111  C12  C11   109.34  3.000
 Z6W  C13   C12  C11   113.45  3.000
 Z6W  H122  C13  H121  106.02  3.000
 Z6W  H122  C13  C14   109.55  3.000
 Z6W  H121  C13  C14   109.63  3.000
 Z6W  H122  C13  C12   109.30  3.000
 Z6W  H121  C13  C12   109.31  3.000
 Z6W  C14   C13  C12   112.80  3.000
 Z6W  H133  C14  H132  107.46  3.000
 Z6W  H133  C14  H131  107.62  3.000
 Z6W  H132  C14  H131  107.59  3.000
 Z6W  H133  C14  C13   111.18  3.000
 Z6W  H132  C14  C13   111.09  3.000
 Z6W  H131  C14  C13   111.70  3.000
 Z6W  HO7   O7   C7    107.89  3.000
 Z6W  H62   C6   H61   106.97  3.000
 Z6W  H62   C6   C7    110.83  3.000
 Z6W  H61   C6   C7    108.50  3.000
 Z6W  H62   C6   C5    109.73  3.000
 Z6W  H61   C6   C5    107.38  3.000
 Z6W  C7    C6   C5    113.18  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
 Z6W  Var_01  C10   C9   C8   C7   -179.30  30.0  3
 Z6W  Var_02  C11   C10  C9   C8   -178.19  30.0  3
 Z6W  Var_03  C12   C11  C10  C9   -179.12  30.0  3
 Z6W  Var_04  C13   C12  C11  C10  -178.99  30.0  3
 Z6W  Var_05  C14   C13  C12  C11  -179.75  30.0  3
 Z6W  Var_06  H131  C14  C13  C12  -179.28  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
 Z6W  chir_01  C2  C1  C3  O5  positiv
 Z6W  chir_02  C3  O3  C2  C4  positiv
 Z6W  chir_03  C4  O4  C3  C5  negativ
 Z6W  chir_04  C5  O5  C6  C4  positiv
 Z6W  chir_05  C7  O7  C6  C8  negativ

