# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 18:19:17 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(3-chloro-2,5-dihydroxyphenyl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2cc(O)cc(Cl)c2O
#
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
 Z16  Z16  (1S)-1,5-anhydro-1-(3-chloro-2,5-dihydroxyphenyl)-D-glucitol  D-saccharide  35  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 PERFECT
;

data_comp_Z16
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
 Z16  C1    C   CR6   0   0.354   1.8936  -0.5401  -0.3281
 Z16  O1    O   OH1   0  -0.648   1.7384  -1.6966  -1.0062
 Z16  C2    C   CR6   0  -0.020   0.8120   0.2398   0.1040
 Z16  C3    C   CR16  0  -0.403   1.0382   1.4166   0.8028
 Z16  C4    C   CR6   0   0.365   2.3334   1.8576   1.0558
 Z16  O4    O   OH1   0  -0.638   2.4810   3.0147   1.7359
 Z16  C5    C   CR16  0  -0.362   3.4138   1.1143   0.6025
 Z16  C6    C   CR6   0  -0.126   3.1777  -0.0726  -0.0739
 Z16  CL6   CL  CL    0  -0.113   4.5254  -1.0085  -0.6220
 Z16  C1'   C   CH1   0  -0.020  -0.5968  -0.1997  -0.2197
 Z16  C2'   C   CH1   0   0.065  -1.1059  -1.2945   0.7249
 Z16  O2'   O   OH1   0  -0.688  -0.2358  -2.4002   0.6302
 Z16  C3'   C   CH1   0  -0.029  -2.5229  -1.6657   0.3192
 Z16  O3'   O   OH1   0  -0.674  -2.9906  -2.6447   1.2211
 Z16  C4'   C   CH1   0   0.019  -3.4131  -0.4253   0.3123
 Z16  O4'   O   OH1   0  -0.672  -4.6878  -0.7205  -0.2076
 Z16  C5'   C   CH1   0  -0.013  -2.7751   0.6550  -0.5642
 Z16  O5'   O   O2    0  -0.492  -1.4529   0.9068  -0.1294
 Z16  C6'   C   CH2   0  -0.156  -3.5356   1.9611  -0.4915
 Z16  O6'   O   OH1   0  -0.670  -2.9624   2.8752  -1.3952
 Z16  HO1   H   HOH1  0   0.476   1.0151  -2.2030  -0.5869
 Z16  H3    H   HCR6  0   0.268   0.2046   2.0171   1.1414
 Z16  HO4   H   HOH1  0   0.475   3.4136   3.2405   1.8211
 Z16  H5    H   HCR6  0   0.291   4.4310   1.4422   0.7788
 Z16  H1'   H   HCH1  0   0.243  -0.6122  -0.6012  -1.2475
 Z16  H2'   H   HCH1  0   0.235  -1.1054  -0.8942   1.7496
 Z16  HO2'  H   HOH1  0   0.473  -0.6367  -3.1647   1.0611
 Z16  H3'   H   HCH1  0   0.229  -2.4862  -2.0654  -0.7054
 Z16  HO3'  H   HOH1  0   0.463  -3.5793  -3.2451   0.7555
 Z16  H4'   H   HCH1  0   0.221  -3.4863  -0.0385   1.3397
 Z16  HO4'  H   HOH1  0   0.459  -5.2102  -1.1408   0.4818
 Z16  H5'   H   HCH1  0   0.224  -2.7621   0.3007  -1.6081
 Z16  H6'   H   HCH2  0   0.212  -4.5850   1.7606  -0.7294
 Z16  H6'A  H   HCH2  0   0.197  -3.5028   2.3322   0.5425
 Z16  HO6'  H   HOH1  0   0.457  -3.4908   3.6780  -1.3795

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
 Z16  C2   C1    aromatic  1.402  0.020  1.402
 Z16  C1   O1    single    1.350  0.020  1.350
 Z16  C1   C6    aromatic  1.390  0.020  1.390
 Z16  O1   HO1   single    0.850  0.020  0.980
 Z16  C1'  C2    single    1.511  0.020  1.511
 Z16  C3   C2    aromatic  1.387  0.020  1.387
 Z16  C3   C4    aromatic  1.391  0.020  1.391
 Z16  C3   H3    single    0.930  0.020  1.080
 Z16  O4   C4    single    1.350  0.020  1.350
 Z16  C4   C5    aromatic  1.388  0.020  1.388
 Z16  O4   HO4   single    0.850  0.020  0.980
 Z16  C5   C6    aromatic  1.386  0.020  1.386
 Z16  C5   H5    single    0.930  0.020  1.080
 Z16  C6   CL6   single    1.730  0.020  1.730
 Z16  C2'  C1'   single    1.533  0.020  1.533
 Z16  C1'  O5'   single    1.402  0.020  1.402
 Z16  C1'  H1'   single    0.970  0.020  1.090
 Z16  C3'  C2'   single    1.520  0.020  1.520
 Z16  O2'  C2'   single    1.410  0.020  1.410
 Z16  C2'  H2'   single    0.970  0.020  1.090
 Z16  O2'  HO2'  single    0.850  0.020  0.980
 Z16  O3'  C3'   single    1.411  0.020  1.411
 Z16  C3'  C4'   single    1.527  0.020  1.527
 Z16  C3'  H3'   single    0.970  0.020  1.090
 Z16  O3'  HO3'  single    0.850  0.020  0.980
 Z16  O4'  C4'   single    1.408  0.020  1.408
 Z16  C4'  C5'   single    1.530  0.020  1.530
 Z16  C4'  H4'   single    0.970  0.020  1.090
 Z16  O4'  HO4'  single    0.850  0.020  0.980
 Z16  C5'  C6'   single    1.513  0.020  1.513
 Z16  C5'  O5'   single    1.414  0.020  1.414
 Z16  C5'  H5'   single    0.970  0.020  1.090
 Z16  O6'  C6'   single    1.407  0.020  1.407
 Z16  C6'  H6'   single    0.970  0.020  1.090
 Z16  C6'  H6'A  single    0.970  0.020  1.090
 Z16  O6'  HO6'  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
 Z16  C6    C1   C2   118.00  3.000
 Z16  C6    C1   O1   119.10  3.000
 Z16  C2    C1   O1   122.88  3.000
 Z16  HO1   O1   C1   108.27  3.000
 Z16  C1'   C2   C3   120.45  3.000
 Z16  C3    C2   C1   120.09  3.000
 Z16  C1'   C2   C1   119.45  3.000
 Z16  H3    C3   C4   118.97  3.000
 Z16  H3    C3   C2   120.20  3.000
 Z16  C4    C3   C2   120.81  3.000
 Z16  C5    C4   O4   122.58  3.000
 Z16  C5    C4   C3   119.71  3.000
 Z16  O4    C4   C3   117.71  3.000
 Z16  HO4   O4   C4   110.57  3.000
 Z16  H5    C5   C6   119.90  3.000
 Z16  H5    C5   C4   121.06  3.000
 Z16  C6    C5   C4   119.04  3.000
 Z16  CL6   C6   C5   119.01  3.000
 Z16  CL6   C6   C1   118.68  3.000
 Z16  C5    C6   C1   122.31  3.000
 Z16  H1'   C1'  O5'  109.80  3.000
 Z16  H1'   C1'  C2'  108.03  3.000
 Z16  O5'   C1'  C2'  108.73  3.000
 Z16  H1'   C1'  C2   108.56  3.000
 Z16  O5'   C1'  C2   109.03  3.000
 Z16  C2'   C1'  C2   112.66  3.000
 Z16  H2'   C2'  C3'  109.75  3.000
 Z16  H2'   C2'  O2'  110.34  3.000
 Z16  C3'   C2'  O2'  111.46  3.000
 Z16  H2'   C2'  C1'  108.30  3.000
 Z16  O2'   C2'  C1'  108.28  3.000
 Z16  C3'   C2'  C1'  108.63  3.000
 Z16  HO2'  O2'  C2'  109.56  3.000
 Z16  H3'   C3'  C4'  108.07  3.000
 Z16  H3'   C3'  O3'  110.75  3.000
 Z16  C4'   C3'  O3'  111.92  3.000
 Z16  H3'   C3'  C2'  107.83  3.000
 Z16  C4'   C3'  C2'  110.27  3.000
 Z16  O3'   C3'  C2'  107.93  3.000
 Z16  HO3'  O3'  C3'  109.07  3.000
 Z16  H4'   C4'  C5'  108.32  3.000
 Z16  H4'   C4'  O4'  110.99  3.000
 Z16  C5'   C4'  O4'  108.30  3.000
 Z16  H4'   C4'  C3'  108.67  3.000
 Z16  C5'   C4'  C3'  109.45  3.000
 Z16  O4'   C4'  C3'  111.06  3.000
 Z16  HO4'  O4'  C4'  108.59  3.000
 Z16  H5'   C5'  C6'  109.20  3.000
 Z16  H5'   C5'  O5'  109.72  3.000
 Z16  C6'   C5'  O5'  107.54  3.000
 Z16  H5'   C5'  C4'  108.68  3.000
 Z16  O5'   C5'  C4'  109.83  3.000
 Z16  C6'   C5'  C4'  111.85  3.000
 Z16  C5'   O5'  C1'  114.23  3.000
 Z16  H6'A  C6'  H6'  107.16  3.000
 Z16  H6'A  C6'  O6'  111.88  3.000
 Z16  H6'   C6'  O6'  111.71  3.000
 Z16  H6'A  C6'  C5'  108.76  3.000
 Z16  H6'   C6'  C5'  108.25  3.000
 Z16  O6'   C6'  C5'  108.96  3.000
 Z16  HO6'  O6'  C6'  107.94  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
 Z16  CONST_01  C4   C3  C2  C1    0.00  0.0  0
 Z16  CONST_02  C4   C5  C6  C1    0.00  0.0  0
 Z16  CONST_03  C5   C6  C1  C2    0.00  0.0  0
 Z16  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 Z16  CONST_05  C6   C1  C2  C3    0.00  0.0  0
 Z16  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 Z16  CONST_07  C1'  C2  C3  C4  180.00  0.0  0
 Z16  CONST_08  C1'  C2  C1  C6  180.00  0.0  0
 Z16  CONST_09  C1'  C2  C1  O1    0.00  0.0  0
 Z16  CONST_10  C3   C2  C1  O1  180.00  0.0  0
 Z16  CONST_11  C5   C6  C1  O1  180.00  0.0  0
 Z16  CONST_12  CL6  C6  C1  C2  180.00  0.0  0
 Z16  CONST_13  O4   C4  C3  C2  180.00  0.0  0
 Z16  CONST_14  CL6  C6  C5  C4  180.00  0.0  0
 Z16  CONST_15  C6   C5  C4  O4  180.00  0.0  0
 Z16  CONST_16  H3   C3  C2  C1  180.00  0.0  0
 Z16  CONST_17  H5   C5  C6  C1  180.00  0.0  0

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
 Z16  chir_01  C1'  C2   C2'  O5'  negativ
 Z16  chir_02  C2'  O2'  C1'  C3'  negativ
 Z16  chir_03  C3'  O3'  C2'  C4'  positiv
 Z16  chir_04  C4'  O4'  C5'  C3'  positiv
 Z16  chir_05  C5'  O5'  C6'  C4'  positiv

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
 Z16  plan-1  C1   0.020
 Z16  plan-1  O1   0.020
 Z16  plan-1  C2   0.020
 Z16  plan-1  C3   0.020
 Z16  plan-1  C4   0.020
 Z16  plan-1  O4   0.020
 Z16  plan-1  C5   0.020
 Z16  plan-1  C6   0.020
 Z16  plan-1  CL6  0.020
 Z16  plan-1  C1'  0.020
 Z16  plan-1  H3   0.020
 Z16  plan-1  H5   0.020

