# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:35:55 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(4-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)c(Cl)cc2O
#
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
 Z15  Z15  (1S)-1,5-anhydro-1-(4-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_Z15
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
 Z15  C1    C   CR6   0   0.300   1.6009  -1.0654  -0.8352
 Z15  O1    O   OH1   0  -0.667   1.1607  -2.0947  -1.5976
 Z15  C2    C   CR6   0  -0.016   0.7270  -0.1635  -0.2128
 Z15  C3    C   CR16  0  -0.404   1.2511   0.8570   0.5675
 Z15  C4    C   CR6   0   0.418   2.6219   1.0323   0.7232
 Z15  O4    O   OH1   0  -0.622   3.0498   2.0494   1.4943
 Z15  C5    C   CR6   0  -0.168   3.4690   0.1486   0.0632
 Z15  CL5   CL  CL    0  -0.118   5.1858   0.3510   0.2212
 Z15  C6    C   CR16  0  -0.299   2.9709  -0.8943  -0.6991
 Z15  C1'   C   CH1   0  -0.017  -0.7655  -0.2926  -0.4025
 Z15  C2'   C   CH1   0   0.061  -1.3768  -1.3660   0.5053
 Z15  O2'   O   OH1   0  -0.688  -0.7744  -2.5993   0.1814
 Z15  C3'   C   CH1   0  -0.022  -2.8804  -1.4071   0.2892
 Z15  O3'   O   OH1   0  -0.674  -3.4142  -2.3571   1.1847
 Z15  C4'   C   CH1   0   0.015  -3.4857  -0.0203   0.4948
 Z15  O4'   O   OH1   0  -0.673  -4.8509  -0.0120   0.1469
 Z15  C5'   C   CH1   0  -0.013  -2.7542   0.9906  -0.3907
 Z15  O5'   O   O2    0  -0.491  -1.3666   0.9423  -0.1231
 Z15  C6'   C   CH2   0  -0.156  -3.2192   2.4071  -0.1310
 Z15  O6'   O   OH1   0  -0.670  -2.5740   3.2734  -1.0332
 Z15  HO1   H   HOH1  0   0.473   0.3961  -2.5029  -1.1493
 Z15  H3    H   HCR6  0   0.273   0.5901   1.5565   1.0622
 Z15  HO4   H   HOH1  0   0.467   4.0133   2.0592   1.5502
 Z15  H6    H   HCR6  0   0.285   3.6480  -1.5831  -1.1874
 Z15  H1'   H   HCH1  0   0.241  -0.9628  -0.5792  -1.4495
 Z15  H2'   H   HCH1  0   0.235  -1.1632  -1.0963   1.5498
 Z15  HO2'  H   HOH1  0   0.473  -1.2161  -3.3125   0.6567
 Z15  H3'   H   HCH1  0   0.225  -3.0655  -1.7084  -0.7533
 Z15  HO3'  H   HOH1  0   0.461  -4.2289  -2.7112   0.8169
 Z15  H4'   H   HCH1  0   0.223  -3.3453   0.2757   1.5453
 Z15  HO4'  H   HOH1  0   0.460  -5.3637  -0.3105   0.9032
 Z15  H5'   H   HCH1  0   0.223  -2.9389   0.7346  -1.4475
 Z15  H6'   H   HCH2  0   0.212  -4.3073   2.4378  -0.2470
 Z15  H6'A  H   HCH2  0   0.197  -2.9977   2.6661   0.9141
 Z15  HO6'  H   HOH1  0   0.457  -2.9076   4.1616  -0.8797

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
 Z15  C2   C1    aromatic  1.402  0.020  1.402
 Z15  C1   O1    single    1.354  0.020  1.354
 Z15  C1   C6    aromatic  1.387  0.020  1.387
 Z15  O1   HO1   single    0.850  0.020  0.980
 Z15  C1'  C2    single    1.510  0.020  1.510
 Z15  C3   C2    aromatic  1.387  0.020  1.387
 Z15  C3   C4    aromatic  1.391  0.020  1.391
 Z15  C3   H3    single    0.930  0.020  1.080
 Z15  O4   C4    single    1.346  0.020  1.346
 Z15  C4   C5    aromatic  1.391  0.020  1.391
 Z15  O4   HO4   single    0.850  0.020  0.980
 Z15  C5   C6    aromatic  1.385  0.020  1.385
 Z15  C5   CL5   single    1.736  0.020  1.736
 Z15  C6   H6    single    0.930  0.020  1.080
 Z15  C2'  C1'   single    1.533  0.020  1.533
 Z15  C1'  O5'   single    1.402  0.020  1.402
 Z15  C1'  H1'   single    0.970  0.020  1.090
 Z15  C3'  C2'   single    1.520  0.020  1.520
 Z15  O2'  C2'   single    1.410  0.020  1.410
 Z15  C2'  H2'   single    0.970  0.020  1.090
 Z15  O2'  HO2'  single    0.850  0.020  0.980
 Z15  O3'  C3'   single    1.410  0.020  1.410
 Z15  C3'  C4'   single    1.527  0.020  1.527
 Z15  C3'  H3'   single    0.970  0.020  1.090
 Z15  O3'  HO3'  single    0.850  0.020  0.980
 Z15  O4'  C4'   single    1.409  0.020  1.409
 Z15  C4'  C5'   single    1.530  0.020  1.530
 Z15  C4'  H4'   single    0.970  0.020  1.090
 Z15  O4'  HO4'  single    0.850  0.020  0.980
 Z15  C5'  C6'   single    1.513  0.020  1.513
 Z15  C5'  O5'   single    1.414  0.020  1.414
 Z15  C5'  H5'   single    0.970  0.020  1.090
 Z15  O6'  C6'   single    1.407  0.020  1.407
 Z15  C6'  H6'   single    0.970  0.020  1.090
 Z15  C6'  H6'A  single    0.970  0.020  1.090
 Z15  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
 Z15  C6    C1   C2   119.53  3.000
 Z15  C6    C1   O1   118.02  3.000
 Z15  C2    C1   O1   122.44  3.000
 Z15  HO1   O1   C1   108.29  3.000
 Z15  C1'   C2   C3   120.45  3.000
 Z15  C3    C2   C1   119.18  3.000
 Z15  C1'   C2   C1   120.36  3.000
 Z15  H3    C3   C4   118.00  3.000
 Z15  H3    C3   C2   120.12  3.000
 Z15  C4    C3   C2   121.87  3.000
 Z15  C5    C4   O4   123.94  3.000
 Z15  C5    C4   C3   117.85  3.000
 Z15  O4    C4   C3   118.21  3.000
 Z15  HO4   O4   C4   110.99  3.000
 Z15  C6    C5   CL5  119.59  3.000
 Z15  CL5   C5   C4   119.02  3.000
 Z15  C6    C5   C4   121.39  3.000
 Z15  H6    C6   C5   120.18  3.000
 Z15  H6    C6   C1   119.68  3.000
 Z15  C5    C6   C1   120.14  3.000
 Z15  H1'   C1'  O5'  109.96  3.000
 Z15  H1'   C1'  C2'  107.99  3.000
 Z15  O5'   C1'  C2'  109.14  3.000
 Z15  H1'   C1'  C2   108.55  3.000
 Z15  O5'   C1'  C2   108.88  3.000
 Z15  C2'   C1'  C2   112.31  3.000
 Z15  H2'   C2'  C3'  109.51  3.000
 Z15  H2'   C2'  O2'  110.47  3.000
 Z15  C3'   C2'  O2'  111.49  3.000
 Z15  H2'   C2'  C1'  108.26  3.000
 Z15  O2'   C2'  C1'  107.82  3.000
 Z15  C3'   C2'  C1'  109.22  3.000
 Z15  HO2'  O2'  C2'  109.75  3.000
 Z15  H3'   C3'  C4'  108.02  3.000
 Z15  H3'   C3'  O3'  110.69  3.000
 Z15  C4'   C3'  O3'  112.10  3.000
 Z15  H3'   C3'  C2'  107.97  3.000
 Z15  C4'   C3'  C2'  110.40  3.000
 Z15  O3'   C3'  C2'  107.60  3.000
 Z15  HO3'  O3'  C3'  109.02  3.000
 Z15  H4'   C4'  C5'  108.29  3.000
 Z15  H4'   C4'  O4'  110.97  3.000
 Z15  C5'   C4'  O4'  108.45  3.000
 Z15  H4'   C4'  C3'  108.80  3.000
 Z15  C5'   C4'  C3'  109.42  3.000
 Z15  O4'   C4'  C3'  110.86  3.000
 Z15  HO4'  O4'  C4'  108.71  3.000
 Z15  H5'   C5'  C6'  109.28  3.000
 Z15  H5'   C5'  O5'  109.74  3.000
 Z15  C6'   C5'  O5'  107.52  3.000
 Z15  H5'   C5'  C4'  108.73  3.000
 Z15  O5'   C5'  C4'  109.70  3.000
 Z15  C6'   C5'  C4'  111.85  3.000
 Z15  C5'   O5'  C1'  114.41  3.000
 Z15  H6'A  C6'  H6'  107.13  3.000
 Z15  H6'A  C6'  O6'  111.85  3.000
 Z15  H6'   C6'  O6'  111.74  3.000
 Z15  H6'A  C6'  C5'  108.77  3.000
 Z15  H6'   C6'  C5'  108.27  3.000
 Z15  O6'   C6'  C5'  108.98  3.000
 Z15  HO6'  O6'  C6'  107.90  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
 Z15  CONST_01  C4   C3  C2  C1    0.00  0.0  0
 Z15  CONST_02  C4   C5  C6  C1    0.00  0.0  0
 Z15  CONST_03  C5   C6  C1  C2    0.00  0.0  0
 Z15  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 Z15  CONST_05  C6   C1  C2  C3    0.00  0.0  0
 Z15  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 Z15  CONST_07  C1'  C2  C3  C4  180.00  0.0  0
 Z15  CONST_08  C1'  C2  C1  C6  180.00  0.0  0
 Z15  CONST_09  CL5  C5  C6  C1  180.00  0.0  0
 Z15  CONST_10  C1'  C2  C1  O1    0.00  0.0  0
 Z15  CONST_11  C3   C2  C1  O1  180.00  0.0  0
 Z15  CONST_12  C5   C6  C1  O1  180.00  0.0  0
 Z15  CONST_13  O4   C4  C3  C2  180.00  0.0  0
 Z15  CONST_14  CL5  C5  C4  C3  180.00  0.0  0
 Z15  CONST_15  C6   C5  C4  O4  180.00  0.0  0
 Z15  CONST_16  H3   C3  C2  C1  180.00  0.0  0
 Z15  CONST_17  H6   C6  C1  C2  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
 Z15  chir_01  C1'  C2   C2'  O5'  negativ
 Z15  chir_02  C2'  O2'  C1'  C3'  negativ
 Z15  chir_03  C3'  O3'  C2'  C4'  positiv
 Z15  chir_04  C4'  O4'  C5'  C3'  positiv
 Z15  chir_05  C5'  O5'  C4'  C6'  negativ

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
 Z15  plan-1  C1   0.020
 Z15  plan-1  O1   0.020
 Z15  plan-1  C2   0.020
 Z15  plan-1  C3   0.020
 Z15  plan-1  C4   0.020
 Z15  plan-1  O4   0.020
 Z15  plan-1  C5   0.020
 Z15  plan-1  CL5  0.020
 Z15  plan-1  C6   0.020
 Z15  plan-1  C1'  0.020
 Z15  plan-1  H3   0.020
 Z15  plan-1  H6   0.020

