# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:22:49 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(3-chloro-2-hydroxy-5-methoxyphenyl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cl)c(O)c(c1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
#
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
 Z2T  Z2T  (1S)-1,5-anhydro-1-(3-chloro-2-hydroxy-5-methoxyphenyl)-D-glucitol  D-saccharide  38  21  .  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_Z2T
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
 Z2T  C1    C   CR6   0   0.355   1.6662  -0.9198  -0.4959
 Z2T  O1    O   OH1   0  -0.648   1.3583  -2.1164  -1.0376
 Z2T  C2    C   CR6   0  -0.020   0.6939   0.0143  -0.1073
 Z2T  C3    C   CR16  0  -0.411   1.0802   1.2199   0.4535
 Z2T  C4    C   CR6   0   0.393   2.4272   1.5420   0.6148
 Z2T  O4    O   O2    0  -0.475   2.6923   2.7422   1.1697
 Z2T  C5    C   CR16  0  -0.359   3.4001   0.6426   0.2011
 Z2T  C6    C   CR6   0  -0.126   3.0010  -0.5720  -0.3408
 Z2T  CL6   CL  CL    0  -0.113   4.2147  -1.7010  -0.8389
 Z2T  C7    C   CH3   0  -0.439   4.0431   3.1038   1.3708
 Z2T  C1'   C   CH1   0  -0.013  -0.7712  -0.2971  -0.3155
 Z2T  C2'   C   CH1   0   0.059  -1.3266  -1.2192   0.7764
 Z2T  O2'   O   OH1   0  -0.688  -0.6215  -2.4394   0.7037
 Z2T  C3'   C   CH1   0  -0.021  -2.8160  -1.4297   0.5553
 Z2T  O3'   O   OH1   0  -0.673  -3.2992  -2.2051   1.6300
 Z2T  C4'   C   CH1   0   0.016  -3.5413  -0.0916   0.4418
 Z2T  O4'   O   OH1   0  -0.672  -4.8884  -0.2808   0.0747
 Z2T  C5'   C   CH1   0  -0.013  -2.8621   0.7623  -0.6288
 Z2T  O5'   O   O2    0  -0.493  -1.4908   0.9050  -0.3160
 Z2T  C6'   C   CH2   0  -0.155  -3.4599   2.1497  -0.7175
 Z2T  O6'   O   OH1   0  -0.670  -2.8521   2.8374  -1.7849
 Z2T  HO1   H   HOH1  0   0.477   0.6052  -2.4922  -0.5410
 Z2T  H3    H   HCR6  0   0.265   0.3344   1.9416   0.7583
 Z2T  H5    H   HCR6  0   0.297   4.4560   0.8527   0.2982
 Z2T  H7    H   HCH3  0   0.228   4.5951   3.1653   0.4288
 Z2T  H7A   H   HCH3  0   0.261   4.0350   4.0869   1.8348
 Z2T  H7B   H   HCH3  0   0.229   4.5582   2.4053   2.0359
 Z2T  H1'   H   HCH1  0   0.244  -0.8906  -0.8051  -1.2876
 Z2T  H2'   H   HCH1  0   0.237  -1.1612  -0.7402   1.7524
 Z2T  HO2'  H   HOH1  0   0.475  -1.0016  -3.0762   1.3197
 Z2T  H3'   H   HCH1  0   0.225  -2.9437  -1.9662  -0.3976
 Z2T  HO3'  H   HOH1  0   0.460  -4.0725  -2.6958   1.3379
 Z2T  H4'   H   HCH1  0   0.223  -3.4666   0.4374   1.4033
 Z2T  HO4'  H   HOH1  0   0.458  -5.3954  -0.4957   0.8628
 Z2T  H5'   H   HCH1  0   0.223  -2.9722   0.2629  -1.6056
 Z2T  H6'   H   HCH2  0   0.213  -4.5398   2.0481  -0.8636
 Z2T  H6'A  H   HCH2  0   0.197  -3.3094   2.6670   0.2405
 Z2T  HO6'  H   HOH1  0   0.457  -3.2735   3.6980  -1.8602

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
 Z2T  C2   C1    aromatic  1.403  0.020  1.403
 Z2T  C1   O1    single    1.349  0.020  1.349
 Z2T  C1   C6    aromatic  1.388  0.020  1.388
 Z2T  O1   HO1   single    0.850  0.020  0.980
 Z2T  C1'  C2    single    1.512  0.020  1.512
 Z2T  C3   C2    aromatic  1.385  0.020  1.385
 Z2T  C3   C4    aromatic  1.394  0.020  1.394
 Z2T  C3   H3    single    0.930  0.020  1.080
 Z2T  O4   C4    single    1.349  0.020  1.349
 Z2T  C4   C5    aromatic  1.388  0.020  1.388
 Z2T  O4   C7    single    1.413  0.020  1.413
 Z2T  C5   C6    aromatic  1.389  0.020  1.389
 Z2T  C5   H5    single    0.930  0.020  1.080
 Z2T  C6   CL6   single    1.731  0.020  1.731
 Z2T  C7   H7    single    0.970  0.020  1.090
 Z2T  C7   H7A   single    0.970  0.020  1.090
 Z2T  C7   H7B   single    0.970  0.020  1.090
 Z2T  C2'  C1'   single    1.533  0.020  1.533
 Z2T  C1'  O5'   single    1.401  0.020  1.401
 Z2T  C1'  H1'   single    0.970  0.020  1.090
 Z2T  C3'  C2'   single    1.520  0.020  1.520
 Z2T  O2'  C2'   single    1.411  0.020  1.411
 Z2T  C2'  H2'   single    0.970  0.020  1.090
 Z2T  O2'  HO2'  single    0.850  0.020  0.980
 Z2T  O3'  C3'   single    1.411  0.020  1.411
 Z2T  C3'  C4'   single    1.526  0.020  1.526
 Z2T  C3'  H3'   single    0.970  0.020  1.090
 Z2T  O3'  HO3'  single    0.850  0.020  0.980
 Z2T  O4'  C4'   single    1.409  0.020  1.409
 Z2T  C4'  C5'   single    1.529  0.020  1.529
 Z2T  C4'  H4'   single    0.970  0.020  1.090
 Z2T  O4'  HO4'  single    0.850  0.020  0.980
 Z2T  C5'  C6'   single    1.513  0.020  1.513
 Z2T  C5'  O5'   single    1.414  0.020  1.414
 Z2T  C5'  H5'   single    0.970  0.020  1.090
 Z2T  O6'  C6'   single    1.408  0.020  1.408
 Z2T  C6'  H6'   single    0.970  0.020  1.090
 Z2T  C6'  H6'A  single    0.970  0.020  1.090
 Z2T  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
 Z2T  C6    C1   C2   117.94  3.000
 Z2T  C6    C1   O1   119.12  3.000
 Z2T  C2    C1   O1   122.92  3.000
 Z2T  HO1   O1   C1   108.23  3.000
 Z2T  C1'   C2   C3   120.36  3.000
 Z2T  C3    C2   C1   119.90  3.000
 Z2T  C1'   C2   C1   119.74  3.000
 Z2T  H3    C3   C4   118.65  3.000
 Z2T  H3    C3   C2   120.17  3.000
 Z2T  C4    C3   C2   121.17  3.000
 Z2T  C5    C4   O4   124.16  3.000
 Z2T  C5    C4   C3   119.53  3.000
 Z2T  O4    C4   C3   116.30  3.000
 Z2T  C7    O4   C4   118.32  3.000
 Z2T  H5    C5   C6   119.07  3.000
 Z2T  H5    C5   C4   122.13  3.000
 Z2T  C6    C5   C4   118.79  3.000
 Z2T  CL6   C6   C5   118.77  3.000
 Z2T  CL6   C6   C1   118.60  3.000
 Z2T  C5    C6   C1   122.63  3.000
 Z2T  H7B   C7   H7A  108.76  3.000
 Z2T  H7B   C7   H7   108.79  3.000
 Z2T  H7A   C7   H7   108.69  3.000
 Z2T  H7B   C7   O4   111.93  3.000
 Z2T  H7A   C7   O4   106.57  3.000
 Z2T  H7    C7   O4   111.99  3.000
 Z2T  H1'   C1'  O5'  109.82  3.000
 Z2T  H1'   C1'  C2'  108.14  3.000
 Z2T  O5'   C1'  C2'  109.28  3.000
 Z2T  H1'   C1'  C2   108.72  3.000
 Z2T  O5'   C1'  C2   108.72  3.000
 Z2T  C2'   C1'  C2   112.13  3.000
 Z2T  H2'   C2'  C3'  109.67  3.000
 Z2T  H2'   C2'  O2'  110.32  3.000
 Z2T  C3'   C2'  O2'  111.24  3.000
 Z2T  H2'   C2'  C1'  108.40  3.000
 Z2T  O2'   C2'  C1'  107.60  3.000
 Z2T  C3'   C2'  C1'  109.54  3.000
 Z2T  HO2'  O2'  C2'  109.95  3.000
 Z2T  H3'   C3'  C4'  107.93  3.000
 Z2T  H3'   C3'  O3'  110.59  3.000
 Z2T  C4'   C3'  O3'  112.07  3.000
 Z2T  H3'   C3'  C2'  107.88  3.000
 Z2T  C4'   C3'  C2'  110.80  3.000
 Z2T  O3'   C3'  C2'  107.51  3.000
 Z2T  HO3'  O3'  C3'  108.95  3.000
 Z2T  H4'   C4'  C5'  108.26  3.000
 Z2T  H4'   C4'  O4'  110.93  3.000
 Z2T  C5'   C4'  O4'  108.51  3.000
 Z2T  H4'   C4'  C3'  108.93  3.000
 Z2T  C5'   C4'  C3'  109.31  3.000
 Z2T  O4'   C4'  C3'  110.86  3.000
 Z2T  HO4'  O4'  C4'  108.70  3.000
 Z2T  H5'   C5'  C6'  108.89  3.000
 Z2T  H5'   C5'  O5'  109.79  3.000
 Z2T  C6'   C5'  O5'  107.68  3.000
 Z2T  H5'   C5'  C4'  108.85  3.000
 Z2T  O5'   C5'  C4'  109.42  3.000
 Z2T  C6'   C5'  C4'  112.19  3.000
 Z2T  C5'   O5'  C1'  114.31  3.000
 Z2T  H6'A  C6'  H6'  107.16  3.000
 Z2T  H6'A  C6'  O6'  111.83  3.000
 Z2T  H6'   C6'  O6'  111.73  3.000
 Z2T  H6'A  C6'  C5'  109.04  3.000
 Z2T  H6'   C6'  C5'  108.21  3.000
 Z2T  O6'   C6'  C5'  108.77  3.000
 Z2T  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
 Z2T  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 Z2T  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 Z2T  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 Z2T  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 Z2T  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 Z2T  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 Z2T  CONST_07  C1'  C2  C3  C4  180.00   0.0  0
 Z2T  CONST_08  C1'  C2  C1  C6  180.00   0.0  0
 Z2T  CONST_09  C1'  C2  C1  O1    0.00   0.0  0
 Z2T  CONST_10  C3   C2  C1  O1  180.00   0.0  0
 Z2T  CONST_11  C5   C6  C1  O1  180.00   0.0  0
 Z2T  CONST_12  CL6  C6  C1  C2  180.00   0.0  0
 Z2T  CONST_13  O4   C4  C3  C2  180.00   0.0  0
 Z2T  CONST_14  CL6  C6  C5  C4  180.00   0.0  0
 Z2T  CONST_15  C6   C5  C4  O4  180.00   0.0  0
 Z2T  CONST_16  H3   C3  C2  C1  180.00   0.0  0
 Z2T  CONST_17  H5   C5  C6  C1  180.00   0.0  0
 Z2T  Var_01    H7   C7  O4  C4   62.04  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
 Z2T  chir_01  C1'  C2   C2'  O5'  negativ
 Z2T  chir_02  C2'  O2'  C1'  C3'  negativ
 Z2T  chir_03  C3'  O3'  C2'  C4'  positiv
 Z2T  chir_04  C4'  O4'  C5'  C3'  positiv
 Z2T  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
 Z2T  plan-1  C1   0.020
 Z2T  plan-1  O1   0.020
 Z2T  plan-1  C2   0.020
 Z2T  plan-1  C3   0.020
 Z2T  plan-1  C4   0.020
 Z2T  plan-1  O4   0.020
 Z2T  plan-1  C5   0.020
 Z2T  plan-1  C6   0.020
 Z2T  plan-1  CL6  0.020
 Z2T  plan-1  C1'  0.020
 Z2T  plan-1  H3   0.020
 Z2T  plan-1  H5   0.020

