# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 18:30:15 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(4-bromo-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(Br)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
 Z57  Z57  (1S)-1,5-anhydro-1-(4-bromo-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_Z57
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
 Z57  C1    C   CR6   0   0.319   0.9026  -1.1233  -0.9388
 Z57  O1    O   OH1   0  -0.662   0.4466  -2.1666  -1.6643
 Z57  C2    C   CR6   0  -0.033   0.0444  -0.2094  -0.3125
 Z57  C3    C   CR16  0  -0.389   0.6003   0.8224   0.4327
 Z57  C4    C   CR6   0   0.376   1.9737   0.9952   0.5453
 Z57  O4    O   OH1   0  -0.652   2.4825   2.0500   1.2399
 Z57  C5    C   CR6   0  -0.203   2.8040   0.0982  -0.1179
 Z57  BR5   BR  BR    0  -0.036   4.6710   0.3144  -0.0059
 Z57  C6    C   CR16  0  -0.316   2.2803  -0.9553  -0.8485
 Z57  C1'   C   CH1   0  -0.011  -1.4551  -0.3221  -0.4687
 Z57  C2'   C   CH1   0   0.052  -2.0582  -1.3902   0.4519
 Z57  O2'   O   OH1   0  -0.689  -1.5239  -2.6353   0.0561
 Z57  C3'   C   CH1   0  -0.014  -3.5738  -1.3828   0.3307
 Z57  O3'   O   OH1   0  -0.674  -4.0806  -2.3089   1.2657
 Z57  C4'   C   CH1   0   0.016  -4.1253   0.0223   0.5603
 Z57  O4'   O   OH1   0  -0.673  -5.5094   0.0691   0.3023
 Z57  C5'   C   CH1   0  -0.015  -3.4220   0.9975  -0.3841
 Z57  O5'   O   O2    0  -0.492  -2.0255   0.9244  -0.1770
 Z57  C6'   C   CH2   0  -0.154  -3.8446   2.4303  -0.1421
 Z57  O6'   O   OH1   0  -0.670  -3.2187   3.2573  -1.0936
 Z57  HO1   H   HOH1  0   0.477  -0.3348  -2.5402  -1.2105
 Z57  H3    H   HCR6  0   0.273  -0.0414   1.5401   0.9264
 Z57  HO4   H   HOH1  0   0.477   2.6139   1.8053   2.1637
 Z57  H6    H   HCR6  0   0.283   2.9284  -1.6642  -1.3475
 Z57  H1'   H   HCH1  0   0.242  -1.6812  -0.6052  -1.5111
 Z57  H2'   H   HCH1  0   0.240  -1.7700  -1.1576   1.4869
 Z57  HO2'  H   HOH1  0   0.476  -1.7959  -3.3253   0.6709
 Z57  H3'   H   HCH1  0   0.223  -3.8315  -1.6846  -0.6962
 Z57  HO3'  H   HOH1  0   0.460  -4.9247  -2.6433   0.9496
 Z57  H4'   H   HCH1  0   0.221  -3.9059   0.3268   1.5947
 Z57  HO4'  H   HOH1  0   0.459  -5.9792  -0.2453   1.0799
 Z57  H5'   H   HCH1  0   0.222  -3.6607   0.7209  -1.4247
 Z57  H6'   H   HCH2  0   0.213  -4.9355   2.4829  -0.2146
 Z57  H6'A  H   HCH2  0   0.196  -3.5746   2.7121   0.8854
 Z57  HO6'  H   HOH1  0   0.457  -3.5489   4.1515  -0.9707

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
 Z57  C2   C1    aromatic  1.401  0.020  1.401
 Z57  C1   O1    single    1.350  0.020  1.350
 Z57  C1   C6    aromatic  1.391  0.020  1.391
 Z57  O1   HO1   single    0.850  0.020  0.980
 Z57  C1'  C2    single    1.512  0.020  1.512
 Z57  C3   C2    aromatic  1.389  0.020  1.389
 Z57  C3   C4    aromatic  1.389  0.020  1.389
 Z57  C3   H3    single    0.930  0.020  1.080
 Z57  O4   C4    single    1.362  0.020  1.362
 Z57  C4   C5    aromatic  1.391  0.020  1.391
 Z57  O4   HO4   single    0.850  0.020  0.980
 Z57  C5   C6    aromatic  1.385  0.020  1.385
 Z57  C5   BR5   single    1.883  0.020  1.883
 Z57  C6   H6    single    0.930  0.020  1.080
 Z57  C2'  C1'   single    1.534  0.020  1.534
 Z57  C1'  O5'   single    1.401  0.020  1.401
 Z57  C1'  H1'   single    0.970  0.020  1.090
 Z57  C3'  C2'   single    1.521  0.020  1.521
 Z57  O2'  C2'   single    1.412  0.020  1.412
 Z57  C2'  H2'   single    0.970  0.020  1.090
 Z57  O2'  HO2'  single    0.850  0.020  0.980
 Z57  O3'  C3'   single    1.410  0.020  1.410
 Z57  C3'  C4'   single    1.527  0.020  1.527
 Z57  C3'  H3'   single    0.970  0.020  1.090
 Z57  O3'  HO3'  single    0.850  0.020  0.980
 Z57  O4'  C4'   single    1.409  0.020  1.409
 Z57  C4'  C5'   single    1.529  0.020  1.529
 Z57  C4'  H4'   single    0.970  0.020  1.090
 Z57  O4'  HO4'  single    0.850  0.020  0.980
 Z57  C5'  C6'   single    1.513  0.020  1.513
 Z57  C5'  O5'   single    1.414  0.020  1.414
 Z57  C5'  H5'   single    0.970  0.020  1.090
 Z57  O6'  C6'   single    1.407  0.020  1.407
 Z57  C6'  H6'   single    0.970  0.020  1.090
 Z57  C6'  H6'A  single    0.970  0.020  1.090
 Z57  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
 Z57  C6    C1   C2   119.92  3.000
 Z57  C6    C1   O1   117.57  3.000
 Z57  C2    C1   O1   122.50  3.000
 Z57  HO1   O1   C1   108.41  3.000
 Z57  C1'   C2   C3   120.52  3.000
 Z57  C3    C2   C1   118.63  3.000
 Z57  C1'   C2   C1   120.84  3.000
 Z57  H3    C3   C4   117.84  3.000
 Z57  H3    C3   C2   120.01  3.000
 Z57  C4    C3   C2   122.13  3.000
 Z57  C5    C4   O4   121.33  3.000
 Z57  C5    C4   C3   118.13  3.000
 Z57  O4    C4   C3   120.48  3.000
 Z57  HO4   O4   C4   110.05  3.000
 Z57  C6    C5   BR5  119.58  3.000
 Z57  BR5   C5   C4   119.32  3.000
 Z57  C6    C5   C4   121.10  3.000
 Z57  H6    C6   C5   121.00  3.000
 Z57  H6    C6   C1   118.95  3.000
 Z57  C5    C6   C1   120.05  3.000
 Z57  H1'   C1'  O5'  109.96  3.000
 Z57  H1'   C1'  C2'  107.92  3.000
 Z57  O5'   C1'  C2'  109.54  3.000
 Z57  H1'   C1'  C2   108.66  3.000
 Z57  O5'   C1'  C2   108.41  3.000
 Z57  C2'   C1'  C2   112.33  3.000
 Z57  H2'   C2'  C3'  109.59  3.000
 Z57  H2'   C2'  O2'  110.57  3.000
 Z57  C3'   C2'  O2'  111.05  3.000
 Z57  H2'   C2'  C1'  108.35  3.000
 Z57  O2'   C2'  C1'  107.29  3.000
 Z57  C3'   C2'  C1'  109.92  3.000
 Z57  HO2'  O2'  C2'  110.24  3.000
 Z57  H3'   C3'  C4'  107.94  3.000
 Z57  H3'   C3'  O3'  110.75  3.000
 Z57  C4'   C3'  O3'  112.02  3.000
 Z57  H3'   C3'  C2'  107.84  3.000
 Z57  C4'   C3'  C2'  110.64  3.000
 Z57  O3'   C3'  C2'  107.59  3.000
 Z57  HO3'  O3'  C3'  109.03  3.000
 Z57  H4'   C4'  C5'  108.21  3.000
 Z57  H4'   C4'  O4'  111.03  3.000
 Z57  C5'   C4'  O4'  108.52  3.000
 Z57  H4'   C4'  C3'  108.90  3.000
 Z57  C5'   C4'  C3'  109.15  3.000
 Z57  O4'   C4'  C3'  110.97  3.000
 Z57  HO4'  O4'  C4'  108.73  3.000
 Z57  H5'   C5'  C6'  109.14  3.000
 Z57  H5'   C5'  O5'  109.82  3.000
 Z57  C6'   C5'  O5'  107.54  3.000
 Z57  H5'   C5'  C4'  108.86  3.000
 Z57  O5'   C5'  C4'  109.33  3.000
 Z57  C6'   C5'  C4'  112.13  3.000
 Z57  C5'   O5'  C1'  114.68  3.000
 Z57  H6'A  C6'  H6'  107.12  3.000
 Z57  H6'A  C6'  O6'  111.84  3.000
 Z57  H6'   C6'  O6'  111.73  3.000
 Z57  H6'A  C6'  C5'  108.88  3.000
 Z57  H6'   C6'  C5'  108.25  3.000
 Z57  O6'   C6'  C5'  108.91  3.000
 Z57  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
 Z57  CONST_01  C4   C3  C2  C1    0.00  0.0  0
 Z57  CONST_02  C4   C5  C6  C1    0.00  0.0  0
 Z57  CONST_03  C5   C6  C1  C2    0.00  0.0  0
 Z57  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 Z57  CONST_05  C6   C1  C2  C3    0.00  0.0  0
 Z57  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 Z57  CONST_07  C1'  C2  C3  C4  180.00  0.0  0
 Z57  CONST_08  C1'  C2  C1  C6  180.00  0.0  0
 Z57  CONST_09  BR5  C5  C6  C1  180.00  0.0  0
 Z57  CONST_10  C1'  C2  C1  O1    0.00  0.0  0
 Z57  CONST_11  C3   C2  C1  O1  180.00  0.0  0
 Z57  CONST_12  C5   C6  C1  O1  180.00  0.0  0
 Z57  CONST_13  O4   C4  C3  C2  180.00  0.0  0
 Z57  CONST_14  BR5  C5  C4  C3  180.00  0.0  0
 Z57  CONST_15  C6   C5  C4  O4  180.00  0.0  0
 Z57  CONST_16  H3   C3  C2  C1  180.00  0.0  0
 Z57  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
 Z57  chir_01  C1'  C2   C2'  O5'  negativ
 Z57  chir_02  C2'  O2'  C1'  C3'  negativ
 Z57  chir_03  C3'  O3'  C2'  C4'  positiv
 Z57  chir_04  C4'  O4'  C5'  C3'  positiv
 Z57  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
 Z57  plan-1  C1   0.020
 Z57  plan-1  O1   0.020
 Z57  plan-1  C2   0.020
 Z57  plan-1  C3   0.020
 Z57  plan-1  C4   0.020
 Z57  plan-1  O4   0.020
 Z57  plan-1  C5   0.020
 Z57  plan-1  BR5  0.020
 Z57  plan-1  C6   0.020
 Z57  plan-1  C1'  0.020
 Z57  plan-1  H3   0.020
 Z57  plan-1  H6   0.020

