# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:23:07 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(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)ccc2O
#
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
 H53  H53  (1S)-1,5-anhydro-1-(2,5-dihydroxyphenyl)-D-glucitol  D-saccharide  35  19  .  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_H53
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
 H53  O5    O  O2    0  -0.492   0.6945   0.9282   0.1187
 H53  C5    C  CH1   0  -0.012   2.0836   0.9508   0.3785
 H53  C4    C  CH1   0   0.018   2.7878  -0.0948  -0.4882
 H53  C3    C  CH1   0  -0.025   2.1522  -1.4623  -0.2498
 H53  C2    C  CH1   0   0.060   0.6489  -1.3915  -0.4629
 H53  C1    C  CH1   0  -0.018   0.0638  -0.2871   0.4243
 H53  C7    C  CR6   0  -0.017  -1.4258  -0.1259   0.2342
 H53  C12   C  CR6   0   0.286  -2.3190  -0.9845   0.8824
 H53  O12   O  OH1   0  -0.672  -1.9005  -2.0034   1.6786
 H53  C11   C  CR16  0  -0.322  -3.6869  -0.7783   0.7397
 H53  C10   C  CR16  0  -0.339  -4.1781   0.2476  -0.0499
 H53  C9    C  CR6   0   0.361  -3.2939   1.0790  -0.7280
 H53  O9    O  OH1   0  -0.643  -3.8115   2.0562  -1.5096
 H53  C8    C  CR16  0  -0.447  -1.9257   0.8876  -0.5788
 H53  O2    O  OH1   0  -0.686   0.0218  -2.6053  -0.1150
 H53  O3    O  OH1   0  -0.675   2.6655  -2.4416  -1.1274
 H53  O4    O  OH1   0  -0.673   4.1546  -0.1047  -0.1487
 H53  C6    C  CH2   0  -0.156   2.5783   2.3507   0.0842
 H53  O6    O  OH1   0  -0.670   1.9618   3.2506   0.9736
 H53  H5    H  HCH1  0   0.222   2.2692   0.7151   1.4398
 H53  H4    H  HCH1  0   0.220   2.6470   0.1814  -1.5445
 H53  H3    H  HCH1  0   0.225   2.3342  -1.7463   0.7977
 H53  H2    H  HCH1  0   0.232   0.4393  -1.1368  -1.5122
 H53  H1    H  HCH1  0   0.238   0.2581  -0.5568   1.4765
 H53  HO12  H  HOH1  0   0.470  -1.1506  -2.4458   1.2417
 H53  H11   H  HCR6  0   0.260  -4.3752  -1.4373   1.2540
 H53  H10   H  HCR6  0   0.262  -5.2464   0.3938  -0.1498
 H53  HO9   H  HOH1  0   0.471  -3.1033   2.5615  -1.9229
 H53  H8    H  HCR6  0   0.268  -1.2359   1.5478  -1.0910
 H53  HO2   H  HOH1  0   0.471   0.4522  -3.3347  -0.5758
 H53  HO3   H  HOH1  0   0.462   3.4381  -2.8494  -0.7262
 H53  HO4   H  HOH1  0   0.458   4.6465  -0.5094  -0.8691
 H53  H61   H  HCH2  0   0.197   2.3517   2.5914  -0.9640
 H53  H62   H  HCH2  0   0.212   3.6680   2.3603   0.1889
 H53  HO6   H  HOH1  0   0.457   2.3106   4.1282   0.7950

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
 H53  O5   C5    single    1.413  0.020  1.413
 H53  O5   C1    single    1.403  0.020  1.403
 H53  C5   C4    single    1.530  0.020  1.530
 H53  C5   C6    single    1.514  0.020  1.514
 H53  C5   H5    single    0.970  0.020  1.090
 H53  C4   C3    single    1.527  0.020  1.527
 H53  C4   O4    single    1.408  0.020  1.408
 H53  C4   H4    single    0.970  0.020  1.090
 H53  C3   C2    single    1.520  0.020  1.520
 H53  C3   O3    single    1.412  0.020  1.412
 H53  C3   H3    single    0.970  0.020  1.090
 H53  C2   C1    single    1.533  0.020  1.533
 H53  C2   O2    single    1.410  0.020  1.410
 H53  C2   H2    single    0.970  0.020  1.090
 H53  C1   C7    single    1.510  0.020  1.510
 H53  C1   H1    single    0.970  0.020  1.090
 H53  C7   C12   aromatic  1.398  0.020  1.398
 H53  C7   C8    aromatic  1.392  0.020  1.392
 H53  C12  O12   single    1.359  0.020  1.359
 H53  C12  C11   aromatic  1.391  0.020  1.391
 H53  O12  HO12  single    0.850  0.020  0.980
 H53  C11  C10   aromatic  1.385  0.020  1.385
 H53  C11  H11   single    0.930  0.020  1.080
 H53  C10  C9    aromatic  1.390  0.020  1.390
 H53  C10  H10   single    0.930  0.020  1.080
 H53  C9   O9    single    1.354  0.020  1.354
 H53  C9   C8    aromatic  1.390  0.020  1.390
 H53  O9   HO9   single    0.850  0.020  0.980
 H53  C8   H8    single    0.930  0.020  1.080
 H53  O2   HO2   single    0.850  0.020  0.980
 H53  O3   HO3   single    0.850  0.020  0.980
 H53  O4   HO4   single    0.850  0.020  0.980
 H53  C6   O6    single    1.408  0.020  1.408
 H53  C6   H61   single    0.970  0.020  1.090
 H53  C6   H62   single    0.970  0.020  1.090
 H53  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
 H53  C1    O5   C5   114.56  3.000
 H53  H5    C5   C6   109.25  3.000
 H53  H5    C5   C4   108.76  3.000
 H53  C6    C5   C4   111.81  3.000
 H53  H5    C5   O5   109.81  3.000
 H53  C6    C5   O5   107.47  3.000
 H53  C4    C5   O5   109.72  3.000
 H53  H4    C4   O4   110.93  3.000
 H53  H4    C4   C3   108.74  3.000
 H53  O4    C4   C3   111.11  3.000
 H53  H4    C4   C5   108.26  3.000
 H53  O4    C4   C5   108.36  3.000
 H53  C3    C4   C5   109.40  3.000
 H53  H3    C3   O3   110.65  3.000
 H53  H3    C3   C2   108.00  3.000
 H53  O3    C3   C2   107.75  3.000
 H53  H3    C3   C4   108.12  3.000
 H53  O3    C3   C4   111.90  3.000
 H53  C2    C3   C4   110.37  3.000
 H53  H2    C2   O2   110.49  3.000
 H53  H2    C2   C1   108.21  3.000
 H53  O2    C2   C1   107.92  3.000
 H53  H2    C2   C3   109.46  3.000
 H53  O2    C2   C3   111.42  3.000
 H53  C1    C2   C3   109.27  3.000
 H53  H1    C1   C7   108.65  3.000
 H53  H1    C1   C2   107.98  3.000
 H53  C7    C1   C2   112.37  3.000
 H53  H1    C1   O5   109.89  3.000
 H53  C7    C1   O5   108.87  3.000
 H53  C2    C1   O5   109.06  3.000
 H53  C8    C7   C12  119.24  3.000
 H53  C8    C7   C1   120.36  3.000
 H53  C12   C7   C1   120.40  3.000
 H53  C11   C12  O12  118.30  3.000
 H53  C11   C12  C7   119.32  3.000
 H53  O12   C12  C7   122.36  3.000
 H53  HO12  O12  C12  108.34  3.000
 H53  H11   C11  C10  119.75  3.000
 H53  H11   C11  C12  119.10  3.000
 H53  C10   C11  C12  121.15  3.000
 H53  H10   C10  C9   120.11  3.000
 H53  H10   C10  C11  120.17  3.000
 H53  C9    C10  C11  119.71  3.000
 H53  C8    C9   O9   122.53  3.000
 H53  C8    C9   C10  119.44  3.000
 H53  O9    C9   C10  118.03  3.000
 H53  HO9   O9   C9   110.19  3.000
 H53  H8    C8   C9   119.48  3.000
 H53  H8    C8   C7   119.41  3.000
 H53  C9    C8   C7   121.10  3.000
 H53  HO2   O2   C2   109.56  3.000
 H53  HO3   O3   C3   109.09  3.000
 H53  HO4   O4   C4   108.59  3.000
 H53  H62   C6   H61  107.13  3.000
 H53  H62   C6   O6   111.71  3.000
 H53  H61   C6   O6   111.86  3.000
 H53  H62   C6   C5   108.35  3.000
 H53  H61   C6   C5   108.70  3.000
 H53  O6    C6   C5   108.98  3.000
 H53  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
 H53  CONST_01  C10  C11  C12  C7     0.00  0.0  0
 H53  CONST_02  C10  C9   C8   C7     0.00  0.0  0
 H53  CONST_03  C9   C8   C7   C12    0.00  0.0  0
 H53  CONST_04  C9   C10  C11  C12    0.00  0.0  0
 H53  CONST_05  C8   C7   C12  C11    0.00  0.0  0
 H53  CONST_06  C8   C9   C10  C11    0.00  0.0  0
 H53  CONST_07  C11  C12  C7   C1   180.00  0.0  0
 H53  CONST_08  C9   C8   C7   C1   180.00  0.0  0
 H53  CONST_09  O12  C12  C7   C1     0.00  0.0  0
 H53  CONST_10  O9   C9   C8   C7   180.00  0.0  0
 H53  CONST_11  C8   C7   C12  O12  180.00  0.0  0
 H53  CONST_12  C10  C11  C12  O12  180.00  0.0  0
 H53  CONST_13  O9   C9   C10  C11  180.00  0.0  0
 H53  CONST_14  H8   C8   C7   C1     0.00  0.0  0
 H53  CONST_15  H11  C11  C12  C7   180.00  0.0  0
 H53  CONST_16  H10  C10  C11  C12  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
 H53  chir_01  C5  O5  C4  C6  negativ
 H53  chir_02  C4  O4  C5  C3  positiv
 H53  chir_03  C3  O3  C4  C2  negativ
 H53  chir_04  C2  O2  C3  C1  positiv
 H53  chir_05  C1  O5  C2  C7  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
 H53  plan-1  C1   0.020
 H53  plan-1  C7   0.020
 H53  plan-1  C12  0.020
 H53  plan-1  O12  0.020
 H53  plan-1  C11  0.020
 H53  plan-1  C10  0.020
 H53  plan-1  C9   0.020
 H53  plan-1  O9   0.020
 H53  plan-1  C8   0.020
 H53  plan-1  H11  0.020
 H53  plan-1  H10  0.020
 H53  plan-1  H8   0.020

