# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:31:11 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (1~{S},2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 M96  M96  (1~{S},2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol  ligand  26  12  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M96
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
 M96  C1   C  CH1   0  -0.006  -0.5828   1.7566   0.0572
 M96  O1   O  OH1   0  -0.671  -0.4632   2.0323   1.4379
 M96  C7   C  CH2   0  -0.438   0.7548   1.2390  -0.4431
 M96  C5   C  CH1   0  -0.318   1.1313  -0.1225   0.1457
 M96  C6   C  CH2   0  -0.126   2.4580  -0.6203  -0.4118
 M96  O6   O  OH1   0  -0.674   3.4717   0.3071  -0.0863
 M96  C4   C  CH1   0   0.069   0.0206  -1.1329  -0.1317
 M96  O4   O  OH1   0  -0.682   0.3501  -2.3533   0.4979
 M96  C3   C  CH1   0   0.030  -1.3202  -0.6198   0.3881
 M96  O3   O  OH1   0  -0.681  -2.2844  -1.6119   0.1040
 M96  C2   C  CH1   0  -0.038  -1.6954   0.7325  -0.2094
 M96  O2   O  OH1   0  -0.669  -1.9065   0.5673  -1.5920
 M96  H1   H  HCH1  0   0.223  -0.8311   2.6784  -0.4922
 M96  H2   H  HOH1  0   0.450  -1.3066   2.3684   1.7580
 M96  H3   H  HCH2  0   0.225   0.7042   1.1599  -1.5326
 M96  H4   H  HCH2  0   0.249   1.5311   1.9746  -0.2262
 M96  H5   H  HCH1  0   0.229   1.2348  -0.0267   1.2332
 M96  H6   H  HCH2  0   0.208   2.6860  -1.6075   0.0038
 M96  H7   H  HCH2  0   0.182   2.3621  -0.7432  -1.5006
 M96  H8   H  HOH1  0   0.453   4.2974  -0.0109  -0.4617
 M96  H9   H  HCH1  0   0.196  -0.0544  -1.2755  -1.2215
 M96  H10  H  HOH1  0   0.445  -0.3980  -2.9497   0.3869
 M96  H11  H  HCH1  0   0.214  -1.2199  -0.4806   1.4727
 M96  H12  H  HOH1  0   0.455  -3.0502  -1.4676   0.6677
 M96  H13  H  HCH1  0   0.222  -2.6198   1.0822   0.2814
 M96  H14  H  HOH1  0   0.452  -2.1590   1.4184  -1.9638

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
 M96  C6  C5   single  1.523  0.020  1.523
 M96  C6  O6   single  1.412  0.020  1.412
 M96  O1  C1   single  1.413  0.020  1.413
 M96  C7  C5   single  1.530  0.020  1.530
 M96  C7  C1   single  1.519  0.020  1.519
 M96  C5  C4   single  1.527  0.020  1.527
 M96  C1  C2   single  1.536  0.020  1.536
 M96  C4  O4   single  1.412  0.020  1.412
 M96  C4  C3   single  1.527  0.020  1.527
 M96  C2  C3   single  1.525  0.020  1.525
 M96  C2  O2   single  1.408  0.020  1.408
 M96  C3  O3   single  1.412  0.020  1.412
 M96  C1  H1   single  0.970  0.020  1.090
 M96  O1  H2   single  0.850  0.020  0.980
 M96  C7  H3   single  0.970  0.020  1.090
 M96  C7  H4   single  0.970  0.020  1.090
 M96  C5  H5   single  0.970  0.020  1.090
 M96  C6  H6   single  0.970  0.020  1.090
 M96  C6  H7   single  0.970  0.020  1.090
 M96  O6  H8   single  0.850  0.020  0.980
 M96  C4  H9   single  0.970  0.020  1.090
 M96  O4  H10  single  0.850  0.020  0.980
 M96  C3  H11  single  0.970  0.020  1.090
 M96  O3  H12  single  0.850  0.020  0.980
 M96  C2  H13  single  0.970  0.020  1.090
 M96  O2  H14  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
 M96  H1   C1  C2  107.95  3.000
 M96  H1   C1  C7  108.63  3.000
 M96  C2   C1  C7  110.71  3.000
 M96  H1   C1  O1  110.07  3.000
 M96  C2   C1  O1  111.17  3.000
 M96  C7   C1  O1  108.29  3.000
 M96  H2   O1  C1  108.60  3.000
 M96  H4   C7  H3  106.24  3.000
 M96  H4   C7  C5  110.38  3.000
 M96  H3   C7  C5  109.29  3.000
 M96  H4   C7  C1  109.34  3.000
 M96  H3   C7  C1  108.18  3.000
 M96  C5   C7  C1  113.15  3.000
 M96  H5   C5  C4  107.85  3.000
 M96  H5   C5  C6  108.02  3.000
 M96  C4   C5  C6  110.55  3.000
 M96  H5   C5  C7  109.09  3.000
 M96  C4   C5  C7  109.87  3.000
 M96  C6   C5  C7  111.37  3.000
 M96  H7   C6  H6  107.04  3.000
 M96  H7   C6  O6  111.36  3.000
 M96  H6   C6  O6  110.80  3.000
 M96  H7   C6  C5  108.84  3.000
 M96  H6   C6  C5  109.70  3.000
 M96  O6   C6  C5  109.05  3.000
 M96  H8   O6  C6  108.03  3.000
 M96  H9   C4  C3  108.70  3.000
 M96  H9   C4  O4  110.19  3.000
 M96  C3   C4  O4  110.09  3.000
 M96  H9   C4  C5  108.36  3.000
 M96  C3   C4  C5  110.77  3.000
 M96  O4   C4  C5  108.73  3.000
 M96  H10  O4  C4  107.60  3.000
 M96  H11  C3  C2  107.28  3.000
 M96  H11  C3  O3  110.49  3.000
 M96  C2   C3  O3  112.09  3.000
 M96  H11  C3  C4  107.38  3.000
 M96  O3   C3  C4  107.15  3.000
 M96  C2   C3  C4  112.37  3.000
 M96  H12  O3  C3  108.68  3.000
 M96  H13  C2  O2  110.38  3.000
 M96  H13  C2  C3  108.23  3.000
 M96  O2   C2  C3  108.51  3.000
 M96  H13  C2  C1  108.57  3.000
 M96  O2   C2  C1  110.93  3.000
 M96  C3   C2  C1  110.18  3.000
 M96  H14  O2  C2  108.35  3.000

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
 M96  chir_01  C1  O1  C7  C2  negativ
 M96  chir_02  C5  C6  C7  C4  negativ
 M96  chir_03  C4  O4  C5  C3  positiv
 M96  chir_04  C3  O3  C4  C2  negativ
 M96  chir_05  C2  O2  C3  C1  negativ

