# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 23:41:03 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: (1~{R},2~{R},3~{R},4~{S},5~{R})-4-[[(1~{S},2~{S},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-2,3,4-tris(oxidanyl)cyclohexyl]oxymethyl]cyclohexane-1,2,3,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@H](OC[C@H]2[C@H](O)C[C@@H](O)[C@@H](O)[C@@H]2O)[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
 QE8  QE8  (1~{R},2~{R},3~{R},4~{S},5~{R})-4-[[(1~{S},2~{S},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-2,3,4-tris(oxidanyl)cyclohexyl]oxymethyl]cyclohexane-1,2,3,5-tetrol  ligand  49  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QE8
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
 QE8  O3   O  OH1   0  -0.673  20.6431   2.1801  17.3036
 QE8  C4   C  CR16  0   0.025  18.9032   3.3034  18.5669
 QE8  C5   C  CH1   0  -0.309  15.5128   7.1248  22.1198
 QE8  O4   O  OH1   0  -0.677  13.4334   7.1994  23.2921
 QE8  C6   C  CH2   0  -0.152  15.5660   8.6381  21.9811
 QE8  C7   C  CH2   0  -0.450  16.9139   6.5115  22.1293
 QE8  O6   O  O2    0  -0.518  16.2616   4.4447  21.0195
 QE8  C11  C  CH1   0   0.007  16.8818   4.9895  22.1746
 QE8  O8   O  OH1   0  -0.688  16.3899   1.6393  20.8563
 QE8  C1   C  C     0  -0.517  18.0579   0.6677  19.4998
 QE8  C51  C  CR16  0  -0.364  17.9795   3.1745  19.7852
 QE8  C61  C  CH2   0  -0.174  17.0806   4.4090  19.8633
 QE8  O61  O  OH1   0  -0.671  16.2263   9.1978  23.0951
 QE8  C41  C  CH1   0   0.091  14.7362   6.6621  23.3498
 QE8  O41  O  OH1   0  -0.678  19.7762   4.4138  18.6938
 QE8  C3   C  CR16  0   0.061  19.7880   2.0675  18.4122
 QE8  C31  C  CH1   0  -0.025  14.6841   5.1373  23.4021
 QE8  O31  O  OH1   0  -0.675  14.0114   4.7868  24.6001
 QE8  C2   C  CR16  0  -0.001  18.9567   0.8025  18.2774
 QE8  C21  C  CH1   0  -0.006  16.0759   4.5002  23.3758
 QE8  O2   O  OH1   0  -0.667  18.2215   0.8803  17.0739
 QE8  O21  O  OH1   0  -0.668  16.8111   4.8226  24.5317
 QE8  C71  C  CR16  0   0.112  17.1590   1.8786  19.6967
 QE8  H1   H  HOH1  0   0.441  21.0919   3.0298  17.3750
 QE8  H2   H  HCR6  0   0.221  18.2876   3.4090  17.6638
 QE8  H4   H  HOH1  0   0.443  12.9502   6.8862  24.0636
 QE8  H5   H  HCH2  0   0.198  16.0924   8.8755  21.0459
 QE8  H6   H  HCH2  0   0.206  14.5497   9.0345  21.8765
 QE8  H7   H  HCH2  0   0.245  17.4699   6.8521  21.2514
 QE8  H8   H  HCH2  0   0.242  17.4786   6.8665  22.9937
 QE8  H9   H  HCH1  0   0.244  17.9073   4.6063  22.2706
 QE8  H10  H  HOH1  0   0.447  15.9429   2.4635  21.0849
 QE8  H11  H  H     0   0.249  17.4477  -0.2367  19.4140
 QE8  H12  H  H     0   0.232  18.6874   0.5378  20.3859
 QE8  H13  H  HCR6  0   0.238  18.6115   3.1213  20.6824
 QE8  H14  H  HCH2  0   0.229  17.6827   5.3203  19.7985
 QE8  H15  H  HCH2  0   0.236  16.4038   4.4135  19.0031
 QE8  H16  H  HOH1  0   0.452  16.2248  10.1537  22.9975
 QE8  H17  H  HCH1  0   0.196  15.2593   7.0195  24.2487
 QE8  H18  H  HOH1  0   0.458  19.4250   5.1541  18.1924
 QE8  H19  H  HCR6  0   0.201  20.3700   1.9620  19.3432
 QE8  H20  H  HCH1  0   0.221  14.1236   4.7840  22.5266
 QE8  H21  H  HOH1  0   0.457  13.6780   3.8874  24.5181
 QE8  H22  H  HCR6  0   0.227  19.6411  -0.0577  18.2531
 QE8  H23  H  HCH1  0   0.218  15.9517   3.4082  23.2936
 QE8  H24  H  HOH1  0   0.450  17.6806   0.0876  17.0019
 QE8  H25  H  HOH1  0   0.446  16.2277   4.6926  25.2882
 QE8  H26  H  HCR6  0   0.184  16.5007   1.9702  18.8183
 QE8  H3   H  HCH1  0   0.236  14.9826   6.7635  21.2300

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
 QE8  O3   C3   single  1.405  0.020  1.405
 QE8  O2   C2   single  1.412  0.020  1.412
 QE8  C2   C3   single  1.520  0.020  1.520
 QE8  C2   C1   single  1.523  0.020  1.523
 QE8  C3   C4   single  1.528  0.020  1.528
 QE8  C4   O41  single  1.418  0.020  1.418
 QE8  C4   C51  single  1.534  0.020  1.534
 QE8  C1   C71  single  1.521  0.020  1.521
 QE8  C71  C51  single  1.536  0.020  1.536
 QE8  C71  O8   single  1.412  0.020  1.412
 QE8  C51  C61  single  1.529  0.020  1.529
 QE8  C61  O6   single  1.417  0.020  1.417
 QE8  O6   C11  single  1.420  0.020  1.420
 QE8  C6   C5   single  1.521  0.020  1.521
 QE8  C6   O61  single  1.411  0.020  1.411
 QE8  C5   C7   single  1.529  0.020  1.529
 QE8  C5   C41  single  1.526  0.020  1.526
 QE8  C7   C11  single  1.523  0.020  1.523
 QE8  C11  C21  single  1.527  0.020  1.527
 QE8  O4   C41  single  1.411  0.020  1.411
 QE8  C41  C31  single  1.527  0.020  1.527
 QE8  C31  C21  single  1.531  0.020  1.531
 QE8  C31  O31  single  1.418  0.020  1.418
 QE8  C21  O21  single  1.407  0.020  1.407
 QE8  O3   H1   single  0.850  0.020  0.980
 QE8  C4   H2   single  0.970  0.020  1.090
 QE8  C5   H3   single  0.970  0.020  1.090
 QE8  O4   H4   single  0.850  0.020  0.980
 QE8  C6   H5   single  0.970  0.020  1.090
 QE8  C6   H6   single  0.970  0.020  1.090
 QE8  C7   H7   single  0.970  0.020  1.090
 QE8  C7   H8   single  0.970  0.020  1.090
 QE8  C11  H9   single  0.970  0.020  1.090
 QE8  O8   H10  single  0.850  0.020  0.980
 QE8  C1   H11  single  0.970  0.020  1.090
 QE8  C1   H12  single  0.970  0.020  1.090
 QE8  C51  H13  single  0.970  0.020  1.090
 QE8  C61  H14  single  0.970  0.020  1.090
 QE8  C61  H15  single  0.970  0.020  1.090
 QE8  O61  H16  single  0.850  0.020  0.980
 QE8  C41  H17  single  0.970  0.020  1.090
 QE8  O41  H18  single  0.850  0.020  0.980
 QE8  C3   H19  single  0.970  0.020  1.090
 QE8  C31  H20  single  0.970  0.020  1.090
 QE8  O31  H21  single  0.850  0.020  0.980
 QE8  C2   H22  single  0.970  0.020  1.090
 QE8  C21  H23  single  0.970  0.020  1.090
 QE8  O2   H24  single  0.850  0.020  0.980
 QE8  O21  H25  single  0.850  0.020  0.980
 QE8  C71  H26  single  0.970  0.020  1.090

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
 QE8  H1   O3   C3   107.21  3.000
 QE8  H2   C4   C3   108.62  3.000
 QE8  H2   C4   O41  110.08  3.000
 QE8  C3   C4   O41  106.61  3.000
 QE8  H2   C4   C51  108.88  3.000
 QE8  O41  C4   C51  111.42  3.000
 QE8  C3   C4   C51  111.17  3.000
 QE8  H3   C5   C41  107.93  3.000
 QE8  H3   C5   C7   108.40  3.000
 QE8  C41  C5   C7   109.84  3.000
 QE8  H3   C5   C6   105.71  3.000
 QE8  C41  C5   C6   113.14  3.000
 QE8  C7   C5   C6   111.57  3.000
 QE8  H4   O4   C41  107.87  3.000
 QE8  H6   C6   H5   106.55  3.000
 QE8  H6   C6   O61  111.47  3.000
 QE8  H5   C6   O61  111.22  3.000
 QE8  H6   C6   C5   109.65  3.000
 QE8  H5   C6   C5   108.02  3.000
 QE8  O61  C6   C5   109.83  3.000
 QE8  H8   C7   H7   105.74  3.000
 QE8  H8   C7   C11  108.20  3.000
 QE8  H7   C7   C11  110.23  3.000
 QE8  H8   C7   C5   110.39  3.000
 QE8  H7   C7   C5   109.62  3.000
 QE8  C11  C7   C5   112.44  3.000
 QE8  C61  O6   C11  114.90  3.000
 QE8  H9   C11  C21  108.18  3.000
 QE8  H9   C11  O6   110.18  3.000
 QE8  C21  C11  O6   106.65  3.000
 QE8  H9   C11  C7   109.35  3.000
 QE8  C21  C11  C7   110.78  3.000
 QE8  O6   C11  C7   111.62  3.000
 QE8  H10  O8   C71  107.58  3.000
 QE8  H12  C1   H11  106.61  3.000
 QE8  H12  C1   C71  109.24  3.000
 QE8  H11  C1   C71  109.79  3.000
 QE8  H12  C1   C2   108.71  3.000
 QE8  H11  C1   C2   109.83  3.000
 QE8  C71  C1   C2   112.48  3.000
 QE8  H13  C51  C71  108.26  3.000
 QE8  H13  C51  C61  109.60  3.000
 QE8  C71  C51  C61  111.71  3.000
 QE8  H13  C51  C4   107.83  3.000
 QE8  C61  C51  C4   109.07  3.000
 QE8  C71  C51  C4   110.28  3.000
 QE8  H15  C61  H14  106.88  3.000
 QE8  H15  C61  C51  109.07  3.000
 QE8  H14  C61  C51  110.24  3.000
 QE8  H15  C61  O6   106.48  3.000
 QE8  H14  C61  O6   110.20  3.000
 QE8  C51  C61  O6   113.69  3.000
 QE8  H16  O61  C6   108.28  3.000
 QE8  H17  C41  C31  108.23  3.000
 QE8  H17  C41  O4   110.43  3.000
 QE8  C31  C41  O4   110.51  3.000
 QE8  H17  C41  C5   108.56  3.000
 QE8  C31  C41  C5   110.35  3.000
 QE8  O4   C41  C5   108.75  3.000
 QE8  H18  O41  C4   109.36  3.000
 QE8  H19  C3   C2   106.49  3.000
 QE8  H19  C3   C4   107.31  3.000
 QE8  C2   C3   C4   111.44  3.000
 QE8  H19  C3   O3   110.65  3.000
 QE8  C4   C3   O3   111.57  3.000
 QE8  C2   C3   O3   109.26  3.000
 QE8  H20  C31  C21  108.45  3.000
 QE8  H20  C31  O31  110.61  3.000
 QE8  C21  C31  O31  110.06  3.000
 QE8  H20  C31  C41  108.15  3.000
 QE8  O31  C31  C41  106.98  3.000
 QE8  C21  C31  C41  112.58  3.000
 QE8  H21  O31  C31  108.86  3.000
 QE8  H22  C2   O2   110.38  3.000
 QE8  H22  C2   C3   108.22  3.000
 QE8  O2   C2   C3   108.33  3.000
 QE8  H22  C2   C1   108.41  3.000
 QE8  C3   C2   C1   108.98  3.000
 QE8  O2   C2   C1   112.43  3.000
 QE8  H23  C21  O21  110.31  3.000
 QE8  H23  C21  C31  108.13  3.000
 QE8  O21  C21  C31  111.44  3.000
 QE8  H23  C21  C11  108.56  3.000
 QE8  O21  C21  C11  107.27  3.000
 QE8  C31  C21  C11  111.10  3.000
 QE8  H24  O2   C2   108.11  3.000
 QE8  H25  O21  C21  107.30  3.000
 QE8  H26  C71  C51  107.15  3.000
 QE8  H26  C71  C1   108.43  3.000
 QE8  C51  C71  C1   111.30  3.000
 QE8  H26  C71  O8   110.09  3.000
 QE8  C51  C71  O8   112.74  3.000
 QE8  C1   C71  O8   107.06  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
 QE8  Var_01  C51  C61  O6  C11  84.85  30.0  1

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
 QE8  chir_01  C4   C3   O41  C51  positiv
 QE8  chir_02  C5   C6   C7   C41  negativ
 QE8  chir_03  C11  O6   C7   C21  negativ
 QE8  chir_04  C51  C4   C71  C61  positiv
 QE8  chir_05  C41  C5   O4   C31  negativ
 QE8  chir_06  C3   O3   C2   C4   positiv
 QE8  chir_07  C31  C41  C21  O31  negativ
 QE8  chir_08  C2   O2   C3   C1   negativ
 QE8  chir_09  C21  C11  C31  O21  positiv
 QE8  chir_10  C71  O8   C1   C51  positiv

