# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 19:46:03 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: (1~{R},2~{S},4~{R},5~{S},6~{R})-6-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-heptoxy-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl]oxy-5-(hydroxymethyl)cyclohexane-1,2,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCO[C@H]1[C@H](O)[C@@H](O)[C@H](O[C@@H]1CO)O[C@H]2[C@H](O)[C@@H](O)C[C@@H](O)[C@@H]2CO
#
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
 QJN  QJN  (1~{R},2~{S},4~{R},5~{S},6~{R})-6-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-heptoxy-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl]oxy-5-(hydroxymethyl)cyclohexane-1,2,4-triol  ligand  68  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QJN
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
 QJN  C2    C  CH1   0  -0.017  -4.7350  18.8374  -43.3039
 QJN  C4    C  CH1   0   0.050  -3.7238  20.5903  -44.7416
 QJN  C5    C  CH1   0  -0.011  -3.9203  21.5639  -43.5736
 QJN  C6    C  CH2   0  -0.189  -4.1707  22.9909  -44.0072
 QJN  C1'   C  CH2   0  -0.517  -2.9932  19.3921  -37.2260
 QJN  C2'   C  CH1   0   0.027  -3.2343  18.1420  -38.0546
 QJN  O2'   O  OH1   0  -0.673  -2.3078  17.1156  -37.7704
 QJN  C3'   C  CH1   0   0.055  -3.0932  18.4608  -39.5347
 QJN  O3'   O  OH1   0  -0.681  -3.3835  17.3270  -40.3236
 QJN  C4'   C  CH1   0   0.054  -4.0492  19.5759  -39.9451
 QJN  C5'   C  CH1   0  -0.334  -3.8211  20.8403  -39.1021
 QJN  C6'   C  CH2   0  -0.173  -4.7229  21.9880  -39.5296
 QJN  C7'   C  CH1   0   0.086  -3.9668  20.4972  -37.6159
 QJN  O1    O  O2    0  -0.524  -3.8248  19.8234  -41.3198
 QJN  C1    C  CH1   0   0.234  -4.9097  19.8879  -42.2027
 QJN  O5    O  O2    0  -0.499  -5.0202  21.1554  -42.7719
 QJN  O6    O  OH1   0  -0.668  -5.3062  23.0532  -44.8368
 QJN  O4    O  O2    0  -0.504  -2.5898  20.9762  -45.4782
 QJN  C3    C  CH1   0   0.011  -3.5420  19.1828  -44.1938
 QJN  O3    O  OH1   0  -0.667  -3.4396  18.2900  -45.2762
 QJN  O2    O  OH1   0  -0.692  -4.6634  17.5303  -42.8040
 QJN  O7    O  OH1   0  -0.670  -3.7340  21.6704  -36.8678
 QJN  C10   C  CH2   0  -0.418  -0.5337  20.3402  -47.4968
 QJN  C11   C  CH2   0  -0.426   0.7603  20.5817  -48.2696
 QJN  C12   C  CH2   0  -0.420   0.5790  20.6672  -49.7825
 QJN  C13   C  CH2   0  -0.422   1.8901  20.7603  -50.5598
 QJN  C14   C  CH3   0  -0.664   2.6824  22.0326  -50.2873
 QJN  H2    H  HCH1  0   0.229  -5.6372  18.8790  -43.9264
 QJN  H4    H  HCH1  0   0.224  -4.6258  20.6030  -45.3682
 QJN  H5    H  HCH1  0   0.227  -2.9975  21.5800  -42.9773
 QJN  H62   H  HCH2  0   0.210  -3.2695  23.3515  -44.5152
 QJN  H61   H  HCH2  0   0.217  -4.2917  23.6061  -43.1051
 QJN  H1'1  H  HCH2  0   0.246  -3.1075  19.1546  -36.1632
 QJN  H6    H  HCH2  0   0.230  -1.9660  19.7421  -37.3744
 QJN  H2'   H  HCH1  0   0.210  -4.2632  17.7913  -37.8798
 QJN  HO2'  H  HOH1  0   0.454  -2.5086  16.7530  -36.9021
 QJN  H3'   H  HCH1  0   0.216  -2.0630  18.8064  -39.7172
 QJN  HO3'  H  HOH1  0   0.461  -2.7736  16.6200  -40.0856
 QJN  H4'   H  HCH1  0   0.232  -5.0774  19.2210  -39.7923
 QJN  H5'   H  HCH1  0   0.243  -2.7875  21.1744  -39.2662
 QJN  HO6'  H  HOH1  0   0.453  -6.6246  22.2875  -39.7803
 QJN  H6'1  H  HCH2  0   0.221  -4.4699  22.2841  -40.5519
 QJN  H6'2  H  HCH2  0   0.214  -4.5159  22.8563  -38.8949
 QJN  H7'   H  HCH1  0   0.203  -4.9904  20.1320  -37.4426
 QJN  H1    H  HCH1  0   0.243  -5.8496  19.7134  -41.6675
 QJN  HO6   H  HOH1  0   0.456  -5.3836  23.9507  -45.1716
 QJN  H3    H  HCH1  0   0.200  -2.6222  19.1617  -43.5868
 QJN  HO3   H  HOH1  0   0.444  -3.4057  17.3975  -44.9152
 QJN  HO2   H  HOH1  0   0.453  -4.0652  17.4993  -42.0362
 QJN  HO7   H  HOH1  0   0.449  -3.9158  21.4764  -35.9429
 QJN  H91   H  HCH2  0   0.217  -1.0329  22.4042  -47.1148
 QJN  H9    H  HCH2  0   0.228  -1.7456  21.7677  -48.5788
 QJN  H101  H  HCH2  0   0.205  -1.0294  19.4448  -47.8893
 QJN  H10   H  HCH2  0   0.223  -0.2872  20.1175  -46.4562
 QJN  H111  H  HCH2  0   0.214   1.4593  19.7680  -48.0500
 QJN  H11   H  HCH2  0   0.212   1.2357  21.4940  -47.8952
 QJN  H121  H  HCH2  0   0.210  -0.0465  21.5272  -50.0421
 QJN  H12   H  HCH2  0   0.213   0.0307  19.7811  -50.1193
 QJN  H131  H  HCH2  0   0.218   1.6702  20.7008  -51.6292
 QJN  H13   H  HCH2  0   0.208   2.5101  19.8875  -50.3311
 QJN  H14   H  HCH3  0   0.225   3.5733  22.0839  -50.9143
 QJN  H141  H  HCH3  0   0.213   2.0813  22.9203  -50.4947
 QJN  H7    H  HCH3  0   0.220   3.0123  22.0944  -49.2496
 QJN  C8    C  CH2   0  -0.151  -2.8243  21.2469  -46.8450
 QJN  O6'   O  OH1   0  -0.674  -6.0724  21.5839  -39.4288
 QJN  C9    C  CH2   0  -0.469  -1.5070  21.5143  -47.5423
 QJN  H81   H  HCH2  0   0.208  -3.4892  22.1132  -46.9549
 QJN  H8    H  HCH2  0   0.199  -3.3247  20.3956  -47.3245

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
 QJN  C13  C14   single  1.523  0.020  1.523
 QJN  C13  C12   single  1.527  0.020  1.527
 QJN  C12  C11   single  1.526  0.020  1.526
 QJN  C11  C10   single  1.527  0.020  1.527
 QJN  C10  C9    single  1.526  0.020  1.526
 QJN  C9   C8    single  1.514  0.020  1.514
 QJN  C8   O4    single  1.413  0.020  1.413
 QJN  O4   C4    single  1.406  0.020  1.406
 QJN  O3   C3    single  1.407  0.020  1.407
 QJN  O6   C6    single  1.408  0.020  1.408
 QJN  C4   C3    single  1.521  0.020  1.521
 QJN  C4   C5    single  1.533  0.020  1.533
 QJN  C3   C2    single  1.528  0.020  1.528
 QJN  C6   C5    single  1.512  0.020  1.512
 QJN  C5   O5    single  1.421  0.020  1.421
 QJN  C2   O2    single  1.401  0.020  1.401
 QJN  C2   C1    single  1.532  0.020  1.532
 QJN  O5   C1    single  1.394  0.020  1.394
 QJN  C1   O1    single  1.400  0.020  1.400
 QJN  O1   C4'   single  1.415  0.020  1.415
 QJN  O6'  C6'   single  1.412  0.020  1.412
 QJN  O3'  C3'   single  1.412  0.020  1.412
 QJN  C4'  C3'   single  1.525  0.020  1.525
 QJN  C4'  C5'   single  1.537  0.020  1.537
 QJN  C6'  C5'   single  1.521  0.020  1.521
 QJN  C3'  C2'   single  1.521  0.020  1.521
 QJN  C5'  C7'   single  1.532  0.020  1.532
 QJN  C2'  O2'   single  1.412  0.020  1.412
 QJN  C2'  C1'   single  1.519  0.020  1.519
 QJN  C7'  C1'   single  1.524  0.020  1.524
 QJN  C7'  O7    single  1.411  0.020  1.411
 QJN  C2   H2    single  0.970  0.020  1.090
 QJN  C4   H4    single  0.970  0.020  1.090
 QJN  C5   H5    single  0.970  0.020  1.090
 QJN  C6   H62   single  0.970  0.020  1.090
 QJN  C6   H61   single  0.970  0.020  1.090
 QJN  C8   H81   single  0.970  0.020  1.090
 QJN  C8   H8    single  0.970  0.020  1.090
 QJN  C1'  H1'1  single  0.970  0.020  1.090
 QJN  C1'  H6    single  0.970  0.020  1.090
 QJN  C2'  H2'   single  0.970  0.020  1.090
 QJN  O2'  HO2'  single  0.850  0.020  0.980
 QJN  C3'  H3'   single  0.970  0.020  1.090
 QJN  O3'  HO3'  single  0.850  0.020  0.980
 QJN  C4'  H4'   single  0.970  0.020  1.090
 QJN  C5'  H5'   single  0.970  0.020  1.090
 QJN  O6'  HO6'  single  0.850  0.020  0.980
 QJN  C6'  H6'1  single  0.970  0.020  1.090
 QJN  C6'  H6'2  single  0.970  0.020  1.090
 QJN  C7'  H7'   single  0.970  0.020  1.090
 QJN  C1   H1    single  0.970  0.020  1.090
 QJN  O6   HO6   single  0.850  0.020  0.980
 QJN  C3   H3    single  0.970  0.020  1.090
 QJN  O3   HO3   single  0.850  0.020  0.980
 QJN  O2   HO2   single  0.850  0.020  0.980
 QJN  O7   HO7   single  0.850  0.020  0.980
 QJN  C9   H91   single  0.970  0.020  1.090
 QJN  C9   H9    single  0.970  0.020  1.090
 QJN  C10  H101  single  0.970  0.020  1.090
 QJN  C10  H10   single  0.970  0.020  1.090
 QJN  C11  H111  single  0.970  0.020  1.090
 QJN  C11  H11   single  0.970  0.020  1.090
 QJN  C12  H121  single  0.970  0.020  1.090
 QJN  C12  H12   single  0.970  0.020  1.090
 QJN  C13  H131  single  0.970  0.020  1.090
 QJN  C13  H13   single  0.970  0.020  1.090
 QJN  C14  H14   single  0.970  0.020  1.090
 QJN  C14  H141  single  0.970  0.020  1.090
 QJN  C14  H7    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
 QJN  H2    C2   O2    106.25  3.000
 QJN  H2    C2   C3    107.64  3.000
 QJN  O2    C2   C3    112.26  3.000
 QJN  H2    C2   C1    106.75  3.000
 QJN  O2    C2   C1    112.90  3.000
 QJN  C3    C2   C1    110.65  3.000
 QJN  H4    C4   C3    108.31  3.000
 QJN  H4    C4   O4    111.11  3.000
 QJN  C3    C4   O4    110.26  3.000
 QJN  H4    C4   C5    108.78  3.000
 QJN  C3    C4   C5    109.18  3.000
 QJN  O4    C4   C5    109.16  3.000
 QJN  H5    C5   O5    110.37  3.000
 QJN  H5    C5   C6    106.31  3.000
 QJN  O5    C5   C6    107.75  3.000
 QJN  H5    C5   C4    108.36  3.000
 QJN  O5    C5   C4    110.27  3.000
 QJN  C6    C5   C4    113.70  3.000
 QJN  H61   C6   H62   106.68  3.000
 QJN  H61   C6   O6    111.74  3.000
 QJN  H62   C6   O6    112.07  3.000
 QJN  H61   C6   C5    108.13  3.000
 QJN  H62   C6   C5    107.90  3.000
 QJN  O6    C6   C5    110.14  3.000
 QJN  H6    C1'  H1'1  107.38  3.000
 QJN  H6    C1'  C7'   109.44  3.000
 QJN  H1'1  C1'  C7'   109.81  3.000
 QJN  H6    C1'  C2'   109.75  3.000
 QJN  H1'1  C1'  C2'   109.54  3.000
 QJN  C7'   C1'  C2'   110.85  3.000
 QJN  H2'   C2'  C3'   107.95  3.000
 QJN  H2'   C2'  O2'   110.47  3.000
 QJN  C3'   C2'  O2'   106.71  3.000
 QJN  H2'   C2'  C1'   108.90  3.000
 QJN  O2'   C2'  C1'   112.60  3.000
 QJN  C3'   C2'  C1'   110.10  3.000
 QJN  HO2'  O2'  C2'   108.58  3.000
 QJN  H3'   C3'  C4'   108.19  3.000
 QJN  H3'   C3'  O3'   110.59  3.000
 QJN  C4'   C3'  O3'   107.94  3.000
 QJN  H3'   C3'  C2'   108.29  3.000
 QJN  C4'   C3'  C2'   110.92  3.000
 QJN  O3'   C3'  C2'   110.89  3.000
 QJN  HO3'  O3'  C3'   108.73  3.000
 QJN  H4'   C4'  O1    109.89  3.000
 QJN  H4'   C4'  C5'   109.18  3.000
 QJN  O1    C4'  C5'   111.44  3.000
 QJN  H4'   C4'  C3'   108.25  3.000
 QJN  C5'   C4'  C3'   111.16  3.000
 QJN  O1    C4'  C3'   106.86  3.000
 QJN  H5'   C5'  C7'   107.61  3.000
 QJN  H5'   C5'  C6'   106.64  3.000
 QJN  C7'   C5'  C6'   112.66  3.000
 QJN  H5'   C5'  C4'   107.94  3.000
 QJN  C7'   C5'  C4'   109.50  3.000
 QJN  C6'   C5'  C4'   112.25  3.000
 QJN  H6'2  C6'  H6'1  106.45  3.000
 QJN  H6'2  C6'  O6'   111.48  3.000
 QJN  H6'1  C6'  O6'   111.41  3.000
 QJN  H6'2  C6'  C5'   108.86  3.000
 QJN  H6'1  C6'  C5'   109.25  3.000
 QJN  O6'   C6'  C5'   109.31  3.000
 QJN  H7'   C7'  O7    110.24  3.000
 QJN  H7'   C7'  C5'   108.39  3.000
 QJN  O7    C7'  C5'   108.21  3.000
 QJN  H7'   C7'  C1'   108.26  3.000
 QJN  O7    C7'  C1'   111.23  3.000
 QJN  C5'   C7'  C1'   110.48  3.000
 QJN  C1    O1   C4'   119.86  3.000
 QJN  H1    C1   O5    106.04  3.000
 QJN  H1    C1   O1    110.44  3.000
 QJN  O5    C1   O1    111.15  3.000
 QJN  H1    C1   C2    109.86  3.000
 QJN  O1    C1   C2    109.47  3.000
 QJN  O5    C1   C2    109.82  3.000
 QJN  C1    O5   C5    115.49  3.000
 QJN  HO6   O6   C6    108.16  3.000
 QJN  C8    O4   C4    115.18  3.000
 QJN  H3    C3   O3    110.53  3.000
 QJN  H3    C3   C4    108.40  3.000
 QJN  O3    C3   C4    108.59  3.000
 QJN  H3    C3   C2    109.06  3.000
 QJN  C4    C3   C2    109.01  3.000
 QJN  O3    C3   C2    111.19  3.000
 QJN  HO3   O3   C3    107.59  3.000
 QJN  HO2   O2   C2    110.02  3.000
 QJN  HO7   O7   C7'   108.11  3.000
 QJN  H10   C10  H101  106.06  3.000
 QJN  H10   C10  C11   108.86  3.000
 QJN  H101  C10  C11   109.35  3.000
 QJN  H10   C10  C9    109.22  3.000
 QJN  H101  C10  C9    109.24  3.000
 QJN  C11   C10  C9    113.82  3.000
 QJN  H11   C11  H111  105.87  3.000
 QJN  H11   C11  C12   110.12  3.000
 QJN  H111  C11  C12   108.44  3.000
 QJN  H11   C11  C10   109.08  3.000
 QJN  H111  C11  C10   108.78  3.000
 QJN  C12   C11  C10   114.21  3.000
 QJN  H12   C12  H121  106.06  3.000
 QJN  H12   C12  C13   108.82  3.000
 QJN  H121  C12  C13   108.78  3.000
 QJN  H12   C12  C11   108.61  3.000
 QJN  H121  C12  C11   110.31  3.000
 QJN  C13   C12  C11   113.95  3.000
 QJN  H13   C13  H131  105.95  3.000
 QJN  H13   C13  C14   109.51  3.000
 QJN  H131  C13  C14   108.96  3.000
 QJN  H13   C13  C12   109.35  3.000
 QJN  H131  C13  C12   108.77  3.000
 QJN  C14   C13  C12   113.98  3.000
 QJN  H7    C14  H141  107.52  3.000
 QJN  H7    C14  H14   107.29  3.000
 QJN  H141  C14  H14   107.59  3.000
 QJN  H7    C14  C13   112.02  3.000
 QJN  H141  C14  C13   111.02  3.000
 QJN  H14   C14  C13   111.18  3.000
 QJN  H8    C8   H81   106.99  3.000
 QJN  H8    C8   C9    109.41  3.000
 QJN  H81   C8   C9    109.97  3.000
 QJN  H8    C8   O4    110.47  3.000
 QJN  H81   C8   O4    110.40  3.000
 QJN  C9    C8   O4    109.57  3.000
 QJN  HO6'  O6'  C6'   108.27  3.000
 QJN  H9    C9   H91   106.03  3.000
 QJN  H9    C9   C10   110.23  3.000
 QJN  H91   C9   C10   109.72  3.000
 QJN  H9    C9   C8    106.72  3.000
 QJN  H91   C9   C8    109.89  3.000
 QJN  C10   C9   C8    113.91  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
 QJN  Var_01  C9   C8   O4   C4   -174.43  30.0  1
 QJN  Var_02  C11  C10  C9   C8    176.62  30.0  1
 QJN  Var_03  C10  C9   C8   O4     60.98  30.0  2
 QJN  Var_04  C12  C11  C10  C9    -67.89  30.0  1
 QJN  Var_05  C13  C12  C11  C10  -173.86  30.0  1
 QJN  Var_06  C14  C13  C12  C11   -64.66  30.0  1
 QJN  Var_07  H14  C14  C13  C12  -176.13  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
 QJN  chir_01  C2   C3   O2   C1   negativ
 QJN  chir_02  C4   O4   C5   C3   positiv
 QJN  chir_03  C5   O5   C4   C6   negativ
 QJN  chir_04  C2'  C3'  O2'  C1'  negativ
 QJN  chir_05  C3'  O3'  C4'  C2'  negativ
 QJN  chir_06  C4'  O1   C3'  C5'  negativ
 QJN  chir_07  C5'  C4'  C6'  C7'  negativ
 QJN  chir_08  C7'  O7   C5'  C1'  negativ
 QJN  chir_09  C1   O1   O5   C2   negativ
 QJN  chir_10  C3   O3   C2   C4   positiv

