# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 06:23:46 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(9-methoxynonyl)amino]cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCCCCCCCN[C@H]1C[C@](O)(CO)[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
 W9G  W9G  "(1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(9-methoxynonyl)amino]cyclohexane-1,2,3,4-tetrol"
  ligand  59  24  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W9G
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
 W9G  N1   N  NH1   0  -0.648   7.4458  24.6853  16.3057
 W9G  C4   C  CH2   0  -0.476   7.6902  26.0830  14.2907
 W9G  C5   C  CH1   0  -0.118   7.4582  26.0594  15.8013
 W9G  C6   C  CH2   0  -0.257   8.7749  24.1319  16.5166
 W9G  C7   C  CH2   0  -0.445   8.7042  22.6888  16.9931
 W9G  C8   C  CH2   0  -0.435  10.0735  22.0911  17.3056
 W9G  C10  C  CH2   0  -0.417  12.3703  21.4119  16.4053
 W9G  C13  C  CH2   0  -0.461  13.9361  18.1914  17.9566
 W9G  C15  C  CH3   0  -0.398  15.2531  15.4348  18.1558
 W9G  C17  C  CH1   0   0.003   4.9701  26.1280  15.3407
 W9G  C1   C  CH1   0   0.073   5.2479  26.1159  13.8396
 W9G  C11  C  CH2   0  -0.415  12.4310  20.0249  17.0363
 W9G  C12  C  CH2   0  -0.415  13.8587  19.5646  17.2989
 W9G  C14  C  CH2   0  -0.147  15.3793  17.7907  18.2268
 W9G  C16  C  CH1   0   0.014   6.1294  26.7539  16.1076
 W9G  C2   C  CT    0   0.152   6.5622  25.3866  13.5177
 W9G  C3   C  CH2   0  -0.155   6.8544  25.4012  12.0167
 W9G  C9   C  CH2   0  -0.429  10.9622  21.9009  16.0790
 W9G  O1   O  OH1   0  -0.677   4.1954  25.4976  13.1416
 W9G  O2   O  OH1   0  -0.669   6.8862  26.7274  11.5446
 W9G  O3   O  OH1   0  -0.712   6.4840  24.0207  13.8633
 W9G  O4   O  O2    0  -0.483  15.5322  16.5769  18.9239
 W9G  O5   O  OH1   0  -0.667   5.7979  26.6963  17.4789
 W9G  O6   O  OH1   0  -0.677   3.7802  26.8690  15.5214
 W9G  H1   H  HNH1  0   0.358   6.9431  24.6687  17.1869
 W9G  H3   H  HCH2  0   0.252   8.6439  25.6077  14.0453
 W9G  H4   H  HCH2  0   0.246   7.7807  27.1228  13.9677
 W9G  H5   H  HCH1  0   0.231   8.2583  26.6419  16.2859
 W9G  H6   H  HCH2  0   0.205   9.3477  24.7303  17.2411
 W9G  H7   H  HCH2  0   0.229   9.3258  24.1845  15.5755
 W9G  H8   H  HCH2  0   0.225   8.0812  22.6454  17.8921
 W9G  H9   H  HCH2  0   0.217   8.1971  22.0815  16.2365
 W9G  H10  H  HCH2  0   0.229   9.9263  21.1299  17.8036
 W9G  H11  H  HCH2  0   0.208  10.5885  22.7315  18.0307
 W9G  H12  H  HCH2  0   0.216  12.9657  21.4070  15.4867
 W9G  H13  H  HCH2  0   0.206  12.8541  22.1330  17.0736
 W9G  H14  H  HCH2  0   0.216  13.3810  18.2044  18.8999
 W9G  H15  H  HCH2  0   0.221  13.4449  17.4563  17.3117
 W9G  H16  H  HCH3  0   0.229  15.5372  14.5606  18.7415
 W9G  H17  H  HCH3  0   0.204  14.1927  15.3378  17.8989
 W9G  H18  H  HCH3  0   0.199  15.8263  15.4209  17.2203
 W9G  H19  H  HCH1  0   0.208   4.8250  25.0935  15.6839
 W9G  H20  H  HCH1  0   0.199   5.3608  27.1639  13.5211
 W9G  H21  H  HCH2  0   0.214  11.8762  20.0159  17.9792
 W9G  H22  H  HCH2  0   0.207  11.9290  19.3056  16.3797
 W9G  H23  H  HCH2  0   0.212  14.4154  19.5509  16.3556
 W9G  H24  H  HCH2  0   0.210  14.3619  20.2999  17.9365
 W9G  H25  H  HCH2  0   0.188  15.9339  17.7609  17.2764
 W9G  H26  H  HCH2  0   0.219  15.8528  18.5572  18.8467
 W9G  H27  H  HCH1  0   0.223   6.2290  27.7978  15.7758
 W9G  H28  H  HCH2  0   0.205   6.0937  24.8051  11.4976
 W9G  H29  H  HCH2  0   0.199   7.8187  24.8982  11.8615
 W9G  H30  H  HCH2  0   0.224  11.0460  22.8461  15.5362
 W9G  H31  H  HCH2  0   0.208  10.4806  21.1983  15.3898
 W9G  H32  H  HOH1  0   0.443   3.3787  25.9406  13.3939
 W9G  H33  H  HOH1  0   0.456   7.0917  26.7077  10.6061
 W9G  H34  H  HOH1  0   0.449   6.7320  23.9660  14.8138
 W9G  H35  H  HOH1  0   0.455   6.3924  27.2764  17.9653
 W9G  H36  H  HOH1  0   0.450   3.4845  26.7572  16.4299

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
 W9G  O2   C3   single  1.408  0.020  1.408
 W9G  C3   C2   single  1.529  0.020  1.529
 W9G  O1   C1   single  1.406  0.020  1.406
 W9G  C1   C2   single  1.537  0.020  1.537
 W9G  C1   C17  single  1.527  0.020  1.527
 W9G  C2   O3   single  1.411  0.020  1.411
 W9G  C2   C4   single  1.535  0.020  1.535
 W9G  O6   C17  single  1.413  0.020  1.413
 W9G  C17  C16  single  1.524  0.020  1.524
 W9G  C4   C5   single  1.528  0.020  1.528
 W9G  C10  C9   single  1.526  0.020  1.526
 W9G  C10  C11  single  1.525  0.020  1.525
 W9G  C9   C8   single  1.527  0.020  1.527
 W9G  C5   C16  single  1.530  0.020  1.530
 W9G  C5   N1   single  1.464  0.020  1.464
 W9G  C16  O5   single  1.412  0.020  1.412
 W9G  C6   C7   single  1.521  0.020  1.521
 W9G  C6   N1   single  1.455  0.020  1.455
 W9G  C7   C8   single  1.526  0.020  1.526
 W9G  C12  C11  single  1.523  0.020  1.523
 W9G  C12  C13  single  1.525  0.020  1.525
 W9G  C14  C13  single  1.522  0.020  1.522
 W9G  C14  O4   single  1.408  0.020  1.408
 W9G  C15  O4   single  1.404  0.020  1.404
 W9G  N1   H1   single  0.890  0.020  1.040
 W9G  C4   H3   single  0.970  0.020  1.090
 W9G  C4   H4   single  0.970  0.020  1.090
 W9G  C5   H5   single  0.970  0.020  1.090
 W9G  C6   H6   single  0.970  0.020  1.090
 W9G  C6   H7   single  0.970  0.020  1.090
 W9G  C7   H8   single  0.970  0.020  1.090
 W9G  C7   H9   single  0.970  0.020  1.090
 W9G  C8   H10  single  0.970  0.020  1.090
 W9G  C8   H11  single  0.970  0.020  1.090
 W9G  C10  H12  single  0.970  0.020  1.090
 W9G  C10  H13  single  0.970  0.020  1.090
 W9G  C13  H14  single  0.970  0.020  1.090
 W9G  C13  H15  single  0.970  0.020  1.090
 W9G  C15  H16  single  0.970  0.020  1.090
 W9G  C15  H17  single  0.970  0.020  1.090
 W9G  C15  H18  single  0.970  0.020  1.090
 W9G  C17  H19  single  0.970  0.020  1.090
 W9G  C1   H20  single  0.970  0.020  1.090
 W9G  C11  H21  single  0.970  0.020  1.090
 W9G  C11  H22  single  0.970  0.020  1.090
 W9G  C12  H23  single  0.970  0.020  1.090
 W9G  C12  H24  single  0.970  0.020  1.090
 W9G  C14  H25  single  0.970  0.020  1.090
 W9G  C14  H26  single  0.970  0.020  1.090
 W9G  C16  H27  single  0.970  0.020  1.090
 W9G  C3   H28  single  0.970  0.020  1.090
 W9G  C3   H29  single  0.970  0.020  1.090
 W9G  C9   H30  single  0.970  0.020  1.090
 W9G  C9   H31  single  0.970  0.020  1.090
 W9G  O1   H32  single  0.850  0.020  0.980
 W9G  O2   H33  single  0.850  0.020  0.980
 W9G  O3   H34  single  0.850  0.020  0.980
 W9G  O5   H35  single  0.850  0.020  0.980
 W9G  O6   H36  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
 W9G  H1   N1   C6   108.69  3.000
 W9G  H1   N1   C5   108.60  3.000
 W9G  C6   N1   C5   113.53  3.000
 W9G  H4   C4   H3   105.96  3.000
 W9G  H4   C4   C2   110.12  3.000
 W9G  H3   C4   C2   109.31  3.000
 W9G  H4   C4   C5   108.63  3.000
 W9G  H3   C4   C5   110.33  3.000
 W9G  C2   C4   C5   112.29  3.000
 W9G  H5   C5   C16  107.61  3.000
 W9G  H5   C5   C4   108.44  3.000
 W9G  C16  C5   C4   108.82  3.000
 W9G  H5   C5   N1   110.53  3.000
 W9G  C16  C5   N1   110.47  3.000
 W9G  C4   C5   N1   110.88  3.000
 W9G  H7   C6   H6   106.18  3.000
 W9G  H7   C6   C7   109.83  3.000
 W9G  H6   C6   C7   109.50  3.000
 W9G  H7   C6   N1   108.52  3.000
 W9G  H6   C6   N1   111.35  3.000
 W9G  C7   C6   N1   111.33  3.000
 W9G  H9   C7   H8   106.38  3.000
 W9G  H9   C7   C8   109.87  3.000
 W9G  H8   C7   C8   109.08  3.000
 W9G  H9   C7   C6   109.34  3.000
 W9G  H8   C7   C6   108.74  3.000
 W9G  C8   C7   C6   113.20  3.000
 W9G  H11  C8   H10  106.02  3.000
 W9G  H11  C8   C9   109.32  3.000
 W9G  H10  C8   C9   109.58  3.000
 W9G  H11  C8   C7   109.16  3.000
 W9G  H10  C8   C7   108.48  3.000
 W9G  C9   C8   C7   113.98  3.000
 W9G  H13  C10  H12  105.94  3.000
 W9G  H13  C10  C9   109.08  3.000
 W9G  H12  C10  C9   108.90  3.000
 W9G  H13  C10  C11  109.19  3.000
 W9G  H12  C10  C11  108.75  3.000
 W9G  C9   C10  C11  114.63  3.000
 W9G  H15  C13  H14  106.76  3.000
 W9G  H15  C13  C14  110.69  3.000
 W9G  H14  C13  C14  109.33  3.000
 W9G  H15  C13  C12  109.15  3.000
 W9G  H14  C13  C12  109.59  3.000
 W9G  C14  C13  C12  111.21  3.000
 W9G  H18  C15  H17  107.74  3.000
 W9G  H18  C15  H16  108.17  3.000
 W9G  H17  C15  H16  107.90  3.000
 W9G  H18  C15  O4   111.89  3.000
 W9G  H17  C15  O4   113.12  3.000
 W9G  H16  C15  O4   107.85  3.000
 W9G  H19  C17  O6   110.02  3.000
 W9G  H19  C17  C16  109.24  3.000
 W9G  O6   C17  C16  111.14  3.000
 W9G  H19  C17  C1   108.87  3.000
 W9G  C16  C17  C1   111.07  3.000
 W9G  O6   C17  C1   106.45  3.000
 W9G  H20  C1   O1   110.58  3.000
 W9G  H20  C1   C2   107.66  3.000
 W9G  O1   C1   C2   109.11  3.000
 W9G  H20  C1   C17  107.19  3.000
 W9G  C2   C1   C17  111.43  3.000
 W9G  O1   C1   C17  110.81  3.000
 W9G  H22  C11  H21  106.18  3.000
 W9G  H22  C11  C12  109.54  3.000
 W9G  H21  C11  C12  108.92  3.000
 W9G  H22  C11  C10  109.33  3.000
 W9G  H21  C11  C10  110.12  3.000
 W9G  C12  C11  C10  112.56  3.000
 W9G  H24  C12  H23  106.03  3.000
 W9G  H24  C12  C11  109.15  3.000
 W9G  H23  C12  C11  109.37  3.000
 W9G  H24  C12  C13  109.28  3.000
 W9G  H23  C12  C13  109.54  3.000
 W9G  C11  C12  C13  113.22  3.000
 W9G  H26  C14  H25  106.88  3.000
 W9G  H26  C14  O4   106.05  3.000
 W9G  H25  C14  O4   110.46  3.000
 W9G  H26  C14  C13  109.06  3.000
 W9G  H25  C14  C13  109.36  3.000
 W9G  O4   C14  C13  114.70  3.000
 W9G  H27  C16  O5   110.66  3.000
 W9G  H27  C16  C17  107.87  3.000
 W9G  O5   C16  C17  107.05  3.000
 W9G  H27  C16  C5   106.96  3.000
 W9G  O5   C16  C5   112.32  3.000
 W9G  C17  C16  C5   111.92  3.000
 W9G  O3   C2   C3   105.09  3.000
 W9G  O3   C2   C1   111.13  3.000
 W9G  C3   C2   C1   111.37  3.000
 W9G  O3   C2   C4   110.89  3.000
 W9G  C1   C2   C4   107.92  3.000
 W9G  C3   C2   C4   110.46  3.000
 W9G  H29  C3   H28  107.04  3.000
 W9G  H29  C3   O2   111.35  3.000
 W9G  H28  C3   O2   111.64  3.000
 W9G  H29  C3   C2   107.58  3.000
 W9G  H28  C3   C2   109.07  3.000
 W9G  O2   C3   C2   110.03  3.000
 W9G  H31  C9   H30  106.01  3.000
 W9G  H31  C9   C10  109.54  3.000
 W9G  H30  C9   C10  108.21  3.000
 W9G  H31  C9   C8   109.24  3.000
 W9G  H30  C9   C8   109.63  3.000
 W9G  C10  C9   C8   113.91  3.000
 W9G  H32  O1   C1   107.61  3.000
 W9G  H33  O2   C3   108.24  3.000
 W9G  H34  O3   C2   106.05  3.000
 W9G  C14  O4   C15  114.12  3.000
 W9G  H35  O5   C16  108.73  3.000
 W9G  H36  O6   C17  108.58  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
 W9G  Var_01  C7   C6   N1   C5   -177.99  30.0  1
 W9G  Var_02  H6   C6   N1   C5     59.50  30.0  1
 W9G  Var_03  H7   C6   N1   C5    -57.01  30.0  1
 W9G  Var_04  C8   C7   C6   N1   -176.66  30.0  3
 W9G  Var_05  C9   C8   C7   C6    -67.56  30.0  3
 W9G  Var_06  C10  C9   C8   C7    175.23  30.0  1
 W9G  Var_07  C11  C10  C9   C8     63.95  30.0  1
 W9G  Var_08  C13  C12  C11  C10   178.80  30.0  1
 W9G  Var_09  C15  O4   C14  C13    73.02  30.0  3
 W9G  Var_10  C14  C13  C12  C11  -178.71  30.0  3
 W9G  Var_11  C9   C10  C11  C12   178.07  30.0  1
 W9G  Var_12  O4   C14  C13  C12   175.51  30.0  1
 W9G  Var_13  H8   C7   C6   N1    -55.27  30.0  3
 W9G  Var_14  H9   C7   C6   N1     60.50  30.0  3
 W9G  Var_15  H10  C8   C7   C6    170.08  30.0  3
 W9G  Var_16  H11  C8   C7   C6     54.99  30.0  3
 W9G  Var_17  H1   N1   C6   C7     61.05  30.0  3
 W9G  Var_18  H30  C9   C8   C7     53.83  30.0  1
 W9G  Var_19  H31  C9   C8   C7    -61.94  30.0  1
 W9G  Var_20  H12  C10  C9   C8   -173.99  30.0  1
 W9G  Var_21  H13  C10  C9   C8    -58.80  30.0  1
 W9G  Var_22  H6   C6   C7   C8    -53.10  30.0  1
 W9G  Var_23  H7   C6   C7   C8     63.13  30.0  1
 W9G  Var_24  H10  C8   C9   C10   -63.01  30.0  3
 W9G  Var_25  H11  C8   C9   C10    52.77  30.0  3
 W9G  Var_26  H23  C12  C11  C10   -58.75  30.0  1
 W9G  Var_27  H24  C12  C11  C10    56.84  30.0  1
 W9G  Var_28  H21  C11  C12  C13    56.38  30.0  3
 W9G  Var_29  H22  C11  C12  C13   -59.36  30.0  3
 W9G  Var_30  H25  C14  O4   C15   -51.11  30.0  1
 W9G  Var_31  H26  C14  O4   C15  -166.56  30.0  1
 W9G  Var_32  H30  C9   C10  C11  -173.86  30.0  3
 W9G  Var_33  H31  C9   C10  C11   -58.71  30.0  3
 W9G  Var_34  H14  C13  C12  C11   -57.70  30.0  3
 W9G  Var_35  H15  C13  C12  C11    58.88  30.0  3
 W9G  Var_36  H12  C10  C11  C12    55.93  30.0  1
 W9G  Var_37  H13  C10  C11  C12   -59.23  30.0  1
 W9G  Var_38  H25  C14  C13  C12   -59.79  30.0  1
 W9G  Var_39  H26  C14  C13  C12    56.76  30.0  1
 W9G  Var_40  H23  C12  C13  C14    58.93  30.0  1
 W9G  Var_41  H24  C12  C13  C14   -56.83  30.0  1
 W9G  Var_42  H16  C15  O4   C14   172.08  30.0  3
 W9G  Var_43  H17  C15  O4   C14   -68.66  30.0  3
 W9G  Var_44  H18  C15  O4   C14    53.24  30.0  3
 W9G  Var_45  H21  C11  C10  C9    -60.19  30.0  3
 W9G  Var_46  H22  C11  C10  C9     56.10  30.0  3
 W9G  Var_47  H8   C7   C8   C9    171.24  30.0  1
 W9G  Var_48  H9   C7   C8   C9     55.00  30.0  1
 W9G  Var_49  H14  C13  C14  O4     54.35  30.0  3
 W9G  Var_50  H15  C13  C14  O4    -62.98  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
 W9G  chir_01  C5   C4  C16  N1  negativ
 W9G  chir_02  C17  O6  C16  C1  positiv
 W9G  chir_03  C1   O1  C17  C2  negativ
 W9G  chir_04  C16  O5  C17  C5  positiv
 W9G  chir_05  C2   C3  C1   C4  positiv

