# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 11:31:47 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-(9-methoxynonyl)piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
#
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
 6A9  6A9  (2R,3R,4R,5S)-2-(hydroxymethyl)-1-(9-methoxynonyl)piperidine-3,4,5-triol  ligand  55  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6A9
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
 6A9  C10  C  CH2   0  -0.411   4.6504  -0.2814   0.2841
 6A9  C12  C  CH2   0  -0.463   7.1840  -0.4116   0.4165
 6A9  C14  C  CH3   0  -0.396  10.8139  -0.0401   0.0484
 6A9  C15  C  CH2   0  -0.331  -3.1636  -1.2454  -0.5349
 6A9  C3   C  CH1   0  -0.091  -4.0356   0.9765  -0.5288
 6A9  C2   C  CH1   0   0.061  -5.2674   0.5027   0.2574
 6A9  O2   O  OH1   0  -0.679  -6.3658   1.3032  -0.1165
 6A9  C1   C  CH1   0   0.005  -5.5654  -0.9638  -0.0159
 6A9  O1   O  OH1   0  -0.679  -6.6648  -1.3276   0.7892
 6A9  N    N  NT    0  -0.444  -2.8984   0.1321  -0.1641
 6A9  C    C  CH1   0   0.033  -4.3355  -1.8030   0.2594
 6A9  O    O  OH1   0  -0.677  -4.6338  -3.1330  -0.1063
 6A9  C5   C  CH2   0  -0.257  -1.6123   0.5849  -0.6735
 6A9  C6   C  CH2   0  -0.445  -0.4191  -0.0906  -0.0086
 6A9  C7   C  CH2   0  -0.416   0.9018   0.4838  -0.5065
 6A9  C8   C  CH2   0  -0.412   2.1146  -0.1672   0.1459
 6A9  C9   C  CH2   0  -0.413   3.4413   0.3765  -0.3681
 6A9  C11  C  CH2   0  -0.424   5.9782   0.2522  -0.2373
 6A9  C13  C  CH2   0  -0.120   8.4898   0.1365  -0.1219
 6A9  O4   O  O2    0  -0.488   9.5722  -0.5060   0.5075
 6A9  H1   H  HCH2  0   0.209   4.6011  -0.1376   1.3690
 6A9  H2   H  HCH2  0   0.209   4.6052  -1.3639   0.1214
 6A9  H3   H  HCH2  0   0.221   7.1426  -0.2602   1.4997
 6A9  H4   H  HCH2  0   0.221   7.1434  -1.4921   0.2467
 6A9  H5   H  HCH3  0   0.201  10.9428  -0.2042  -1.0284
 6A9  H6   H  HCH3  0   0.201  10.9482   1.0317   0.2391
 6A9  H7   H  HCH3  0   0.231  11.5978  -0.5837   0.5750
 6A9  H8   H  HCH2  0   0.196  -3.3703  -1.3495  -1.6160
 6A9  H9   H  HCH2  0   0.247  -2.2861  -1.8587  -0.3249
 6A9  H10  H  HOH1  0   0.455  -3.4167   3.6329   1.1951
 6A9  H13  H  HCH1  0   0.204  -4.2650   0.8773  -1.6078
 6A9  H14  H  HCH1  0   0.205  -5.0470   0.6175   1.3284
 6A9  H15  H  HOH1  0   0.451  -7.1280   1.0171   0.3969
 6A9  H16  H  HCH1  0   0.199  -5.8140  -1.0660  -1.0855
 6A9  H17  H  HOH1  0   0.453  -6.9178  -2.2295   0.5693
 6A9  H19  H  HCH1  0   0.205  -4.0909  -1.7336   1.3288
 6A9  H20  H  HOH1  0   0.455  -3.9404  -3.7056   0.2353
 6A9  H21  H  HCH2  0   0.185  -1.5414   0.4635  -1.7684
 6A9  H22  H  HCH2  0   0.241  -1.5091   1.6511  -0.4788
 6A9  H23  H  HCH2  0   0.216  -0.4978   0.0429   1.0748
 6A9  H24  H  HCH2  0   0.220  -0.4164  -1.1690  -0.1891
 6A9  H25  H  HCH2  0   0.211   0.9658   0.3594  -1.5930
 6A9  H26  H  HCH2  0   0.211   0.9259   1.5638  -0.3241
 6A9  H27  H  HCH2  0   0.209   2.0603  -0.0293   1.2314
 6A9  H28  H  HCH2  0   0.208   2.0775  -1.2493  -0.0221
 6A9  H29  H  HCH2  0   0.208   3.4822   1.4586  -0.2012
 6A9  H30  H  HCH2  0   0.208   3.4945   0.2368  -1.4536
 6A9  H31  H  HCH2  0   0.213   6.0253   0.1076  -1.3221
 6A9  H32  H  HCH2  0   0.213   6.0235   1.3345  -0.0746
 6A9  H33  H  HCH2  0   0.190   8.5361  -0.0109  -1.2117
 6A9  H34  H  HCH2  0   0.190   8.5368   1.2233   0.0461
 6A9  C4   C  CH2   0  -0.211  -3.7963   2.4613  -0.2972
 6A9  H11  H  HCH2  0   0.230  -4.7189   2.9904  -0.5548
 6A9  O3   O  OH1   0  -0.672  -3.4219   2.6841   1.0428
 6A9  H12  H  HCH2  0   0.212  -3.0364   2.8298  -0.9968

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
 6A9  O1   C1   single  1.410  0.020  1.410
 6A9  O2   C2   single  1.410  0.020  1.410
 6A9  C1   C2   single  1.521  0.020  1.521
 6A9  C1   C    single  1.514  0.020  1.514
 6A9  C2   C3   single  1.536  0.020  1.536
 6A9  O    C    single  1.411  0.020  1.411
 6A9  C    C15  single  1.522  0.020  1.522
 6A9  C3   C4   single  1.522  0.020  1.522
 6A9  C3   N    single  1.463  0.020  1.463
 6A9  C12  C13  single  1.515  0.020  1.515
 6A9  C12  C11  single  1.524  0.020  1.524
 6A9  C15  N    single  1.451  0.020  1.451
 6A9  C13  O4   single  1.407  0.020  1.407
 6A9  O4   C14  single  1.403  0.020  1.403
 6A9  C4   O3   single  1.409  0.020  1.409
 6A9  N    C5   single  1.456  0.020  1.456
 6A9  C11  C10  single  1.523  0.020  1.523
 6A9  C6   C5   single  1.524  0.020  1.524
 6A9  C6   C7   single  1.524  0.020  1.524
 6A9  C8   C7   single  1.523  0.020  1.523
 6A9  C8   C9   single  1.523  0.020  1.523
 6A9  C10  C9   single  1.523  0.020  1.523
 6A9  C10  H1   single  0.970  0.020  1.090
 6A9  C10  H2   single  0.970  0.020  1.090
 6A9  C12  H3   single  0.970  0.020  1.090
 6A9  C12  H4   single  0.970  0.020  1.090
 6A9  C14  H5   single  0.970  0.020  1.090
 6A9  C14  H6   single  0.970  0.020  1.090
 6A9  C14  H7   single  0.970  0.020  1.090
 6A9  C15  H8   single  0.970  0.020  1.090
 6A9  C15  H9   single  0.970  0.020  1.090
 6A9  O3   H10  single  0.850  0.020  0.980
 6A9  C4   H11  single  0.970  0.020  1.090
 6A9  C4   H12  single  0.970  0.020  1.090
 6A9  C3   H13  single  0.970  0.020  1.090
 6A9  C2   H14  single  0.970  0.020  1.090
 6A9  O2   H15  single  0.850  0.020  0.980
 6A9  C1   H16  single  0.970  0.020  1.090
 6A9  O1   H17  single  0.850  0.020  0.980
 6A9  C    H19  single  0.970  0.020  1.090
 6A9  O    H20  single  0.850  0.020  0.980
 6A9  C5   H21  single  0.970  0.020  1.090
 6A9  C5   H22  single  0.970  0.020  1.090
 6A9  C6   H23  single  0.970  0.020  1.090
 6A9  C6   H24  single  0.970  0.020  1.090
 6A9  C7   H25  single  0.970  0.020  1.090
 6A9  C7   H26  single  0.970  0.020  1.090
 6A9  C8   H27  single  0.970  0.020  1.090
 6A9  C8   H28  single  0.970  0.020  1.090
 6A9  C9   H29  single  0.970  0.020  1.090
 6A9  C9   H30  single  0.970  0.020  1.090
 6A9  C11  H31  single  0.970  0.020  1.090
 6A9  C11  H32  single  0.970  0.020  1.090
 6A9  C13  H33  single  0.970  0.020  1.090
 6A9  C13  H34  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
 6A9  H2   C10  H1   105.96  3.000
 6A9  H2   C10  C11  109.34  3.000
 6A9  H1   C10  C11  109.40  3.000
 6A9  H2   C10  C9   109.30  3.000
 6A9  H1   C10  C9   109.37  3.000
 6A9  C11  C10  C9   113.21  3.000
 6A9  H4   C12  H3   106.78  3.000
 6A9  H4   C12  C13  109.51  3.000
 6A9  H3   C12  C13  109.53  3.000
 6A9  H4   C12  C11  109.51  3.000
 6A9  H3   C12  C11  109.54  3.000
 6A9  C13  C12  C11  111.83  3.000
 6A9  H7   C14  H6   108.38  3.000
 6A9  H7   C14  H5   108.38  3.000
 6A9  H6   C14  H5   107.60  3.000
 6A9  H7   C14  O4   108.23  3.000
 6A9  H6   C14  O4   112.07  3.000
 6A9  H5   C14  O4   112.05  3.000
 6A9  H9   C15  H8   106.60  3.000
 6A9  H9   C15  C    108.24  3.000
 6A9  H8   C15  C    109.39  3.000
 6A9  H9   C15  N    109.72  3.000
 6A9  H8   C15  N    111.93  3.000
 6A9  C    C15  N    110.81  3.000
 6A9  H13  C3   N    110.63  3.000
 6A9  H13  C3   C2   107.75  3.000
 6A9  N    C3   C2   108.53  3.000
 6A9  H13  C3   C4   105.56  3.000
 6A9  N    C3   C4   113.78  3.000
 6A9  C2   C3   C4   110.43  3.000
 6A9  H14  C2   C1   108.36  3.000
 6A9  H14  C2   O2   110.81  3.000
 6A9  C1   C2   O2   110.31  3.000
 6A9  H14  C2   C3   107.80  3.000
 6A9  C1   C2   C3   111.25  3.000
 6A9  O2   C2   C3   108.30  3.000
 6A9  H15  O2   C2   107.86  3.000
 6A9  H16  C1   C    107.94  3.000
 6A9  H16  C1   O1   110.74  3.000
 6A9  C    C1   O1   112.73  3.000
 6A9  H16  C1   C2   107.92  3.000
 6A9  C    C1   C2   110.03  3.000
 6A9  O1   C1   C2   107.38  3.000
 6A9  H17  O1   C1   108.43  3.000
 6A9  C5   N    C3   114.84  3.000
 6A9  C5   N    C15  111.55  3.000
 6A9  C3   N    C15  110.02  3.000
 6A9  H19  C    O    111.02  3.000
 6A9  H19  C    C1   108.82  3.000
 6A9  O    C    C1   107.67  3.000
 6A9  H19  C    C15  108.26  3.000
 6A9  O    C    C15  111.89  3.000
 6A9  C1   C    C15  109.12  3.000
 6A9  H20  O    C    108.46  3.000
 6A9  H22  C5   H21  106.20  3.000
 6A9  H22  C5   C6   106.37  3.000
 6A9  H21  C5   C6   109.49  3.000
 6A9  H22  C5   N    109.02  3.000
 6A9  H21  C5   N    111.70  3.000
 6A9  C6   C5   N    113.66  3.000
 6A9  H24  C6   H23  106.49  3.000
 6A9  H24  C6   C7   108.40  3.000
 6A9  H23  C6   C7   109.86  3.000
 6A9  H24  C6   C5   111.54  3.000
 6A9  H23  C6   C5   108.76  3.000
 6A9  C7   C6   C5   111.66  3.000
 6A9  H26  C7   H25  106.00  3.000
 6A9  H26  C7   C8   109.42  3.000
 6A9  H25  C7   C8   109.26  3.000
 6A9  H26  C7   C6   109.64  3.000
 6A9  H25  C7   C6   109.38  3.000
 6A9  C8   C7   C6   112.90  3.000
 6A9  H28  C8   H27  105.93  3.000
 6A9  H28  C8   C9   109.28  3.000
 6A9  H27  C8   C9   109.43  3.000
 6A9  H28  C8   C7   109.24  3.000
 6A9  H27  C8   C7   109.34  3.000
 6A9  C9   C8   C7   113.36  3.000
 6A9  H30  C9   H29  105.96  3.000
 6A9  H30  C9   C8   109.34  3.000
 6A9  H29  C9   C8   109.49  3.000
 6A9  H30  C9   C10  109.31  3.000
 6A9  H29  C9   C10  109.37  3.000
 6A9  C8   C9   C10  113.13  3.000
 6A9  H32  C11  H31  106.00  3.000
 6A9  H32  C11  C12  109.51  3.000
 6A9  H31  C11  C12  109.48  3.000
 6A9  H32  C11  C10  109.35  3.000
 6A9  H31  C11  C10  109.29  3.000
 6A9  C12  C11  C10  112.98  3.000
 6A9  H34  C13  H33  106.35  3.000
 6A9  H34  C13  O4   110.47  3.000
 6A9  H33  C13  O4   110.45  3.000
 6A9  H34  C13  C12  109.87  3.000
 6A9  H33  C13  C12  109.86  3.000
 6A9  O4   C13  C12  109.80  3.000
 6A9  C13  O4   C14  112.50  3.000
 6A9  H12  C4   H11  105.76  3.000
 6A9  H12  C4   C3   109.86  3.000
 6A9  H11  C4   C3   107.66  3.000
 6A9  H12  C4   O3   111.68  3.000
 6A9  H11  C4   O3   111.81  3.000
 6A9  C3   C4   O3   109.92  3.000
 6A9  H10  O3   C4   107.95  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
 6A9  Var_01  C    C15  N    C3    -64.46  30.0  1
 6A9  Var_02  C6   C5   N    C15   -68.40  30.0  3
 6A9  Var_03  C7   C6   C5   N    -176.10  30.0  1
 6A9  Var_04  C13  C12  C11  C10   179.92  30.0  1
 6A9  Var_05  C7   C8   C9   C10  -179.80  30.0  1
 6A9  Var_06  C9   C10  C11  C12  -179.88  30.0  3
 6A9  Var_07  C8   C7   C6   C5    179.71  30.0  3
 6A9  Var_08  C9   C8   C7   C6    178.65  30.0  1
 6A9  Var_09  C11  C10  C9   C8    179.50  30.0  1
 6A9  Var_10  O4   C13  C12  C11  -179.90  30.0  3
 6A9  Var_11  H33  C13  O4   C14    58.65  30.0  1
 6A9  Var_12  H5   C14  O4   C13   -60.32  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
 6A9  chir_01  C3  C2  C4  N    negativ
 6A9  chir_02  C2  O2  C3  C1   positiv
 6A9  chir_03  C1  O1  C2  C    negativ
 6A9  chir_04  C   O   C1  C15  positiv

