# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:02:40 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-nonylpiperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCN1C[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
 NND  NND  (2R,3R,4R,5S)-2-(hydroxymethyl)-1-nonylpiperidine-3,4,5-triol  ligand  51  20  .  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_NND
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
 NND  O6    O  OH1   0  -0.671  -2.3555   2.6846   1.0584
 NND  C6    C  CH2   0  -0.211  -2.7236   2.4812  -0.2863
 NND  C5    C  CR16  0  -0.092  -2.9727   1.0010  -0.5365
 NND  C4    C  CR16  0   0.064  -4.2109   0.5268   0.2392
 NND  O4    O  OH1   0  -0.680  -5.3019   1.3410  -0.1264
 NND  O3    O  OH1   0  -0.679  -5.6252  -1.2981   0.7409
 NND  C2    C  CR16  0   0.034  -3.2977  -1.7870   0.2126
 NND  O2    O  OH1   0  -0.677  -3.6057  -3.1084  -0.1754
 NND  N1    N  NR6   0  -0.444  -1.8442   0.1435  -0.1760
 NND  C8    C  CH2   0  -0.257  -0.5501   0.5922  -0.6686
 NND  C7    C  CH2   0  -0.444   0.6301  -0.0949   0.0073
 NND  C1    C  C     0  -0.331  -2.1178  -1.2265  -0.5679
 NND  C9    C  CH2   0  -0.416   1.9631   0.4642  -0.4760
 NND  C10   C  CH2   0  -0.412   3.1595  -0.2027   0.1901
 NND  C14   C  CH2   0  -0.412   4.5007   0.3201  -0.3080
 NND  C13   C  CH2   0  -0.412   5.6910  -0.3578   0.3586
 NND  C12   C  CH2   0  -0.406   7.0367   0.1530  -0.1387
 NND  C16   C  CH3   0  -0.661   9.5652  -0.0184   0.0285
 NND  C11   C  CH2   0  -0.420   8.2224  -0.5329   0.5282
 NND  C31   C  CR16  0   0.003  -4.5193  -0.9333  -0.0554
 NND  H6    H  HOH1  0   0.455  -2.3226   3.6321   1.2164
 NND  H6C1  H  HCH2  0   0.230  -3.6410   3.0203  -0.5426
 NND  H6C2  H  HCH2  0   0.213  -1.9573   2.8521  -0.9774
 NND  H5    H  HCR6  0   0.204  -3.1980   0.9159  -1.6173
 NND  H4    H  HCR6  0   0.205  -3.9923   0.6249   1.3124
 NND  HA    H  HOH1  0   0.450  -6.0770   1.0269   0.3504
 NND  H31   H  HCR6  0   0.199  -4.7657  -1.0186  -1.1268
 NND  H3    H  HOH1  0   0.453  -5.8949  -2.1893   0.4983
 NND  H2    H  HCR6  0   0.206  -3.0580  -1.7359   1.2841
 NND  HB    H  HOH1  0   0.455  -2.9178  -3.6922   0.1583
 NND  H1C1  H  H     0   0.247  -1.2459  -1.8498  -0.3636
 NND  H1C2  H  H     0   0.196  -2.3202  -1.3138  -1.6516
 NND  H8C1  H  HCH2  0   0.186  -0.4668   0.4759  -1.7632
 NND  H8C2  H  HCH2  0   0.241  -0.4425   1.6568  -0.4675
 NND  H7C1  H  HCH2  0   0.216   0.5416   0.0384   1.0899
 NND  H7C2  H  HCH2  0   0.220   0.6229  -1.1731  -0.1740
 NND  H9C1  H  HCH2  0   0.210   2.0373   0.3399  -1.5620
 NND  H9C2  H  HCH2  0   0.211   1.9987   1.5437  -0.2924
 NND  H101  H  HCH2  0   0.208   3.0947  -0.0628   1.2748
 NND  H102  H  HCH2  0   0.207   3.1085  -1.2844   0.0231
 NND  H141  H  HCH2  0   0.207   4.5645   0.1811  -1.3930
 NND  H142  H  HCH2  0   0.207   4.5566   1.4013  -0.1392
 NND  H131  H  HCH2  0   0.207   5.6274  -0.2164   1.4434
 NND  H132  H  HCH2  0   0.206   5.6295  -1.4393   0.1927
 NND  H121  H  HCH2  0   0.206   7.1010   0.0132  -1.2237
 NND  H122  H  HCH2  0   0.206   7.1015   1.2338   0.0297
 NND  H111  H  HCH2  0   0.210   8.1566  -0.3947   1.6119
 NND  H112  H  HCH2  0   0.210   8.1580  -1.6121   0.3567
 NND  H161  H  HCH3  0   0.215   9.6710  -0.1733  -1.0469
 NND  H162  H  HCH3  0   0.215   9.6721   1.0516   0.2165
 NND  H163  H  HCH3  0   0.225  10.3975  -0.5247   0.5187

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
 NND  O6   C6    single  1.409  0.020  1.409
 NND  O6   H6    single  0.850  0.020  0.980
 NND  C6   C5    single  1.522  0.020  1.522
 NND  C6   H6C1  single  0.970  0.020  1.090
 NND  C6   H6C2  single  0.970  0.020  1.090
 NND  C5   C4    single  1.536  0.020  1.536
 NND  C5   N1    single  1.463  0.020  1.463
 NND  C5   H5    single  0.970  0.020  1.090
 NND  C4   O4    single  1.410  0.020  1.410
 NND  C4   C31   single  1.521  0.020  1.521
 NND  C4   H4    single  0.970  0.020  1.090
 NND  O4   HA    single  0.850  0.020  0.980
 NND  O3   C31   single  1.411  0.020  1.411
 NND  O3   H3    single  0.850  0.020  0.980
 NND  C2   O2    single  1.411  0.020  1.411
 NND  C2   C1    single  1.522  0.020  1.522
 NND  C2   C31   single  1.514  0.020  1.514
 NND  C2   H2    single  0.970  0.020  1.090
 NND  O2   HB    single  0.850  0.020  0.980
 NND  N1   C8    single  1.456  0.020  1.456
 NND  N1   C1    single  1.451  0.020  1.451
 NND  C8   C7    single  1.524  0.020  1.524
 NND  C8   H8C1  single  0.970  0.020  1.090
 NND  C8   H8C2  single  0.970  0.020  1.090
 NND  C7   C9    single  1.524  0.020  1.524
 NND  C7   H7C1  single  0.970  0.020  1.090
 NND  C7   H7C2  single  0.970  0.020  1.090
 NND  C1   H1C1  single  0.970  0.020  1.090
 NND  C1   H1C2  single  0.970  0.020  1.090
 NND  C9   C10   single  1.523  0.020  1.523
 NND  C9   H9C1  single  0.970  0.020  1.090
 NND  C9   H9C2  single  0.970  0.020  1.090
 NND  C10  C14   single  1.523  0.020  1.523
 NND  C10  H101  single  0.970  0.020  1.090
 NND  C10  H102  single  0.970  0.020  1.090
 NND  C14  C13   single  1.523  0.020  1.523
 NND  C14  H141  single  0.970  0.020  1.090
 NND  C14  H142  single  0.970  0.020  1.090
 NND  C13  C12   single  1.523  0.020  1.523
 NND  C13  H131  single  0.970  0.020  1.090
 NND  C13  H132  single  0.970  0.020  1.090
 NND  C12  C11   single  1.523  0.020  1.523
 NND  C12  H121  single  0.970  0.020  1.090
 NND  C12  H122  single  0.970  0.020  1.090
 NND  C16  C11   single  1.522  0.020  1.522
 NND  C16  H161  single  0.970  0.020  1.090
 NND  C16  H162  single  0.970  0.020  1.090
 NND  C16  H163  single  0.970  0.020  1.090
 NND  C11  H111  single  0.970  0.020  1.090
 NND  C11  H112  single  0.970  0.020  1.090
 NND  C31  H31   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
 NND  H6    O6   C6    107.95  3.000
 NND  H6C2  C6   H6C1  105.75  3.000
 NND  H6C2  C6   C5    109.86  3.000
 NND  H6C1  C6   C5    107.66  3.000
 NND  H6C2  C6   O6    111.72  3.000
 NND  H6C1  C6   O6    111.80  3.000
 NND  C5    C6   O6    109.89  3.000
 NND  H5    C5   N1    110.64  3.000
 NND  H5    C5   C4    107.77  3.000
 NND  N1    C5   C4    108.45  3.000
 NND  H5    C5   C6    105.58  3.000
 NND  N1    C5   C6    113.80  3.000
 NND  C4    C5   C6    110.44  3.000
 NND  H4    C4   C31   108.36  3.000
 NND  H4    C4   O4    110.82  3.000
 NND  C31   C4   O4    110.32  3.000
 NND  H4    C4   C5    107.76  3.000
 NND  C31   C4   C5    111.22  3.000
 NND  O4    C4   C5    108.33  3.000
 NND  HA    O4   C4    107.83  3.000
 NND  H3    O3   C31   108.47  3.000
 NND  H2    C2   C31   108.80  3.000
 NND  H2    C2   C1    108.29  3.000
 NND  C31   C2   C1    109.10  3.000
 NND  H2    C2   O2    111.04  3.000
 NND  C31   C2   O2    107.65  3.000
 NND  C1    C2   O2    111.91  3.000
 NND  HB    O2   C2    108.47  3.000
 NND  C1    N1   C8    111.55  3.000
 NND  C1    N1   C5    109.97  3.000
 NND  C8    N1   C5    114.95  3.000
 NND  H8C2  C8   H8C1  106.19  3.000
 NND  H8C2  C8   C7    106.41  3.000
 NND  H8C1  C8   C7    109.50  3.000
 NND  H8C2  C8   N1    109.08  3.000
 NND  H8C1  C8   N1    111.72  3.000
 NND  C7    C8   N1    113.54  3.000
 NND  H7C2  C7   H7C1  106.48  3.000
 NND  H7C2  C7   C9    108.36  3.000
 NND  H7C1  C7   C9    109.87  3.000
 NND  H7C2  C7   C8    111.47  3.000
 NND  H7C1  C7   C8    108.73  3.000
 NND  C9    C7   C8    111.79  3.000
 NND  H1C2  C1   H1C1  106.54  3.000
 NND  H1C2  C1   N1    111.95  3.000
 NND  H1C1  C1   N1    109.76  3.000
 NND  H1C2  C1   C2    109.37  3.000
 NND  H1C1  C1   C2    108.25  3.000
 NND  N1    C1   C2    110.82  3.000
 NND  H9C2  C9   H9C1  106.01  3.000
 NND  H9C2  C9   C10   109.43  3.000
 NND  H9C1  C9   C10   109.31  3.000
 NND  H9C2  C9   C7    109.68  3.000
 NND  H9C1  C9   C7    109.39  3.000
 NND  C10   C9   C7    112.81  3.000
 NND  H102  C10  H101  105.91  3.000
 NND  H102  C10  C14   109.27  3.000
 NND  H101  C10  C14   109.39  3.000
 NND  H102  C10  C9    109.21  3.000
 NND  H101  C10  C9    109.30  3.000
 NND  C14   C10  C9    113.48  3.000
 NND  H142  C14  H141  105.95  3.000
 NND  H142  C14  C13   109.38  3.000
 NND  H141  C14  C13   109.35  3.000
 NND  H142  C14  C10   109.47  3.000
 NND  H141  C14  C10   109.36  3.000
 NND  C13   C14  C10   113.09  3.000
 NND  H132  C13  H131  105.90  3.000
 NND  H132  C13  C12   109.34  3.000
 NND  H131  C13  C12   109.34  3.000
 NND  H132  C13  C14   109.21  3.000
 NND  H131  C13  C14   109.29  3.000
 NND  C12   C13  C14   113.48  3.000
 NND  H122  C12  H121  105.93  3.000
 NND  H122  C12  C11   109.32  3.000
 NND  H121  C12  C11   109.29  3.000
 NND  H122  C12  C13   109.44  3.000
 NND  H121  C12  C13   109.41  3.000
 NND  C11   C12  C13   113.19  3.000
 NND  H163  C16  H162  107.63  3.000
 NND  H163  C16  H161  107.63  3.000
 NND  H162  C16  H161  107.41  3.000
 NND  H163  C16  C11   111.64  3.000
 NND  H162  C16  C11   111.17  3.000
 NND  H161  C16  C11   111.15  3.000
 NND  H112  C11  H111  106.03  3.000
 NND  H112  C11  C16   109.49  3.000
 NND  H111  C11  C16   109.60  3.000
 NND  H112  C11  C12   109.24  3.000
 NND  H111  C11  C12   109.25  3.000
 NND  C16   C11  C12   112.99  3.000
 NND  H31   C31  C2    107.97  3.000
 NND  H31   C31  O3    110.69  3.000
 NND  C2    C31  O3    112.76  3.000
 NND  H31   C31  C4    107.92  3.000
 NND  C2    C31  C4    110.08  3.000
 NND  O3    C31  C4    107.33  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
 NND  Var_01  C2    C1   N1   C5    -64.56  30.0  1
 NND  Var_02  C7    C8   N1   C5    165.01  30.0  3
 NND  Var_03  C9    C7   C8   N1   -176.51  30.0  3
 NND  Var_04  C10   C9   C7   C8    179.74  30.0  3
 NND  Var_05  C14   C10  C9   C7    178.53  30.0  3
 NND  Var_06  C13   C14  C10  C9   -179.70  30.0  3
 NND  Var_07  C12   C13  C14  C10   179.68  30.0  3
 NND  Var_08  C11   C12  C13  C14  -179.78  30.0  3
 NND  Var_09  C16   C11  C12  C13  -179.96  30.0  3
 NND  Var_10  H161  C16  C11  C12   -59.72  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
 NND  chir_01  C5   C6  C4   N1   positiv
 NND  chir_02  C4   O4  C5   C31  positiv
 NND  chir_03  C2   O2  C31  C1   positiv
 NND  chir_04  C31  O3  C2   C4   positiv

