# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:43:04 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2R,3R,4R,5S)-1-butyl-2-(hydroxymethyl)piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1C[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
 NBV  NBV  (2R,3R,4R,5S)-1-butyl-2-(hydroxymethyl)piperidine-3,4,5-triol  ligand  36  15  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NBV
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
 NBV  O9    O  OH1   0  -0.672   0.1175   2.6846   1.0073
 NBV  C12   C  CH2   0  -0.211  -0.1834   2.4608  -0.3509
 NBV  C11   C  CH1   0  -0.092  -0.5645   1.0033  -0.5640
 NBV  C10   C  CH1   0   0.065  -1.8846   0.6811   0.1512
 NBV  O1    O  OH1   0  -0.680  -2.8668   1.5850  -0.3010
 NBV  C9    C  CH1   0   0.001  -2.3183  -0.7518  -0.1207
 NBV  O8    O  OH1   0  -0.678  -3.5014  -0.9789   0.6128
 NBV  C8    C  CH1   0   0.035  -1.2056  -1.7087   0.2522
 NBV  O7    O  OH1   0  -0.676  -1.6176  -3.0085  -0.1104
 NBV  N1    N  NT    0  -0.444   0.4524   0.0548  -0.1100
 NBV  C7    C  CH2   0  -0.330   0.0677  -1.2963  -0.4723
 NBV  C13   C  CH2   0  -0.256   1.8073   0.3662  -0.5443
 NBV  C14   C  CH2   0  -0.440   2.8843  -0.4357   0.1764
 NBV  C15   C  CH2   0  -0.421   4.2848   0.0044  -0.2350
 NBV  C16   C  CH3   0  -0.663   5.3766  -0.7735   0.4859
 NBV  H9    H  HOH1  0   0.455   0.2051   3.6324   1.1396
 NBV  H121  H  HCH2  0   0.230  -1.0226   3.0765  -0.6890
 NBV  H122  H  HCH2  0   0.213   0.6595   2.7229  -1.0015
 NBV  H11   H  HCH1  0   0.204  -0.7365   0.8983  -1.6534
 NBV  H10   H  HCH1  0   0.204  -1.7171   0.7924   1.2325
 NBV  H1    H  HOH1  0   0.450  -3.6963   1.3571   0.1312
 NBV  HA    H  HCH1  0   0.200  -2.5038  -0.8519  -1.2031
 NBV  H8    H  HOH1  0   0.454  -3.8640  -1.8312   0.3522
 NBV  HB    H  HCH1  0   0.205  -1.0260  -1.6378   1.3344
 NBV  H7    H  HOH1  0   0.455  -1.0020  -3.6417   0.2711
 NBV  H7C1  H  HCH2  0   0.247   0.8593  -1.9936  -0.1950
 NBV  H7C2  H  HCH2  0   0.195  -0.0828  -1.4042  -1.5623
 NBV  H131  H  HCH2  0   0.185   1.9231   0.2430  -1.6353
 NBV  H132  H  HCH2  0   0.240   2.0105   1.4143  -0.3306
 NBV  H141  H  HCH2  0   0.215   2.7577  -0.3067   1.2559
 NBV  H142  H  HCH2  0   0.219   2.7878  -1.5059  -0.0229
 NBV  H151  H  HCH2  0   0.214   4.3990  -0.1198  -1.3162
 NBV  H152  H  HCH2  0   0.214   4.4039   1.0741  -0.0379
 NBV  H161  H  HCH3  0   0.217   5.2985  -1.8431   0.2825
 NBV  H162  H  HCH3  0   0.228   6.3706  -0.4502   0.1757
 NBV  H163  H  HCH3  0   0.217   5.3072  -0.6398   1.5671

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
 NBV  O9   C12   single  1.409  0.020  1.409
 NBV  O9   H9    single  0.850  0.020  0.980
 NBV  C12  C11   single  1.522  0.020  1.522
 NBV  C12  H121  single  0.970  0.020  1.090
 NBV  C12  H122  single  0.970  0.020  1.090
 NBV  C11  C10   single  1.536  0.020  1.536
 NBV  C11  N1    single  1.463  0.020  1.463
 NBV  C11  H11   single  0.970  0.020  1.090
 NBV  C10  O1    single  1.409  0.020  1.409
 NBV  C10  C9    single  1.522  0.020  1.522
 NBV  C10  H10   single  0.970  0.020  1.090
 NBV  O1   H1    single  0.850  0.020  0.980
 NBV  C9   O8    single  1.410  0.020  1.410
 NBV  C9   C8    single  1.514  0.020  1.514
 NBV  C9   HA    single  0.970  0.020  1.090
 NBV  O8   H8    single  0.850  0.020  0.980
 NBV  C8   O7    single  1.411  0.020  1.411
 NBV  C8   C7    single  1.522  0.020  1.522
 NBV  C8   HB    single  0.970  0.020  1.090
 NBV  O7   H7    single  0.850  0.020  0.980
 NBV  N1   C7    single  1.451  0.020  1.451
 NBV  N1   C13   single  1.456  0.020  1.456
 NBV  C7   H7C1  single  0.970  0.020  1.090
 NBV  C7   H7C2  single  0.970  0.020  1.090
 NBV  C13  C14   single  1.524  0.020  1.524
 NBV  C13  H131  single  0.970  0.020  1.090
 NBV  C13  H132  single  0.970  0.020  1.090
 NBV  C14  C15   single  1.525  0.020  1.525
 NBV  C14  H141  single  0.970  0.020  1.090
 NBV  C14  H142  single  0.970  0.020  1.090
 NBV  C15  C16   single  1.522  0.020  1.522
 NBV  C15  H151  single  0.970  0.020  1.090
 NBV  C15  H152  single  0.970  0.020  1.090
 NBV  C16  H161  single  0.970  0.020  1.090
 NBV  C16  H162  single  0.970  0.020  1.090
 NBV  C16  H163  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
 NBV  H9    O9   C12   107.99  3.000
 NBV  H122  C12  H121  105.76  3.000
 NBV  H122  C12  C11   109.78  3.000
 NBV  H121  C12  C11   107.67  3.000
 NBV  H122  C12  O9    111.71  3.000
 NBV  H121  C12  O9    111.86  3.000
 NBV  C11   C12  O9    109.92  3.000
 NBV  H11   C11  N1    110.59  3.000
 NBV  H11   C11  C10   107.74  3.000
 NBV  N1    C11  C10   108.48  3.000
 NBV  H11   C11  C12   105.51  3.000
 NBV  N1    C11  C12   113.79  3.000
 NBV  C10   C11  C12   110.55  3.000
 NBV  H10   C10  C9    108.32  3.000
 NBV  H10   C10  O1    110.90  3.000
 NBV  C9    C10  O1    110.36  3.000
 NBV  H10   C10  C11   107.81  3.000
 NBV  C9    C10  C11   111.06  3.000
 NBV  O1    C10  C11   108.37  3.000
 NBV  H1    O1   C10   107.73  3.000
 NBV  HA    C9   C8    107.93  3.000
 NBV  HA    C9   O8    110.77  3.000
 NBV  C8    C9   O8    112.74  3.000
 NBV  HA    C9   C10   107.99  3.000
 NBV  C8    C9   C10   109.98  3.000
 NBV  O8    C9   C10   107.33  3.000
 NBV  H8    O8   C9    108.54  3.000
 NBV  HB    C8   C7    108.33  3.000
 NBV  HB    C8   O7    111.11  3.000
 NBV  C7    C8   O7    111.82  3.000
 NBV  HB    C8   C9    108.77  3.000
 NBV  C7    C8   C9    109.04  3.000
 NBV  O7    C8   C9    107.72  3.000
 NBV  H7    O7   C8    108.51  3.000
 NBV  C13   N1   C7    111.80  3.000
 NBV  C13   N1   C11   114.55  3.000
 NBV  C7    N1   C11   109.99  3.000
 NBV  H7C2  C7   H7C1  106.68  3.000
 NBV  H7C2  C7   N1    111.92  3.000
 NBV  H7C1  C7   N1    109.84  3.000
 NBV  H7C2  C7   C8    109.21  3.000
 NBV  H7C1  C7   C8    108.23  3.000
 NBV  N1    C7   C8    110.81  3.000
 NBV  H132  C13  H131  106.36  3.000
 NBV  H132  C13  C14   106.37  3.000
 NBV  H131  C13  C14   109.55  3.000
 NBV  H132  C13  N1    108.72  3.000
 NBV  H131  C13  N1    111.62  3.000
 NBV  C14   C13  N1    113.82  3.000
 NBV  H142  C14  H141  106.57  3.000
 NBV  H142  C14  C15   108.33  3.000
 NBV  H141  C14  C15   109.78  3.000
 NBV  H142  C14  C13   111.51  3.000
 NBV  H141  C14  C13   108.83  3.000
 NBV  C15   C14  C13   111.69  3.000
 NBV  H152  C15  H151  106.11  3.000
 NBV  H152  C15  C16   109.65  3.000
 NBV  H151  C15  C16   109.58  3.000
 NBV  H152  C15  C14   109.48  3.000
 NBV  H151  C15  C14   109.26  3.000
 NBV  C16   C15  C14   112.55  3.000
 NBV  H163  C16  H162  107.67  3.000
 NBV  H163  C16  H161  107.46  3.000
 NBV  H162  C16  H161  107.62  3.000
 NBV  H163  C16  C15   111.16  3.000
 NBV  H162  C16  C15   111.57  3.000
 NBV  H161  C16  C15   111.17  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
 NBV  Var_01  C8    C7   N1   C11   -64.39  30.0  1
 NBV  Var_02  C14   C13  N1   C11   167.20  30.0  3
 NBV  Var_03  C15   C14  C13  N1   -175.53  30.0  3
 NBV  Var_04  C16   C15  C14  C13   179.33  30.0  3
 NBV  Var_05  H161  C16  C15  C14    59.53  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
 NBV  chir_01  C11  C12  C10  N1  positiv
 NBV  chir_02  C10  O1   C11  C9  positiv
 NBV  chir_03  C9   O8   C10  C8  negativ
 NBV  chir_04  C8   O7   C9   C7  positiv

