# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:01:48 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1NC[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
 DNJ  DNJ  (2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol  ligand  24  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DNJ
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
 DNJ  C1   C  CH2   0  -0.331   1.7760   0.2189  -0.5208
 DNJ  C2   C  CH1   0   0.033   0.8250  -0.2537  -1.6127
 DNJ  O2   O  OH1   0  -0.676   1.1660   0.2642  -2.8804
 DNJ  C3   C  CH1   0   0.004  -0.5832   0.2239  -1.2913
 DNJ  O3   O  OH1   0  -0.678  -1.5408  -0.2837  -2.1935
 DNJ  C4   C  CH1   0   0.067  -1.0050  -0.2105   0.1085
 DNJ  O4   O  OH1   0  -0.676  -2.2535   0.3442   0.4519
 DNJ  C5   C  CH1   0  -0.135   0.0273   0.2420   1.1394
 DNJ  C6   C  CH2   0  -0.141  -0.3404  -0.2485   2.5290
 DNJ  O6   O  OH1   0  -0.675   0.6307   0.2253   3.4384
 DNJ  N5   N  NH1   0  -0.614   1.3175  -0.2984   0.7512
 DNJ  H11  H  HCH2  0   0.196   1.8322   1.3200  -0.5471
 DNJ  H12  H  HCH2  0   0.242   2.7818  -0.1596  -0.7174
 DNJ  H2   H  HCH1  0   0.206   0.8312  -1.3530  -1.6221
 DNJ  HO2  H  HOH1  0   0.456   1.9388  -0.2076  -3.2049
 DNJ  H3   H  HCH1  0   0.200  -0.5768   1.3273  -1.3100
 DNJ  HO3  H  HOH1  0   0.453  -1.3352   0.0505  -3.0722
 DNJ  H4   H  HCH1  0   0.199  -1.0452  -1.3114   0.1325
 DNJ  HO4  H  HOH1  0   0.451  -2.8950   0.0708  -0.2118
 DNJ  H5   H  HCH1  0   0.205   0.0296   1.3477   1.1504
 DNJ  H61  H  HCH2  0   0.191  -0.3771  -1.3461   2.5168
 DNJ  H62  H  HCH2  0   0.207  -1.3398   0.1127   2.7910
 DNJ  HO6  H  HOH1  0   0.458   0.4475  -0.1567   4.3011
 DNJ  HN5  H  HNH1  0   0.358   1.9990  -0.0996   1.4706

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
 DNJ  C1  C2   single  1.523  0.020  1.523
 DNJ  C1  N5   single  1.448  0.020  1.448
 DNJ  C1  H11  single  0.970  0.020  1.090
 DNJ  C1  H12  single  0.970  0.020  1.090
 DNJ  C2  O2   single  1.411  0.020  1.411
 DNJ  C2  C3   single  1.521  0.020  1.521
 DNJ  C2  H2   single  0.970  0.020  1.090
 DNJ  O2  HO2  single  0.850  0.020  0.980
 DNJ  C3  O3   single  1.410  0.020  1.410
 DNJ  C3  C4   single  1.525  0.020  1.525
 DNJ  C3  H3   single  0.970  0.020  1.090
 DNJ  O3  HO3  single  0.850  0.020  0.980
 DNJ  C4  O4   single  1.409  0.020  1.409
 DNJ  C4  C5   single  1.527  0.020  1.527
 DNJ  C4  H4   single  0.970  0.020  1.090
 DNJ  O4  HO4  single  0.850  0.020  0.980
 DNJ  C5  C6   single  1.519  0.020  1.519
 DNJ  C5  N5   single  1.452  0.020  1.452
 DNJ  C5  H5   single  0.970  0.020  1.090
 DNJ  C6  O6   single  1.412  0.020  1.412
 DNJ  C6  H61  single  0.970  0.020  1.090
 DNJ  C6  H62  single  0.970  0.020  1.090
 DNJ  O6  HO6  single  0.850  0.020  0.980
 DNJ  N5  HN5  single  0.890  0.020  1.040

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
 DNJ  H12  C1  H11  107.13  3.000
 DNJ  H12  C1  N5   109.02  3.000
 DNJ  H11  C1  N5   113.19  3.000
 DNJ  H12  C1  C2   109.78  3.000
 DNJ  H11  C1  C2   108.94  3.000
 DNJ  N5   C1  C2   108.74  3.000
 DNJ  H2   C2  C3   108.72  3.000
 DNJ  H2   C2  O2   110.97  3.000
 DNJ  C3   C2  O2   107.35  3.000
 DNJ  H2   C2  C1   108.23  3.000
 DNJ  C3   C2  C1   109.21  3.000
 DNJ  O2   C2  C1   112.29  3.000
 DNJ  HO2  O2  C2   108.49  3.000
 DNJ  H3   C3  C4   107.57  3.000
 DNJ  H3   C3  O3   110.66  3.000
 DNJ  C4   C3  O3   107.27  3.000
 DNJ  H3   C3  C2   107.76  3.000
 DNJ  C4   C3  C2   111.13  3.000
 DNJ  O3   C3  C2   112.36  3.000
 DNJ  HO3  O3  C3   108.31  3.000
 DNJ  H4   C4  C5   107.81  3.000
 DNJ  H4   C4  O4   110.84  3.000
 DNJ  C5   C4  O4   108.53  3.000
 DNJ  H4   C4  C3   108.34  3.000
 DNJ  C5   C4  C3   110.37  3.000
 DNJ  O4   C4  C3   110.90  3.000
 DNJ  HO4  O4  C4   108.11  3.000
 DNJ  H5   C5  N5   111.90  3.000
 DNJ  H5   C5  C6   108.32  3.000
 DNJ  N5   C5  C6   109.86  3.000
 DNJ  H5   C5  C4   107.72  3.000
 DNJ  N5   C5  C4   108.06  3.000
 DNJ  C6   C5  C4   110.99  3.000
 DNJ  H62  C6  H61  107.58  3.000
 DNJ  H62  C6  O6   111.28  3.000
 DNJ  H61  C6  O6   111.43  3.000
 DNJ  H62  C6  C5   109.48  3.000
 DNJ  H61  C6  C5   108.70  3.000
 DNJ  O6   C6  C5   108.32  3.000
 DNJ  HO6  O6  C6   108.27  3.000
 DNJ  HN5  N5  C5   109.62  3.000
 DNJ  HN5  N5  C1   109.98  3.000
 DNJ  C5   N5  C1   112.55  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
 DNJ  Var_01  C5  N5  C1  C2  -64.91  30.0  1

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
 DNJ  chir_01  C2  C1  O2  C3  positiv
 DNJ  chir_02  C3  O3  C2  C4  positiv
 DNJ  chir_03  C4  O4  C3  C5  negativ
 DNJ  chir_04  C5  N5  C4  C6  negativ

