# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:10:37 2022
#   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
 NOJ  NOJ  (2R,3R,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol  ligand  24  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NOJ
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
 NOJ  C1   C  CH2   0  -0.354  -0.5670  -1.7882  -0.2013
 NOJ  C2   C  CH1   0   0.018  -1.6388  -0.8006   0.2575
 NOJ  O2   O  OH1   0  -0.676  -2.9118  -1.1083  -0.2709
 NOJ  C3   C  CH1   0   0.008  -1.2707   0.5947  -0.2196
 NOJ  O3   O  OH1   0  -0.679  -2.1553   1.5793   0.2691
 NOJ  C4   C  CH1   0   0.056   0.1308   0.9778   0.2440
 NOJ  O4   O  OH1   0  -0.677   0.5114   2.2262  -0.2873
 NOJ  C5   C  CH1   0  -0.162   1.1475  -0.0820  -0.2004
 NOJ  N5   N  NH1   0  -0.576   0.7664  -1.4167   0.2268
 NOJ  C6   C  CH2   0  -0.140   2.5385   0.2592   0.3081
 NOJ  O6   O  OH1   0  -0.669   3.4638  -0.6726  -0.2012
 NOJ  H11  H  HCH2  0   0.245  -0.7949  -2.7891   0.1729
 NOJ  H12  H  HCH2  0   0.224  -0.5824  -1.8493  -1.2953
 NOJ  H2   H  HCH1  0   0.205  -1.6656  -0.7990   1.3578
 NOJ  HO2  H  HOH1  0   0.456  -3.2601  -1.8728   0.1975
 NOJ  H3   H  HCH1  0   0.203  -1.2701   0.5873  -1.3232
 NOJ  HO3  H  HOH1  0   0.453  -3.0292   1.4100  -0.0964
 NOJ  H4   H  HCH1  0   0.195   0.1326   1.0079   1.3471
 NOJ  HO4  H  HOH1  0   0.450  -0.1617   2.8718  -0.0472
 NOJ  H5   H  HCH1  0   0.230   1.1708  -0.0798  -1.2988
 NOJ  HN5  H  HNH1  0   0.341   0.8348  -1.4863   1.2366
 NOJ  H61  H  HCH2  0   0.211   2.7893   1.2796   0.0015
 NOJ  H62  H  HCH2  0   0.185   2.5238   0.2517   1.4089
 NOJ  HO6  H  HOH1  0   0.453   4.3388  -0.4098   0.0975

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
 NOJ  C1  C2   single  1.528  0.020  1.528
 NOJ  C1  N5   single  1.449  0.020  1.449
 NOJ  C1  H11  single  0.970  0.020  1.090
 NOJ  C1  H12  single  0.970  0.020  1.090
 NOJ  C2  O2   single  1.412  0.020  1.412
 NOJ  C2  C3   single  1.520  0.020  1.520
 NOJ  C2  H2   single  0.970  0.020  1.090
 NOJ  O2  HO2  single  0.850  0.020  0.980
 NOJ  C3  O3   single  1.411  0.020  1.411
 NOJ  C3  C4   single  1.525  0.020  1.525
 NOJ  C3  H3   single  0.970  0.020  1.090
 NOJ  O3  HO3  single  0.850  0.020  0.980
 NOJ  C4  O4   single  1.409  0.020  1.409
 NOJ  C4  C5   single  1.534  0.020  1.534
 NOJ  C4  H4   single  0.970  0.020  1.090
 NOJ  O4  HO4  single  0.850  0.020  0.980
 NOJ  C5  N5   single  1.452  0.020  1.452
 NOJ  C5  C6   single  1.520  0.020  1.520
 NOJ  C5  H5   single  0.970  0.020  1.090
 NOJ  N5  HN5  single  0.890  0.020  1.040
 NOJ  C6  O6   single  1.408  0.020  1.408
 NOJ  C6  H61  single  0.970  0.020  1.090
 NOJ  C6  H62  single  0.970  0.020  1.090
 NOJ  O6  HO6  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
 NOJ  H12  C1  H11  106.73  3.000
 NOJ  H12  C1  N5   108.80  3.000
 NOJ  H11  C1  N5   109.00  3.000
 NOJ  H12  C1  C2   109.03  3.000
 NOJ  H11  C1  C2   110.06  3.000
 NOJ  N5   C1  C2   113.02  3.000
 NOJ  H2   C2  C3   108.56  3.000
 NOJ  H2   C2  O2   110.64  3.000
 NOJ  C3   C2  O2   107.51  3.000
 NOJ  H2   C2  C1   108.56  3.000
 NOJ  C3   C2  C1   109.22  3.000
 NOJ  O2   C2  C1   112.28  3.000
 NOJ  HO2  O2  C2   108.51  3.000
 NOJ  H3   C3  C4   107.77  3.000
 NOJ  H3   C3  O3   110.57  3.000
 NOJ  C4   C3  O3   107.19  3.000
 NOJ  H3   C3  C2   107.93  3.000
 NOJ  C4   C3  C2   110.96  3.000
 NOJ  O3   C3  C2   112.34  3.000
 NOJ  HO3  O3  C3   108.36  3.000
 NOJ  H4   C4  C5   107.90  3.000
 NOJ  H4   C4  O4   110.63  3.000
 NOJ  C5   C4  O4   108.89  3.000
 NOJ  H4   C4  C3   108.19  3.000
 NOJ  C5   C4  C3   110.33  3.000
 NOJ  O4   C4  C3   110.86  3.000
 NOJ  HO4  O4  C4   108.13  3.000
 NOJ  H5   C5  C6   108.34  3.000
 NOJ  H5   C5  N5   107.54  3.000
 NOJ  C6   C5  N5   110.37  3.000
 NOJ  H5   C5  C4   107.60  3.000
 NOJ  C6   C5  C4   110.76  3.000
 NOJ  N5   C5  C4   112.07  3.000
 NOJ  HN5  N5  C5   109.76  3.000
 NOJ  HN5  N5  C1   109.79  3.000
 NOJ  C5   N5  C1   112.97  3.000
 NOJ  H62  C6  H61  106.83  3.000
 NOJ  H62  C6  O6   111.46  3.000
 NOJ  H61  C6  O6   111.40  3.000
 NOJ  H62  C6  C5   108.71  3.000
 NOJ  H61  C6  C5   108.98  3.000
 NOJ  O6   C6  C5   109.38  3.000
 NOJ  HO6  O6  C6   107.75  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
 NOJ  Var_01  C5  N5  C1  C2  -55.97  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
 NOJ  chir_01  C2  C1  O2  C3  positiv
 NOJ  chir_02  C3  O3  C2  C4  positiv
 NOJ  chir_03  C4  O4  C3  C5  negativ
 NOJ  chir_04  C5  N5  C4  C6  negativ

