# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:30:51 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3S,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
 DGJ  DGJ  (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol  ligand  24  11  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DGJ
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
 DGJ  C1   C  CH2   0  -0.352  -0.4342  -1.7381   0.1270
 DGJ  C2   C  CH1   0   0.020  -1.5495  -0.7007   0.2711
 DGJ  O2   O  OH1   0  -0.678  -2.8006  -1.1978  -0.1619
 DGJ  C3   C  CH1   0   0.015  -1.2282   0.5147  -0.5851
 DGJ  O3   O  OH1   0  -0.680  -2.1668   1.5538  -0.4168
 DGJ  C4   C  CH1   0   0.013   0.1488   1.0740  -0.2360
 DGJ  O4   O  OH1   0  -0.676   0.1831   1.5854   1.0775
 DGJ  C5   C  CH1   0  -0.154   1.1976  -0.0349  -0.3559
 DGJ  N5   N  NH1   0  -0.575   0.8818  -1.2134   0.4337
 DGJ  C6   C  CH2   0  -0.138   2.5869   0.4839  -0.0265
 DGJ  O6   O  OH1   0  -0.670   3.5415  -0.4724  -0.4263
 DGJ  H1   H  HCH2  0   0.243  -0.6377  -2.5920   0.7780
 DGJ  H1A  H  HCH2  0   0.222  -0.4320  -2.1174  -0.9017
 DGJ  H2   H  HCH1  0   0.207  -1.6029  -0.3863   1.3228
 DGJ  HO2  H  HOH1  0   0.456  -3.1223  -1.8262   0.4916
 DGJ  H3   H  HCH1  0   0.204  -1.1951   0.1876  -1.6372
 DGJ  HO3  H  HOH1  0   0.452  -3.0496   1.1682  -0.4293
 DGJ  H4   H  HCH1  0   0.218   0.3909   1.8621  -0.9663
 DGJ  HO4  H  HOH1  0   0.449  -0.5865   2.1529   1.1959
 DGJ  H5   H  HCH1  0   0.236   1.2002  -0.3380  -1.4112
 DGJ  HN5  H  HNH1  0   0.340   0.9345  -0.9855   1.4204
 DGJ  H6   H  HCH2  0   0.198   2.7366   1.4393  -0.5476
 DGJ  H6A  H  HCH2  0   0.197   2.6578   0.6959   1.0480
 DGJ  HO6  H  HOH1  0   0.453   4.4092  -0.1505  -0.1669

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
 DGJ  N5  C1   single  1.450  0.020  1.450
 DGJ  C2  C1   single  1.530  0.020  1.530
 DGJ  C1  H1   single  0.970  0.020  1.090
 DGJ  C1  H1A  single  0.970  0.020  1.090
 DGJ  C3  C2   single  1.521  0.020  1.521
 DGJ  C2  O2   single  1.414  0.020  1.414
 DGJ  C2  H2   single  0.970  0.020  1.090
 DGJ  O2  HO2  single  0.850  0.020  0.980
 DGJ  C4  C3   single  1.527  0.020  1.527
 DGJ  O3  C3   single  1.410  0.020  1.410
 DGJ  C3  H3   single  0.970  0.020  1.090
 DGJ  O3  HO3  single  0.850  0.020  0.980
 DGJ  O4  C4   single  1.410  0.020  1.410
 DGJ  C4  C5   single  1.531  0.020  1.531
 DGJ  C4  H4   single  0.970  0.020  1.090
 DGJ  O4  HO4  single  0.850  0.020  0.980
 DGJ  C6  C5   single  1.519  0.020  1.519
 DGJ  C5  N5   single  1.453  0.020  1.453
 DGJ  C5  H5   single  0.970  0.020  1.090
 DGJ  N5  HN5  single  0.890  0.020  1.040
 DGJ  C6  O6   single  1.409  0.020  1.409
 DGJ  C6  H6   single  0.970  0.020  1.090
 DGJ  C6  H6A  single  0.970  0.020  1.090
 DGJ  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
 DGJ  H1A  C1  H1  106.80  3.000
 DGJ  H1A  C1  N5  108.78  3.000
 DGJ  H1   C1  N5  109.01  3.000
 DGJ  H1A  C1  C2  108.93  3.000
 DGJ  H1   C1  C2  109.75  3.000
 DGJ  N5   C1  C2  113.35  3.000
 DGJ  H2   C2  C3  108.69  3.000
 DGJ  H2   C2  O2  110.52  3.000
 DGJ  C3   C2  O2  107.18  3.000
 DGJ  H2   C2  C1  108.64  3.000
 DGJ  O2   C2  C1  112.19  3.000
 DGJ  C3   C2  C1  109.56  3.000
 DGJ  HO2  O2  C2  108.51  3.000
 DGJ  H3   C3  C4  107.45  3.000
 DGJ  H3   C3  O3  110.64  3.000
 DGJ  C4   C3  O3  107.64  3.000
 DGJ  H3   C3  C2  107.85  3.000
 DGJ  O3   C3  C2  112.39  3.000
 DGJ  C4   C3  C2  110.76  3.000
 DGJ  HO3  O3  C3  108.27  3.000
 DGJ  H4   C4  C5  108.41  3.000
 DGJ  H4   C4  O4  110.66  3.000
 DGJ  C5   C4  O4  108.60  3.000
 DGJ  H4   C4  C3  107.98  3.000
 DGJ  C5   C4  C3  109.55  3.000
 DGJ  O4   C4  C3  111.58  3.000
 DGJ  HO4  O4  C4  107.98  3.000
 DGJ  H5   C5  C6  107.49  3.000
 DGJ  H5   C5  N5  107.39  3.000
 DGJ  C6   C5  N5  110.97  3.000
 DGJ  H5   C5  C4  106.07  3.000
 DGJ  N5   C5  C4  113.32  3.000
 DGJ  C6   C5  C4  111.23  3.000
 DGJ  HN5  N5  C5  109.58  3.000
 DGJ  HN5  N5  C1  109.54  3.000
 DGJ  C5   N5  C1  112.08  3.000
 DGJ  H6A  C6  H6  106.72  3.000
 DGJ  H6A  C6  O6  111.41  3.000
 DGJ  H6   C6  O6  111.30  3.000
 DGJ  H6A  C6  C5  109.71  3.000
 DGJ  H6   C6  C5  108.59  3.000
 DGJ  O6   C6  C5  109.04  3.000
 DGJ  HO6  O6  C6  107.92  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
 DGJ  Var_01  C5  N5  C1  C2  -54.90  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
 DGJ  chir_01  C2  C1  C3  O2  negativ
 DGJ  chir_02  C3  O3  C2  C4  positiv
 DGJ  chir_03  C4  O4  C3  C5  positiv
 DGJ  chir_04  C5  N5  C4  C6  negativ

