# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:23:43 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3R,4R,5R)-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
 DMJ  DMJ  (2R,3R,4R,5R)-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_DMJ
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
 DMJ  C4   C  CH1   0   0.065   0.9263   0.2048  -0.1417
 DMJ  O4   O  OH1   0  -0.680   2.2817  -0.1035   0.0953
 DMJ  C3   C  CH1   0   0.011   0.4393  -0.4592  -1.4276
 DMJ  O3   O  OH1   0  -0.677   1.2189   0.0528  -2.4846
 DMJ  C2   C  CH1   0   0.016  -1.0574  -0.2521  -1.6339
 DMJ  O2   O  OH1   0  -0.670  -1.2862   1.1129  -1.8946
 DMJ  C1   C  CH2   0  -0.347  -1.7790  -0.7461  -0.3864
 DMJ  N5   N  NH1   0  -0.604  -1.2964  -0.0358   0.7786
 DMJ  C5   C  CH1   0  -0.134   0.1056  -0.2921   1.0490
 DMJ  C6   C  CH2   0  -0.141   0.5187   0.4175   2.3269
 DMJ  O6   O  OH1   0  -0.675  -0.2318  -0.1179   3.3971
 DMJ  H4   H  HCH1  0   0.201   0.7814   1.2920  -0.2270
 DMJ  HO4  H  HOH1  0   0.449   2.7842   0.1736  -0.6777
 DMJ  H3   H  HCH1  0   0.210   0.5977  -1.5428  -1.3167
 DMJ  HO3  H  HOH1  0   0.455   1.1113  -0.5179  -3.2514
 DMJ  H2   H  HCH1  0   0.213  -1.3825  -0.8725  -2.4840
 DMJ  HO2  H  HOH1  0   0.449  -2.2365   1.2623  -1.9006
 DMJ  H11  H  HCH2  0   0.202  -1.6367  -1.8375  -0.3204
 DMJ  H12  H  HCH2  0   0.247  -2.8552  -0.5800  -0.4847
 DMJ  HN5  H  HNH1  0   0.355  -1.8481  -0.2900   1.5868
 DMJ  H5   H  HCH1  0   0.202   0.3115  -1.3726   1.1681
 DMJ  H61  H  HCH2  0   0.191   0.3327   1.4927   2.2043
 DMJ  H62  H  HCH2  0   0.205   1.5933   0.2848   2.4891
 DMJ  HO6  H  HOH1  0   0.457  -0.0682   0.4189   4.1773

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
 DMJ  C4  O4   single  1.410  0.020  1.410
 DMJ  C4  C3   single  1.527  0.020  1.527
 DMJ  C4  C5   single  1.529  0.020  1.529
 DMJ  C4  H4   single  0.970  0.020  1.090
 DMJ  O4  HO4  single  0.850  0.020  0.980
 DMJ  C3  O3   single  1.410  0.020  1.410
 DMJ  C3  C2   single  1.525  0.020  1.525
 DMJ  C3  H3   single  0.970  0.020  1.090
 DMJ  O3  HO3  single  0.850  0.020  0.980
 DMJ  C2  O2   single  1.408  0.020  1.408
 DMJ  C2  C1   single  1.524  0.020  1.524
 DMJ  C2  H2   single  0.970  0.020  1.090
 DMJ  O2  HO2  single  0.850  0.020  0.980
 DMJ  C1  N5   single  1.447  0.020  1.447
 DMJ  C1  H11  single  0.970  0.020  1.090
 DMJ  C1  H12  single  0.970  0.020  1.090
 DMJ  N5  C5   single  1.451  0.020  1.451
 DMJ  N5  HN5  single  0.890  0.020  1.040
 DMJ  C5  C6   single  1.519  0.020  1.519
 DMJ  C5  H5   single  0.970  0.020  1.090
 DMJ  C6  O6   single  1.413  0.020  1.413
 DMJ  C6  H61  single  0.970  0.020  1.090
 DMJ  C6  H62  single  0.970  0.020  1.090
 DMJ  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
 DMJ  H4   C4  C5   108.11  3.000
 DMJ  H4   C4  C3   108.81  3.000
 DMJ  C5   C4  C3   110.08  3.000
 DMJ  H4   C4  O4   110.83  3.000
 DMJ  C5   C4  O4   108.30  3.000
 DMJ  C3   C4  O4   110.67  3.000
 DMJ  HO4  O4  C4   107.69  3.000
 DMJ  H3   C3  C2   106.77  3.000
 DMJ  H3   C3  O3   110.70  3.000
 DMJ  C2   C3  O3   113.08  3.000
 DMJ  H3   C3  C4   107.29  3.000
 DMJ  C2   C3  C4   111.59  3.000
 DMJ  O3   C3  C4   107.29  3.000
 DMJ  HO3  O3  C3   108.69  3.000
 DMJ  H2   C2  C1   108.03  3.000
 DMJ  H2   C2  O2   110.80  3.000
 DMJ  C1   C2  O2   112.88  3.000
 DMJ  H2   C2  C3   108.52  3.000
 DMJ  C1   C2  C3   108.06  3.000
 DMJ  O2   C2  C3   108.43  3.000
 DMJ  HO2  O2  C2   108.19  3.000
 DMJ  H12  C1  H11  106.43  3.000
 DMJ  H12  C1  N5   109.02  3.000
 DMJ  H11  C1  N5   113.24  3.000
 DMJ  H12  C1  C2   110.08  3.000
 DMJ  H11  C1  C2   107.99  3.000
 DMJ  N5   C1  C2   110.00  3.000
 DMJ  HN5  N5  C5   109.50  3.000
 DMJ  HN5  N5  C1   109.76  3.000
 DMJ  C5   N5  C1   112.68  3.000
 DMJ  H5   C5  C6   108.36  3.000
 DMJ  H5   C5  N5   111.87  3.000
 DMJ  C6   C5  N5   109.70  3.000
 DMJ  H5   C5  C4   107.53  3.000
 DMJ  C6   C5  C4   110.94  3.000
 DMJ  N5   C5  C4   108.43  3.000
 DMJ  H62  C6  H61  107.54  3.000
 DMJ  H62  C6  O6   111.31  3.000
 DMJ  H61  C6  O6   111.45  3.000
 DMJ  H62  C6  C5   109.57  3.000
 DMJ  H61  C6  C5   108.51  3.000
 DMJ  O6   C6  C5   108.41  3.000
 DMJ  HO6  O6  C6   108.24  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
 DMJ  Var_01  C5  N5  C1  C2  -64.03  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
 DMJ  chir_01  C4  O4  C3  C5  negativ
 DMJ  chir_02  C3  O3  C4  C2  negativ
 DMJ  chir_03  C2  O2  C3  C1  negativ
 DMJ  chir_04  C5  N5  C4  C6  negativ

