# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:30:42 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
 DDM  DDM  (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_DDM
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
 DDM  C2    C  CH1   0   0.015  -1.0652  -0.2460  -1.6235
 DDM  C3    C  CH1   0   0.012   0.4286  -0.4643  -1.4072
 DDM  C1    C  CH2   0  -0.345  -1.7978  -0.7229  -0.3754
 DDM  C4    C  CH1   0   0.065   0.9138   0.2083  -0.1251
 DDM  C5    C  CH1   0  -0.134   0.0830  -0.2713   1.0658
 DDM  C6    C  CH2   0  -0.141   0.4951   0.4462   2.3397
 DDM  O2    O  OH1   0  -0.670  -1.2802   1.1186  -1.8963
 DDM  O3    O  OH1   0  -0.677   1.2191   0.0298  -2.4643
 DDM  O4    O  OH1   0  -0.680   2.2656  -0.1079   0.1228
 DDM  N5    N  NH1   0  -0.605  -1.3154  -0.0069   0.7860
 DDM  O6    O  OH1   0  -0.675  -0.2664  -0.0732   3.4101
 DDM  HC2   H  HCH1  0   0.214  -1.3916  -0.8707  -2.4698
 DDM  HC3   H  HCH1  0   0.210   0.5766  -1.5482  -1.2842
 DDM  HC11  H  HCH2  0   0.201  -1.6647  -1.8150  -0.2991
 DDM  HC12  H  HCH2  0   0.246  -2.8719  -0.5486  -0.4813
 DDM  HC4   H  HCH1  0   0.201   0.7775   1.2957  -0.2215
 DDM  HC5   H  HCH1  0   0.201   0.2805  -1.3523   1.1951
 DDM  HC61  H  HCH2  0   0.191   0.3191   1.5219   2.2071
 DDM  HC62  H  HCH2  0   0.205   1.5677   0.3056   2.5094
 DDM  HO2   H  HOH1  0   0.449  -2.2292   1.2707  -1.9378
 DDM  HO3   H  HOH1  0   0.455   1.1006  -0.5399  -3.2303
 DDM  HO4   H  HOH1  0   0.449   2.7756   0.1617  -0.6478
 DDM  HN5   H  HNH1  0   0.355  -1.8736  -0.2483   1.5936
 DDM  HO6   H  HOH1  0   0.457  -0.1003   0.4672   4.1873

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
 DDM  C2  C3    single  1.525  0.020  1.525
 DDM  C2  C1    single  1.524  0.020  1.524
 DDM  C2  O2    single  1.408  0.020  1.408
 DDM  C2  HC2   single  0.970  0.020  1.090
 DDM  C3  C4    single  1.527  0.020  1.527
 DDM  C3  O3    single  1.409  0.020  1.409
 DDM  C3  HC3   single  0.970  0.020  1.090
 DDM  C1  N5    single  1.447  0.020  1.447
 DDM  C1  HC11  single  0.970  0.020  1.090
 DDM  C1  HC12  single  0.970  0.020  1.090
 DDM  C4  C5    single  1.529  0.020  1.529
 DDM  C4  O4    single  1.410  0.020  1.410
 DDM  C4  HC4   single  0.970  0.020  1.090
 DDM  C5  C6    single  1.519  0.020  1.519
 DDM  C5  N5    single  1.450  0.020  1.450
 DDM  C5  HC5   single  0.970  0.020  1.090
 DDM  C6  O6    single  1.413  0.020  1.413
 DDM  C6  HC61  single  0.970  0.020  1.090
 DDM  C6  HC62  single  0.970  0.020  1.090
 DDM  O2  HO2   single  0.850  0.020  0.980
 DDM  O3  HO3   single  0.850  0.020  0.980
 DDM  O4  HO4   single  0.850  0.020  0.980
 DDM  N5  HN5   single  0.890  0.020  1.040
 DDM  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
 DDM  HC2   C2  O2    110.83  3.000
 DDM  HC2   C2  C1    108.02  3.000
 DDM  O2    C2  C1    112.87  3.000
 DDM  HC2   C2  C3    108.55  3.000
 DDM  O2    C2  C3    108.41  3.000
 DDM  C1    C2  C3    108.06  3.000
 DDM  HC3   C3  O3    110.71  3.000
 DDM  HC3   C3  C4    107.29  3.000
 DDM  O3    C3  C4    107.28  3.000
 DDM  HC3   C3  C2    106.76  3.000
 DDM  O3    C3  C2    113.13  3.000
 DDM  C4    C3  C2    111.54  3.000
 DDM  HC12  C1  HC11  106.45  3.000
 DDM  HC12  C1  N5    109.05  3.000
 DDM  HC11  C1  N5    113.22  3.000
 DDM  HC12  C1  C2    110.07  3.000
 DDM  HC11  C1  C2    107.98  3.000
 DDM  N5    C1  C2    110.01  3.000
 DDM  HC4   C4  O4    110.85  3.000
 DDM  HC4   C4  C5    108.11  3.000
 DDM  O4    C4  C5    108.27  3.000
 DDM  HC4   C4  C3    108.81  3.000
 DDM  O4    C4  C3    110.69  3.000
 DDM  C5    C4  C3    110.07  3.000
 DDM  HC5   C5  N5    111.88  3.000
 DDM  HC5   C5  C6    108.36  3.000
 DDM  N5    C5  C6    109.71  3.000
 DDM  HC5   C5  C4    107.49  3.000
 DDM  N5    C5  C4    108.45  3.000
 DDM  C6    C5  C4    110.95  3.000
 DDM  HC62  C6  HC61  107.55  3.000
 DDM  HC62  C6  O6    111.32  3.000
 DDM  HC61  C6  O6    111.43  3.000
 DDM  HC62  C6  C5    109.58  3.000
 DDM  HC61  C6  C5    108.53  3.000
 DDM  O6    C6  C5    108.40  3.000
 DDM  HO2   O2  C2    108.19  3.000
 DDM  HO3   O3  C3    108.69  3.000
 DDM  HO4   O4  C4    107.72  3.000
 DDM  HN5   N5  C5    109.56  3.000
 DDM  HN5   N5  C1    109.80  3.000
 DDM  C5    N5  C1    112.71  3.000
 DDM  HO6   O6  C6    108.23  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
 DDM  Var_01  C5  N5  C1  C2  -63.95  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
 DDM  chir_01  C2  C3  C1  O2  negativ
 DDM  chir_02  C3  O3  C2  C4  positiv
 DDM  chir_03  C4  O4  C3  C5  negativ
 DDM  chir_04  C5  N5  C4  C6  negativ

