# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:29:41 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN[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
 MNM  MNM  (2S,3S,4R,5R)-5-(hydroxymethyl)piperidine-2,3,4-triol  ligand  24  11  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MNM
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
 MNM  C1    C  CH1   0   0.028  -1.3681   0.4642  -0.4260
 MNM  C2    C  CH1   0   0.106  -1.5967  -1.0306  -0.2042
 MNM  C3    C  CH1   0   0.050  -0.0706   0.9295   0.2307
 MNM  O4    O  OH1   0  -0.676  -2.4085   1.2575   0.0950
 MNM  O5    O  OH1   0  -0.672  -1.8550  -1.2239   1.1727
 MNM  N6    N  NH1   0  -0.625  -0.4547  -1.7273  -0.7195
 MNM  O7    O  OH1   0  -0.677   0.1827   2.2844  -0.0737
 MNM  C8    C  CH1   0  -0.314   1.1090   0.0898  -0.2542
 MNM  C9    C  CH2   0  -0.131   2.3859   0.4869   0.4712
 MNM  C10   C  CH2   0  -0.270   0.7964  -1.3924  -0.0624
 MNM  O11   O  OH1   0  -0.674   3.4587  -0.2789  -0.0350
 MNM  HC1   H  HCH1  0   0.213  -1.2670   0.6104  -1.5104
 MNM  HC2   H  HCH1  0   0.225  -2.4647  -1.3533  -0.7960
 MNM  HC3   H  HCH1  0   0.198  -0.1662   0.7948   1.3200
 MNM  HO4   H  HOH1  0   0.455  -3.1817   1.1614  -0.4688
 MNM  HO5   H  HOH1  0   0.448  -2.0561  -2.1550   1.3119
 MNM  HN6   H  HNH1  0   0.359  -0.6068  -2.7271  -0.7260
 MNM  HO7   H  HOH1  0   0.447  -0.5742   2.7986   0.2259
 MNM  HC8   H  HCH1  0   0.230   1.2376   0.2763  -1.3280
 MNM  HC91  H  HCH2  0   0.185   2.2485   0.3178   1.5490
 MNM  HC92  H  HCH2  0   0.210   2.5685   1.5585   0.3367
 MNM  H1    H  HCH2  0   0.241   1.5860  -1.9943  -0.5110
 MNM  H10   H  HCH2  0   0.194   0.7931  -1.6240   1.0131
 MNM  H11   H  HOH1  0   0.454   4.2508  -0.0406   0.4544

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
 MNM  C1   C2    single  1.528  0.020  1.528
 MNM  C1   C3    single  1.527  0.020  1.527
 MNM  C1   O4    single  1.408  0.020  1.408
 MNM  C1   HC1   single  0.970  0.020  1.090
 MNM  C2   O5    single  1.414  0.020  1.414
 MNM  C2   N6    single  1.433  0.020  1.433
 MNM  C2   HC2   single  0.970  0.020  1.090
 MNM  C3   O7    single  1.412  0.020  1.412
 MNM  C3   C8    single  1.527  0.020  1.527
 MNM  C3   HC3   single  0.970  0.020  1.090
 MNM  O4   HO4   single  0.850  0.020  0.980
 MNM  O5   HO5   single  0.850  0.020  0.980
 MNM  N6   C10   single  1.452  0.020  1.452
 MNM  N6   HN6   single  0.890  0.020  1.040
 MNM  O7   HO7   single  0.850  0.020  0.980
 MNM  C8   C9    single  1.521  0.020  1.521
 MNM  C8   C10   single  1.527  0.020  1.527
 MNM  C8   HC8   single  0.970  0.020  1.090
 MNM  C9   O11   single  1.412  0.020  1.412
 MNM  C9   HC91  single  0.970  0.020  1.090
 MNM  C9   HC92  single  0.970  0.020  1.090
 MNM  C10  H1    single  0.970  0.020  1.090
 MNM  C10  H10   single  0.970  0.020  1.090
 MNM  O11  H11   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
 MNM  HC1   C1   O4    110.99  3.000
 MNM  HC1   C1   C3    107.80  3.000
 MNM  O4    C1   C3    107.28  3.000
 MNM  HC1   C1   C2    106.68  3.000
 MNM  O4    C1   C2    112.75  3.000
 MNM  C3    C1   C2    111.26  3.000
 MNM  HC2   C2   N6    107.04  3.000
 MNM  HC2   C2   O5    109.87  3.000
 MNM  N6    C2   O5    115.41  3.000
 MNM  HC2   C2   C1    109.09  3.000
 MNM  N6    C2   C1    107.70  3.000
 MNM  O5    C2   C1    107.60  3.000
 MNM  HC3   C3   C8    108.29  3.000
 MNM  HC3   C3   O7    110.25  3.000
 MNM  C8    C3   O7    108.71  3.000
 MNM  HC3   C3   C1    108.32  3.000
 MNM  C8    C3   C1    110.63  3.000
 MNM  O7    C3   C1    110.62  3.000
 MNM  HO4   O4   C1    108.71  3.000
 MNM  HO5   O5   C2    108.13  3.000
 MNM  HN6   N6   C10   111.12  3.000
 MNM  HN6   N6   C2    111.28  3.000
 MNM  C10   N6   C2    114.30  3.000
 MNM  HO7   O7   C3    107.73  3.000
 MNM  HC8   C8   C10   108.17  3.000
 MNM  HC8   C8   C9    108.89  3.000
 MNM  C10   C8   C9    111.43  3.000
 MNM  HC8   C8   C3    107.92  3.000
 MNM  C10   C8   C3    109.62  3.000
 MNM  C9    C8   C3    110.70  3.000
 MNM  HC92  C9   HC91  106.95  3.000
 MNM  HC92  C9   O11   111.10  3.000
 MNM  HC91  C9   O11   111.28  3.000
 MNM  HC92  C9   C8    109.68  3.000
 MNM  HC91  C9   C8    108.80  3.000
 MNM  O11   C9   C8    108.98  3.000
 MNM  H10   C10  H1    106.76  3.000
 MNM  H10   C10  C8    109.13  3.000
 MNM  H1    C10  C8    109.64  3.000
 MNM  H10   C10  N6    113.03  3.000
 MNM  H1    C10  N6    108.10  3.000
 MNM  C8    C10  N6    110.08  3.000
 MNM  H11   O11  C9    108.01  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
 MNM  Var_01  C8  C10  N6  C2  -61.77  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
 MNM  chir_01  C1  C2  C3  O4   positiv
 MNM  chir_02  C2  O5  N6  C1   positiv
 MNM  chir_03  C3  O7  C1  C8   negativ
 MNM  chir_04  C8  C3  C9  C10  negativ

