# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:56:04 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2~{R},3~{R},4~{R},5~{R})-5-azanyl-2-(hydroxymethyl)piperidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CN[C@H](CO)[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
 G63  G63  (2~{R},3~{R},4~{R},5~{R})-5-azanyl-2-(hydroxymethyl)piperidine-3,4-diol  ligand  25  11  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G63
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
 G63  O3   O  OH1   0  -0.677  -2.4295  -1.2724  -0.0328
 G63  C3   C  CH1   0   0.052  -1.3909  -0.4530   0.4506
 G63  C2   C  CH1   0  -0.157  -1.6162   1.0410   0.1954
 G63  N2   N  NH2   0  -0.791  -1.9174   1.3109  -1.2021
 G63  C4   C  CH1   0   0.055  -0.0971  -0.9454  -0.1925
 G63  O4   O  OH1   0  -0.679   0.1671  -2.2845   0.1629
 G63  C5   C  CH1   0  -0.128   1.0822  -0.0871   0.2667
 G63  C6   C  CH2   0  -0.142   2.3595  -0.4919  -0.4484
 G63  O6   O  OH1   0  -0.675   3.4207   0.2925   0.0554
 G63  N7   N  NH1   0  -0.609   0.7777   1.3025  -0.0186
 G63  C1   C  CH2   0  -0.311  -0.3805   1.7783   0.7119
 G63  H1   H  HOH1  0   0.452  -3.2291  -1.0788   0.4656
 G63  H2   H  HCH1  0   0.199  -1.2761  -0.5791   1.5394
 G63  H3   H  HCH1  0   0.239  -2.4817   1.3557   0.7881
 G63  H4   H  HNH2  0   0.345  -2.2872   2.2504  -1.2787
 G63  H5   H  HNH2  0   0.335  -1.0492   1.3220  -1.7256
 G63  H7   H  HCH1  0   0.197  -0.1854  -0.8477  -1.2864
 G63  H8   H  HOH1  0   0.449  -0.5960  -2.8127  -0.0928
 G63  H9   H  HCH1  0   0.201   1.2180  -0.2621   1.3505
 G63  H10  H  HCH2  0   0.205   2.5441  -1.5597  -0.2924
 G63  H11  H  HCH2  0   0.191   2.2209  -0.3335  -1.5260
 G63  H12  H  HOH1  0   0.457   4.1974   0.1316  -0.4874
 G63  H13  H  HNH1  0   0.356   1.5833   1.8764   0.1902
 G63  H15  H  HCH2  0   0.239  -0.4929   2.8511   0.5408
 G63  H16  H  HCH2  0   0.196  -0.2888   1.6341   1.8014

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
 G63  C6  C5   single  1.519  0.020  1.519
 G63  C6  O6   single  1.413  0.020  1.413
 G63  C5  N7   single  1.451  0.020  1.451
 G63  C5  C4   single  1.529  0.020  1.529
 G63  N7  C1   single  1.450  0.020  1.450
 G63  C1  C2   single  1.529  0.020  1.529
 G63  C4  O4   single  1.410  0.020  1.410
 G63  C4  C3   single  1.526  0.020  1.526
 G63  C3  C2   single  1.532  0.020  1.532
 G63  C3  O3   single  1.408  0.020  1.408
 G63  C2  N2   single  1.455  0.020  1.455
 G63  O3  H1   single  0.850  0.020  0.980
 G63  C3  H2   single  0.970  0.020  1.090
 G63  C2  H3   single  0.970  0.020  1.090
 G63  N2  H4   single  0.890  0.020  1.040
 G63  N2  H5   single  0.890  0.020  1.040
 G63  C4  H7   single  0.970  0.020  1.090
 G63  O4  H8   single  0.850  0.020  0.980
 G63  C5  H9   single  0.970  0.020  1.090
 G63  C6  H10  single  0.970  0.020  1.090
 G63  C6  H11  single  0.970  0.020  1.090
 G63  O6  H12  single  0.850  0.020  0.980
 G63  N7  H13  single  0.890  0.020  1.040
 G63  C1  H15  single  0.970  0.020  1.090
 G63  C1  H16  single  0.970  0.020  1.090

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
 G63  H1   O3  C3   108.54  3.000
 G63  H2   C3  C4   106.92  3.000
 G63  H2   C3  C2   106.94  3.000
 G63  C4   C3  C2   111.65  3.000
 G63  H2   C3  O3   110.45  3.000
 G63  C2   C3  O3   113.68  3.000
 G63  C4   C3  O3   107.02  3.000
 G63  H3   C2  C1   108.50  3.000
 G63  H3   C2  N2   107.64  3.000
 G63  C1   C2  N2   113.73  3.000
 G63  H3   C2  C3   107.83  3.000
 G63  N2   C2  C3   111.80  3.000
 G63  C1   C2  C3   107.17  3.000
 G63  H5   N2  H4   105.28  3.000
 G63  H5   N2  C2   108.70  3.000
 G63  H4   N2  C2   108.69  3.000
 G63  H7   C4  C5   108.07  3.000
 G63  H7   C4  O4   110.45  3.000
 G63  C5   C4  O4   108.23  3.000
 G63  H7   C4  C3   108.77  3.000
 G63  O4   C4  C3   111.03  3.000
 G63  C5   C4  C3   110.26  3.000
 G63  H8   O4  C4   107.79  3.000
 G63  H9   C5  N7   111.71  3.000
 G63  H9   C5  C6   108.42  3.000
 G63  N7   C5  C6   109.83  3.000
 G63  H9   C5  C4   107.46  3.000
 G63  N7   C5  C4   108.46  3.000
 G63  C6   C5  C4   110.96  3.000
 G63  H11  C6  H10  107.57  3.000
 G63  H11  C6  O6   111.40  3.000
 G63  H10  C6  O6   111.35  3.000
 G63  H11  C6  C5   108.51  3.000
 G63  H10  C6  C5   109.55  3.000
 G63  O6   C6  C5   108.41  3.000
 G63  H12  O6  C6   108.22  3.000
 G63  H13  N7  C1   110.26  3.000
 G63  H13  N7  C5   109.63  3.000
 G63  C1   N7  C5   112.52  3.000
 G63  H16  C1  H15  106.97  3.000
 G63  H16  C1  N7   112.86  3.000
 G63  H15  C1  N7   109.00  3.000
 G63  H16  C1  C2   109.75  3.000
 G63  H15  C1  C2   109.73  3.000
 G63  N7   C1  C2   108.49  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
 G63  Var_01  C5  N7  C1  C2  -66.64  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
 G63  chir_01  C3  C4  C2  O3  negativ
 G63  chir_02  C2  N2  C3  C1  negativ
 G63  chir_03  C4  O4  C3  C5  negativ
 G63  chir_04  C5  N7  C4  C6  negativ

