# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:48:07 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: (3R,4r,5S)-piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CNC[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
 XDN  XDN  (3R,4r,5S)-piperidine-3,4,5-triol  ligand  20  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDN
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
 XDN  C1   C  CH2   0  -0.356  -1.2666   1.3753   0.1695
 XDN  C2   C  CH1   0   0.031  -1.2614  -0.1030  -0.2354
 XDN  O2   O  OH1   0  -0.670  -2.3621  -0.7916   0.3133
 XDN  C3   C  CH1   0   0.030   0.0108  -0.7677   0.2627
 XDN  O3   O  OH1   0  -0.674   0.0299  -2.1037  -0.1799
 XDN  C4   C  CH1   0   0.008   1.2263   0.0070  -0.2362
 XDN  O4   O  OH1   0  -0.677   2.3708  -0.6221   0.3047
 XDN  C5   C  CH2   0  -0.350   1.1313   1.4759   0.1773
 XDN  N5   N  NH1   0  -0.581  -0.0955   2.1126  -0.2624
 XDN  H11  H  HCH2  0   0.245  -2.1598   1.8611  -0.2328
 XDN  H12  H  HCH2  0   0.224  -1.3393   1.4395   1.2615
 XDN  H2   H  HCH1  0   0.200  -1.2719  -0.1624  -1.3355
 XDN  HO2  H  HOH1  0   0.451  -3.1643  -0.4310  -0.0768
 XDN  H3   H  HCH1  0   0.196   0.0107  -0.7192   1.3662
 XDN  HO3  H  HOH1  0   0.445   0.8777  -2.4817   0.0764
 XDN  H4   H  HCH1  0   0.207   1.2397  -0.0474  -1.3355
 XDN  HO4  H  HOH1  0   0.457   3.1386  -0.3501  -0.2066
 XDN  H51  H  HCH2  0   0.224   1.1922   1.5445   1.2696
 XDN  H52  H  HCH2  0   0.243   1.9841   2.0306  -0.2217
 XDN  HN5  H  HNH1  0   0.348  -0.0954   2.1920  -1.2723

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
 XDN  C1  C2   single  1.533  0.020  1.533
 XDN  C1  N5   single  1.450  0.020  1.450
 XDN  C1  H11  single  0.970  0.020  1.090
 XDN  C1  H12  single  0.970  0.020  1.090
 XDN  C2  O2   single  1.410  0.020  1.410
 XDN  C2  C3   single  1.519  0.020  1.519
 XDN  C2  H2   single  0.970  0.020  1.090
 XDN  O2  HO2  single  0.850  0.020  0.980
 XDN  C3  O3   single  1.408  0.020  1.408
 XDN  C3  C4   single  1.525  0.020  1.525
 XDN  C3  H3   single  0.970  0.020  1.090
 XDN  O3  HO3  single  0.850  0.020  0.980
 XDN  C4  O4   single  1.414  0.020  1.414
 XDN  C4  C5   single  1.529  0.020  1.529
 XDN  C4  H4   single  0.970  0.020  1.090
 XDN  O4  HO4  single  0.850  0.020  0.980
 XDN  C5  N5   single  1.450  0.020  1.450
 XDN  C5  H51  single  0.970  0.020  1.090
 XDN  C5  H52  single  0.970  0.020  1.090
 XDN  N5  HN5  single  0.890  0.020  1.040

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
 XDN  H12  C1  H11  106.64  3.000
 XDN  H12  C1  N5   108.70  3.000
 XDN  H11  C1  N5   108.92  3.000
 XDN  H12  C1  C2   108.65  3.000
 XDN  H11  C1  C2   109.52  3.000
 XDN  N5   C1  C2   114.14  3.000
 XDN  H2   C2  C3   108.16  3.000
 XDN  H2   C2  O2   110.79  3.000
 XDN  C3   C2  O2   108.21  3.000
 XDN  H2   C2  C1   108.41  3.000
 XDN  C3   C2  C1   109.76  3.000
 XDN  O2   C2  C1   111.45  3.000
 XDN  HO2  O2  C2   108.07  3.000
 XDN  H3   C3  C4   107.73  3.000
 XDN  H3   C3  O3   110.84  3.000
 XDN  C4   C3  O3   111.62  3.000
 XDN  H3   C3  C2   107.96  3.000
 XDN  C4   C3  C2   109.74  3.000
 XDN  O3   C3  C2   108.88  3.000
 XDN  HO3  O3  C3   107.51  3.000
 XDN  H4   C4  C5   108.57  3.000
 XDN  H4   C4  O4   110.51  3.000
 XDN  C5   C4  O4   111.99  3.000
 XDN  H4   C4  C3   108.13  3.000
 XDN  C5   C4  C3   110.49  3.000
 XDN  O4   C4  C3   107.10  3.000
 XDN  HO4  O4  C4   108.48  3.000
 XDN  H52  C5  H51  106.77  3.000
 XDN  H52  C5  N5   109.06  3.000
 XDN  H51  C5  N5   108.76  3.000
 XDN  H52  C5  C4   109.90  3.000
 XDN  H51  C5  C4   109.04  3.000
 XDN  N5   C5  C4   113.10  3.000
 XDN  HN5  N5  C5   109.66  3.000
 XDN  HN5  N5  C1   109.70  3.000
 XDN  C5   N5  C1   111.70  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
 XDN  Var_01  C4  C5  N5  C1   53.96  30.0  1
 XDN  Var_02  C5  N5  C1  C2  -54.08  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
 XDN  chir_01  C2  C1  O2  C3  positiv
 XDN  chir_02  C3  O3  C2  C4  positiv
 XDN  chir_03  C4  O4  C3  C5  negativ

