# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 07:34:44 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: (2~{S},3~{R})-2-(hydroxymethyl)piperidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1NCCC[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
 KFW  KFW  (2~{S},3~{R})-2-(hydroxymethyl)piperidin-3-ol  ligand  22  9  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KFW
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
 KFW  N1   N  NH1   0  -0.603  47.8991  -13.0426   -7.3557
 KFW  C1   C  CH2   0  -0.197  45.8217  -13.8106   -6.3128
 KFW  C2   C  CH1   0  -0.112  46.7970  -13.9844   -7.4639
 KFW  C3   C  CH2   0  -0.291  48.9490  -13.3216   -8.3195
 KFW  C4   C  CH2   0  -0.436  48.4012  -13.1704   -9.7295
 KFW  C5   C  CH2   0  -0.466  47.1835  -14.0669   -9.9286
 KFW  C6   C  CH1   0   0.079  46.1479  -13.8113   -8.8442
 KFW  O1   O  OH1   0  -0.671  45.1571  -12.5721   -6.4138
 KFW  O2   O  OH1   0  -0.680  45.0727  -14.7066   -9.0398
 KFW  H1   H  HNH1  0   0.347  48.2825  -13.0849   -6.4195
 KFW  H3   H  HCH2  0   0.203  45.1178  -14.6521   -6.3197
 KFW  H4   H  HCH2  0   0.210  46.3817  -13.8920   -5.3699
 KFW  H5   H  HCH1  0   0.196  47.1514  -15.0310   -7.3996
 KFW  H6   H  HCH2  0   0.185  49.3613  -14.3386   -8.2058
 KFW  H7   H  HCH2  0   0.232  49.7718  -12.6232   -8.1556
 KFW  H8   H  HCH2  0   0.233  49.1762  -13.4169  -10.4581
 KFW  H9   H  HCH2  0   0.218  48.1245  -12.1256   -9.8979
 KFW  H10  H  HCH2  0   0.236  46.7423  -13.9025  -10.9149
 KFW  H11  H  HCH2  0   0.214  47.4945  -15.1172   -9.8836
 KFW  H12  H  HCH1  0   0.198  45.8078  -12.7709   -8.9327
 KFW  H13  H  HOH1  0   0.456  44.5089  -12.5231   -5.7060
 KFW  H14  H  HOH1  0   0.450  44.3226  -14.4013   -8.5211

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
 KFW  C5  C4   single  1.525  0.020  1.525
 KFW  C5  C6   single  1.521  0.020  1.521
 KFW  C4  C3   single  1.520  0.020  1.520
 KFW  O2  C6   single  1.413  0.020  1.413
 KFW  C6  C2   single  1.535  0.020  1.535
 KFW  C3  N1   single  1.452  0.020  1.452
 KFW  C2  N1   single  1.454  0.020  1.454
 KFW  C2  C1   single  1.519  0.020  1.519
 KFW  O1  C1   single  1.409  0.020  1.409
 KFW  N1  H1   single  0.890  0.020  1.040
 KFW  C1  H3   single  0.970  0.020  1.090
 KFW  C1  H4   single  0.970  0.020  1.090
 KFW  C2  H5   single  0.970  0.020  1.090
 KFW  C3  H6   single  0.970  0.020  1.090
 KFW  C3  H7   single  0.970  0.020  1.090
 KFW  C4  H8   single  0.970  0.020  1.090
 KFW  C4  H9   single  0.970  0.020  1.090
 KFW  C5  H10  single  0.970  0.020  1.090
 KFW  C5  H11  single  0.970  0.020  1.090
 KFW  C6  H12  single  0.970  0.020  1.090
 KFW  O1  H13  single  0.850  0.020  0.980
 KFW  O2  H14  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
 KFW  H1   N1  C3   109.38  3.000
 KFW  H1   N1  C2   109.20  3.000
 KFW  C3   N1  C2   111.98  3.000
 KFW  H4   C1  H3   105.99  3.000
 KFW  H4   C1  O1   111.51  3.000
 KFW  H3   C1  O1   111.78  3.000
 KFW  H4   C1  C2   108.33  3.000
 KFW  H3   C1  C2   108.63  3.000
 KFW  O1   C1  C2   110.43  3.000
 KFW  H5   C2  C6   107.11  3.000
 KFW  H5   C2  C1   105.65  3.000
 KFW  C6   C2  C1   113.40  3.000
 KFW  H5   C2  N1   111.44  3.000
 KFW  C1   C2  N1   110.87  3.000
 KFW  C6   C2  N1   108.32  3.000
 KFW  H7   C3  H6   107.02  3.000
 KFW  H7   C3  C4   110.32  3.000
 KFW  H6   C3  C4   108.78  3.000
 KFW  H7   C3  N1   108.81  3.000
 KFW  H6   C3  N1   112.26  3.000
 KFW  C4   C3  N1   109.63  3.000
 KFW  H9   C4  H8   107.00  3.000
 KFW  H9   C4  C5   109.84  3.000
 KFW  H8   C4  C5   110.29  3.000
 KFW  H9   C4  C3   109.21  3.000
 KFW  H8   C4  C3   109.92  3.000
 KFW  C5   C4  C3   110.51  3.000
 KFW  H11  C5  H10  107.20  3.000
 KFW  H11  C5  C6   108.95  3.000
 KFW  H10  C5  C6   110.07  3.000
 KFW  H11  C5  C4   109.35  3.000
 KFW  H10  C5  C4   110.59  3.000
 KFW  C6   C5  C4   110.60  3.000
 KFW  H12  C6  O2   110.70  3.000
 KFW  H12  C6  C5   108.22  3.000
 KFW  O2   C6  C5   108.24  3.000
 KFW  H12  C6  C2   108.07  3.000
 KFW  O2   C6  C2   112.01  3.000
 KFW  C5   C6  C2   109.52  3.000
 KFW  H13  O1  C1   108.07  3.000
 KFW  H14  O2  C6   108.53  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
 KFW  Var_01  C5  C4  C3  N1  -55.84  30.0  1
 KFW  Var_02  C4  C3  N1  C2   62.49  30.0  1
 KFW  Var_03  C6  C5  C4  C3   53.43  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
 KFW  chir_01  C2  C6  N1  C1  negativ
 KFW  chir_02  C6  O2  C2  C5  negativ

