# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:10:34 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-2-propyl-piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H]1NC[C@@H](O)[C@H](O)[C@H]1C(O)=O
#
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
 CKX  CKX  '(2~{S},3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-2-propyl-piperidine-3-carboxylic acid'  ligand  30  14  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CKX
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
 CKX  N    N  NH1    0  -0.616  124.4086  -880.7550  303.0914
 CKX  C10  C  CH3    0  -0.656  125.5960  -881.9392  307.1969
 CKX  C2   C  CH2    0  -0.332  123.8361  -880.0200  301.9865
 CKX  C3   C  CH1    0   0.058  124.8988  -879.8200  300.9155
 CKX  C4   C  CH1    0   0.069  126.0451  -879.0180  301.5018
 CKX  C5   C  CH1    0  -0.444  126.5749  -879.6775  302.7971
 CKX  C6   C  C      0   0.467  127.6767  -878.7489  303.3582
 CKX  C7   C  CH1    0  -0.034  125.4604  -880.0229  303.7878
 CKX  C8   C  CH2    0  -0.409  125.9874  -880.8873  304.9321
 CKX  C9   C  CH2    0  -0.439  124.9635  -881.2140  306.0162
 CKX  O3   O  OH1    0  -0.671  124.3962  -879.1215  299.7982
 CKX  O4   O  OH1    0  -0.708  127.0670  -878.8827  300.5488
 CKX  O61  O  O      0  -0.619  128.6541  -878.5630  302.5793
 CKX  O62  O  OC    -1  -0.557  127.5367  -878.2220  304.4695
 CKX  H1   H  HNH1   0   0.353  123.6736  -880.9887  303.7451
 CKX  H3   H  HCH3   0   0.224  124.8590  -882.1757  307.9651
 CKX  H4   H  HCH3   0   0.215  126.0576  -882.8768  306.8814
 CKX  H5   H  HCH3   0   0.216  126.3744  -881.3302  307.6599
 CKX  H6   H  HCH2   0   0.186  123.4332  -879.0343  302.2772
 CKX  H7   H  HCH2   0   0.231  123.0013  -880.5957  301.5760
 CKX  H8   H  HCH1   0   0.183  125.2813  -880.8115  300.6276
 CKX  H9   H  HCH1   0   0.165  125.6324  -878.0286  301.7783
 CKX  H10  H  HCH1   0   0.220  127.0499  -880.6213  302.4937
 CKX  H11  H  HCH1   0   0.177  125.0718  -879.0817  304.2143
 CKX  H12  H  HCH2   0   0.199  126.3825  -881.8197  304.5130
 CKX  H13  H  HCH2   0   0.224  126.8267  -880.3724  305.3995
 CKX  H14  H  HCH2   0   0.211  124.4951  -880.2879  306.3650
 CKX  H15  H  HCH2   0   0.210  124.1563  -881.8338  305.6153
 CKX  H16  H  HOH1   0   0.445  123.6922  -879.6486  299.4081
 CKX  H17  H  HOH1   0   0.433  127.8773  -878.7382  301.0932

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
 CKX  O3   C3   single  1.410  0.020  1.410
 CKX  O4   C4   single  1.404  0.020  1.404
 CKX  C3   C4   single  1.517  0.020  1.517
 CKX  C3   C2   single  1.522  0.020  1.522
 CKX  C4   C5   single  1.547  0.020  1.547
 CKX  C2   N    single  1.445  0.020  1.445
 CKX  C5   C6   single  1.546  0.020  1.546
 CKX  C5   C7   single  1.531  0.020  1.531
 CKX  O61  C6   deloc   1.264  0.020  1.264
 CKX  N    C7   single  1.458  0.020  1.458
 CKX  C6   O62  deloc   1.238  0.020  1.238
 CKX  C7   C8   single  1.528  0.020  1.528
 CKX  C8   C9   single  1.527  0.020  1.527
 CKX  C9   C10  single  1.523  0.020  1.523
 CKX  N    H1   single  0.890  0.020  1.040
 CKX  C10  H3   single  0.970  0.020  1.090
 CKX  C10  H4   single  0.970  0.020  1.090
 CKX  C10  H5   single  0.970  0.020  1.090
 CKX  C2   H6   single  0.970  0.020  1.090
 CKX  C2   H7   single  0.970  0.020  1.090
 CKX  C3   H8   single  0.970  0.020  1.090
 CKX  C4   H9   single  0.970  0.020  1.090
 CKX  C5   H10  single  0.970  0.020  1.090
 CKX  C7   H11  single  0.970  0.020  1.090
 CKX  C8   H12  single  0.970  0.020  1.090
 CKX  C8   H13  single  0.970  0.020  1.090
 CKX  C9   H14  single  0.970  0.020  1.090
 CKX  C9   H15  single  0.970  0.020  1.090
 CKX  O3   H16  single  0.850  0.020  0.980
 CKX  O4   H17  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
 CKX  H1   N    C7   109.37  3.000
 CKX  H1   N    C2   108.89  3.000
 CKX  C7   N    C2   113.29  3.000
 CKX  H5   C10  H4   107.48  3.000
 CKX  H5   C10  H3   107.71  3.000
 CKX  H4   C10  H3   107.65  3.000
 CKX  H5   C10  C9   111.05  3.000
 CKX  H4   C10  C9   111.13  3.000
 CKX  H3   C10  C9   111.63  3.000
 CKX  H7   C2   H6   106.87  3.000
 CKX  H7   C2   C3   109.75  3.000
 CKX  H6   C2   C3   108.84  3.000
 CKX  H7   C2   N    108.75  3.000
 CKX  H6   C2   N    113.41  3.000
 CKX  C3   C2   N    109.16  3.000
 CKX  H8   C3   O3   111.26  3.000
 CKX  H8   C3   C4   108.34  3.000
 CKX  O3   C3   C4   108.28  3.000
 CKX  H8   C3   C2   107.96  3.000
 CKX  C4   C3   C2   108.97  3.000
 CKX  O3   C3   C2   111.95  3.000
 CKX  H9   C4   O4   110.78  3.000
 CKX  H9   C4   C5   107.43  3.000
 CKX  O4   C4   C5   111.11  3.000
 CKX  H9   C4   C3   106.70  3.000
 CKX  C5   C4   C3   110.91  3.000
 CKX  O4   C4   C3   109.79  3.000
 CKX  H10  C5   C7   107.43  3.000
 CKX  H10  C5   C6   107.93  3.000
 CKX  C7   C5   C6   114.80  3.000
 CKX  H10  C5   C4   106.43  3.000
 CKX  C7   C5   C4   112.88  3.000
 CKX  C6   C5   C4   106.97  3.000
 CKX  O62  C6   O61  125.33  3.000
 CKX  O62  C6   C5   120.05  3.000
 CKX  O61  C6   C5   114.58  3.000
 CKX  H11  C7   C8   108.32  3.000
 CKX  H11  C7   C5   108.30  3.000
 CKX  C8   C7   C5   111.17  3.000
 CKX  H11  C7   N    111.01  3.000
 CKX  C8   C7   N    108.80  3.000
 CKX  C5   C7   N    109.23  3.000
 CKX  H13  C8   H12  106.76  3.000
 CKX  H13  C8   C9   108.24  3.000
 CKX  H12  C8   C9   109.34  3.000
 CKX  H13  C8   C7   108.64  3.000
 CKX  H12  C8   C7   108.62  3.000
 CKX  C9   C8   C7   114.94  3.000
 CKX  H15  C9   H14  106.28  3.000
 CKX  H15  C9   C8   110.85  3.000
 CKX  H14  C9   C8   109.40  3.000
 CKX  H15  C9   C10  108.71  3.000
 CKX  H14  C9   C10  109.48  3.000
 CKX  C8   C9   C10  111.95  3.000
 CKX  H16  O3   C3   108.10  3.000
 CKX  H17  O4   C4   103.73  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
 CKX  Var_01  C7  N    C2  C3     65.25  30.0  1
 CKX  Var_02  C7  C8   C9  C10  -173.46  30.0  1
 CKX  Var_03  H3  C10  C9  C8   -179.64  30.0  3

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
 CKX  chir_01  C3  O3  C4  C2  negativ
 CKX  chir_02  C4  O4  C5  C3  positiv
 CKX  chir_03  C5  C4  C6  C7  negativ
 CKX  chir_04  C7  N   C8  C5  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CKX  plan-1  C5   0.020
 CKX  plan-1  C6   0.020
 CKX  plan-1  O61  0.020
 CKX  plan-1  O62  0.020

