# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:04:27 2021
#   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  31  14  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.612  124.4686  -880.8235  303.0587
 CKX  C10  C  CH3   0  -0.659  125.5521  -881.9149  307.2457
 CKX  C2   C  CH2   0  -0.333  123.8797  -880.0346  301.9955
 CKX  C3   C  CH1   0   0.036  124.9404  -879.7277  300.9452
 CKX  C4   C  CH1   0   0.059  126.0910  -878.9859  301.6055
 CKX  C5   C  CH1   0  -0.392  126.6318  -879.8089  302.7747
 CKX  C6   C  C     0   0.543  127.8087  -879.1031  303.4022
 CKX  C7   C  CH1   0  -0.055  125.5070  -880.1096  303.7825
 CKX  C8   C  CH2   0  -0.424  126.0064  -880.9483  304.9546
 CKX  C9   C  CH2   0  -0.439  124.9672  -881.1781  306.0481
 CKX  O3   O  OH1   0  -0.676  124.4448  -878.8963  299.9198
 CKX  O4   O  OH1   0  -0.671  127.1634  -878.7463  300.7272
 CKX  O61  O  O     0  -0.438  128.9287  -879.5480  303.4500
 CKX  O62  O  OH1   0  -0.591  127.4769  -877.9228  303.9133
 CKX  H1   H  HNH1  0   0.363  123.7402  -881.1103  303.6982
 CKX  H3   H  HCH3  0   0.230  124.8053  -882.0606  308.0267
 CKX  H4   H  HCH3  0   0.219  125.9270  -882.8988  306.9588
 CKX  H5   H  HCH3  0   0.219  126.3839  -881.3583  307.6808
 CKX  H6   H  HCH2  0   0.199  123.4497  -879.0833  302.3512
 CKX  H7   H  HCH2  0   0.244  123.0670  -880.6062  301.5417
 CKX  H8   H  HCH1  0   0.210  125.3197  -880.6768  300.5403
 CKX  H9   H  HCH1  0   0.209  125.6879  -878.0387  301.9984
 CKX  H10  H  HCH1  0   0.269  127.0007  -880.7659  302.3921
 CKX  H11  H  HCH1  0   0.208  125.1330  -879.1481  304.1773
 CKX  H12  H  HCH2  0   0.223  126.3679  -881.9101  304.5757
 CKX  H13  H  HCH2  0   0.228  126.8681  -880.4526  305.4125
 CKX  H14  H  HCH2  0   0.220  124.5644  -880.2136  306.3713
 CKX  H15  H  HCH2  0   0.218  124.1189  -881.7521  305.6646
 CKX  H16  H  HOH1  0   0.458  123.8759  -879.4185  299.3463
 CKX  H17  H  HOH1  0   0.453  126.8362  -878.2235  299.9875
 CKX  H18  H  HOH1  0   0.482  128.2555  -877.4977  304.3039

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  1.407  0.020  1.407
 CKX  C3   C4   single  1.520  0.020  1.520
 CKX  C3   C2   single  1.524  0.020  1.524
 CKX  C4   C5   single  1.529  0.020  1.529
 CKX  C2   N    single  1.449  0.020  1.449
 CKX  C5   C6   single  1.509  0.020  1.509
 CKX  C5   C7   single  1.540  0.020  1.540
 CKX  O61  C6   double  1.206  0.020  1.206
 CKX  N    C7   single  1.453  0.020  1.453
 CKX  C6   O62  single  1.328  0.020  1.328
 CKX  C7   C8   single  1.525  0.020  1.525
 CKX  C8   C9   single  1.526  0.020  1.526
 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
 CKX  O62  H18  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   109.83  3.000
 CKX  H1   N    C2   109.01  3.000
 CKX  C7   N    C2   112.85  3.000
 CKX  H5   C10  H4   107.62  3.000
 CKX  H5   C10  H3   107.74  3.000
 CKX  H4   C10  H3   107.65  3.000
 CKX  H5   C10  C9   111.07  3.000
 CKX  H4   C10  C9   111.18  3.000
 CKX  H3   C10  C9   111.41  3.000
 CKX  H7   C2   H6   107.17  3.000
 CKX  H7   C2   C3   109.69  3.000
 CKX  H6   C2   C3   108.66  3.000
 CKX  H7   C2   N    108.80  3.000
 CKX  H6   C2   N    113.05  3.000
 CKX  C3   C2   N    109.42  3.000
 CKX  H8   C3   O3   111.25  3.000
 CKX  H8   C3   C4   108.67  3.000
 CKX  O3   C3   C4   107.11  3.000
 CKX  H8   C3   C2   108.67  3.000
 CKX  C4   C3   C2   109.01  3.000
 CKX  O3   C3   C2   112.04  3.000
 CKX  H9   C4   O4   110.80  3.000
 CKX  H9   C4   C5   108.63  3.000
 CKX  O4   C4   C5   107.43  3.000
 CKX  H9   C4   C3   107.31  3.000
 CKX  C5   C4   C3   109.71  3.000
 CKX  O4   C4   C3   112.89  3.000
 CKX  H10  C5   C7   107.71  3.000
 CKX  H10  C5   C6   106.94  3.000
 CKX  C7   C5   C6   112.88  3.000
 CKX  H10  C5   C4   108.82  3.000
 CKX  C7   C5   C4   110.32  3.000
 CKX  C6   C5   C4   110.01  3.000
 CKX  O62  C6   O61  122.99  3.000
 CKX  O62  C6   C5   112.38  3.000
 CKX  O61  C6   C5   124.62  3.000
 CKX  H11  C7   C8   108.36  3.000
 CKX  H11  C7   C5   108.13  3.000
 CKX  C8   C7   C5   111.78  3.000
 CKX  H11  C7   N    111.33  3.000
 CKX  C8   C7   N    110.27  3.000
 CKX  C5   C7   N    106.97  3.000
 CKX  H13  C8   H12  106.42  3.000
 CKX  H13  C8   C9   107.73  3.000
 CKX  H12  C8   C9   109.90  3.000
 CKX  H13  C8   C7   109.28  3.000
 CKX  H12  C8   C7   108.98  3.000
 CKX  C9   C8   C7   114.23  3.000
 CKX  H15  C9   H14  106.30  3.000
 CKX  H15  C9   C8   110.85  3.000
 CKX  H14  C9   C8   109.25  3.000
 CKX  H15  C9   C10  108.65  3.000
 CKX  H14  C9   C10  109.61  3.000
 CKX  C8   C9   C10  112.02  3.000
 CKX  H16  O3   C3   108.75  3.000
 CKX  H17  O4   C4   108.24  3.000
 CKX  H18  O62  C6   110.12  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  CONST_01  H18  O62  C6  C5    180.00   0.0  0
 CKX  Var_01    C7   N    C2  C3     63.92  30.0  1
 CKX  Var_02    C7   C8   C9  C10  -175.01  30.0  1
 CKX  Var_03    H3   C10  C9  C8    179.16  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
 CKX  plan-1  H18  0.020

