# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:29:54 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: (3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-1-propyl-piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN1C[C@@H](O)[C@H](O)[C@H](C1)C(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
 CKU  CKU  '(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-1-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_CKU
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
 CKU  C10  C  CH1   0  -0.458  155.6823  -864.4510  272.6737
 CKU  C01  C  CH3   0  -0.671  157.1839  -862.7650  267.2748
 CKU  C02  C  CH2   0  -0.500  157.0844  -862.0111  268.5968
 CKU  C03  C  CH2   0  -0.281  157.4928  -862.8171  269.8344
 CKU  N04  N  NT    0  -0.384  156.3831  -863.3988  270.5763
 CKU  C05  C  CH2   0  -0.334  155.5933  -864.3329  269.8020
 CKU  C06  C  CH1   0   0.013  154.3760  -864.7831  270.5921
 CKU  O07  O  OH1   0  -0.731  153.6500  -865.6837  269.7940
 CKU  C08  C  CH1   0   0.045  154.8085  -865.4307  271.8946
 CKU  O09  O  OH1   0  -0.653  153.6392  -865.7994  272.5877
 CKU  C11  C  CH2   0  -0.241  156.8607  -863.9982  271.8061
 CKU  C12  C  C     0   0.469  156.1512  -865.0523  273.9760
 CKU  O13  O  OH1   0  -0.414  156.8645  -864.2015  274.6915
 CKU  O14  O  O     0  -0.438  155.9059  -866.1769  274.3448
 CKU  H1   H  HCH1  0   0.207  155.0907  -863.5602  272.9203
 CKU  H2   H  HCH3  0   0.199  156.9130  -862.1200  266.4381
 CKU  H3   H  HCH3  0   0.256  158.2037  -863.1132  267.1034
 CKU  H4   H  HCH3  0   0.223  156.5319  -863.6381  267.2376
 CKU  H5   H  HCH2  0   0.214  157.7356  -861.1365  268.5355
 CKU  H6   H  HCH2  0   0.263  156.0753  -861.6158  268.7420
 CKU  H7   H  HCH2  0   0.240  158.2276  -863.5872  269.5411
 CKU  H8   H  HCH2  0   0.222  158.0159  -862.1563  270.5295
 CKU  H10  H  HCH2  0   0.279  155.2489  -863.8450  268.8900
 CKU  H11  H  HCH2  0   0.196  156.1781  -865.2194  269.4940
 CKU  H12  H  HCH1  0   0.255  153.7742  -863.8922  270.8310
 CKU  H13  H  HOH1  0   0.432  152.9184  -866.0223  270.3200
 CKU  H14  H  HCH1  0   0.203  155.4125  -866.3161  271.6411
 CKU  H15  H  HOH1  0   0.458  153.8980  -866.3413  273.3403
 CKU  H16  H  HCH2  0   0.201  157.5286  -864.8572  271.6145
 CKU  H17  H  HCH2  0   0.242  157.4514  -863.2558  272.3446
 CKU  H18  H  HOH1  0   0.491  157.1494  -864.6143  275.5206

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
 CKU  C01  C02  single  1.525  0.020  1.525
 CKU  C02  C03  single  1.532  0.020  1.532
 CKU  C03  N04  single  1.456  0.020  1.456
 CKU  C05  N04  single  1.448  0.020  1.448
 CKU  C05  C06  single  1.520  0.020  1.520
 CKU  O07  C06  single  1.405  0.020  1.405
 CKU  N04  C11  single  1.449  0.020  1.449
 CKU  C06  C08  single  1.518  0.020  1.518
 CKU  C11  C10  single  1.532  0.020  1.532
 CKU  C08  C10  single  1.527  0.020  1.527
 CKU  C08  O09  single  1.408  0.020  1.408
 CKU  C10  C12  single  1.509  0.020  1.509
 CKU  O14  C12  double  1.209  0.020  1.209
 CKU  C12  O13  single  1.321  0.020  1.321
 CKU  C10  H1   single  0.970  0.020  1.090
 CKU  C01  H2   single  0.970  0.020  1.090
 CKU  C01  H3   single  0.970  0.020  1.090
 CKU  C01  H4   single  0.970  0.020  1.090
 CKU  C02  H5   single  0.970  0.020  1.090
 CKU  C02  H6   single  0.970  0.020  1.090
 CKU  C03  H7   single  0.970  0.020  1.090
 CKU  C03  H8   single  0.970  0.020  1.090
 CKU  C05  H10  single  0.970  0.020  1.090
 CKU  C05  H11  single  0.970  0.020  1.090
 CKU  C06  H12  single  0.970  0.020  1.090
 CKU  O07  H13  single  0.850  0.020  0.980
 CKU  C08  H14  single  0.970  0.020  1.090
 CKU  O09  H15  single  0.850  0.020  0.980
 CKU  C11  H16  single  0.970  0.020  1.090
 CKU  C11  H17  single  0.970  0.020  1.090
 CKU  O13  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
 CKU  H1   C10  C12  107.28  3.000
 CKU  H1   C10  C11  107.58  3.000
 CKU  C12  C10  C11  111.56  3.000
 CKU  H1   C10  C08  109.09  3.000
 CKU  C12  C10  C08  111.26  3.000
 CKU  C11  C10  C08  109.94  3.000
 CKU  H4   C01  H3   107.34  3.000
 CKU  H4   C01  H2   107.40  3.000
 CKU  H3   C01  H2   107.48  3.000
 CKU  H4   C01  C02  112.73  3.000
 CKU  H3   C01  C02  110.78  3.000
 CKU  H2   C01  C02  110.88  3.000
 CKU  H6   C02  H5   105.56  3.000
 CKU  H6   C02  C03  109.20  3.000
 CKU  H5   C02  C03  107.92  3.000
 CKU  H6   C02  C01  110.73  3.000
 CKU  H5   C02  C01  107.95  3.000
 CKU  C03  C02  C01  115.01  3.000
 CKU  H8   C03  H7   105.80  3.000
 CKU  H8   C03  N04  106.40  3.000
 CKU  H7   C03  N04  111.34  3.000
 CKU  H8   C03  C02  108.87  3.000
 CKU  H7   C03  C02  109.25  3.000
 CKU  N04  C03  C02  114.74  3.000
 CKU  C11  N04  C05  111.52  3.000
 CKU  C11  N04  C03  110.28  3.000
 CKU  C05  N04  C03  113.64  3.000
 CKU  H11  C05  H10  107.03  3.000
 CKU  H11  C05  C06  109.33  3.000
 CKU  H10  C05  C06  108.33  3.000
 CKU  H11  C05  N04  112.20  3.000
 CKU  H10  C05  N04  109.33  3.000
 CKU  C06  C05  N04  110.49  3.000
 CKU  H12  C06  C08  108.35  3.000
 CKU  H12  C06  O07  111.06  3.000
 CKU  C08  C06  O07  111.17  3.000
 CKU  H12  C06  C05  108.11  3.000
 CKU  C08  C06  C05  110.15  3.000
 CKU  O07  C06  C05  107.96  3.000
 CKU  H13  O07  C06  107.92  3.000
 CKU  H14  C08  O09  110.99  3.000
 CKU  H14  C08  C06  107.57  3.000
 CKU  O09  C08  C06  107.31  3.000
 CKU  H14  C08  C10  108.63  3.000
 CKU  O09  C08  C10  113.08  3.000
 CKU  C06  C08  C10  109.10  3.000
 CKU  H15  O09  C08  108.00  3.000
 CKU  H17  C11  H16  106.70  3.000
 CKU  H17  C11  N04  108.41  3.000
 CKU  H16  C11  N04  111.94  3.000
 CKU  H17  C11  C10  109.77  3.000
 CKU  H16  C11  C10  109.48  3.000
 CKU  N04  C11  C10  110.45  3.000
 CKU  O14  C12  O13  122.93  3.000
 CKU  O13  C12  C10  112.25  3.000
 CKU  O14  C12  C10  124.82  3.000
 CKU  H18  O13  C12  110.36  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
 CKU  CONST_01  H18  O13  C12  C10   180.00   0.0  0
 CKU  Var_01    C05  N04  C11  C10   -60.02  30.0  1
 CKU  Var_02    C11  N04  C05  C06    60.57  30.0  1
 CKU  Var_03    N04  C03  C02  C01   -98.17  30.0  3
 CKU  Var_04    H2   C01  C02  C03  -177.96  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
 CKU  chir_01  C10  C11  C08  C12  negativ
 CKU  chir_02  C06  O07  C08  C05  negativ
 CKU  chir_03  C08  O09  C06  C10  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
 CKU  plan-1  C10  0.020
 CKU  plan-1  C12  0.020
 CKU  plan-1  O13  0.020
 CKU  plan-1  O14  0.020
 CKU  plan-1  H18  0.020

