# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 05:28:09 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[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
 E8X  E8X  '(2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid'  ligand  39  17  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E8X
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
 E8X  C6   C  C      0   0.413  -33.3661  33.8547  -31.3461
 E8X  C5   C  CH1    0  -0.365  -33.6710  34.5600  -30.0050
 E8X  C4   C  CH1    0   0.062  -33.9003  33.5353  -28.9017
 E8X  O4   O  OH1    0  -0.676  -32.7410  32.7347  -28.7928
 E8X  C3   C  CH1    0   0.027  -34.2319  34.2236  -27.5882
 E8X  O3   O  OH1    0  -0.677  -34.4853  33.2170  -26.6262
 E8X  C2   C  CH2    0  -0.347  -35.4394  35.1383  -27.7865
 E8X  C7   C  CH1    0  -0.076  -34.8964  35.4883  -30.1189
 E8X  C8   C  CH2    0  -0.428  -34.6950  36.5733  -31.1736
 E8X  C9   C  CH2    0  -0.398  -35.9052  37.4755  -31.3825
 E8X  N    N  NH1    0  -0.580  -35.2576  36.1058  -28.8474
 E8X  O61  O  O      0  -0.610  -34.2313  33.0500  -31.7518
 E8X  O62  O  OC    -1  -0.607  -32.3017  34.1547  -31.9220
 E8X  C10  C  CH2    0  -0.416  -35.7230  38.4548  -32.5357
 E8X  C11  C  CH2    0  -0.415  -36.9197  39.3824  -32.7130
 E8X  C12  C  CH2    0  -0.424  -36.7689  40.4031  -33.8380
 E8X  C13  C  CH3    0  -0.664  -36.7071  39.7865  -35.2299
 E8X  H1   H  HCH1   0   0.188  -32.8123  35.1838  -29.7223
 E8X  H2   H  HCH1   0   0.178  -34.7688  32.9172  -29.1826
 E8X  H3   H  HOH1   0   0.439  -32.8891  32.0980  -28.0861
 E8X  H4   H  HCH1   0   0.191  -33.3675  34.8367  -27.2876
 E8X  H5   H  HOH1   0   0.450  -34.5337  33.6288  -25.7580
 E8X  H6   H  HCH2   0   0.233  -35.6671  35.6669  -26.8564
 E8X  H7   H  HCH2   0   0.216  -36.3142  34.5206  -28.0205
 E8X  H8   H  HCH1   0   0.203  -35.7530  34.8742  -30.4264
 E8X  H9   H  HCH2   0   0.225  -34.4427  36.0990  -32.1257
 E8X  H10  H  HCH2   0   0.204  -33.8234  37.1818  -30.9021
 E8X  H11  H  HCH2   0   0.208  -36.1198  38.0315  -30.4666
 E8X  H12  H  HCH2   0   0.201  -36.7881  36.8544  -31.5725
 E8X  H13  H  HNH1   0   0.333  -34.5312  36.7640  -28.5834
 E8X  H16  H  HCH2   0   0.210  -35.5401  37.8931  -33.4571
 E8X  H17  H  HCH2   0   0.203  -34.8240  39.0586  -32.3657
 E8X  H18  H  HCH2   0   0.213  -37.0911  39.9150  -31.7720
 E8X  H19  H  HCH2   0   0.203  -37.8201  38.7826  -32.8876
 E8X  H20  H  HCH2   0   0.208  -35.8714  41.0052  -33.6635
 E8X  H21  H  HCH2   0   0.218  -37.6105  41.0999  -33.7955
 E8X  H22  H  HCH3   0   0.225  -36.6447  40.5557  -36.0005
 E8X  H23  H  HCH3   0   0.220  -35.8406  39.1352  -35.3503
 E8X  H24  H  HCH3   0   0.213  -37.5978  39.1882  -35.4322

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
 E8X  C13  C12  single  1.524  0.020  1.524
 E8X  C12  C11  single  1.526  0.020  1.526
 E8X  C11  C10  single  1.524  0.020  1.524
 E8X  C10  C9   single  1.524  0.020  1.524
 E8X  O61  C6   deloc   1.249  0.020  1.249
 E8X  O62  C6   deloc   1.247  0.020  1.247
 E8X  C9   C8   single  1.524  0.020  1.524
 E8X  C6   C5   single  1.546  0.020  1.546
 E8X  C8   C7   single  1.527  0.020  1.527
 E8X  C5   C7   single  1.542  0.020  1.542
 E8X  C5   C4   single  1.523  0.020  1.523
 E8X  C7   N    single  1.459  0.020  1.459
 E8X  O4   C4   single  1.413  0.020  1.413
 E8X  C4   C3   single  1.520  0.020  1.520
 E8X  N    C2   single  1.447  0.020  1.447
 E8X  C3   C2   single  1.528  0.020  1.528
 E8X  C3   O3   single  1.415  0.020  1.415
 E8X  C5   H1   single  0.970  0.020  1.090
 E8X  C4   H2   single  0.970  0.020  1.090
 E8X  O4   H3   single  0.850  0.020  0.980
 E8X  C3   H4   single  0.970  0.020  1.090
 E8X  O3   H5   single  0.850  0.020  0.980
 E8X  C2   H6   single  0.970  0.020  1.090
 E8X  C2   H7   single  0.970  0.020  1.090
 E8X  C7   H8   single  0.970  0.020  1.090
 E8X  C8   H9   single  0.970  0.020  1.090
 E8X  C8   H10  single  0.970  0.020  1.090
 E8X  C9   H11  single  0.970  0.020  1.090
 E8X  C9   H12  single  0.970  0.020  1.090
 E8X  N    H13  single  0.890  0.020  1.040
 E8X  C10  H16  single  0.970  0.020  1.090
 E8X  C10  H17  single  0.970  0.020  1.090
 E8X  C11  H18  single  0.970  0.020  1.090
 E8X  C11  H19  single  0.970  0.020  1.090
 E8X  C12  H20  single  0.970  0.020  1.090
 E8X  C12  H21  single  0.970  0.020  1.090
 E8X  C13  H22  single  0.970  0.020  1.090
 E8X  C13  H23  single  0.970  0.020  1.090
 E8X  C13  H24  single  0.970  0.020  1.090

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
 E8X  O62  C6   O61  126.60  3.000
 E8X  O62  C6   C5   117.35  3.000
 E8X  O61  C6   C5   116.05  3.000
 E8X  H1   C5   C7   107.37  3.000
 E8X  H1   C5   C4   108.26  3.000
 E8X  C7   C5   C4   109.81  3.000
 E8X  H1   C5   C6   109.17  3.000
 E8X  C4   C5   C6   110.57  3.000
 E8X  C7   C5   C6   111.56  3.000
 E8X  H2   C4   C3   107.60  3.000
 E8X  H2   C4   O4   110.38  3.000
 E8X  C3   C4   O4   111.66  3.000
 E8X  H2   C4   C5   108.13  3.000
 E8X  C3   C4   C5   110.75  3.000
 E8X  O4   C4   C5   108.26  3.000
 E8X  H3   O4   C4   107.76  3.000
 E8X  H4   C3   C2   108.81  3.000
 E8X  H4   C3   O3   110.54  3.000
 E8X  C2   C3   O3   111.87  3.000
 E8X  H4   C3   C4   108.47  3.000
 E8X  O3   C3   C4   107.73  3.000
 E8X  C2   C3   C4   109.36  3.000
 E8X  H5   O3   C3   108.54  3.000
 E8X  H7   C2   H6   106.72  3.000
 E8X  H7   C2   N    108.69  3.000
 E8X  H6   C2   N    109.05  3.000
 E8X  H7   C2   C3   108.74  3.000
 E8X  H6   C2   C3   110.09  3.000
 E8X  N    C2   C3   113.34  3.000
 E8X  H8   C7   N    106.72  3.000
 E8X  H8   C7   C8   107.88  3.000
 E8X  N    C7   C8   109.51  3.000
 E8X  H8   C7   C5   107.70  3.000
 E8X  N    C7   C5   112.79  3.000
 E8X  C8   C7   C5   111.97  3.000
 E8X  H10  C8   H9   105.83  3.000
 E8X  H10  C8   C9   109.66  3.000
 E8X  H9   C8   C9   108.71  3.000
 E8X  H10  C8   C7   109.15  3.000
 E8X  H9   C8   C7   108.89  3.000
 E8X  C9   C8   C7   114.25  3.000
 E8X  H12  C9   H11  105.99  3.000
 E8X  H12  C9   C10  109.23  3.000
 E8X  H11  C9   C10  109.32  3.000
 E8X  H12  C9   C8   109.14  3.000
 E8X  H11  C9   C8   110.02  3.000
 E8X  C10  C9   C8   112.91  3.000
 E8X  H13  N    C7   108.90  3.000
 E8X  H13  N    C2   109.43  3.000
 E8X  C7   N    C2   112.77  3.000
 E8X  H17  C10  H16  106.03  3.000
 E8X  H17  C10  C11  109.07  3.000
 E8X  H16  C10  C11  110.22  3.000
 E8X  H17  C10  C9   109.55  3.000
 E8X  H16  C10  C9   109.10  3.000
 E8X  C11  C10  C9   112.66  3.000
 E8X  H19  C11  H18  105.93  3.000
 E8X  H19  C11  C12  109.25  3.000
 E8X  H18  C11  C12  108.88  3.000
 E8X  H19  C11  C10  109.29  3.000
 E8X  H18  C11  C10  108.60  3.000
 E8X  C12  C11  C10  114.53  3.000
 E8X  H21  C12  H20  105.93  3.000
 E8X  H21  C12  C13  108.94  3.000
 E8X  H20  C12  C13  109.56  3.000
 E8X  H21  C12  C11  108.75  3.000
 E8X  H20  C12  C11  109.34  3.000
 E8X  C13  C12  C11  114.00  3.000
 E8X  H24  C13  H23  107.48  3.000
 E8X  H24  C13  H22  107.59  3.000
 E8X  H23  C13  H22  107.33  3.000
 E8X  H24  C13  C12  110.97  3.000
 E8X  H23  C13  C12  112.01  3.000
 E8X  H22  C13  C12  111.25  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
 E8X  Var_01  C7   N    C2   C3     54.70  30.0  1
 E8X  Var_02  C10  C9   C8   C7   -174.21  30.0  1
 E8X  Var_03  C11  C10  C9   C8   -178.28  30.0  1
 E8X  Var_04  C12  C11  C10  C9    178.69  30.0  2
 E8X  Var_05  C13  C12  C11  C10    65.80  30.0  2
 E8X  Var_06  H22  C13  C12  C11   177.44  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
 E8X  chir_01  C5  C6  C7  C4  negativ
 E8X  chir_02  C4  O4  C5  C3  positiv
 E8X  chir_03  C3  O3  C4  C2  negativ
 E8X  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
 E8X  plan-1  C6   0.020
 E8X  plan-1  C5   0.020
 E8X  plan-1  O61  0.020
 E8X  plan-1  O62  0.020

