# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 07:14:21 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC[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
 E9O  E9O  '(2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid'  ligand  48  20  .  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_E9O
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
 E9O  C2   C  CH2    0  -0.319  -1.3715  -14.2850  -54.2719
 E9O  C3   C  CH1    0   0.067  -2.3733  -13.1816  -54.5506
 E9O  O3   O  OH1    0  -0.676  -2.9777  -13.4252  -55.8011
 E9O  N    N  NH1    0  -0.617  -0.7025  -13.9923  -53.0227
 E9O  C7   C  CH1    0  -0.036  -1.5864  -14.0189  -51.8602
 E9O  C5   C  CH1    0  -0.444  -2.7067  -12.9930  -52.0533
 E9O  C6   C  C      0   0.470  -3.8218  -13.0251  -50.9830
 E9O  O62  O  OC    -1  -0.555  -3.8231  -13.9002  -50.1083
 E9O  C4   C  CH1    0   0.050  -3.3929  -13.1470  -53.4265
 E9O  O4   O  OH1    0  -0.716  -4.3026  -12.1035  -53.6730
 E9O  O61  O  O      0  -0.621  -4.7062  -12.1324  -51.1242
 E9O  C8   C  CH2    0  -0.414  -0.7575  -13.7156  -50.6135
 E9O  C9   C  CH2    0  -0.431   0.2640  -14.7888  -50.2504
 E9O  C10  C  CH2    0  -0.407   0.9869  -14.4850  -48.9438
 E9O  C1   C  CH2    0  -0.410   2.0090  -15.5447  -48.5553
 E9O  C11  C  CH2    0  -0.409   2.7311  -15.2326  -47.2510
 E9O  C12  C  CH2    0  -0.409   3.7525  -16.2909  -46.8568
 E9O  C13  C  CH2    0  -0.404   4.4846  -15.9690  -45.5606
 E9O  C14  C  CH2    0  -0.417   5.4980  -17.0327  -45.1584
 E9O  C15  C  CH3    0  -0.659   6.2379  -16.6920  -43.8723
 E9O  H1   H  HCH2   0   0.187  -1.8965  -15.2555  -54.2683
 E9O  H2   H  HCH2   0   0.234  -0.6268  -14.3259  -55.0705
 E9O  H3   H  HCH1   0   0.180  -1.8314  -12.2227  -54.5529
 E9O  H4   H  HOH1   0   0.443  -3.6691  -12.7670  -55.9257
 E9O  H5   H  HNH1   0   0.353   0.0436  -14.6608  -52.8882
 E9O  H7   H  HCH1   0   0.177  -2.0471  -15.0146  -51.7395
 E9O  H8   H  HCH1   0   0.222  -2.2480  -11.9939  -52.0376
 E9O  H10  H  HCH1   0   0.166  -3.9122  -14.1246  -53.4328
 E9O  H11  H  HOH1   0   0.437  -4.6592  -11.8884  -52.7759
 E9O  H12  H  HCH2   0   0.199  -0.2473  -12.7576  -50.7628
 E9O  H13  H  HCH2   0   0.226  -1.4321  -13.5842  -49.7677
 E9O  H14  H  HCH2   0   0.207  -0.2429  -15.7568  -50.1686
 E9O  H15  H  HCH2   0   0.206   1.0133  -14.9034  -51.0415
 E9O  H16  H  HCH2   0   0.206   1.4856  -13.5128  -49.0236
 E9O  H17  H  HCH2   0   0.206   0.2491  -14.3801  -48.1405
 E9O  H18  H  HCH2   0   0.205   1.5103  -16.5166  -48.4713
 E9O  H19  H  HCH2   0   0.205   2.7454  -15.6517  -49.3596
 E9O  H20  H  HCH2   0   0.205   3.2307  -14.2613  -47.3370
 E9O  H21  H  HCH2   0   0.205   1.9942  -15.1224  -46.4476
 E9O  H22  H  HCH2   0   0.205   3.2520  -17.2607  -46.7607
 E9O  H23  H  HCH2   0   0.205   4.4837  -16.4077  -47.6644
 E9O  H24  H  HCH2   0   0.204   4.9939  -15.0042  -45.6617
 E9O  H25  H  HCH2   0   0.204   3.7547  -15.8415  -44.7533
 E9O  H26  H  HCH2   0   0.209   4.9870  -17.9937  -45.0446
 E9O  H27  H  HCH2   0   0.208   6.2203  -17.1692  -45.9693
 E9O  H28  H  HCH3   0   0.224   6.9515  -17.4712  -43.6017
 E9O  H29  H  HCH3   0   0.214   6.7927  -15.7572  -43.9723
 E9O  H30  H  HCH3   0   0.214   5.5453  -16.5745  -43.0369

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
 E9O  O3   C3   single  1.410  0.020  1.410
 E9O  C3   C2   single  1.516  0.020  1.516
 E9O  C3   C4   single  1.518  0.020  1.518
 E9O  C2   N    single  1.447  0.020  1.447
 E9O  C4   O4   single  1.406  0.020  1.406
 E9O  C4   C5   single  1.543  0.020  1.543
 E9O  N    C7   single  1.461  0.020  1.461
 E9O  C5   C7   single  1.531  0.020  1.531
 E9O  C5   C6   single  1.546  0.020  1.546
 E9O  C7   C8   single  1.527  0.020  1.527
 E9O  C6   O61  deloc   1.265  0.020  1.265
 E9O  C6   O62  deloc   1.237  0.020  1.237
 E9O  C8   C9   single  1.525  0.020  1.525
 E9O  C9   C10  single  1.524  0.020  1.524
 E9O  C10  C1   single  1.523  0.020  1.523
 E9O  C1   C11  single  1.523  0.020  1.523
 E9O  C11  C12  single  1.523  0.020  1.523
 E9O  C12  C13  single  1.523  0.020  1.523
 E9O  C13  C14  single  1.523  0.020  1.523
 E9O  C14  C15  single  1.522  0.020  1.522
 E9O  C2   H1   single  0.970  0.020  1.090
 E9O  C2   H2   single  0.970  0.020  1.090
 E9O  C3   H3   single  0.970  0.020  1.090
 E9O  O3   H4   single  0.850  0.020  0.980
 E9O  N    H5   single  0.890  0.020  1.040
 E9O  C7   H7   single  0.970  0.020  1.090
 E9O  C5   H8   single  0.970  0.020  1.090
 E9O  C4   H10  single  0.970  0.020  1.090
 E9O  O4   H11  single  0.850  0.020  0.980
 E9O  C8   H12  single  0.970  0.020  1.090
 E9O  C8   H13  single  0.970  0.020  1.090
 E9O  C9   H14  single  0.970  0.020  1.090
 E9O  C9   H15  single  0.970  0.020  1.090
 E9O  C10  H16  single  0.970  0.020  1.090
 E9O  C10  H17  single  0.970  0.020  1.090
 E9O  C1   H18  single  0.970  0.020  1.090
 E9O  C1   H19  single  0.970  0.020  1.090
 E9O  C11  H20  single  0.970  0.020  1.090
 E9O  C11  H21  single  0.970  0.020  1.090
 E9O  C12  H22  single  0.970  0.020  1.090
 E9O  C12  H23  single  0.970  0.020  1.090
 E9O  C13  H24  single  0.970  0.020  1.090
 E9O  C13  H25  single  0.970  0.020  1.090
 E9O  C14  H26  single  0.970  0.020  1.090
 E9O  C14  H27  single  0.970  0.020  1.090
 E9O  C15  H28  single  0.970  0.020  1.090
 E9O  C15  H29  single  0.970  0.020  1.090
 E9O  C15  H30  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
 E9O  H2   C2   H1   107.09  3.000
 E9O  H2   C2   N    108.87  3.000
 E9O  H1   C2   N    113.26  3.000
 E9O  H2   C2   C3   110.07  3.000
 E9O  H1   C2   C3   109.05  3.000
 E9O  N    C2   C3   108.48  3.000
 E9O  H3   C3   C4   108.19  3.000
 E9O  H3   C3   O3   111.07  3.000
 E9O  C4   C3   O3   111.88  3.000
 E9O  H3   C3   C2   107.99  3.000
 E9O  C4   C3   C2   108.92  3.000
 E9O  O3   C3   C2   108.69  3.000
 E9O  H4   O3   C3   107.73  3.000
 E9O  H5   N    C7   109.20  3.000
 E9O  H5   N    C2   108.81  3.000
 E9O  C7   N    C2   113.81  3.000
 E9O  H7   C7   C8   108.44  3.000
 E9O  H7   C7   C5   108.23  3.000
 E9O  C8   C7   C5   111.53  3.000
 E9O  H7   C7   N    110.85  3.000
 E9O  C8   C7   N    108.52  3.000
 E9O  C5   C7   N    109.28  3.000
 E9O  H8   C5   C4   106.80  3.000
 E9O  H8   C5   C6   108.06  3.000
 E9O  C4   C5   C6   107.06  3.000
 E9O  H8   C5   C7   107.56  3.000
 E9O  C6   C5   C7   115.25  3.000
 E9O  C4   C5   C7   111.77  3.000
 E9O  O61  C6   O62  125.27  3.000
 E9O  O62  C6   C5   120.33  3.000
 E9O  O61  C6   C5   114.36  3.000
 E9O  H10  C4   O4   110.54  3.000
 E9O  H10  C4   C5   107.57  3.000
 E9O  O4   C4   C5   111.70  3.000
 E9O  H10  C4   C3   106.90  3.000
 E9O  C5   C4   C3   111.26  3.000
 E9O  O4   C4   C3   108.76  3.000
 E9O  H11  O4   C4   103.63  3.000
 E9O  H13  C8   H12  106.77  3.000
 E9O  H13  C8   C9   108.34  3.000
 E9O  H12  C8   C9   109.62  3.000
 E9O  H13  C8   C7   108.75  3.000
 E9O  H12  C8   C7   108.37  3.000
 E9O  C9   C8   C7   114.71  3.000
 E9O  H15  C9   H14  106.13  3.000
 E9O  H15  C9   C10  108.40  3.000
 E9O  H14  C9   C10  109.36  3.000
 E9O  H15  C9   C8   111.08  3.000
 E9O  H14  C9   C8   109.24  3.000
 E9O  C10  C9   C8   112.43  3.000
 E9O  H17  C10  H16  105.96  3.000
 E9O  H17  C10  C1   109.37  3.000
 E9O  H16  C10  C1   109.31  3.000
 E9O  H17  C10  C9   109.16  3.000
 E9O  H16  C10  C9   109.29  3.000
 E9O  C1   C10  C9   113.48  3.000
 E9O  H19  C1   H18  106.00  3.000
 E9O  H19  C1   C11  109.27  3.000
 E9O  H18  C1   C11  109.38  3.000
 E9O  H19  C1   C10  109.38  3.000
 E9O  H18  C1   C10  109.36  3.000
 E9O  C11  C1   C10  113.20  3.000
 E9O  H21  C11  H20  105.97  3.000
 E9O  H21  C11  C12  109.34  3.000
 E9O  H20  C11  C12  109.31  3.000
 E9O  H21  C11  C1   109.25  3.000
 E9O  H20  C11  C1   109.31  3.000
 E9O  C12  C11  C1   113.40  3.000
 E9O  H23  C12  H22  105.97  3.000
 E9O  H23  C12  C13  109.21  3.000
 E9O  H22  C12  C13  109.39  3.000
 E9O  H23  C12  C11  109.32  3.000
 E9O  H22  C12  C11  109.36  3.000
 E9O  C13  C12  C11  113.32  3.000
 E9O  H25  C13  H24  105.97  3.000
 E9O  H25  C13  C14  109.26  3.000
 E9O  H24  C13  C14  109.27  3.000
 E9O  H25  C13  C12  109.36  3.000
 E9O  H24  C13  C12  109.33  3.000
 E9O  C14  C13  C12  113.39  3.000
 E9O  H27  C14  H26  106.00  3.000
 E9O  H27  C14  C15  109.46  3.000
 E9O  H26  C14  C15  109.61  3.000
 E9O  H27  C14  C13  109.30  3.000
 E9O  H26  C14  C13  109.27  3.000
 E9O  C15  C14  C13  112.96  3.000
 E9O  H30  C15  H29  107.48  3.000
 E9O  H30  C15  H28  107.59  3.000
 E9O  H29  C15  H28  107.58  3.000
 E9O  H30  C15  C14  111.24  3.000
 E9O  H29  C15  C14  111.18  3.000
 E9O  H28  C15  C14  111.58  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
 E9O  Var_01  C7   N    C2   C3     64.89  30.0  1
 E9O  Var_02  C10  C9   C8   C7   -175.68  30.0  3
 E9O  Var_03  C1   C10  C9   C8    179.77  30.0  3
 E9O  Var_04  C11  C1   C10  C9    179.81  30.0  3
 E9O  Var_05  C12  C11  C1   C10   179.89  30.0  3
 E9O  Var_06  C13  C12  C11  C1    179.35  30.0  3
 E9O  Var_07  C14  C13  C12  C11   179.49  30.0  3
 E9O  Var_08  C15  C14  C13  C12   179.19  30.0  3
 E9O  Var_09  H28  C15  C14  C13   179.57  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
 E9O  chir_01  C3  O3  C2  C4  positiv
 E9O  chir_02  C7  N   C8  C5  negativ
 E9O  chir_03  C5  C4  C7  C6  positiv
 E9O  chir_04  C4  O4  C5  C3  positiv

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
 E9O  plan-1  C5   0.020
 E9O  plan-1  C6   0.020
 E9O  plan-1  O62  0.020
 E9O  plan-1  O61  0.020

