# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 23:06:04 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-methyl-~{N}-octyl-piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCNC(=O)N1CCC(C)CC1
#
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
 UBN  UBN  "4-methyl-~{N}-[(~{E})-oct-5-enyl]piperidine-1-carboxamide"  ligand  48  18  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UBN
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
 UBN  C4   C  CH2   0  -0.407  -18.4480  -31.4673   0.2054
 UBN  C14  C  CH2   0  -0.420   -9.2687  -27.1375   2.7707
 UBN  C5   C  CH2   0  -0.421  -17.0637  -31.0121   0.6494
 UBN  C6   C  CH2   0  -0.429  -16.9917  -30.7212   2.1447
 UBN  C11  C  CH2   0  -0.412  -10.3097  -27.9125   4.8644
 UBN  C7   C  CH2   0  -0.447  -15.5968  -30.3806   2.6584
 UBN  C8   C  CH2   0  -0.253  -14.9983  -29.1452   1.9981
 UBN  C9   C  C     0   0.726  -12.6974  -28.2593   2.0116
 UBN  C10  C  CH2   0  -0.314  -11.6881  -27.7809   4.2308
 UBN  C12  C  CH1   0  -0.242   -9.3028  -26.9323   4.2792
 UBN  C13  C  CH3   0  -0.650   -7.9277  -27.0890   4.9105
 UBN  N1   N  NH1   0  -0.691  -13.7891  -28.7266   2.6725
 UBN  N2   N  NT    0  -0.499  -11.6254  -27.8670   2.7800
 UBN  C3   C  CH2   0  -0.404  -18.5515  -31.7063  -1.2951
 UBN  C1   C  CH3   0  -0.659  -20.0267  -32.4034  -3.2391
 UBN  C2   C  CH2   0  -0.417  -19.9331  -32.1716  -1.7377
 UBN  O1   O  O     0  -0.544  -12.6551  -28.2238   0.7845
 UBN  C15  C  CH2   0  -0.284  -10.6494  -26.9827   2.1560
 UBN  H1   H  HCH2  0   0.206  -19.1886  -30.7167   0.5031
 UBN  H2   H  HCH2  0   0.215   -8.8748  -28.1353   2.5484
 UBN  H3   H  HCH2  0   0.232   -8.5968  -26.4163   2.2982
 UBN  H4   H  HCH2  0   0.208  -16.3252  -31.7796   0.3919
 UBN  H5   H  HCH2  0   0.214  -16.7842  -30.1197   0.0802
 UBN  H6   H  HCH2  0   0.212  -17.6772  -29.9016   2.3854
 UBN  H7   H  HCH2  0   0.222  -17.3603  -31.5922   2.6946
 UBN  H8   H  HCH2  0   0.236  -10.4157  -27.7642   5.9418
 UBN  H9   H  HCH2  0   0.218   -9.9435  -28.9343   4.7182
 UBN  H10  H  HCH2  0   0.220  -14.9242  -31.2303   2.5078
 UBN  H11  H  HCH2  0   0.226  -15.6528  -30.2179   3.7392
 UBN  H12  H  HCH2  0   0.243  -14.7566  -29.3479   0.9574
 UBN  H13  H  HCH2  0   0.219  -15.7369  -28.3341   1.9995
 UBN  H14  H  HCH2  0   0.225  -12.1478  -26.8340   4.5453
 UBN  H15  H  HCH2  0   0.245  -12.3000  -28.5900   4.6275
 UBN  H16  H  HCH1  0   0.213   -9.6638  -25.9138   4.4738
 UBN  H17  H  HCH3  0   0.225   -7.9635  -26.9198   5.9879
 UBN  H18  H  HCH3  0   0.214   -7.5366  -28.0952   4.7446
 UBN  H19  H  HCH3  0   0.225   -7.2139  -26.3812   4.4857
 UBN  H20  H  HNH1  0   0.397  -13.8922  -28.5454   3.6559
 UBN  H21  H  HCH2  0   0.205  -17.8044  -32.4480  -1.5983
 UBN  H22  H  HCH3  0   0.224  -21.0236  -32.7336  -3.5335
 UBN  H23  H  HCH3  0   0.215  -19.8034  -31.4901  -3.7937
 UBN  H24  H  HCH3  0   0.215  -19.3165  -33.1656  -3.5651
 UBN  H25  H  HCH2  0   0.209  -20.6781  -31.4296  -1.4337
 UBN  H26  H  HCH2  0   0.209  -20.1914  -33.0936  -1.2076
 UBN  H27  H  HCH2  0   0.212  -10.9728  -25.9376   2.2618
 UBN  H28  H  HCH2  0   0.256  -10.6093  -27.1996   1.0926
 UBN  H29  H  HCH2  0   0.206  -18.7169  -32.3854   0.7393
 UBN  H30  H  HCH2  0   0.205  -18.2933  -30.7837  -1.8267

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
 UBN  C1   C2   single  1.522  0.020  1.522
 UBN  C2   C3   single  1.524  0.020  1.524
 UBN  C3   C4   single  1.523  0.020  1.523
 UBN  C4   C5   single  1.523  0.020  1.523
 UBN  C5   C6   single  1.525  0.020  1.525
 UBN  O1   C9   double  1.228  0.020  1.228
 UBN  C8   C7   single  1.523  0.020  1.523
 UBN  C8   N1   single  1.446  0.020  1.446
 UBN  C9   N1   single  1.359  0.020  1.359
 UBN  C9   N2   single  1.376  0.020  1.376
 UBN  C6   C7   single  1.525  0.020  1.525
 UBN  C15  C14  single  1.519  0.020  1.519
 UBN  C15  N2   single  1.457  0.020  1.457
 UBN  C14  C12  single  1.523  0.020  1.523
 UBN  N2   C10  single  1.455  0.020  1.455
 UBN  C10  C11  single  1.523  0.020  1.523
 UBN  C12  C11  single  1.522  0.020  1.522
 UBN  C12  C13  single  1.521  0.020  1.521
 UBN  C4   H1   single  0.970  0.020  1.090
 UBN  C14  H2   single  0.970  0.020  1.090
 UBN  C14  H3   single  0.970  0.020  1.090
 UBN  C5   H4   single  0.970  0.020  1.090
 UBN  C5   H5   single  0.970  0.020  1.090
 UBN  C6   H6   single  0.970  0.020  1.090
 UBN  C6   H7   single  0.970  0.020  1.090
 UBN  C11  H8   single  0.970  0.020  1.090
 UBN  C11  H9   single  0.970  0.020  1.090
 UBN  C7   H10  single  0.970  0.020  1.090
 UBN  C7   H11  single  0.970  0.020  1.090
 UBN  C8   H12  single  0.970  0.020  1.090
 UBN  C8   H13  single  0.970  0.020  1.090
 UBN  C10  H14  single  0.970  0.020  1.090
 UBN  C10  H15  single  0.970  0.020  1.090
 UBN  C12  H16  single  0.970  0.020  1.090
 UBN  C13  H17  single  0.970  0.020  1.090
 UBN  C13  H18  single  0.970  0.020  1.090
 UBN  C13  H19  single  0.970  0.020  1.090
 UBN  N1   H20  single  0.860  0.020  1.020
 UBN  C3   H21  single  0.970  0.020  1.090
 UBN  C1   H22  single  0.970  0.020  1.090
 UBN  C1   H23  single  0.970  0.020  1.090
 UBN  C1   H24  single  0.970  0.020  1.090
 UBN  C2   H25  single  0.970  0.020  1.090
 UBN  C2   H26  single  0.970  0.020  1.090
 UBN  C15  H27  single  0.970  0.020  1.090
 UBN  C15  H28  single  0.970  0.020  1.090
 UBN  C4   H29  single  0.970  0.020  1.090
 UBN  C3   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
 UBN  H29  C4   H1   106.00  3.000
 UBN  H29  C4   C3   109.39  3.000
 UBN  H1   C4   C3   109.23  3.000
 UBN  H29  C4   C5   109.35  3.000
 UBN  H1   C4   C5   109.29  3.000
 UBN  C3   C4   C5   113.32  3.000
 UBN  H3   C14  H2   106.99  3.000
 UBN  H3   C14  C15  108.46  3.000
 UBN  H2   C14  C15  109.72  3.000
 UBN  H3   C14  C12  110.67  3.000
 UBN  H2   C14  C12  109.38  3.000
 UBN  C15  C14  C12  111.52  3.000
 UBN  H5   C5   H4   106.06  3.000
 UBN  H5   C5   C6   110.01  3.000
 UBN  H4   C5   C6   109.40  3.000
 UBN  H5   C5   C4   108.91  3.000
 UBN  H4   C5   C4   109.55  3.000
 UBN  C6   C5   C4   112.69  3.000
 UBN  H7   C6   H6   105.93  3.000
 UBN  H7   C6   C7   108.46  3.000
 UBN  H6   C6   C7   109.35  3.000
 UBN  H7   C6   C5   108.96  3.000
 UBN  H6   C6   C5   109.19  3.000
 UBN  C7   C6   C5   114.59  3.000
 UBN  H9   C11  H8   106.90  3.000
 UBN  H9   C11  C12  109.17  3.000
 UBN  H8   C11  C12  110.84  3.000
 UBN  H9   C11  C10  109.14  3.000
 UBN  H8   C11  C10  108.10  3.000
 UBN  C12  C11  C10  112.53  3.000
 UBN  H11  C7   H10  106.43  3.000
 UBN  H11  C7   C8   109.12  3.000
 UBN  H10  C7   C8   109.19  3.000
 UBN  H11  C7   C6   108.61  3.000
 UBN  H10  C7   C6   110.03  3.000
 UBN  C8   C7   C6   113.23  3.000
 UBN  H13  C8   H12  106.78  3.000
 UBN  H13  C8   N1   110.38  3.000
 UBN  H12  C8   N1   108.32  3.000
 UBN  H13  C8   C7   109.55  3.000
 UBN  H12  C8   C7   110.55  3.000
 UBN  N1   C8   C7   111.17  3.000
 UBN  O1   C9   N2   121.52  3.000
 UBN  N2   C9   N1   116.89  3.000
 UBN  O1   C9   N1   121.56  3.000
 UBN  H15  C10  H14  107.52  3.000
 UBN  H15  C10  N2   110.09  3.000
 UBN  H14  C10  N2   110.77  3.000
 UBN  H15  C10  C11  107.02  3.000
 UBN  H14  C10  C11  109.52  3.000
 UBN  N2   C10  C11  111.76  3.000
 UBN  H16  C12  C13  108.61  3.000
 UBN  H16  C12  C11  108.16  3.000
 UBN  C13  C12  C11  111.84  3.000
 UBN  H16  C12  C14  107.94  3.000
 UBN  C13  C12  C14  112.15  3.000
 UBN  C11  C12  C14  107.99  3.000
 UBN  H19  C13  H18  107.70  3.000
 UBN  H19  C13  H17  107.78  3.000
 UBN  H18  C13  H17  107.73  3.000
 UBN  H19  C13  C12  111.28  3.000
 UBN  H18  C13  C12  110.83  3.000
 UBN  H17  C13  C12  111.36  3.000
 UBN  H20  N1   C9   119.74  3.000
 UBN  H20  N1   C8   115.00  3.000
 UBN  C9   N1   C8   122.98  3.000
 UBN  C15  N2   C10  114.83  3.000
 UBN  C10  N2   C9   122.70  3.000
 UBN  C15  N2   C9   117.11  3.000
 UBN  H30  C3   H21  105.97  3.000
 UBN  H30  C3   C2   109.26  3.000
 UBN  H21  C3   C2   109.35  3.000
 UBN  H30  C3   C4   109.26  3.000
 UBN  H21  C3   C4   109.42  3.000
 UBN  C2   C3   C4   113.32  3.000
 UBN  H24  C1   H23  107.41  3.000
 UBN  H24  C1   H22  107.62  3.000
 UBN  H23  C1   H22  107.65  3.000
 UBN  H24  C1   C2   111.16  3.000
 UBN  H23  C1   C2   111.17  3.000
 UBN  H22  C1   C2   111.63  3.000
 UBN  H26  C2   H25  106.02  3.000
 UBN  H26  C2   C1   109.57  3.000
 UBN  H25  C2   C1   109.59  3.000
 UBN  H26  C2   C3   109.30  3.000
 UBN  H25  C2   C3   109.24  3.000
 UBN  C1   C2   C3   112.88  3.000
 UBN  H28  C15  H27  107.16  3.000
 UBN  H28  C15  N2   108.83  3.000
 UBN  H27  C15  N2   109.80  3.000
 UBN  H28  C15  C14  110.02  3.000
 UBN  H27  C15  C14  108.98  3.000
 UBN  N2   C15  C14  111.94  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
 UBN  CONST_01  O1   C9   N2   C10   180.00   0.0  0
 UBN  CONST_03  N1   C9   N2   C10     0.00   0.0  0
 UBN  CONST_05  N2   C9   N1   C8    180.00   0.0  0
 UBN  CONST_07  O1   C9   N1   C8      0.00   0.0  0
 UBN  CONST_08  H20  N1   C9   O1    180.00   0.0  0
 UBN  Var_01    C10  N2   C15  C14    52.26  30.0  1
 UBN  Var_02    C15  N2   C10  C11   -50.92  30.0  1
 UBN  Var_03    N2   C15  C14  C12   -55.05  30.0  1
 UBN  Var_04    N2   C10  C11  C12    53.03  30.0  1
 UBN  Var_05    C9   N2   C15  C14  -152.84  30.0  1
 UBN  Var_06    C9   N2   C10  C11   155.75  30.0  1
 UBN  Var_07    H27  C15  N2   C10   -68.92  30.0  1
 UBN  Var_08    H28  C15  N2   C10   174.08  30.0  1
 UBN  Var_09    H27  C15  C14  C12    66.60  30.0  1
 UBN  Var_10    H28  C15  C14  C12  -176.18  30.0  1
 UBN  Var_11    H14  C10  C11  C12   -70.10  30.0  1
 UBN  Var_12    H15  C10  C11  C12   173.63  30.0  1
 UBN  Var_13    H2   C14  C15  N2     66.30  30.0  1
 UBN  Var_14    H3   C14  C15  N2   -177.16  30.0  1
 UBN  Var_15    H8   C11  C10  N2    175.77  30.0  1
 UBN  Var_16    H9   C11  C10  N2    -68.31  30.0  1
 UBN  Var_17    H14  C10  N2   C15    71.51  30.0  1
 UBN  Var_18    H15  C10  N2   C15  -169.71  30.0  1
 UBN  Var_19    H27  C15  N2   C9     85.98  30.0  1
 UBN  Var_20    H28  C15  N2   C9    -31.02  30.0  1
 UBN  Var_21    H14  C10  N2   C9    -81.83  30.0  1
 UBN  Var_22    H15  C10  N2   C9     36.95  30.0  1
 UBN  Var_23    C1   C2   C3   C4    179.83  30.0  1
 UBN  Var_24    C7   C6   C5   C4    174.88  30.0  3
 UBN  Var_25    C2   C3   C4   C5    179.57  30.0  1
 UBN  Var_26    C8   C7   C6   C5     60.15  30.0  3
 UBN  Var_27    C3   C4   C5   C6    177.61  30.0  1
 UBN  Var_28    N1   C8   C7   C6    170.01  30.0  1
 UBN  Var_29    C9   N1   C8   C7    141.09  30.0  3
 UBN  Var_30    H25  C2   C3   C4     57.63  30.0  1
 UBN  Var_31    H26  C2   C3   C4    -57.96  30.0  1
 UBN  Var_32    H6   C6   C5   C4    -62.09  30.0  3
 UBN  Var_33    H7   C6   C5   C4     53.18  30.0  3
 UBN  Var_34    H21  C3   C4   C5     57.26  30.0  1
 UBN  Var_35    H30  C3   C4   C5    -58.35  30.0  1
 UBN  Var_36    H10  C7   C6   C5    -62.34  30.0  3
 UBN  Var_37    H11  C7   C6   C5   -178.47  30.0  3
 UBN  Var_38    H1   C4   C5   C6     55.55  30.0  1
 UBN  Var_39    H29  C4   C5   C6    -60.08  30.0  1
 UBN  Var_40    H12  C8   C7   C6    -69.65  30.0  1
 UBN  Var_41    H13  C8   C7   C6     47.74  30.0  1
 UBN  Var_42    H20  N1   C8   C7    -56.15  30.0  3
 UBN  Var_43    H4   C5   C6   C7     52.75  30.0  1
 UBN  Var_44    H5   C5   C6   C7    -63.38  30.0  1
 UBN  Var_45    H6   C6   C7   C8    -62.79  30.0  1
 UBN  Var_46    H7   C6   C7   C8   -177.87  30.0  1
 UBN  Var_47    H12  C8   N1   C9     19.44  30.0  1
 UBN  Var_48    H13  C8   N1   C9    -97.13  30.0  1
 UBN  Var_49    H10  C7   C8   N1    -67.03  30.0  3
 UBN  Var_50    H11  C7   C8   N1     48.92  30.0  3
 UBN  Var_51    H22  C1   C2   C3   -179.88  30.0  3
 UBN  Var_52    H23  C1   C2   C3    -59.67  30.0  3
 UBN  Var_53    H24  C1   C2   C3     59.94  30.0  3
 UBN  Var_54    H4   C5   C4   C3    -60.35  30.0  3
 UBN  Var_55    H5   C5   C4   C3     55.24  30.0  3
 UBN  Var_56    H21  C3   C2   C1    -57.82  30.0  3
 UBN  Var_57    H30  C3   C2   C1     57.75  30.0  3
 UBN  Var_58    H1   C4   C3   C2    -58.34  30.0  3
 UBN  Var_59    H29  C4   C3   C2     57.28  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
 UBN  chir_01  C12  C14  C11  C13  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
 UBN  plan-1  C8   0.020
 UBN  plan-1  C9   0.020
 UBN  plan-1  C10  0.020
 UBN  plan-1  N1   0.020
 UBN  plan-1  N2   0.020
 UBN  plan-1  O1   0.020
 UBN  plan-1  C15  0.020
 UBN  plan-1  H20  0.020

