# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 01:39:16 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-methyl-~{N}-pentyl-piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCNC(=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
 UB5  UB5  "4-methyl-~{N}-pentyl-piperidine-1-carboxamide"
  ligand  39  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UB5
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
 UB5  C4   C  CH2   0  -0.465  -15.0958  -29.7728   2.5092
 UB5  C5   C  CH2   0  -0.232  -14.0255  -29.1868   1.6000
 UB5  C6   C  C     0   0.727  -11.9842  -27.8509   1.8264
 UB5  C11  C  CH2   0  -0.461   -8.5676  -27.2103   2.8411
 UB5  C7   C  CH2   0  -0.308  -10.9845  -27.7033   4.0889
 UB5  C8   C  CH2   0  -0.460  -10.0703  -26.7155   4.7955
 UB5  C9   C  CH1   0  -0.215   -8.6130  -26.8232   4.3301
 UB5  C10  C  CH3   0  -0.664   -7.8661  -25.5242   4.6018
 UB5  C12  C  CH2   0  -0.284   -9.8202  -26.7700   2.0999
 UB5  N1   N  NH1   0  -0.695  -12.9440  -28.6396   2.3907
 UB5  N2   N  NT    0  -0.491  -10.9814  -27.4494   2.6546
 UB5  C3   C  CH2   0  -0.420  -16.2415  -30.4290   1.7455
 UB5  C1   C  CH3   0  -0.657  -18.2569  -30.1418   0.2384
 UB5  C2   C  CH2   0  -0.427  -17.0548  -29.4680   0.8851
 UB5  O1   O  O     0  -0.552  -12.0421  -27.5060   0.6474
 UB5  H1   H  HCH2  0   0.228  -14.6375  -30.5172   3.1686
 UB5  H2   H  HCH2  0   0.222  -15.4900  -28.9842   3.1571
 UB5  H3   H  HCH2  0   0.232  -14.4466  -28.3897   0.9876
 UB5  H4   H  HCH2  0   0.211  -13.6697  -29.9615   0.9092
 UB5  H5   H  HCH2  0   0.235   -8.4688  -28.2934   2.7326
 UB5  H6   H  HCH2  0   0.239   -7.6916  -26.7727   2.3565
 UB5  H7   H  HCH2  0   0.247  -11.9982  -27.5876   4.4777
 UB5  H8   H  HCH2  0   0.229  -10.6663  -28.7297   4.3147
 UB5  H9   H  HCH2  0   0.249  -10.1392  -26.8785   5.8727
 UB5  H10  H  HCH2  0   0.229  -10.4462  -25.7033   4.6143
 UB5  H11  H  HCH1  0   0.229   -8.1309  -27.6208   4.9030
 UB5  H12  H  HCH3  0   0.225   -7.9396  -25.2337   5.6516
 UB5  H13  H  HCH3  0   0.226   -6.8073  -25.6175   4.3557
 UB5  H14  H  HCH3  0   0.217   -8.2755  -24.7057   4.0044
 UB5  H15  H  HCH2  0   0.221   -9.9339  -25.6810   2.1594
 UB5  H16  H  HCH2  0   0.250   -9.7361  -27.0189   1.0444
 UB5  H17  H  HNH1  0   0.396  -12.7139  -29.1545   3.2253
 UB5  H18  H  HCH2  0   0.222  -16.9095  -30.9081   2.4675
 UB5  H19  H  HCH2  0   0.212  -15.8494  -31.2365   1.1177
 UB5  H20  H  HCH3  0   0.226  -18.8185  -29.4459  -0.3858
 UB5  H21  H  HCH3  0   0.215  -17.9477  -30.9768  -0.3930
 UB5  H22  H  HCH3  0   0.215  -18.9406  -30.5363   0.9924
 UB5  H23  H  HCH2  0   0.218  -16.4233  -29.0351   0.1048
 UB5  H24  H  HCH2  0   0.211  -17.3918  -28.6289   1.5022

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
 UB5  C1   C2   single  1.522  0.020  1.522
 UB5  C2   C3   single  1.525  0.020  1.525
 UB5  O1   C6   double  1.230  0.020  1.230
 UB5  C5   N1   single  1.447  0.020  1.447
 UB5  C5   C4   single  1.522  0.020  1.522
 UB5  C6   N1   single  1.364  0.020  1.364
 UB5  C6   N2   single  1.361  0.020  1.361
 UB5  C3   C4   single  1.525  0.020  1.525
 UB5  C12  C11  single  1.521  0.020  1.521
 UB5  C12  N2   single  1.455  0.020  1.455
 UB5  C11  C9   single  1.539  0.020  1.539
 UB5  N2   C7   single  1.457  0.020  1.457
 UB5  C9   C10  single  1.523  0.020  1.523
 UB5  C9   C8   single  1.534  0.020  1.534
 UB5  C7   C8   single  1.520  0.020  1.520
 UB5  C4   H1   single  0.970  0.020  1.090
 UB5  C4   H2   single  0.970  0.020  1.090
 UB5  C5   H3   single  0.970  0.020  1.090
 UB5  C5   H4   single  0.970  0.020  1.090
 UB5  C11  H5   single  0.970  0.020  1.090
 UB5  C11  H6   single  0.970  0.020  1.090
 UB5  C7   H7   single  0.970  0.020  1.090
 UB5  C7   H8   single  0.970  0.020  1.090
 UB5  C8   H9   single  0.970  0.020  1.090
 UB5  C8   H10  single  0.970  0.020  1.090
 UB5  C9   H11  single  0.970  0.020  1.090
 UB5  C10  H12  single  0.970  0.020  1.090
 UB5  C10  H13  single  0.970  0.020  1.090
 UB5  C10  H14  single  0.970  0.020  1.090
 UB5  C12  H15  single  0.970  0.020  1.090
 UB5  C12  H16  single  0.970  0.020  1.090
 UB5  N1   H17  single  0.890  0.020  1.040
 UB5  C3   H18  single  0.970  0.020  1.090
 UB5  C3   H19  single  0.970  0.020  1.090
 UB5  C1   H20  single  0.970  0.020  1.090
 UB5  C1   H21  single  0.970  0.020  1.090
 UB5  C1   H22  single  0.970  0.020  1.090
 UB5  C2   H23  single  0.970  0.020  1.090
 UB5  C2   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
 UB5  H2   C4   H1   106.51  3.000
 UB5  H2   C4   C3   109.63  3.000
 UB5  H1   C4   C3   108.87  3.000
 UB5  H2   C4   C5   109.25  3.000
 UB5  H1   C4   C5   109.10  3.000
 UB5  C3   C4   C5   113.26  3.000
 UB5  H4   C5   H3   106.74  3.000
 UB5  H4   C5   N1   111.63  3.000
 UB5  H3   C5   N1   108.62  3.000
 UB5  H4   C5   C4   109.41  3.000
 UB5  H3   C5   C4   110.22  3.000
 UB5  N1   C5   C4   110.17  3.000
 UB5  O1   C6   N2   122.36  3.000
 UB5  N2   C6   N1   115.92  3.000
 UB5  O1   C6   N1   121.70  3.000
 UB5  H6   C11  H5   106.28  3.000
 UB5  H6   C11  C12  109.17  3.000
 UB5  H5   C11  C12  108.24  3.000
 UB5  H6   C11  C9   110.61  3.000
 UB5  H5   C11  C9   110.36  3.000
 UB5  C12  C11  C9   111.99  3.000
 UB5  H8   C7   H7   107.15  3.000
 UB5  H8   C7   N2   111.40  3.000
 UB5  H7   C7   N2   109.52  3.000
 UB5  H8   C7   C8   109.73  3.000
 UB5  H7   C7   C8   108.90  3.000
 UB5  N2   C7   C8   110.07  3.000
 UB5  H10  C8   H9   106.24  3.000
 UB5  H10  C8   C9   109.93  3.000
 UB5  H9   C8   C9   110.43  3.000
 UB5  H10  C8   C7   108.50  3.000
 UB5  H9   C8   C7   108.89  3.000
 UB5  C9   C8   C7   112.62  3.000
 UB5  H11  C9   C10  108.20  3.000
 UB5  H11  C9   C8   108.12  3.000
 UB5  C10  C9   C8   110.61  3.000
 UB5  H11  C9   C11  108.07  3.000
 UB5  C8   C9   C11  109.84  3.000
 UB5  C10  C9   C11  111.88  3.000
 UB5  H14  C10  H13  107.71  3.000
 UB5  H14  C10  H12  107.53  3.000
 UB5  H13  C10  H12  107.76  3.000
 UB5  H14  C10  C9   110.95  3.000
 UB5  H13  C10  C9   111.27  3.000
 UB5  H12  C10  C9   111.44  3.000
 UB5  H16  C12  H15  106.73  3.000
 UB5  H16  C12  N2   108.95  3.000
 UB5  H15  C12  N2   111.11  3.000
 UB5  H16  C12  C11  110.06  3.000
 UB5  H15  C12  C11  110.28  3.000
 UB5  N2   C12  C11  109.66  3.000
 UB5  H17  N1   C6   118.52  3.000
 UB5  H17  N1   C5   115.48  3.000
 UB5  C6   N1   C5   121.22  3.000
 UB5  C12  N2   C7   117.28  3.000
 UB5  C7   N2   C6   123.10  3.000
 UB5  C12  N2   C6   119.58  3.000
 UB5  H19  C3   H18  105.89  3.000
 UB5  H19  C3   C2   109.40  3.000
 UB5  H18  C3   C2   108.82  3.000
 UB5  H19  C3   C4   109.58  3.000
 UB5  H18  C3   C4   108.46  3.000
 UB5  C2   C3   C4   114.33  3.000
 UB5  H22  C1   H21  107.49  3.000
 UB5  H22  C1   H20  107.66  3.000
 UB5  H21  C1   H20  107.64  3.000
 UB5  H22  C1   C2   111.17  3.000
 UB5  H21  C1   C2   111.14  3.000
 UB5  H20  C1   C2   111.56  3.000
 UB5  H24  C2   H23  106.06  3.000
 UB5  H24  C2   C1   109.61  3.000
 UB5  H23  C2   C1   109.16  3.000
 UB5  H24  C2   C3   109.22  3.000
 UB5  H23  C2   C3   110.13  3.000
 UB5  C1   C2   C3   112.46  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
 UB5  CONST_01  O1   C6   N2   C7    180.00   0.0  0
 UB5  CONST_02  O1   C6   N2   C12     0.00   0.0  0
 UB5  CONST_03  N1   C6   N2   C7      0.00   0.0  0
 UB5  CONST_04  N1   C6   N2   C12   180.00   0.0  0
 UB5  CONST_05  N2   C6   N1   C5    180.00   0.0  0
 UB5  CONST_07  O1   C6   N1   C5      0.00   0.0  0
 UB5  Var_01    C7   N2   C12  C11    35.32  30.0  1
 UB5  Var_02    C12  N2   C7   C8     23.87  30.0  1
 UB5  Var_03    N2   C12  C11  C9    -62.68  30.0  1
 UB5  Var_04    N2   C7   C8   C9    -60.97  30.0  1
 UB5  Var_05    C11  C12  N2   C6   -142.76  30.0  1
 UB5  Var_06    C8   C7   N2   C6   -158.12  30.0  1
 UB5  Var_07    H15  C12  N2   C7    -86.85  30.0  1
 UB5  Var_08    H16  C12  N2   C7    155.84  30.0  1
 UB5  Var_09    H15  C12  C11  C9     59.99  30.0  1
 UB5  Var_10    H16  C12  C11  C9    177.48  30.0  1
 UB5  Var_11    H7   C7   C8   C9    178.95  30.0  1
 UB5  Var_12    H8   C7   C8   C9     61.96  30.0  1
 UB5  Var_13    H7   C7   N2   C12   143.57  30.0  1
 UB5  Var_14    H8   C7   N2   C12   -98.08  30.0  1
 UB5  Var_15    H5   C11  C12  N2     59.21  30.0  1
 UB5  Var_16    H6   C11  C12  N2    174.49  30.0  1
 UB5  Var_17    H9   C8   C7   N2    176.19  30.0  1
 UB5  Var_18    H10  C8   C7   N2     60.96  30.0  1
 UB5  Var_19    H15  C12  N2   C6     95.07  30.0  1
 UB5  Var_20    H16  C12  N2   C6    -22.24  30.0  1
 UB5  Var_21    H7   C7   N2   C6    -38.43  30.0  1
 UB5  Var_22    H8   C7   N2   C6     79.92  30.0  1
 UB5  Var_23    C6   N1   C5   C4   -168.20  30.0  3
 UB5  Var_24    C1   C2   C3   C4   -175.04  30.0  1
 UB5  Var_25    C2   C3   C4   C5    -63.97  30.0  1
 UB5  Var_26    C3   C4   C5   N1   -177.30  30.0  3
 UB5  Var_27    H17  N1   C5   C4     36.69  30.0  3
 UB5  Var_28    H23  C2   C3   C4     62.97  30.0  1
 UB5  Var_29    H24  C2   C3   C4    -53.12  30.0  1
 UB5  Var_30    H18  C3   C4   C5    174.41  30.0  1
 UB5  Var_31    H19  C3   C4   C5     59.25  30.0  1
 UB5  Var_32    H3   C5   N1   C6    -47.38  30.0  1
 UB5  Var_33    H4   C5   N1   C6     70.04  30.0  1
 UB5  Var_34    H1   C4   C5   N1    -55.87  30.0  3
 UB5  Var_35    H2   C4   C5   N1     60.19  30.0  3
 UB5  Var_36    H20  C1   C2   C3   -179.08  30.0  3
 UB5  Var_37    H21  C1   C2   C3    -58.95  30.0  3
 UB5  Var_38    H22  C1   C2   C3     60.73  30.0  3
 UB5  Var_39    H3   C5   C4   C3     62.85  30.0  1
 UB5  Var_40    H4   C5   C4   C3    -54.23  30.0  1
 UB5  Var_41    H18  C3   C2   C1    -53.62  30.0  3
 UB5  Var_42    H19  C3   C2   C1     61.65  30.0  3
 UB5  Var_43    H1   C4   C3   C2    174.47  30.0  3
 UB5  Var_44    H2   C4   C3   C2     58.32  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
 UB5  chir_01  C9  C11  C10  C8  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
 UB5  plan-1  C5   0.020
 UB5  plan-1  C6   0.020
 UB5  plan-1  C7   0.020
 UB5  plan-1  C12  0.020
 UB5  plan-1  N1   0.020
 UB5  plan-1  N2   0.020
 UB5  plan-1  O1   0.020
 UB5  plan-1  H17  0.020

