# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:29:33 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (3S)-piperidin-3-yl(piperidin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C([C@H]1CCCNC1)N2CCCCC2
#
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
 46H  46H  (3S)-piperidin-3-yl(piperidin-1-yl)methanone  ligand  34  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_46H
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
 46H  C4   C  CH2   0  -0.326   3.7971  -0.6004  -0.4235
 46H  C5   C  CH2   0  -0.276   2.3415   1.1048   0.4589
 46H  C6   C  CH2   0  -0.303  -2.5799   1.1744   0.2748
 46H  N1   N  NT    0  -0.454  -1.3349   0.4676   0.5385
 46H  C7   C  CH2   0  -0.420  -3.4297   0.4077  -0.7308
 46H  C8   C  CH2   0  -0.432  -3.6924  -1.0121  -0.2403
 46H  C9   C  CH2   0  -0.421  -2.3834  -1.7102   0.1148
 46H  C10  C  CH2   0  -0.301  -1.5509  -0.8662   1.0742
 46H  O    O  O     0  -0.506  -0.0884   2.0832  -0.4133
 46H  C    C  C     0   0.595  -0.1531   0.9877   0.1375
 46H  C1   C  CH1   0  -0.420   1.1151   0.1842   0.3707
 46H  N    N  NH1   0  -0.570   3.5924   0.3869   0.6246
 46H  C3   C  CH2   0  -0.428   2.6406  -1.5835  -0.5681
 46H  C2   C  CH2   0  -0.423   1.3221  -0.8411  -0.7553
 46H  H1   H  HCH2  0   0.232   3.9306  -0.0642  -1.3696
 46H  H2   H  HCH2  0   0.245   4.7315  -1.1310  -0.2290
 46H  H3   H  HCH2  0   0.227   2.4141   1.7069  -0.4500
 46H  H4   H  HCH2  0   0.231   2.2281   1.8020   1.2920
 46H  H6   H  HCH2  0   0.261  -2.3599   2.1786  -0.0751
 46H  H7   H  HCH2  0   0.231  -4.3689   0.9412  -0.8919
 46H  H8   H  HCH2  0   0.218  -2.9078   0.3796  -1.6923
 46H  H9   H  HCH2  0   0.209  -4.3351  -0.9759   0.6454
 46H  H10  H  HCH2  0   0.234  -4.2339  -1.5852  -0.9956
 46H  H11  H  HCH2  0   0.233  -2.5762  -2.6825   0.5732
 46H  H12  H  HCH2  0   0.218  -1.8059  -1.8969  -0.7958
 46H  H13  H  HCH2  0   0.251  -0.6064  -1.3559   1.2918
 46H  H14  H  HCH2  0   0.232  -2.0795  -0.7695   2.0288
 46H  H15  H  HCH1  0   0.230   1.0585  -0.3570   1.3207
 46H  H16  H  HNH1  0   0.317   3.5956  -0.0793   1.5249
 46H  H18  H  HCH2  0   0.225   2.8164  -2.2519  -1.4149
 46H  H19  H  HCH2  0   0.202   2.5824  -2.2147   0.3250
 46H  H20  H  HCH2  0   0.240   0.4958  -1.5543  -0.7956
 46H  H21  H  HCH2  0   0.228   1.3277  -0.3179  -1.7178
 46H  H5   H  HCH2  0   0.221  -3.1243   1.2668   1.2211

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
 46H  C3   C2   single  1.525  0.020  1.525
 46H  C3   C4   single  1.525  0.020  1.525
 46H  C2   C1   single  1.537  0.020  1.537
 46H  C4   N    single  1.454  0.020  1.454
 46H  C6   N1   single  1.456  0.020  1.456
 46H  C6   C7   single  1.524  0.020  1.524
 46H  N1   C10  single  1.454  0.020  1.454
 46H  N1   C    single  1.352  0.020  1.352
 46H  C10  C9   single  1.525  0.020  1.525
 46H  C1   C    single  1.519  0.020  1.519
 46H  C1   C5   single  1.536  0.020  1.536
 46H  C    O    double  1.228  0.020  1.228
 46H  C7   C8   single  1.525  0.020  1.525
 46H  N    C5   single  1.452  0.020  1.452
 46H  C8   C9   single  1.525  0.020  1.525
 46H  C4   H1   single  0.970  0.020  1.090
 46H  C4   H2   single  0.970  0.020  1.090
 46H  C5   H3   single  0.970  0.020  1.090
 46H  C5   H4   single  0.970  0.020  1.090
 46H  C6   H5   single  0.970  0.020  1.090
 46H  C6   H6   single  0.970  0.020  1.090
 46H  C7   H7   single  0.970  0.020  1.090
 46H  C7   H8   single  0.970  0.020  1.090
 46H  C8   H9   single  0.970  0.020  1.090
 46H  C8   H10  single  0.970  0.020  1.090
 46H  C9   H11  single  0.970  0.020  1.090
 46H  C9   H12  single  0.970  0.020  1.090
 46H  C10  H13  single  0.970  0.020  1.090
 46H  C10  H14  single  0.970  0.020  1.090
 46H  C1   H15  single  0.970  0.020  1.090
 46H  N    H16  single  0.890  0.020  1.040
 46H  C3   H18  single  0.970  0.020  1.090
 46H  C3   H19  single  0.970  0.020  1.090
 46H  C2   H20  single  0.970  0.020  1.090
 46H  C2   H21  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
 46H  H2   C4   H1   106.69  3.000
 46H  H2   C4   C3   110.65  3.000
 46H  H1   C4   C3   109.03  3.000
 46H  H2   C4   N    108.78  3.000
 46H  H1   C4   N    107.89  3.000
 46H  C3   C4   N    113.54  3.000
 46H  H4   C5   H3   106.84  3.000
 46H  H4   C5   N    108.55  3.000
 46H  H3   C5   N    108.07  3.000
 46H  H4   C5   C1   110.09  3.000
 46H  H3   C5   C1   109.61  3.000
 46H  N    C5   C1   113.46  3.000
 46H  H6   C6   H5   107.52  3.000
 46H  H6   C6   C7   111.45  3.000
 46H  H5   C6   C7   109.60  3.000
 46H  H6   C6   N1   109.51  3.000
 46H  H5   C6   N1   108.02  3.000
 46H  C7   C6   N1   110.63  3.000
 46H  C    N1   C10  126.31  3.000
 46H  C    N1   C6   120.47  3.000
 46H  C10  N1   C6   112.66  3.000
 46H  H8   C7   H7   107.04  3.000
 46H  H8   C7   C8   109.93  3.000
 46H  H7   C7   C8   110.74  3.000
 46H  H8   C7   C6   109.08  3.000
 46H  H7   C7   C6   109.34  3.000
 46H  C8   C7   C6   110.63  3.000
 46H  H10  C8   H9   106.61  3.000
 46H  H10  C8   C9   110.27  3.000
 46H  H9   C8   C9   109.30  3.000
 46H  H10  C8   C7   110.59  3.000
 46H  H9   C8   C7   109.30  3.000
 46H  C9   C8   C7   110.68  3.000
 46H  H12  C9   H11  106.90  3.000
 46H  H12  C9   C10  109.26  3.000
 46H  H11  C9   C10  108.97  3.000
 46H  H12  C9   C8   109.70  3.000
 46H  H11  C9   C8   110.71  3.000
 46H  C10  C9   C8   111.20  3.000
 46H  H14  C10  H13  106.56  3.000
 46H  H14  C10  C9   109.49  3.000
 46H  H13  C10  C9   110.57  3.000
 46H  H14  C10  N1   108.17  3.000
 46H  H13  C10  N1   111.00  3.000
 46H  C9   C10  N1   110.92  3.000
 46H  C1   C    O    119.78  3.000
 46H  O    C    N1   121.49  3.000
 46H  C1   C    N1   118.73  3.000
 46H  H15  C1   C2   108.24  3.000
 46H  H15  C1   C    110.58  3.000
 46H  C2   C1   C    110.66  3.000
 46H  H15  C1   C5   106.72  3.000
 46H  C    C1   C5   110.99  3.000
 46H  C2   C1   C5   109.53  3.000
 46H  H16  N    C5   109.36  3.000
 46H  H16  N    C4   109.10  3.000
 46H  C5   N    C4   112.01  3.000
 46H  H19  C3   H18  106.73  3.000
 46H  H19  C3   C2   109.56  3.000
 46H  H18  C3   C2   109.99  3.000
 46H  H19  C3   C4   109.55  3.000
 46H  H18  C3   C4   110.23  3.000
 46H  C2   C3   C4   110.71  3.000
 46H  H21  C2   H20  106.45  3.000
 46H  H21  C2   C3   109.63  3.000
 46H  H20  C2   C3   109.93  3.000
 46H  H21  C2   C1   109.01  3.000
 46H  H20  C2   C1   111.14  3.000
 46H  C3   C2   C1   110.57  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
 46H  CONST_01  C1   C    N1   C6   180.00   0.0  0
 46H  CONST_02  C1   C    N1   C10    0.00   0.0  0
 46H  CONST_03  O    C    N1   C6     0.00   0.0  0
 46H  CONST_04  O    C    N1   C10  180.00   0.0  0
 46H  Var_01    C1   C2   C3   C4   -53.43  30.0  1
 46H  Var_02    C1   C5   N    C4    55.23  30.0  1
 46H  Var_03    C3   C4   N    C5   -54.37  30.0  1
 46H  Var_04    C9   C10  N1   C6    58.55  30.0  1
 46H  Var_05    C9   C8   C7   C6   -53.04  30.0  1
 46H  Var_06    C8   C7   C6   N1    56.21  30.0  1
 46H  Var_07    C8   C9   C10  N1   -54.36  30.0  1
 46H  Var_08    C10  N1   C6   C7   -59.59  30.0  1
 46H  Var_09    C10  C9   C8   C7    52.20  30.0  1
 46H  Var_10    C2   C3   C4   N     53.92  30.0  1

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
 46H  chir_01  C1  C2  C  C5  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
 46H  plan-1  C6   0.020
 46H  plan-1  N1   0.020
 46H  plan-1  C10  0.020
 46H  plan-1  O    0.020
 46H  plan-1  C    0.020
 46H  plan-1  C1   0.020

