# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:41:30 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (3R)-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
 46J  46J  (3R)-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 GRAND
;

data_comp_46J
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
 46J  C1   C  CH1   0  -0.412  -1.0908  -0.0657   0.2001
 46J  C2   C  CH2   0  -0.413  -2.0802  -0.9248   0.9829
 46J  N1   N  NT    0  -0.454   1.2770  -0.1426  -0.4880
 46J  C3   C  CH2   0  -0.438  -3.3608  -0.1406   1.2495
 46J  C    C  C     0   0.581   0.1613  -0.8421  -0.1796
 46J  C10  C  CH2   0  -0.323   1.4835   1.2834  -0.2890
 46J  C9   C  CH2   0  -0.425   2.5089   1.5265   0.8135
 46J  C8   C  CH2   0  -0.445   3.8147   0.7941   0.5213
 46J  C7   C  CH2   0  -0.433   3.5578  -0.6807   0.2279
 46J  C6   C  CH2   0  -0.315   2.5016  -0.8370  -0.8590
 46J  C5   C  CH2   0  -0.270  -1.7599   0.4748  -1.0710
 46J  N    N  NH1   0  -0.597  -2.9547   1.2181  -0.7250
 46J  C4   C  CH2   0  -0.291  -3.9402   0.3898  -0.0523
 46J  H1   H  HCH1  0   0.253  -0.8333   0.7900   0.8302
 46J  H2   H  HCH2  0   0.218  -2.3240  -1.8244   0.4127
 46J  H3   H  HCH2  0   0.236  -1.6332  -1.2570   1.9225
 46J  H4   H  HCH2  0   0.231  -4.0943  -0.7791   1.7466
 46J  H5   H  HCH2  0   0.214  -3.1582   0.6961   1.9252
 46J  H6   H  HCH2  0   0.241   1.8405   1.7141  -1.2306
 46J  H7   H  HCH2  0   0.265   0.5512   1.7878  -0.0535
 46J  H8   H  HCH2  0   0.238   2.6825   2.6006   0.9075
 46J  H9   H  HCH2  0   0.223   2.0915   1.1838   1.7656
 46J  H10  H  HCH2  0   0.217   4.2996   1.2552  -0.3458
 46J  H11  H  HCH2  0   0.238   4.5064   0.9031   1.3591
 46J  H12  H  HCH2  0   0.236   4.4780  -1.1766  -0.0888
 46J  H13  H  HCH2  0   0.224   3.2162  -1.1901   1.1344
 46J  H14  H  HCH2  0   0.261   2.2820  -1.8832  -1.0494
 46J  H15  H  HCH2  0   0.235   2.8671  -0.4031  -1.7961
 46J  H16  H  HCH2  0   0.242  -1.0800   1.1406  -1.6077
 46J  H17  H  HCH2  0   0.198  -1.9634  -0.3757  -1.7433
 46J  H18  H  HNH1  0   0.353  -3.3562   1.6085  -1.5673
 46J  H20  H  HCH2  0   0.186  -4.2617  -0.4670  -0.6683
 46J  H21  H  HCH2  0   0.231  -4.8298   0.9920   0.1433
 46J  O    O  O     0  -0.506   0.1292  -2.0660  -0.2553

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
 46J  C7   C8   single  1.525  0.020  1.525
 46J  C7   C6   single  1.524  0.020  1.524
 46J  C8   C9   single  1.525  0.020  1.525
 46J  C3   C4   single  1.520  0.020  1.520
 46J  C3   C2   single  1.525  0.020  1.525
 46J  C6   N1   single  1.456  0.020  1.456
 46J  N    C4   single  1.453  0.020  1.453
 46J  N    C5   single  1.449  0.020  1.449
 46J  C1   C2   single  1.526  0.020  1.526
 46J  C1   C5   single  1.535  0.020  1.535
 46J  C1   C    single  1.521  0.020  1.521
 46J  C9   C10  single  1.525  0.020  1.525
 46J  N1   C    single  1.352  0.020  1.352
 46J  N1   C10  single  1.455  0.020  1.455
 46J  C    O    double  1.227  0.020  1.227
 46J  C1   H1   single  0.970  0.020  1.090
 46J  C2   H2   single  0.970  0.020  1.090
 46J  C2   H3   single  0.970  0.020  1.090
 46J  C3   H4   single  0.970  0.020  1.090
 46J  C3   H5   single  0.970  0.020  1.090
 46J  C10  H6   single  0.970  0.020  1.090
 46J  C10  H7   single  0.970  0.020  1.090
 46J  C9   H8   single  0.970  0.020  1.090
 46J  C9   H9   single  0.970  0.020  1.090
 46J  C8   H10  single  0.970  0.020  1.090
 46J  C8   H11  single  0.970  0.020  1.090
 46J  C7   H12  single  0.970  0.020  1.090
 46J  C7   H13  single  0.970  0.020  1.090
 46J  C6   H14  single  0.970  0.020  1.090
 46J  C6   H15  single  0.970  0.020  1.090
 46J  C5   H16  single  0.970  0.020  1.090
 46J  C5   H17  single  0.970  0.020  1.090
 46J  N    H18  single  0.890  0.020  1.040
 46J  C4   H20  single  0.970  0.020  1.090
 46J  C4   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
 46J  H1   C1   C5   107.72  3.000
 46J  H1   C1   C    110.45  3.000
 46J  C5   C1   C    109.38  3.000
 46J  H1   C1   C2   107.31  3.000
 46J  C    C1   C2   111.98  3.000
 46J  C5   C1   C2   109.90  3.000
 46J  H3   C2   H2   106.85  3.000
 46J  H3   C2   C3   110.46  3.000
 46J  H2   C2   C3   109.10  3.000
 46J  H3   C2   C1   110.31  3.000
 46J  H2   C2   C1   109.90  3.000
 46J  C3   C2   C1   110.16  3.000
 46J  C6   N1   C10  112.52  3.000
 46J  C10  N1   C    126.37  3.000
 46J  C6   N1   C    120.35  3.000
 46J  H5   C3   H4   106.88  3.000
 46J  H5   C3   C4   109.42  3.000
 46J  H4   C3   C4   109.74  3.000
 46J  H5   C3   C2   110.22  3.000
 46J  H4   C3   C2   110.05  3.000
 46J  C4   C3   C2   110.47  3.000
 46J  O    C    N1   121.57  3.000
 46J  O    C    C1   120.20  3.000
 46J  N1   C    C1   118.16  3.000
 46J  H7   C10  H6   106.48  3.000
 46J  H7   C10  C9   110.28  3.000
 46J  H6   C10  C9   109.86  3.000
 46J  H7   C10  N1   111.29  3.000
 46J  H6   C10  N1   108.31  3.000
 46J  C9   C10  N1   110.53  3.000
 46J  H9   C9   H8   107.07  3.000
 46J  H9   C9   C8   110.04  3.000
 46J  H8   C9   C8   110.65  3.000
 46J  H9   C9   C10  108.81  3.000
 46J  H8   C9   C10  109.02  3.000
 46J  C8   C9   C10  111.14  3.000
 46J  H11  C8   H10  106.56  3.000
 46J  H11  C8   C7   110.54  3.000
 46J  H10  C8   C7   109.22  3.000
 46J  H11  C8   C9   110.33  3.000
 46J  H10  C8   C9   109.17  3.000
 46J  C7   C8   C9   110.91  3.000
 46J  H13  C7   H12  106.96  3.000
 46J  H13  C7   C6   109.07  3.000
 46J  H12  C7   C6   109.31  3.000
 46J  H13  C7   C8   110.07  3.000
 46J  H12  C7   C8   110.66  3.000
 46J  C6   C7   C8   110.68  3.000
 46J  H15  C6   H14  107.40  3.000
 46J  H15  C6   C7   109.78  3.000
 46J  H14  C6   C7   111.36  3.000
 46J  H15  C6   N1   108.04  3.000
 46J  H14  C6   N1   109.51  3.000
 46J  C7   C6   N1   110.63  3.000
 46J  H17  C5   H16  106.58  3.000
 46J  H17  C5   N    112.89  3.000
 46J  H16  C5   N    108.53  3.000
 46J  H17  C5   C1   108.28  3.000
 46J  H16  C5   C1   110.49  3.000
 46J  N    C5   C1   110.02  3.000
 46J  H18  N    C4   109.66  3.000
 46J  H18  N    C5   109.05  3.000
 46J  C4   N    C5   112.18  3.000
 46J  H21  C4   H20  106.92  3.000
 46J  H21  C4   N    108.74  3.000
 46J  H20  C4   N    112.46  3.000
 46J  H21  C4   C3   110.46  3.000
 46J  H20  C4   C3   108.56  3.000
 46J  N    C4   C3   109.69  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
 46J  CONST_01  C6   N1  C    C1   180.00   0.0  0
 46J  CONST_02  C10  N1  C    C1     0.00   0.0  0
 46J  CONST_03  C6   N1  C    O      0.00   0.0  0
 46J  CONST_04  C10  N1  C    O    180.00   0.0  0
 46J  Var_01    C4   C3  C2   C1    54.64  30.0  1
 46J  Var_02    C4   N   C5   C1   -61.29  30.0  1
 46J  Var_03    N    C4  C3   C2   -57.40  30.0  1
 46J  Var_04    C8   C7  C6   N1   -55.74  30.0  1
 46J  Var_05    C8   C9  C10  N1    54.94  30.0  1
 46J  Var_06    C5   N   C4   C3    61.51  30.0  1
 46J  Var_07    C7   C8  C9   C10  -52.11  30.0  1
 46J  Var_08    C7   C6  N1   C10   60.05  30.0  1
 46J  Var_09    C6   C7  C8   C9    52.38  30.0  1
 46J  Var_10    C6   N1  C10  C9   -59.45  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
 46J  chir_01  C1  C2  C5  C  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
 46J  plan-1  C1   0.020
 46J  plan-1  N1   0.020
 46J  plan-1  C    0.020
 46J  plan-1  C10  0.020
 46J  plan-1  C6   0.020
 46J  plan-1  O    0.020

