# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 22:19:42 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: ~{N}-[(1-pyridin-2-ylpiperidin-4-yl)methyl]pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1CCN(CC1)c2ccccn2)N3CCCC3
#
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
 841  841  ~{N}-[(1-pyridin-2-ylpiperidin-4-yl)methyl]pyrrolidine-1-carboxamide  ligand  45  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_841
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
 841  O    O  O     0  -0.555  -2.5976   0.4969   1.8982
 841  C11  C  C     0   0.743  -2.9479  -0.0484   0.8543
 841  N3   N  NT    0  -0.514  -4.1547   0.2003   0.2875
 841  C15  C  CH2   0  -0.270  -4.6217  -0.3342  -0.9810
 841  C14  C  CH2   0  -0.460  -6.0528   0.1846  -1.0804
 841  C13  C  CH2   0  -0.465  -6.0021   1.4987  -0.3087
 841  C12  C  CH2   0  -0.236  -5.0639   1.1877   0.8514
 841  N2   N  NH1   0  -0.685  -2.1435  -0.9203   0.1845
 841  C10  C  CH2   0  -0.216  -0.8962  -1.3893   0.7407
 841  C7   C  CH1   0  -0.302   0.0271  -1.9230  -0.3523
 841  C6   C  CH2   0  -0.417   1.3040  -2.4975   0.2506
 841  C5   C  CH2   0  -0.287   2.2433  -1.4284   0.7940
 841  C8   C  CH2   0  -0.417   0.4169  -0.8706  -1.3874
 841  C9   C  CH2   0  -0.300   1.3569   0.1822  -0.8239
 841  N1   N  NT    0  -0.500   2.5306  -0.4168  -0.2033
 841  C3   C  CR6   0   0.534   3.6929   0.3153  -0.1433
 841  C4   C  CR16  0  -0.398   4.7102   0.0594   0.7955
 841  C    C  CR16  0  -0.124   5.8713   0.8024   0.7380
 841  N    N  N     0  -0.449   3.8334   1.2867  -1.0461
 841  C2   C  CR16  0  -0.032   4.9511   1.9913  -1.0793
 841  C1   C  CR16  0  -0.342   6.0182   1.7950  -0.2218
 841  H1   H  HCH2  0   0.230  -4.0112   0.0282  -1.8156
 841  H2   H  HCH2  0   0.223  -4.5978  -1.4275  -1.0017
 841  H3   H  HCH2  0   0.243  -6.3745   0.3012  -2.1140
 841  H4   H  HCH2  0   0.232  -6.7381  -0.5133  -0.5955
 841  H5   H  HCH2  0   0.229  -5.5752   2.2857  -0.9338
 841  H6   H  HCH2  0   0.240  -6.9807   1.8368   0.0284
 841  H7   H  HCH2  0   0.217  -5.6121   0.7762   1.7050
 841  H8   H  HCH2  0   0.237  -4.5269   2.0682   1.2022
 841  H9   H  HNH1  0   0.372  -2.5423  -1.4938  -0.5396
 841  H10  H  HCH2  0   0.229  -0.4309  -0.5639   1.2786
 841  H11  H  HCH2  0   0.223  -1.0628  -2.1829   1.4788
 841  H12  H  HCH1  0   0.232  -0.4966  -2.7399  -0.8616
 841  H13  H  HCH2  0   0.234   1.0773  -3.1969   1.0585
 841  H14  H  HCH2  0   0.233   1.8331  -3.0695  -0.5156
 841  H15  H  HCH2  0   0.213   1.8312  -0.9769   1.7080
 841  H16  H  HCH2  0   0.242   3.1634  -1.9306   1.0858
 841  H17  H  HCH2  0   0.226   0.9026  -1.3694  -2.2304
 841  H18  H  HCH2  0   0.229  -0.4655  -0.3680  -1.7881
 841  H19  H  HCH2  0   0.277   1.6854   0.8433  -1.6199
 841  H20  H  HCH2  0   0.206   0.8258   0.8112  -0.0939
 841  H21  H  HCR6  0   0.240   4.6037  -0.6869   1.5675
 841  H22  H  HCR6  0   0.233   6.6586   0.6097   1.4556
 841  H23  H  HCR6  0   0.226   4.9960   2.7634  -1.8405
 841  H24  H  HCR6  0   0.225   6.9123   2.3973  -0.2930

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
 841  C14  C15  single    1.525  0.020  1.525
 841  C14  C13  single    1.525  0.020  1.525
 841  C15  N3   single    1.454  0.020  1.454
 841  C13  C12  single    1.524  0.020  1.524
 841  N3   C12  single    1.456  0.020  1.456
 841  N3   C11  single    1.356  0.020  1.356
 841  O    C11  double    1.229  0.020  1.229
 841  C11  N2   single    1.362  0.020  1.362
 841  C9   C8   single    1.520  0.020  1.520
 841  C9   N1   single    1.457  0.020  1.457
 841  C8   C7   single    1.527  0.020  1.527
 841  N2   C10  single    1.444  0.020  1.444
 841  C7   C10  single    1.527  0.020  1.527
 841  C7   C6   single    1.524  0.020  1.524
 841  N1   C5   single    1.449  0.020  1.449
 841  N1   C3   single    1.375  0.020  1.375
 841  C5   C6   single    1.523  0.020  1.523
 841  N    C3   aromatic  1.334  0.020  1.334
 841  N    C2   aromatic  1.322  0.020  1.322
 841  C3   C4   aromatic  1.408  0.020  1.408
 841  C2   C1   aromatic  1.383  0.020  1.383
 841  C4   C    aromatic  1.380  0.020  1.380
 841  C1   C    aromatic  1.389  0.020  1.389
 841  C15  H1   single    0.970  0.020  1.090
 841  C15  H2   single    0.970  0.020  1.090
 841  C14  H3   single    0.970  0.020  1.090
 841  C14  H4   single    0.970  0.020  1.090
 841  C13  H5   single    0.970  0.020  1.090
 841  C13  H6   single    0.970  0.020  1.090
 841  C12  H7   single    0.970  0.020  1.090
 841  C12  H8   single    0.970  0.020  1.090
 841  N2   H9   single    0.890  0.020  1.040
 841  C10  H10  single    0.970  0.020  1.090
 841  C10  H11  single    0.970  0.020  1.090
 841  C7   H12  single    0.970  0.020  1.090
 841  C6   H13  single    0.970  0.020  1.090
 841  C6   H14  single    0.970  0.020  1.090
 841  C5   H15  single    0.970  0.020  1.090
 841  C5   H16  single    0.970  0.020  1.090
 841  C8   H17  single    0.970  0.020  1.090
 841  C8   H18  single    0.970  0.020  1.090
 841  C9   H19  single    0.970  0.020  1.090
 841  C9   H20  single    0.970  0.020  1.090
 841  C4   H21  single    0.930  0.020  1.080
 841  C    H22  single    0.930  0.020  1.080
 841  C2   H23  single    0.930  0.020  1.080
 841  C1   H24  single    0.930  0.020  1.080

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
 841  N2   C11  N3   115.93  3.000
 841  N2   C11  O    122.23  3.000
 841  N3   C11  O    121.82  3.000
 841  C12  N3   C15  112.76  3.000
 841  C12  N3   C11  121.21  3.000
 841  C15  N3   C11  125.67  3.000
 841  H2   C15  H1   107.70  3.000
 841  H2   C15  C14  111.05  3.000
 841  H1   C15  C14  111.14  3.000
 841  H2   C15  N3   112.15  3.000
 841  H1   C15  N3   111.35  3.000
 841  C14  C15  N3   103.49  3.000
 841  H4   C14  H3   107.74  3.000
 841  H4   C14  C13  110.31  3.000
 841  H3   C14  C13  113.46  3.000
 841  H4   C14  C15  110.03  3.000
 841  H3   C14  C15  112.05  3.000
 841  C13  C14  C15  103.23  3.000
 841  H6   C13  H5   107.75  3.000
 841  H6   C13  C12  112.39  3.000
 841  H5   C13  C12  110.01  3.000
 841  H6   C13  C14  113.23  3.000
 841  H5   C13  C14  110.14  3.000
 841  C12  C13  C14  103.29  3.000
 841  H8   C12  H7   107.43  3.000
 841  H8   C12  C13  112.56  3.000
 841  H7   C12  C13  111.21  3.000
 841  H8   C12  N3   111.41  3.000
 841  H7   C12  N3   111.09  3.000
 841  C13  C12  N3   103.18  3.000
 841  H9   N2   C10  115.76  3.000
 841  H9   N2   C11  118.98  3.000
 841  C10  N2   C11  121.91  3.000
 841  H11  C10  H10  106.31  3.000
 841  H11  C10  C7   108.71  3.000
 841  H10  C10  C7   111.09  3.000
 841  H11  C10  N2   111.29  3.000
 841  H10  C10  N2   108.24  3.000
 841  C7   C10  N2   111.11  3.000
 841  H12  C7   C8   108.71  3.000
 841  H12  C7   C6   107.64  3.000
 841  C8   C7   C6   108.31  3.000
 841  H12  C7   C10  107.71  3.000
 841  C6   C7   C10  110.80  3.000
 841  C8   C7   C10  113.50  3.000
 841  H14  C6   H13  106.50  3.000
 841  H14  C6   C5   108.59  3.000
 841  H13  C6   C5   108.27  3.000
 841  H14  C6   C7   109.00  3.000
 841  H13  C6   C7   111.10  3.000
 841  C5   C6   C7   113.14  3.000
 841  H16  C5   H15  106.47  3.000
 841  H16  C5   N1   109.82  3.000
 841  H15  C5   N1   111.08  3.000
 841  H16  C5   C6   107.05  3.000
 841  H15  C5   C6   110.70  3.000
 841  N1   C5   C6   111.51  3.000
 841  H18  C8   H17  106.62  3.000
 841  H18  C8   C9   108.49  3.000
 841  H17  C8   C9   109.10  3.000
 841  H18  C8   C7   111.09  3.000
 841  H17  C8   C7   108.77  3.000
 841  C9   C8   C7   112.58  3.000
 841  H20  C9   H19  106.52  3.000
 841  H20  C9   N1   109.96  3.000
 841  H19  C9   N1   108.60  3.000
 841  H20  C9   C8   110.09  3.000
 841  H19  C9   C8   109.71  3.000
 841  N1   C9   C8   111.81  3.000
 841  C3   N1   C9   118.74  3.000
 841  C3   N1   C5   120.61  3.000
 841  C9   N1   C5   114.87  3.000
 841  N    C3   C4   120.52  3.000
 841  C4   C3   N1   122.91  3.000
 841  N    C3   N1   116.57  3.000
 841  H21  C4   C    119.03  3.000
 841  H21  C4   C3   122.11  3.000
 841  C    C4   C3   118.85  3.000
 841  H22  C    C1   120.56  3.000
 841  H22  C    C4   119.24  3.000
 841  C1   C    C4   120.19  3.000
 841  C2   N    C3   119.63  3.000
 841  H23  C2   C1   120.26  3.000
 841  H23  C2   N    115.60  3.000
 841  C1   C2   N    124.14  3.000
 841  H24  C1   C2   121.24  3.000
 841  H24  C1   C    122.12  3.000
 841  C2   C1   C    116.64  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
 841  CONST_01  C1   C2   N    C3      0.00   0.0  0
 841  CONST_02  C1   C    C4   C3      0.00   0.0  0
 841  CONST_03  C2   N    C3   C4      0.00   0.0  0
 841  CONST_04  C2   C1   C    C4      0.00   0.0  0
 841  CONST_05  N    C3   C4   C       0.00   0.0  0
 841  CONST_06  N    C2   C1   C       0.00   0.0  0
 841  CONST_07  C2   N    C3   N1    180.00   0.0  0
 841  CONST_08  C    C4   C3   N1    180.00   0.0  0
 841  CONST_09  H21  C4   C3   N1      0.00   0.0  0
 841  CONST_10  H23  C2   N    C3    180.00   0.0  0
 841  CONST_11  H22  C    C4   C3    180.00   0.0  0
 841  CONST_12  H24  C1   C    C4    180.00   0.0  0
 841  CONST_13  C15  N3   C11  O     180.00   0.0  0
 841  CONST_14  C12  N3   C11  O       0.00   0.0  0
 841  CONST_15  N2   C11  N3   C15     0.00   0.0  0
 841  CONST_16  N2   C11  N3   C12   180.00   0.0  0
 841  CONST_17  C10  N2   C11  N3    180.00   0.0  0
 841  CONST_18  H9   N2   C11  N3      0.00   0.0  0
 841  CONST_19  C10  N2   C11  O       0.00   0.0  0
 841  Var_01    C13  C14  C15  N3     29.65  30.0  1
 841  Var_02    C14  C13  C12  N3     31.01  30.0  1
 841  Var_03    C12  C13  C14  C15   -37.74  30.0  1
 841  Var_04    C13  C12  N3   C15   -12.91  30.0  1
 841  Var_05    C12  N3   C15  C14   -10.59  30.0  1
 841  Var_06    N1   C9   C8   C7     53.55  30.0  1
 841  Var_07    N1   C5   C6   C7    -53.13  30.0  1
 841  Var_08    C9   N1   C5   C6     52.45  30.0  1
 841  Var_09    C8   C9   N1   C5    -52.97  30.0  1
 841  Var_10    N    C3   N1   C5   -175.52  30.0  2
 841  Var_11    C7   C10  N2   C11  -159.59  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
 841  chir_01  C7  C8  C10  C6  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
 841  plan-1  O    0.020
 841  plan-1  C11  0.020
 841  plan-1  N3   0.020
 841  plan-1  C15  0.020
 841  plan-1  C12  0.020
 841  plan-1  N2   0.020
 841  plan-1  C10  0.020
 841  plan-1  H9   0.020
 841  plan-2  N1   0.020
 841  plan-2  C3   0.020
 841  plan-2  C4   0.020
 841  plan-2  C    0.020
 841  plan-2  N    0.020
 841  plan-2  C2   0.020
 841  plan-2  C1   0.020
 841  plan-2  H21  0.020
 841  plan-2  H22  0.020
 841  plan-2  H23  0.020
 841  plan-2  H24  0.020

