# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:56:19 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 5-(pyrrolidin-1-yl)pyridine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1ccc(cn1)N2CCCC2
#
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
 JKS  JKS  5-(pyrrolidin-1-yl)pyridine-2-carbonitrile  ligand  24  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JKS
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
 JKS  C10   C  CH2   0  -0.281  -2.3733   1.2231   0.1507
 JKS  C13   C  CH2   0  -0.281  -2.4423  -1.1979   0.2048
 JKS  N01   N  NS    0  -0.264   5.0517   0.0873  -0.2530
 JKS  C03   C  CR6   0   0.136   2.4766  -0.0256  -0.1044
 JKS  C04   C  CR16  0  -0.250   1.8275  -1.2479   0.0425
 JKS  C05   C  CR16  0  -0.266   0.4531  -1.2685   0.1196
 JKS  C06   C  CR6   0   0.359  -0.2638  -0.0587   0.0476
 JKS  C07   C  CR16  0  -0.172   0.5102   1.1233  -0.1065
 JKS  N08   N  N     0  -0.389   1.8189   1.1331  -0.1771
 JKS  N09   N  NR5   0  -0.522  -1.6022  -0.0125   0.1184
 JKS  C11   C  CH2   0  -0.479  -3.7647   0.7605   0.5649
 JKS  C12   C  CH2   0  -0.478  -3.8485  -0.6501  -0.0079
 JKS  H102  H  HCH2  0   0.252  -1.9469   1.9376   0.8575
 JKS  H101  H  HCH2  0   0.242  -2.3880   1.6998  -0.8355
 JKS  H131  H  HCH2  0   0.252  -2.1684  -1.9358  -0.5526
 JKS  H132  H  HCH2  0   0.241  -2.3418  -1.6757   1.1857
 JKS  H041  H  HCR6  0   0.288   2.3942  -2.1673   0.1002
 JKS  H051  H  HCR6  0   0.290  -0.0587  -2.2124   0.2451
 JKS  H071  H  HCR6  0   0.279   0.0225   2.0884  -0.1791
 JKS  H111  H  HCH2  0   0.243  -3.8421   0.7333   1.6536
 JKS  H112  H  HCH2  0   0.256  -4.5432   1.4240   0.1911
 JKS  H122  H  HCH2  0   0.243  -4.0757  -0.6126  -1.0750
 JKS  H121  H  HCH2  0   0.255  -4.6050  -1.2674   0.4742
 JKS  C02   C  CSP   0   0.045   3.9011   0.0410  -0.1868

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
 JKS  N01  C02   triple    1.153  0.020  1.153
 JKS  C02  C03   single    1.428  0.020  1.428
 JKS  C03  N08   aromatic  1.334  0.020  1.334
 JKS  C03  C04   aromatic  1.392  0.020  1.392
 JKS  N08  C07   aromatic  1.311  0.020  1.311
 JKS  C04  C05   aromatic  1.377  0.020  1.377
 JKS  C07  C06   aromatic  1.421  0.020  1.421
 JKS  C05  C06   aromatic  1.408  0.020  1.408
 JKS  C06  N09   single    1.341  0.020  1.341
 JKS  N09  C10   single    1.457  0.020  1.457
 JKS  N09  C13   single    1.456  0.020  1.456
 JKS  C10  C11   single    1.524  0.020  1.524
 JKS  C13  C12   single    1.524  0.020  1.524
 JKS  C12  C11   single    1.525  0.020  1.525
 JKS  C10  H102  single    0.970  0.020  1.090
 JKS  C10  H101  single    0.970  0.020  1.090
 JKS  C13  H131  single    0.970  0.020  1.090
 JKS  C13  H132  single    0.970  0.020  1.090
 JKS  C04  H041  single    0.930  0.020  1.080
 JKS  C05  H051  single    0.930  0.020  1.080
 JKS  C07  H071  single    0.930  0.020  1.080
 JKS  C11  H111  single    0.970  0.020  1.090
 JKS  C11  H112  single    0.970  0.020  1.090
 JKS  C12  H122  single    0.970  0.020  1.090
 JKS  C12  H121  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
 JKS  H101  C10  H102  107.65  3.000
 JKS  H101  C10  C11   111.38  3.000
 JKS  H102  C10  C11   112.30  3.000
 JKS  H101  C10  N09   110.86  3.000
 JKS  H102  C10  N09   111.27  3.000
 JKS  C11   C10  N09   103.41  3.000
 JKS  H132  C13  H131  107.65  3.000
 JKS  H132  C13  C12   111.49  3.000
 JKS  H131  C13  C12   112.17  3.000
 JKS  H132  C13  N09   110.81  3.000
 JKS  H131  C13  N09   111.36  3.000
 JKS  C12   C13  N09   103.39  3.000
 JKS  N08   C03  C04   122.58  3.000
 JKS  C04   C03  C02   120.81  3.000
 JKS  N08   C03  C02   116.61  3.000
 JKS  H041  C04  C05   120.49  3.000
 JKS  H041  C04  C03   120.52  3.000
 JKS  C05   C04  C03   118.99  3.000
 JKS  H051  C05  C06   121.00  3.000
 JKS  H051  C05  C04   119.48  3.000
 JKS  C06   C05  C04   119.51  3.000
 JKS  N09   C06  C07   121.37  3.000
 JKS  N09   C06  C05   122.35  3.000
 JKS  C07   C06  C05   116.28  3.000
 JKS  H071  C07  N08   116.05  3.000
 JKS  H071  C07  C06   120.18  3.000
 JKS  N08   C07  C06   123.77  3.000
 JKS  C07   N08  C03   118.87  3.000
 JKS  C06   N09  C13   123.44  3.000
 JKS  C13   N09  C10   112.57  3.000
 JKS  C06   N09  C10   123.97  3.000
 JKS  H112  C11  H111  107.86  3.000
 JKS  H112  C11  C12   113.29  3.000
 JKS  H111  C11  C12   110.34  3.000
 JKS  H112  C11  C10   111.99  3.000
 JKS  H111  C11  C10   110.08  3.000
 JKS  C12   C11  C10   103.24  3.000
 JKS  H121  C12  H122  107.92  3.000
 JKS  H121  C12  C11   113.35  3.000
 JKS  H122  C12  C11   110.30  3.000
 JKS  H121  C12  C13   112.05  3.000
 JKS  H122  C12  C13   109.93  3.000
 JKS  C11   C12  C13   103.26  3.000
 JKS  C03   C02  N01   180.00  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
 JKS  CONST_01  C06   C07  N08  C03    0.00   0.0  0
 JKS  CONST_02  C06   C05  C04  C03    0.00   0.0  0
 JKS  CONST_03  C07   N08  C03  C04    0.00   0.0  0
 JKS  CONST_04  C07   C06  C05  C04    0.00   0.0  0
 JKS  CONST_05  N08   C03  C04  C05    0.00   0.0  0
 JKS  CONST_06  N08   C07  C06  C05    0.00   0.0  0
 JKS  CONST_07  N09   C06  C05  C04  180.00   0.0  0
 JKS  CONST_08  N09   C06  C07  N08  180.00   0.0  0
 JKS  CONST_09  C07   N08  C03  C02  180.00   0.0  0
 JKS  CONST_10  C05   C04  C03  C02  180.00   0.0  0
 JKS  CONST_11  H071  C07  N08  C03  180.00   0.0  0
 JKS  CONST_12  H051  C05  C04  C03  180.00   0.0  0
 JKS  CONST_13  H041  C04  C05  C06  180.00   0.0  0
 JKS  Var_01    C07   C06  N09  C10   -4.94  30.0  2
 JKS  Var_02    C12   C13  N09  C10   11.88  30.0  1
 JKS  Var_03    C13   C12  C11  C10   37.86  30.0  1
 JKS  Var_04    C11   C10  N09  C13   11.70  30.0  1
 JKS  Var_05    C12   C11  C10  N09  -30.37  30.0  1
 JKS  Var_06    C11   C12  C13  N09  -30.49  30.0  1

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
 JKS  plan-1  N01   0.020
 JKS  plan-1  C03   0.020
 JKS  plan-1  C04   0.020
 JKS  plan-1  C05   0.020
 JKS  plan-1  C06   0.020
 JKS  plan-1  C07   0.020
 JKS  plan-1  N08   0.020
 JKS  plan-1  N09   0.020
 JKS  plan-1  H041  0.020
 JKS  plan-1  H051  0.020
 JKS  plan-1  H071  0.020
 JKS  plan-1  C02   0.020

