# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:00:47 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: N-{[(3R)-pyrrolidin-3-yl]methyl}pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@H](CN1)CNc2ccccn2
#
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
 WNJ  WNJ  N-{[(3R)-pyrrolidin-3-yl]methyl}pyridin-2-amine  ligand  28  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WNJ
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
 WNJ  C10  C  CH2   0  -0.466  -33.1787  -8.5603  -19.2222
 WNJ  N12  N  NH1   0  -0.583  -33.4843  -6.1695  -19.4303
 WNJ  C13  C  CH2   0  -0.310  -32.3580  -6.5401  -20.2747
 WNJ  C01  C  CH2   0  -0.326  -31.2861  -8.7716  -20.9302
 WNJ  C03  C  CR6   0   0.487  -28.9145  -8.0391  -20.9909
 WNJ  C04  C  CR16  0  -0.398  -28.5646  -8.6954  -19.7946
 WNJ  C05  C  CR16  0  -0.156  -27.2862  -8.5313  -19.3053
 WNJ  C06  C  CR16  0  -0.366  -26.3754  -7.7296  -19.9889
 WNJ  C07  C  CR16  0  -0.067  -26.8191  -7.1251  -21.1513
 WNJ  C09  C  CH1   0  -0.260  -31.8978  -7.9344  -19.8111
 WNJ  C11  C  CH2   0  -0.321  -34.2178  -7.4188  -19.2560
 WNJ  N02  N  NH1   0  -0.652  -30.1372  -8.1714  -21.5647
 WNJ  N08  N  N     0  -0.469  -28.0426  -7.2656  -21.6450
 WNJ  H1   H  HCH2  0   0.231  -33.5137  -9.4227  -19.8042
 WNJ  H2   H  HCH2  0   0.236  -33.0091  -8.9138  -18.2045
 WNJ  H3   H  HNH1  0   0.342  -33.1230  -5.8805  -18.5283
 WNJ  H5   H  HCH2  0   0.241  -31.5709  -5.7873  -20.2269
 WNJ  H6   H  HCH2  0   0.214  -32.6981  -6.5898  -21.3164
 WNJ  H7   H  HCH2  0   0.258  -32.0354  -8.9267  -21.7096
 WNJ  H8   H  HCH2  0   0.247  -31.0254  -9.7671  -20.5607
 WNJ  H9   H  HCR6  0   0.268  -29.2745  -9.3159  -19.2659
 WNJ  H10  H  HCR6  0   0.264  -26.9992  -9.0267  -18.3863
 WNJ  H11  H  HCR6  0   0.255  -25.3664  -7.5783  -19.6330
 WNJ  H12  H  HCR6  0   0.253  -26.1514  -6.4859  -21.7200
 WNJ  H13  H  HCH1  0   0.242  -31.1581  -7.8094  -19.0142
 WNJ  H14  H  HCH2  0   0.236  -34.8383  -7.3788  -18.3608
 WNJ  H15  H  HCH2  0   0.221  -34.8910  -7.5533  -20.1072
 WNJ  H16  H  HNH1  0   0.379  -30.3043  -7.5670  -22.3527

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
 WNJ  N08  C07  aromatic  1.327  0.020  1.327
 WNJ  N08  C03  aromatic  1.337  0.020  1.337
 WNJ  N02  C03  single    1.357  0.020  1.357
 WNJ  N02  C01  single    1.443  0.020  1.443
 WNJ  C07  C06  aromatic  1.383  0.020  1.383
 WNJ  C03  C04  aromatic  1.409  0.020  1.409
 WNJ  C01  C09  single    1.526  0.020  1.526
 WNJ  C13  C09  single    1.540  0.020  1.540
 WNJ  C13  N12  single    1.456  0.020  1.456
 WNJ  C06  C05  aromatic  1.393  0.020  1.393
 WNJ  C09  C10  single    1.542  0.020  1.542
 WNJ  N12  C11  single    1.459  0.020  1.459
 WNJ  C04  C05  aromatic  1.379  0.020  1.379
 WNJ  C10  C11  single    1.544  0.020  1.544
 WNJ  C10  H1   single    0.970  0.020  1.090
 WNJ  C10  H2   single    0.970  0.020  1.090
 WNJ  N12  H3   single    0.890  0.020  1.040
 WNJ  C13  H5   single    0.970  0.020  1.090
 WNJ  C13  H6   single    0.970  0.020  1.090
 WNJ  C01  H7   single    0.970  0.020  1.090
 WNJ  C01  H8   single    0.970  0.020  1.090
 WNJ  C04  H9   single    0.930  0.020  1.080
 WNJ  C05  H10  single    0.930  0.020  1.080
 WNJ  C06  H11  single    0.930  0.020  1.080
 WNJ  C07  H12  single    0.930  0.020  1.080
 WNJ  C09  H13  single    0.970  0.020  1.090
 WNJ  C11  H14  single    0.970  0.020  1.090
 WNJ  C11  H15  single    0.970  0.020  1.090
 WNJ  N02  H16  single    0.860  0.020  1.020

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
 WNJ  H2   C10  H1   106.79  3.000
 WNJ  H2   C10  C11  111.39  3.000
 WNJ  H1   C10  C11  111.43  3.000
 WNJ  H2   C10  C09  111.02  3.000
 WNJ  H1   C10  C09  111.80  3.000
 WNJ  C11  C10  C09  104.51  3.000
 WNJ  H3   N12  C11  108.48  3.000
 WNJ  H3   N12  C13  108.23  3.000
 WNJ  C11  N12  C13  103.90  3.000
 WNJ  H6   C13  H5   107.26  3.000
 WNJ  H6   C13  C09  109.73  3.000
 WNJ  H5   C13  C09  113.35  3.000
 WNJ  H6   C13  N12  108.81  3.000
 WNJ  H5   C13  N12  110.94  3.000
 WNJ  C09  C13  N12  106.69  3.000
 WNJ  H8   C01  H7   105.98  3.000
 WNJ  H8   C01  N02  109.72  3.000
 WNJ  H7   C01  N02  106.95  3.000
 WNJ  H8   C01  C09  110.32  3.000
 WNJ  H7   C01  C09  109.05  3.000
 WNJ  N02  C01  C09  114.43  3.000
 WNJ  N08  C03  N02  115.93  3.000
 WNJ  N02  C03  C04  122.51  3.000
 WNJ  N08  C03  C04  121.54  3.000
 WNJ  H9   C04  C05  120.25  3.000
 WNJ  H9   C04  C03  121.31  3.000
 WNJ  C05  C04  C03  118.44  3.000
 WNJ  H10  C05  C06  120.44  3.000
 WNJ  H10  C05  C04  119.51  3.000
 WNJ  C06  C05  C04  120.05  3.000
 WNJ  H11  C06  C07  121.00  3.000
 WNJ  H11  C06  C05  121.98  3.000
 WNJ  C07  C06  C05  117.02  3.000
 WNJ  H12  C07  N08  115.76  3.000
 WNJ  H12  C07  C06  120.03  3.000
 WNJ  N08  C07  C06  124.21  3.000
 WNJ  H13  C09  C01  109.02  3.000
 WNJ  H13  C09  C13  108.53  3.000
 WNJ  C01  C09  C13  113.32  3.000
 WNJ  H13  C09  C10  109.24  3.000
 WNJ  C13  C09  C10  103.55  3.000
 WNJ  C01  C09  C10  112.98  3.000
 WNJ  H15  C11  H14  107.06  3.000
 WNJ  H15  C11  N12  108.77  3.000
 WNJ  H14  C11  N12  110.66  3.000
 WNJ  H15  C11  C10  109.91  3.000
 WNJ  H14  C11  C10  113.10  3.000
 WNJ  N12  C11  C10  107.29  3.000
 WNJ  H16  N02  C03  114.95  3.000
 WNJ  H16  N02  C01  117.49  3.000
 WNJ  C03  N02  C01  124.88  3.000
 WNJ  C07  N08  C03  118.73  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
 WNJ  CONST_01  C06  C07  N08  C03    0.00   0.0  0
 WNJ  CONST_02  C06  C05  C04  C03    0.00   0.0  0
 WNJ  CONST_03  C07  N08  C03  C04    0.00   0.0  0
 WNJ  CONST_04  C07  C06  C05  C04    0.00   0.0  0
 WNJ  CONST_05  N08  C07  C06  C05    0.00   0.0  0
 WNJ  CONST_06  N08  C03  C04  C05    0.00   0.0  0
 WNJ  CONST_07  N02  C03  C04  C05  180.00   0.0  0
 WNJ  CONST_08  N02  C03  N08  C07  180.00   0.0  0
 WNJ  CONST_09  H12  C07  N08  C03  180.00   0.0  0
 WNJ  CONST_10  H10  C05  C04  C03  180.00   0.0  0
 WNJ  CONST_11  H11  C06  C05  C04  180.00   0.0  0
 WNJ  CONST_12  H9   C04  C05  C06  180.00   0.0  0
 WNJ  CONST_13  N08  C03  N02  C01  180.00   0.0  0
 WNJ  CONST_14  C04  C03  N02  C01    0.00   0.0  0
 WNJ  CONST_15  H16  N02  C03  C04  180.00   0.0  0
 WNJ  Var_01    C13  N12  C11  C10   34.07  30.0  1
 WNJ  Var_02    C09  C10  C11  N12  -16.79  30.0  1
 WNJ  Var_03    C11  N12  C13  C09  -38.27  30.0  1
 WNJ  Var_04    C09  C01  N02  C03   71.35  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
 WNJ  chir_01  C09  C01  C13  C10  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
 WNJ  plan-1  C03  0.020
 WNJ  plan-1  C04  0.020
 WNJ  plan-1  C05  0.020
 WNJ  plan-1  C06  0.020
 WNJ  plan-1  C07  0.020
 WNJ  plan-1  N02  0.020
 WNJ  plan-1  N08  0.020
 WNJ  plan-1  H9   0.020
 WNJ  plan-1  H10  0.020
 WNJ  plan-1  H11  0.020
 WNJ  plan-1  H12  0.020
 WNJ  plan-2  C01  0.020
 WNJ  plan-2  C03  0.020
 WNJ  plan-2  N02  0.020
 WNJ  plan-2  H16  0.020

