# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:44:18 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (2S)-pyrrolidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#C[C@@H]1CCCN1
#
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
 QEJ  QEJ  (2S)-pyrrolidine-2-carbonitrile  ligand  15  7  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QEJ
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
 QEJ  C1   C  CSP   0   0.144  -1.6619   0.0379   0.2266
 QEJ  N2   N  NS    0  -0.282  -2.7340   0.0019  -0.1902
 QEJ  CA   C  CH1   0  -0.197  -0.2924   0.0858   0.7508
 QEJ  CB   C  CH2   0  -0.475   0.5121   1.2578   0.1182
 QEJ  CG   C  CH2   0  -0.460   1.8370   0.6019  -0.2650
 QEJ  CD   C  CH2   0  -0.317   1.4067  -0.8276  -0.5777
 QEJ  N    N  NH1   0  -0.587   0.4023  -1.1591   0.4307
 QEJ  HA   H  HCH1  0   0.320  -0.3751   0.2076   1.8325
 QEJ  HB2  H  HCH2  0   0.256   0.0075   1.6391  -0.7706
 QEJ  HB3  H  HCH2  0   0.267   0.6183   2.0846   0.8177
 QEJ  HG2  H  HCH2  0   0.246   2.3208   1.1031  -1.1032
 QEJ  HG3  H  HCH2  0   0.236   2.5300   0.6068   0.5790
 QEJ  HD2  H  HCH2  0   0.230   0.9587  -0.8775  -1.5746
 QEJ  HD3  H  HCH2  0   0.251   2.2202  -1.5513  -0.5467
 QEJ  H    H  HNH1  0   0.368   0.8601  -1.4953   1.2666

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
 QEJ  C1  N2   triple  1.151  0.020  1.151
 QEJ  C1  CA   single  1.467  0.020  1.467
 QEJ  CA  CB   single  1.556  0.020  1.556
 QEJ  CA  N    single  1.461  0.020  1.461
 QEJ  CB  CG   single  1.527  0.020  1.527
 QEJ  CG  CD   single  1.525  0.020  1.525
 QEJ  CD  N    single  1.461  0.020  1.461
 QEJ  CA  HA   single  0.970  0.020  1.090
 QEJ  CB  HB2  single  0.970  0.020  1.090
 QEJ  CB  HB3  single  0.970  0.020  1.090
 QEJ  CG  HG2  single  0.970  0.020  1.090
 QEJ  CG  HG3  single  0.970  0.020  1.090
 QEJ  CD  HD2  single  0.970  0.020  1.090
 QEJ  CD  HD3  single  0.970  0.020  1.090
 QEJ  N   H    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
 QEJ  CA   C1  N2   180.00  3.000
 QEJ  HA   CA  N    110.38  3.000
 QEJ  HA   CA  CB   110.98  3.000
 QEJ  N    CA  CB   107.87  3.000
 QEJ  HA   CA  C1   106.67  3.000
 QEJ  N    CA  C1   109.74  3.000
 QEJ  CB   CA  C1   111.22  3.000
 QEJ  HB3  CB  HB2  107.65  3.000
 QEJ  HB3  CB  CG   113.76  3.000
 QEJ  HB2  CB  CG   110.31  3.000
 QEJ  HB3  CB  CA   111.18  3.000
 QEJ  HB2  CB  CA   110.82  3.000
 QEJ  CG   CB  CA   103.13  3.000
 QEJ  HG3  CG  HG2  108.09  3.000
 QEJ  HG3  CG  CD   109.98  3.000
 QEJ  HG2  CG  CD   113.49  3.000
 QEJ  HG3  CG  CB   110.78  3.000
 QEJ  HG2  CG  CB   112.37  3.000
 QEJ  CD   CG  CB   102.08  3.000
 QEJ  HD3  CD  HD2  107.55  3.000
 QEJ  HD3  CD  N    110.06  3.000
 QEJ  HD2  CD  N    109.69  3.000
 QEJ  HD3  CD  CG   113.96  3.000
 QEJ  HD2  CD  CG   110.19  3.000
 QEJ  N    CD  CG   105.37  3.000
 QEJ  H    N   CD   109.57  3.000
 QEJ  H    N   CA   108.51  3.000
 QEJ  CD   N   CA   106.54  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
 QEJ  Var_01  CD  CG  CB  CA   31.04  30.0  1
 QEJ  Var_02  N   CD  CG  CB  -39.52  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
 QEJ  chir_01  CA  C1  CB  N  positiv

