# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 06:07:17 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: (2S)-5-oxopyrrolidine-2-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C[C@@H]1CCC(=O)N1
#
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
 CGN  CGN  (2S)-5-oxopyrrolidine-2-carbaldehyde  ligand  15  8  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CGN
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
 CGN  CB   C  CH2   0  -0.477   1.5446  -0.2613  -0.0627
 CGN  CG   C  CH2   0  -0.587   1.1813  -0.1995   1.4167
 CGN  CD   C  C     0   0.524  -0.3206   0.0006   1.4272
 CGN  N    N  NH1   0  -0.630  -0.6841   0.3749   0.1834
 CGN  OE1  O  O     0  -0.485  -1.0670  -0.1263   2.3808
 CGN  C    C  C1    0   0.175   0.1244   0.0228  -2.1136
 CGN  CA   C  CH1   0  -0.147   0.4087   0.5393  -0.7354
 CGN  O    O  O     0  -0.368  -0.9138  -0.4789  -2.4580
 CGN  HB1  H  HCH2  0   0.263   1.5283  -1.2975  -0.4058
 CGN  HB2  H  HCH2  0   0.273   2.5231   0.1532  -0.2926
 CGN  HG1  H  HCH2  0   0.282   1.4707  -1.0873   1.9768
 CGN  HG2  H  HCH2  0   0.282   1.6386   0.6644   1.9070
 CGN  HN   H  HNH1  0   0.401  -1.6184   0.6927  -0.0257
 CGN  H    H  H     0   0.207   0.9714   0.1447  -2.8111
 CGN  HA   H  HCH1  0   0.288   0.7050   1.5924  -0.8401

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
 CGN  CB  CG   single  1.525  0.020  1.525
 CGN  CB  CA   single  1.544  0.020  1.544
 CGN  CB  HB1  single  0.970  0.020  1.090
 CGN  CB  HB2  single  0.970  0.020  1.090
 CGN  CG  CD   single  1.515  0.020  1.515
 CGN  CG  HG1  single  0.970  0.020  1.090
 CGN  CG  HG2  single  0.970  0.020  1.090
 CGN  CD  N    single  1.349  0.020  1.349
 CGN  CD  OE1  double  1.218  0.020  1.218
 CGN  N   CA   single  1.437  0.020  1.437
 CGN  N   HN   single  0.860  0.020  1.020
 CGN  C   CA   single  1.499  0.020  1.499
 CGN  C   O    double  1.203  0.020  1.203
 CGN  C   H    single  0.930  0.020  1.080
 CGN  CA  HA   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
 CGN  HB2  CB  HB1  107.99  3.000
 CGN  HB2  CB  CA   111.86  3.000
 CGN  HB1  CB  CA   110.14  3.000
 CGN  HB2  CB  CG   113.84  3.000
 CGN  HB1  CB  CG   109.87  3.000
 CGN  CA   CB  CG   103.09  3.000
 CGN  HG2  CG  HG1  107.60  3.000
 CGN  HG2  CG  CD   107.88  3.000
 CGN  HG1  CG  CD   111.57  3.000
 CGN  HG2  CG  CB   111.56  3.000
 CGN  HG1  CG  CB   113.75  3.000
 CGN  CD   CG  CB   104.38  3.000
 CGN  OE1  CD  N    125.87  3.000
 CGN  OE1  CD  CG   126.82  3.000
 CGN  N    CD  CG   107.30  3.000
 CGN  HN   N   CA   122.39  3.000
 CGN  HN   N   CD   121.88  3.000
 CGN  CA   N   CD   114.61  3.000
 CGN  H    C   O    121.81  3.000
 CGN  H    C   CA   113.41  3.000
 CGN  O    C   CA   124.78  3.000
 CGN  HA   CA  C    107.08  3.000
 CGN  HA   CA  N    112.06  3.000
 CGN  C    CA  N    113.84  3.000
 CGN  HA   CA  CB   109.88  3.000
 CGN  C    CA  CB   111.19  3.000
 CGN  N    CA  CB   102.80  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
 CGN  CONST_01  CA  N   CD  CG     0.00   0.0  0
 CGN  CONST_02  CA  N   CD  OE1  180.00   0.0  0
 CGN  CONST_03  HN  N   CD  CG   180.00   0.0  0
 CGN  Var_01    N   CD  CG  CB   -15.04  30.0  1
 CGN  Var_02    CA  CB  CG  CD    25.59  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
 CGN  chir_01  CA  CB  N  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
 CGN  plan-1  CG   0.020
 CGN  plan-1  CD   0.020
 CGN  plan-1  N    0.020
 CGN  plan-1  OE1  0.020
 CGN  plan-1  CA   0.020
 CGN  plan-1  HN   0.020
 CGN  plan-2  C    0.020
 CGN  plan-2  CA   0.020
 CGN  plan-2  O    0.020
 CGN  plan-2  H    0.020

