# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 00:53:08 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (3S)-3-[(2S)-2-amino-3-oxobutyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@@H](N)C[C@@H]1CCNC1=O
#
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
 KCQ  KCQ  (3S)-3-[(2S)-2-amino-3-oxobutyl]pyrrolidin-2-one  ligand  26  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KCQ
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
 KCQ  OAD   O  O     0  -0.495   2.0469   1.7316   1.1062
 KCQ  CD2   C  C     0   0.572   2.0943   0.6657   0.5133
 KCQ  NAH   N  NH1   0  -0.629   3.1389  -0.1758   0.4731
 KCQ  CAE   C  CH2   0  -0.257   2.9457  -1.3381  -0.3680
 KCQ  CD1   C  CH2   0  -0.467   1.4227  -1.3970  -0.4968
 KCQ  CG    C  CH1   0  -0.420   0.9821   0.0572  -0.3290
 KCQ  CB    C  CH2   0  -0.453  -0.3914   0.2541   0.2908
 KCQ  CA    C  CH1   0  -0.217  -1.5199  -0.3599  -0.5639
 KCQ  N     N  NH2   0  -0.783  -1.6106   0.1314  -1.9193
 KCQ  C     C  C     0   0.406  -2.8357  -0.1540   0.1672
 KCQ  O     O  O     0  -0.396  -3.7013   0.5658  -0.2747
 KCQ  CMK   C  CH3   0  -0.785  -2.9855  -0.8620   1.4872
 KCQ  HN1   H  HNH2  0   0.344  -1.6562   1.1431  -1.9300
 KCQ  HN2   H  HNH2  0   0.355  -0.7795  -0.1259  -2.4354
 KCQ  HA    H  HCH1  0   0.267  -1.3567  -1.4434  -0.6106
 KCQ  HMK1  H  HCH3  0   0.255  -2.4779  -1.8260   1.4899
 KCQ  HMK2  H  HCH3  0   0.274  -2.5372  -0.2589   2.2805
 KCQ  HMK3  H  HCH3  0   0.269  -4.0368  -1.0019   1.7314
 KCQ  HB1   H  HCH2  0   0.248  -0.3940  -0.1937   1.2882
 KCQ  HB2   H  HCH2  0   0.250  -0.5813   1.3235   0.4220
 KCQ  HG    H  HCH1  0   0.275   1.0213   0.5743  -1.2965
 KCQ  HAH   H  HNH1  0   0.397   4.0309   0.0577   0.8814
 KCQ  HAE1  H  HCH2  0   0.237   3.4289  -1.2061  -1.3404
 KCQ  HAE2  H  HCH2  0   0.252   3.3628  -2.2317   0.0947
 KCQ  HD11  H  HCH2  0   0.257   1.1090  -1.8431  -1.4397
 KCQ  HD12  H  HCH2  0   0.247   1.0064  -2.0024   0.3128

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
 KCQ  OAD  CD2   double  1.221  0.020  1.221
 KCQ  CD2  CG    single  1.522  0.020  1.522
 KCQ  CD2  NAH   single  1.342  0.020  1.342
 KCQ  NAH  HAH   single  0.860  0.020  1.020
 KCQ  NAH  CAE   single  1.448  0.020  1.448
 KCQ  CAE  HAE1  single  0.970  0.020  1.090
 KCQ  CAE  HAE2  single  0.970  0.020  1.090
 KCQ  CAE  CD1   single  1.530  0.020  1.530
 KCQ  CD1  CG    single  1.529  0.020  1.529
 KCQ  CD1  HD11  single  0.970  0.020  1.090
 KCQ  CD1  HD12  single  0.970  0.020  1.090
 KCQ  CG   CB    single  1.520  0.020  1.520
 KCQ  CG   HG    single  0.970  0.020  1.090
 KCQ  CB   CA    single  1.543  0.020  1.543
 KCQ  CB   HB1   single  0.970  0.020  1.090
 KCQ  CB   HB2   single  0.970  0.020  1.090
 KCQ  CA   N     single  1.445  0.020  1.445
 KCQ  CA   HA    single  0.970  0.020  1.090
 KCQ  CA   C     single  1.519  0.020  1.519
 KCQ  N    HN1   single  0.890  0.020  1.040
 KCQ  N    HN2   single  0.890  0.020  1.040
 KCQ  C    O     double  1.209  0.020  1.209
 KCQ  C    CMK   single  1.505  0.020  1.505
 KCQ  CMK  HMK1  single  0.970  0.020  1.090
 KCQ  CMK  HMK2  single  0.970  0.020  1.090
 KCQ  CMK  HMK3  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
 KCQ  CG    CD2  NAH   107.55  3.000
 KCQ  NAH   CD2  OAD   126.33  3.000
 KCQ  CG    CD2  OAD   126.12  3.000
 KCQ  HAH   NAH  CAE   122.63  3.000
 KCQ  CAE   NAH  CD2   114.65  3.000
 KCQ  HAH   NAH  CD2   122.08  3.000
 KCQ  HAE2  CAE  HAE1  107.91  3.000
 KCQ  HAE2  CAE  CD1   112.67  3.000
 KCQ  HAE1  CAE  CD1   111.69  3.000
 KCQ  CD1   CAE  NAH   102.28  3.000
 KCQ  HAE2  CAE  NAH   111.15  3.000
 KCQ  HAE1  CAE  NAH   111.14  3.000
 KCQ  HD12  CD1  HD11  107.74  3.000
 KCQ  HD12  CD1  CG    109.62  3.000
 KCQ  HD11  CD1  CG    113.68  3.000
 KCQ  HD12  CD1  CAE   109.76  3.000
 KCQ  HD11  CD1  CAE   112.05  3.000
 KCQ  CG    CD1  CAE   103.95  3.000
 KCQ  HG    CG   CB    109.31  3.000
 KCQ  HG    CG   CD1   109.95  3.000
 KCQ  CB    CG   CD1   115.37  3.000
 KCQ  HG    CG   CD2   105.87  3.000
 KCQ  CB    CG   CD2   112.51  3.000
 KCQ  CD1   CG   CD2   103.32  3.000
 KCQ  HB2   CB   HB1   106.89  3.000
 KCQ  HB2   CB   CA    109.17  3.000
 KCQ  HB1   CB   CA    109.91  3.000
 KCQ  HB2   CB   CG    109.41  3.000
 KCQ  HB1   CB   CG    108.74  3.000
 KCQ  CA    CB   CG    112.56  3.000
 KCQ  HA    CA   C     106.46  3.000
 KCQ  C     CA   N     110.55  3.000
 KCQ  HA    CA   N     107.78  3.000
 KCQ  C     CA   CB    108.24  3.000
 KCQ  HA    CA   CB    107.93  3.000
 KCQ  N     CA   CB    115.49  3.000
 KCQ  HN2   N    HN1   106.61  3.000
 KCQ  HN2   N    CA    109.91  3.000
 KCQ  HN1   N    CA    110.64  3.000
 KCQ  CMK   C    O     121.95  3.000
 KCQ  CMK   C    CA    116.38  3.000
 KCQ  O     C    CA    121.64  3.000
 KCQ  HMK3  CMK  HMK2  107.71  3.000
 KCQ  HMK3  CMK  HMK1  109.61  3.000
 KCQ  HMK2  CMK  HMK1  107.18  3.000
 KCQ  HMK3  CMK  C     110.69  3.000
 KCQ  HMK2  CMK  C     109.65  3.000
 KCQ  HMK1  CMK  C     111.84  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
 KCQ  CONST_01  CG    CD2  NAH  CAE    0.00   0.0  0
 KCQ  CONST_02  CAE   NAH  CD2  OAD  180.00   0.0  0
 KCQ  CONST_03  HAH   NAH  CD2  CG   180.00   0.0  0
 KCQ  Var_01    CD1   CAE  NAH  CD2  -19.52  30.0  1
 KCQ  Var_02    CG    CD1  CAE  NAH   27.61  30.0  1
 KCQ  Var_03    HMK1  CMK  C    CA   -34.23  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
 KCQ  chir_01  CG  CD2  CD1  CB  negativ
 KCQ  chir_02  CA  N    C    CB  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
 KCQ  plan-1  CA   0.020
 KCQ  plan-1  C    0.020
 KCQ  plan-1  O    0.020
 KCQ  plan-1  CMK  0.020
 KCQ  plan-2  OAD  0.020
 KCQ  plan-2  CD2  0.020
 KCQ  plan-2  NAH  0.020
 KCQ  plan-2  CAE  0.020
 KCQ  plan-2  CG   0.020
 KCQ  plan-2  HAH  0.020

