# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 07:37:04 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: (2S)-5-amino-2-(2-oxoazetidin-1-yl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCC[C@H](N1CCC1=O)C(O)=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
 RQJ  RQJ  '(2S)-5-amino-2-(2-oxoazetidin-1-yl)pentanoic acid'  ligand  26  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RQJ
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
 RQJ  N    N  N      0  -0.413   -9.7263  -18.7401  -16.8970
 RQJ  CA   C  CH1    0  -0.239   -8.9873  -17.9201  -15.9785
 RQJ  C    C  C      0   0.421   -9.8079  -17.6182  -14.6870
 RQJ  OXT  O  OC     0  -0.598   -9.3123  -16.7666  -13.9252
 RQJ  CB   C  CH2    0  -0.443   -8.4828  -16.6569  -16.6711
 RQJ  O    O  O     -1  -0.587  -10.8539  -18.2680  -14.5188
 RQJ  CAB  C  C      0   0.502   -9.9409  -20.0690  -16.9327
 RQJ  CAC  C  C      0  -0.643  -11.1075  -19.9156  -17.9016
 RQJ  CAD  C  C      0  -0.237  -10.8677  -18.4012  -17.7363
 RQJ  CAK  C  CH2    0  -0.414   -7.5710  -16.9371  -17.8597
 RQJ  CAL  C  CH2    0  -0.290   -7.0822  -15.6770  -18.5598
 RQJ  NAM  N  NH2    0  -0.801   -6.2340  -14.8666  -17.6954
 RQJ  OAE  O  O      0  -0.479   -9.3899  -20.9963  -16.3774
 RQJ  H1   H  HCH1   0   0.246   -8.1134  -18.5076  -15.6703
 RQJ  H3   H  HCH2   0   0.233   -7.9561  -16.0650  -15.9224
 RQJ  H4   H  HCH2   0   0.214   -9.3356  -16.0496  -16.9984
 RQJ  H5   H  H      0   0.271  -12.0591  -20.2792  -17.5153
 RQJ  H6   H  H      0   0.271  -10.9426  -20.3203  -18.8998
 RQJ  H7   H  H      0   0.234  -10.6070  -17.8573  -18.6455
 RQJ  H8   H  H      0   0.235  -11.6610  -17.8734  -17.2062
 RQJ  H9   H  HCH2   0   0.219   -8.0970  -17.5525  -18.5945
 RQJ  H10  H  HCH2   0   0.208   -6.7065  -17.5213  -17.5266
 RQJ  H11  H  HCH2   0   0.186   -7.9539  -15.1317  -18.9522
 RQJ  H12  H  HCH2   0   0.220   -6.4898  -15.9695  -19.4301
 RQJ  H13  H  HNH2   0   0.344   -5.8531  -14.0957  -18.2288
 RQJ  H14  H  HNH2   0   0.340   -6.7956  -14.4369  -16.9712

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
 RQJ  CAL  NAM  single  1.457  0.020  1.457
 RQJ  CAL  CAK  single  1.522  0.020  1.522
 RQJ  CAC  CAD  single  1.542  0.020  1.542
 RQJ  CAC  CAB  single  1.524  0.020  1.524
 RQJ  CAK  CB   single  1.524  0.020  1.524
 RQJ  CAD  N    single  1.457  0.020  1.457
 RQJ  CAB  N    single  1.347  0.020  1.347
 RQJ  CAB  OAE  double  1.213  0.020  1.213
 RQJ  N    CA   single  1.436  0.020  1.436
 RQJ  CB   CA   single  1.526  0.020  1.526
 RQJ  CA   C    single  1.560  0.020  1.560
 RQJ  C    O    deloc   1.243  0.020  1.243
 RQJ  C    OXT  deloc   1.245  0.020  1.245
 RQJ  CA   H1   single  0.970  0.020  1.090
 RQJ  CB   H3   single  0.970  0.020  1.090
 RQJ  CB   H4   single  0.970  0.020  1.090
 RQJ  CAC  H5   single  0.970  0.020  1.090
 RQJ  CAC  H6   single  0.970  0.020  1.090
 RQJ  CAD  H7   single  0.970  0.020  1.090
 RQJ  CAD  H8   single  0.970  0.020  1.090
 RQJ  CAK  H9   single  0.970  0.020  1.090
 RQJ  CAK  H10  single  0.970  0.020  1.090
 RQJ  CAL  H11  single  0.970  0.020  1.090
 RQJ  CAL  H12  single  0.970  0.020  1.090
 RQJ  NAM  H13  single  0.890  0.020  1.040
 RQJ  NAM  H14  single  0.890  0.020  1.040

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
 RQJ  CAD  N    CAB   95.13  3.000
 RQJ  CAB  N    CA   131.49  3.000
 RQJ  CAD  N    CA   129.71  3.000
 RQJ  H1   CA   CB   107.90  3.000
 RQJ  H1   CA   C    106.86  3.000
 RQJ  CB   CA   C    112.92  3.000
 RQJ  H1   CA   N    106.48  3.000
 RQJ  C    CA   N    111.68  3.000
 RQJ  CB   CA   N    110.64  3.000
 RQJ  O    C    OXT  127.57  3.000
 RQJ  OXT  C    CA   115.43  3.000
 RQJ  O    C    CA   116.98  3.000
 RQJ  H4   CB   H3   106.26  3.000
 RQJ  H4   CB   CAK  109.52  3.000
 RQJ  H3   CB   CAK  110.27  3.000
 RQJ  H4   CB   CA   109.67  3.000
 RQJ  H3   CB   CA   107.30  3.000
 RQJ  CAK  CB   CA   113.55  3.000
 RQJ  OAE  CAB  CAC  135.68  3.000
 RQJ  OAE  CAB  N    132.05  3.000
 RQJ  CAC  CAB  N     92.27  3.000
 RQJ  H6   CAC  H5   109.46  3.000
 RQJ  H6   CAC  CAD  116.06  3.000
 RQJ  H5   CAC  CAD  115.18  3.000
 RQJ  H6   CAC  CAB  115.41  3.000
 RQJ  H5   CAC  CAB  114.18  3.000
 RQJ  CAD  CAC  CAB   84.93  3.000
 RQJ  H8   CAD  H7   109.73  3.000
 RQJ  H8   CAD  CAC  114.47  3.000
 RQJ  H7   CAD  CAC  115.94  3.000
 RQJ  H8   CAD  N    113.74  3.000
 RQJ  H7   CAD  N    114.14  3.000
 RQJ  CAC  CAD  N     87.43  3.000
 RQJ  H10  CAK  H9   106.49  3.000
 RQJ  H10  CAK  CAL  109.15  3.000
 RQJ  H9   CAK  CAL  108.14  3.000
 RQJ  H10  CAK  CB   109.46  3.000
 RQJ  H9   CAK  CB   109.87  3.000
 RQJ  CAL  CAK  CB   113.49  3.000
 RQJ  H12  CAL  H11  106.15  3.000
 RQJ  H12  CAL  NAM  107.81  3.000
 RQJ  H11  CAL  NAM  113.39  3.000
 RQJ  H12  CAL  CAK  108.59  3.000
 RQJ  H11  CAL  CAK  108.65  3.000
 RQJ  NAM  CAL  CAK  111.99  3.000
 RQJ  H14  NAM  H13  105.23  3.000
 RQJ  H14  NAM  CAL  109.73  3.000
 RQJ  H13  NAM  CAL  109.27  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
 RQJ  CONST_01  CAB  CAC  CAD  N      0.00   0.0  0
 RQJ  CONST_04  OAE  CAB  CAC  CAD  180.00   0.0  0
 RQJ  CONST_05  OAE  CAB  N    CAD  180.00   0.0  0
 RQJ  Var_01    H5   CAC  CAD  N    117.79  30.0  1
 RQJ  Var_02    CAL  CAK  CB   CA   179.29  30.0  1
 RQJ  Var_03    NAM  CAL  CAK  CB    64.51  30.0  2
 RQJ  Var_04    H13  NAM  CAL  CAK  173.97  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
 RQJ  chir_01  CA  N  CB  C  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
 RQJ  plan-1  N    0.020
 RQJ  plan-1  CA   0.020
 RQJ  plan-1  CAB  0.020
 RQJ  plan-1  CAC  0.020
 RQJ  plan-1  CAD  0.020
 RQJ  plan-1  OAE  0.020
 RQJ  plan-2  CA   0.020
 RQJ  plan-2  C    0.020
 RQJ  plan-2  OXT  0.020
 RQJ  plan-2  O    0.020

