# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 14:33:37 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 1-{4-oxo-4-[(2S)-pyrrolidin-2-yl]butanoyl}-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCN1C(=O)CCC(=O)[C@@H]2CCCN2
#
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
 28T  28T  1-{4-oxo-4-[(2S)-pyrrolidin-2-yl]butanoyl}-L-proline  ligand  38  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_28T
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
 28T  OAA  O  O      0  -0.532   3.4031   1.0953  -1.5438
 28T  CAN  C  C      0   0.427   3.9066   1.1414  -0.4074
 28T  OAD  O  OC    -1  -0.783   4.7259   1.9768   0.0243
 28T  CAR  C  CH1    0  -0.173   3.5586  -0.0109   0.5565
 28T  CAK  C  CH2    0  -0.472   4.5007  -1.2055   0.3242
 28T  CAF  C  CH2    0  -0.424   3.6181  -2.4303   0.5386
 28T  CAL  C  CH2    0  -0.314   2.2856  -1.9850  -0.0443
 28T  NAS  N  NT     0  -0.375   2.2392  -0.5793   0.3223
 28T  CAP  C  C      0   0.514   1.1455   0.1924   0.3662
 28T  OAC  O  O      0  -0.539   1.2002   1.3705   0.7049
 28T  CAI  C  CH2    0  -0.599  -0.1636  -0.4746  -0.0077
 28T  CAH  C  CH2    0  -0.556  -1.3110   0.5132  -0.0995
 28T  C    C  C      0   0.368  -2.6240  -0.1159  -0.4806
 28T  O    O  O      0  -0.357  -2.7087  -1.2498  -0.8974
 28T  CA   C  CH1    0  -0.181  -3.8431   0.7802  -0.3549
 28T  CB   C  CH2    0  -0.460  -4.3122   0.7948   1.1270
 28T  CG   C  CH2    0  -0.477  -5.4567  -0.2105   1.1356
 28T  CD   C  CH2    0  -0.273  -6.0907   0.0457  -0.2258
 28T  N    N  NH1    0  -0.599  -4.9768   0.3059  -1.1403
 28T  H2   H  HCH1   0   0.284   3.6363   0.3363   1.5913
 28T  H3   H  HCH2   0   0.274   4.8709  -1.2001  -0.7036
 28T  H4   H  HCH2   0   0.250   5.3651  -1.1775   0.9858
 28T  H5   H  HCH2   0   0.277   4.0027  -3.3294   0.0583
 28T  H6   H  HCH2   0   0.169   3.5043  -2.6404   1.6047
 28T  H7   H  HCH2   0   0.259   2.2719  -2.1096  -1.1327
 28T  H8   H  HCH2   0   0.231   1.4429  -2.5400   0.3670
 28T  H9   H  HCH2   0   0.274  -0.0459  -1.0059  -0.9550
 28T  H10  H  HCH2   0   0.228  -0.3915  -1.2445   0.7365
 28T  H11  H  HCH2   0   0.305  -1.4334   1.0707   0.8320
 28T  H12  H  HCH2   0   0.293  -1.1072   1.2780  -0.8576
 28T  H13  H  HCH1   0   0.258  -3.5422   1.7915  -0.6502
 28T  H14  H  HCH2   0   0.247  -3.5174   0.5581   1.8355
 28T  H15  H  HCH2   0   0.261  -4.6783   1.7917   1.3787
 28T  H16  H  HCH2   0   0.219  -5.0723  -1.2320   1.1918
 28T  H17  H  HCH2   0   0.201  -6.1442  -0.0635   1.9691
 28T  H18  H  HCH2   0   0.266  -6.6962  -0.7832  -0.5935
 28T  H19  H  HCH2   0   0.198  -6.7440   0.9221  -0.1702
 28T  H20  H  HNH1   0   0.313  -4.7183  -0.5629  -1.5921

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
 28T  O    C    double  1.211  0.020  1.211
 28T  C    CAH  single  1.505  0.020  1.505
 28T  C    CA   single  1.518  0.020  1.518
 28T  CAL  CAF  single  1.521  0.020  1.521
 28T  CAL  NAS  single  1.453  0.020  1.453
 28T  N    CD   single  1.464  0.020  1.464
 28T  N    CA   single  1.458  0.020  1.458
 28T  CAI  CAH  single  1.517  0.020  1.517
 28T  CAI  CAP  single  1.516  0.020  1.516
 28T  CAF  CAK  single  1.525  0.020  1.525
 28T  CD   CG   single  1.524  0.020  1.524
 28T  CA   CB   single  1.554  0.020  1.554
 28T  NAS  CAP  single  1.339  0.020  1.339
 28T  NAS  CAR  single  1.456  0.020  1.456
 28T  CAP  OAC  double  1.227  0.020  1.227
 28T  CAK  CAR  single  1.539  0.020  1.539
 28T  CB   CG   single  1.523  0.020  1.523
 28T  OAA  CAN  deloc   1.244  0.020  1.244
 28T  CAR  CAN  single  1.542  0.020  1.542
 28T  CAN  OAD  deloc   1.247  0.020  1.247
 28T  CAR  H2   single  0.970  0.020  1.090
 28T  CAK  H3   single  0.970  0.020  1.090
 28T  CAK  H4   single  0.970  0.020  1.090
 28T  CAF  H5   single  0.970  0.020  1.090
 28T  CAF  H6   single  0.970  0.020  1.090
 28T  CAL  H7   single  0.970  0.020  1.090
 28T  CAL  H8   single  0.970  0.020  1.090
 28T  CAI  H9   single  0.970  0.020  1.090
 28T  CAI  H10  single  0.970  0.020  1.090
 28T  CAH  H11  single  0.970  0.020  1.090
 28T  CAH  H12  single  0.970  0.020  1.090
 28T  CA   H13  single  0.970  0.020  1.090
 28T  CB   H14  single  0.970  0.020  1.090
 28T  CB   H15  single  0.970  0.020  1.090
 28T  CG   H16  single  0.970  0.020  1.090
 28T  CG   H17  single  0.970  0.020  1.090
 28T  CD   H18  single  0.970  0.020  1.090
 28T  CD   H19  single  0.970  0.020  1.090
 28T  N    H20  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
 28T  CAR  CAN  OAD  115.62  3.000
 28T  OAD  CAN  OAA  127.37  3.000
 28T  CAR  CAN  OAA  116.87  3.000
 28T  H2   CAR  NAS  109.90  3.000
 28T  H2   CAR  CAK  110.21  3.000
 28T  NAS  CAR  CAK  103.15  3.000
 28T  H2   CAR  CAN  109.75  3.000
 28T  CAK  CAR  CAN  110.33  3.000
 28T  NAS  CAR  CAN  113.32  3.000
 28T  H4   CAK  H3   107.61  3.000
 28T  H4   CAK  CAF  113.25  3.000
 28T  H3   CAK  CAF  109.41  3.000
 28T  H4   CAK  CAR  111.98  3.000
 28T  H3   CAK  CAR  110.22  3.000
 28T  CAF  CAK  CAR  104.35  3.000
 28T  H6   CAF  H5   107.95  3.000
 28T  H6   CAF  CAL  109.82  3.000
 28T  H5   CAF  CAL  112.45  3.000
 28T  H6   CAF  CAK  110.61  3.000
 28T  H5   CAF  CAK  113.36  3.000
 28T  CAL  CAF  CAK  102.59  3.000
 28T  H8   CAL  H7   107.91  3.000
 28T  H8   CAL  NAS  111.88  3.000
 28T  H7   CAL  NAS  111.11  3.000
 28T  H8   CAL  CAF  112.56  3.000
 28T  H7   CAL  CAF  111.00  3.000
 28T  NAS  CAL  CAF  102.38  3.000
 28T  CAP  NAS  CAL  126.27  3.000
 28T  CAP  NAS  CAR  120.66  3.000
 28T  CAL  NAS  CAR  112.91  3.000
 28T  CAI  CAP  OAC  121.93  3.000
 28T  OAC  CAP  NAS  121.73  3.000
 28T  CAI  CAP  NAS  116.34  3.000
 28T  H10  CAI  H9   105.65  3.000
 28T  H10  CAI  CAH  109.98  3.000
 28T  H9   CAI  CAH  110.23  3.000
 28T  H10  CAI  CAP  108.75  3.000
 28T  H9   CAI  CAP  109.56  3.000
 28T  CAH  CAI  CAP  112.44  3.000
 28T  H12  CAH  H11  104.75  3.000
 28T  H12  CAH  C    106.19  3.000
 28T  H11  CAH  C    109.36  3.000
 28T  H12  CAH  CAI  110.84  3.000
 28T  H11  CAH  CAI  111.43  3.000
 28T  C    CAH  CAI  113.77  3.000
 28T  CA   C    O    121.67  3.000
 28T  CA   C    CAH  115.65  3.000
 28T  O    C    CAH  122.65  3.000
 28T  H13  CA   N    111.62  3.000
 28T  H13  CA   CB   109.34  3.000
 28T  N    CA   CB   106.37  3.000
 28T  H13  CA   C    107.57  3.000
 28T  CB   CA   C    109.08  3.000
 28T  N    CA   C    112.81  3.000
 28T  H15  CB   H14  107.03  3.000
 28T  H15  CB   CG   110.46  3.000
 28T  H14  CB   CG   113.61  3.000
 28T  H15  CB   CA   109.25  3.000
 28T  H14  CB   CA   113.41  3.000
 28T  CG   CB   CA   103.06  3.000
 28T  H17  CG   H16  107.96  3.000
 28T  H17  CG   CD   113.45  3.000
 28T  H16  CG   CD   110.45  3.000
 28T  H17  CG   CB   112.90  3.000
 28T  H16  CG   CB   110.67  3.000
 28T  CD   CG   CB   101.34  3.000
 28T  H19  CD   H18  107.12  3.000
 28T  H19  CD   N    110.09  3.000
 28T  H18  CD   N    110.30  3.000
 28T  H19  CD   CG   109.73  3.000
 28T  H18  CD   CG   113.87  3.000
 28T  N    CD   CG   105.75  3.000
 28T  H20  N    CD   108.68  3.000
 28T  H20  N    CA   108.71  3.000
 28T  CD   N    CA   108.22  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
 28T  CONST_01  CAI  CAP  NAS  CAR   180.00   0.0  0
 28T  CONST_02  OAC  CAP  NAS  CAR     0.00   0.0  0
 28T  CONST_03  CAI  CAP  NAS  CAL     0.00   0.0  0
 28T  CONST_04  OAC  CAP  NAS  CAL   180.00   0.0  0
 28T  Var_01    CAF  CAL  NAS  CAR    23.53  30.0  1
 28T  Var_02    NAS  CAL  CAF  CAK   -36.16  30.0  1
 28T  Var_03    CG   CD   N    CA    -24.04  30.0  1
 28T  Var_04    CD   CG   CB   CA    -36.36  30.0  1
 28T  Var_05    N    CD   CG   CB     37.81  30.0  1
 28T  Var_06    CAH  CAI  CAP  NAS  -172.73  30.0  2
 28T  Var_07    CA   C    CAH  CAI   169.94  30.0  1
 28T  Var_08    C    CAH  CAI  CAP   179.51  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
 28T  chir_01  CAR  NAS  CAK  CAN  negativ
 28T  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
 28T  plan-1  CAR  0.020
 28T  plan-1  CAL  0.020
 28T  plan-1  NAS  0.020
 28T  plan-1  CAP  0.020
 28T  plan-1  OAC  0.020
 28T  plan-1  CAI  0.020
 28T  plan-2  CAH  0.020
 28T  plan-2  C    0.020
 28T  plan-2  O    0.020
 28T  plan-2  CA   0.020
 28T  plan-3  OAA  0.020
 28T  plan-3  CAN  0.020
 28T  plan-3  OAD  0.020
 28T  plan-3  CAR  0.020

