# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:32:39 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  39  19  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.440   3.3893   1.4487  -1.3437
 28T  CAN  C  C     0   0.538   3.7474   1.2721  -0.2084
 28T  OAD  O  OH1   0  -0.590   4.4534   2.1478   0.4924
 28T  CAR  C  CH1   0  -0.148   3.5305  -0.0102   0.5666
 28T  CAK  C  CH2   0  -0.484   4.5849  -1.0635   0.1844
 28T  CAF  C  CH2   0  -0.474   3.8201  -2.3779   0.2947
 28T  CAL  C  CH2   0  -0.275   2.4343  -2.0215  -0.2234
 28T  NAS  N  NT    0  -0.490   2.2757  -0.6387   0.2101
 28T  CAP  C  C     0   0.593   1.1233   0.0377   0.3536
 28T  OAC  O  O     0  -0.505   1.1197   1.1867   0.7805
 28T  CAI  C  CH2   0  -0.599  -0.1425  -0.7006  -0.0197
 28T  CAH  C  CH2   0  -0.554  -1.3410   0.2240  -0.1122
 28T  C    C  C     0   0.379  -2.6403  -0.4902  -0.3684
 28T  O    O  O     0  -0.402  -2.7112  -1.6881  -0.5280
 28T  CA   C  CR15  0  -0.169  -3.8685   0.3897  -0.3886
 28T  CB   C  CH2   0  -0.488  -4.2696   0.8196   1.0643
 28T  CG   C  CH2   0  -0.449  -5.7593   0.4649   1.1541
 28T  CD   C  CH2   0  -0.328  -6.1752   0.3075  -0.3100
 28T  N    N  NR15  0  -0.589  -5.0187  -0.2603  -0.9910
 28T  H1   H  HOH1  0   0.483   4.6400   2.9321  -0.0457
 28T  H2   H  HCH1  0   0.285   3.5698   0.1979   1.6395
 28T  H3   H  HCH2  0   0.254   4.9232  -0.9140  -0.8433
 28T  H4   H  HCH2  0   0.271   5.4557  -1.0144   0.8353
 28T  H5   H  HCH2  0   0.261   4.2805  -3.1825  -0.2765
 28T  H6   H  HCH2  0   0.248   3.7594  -2.6960   1.3373
 28T  H7   H  HCH2  0   0.247   2.3830  -2.0969  -1.3137
 28T  H8   H  HCH2  0   0.262   1.6602  -2.6626   0.1971
 28T  H9   H  HCH2  0   0.276   0.0006  -1.2289  -0.9648
 28T  H10  H  HCH2  0   0.284  -0.3159  -1.4760   0.7330
 28T  H11  H  HCH2  0   0.284  -1.4508   0.8234   0.7959
 28T  H12  H  HCH2  0   0.283  -1.2076   0.9544  -0.9166
 28T  H13  H  HCR5  0   0.262  -3.6229   1.2946  -0.9547
 28T  H14  H  HCH2  0   0.247  -3.6898   0.3027   1.8309
 28T  H15  H  HCH2  0   0.249  -4.0957   1.8866   1.2008
 28T  H16  H  HCH2  0   0.231  -5.8959  -0.4812   1.6818
 28T  H17  H  HCH2  0   0.237  -6.3383   1.2222   1.6834
 28T  H18  H  HCH2  0   0.242  -7.0507  -0.3271  -0.4488
 28T  H19  H  HCH2  0   0.223  -6.4052   1.2852  -0.7437
 28T  H20  H  HNR5  0   0.343  -4.9750  -1.2527  -0.7837

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  1.511  0.020  1.511
 28T  CAL  CAF  single  1.522  0.020  1.522
 28T  CAL  NAS  single  1.458  0.020  1.458
 28T  N    CD   single  1.457  0.020  1.457
 28T  N    CA   single  1.452  0.020  1.452
 28T  CAI  CAH  single  1.516  0.020  1.516
 28T  CAI  CAP  single  1.512  0.020  1.512
 28T  CAF  CAK  single  1.525  0.020  1.525
 28T  CD   CG   single  1.530  0.020  1.530
 28T  CA   CB   single  1.567  0.020  1.567
 28T  NAS  CAP  single  1.344  0.020  1.344
 28T  NAS  CAR  single  1.448  0.020  1.448
 28T  CAP  OAC  double  1.226  0.020  1.226
 28T  CAK  CAR  single  1.539  0.020  1.539
 28T  CB   CG   single  1.534  0.020  1.534
 28T  OAA  CAN  double  1.203  0.020  1.203
 28T  CAR  CAN  single  1.514  0.020  1.514
 28T  CAN  OAD  single  1.325  0.020  1.325
 28T  OAD  H1   single  0.850  0.020  0.980
 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  111.42  3.000
 28T  OAD  CAN  OAA  124.08  3.000
 28T  CAR  CAN  OAA  124.38  3.000
 28T  H1   OAD  CAN  110.10  3.000
 28T  H2   CAR  NAS  110.81  3.000
 28T  H2   CAR  CAK  110.45  3.000
 28T  NAS  CAR  CAK  103.62  3.000
 28T  H2   CAR  CAN  109.63  3.000
 28T  CAK  CAR  CAN  110.76  3.000
 28T  NAS  CAR  CAN  111.46  3.000
 28T  H4   CAK  H3   107.98  3.000
 28T  H4   CAK  CAF  113.39  3.000
 28T  H3   CAK  CAF  109.97  3.000
 28T  H4   CAK  CAR  111.65  3.000
 28T  H3   CAK  CAR  110.63  3.000
 28T  CAF  CAK  CAR  103.21  3.000
 28T  H6   CAF  H5   108.01  3.000
 28T  H6   CAF  CAL  110.04  3.000
 28T  H5   CAF  CAL  112.30  3.000
 28T  H6   CAF  CAK  110.38  3.000
 28T  H5   CAF  CAK  112.77  3.000
 28T  CAL  CAF  CAK  103.31  3.000
 28T  H8   CAL  H7   108.11  3.000
 28T  H8   CAL  NAS  111.47  3.000
 28T  H7   CAL  NAS  110.89  3.000
 28T  H8   CAL  CAF  112.20  3.000
 28T  H7   CAL  CAF  111.46  3.000
 28T  NAS  CAL  CAF  102.71  3.000
 28T  CAP  NAS  CAL  127.05  3.000
 28T  CAP  NAS  CAR  119.89  3.000
 28T  CAL  NAS  CAR  112.99  3.000
 28T  CAI  CAP  OAC  122.76  3.000
 28T  OAC  CAP  NAS  120.76  3.000
 28T  CAI  CAP  NAS  116.47  3.000
 28T  H10  CAI  H9   105.85  3.000
 28T  H10  CAI  CAH  110.41  3.000
 28T  H9   CAI  CAH  110.22  3.000
 28T  H10  CAI  CAP  107.98  3.000
 28T  H9   CAI  CAP  109.88  3.000
 28T  CAH  CAI  CAP  112.27  3.000
 28T  H12  CAH  H11  104.87  3.000
 28T  H12  CAH  C    107.27  3.000
 28T  H11  CAH  C    108.35  3.000
 28T  H12  CAH  CAI  110.81  3.000
 28T  H11  CAH  CAI  111.28  3.000
 28T  C    CAH  CAI  113.79  3.000
 28T  CA   C    O    121.80  3.000
 28T  CA   C    CAH  115.33  3.000
 28T  O    C    CAH  122.87  3.000
 28T  H13  CA   N    109.46  3.000
 28T  H13  CA   CB   108.05  3.000
 28T  N    CA   CB   107.74  3.000
 28T  H13  CA   C    107.80  3.000
 28T  CB   CA   C    110.82  3.000
 28T  N    CA   C    112.87  3.000
 28T  H15  CB   H14  106.92  3.000
 28T  H15  CB   CG   111.97  3.000
 28T  H14  CB   CG   111.42  3.000
 28T  H15  CB   CA   110.11  3.000
 28T  H14  CB   CA   112.67  3.000
 28T  CG   CB   CA   103.85  3.000
 28T  H17  CG   H16  107.50  3.000
 28T  H17  CG   CD   113.06  3.000
 28T  H16  CG   CD   109.83  3.000
 28T  H17  CG   CB   112.55  3.000
 28T  H16  CG   CB   110.50  3.000
 28T  CD   CG   CB   103.40  3.000
 28T  H19  CD   H18  107.51  3.000
 28T  H19  CD   N    109.25  3.000
 28T  H18  CD   N    110.55  3.000
 28T  H19  CD   CG   110.15  3.000
 28T  H18  CD   CG   113.58  3.000
 28T  N    CD   CG   105.75  3.000
 28T  H20  N    CD   108.64  3.000
 28T  H20  N    CA   108.60  3.000
 28T  CD   N    CA   105.09  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  CONST_05  H1   OAD  CAN  CAR   180.00   0.0  0
 28T  Var_01    CAF  CAL  NAS  CAR    17.33  30.0  1
 28T  Var_02    NAS  CAL  CAF  CAK   -33.43  30.0  1
 28T  Var_03    CG   CD   N    CA    -38.32  30.0  1
 28T  Var_04    CD   CG   CB   CA    -17.44  30.0  1
 28T  Var_05    N    CD   CG   CB     34.57  30.0  1
 28T  Var_06    CAH  CAI  CAP  NAS  -167.61  30.0  1
 28T  Var_07    CA   C    CAH  CAI   176.66  30.0  2
 28T  Var_08    C    CAH  CAI  CAP  -175.16  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
 28T  plan-3  H1   0.020

