# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:20:22 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-[(2E)-4-carboxy-4-oxobut-2-en-2-yl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C\C(=O)C(O)=O)/N1CCC[C@H]1C(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
 DYJ  DYJ  1-[(2E)-4-carboxy-4-oxobut-2-en-2-yl]-L-proline  L-peptide  27  16  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DYJ
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
 DYJ  O    O  O      0  -0.589   2.0869  -1.3528   1.3863
 DYJ  C    C  C      0   0.410   2.8051  -1.1132   0.4023
 DYJ  N    N  NT     0  -0.462   1.0685   0.5843  -0.3119
 DYJ  C10  C  C      0   0.337  -3.7636   0.3709   0.4121
 DYJ  CA   C  CH1    0  -0.184   2.4396   0.1052  -0.4738
 DYJ  CB   C  CH2    0  -0.481   3.2954   1.3117  -0.0554
 DYJ  CG   C  CH2    0  -0.467   2.3829   2.5089  -0.2750
 DYJ  CD   C  CH2    0  -0.279   1.0240   1.9674   0.1347
 DYJ  C06  C  C      0   0.456  -0.0267  -0.1760  -0.4281
 DYJ  C07  C  CH3    0  -0.740   0.1318  -1.5222  -1.0717
 DYJ  C08  C  C1     0  -0.550  -1.2612   0.2939  -0.0100
 DYJ  C09  C  C      0   0.144  -2.5086  -0.3949  -0.1208
 DYJ  O11  O  O      0  -0.486  -2.6794  -1.5214  -0.5887
 DYJ  O12  O  OC    -1  -0.601  -4.8543  -0.1857   0.2053
 DYJ  O13  O  O      0  -0.591  -3.5718   1.4564   0.9950
 DYJ  OXT  O  OC    -1  -0.611   3.8424  -1.7082   0.0506
 DYJ  H1   H  HCH1   0   0.243   2.6343  -0.1272  -1.5257
 DYJ  H2   H  HCH2   0   0.235   3.5557   1.2423   1.0041
 DYJ  H3   H  HCH2   0   0.251   4.2238   1.3613  -0.6217
 DYJ  H4   H  HCH2   0   0.248   2.6740   3.3838   0.3058
 DYJ  H5   H  HCH2   0   0.236   2.3684   2.7957  -1.3289
 DYJ  H6   H  HCH2   0   0.247   0.1978   2.4995  -0.3389
 DYJ  H7   H  HCH2   0   0.232   0.8806   2.0273   1.2200
 DYJ  H8   H  HCH3   0   0.253  -0.0060  -2.3166  -0.3403
 DYJ  H9   H  HCH3   0   0.258  -0.6277  -1.6608  -1.8361
 DYJ  H10  H  HCH3   0   0.248   1.1049  -1.6559  -1.5351
 DYJ  H11  H  H      0   0.239  -1.3117   1.2596   0.4685

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
 DYJ  O    C    deloc   1.231  0.020  1.231
 DYJ  C    CA   single  1.525  0.021  1.525
 DYJ  CG   CB   single  1.521  0.020  1.521
 DYJ  CG   CD   single  1.519  0.020  1.519
 DYJ  CB   CA   single  1.530  0.020  1.530
 DYJ  CA   N    single  1.466  0.015  1.466
 DYJ  CD   N    single  1.473  0.014  1.473
 DYJ  N    C06  single  1.338  0.020  1.338
 DYJ  C06  C07  single  1.501  0.020  1.501
 DYJ  C06  C08  double  1.385  0.020  1.385
 DYJ  C08  C09  single  1.429  0.020  1.429
 DYJ  C09  O11  double  1.232  0.020  1.232
 DYJ  C09  C10  single  1.564  0.020  1.564
 DYJ  C10  O13  deloc   1.247  0.020  1.247
 DYJ  C10  O12  deloc   1.242  0.020  1.242
 DYJ  C    OXT  deloc   1.246  0.020  1.246
 DYJ  CA   H1   single  0.970  0.020  1.090
 DYJ  CB   H2   single  0.970  0.020  1.090
 DYJ  CB   H3   single  0.970  0.020  1.090
 DYJ  CG   H4   single  0.970  0.020  1.090
 DYJ  CG   H5   single  0.970  0.020  1.090
 DYJ  CD   H6   single  0.970  0.020  1.090
 DYJ  CD   H7   single  0.970  0.020  1.090
 DYJ  C07  H8   single  0.970  0.020  1.090
 DYJ  C07  H9   single  0.970  0.020  1.090
 DYJ  C07  H10  single  0.970  0.020  1.090
 DYJ  C08  H11  single  0.930  0.020  1.080

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
 DYJ  OXT  C    CA   114.42  3.000
 DYJ  OXT  C    O    127.80  3.000
 DYJ  CA   C    O    119.00  3.000
 DYJ  C06  N    CD   122.82  3.000
 DYJ  C06  N    CA   124.89  3.000
 DYJ  CD   N    CA   112.00  3.000
 DYJ  O13  C10  O12  127.09  3.000
 DYJ  O12  C10  C09  115.38  3.000
 DYJ  O13  C10  C09  117.53  3.000
 DYJ  H1   CA   CB   109.21  3.000
 DYJ  H1   CA   N    110.05  3.000
 DYJ  CB   CA   N    103.00  1.100
 DYJ  H1   CA   C    109.61  3.000
 DYJ  N    CA   C    112.10  2.500
 DYJ  CB   CA   C    110.10  1.900
 DYJ  H3   CB   H2   107.70  3.000
 DYJ  H3   CB   CG   113.62  3.000
 DYJ  H2   CB   CG   109.44  3.000
 DYJ  H3   CB   CA   111.65  3.000
 DYJ  H2   CB   CA   110.27  3.000
 DYJ  CG   CB   CA   104.15  3.000
 DYJ  H5   CG   H4   107.88  3.000
 DYJ  H5   CG   CD   109.99  3.000
 DYJ  H4   CG   CD   112.42  3.000
 DYJ  H5   CG   CB   110.72  3.000
 DYJ  H4   CG   CB   113.24  3.000
 DYJ  CD   CG   CB   102.54  3.000
 DYJ  H7   CD   H6   107.70  3.000
 DYJ  H7   CD   CG   111.37  3.000
 DYJ  H6   CD   CG   112.74  3.000
 DYJ  H7   CD   N    111.10  3.000
 DYJ  H6   CD   N    110.73  3.000
 DYJ  CG   CD   N    103.20  1.500
 DYJ  C08  C06  C07  121.86  3.000
 DYJ  C08  C06  N    120.69  3.000
 DYJ  C07  C06  N    117.42  3.000
 DYJ  H10  C07  H9   108.09  3.000
 DYJ  H10  C07  H8   108.07  3.000
 DYJ  H9   C07  H8   106.92  3.000
 DYJ  H10  C07  C06  112.84  3.000
 DYJ  H9   C07  C06  110.03  3.000
 DYJ  H8   C07  C06  110.68  3.000
 DYJ  H11  C08  C09  115.15  3.000
 DYJ  H11  C08  C06  118.62  3.000
 DYJ  C09  C08  C06  126.22  3.000
 DYJ  O11  C09  C08  126.25  3.000
 DYJ  O11  C09  C10  117.77  3.000
 DYJ  C08  C09  C10  115.98  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
 DYJ  Var_01  CB   CG   CD   N     -35.64  30.0  1
 DYJ  Var_02  CD   CG   CB   CA     36.85  30.0  1
 DYJ  Var_03  CG   CD   N    CA     21.80  30.0  1
 DYJ  Var_04  C07  C06  N    CA    -14.77  30.0  2
 DYJ  Var_05  C09  C08  C06  N     177.66   0.0  2
 DYJ  Var_06  H8   C07  C06  N     110.97  30.0  3
 DYJ  Var_07  C06  C08  C09  C10  -179.12  30.0  2
 DYJ  Var_08  O13  C10  C09  C08    -6.26  30.0  2

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
 DYJ  chir_01  CA  C  CB  N  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
 DYJ  plan-1  C10  0.020
 DYJ  plan-1  C08  0.020
 DYJ  plan-1  C09  0.020
 DYJ  plan-1  O11  0.020
 DYJ  plan-2  O    0.020
 DYJ  plan-2  C    0.020
 DYJ  plan-2  CA   0.020
 DYJ  plan-2  OXT  0.020
 DYJ  plan-3  C10  0.020
 DYJ  plan-3  C09  0.020
 DYJ  plan-3  O12  0.020
 DYJ  plan-3  O13  0.020
 DYJ  plan-4  N    0.020
 DYJ  plan-4  C06  0.020
 DYJ  plan-4  C07  0.020
 DYJ  plan-4  C08  0.020
 DYJ  plan-4  C09  0.020
 DYJ  plan-4  H11  0.020

