# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:42:24 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  29  16  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

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  -0.422   2.1115  -1.3932   1.4060
 DYJ  C    C  C     0   0.544   2.7653  -1.0592   0.4537
 DYJ  N    N  NR5   0  -0.467   1.0647   0.5676  -0.2686
 DYJ  C10  C  C     0   0.477  -3.7146   0.3737   0.3617
 DYJ  CA   C  CR15  0  -0.201   2.4307   0.1048  -0.4566
 DYJ  CB   C  CH2   0  -0.480   3.3047   1.3191  -0.0794
 DYJ  CG   C  CH2   0  -0.470   2.3691   2.5020  -0.2742
 DYJ  CD   C  CH2   0  -0.288   1.0278   1.9562   0.1807
 DYJ  C06  C  C     0   0.470  -0.0270  -0.1865  -0.4301
 DYJ  C07  C  CH3   0  -0.756   0.1294  -1.5264  -1.0818
 DYJ  C08  C  C1    0  -0.529  -1.2659   0.2885  -0.0241
 DYJ  C09  C  C     0   0.206  -2.4932  -0.4084  -0.1639
 DYJ  O11  O  O     0  -0.448  -2.7007  -1.5220  -0.6320
 DYJ  O12  O  OH1   0  -0.581  -4.8335  -0.2980   0.1697
 DYJ  O13  O  O     0  -0.423  -3.6609   1.4602   0.8808
 DYJ  OXT  O  OH1   0  -0.585   3.9043  -1.6246   0.0878
 DYJ  H1   H  HCR5  0   0.315   2.6152  -0.1719  -1.4980
 DYJ  H2   H  HCH2  0   0.261   3.6188   1.2616   0.9649
 DYJ  H3   H  HCH2  0   0.279   4.1997   1.3638  -0.6958
 DYJ  H4   H  HCH2  0   0.266   2.6747   3.3769   0.2968
 DYJ  H5   H  HCH2  0   0.252   2.3196   2.7843  -1.3274
 DYJ  H6   H  HCH2  0   0.267   0.1885   2.4803  -0.2742
 DYJ  H7   H  HCH2  0   0.256   0.9154   2.0083   1.2682
 DYJ  H8   H  HCH3  0   0.274  -0.0242  -2.3270  -0.3591
 DYJ  H9   H  HCH3  0   0.281  -0.6221  -1.6511  -1.8564
 DYJ  H10  H  HCH3  0   0.261   1.1021  -1.6660  -1.5446
 DYJ  H11  H  H     0   0.270  -1.3189   1.2502   0.4622
 DYJ  H12  H  HOH1  0   0.483  -5.5848   0.2152   0.5036
 DYJ  HXT  H  HOH1  0   0.489   4.1458  -2.3297   0.7078

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    double  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  1.518  0.020  1.518
 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  1.337  0.020  1.337
 DYJ  C06  C07  single  1.498  0.020  1.498
 DYJ  C06  C08  double  1.388  0.020  1.388
 DYJ  C08  C09  single  1.418  0.020  1.418
 DYJ  C09  O11  double  1.226  0.020  1.226
 DYJ  C09  C10  single  1.543  0.020  1.543
 DYJ  C10  O13  double  1.205  0.020  1.205
 DYJ  C10  O12  single  1.319  0.020  1.319
 DYJ  C    OXT  single  1.323  0.020  1.323
 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
 DYJ  O12  H12  single  0.850  0.020  0.980
 DYJ  OXT  HXT  single  0.850  0.020  0.980

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   110.63  3.000
 DYJ  OXT  C    O    124.63  3.000
 DYJ  CA   C    O    119.00  3.000
 DYJ  C06  N    CD   123.59  3.000
 DYJ  C06  N    CA   124.88  3.000
 DYJ  CD   N    CA   111.48  3.000
 DYJ  O13  C10  O12  124.02  3.000
 DYJ  O12  C10  C09  111.33  3.000
 DYJ  O13  C10  C09  124.65  3.000
 DYJ  H1   CA   CB   109.66  3.000
 DYJ  H1   CA   N    111.24  3.000
 DYJ  CB   CA   N    103.00  1.100
 DYJ  H1   CA   C    109.91  3.000
 DYJ  N    CA   C    112.10  2.500
 DYJ  CB   CA   C    110.10  1.900
 DYJ  H3   CB   H2   107.91  3.000
 DYJ  H3   CB   CG   113.68  3.000
 DYJ  H2   CB   CG   109.90  3.000
 DYJ  H3   CB   CA   111.10  3.000
 DYJ  H2   CB   CA   110.82  3.000
 DYJ  CG   CB   CA   103.43  3.000
 DYJ  H5   CG   H4   108.12  3.000
 DYJ  H5   CG   CD   110.01  3.000
 DYJ  H4   CG   CD   112.33  3.000
 DYJ  H5   CG   CB   110.65  3.000
 DYJ  H4   CG   CB   112.66  3.000
 DYJ  CD   CG   CB   103.04  3.000
 DYJ  H7   CD   H6   108.24  3.000
 DYJ  H7   CD   CG   111.81  3.000
 DYJ  H6   CD   CG   112.51  3.000
 DYJ  H7   CD   N    110.71  3.000
 DYJ  H6   CD   N    110.40  3.000
 DYJ  CG   CD   N    103.20  1.500
 DYJ  C08  C06  C07  121.78  3.000
 DYJ  C08  C06  N    120.05  3.000
 DYJ  C07  C06  N    118.16  3.000
 DYJ  H10  C07  H9   107.51  3.000
 DYJ  H10  C07  H8   108.33  3.000
 DYJ  H9   C07  H8   106.92  3.000
 DYJ  H10  C07  C06  113.19  3.000
 DYJ  H9   C07  C06  109.92  3.000
 DYJ  H8   C07  C06  110.73  3.000
 DYJ  H11  C08  C09  116.10  3.000
 DYJ  H11  C08  C06  118.74  3.000
 DYJ  C09  C08  C06  125.14  3.000
 DYJ  O11  C09  C08  129.09  3.000
 DYJ  O11  C09  C10  117.18  3.000
 DYJ  C08  C09  C10  113.73  3.000
 DYJ  H12  O12  C10  109.74  3.000
 DYJ  HXT  OXT  C    110.39  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  CONST_01  HXT  OXT  C    CA    180.00   0.0  0
 DYJ  CONST_02  H12  O12  C10  C09   180.00   0.0  0
 DYJ  Var_01    CB   CG   CD   N     -36.03  30.0  1
 DYJ  Var_02    CD   CG   CB   CA     36.40  30.0  1
 DYJ  Var_03    CG   CD   N    CA     22.44  30.0  1
 DYJ  Var_04    C07  C06  N    CA    -11.49  30.0  2
 DYJ  Var_05    C09  C08  C06  N     178.88   0.0  2
 DYJ  Var_06    H8   C07  C06  N     110.05  30.0  3
 DYJ  Var_07    C06  C08  C09  C10  -179.26  30.0  2
 DYJ  Var_08    O13  C10  C09  C08    -1.95  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-2  HXT  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-3  H12  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

