# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 09:17:16 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H]1CCNC1=O)/C=C/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
 PJE  PJE  '(E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid'  peptide  28  14  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PJE
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
 PJE  C19  C  CH1   0  -0.143   0.2038  -1.2721  -0.2250
 PJE  C20  C  C1    0  -0.140   1.2720  -0.2302  -0.3020
 PJE  C21  C  C1    0  -0.405   2.5658  -0.4322  -0.0573
 PJE  C22  C  C     0   0.529   3.5322   0.6741  -0.1575
 PJE  O6   O  OH1   0  -0.604   4.7668   0.2706   0.1326
 PJE  C25  C  CH2   0  -0.436  -0.8917  -0.8676   0.7832
 PJE  C26  C  CR15  0  -0.419  -1.5436   0.5121   0.6215
 PJE  C27  C  CH2   0  -0.466  -2.7248   0.6968   1.5792
 PJE  C28  C  CH2   0  -0.260  -3.9418   0.2495   0.7637
 PJE  N6   N  NR15  0  -0.617  -3.5140   0.5135  -0.5930
 PJE  C29  C  CR5   0   0.547  -2.1894   0.6622  -0.7486
 PJE  O8   O  O     0  -0.496  -1.6079   0.8584  -1.8059
 PJE  N5   N  NH2   0  -0.786   0.7513  -2.5870   0.0525
 PJE  O7   O  O     0  -0.454   3.2686   1.8156  -0.4604
 PJE  H1   H  HCH1  0   0.260  -0.2504  -1.3137  -1.2208
 PJE  H2   H  H     0   0.271   0.9435   0.7625  -0.5891
 PJE  H4   H  H     0   0.271   2.9437  -1.4105   0.2110
 PJE  H6   H  HOH1  0   0.479   5.3838   1.0134   0.0565
 PJE  H7   H  HCH2  0   0.245  -1.6668  -1.6401   0.7478
 PJE  H8   H  HCH2  0   0.246  -0.4597  -0.9108   1.7881
 PJE  H9   H  HCR5  0   0.278  -0.7934   1.2932   0.7577
 PJE  H10  H  HCH2  0   0.254  -2.6181   0.1310   2.5041
 PJE  H11  H  HCH2  0   0.258  -2.8289   1.7499   1.8443
 PJE  H12  H  HCH2  0   0.237  -4.1684  -0.8106   0.9083
 PJE  H13  H  HCH2  0   0.254  -4.8387   0.8165   1.0109
 PJE  H14  H  HNR5  0   0.396  -4.1436   0.4707  -1.3794
 PJE  H15  H  HNH2  0   0.344   1.0324  -2.6439   1.0252
 PJE  H16  H  HNH2  0   0.356   0.0240  -3.2814  -0.0640

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
 PJE  C28  C27  single  1.532  0.020  1.532
 PJE  C28  N6   single  1.447  0.020  1.447
 PJE  C27  C26  single  1.532  0.020  1.532
 PJE  N6   C29  single  1.342  0.020  1.342
 PJE  O7   C22  double  1.210  0.020  1.210
 PJE  O6   C22  single  1.331  0.020  1.331
 PJE  C22  C21  single  1.472  0.020  1.472
 PJE  C26  C29  single  1.522  0.020  1.522
 PJE  C26  C25  single  1.534  0.020  1.534
 PJE  C29  O8   double  1.222  0.020  1.222
 PJE  C21  C20  double  1.332  0.020  1.332
 PJE  C25  C19  single  1.543  0.020  1.543
 PJE  C19  C20  single  1.494  0.020  1.494
 PJE  C19  N5   single  1.451  0.020  1.451
 PJE  C19  H1   single  0.970  0.020  1.090
 PJE  C20  H2   single  0.930  0.020  1.080
 PJE  C21  H4   single  0.930  0.020  1.080
 PJE  O6   H6   single  0.850  0.020  0.980
 PJE  C25  H7   single  0.970  0.020  1.090
 PJE  C25  H8   single  0.970  0.020  1.090
 PJE  C26  H9   single  0.970  0.020  1.090
 PJE  C27  H10  single  0.970  0.020  1.090
 PJE  C27  H11  single  0.970  0.020  1.090
 PJE  C28  H12  single  0.970  0.020  1.090
 PJE  C28  H13  single  0.970  0.020  1.090
 PJE  N6   H14  single  0.860  0.020  1.020
 PJE  N5   H15  single  0.890  0.020  1.040
 PJE  N5   H16  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
 PJE  H1   C19  N5   107.21  3.000
 PJE  H1   C19  C25  108.04  3.000
 PJE  N5   C19  C25  112.37  3.000
 PJE  H1   C19  C20  106.02  3.000
 PJE  N5   C19  C20  111.84  3.000
 PJE  C25  C19  C20  111.01  3.000
 PJE  H2   C20  C21  118.79  3.000
 PJE  H2   C20  C19  115.81  3.000
 PJE  C21  C20  C19  125.39  3.000
 PJE  H4   C21  C22  117.83  3.000
 PJE  H4   C21  C20  121.43  3.000
 PJE  C22  C21  C20  120.73  3.000
 PJE  O7   C22  O6   122.86  3.000
 PJE  O6   C22  C21  111.48  3.000
 PJE  O7   C22  C21  125.65  3.000
 PJE  H6   O6   C22  109.96  3.000
 PJE  H8   C25  H7   106.33  3.000
 PJE  H8   C25  C26  107.45  3.000
 PJE  H7   C25  C26  109.28  3.000
 PJE  H8   C25  C19  108.02  3.000
 PJE  H7   C25  C19  107.25  3.000
 PJE  C26  C25  C19  117.94  3.000
 PJE  H9   C26  C29  109.48  3.000
 PJE  H9   C26  C27  111.45  3.000
 PJE  C29  C26  C27  102.93  3.000
 PJE  H9   C26  C25  109.77  3.000
 PJE  C29  C26  C25  111.33  3.000
 PJE  C27  C26  C25  111.72  3.000
 PJE  H11  C27  H10  107.72  3.000
 PJE  H11  C27  C28  109.60  3.000
 PJE  H10  C27  C28  112.22  3.000
 PJE  H11  C27  C26  110.00  3.000
 PJE  H10  C27  C26  113.12  3.000
 PJE  C28  C27  C26  104.16  3.000
 PJE  H13  C28  H12  107.69  3.000
 PJE  H13  C28  N6   111.17  3.000
 PJE  H12  C28  N6   111.23  3.000
 PJE  H13  C28  C27  112.41  3.000
 PJE  H12  C28  C27  112.17  3.000
 PJE  N6   C28  C27  102.18  3.000
 PJE  H14  N6   C29  122.04  3.000
 PJE  H14  N6   C28  122.61  3.000
 PJE  C29  N6   C28  114.89  3.000
 PJE  O8   C29  N6   125.99  3.000
 PJE  O8   C29  C26  126.33  3.000
 PJE  N6   C29  C26  107.67  3.000
 PJE  H16  N5   H15  105.73  3.000
 PJE  H16  N5   C19  109.17  3.000
 PJE  H15  N5   C19  109.80  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
 PJE  CONST_01  C28  N6   C29  C26     0.00   0.0  0
 PJE  CONST_02  O8   C29  N6   C28   180.00   0.0  0
 PJE  CONST_03  H14  N6   C29  C26   180.00   0.0  0
 PJE  CONST_04  H6   O6   C22  C21   180.00   0.0  0
 PJE  Var_01    N6   C28  C27  C26   -27.09  30.0  1
 PJE  Var_02    C29  N6   C28  C27    17.93  30.0  1
 PJE  Var_03    C22  C21  C20  C19  -179.68   0.0  2
 PJE  Var_04    O7   C22  C21  C20    -0.31  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
 PJE  chir_01  C19  C25  C20  N5   negativ
 PJE  chir_02  C26  C27  C29  C25  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
 PJE  plan-1  C26  0.020
 PJE  plan-1  C28  0.020
 PJE  plan-1  N6   0.020
 PJE  plan-1  C29  0.020
 PJE  plan-1  O8   0.020
 PJE  plan-1  H14  0.020
 PJE  plan-2  C21  0.020
 PJE  plan-2  C22  0.020
 PJE  plan-2  O6   0.020
 PJE  plan-2  O7   0.020
 PJE  plan-2  H6   0.020
 PJE  plan-3  C19  0.020
 PJE  plan-3  C20  0.020
 PJE  plan-3  C21  0.020
 PJE  plan-3  C22  0.020
 PJE  plan-3  H2   0.020
 PJE  plan-3  H4   0.020

