# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 01:44:12 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S)-2-amino-4-oxo-4-(piperidin-1-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1CCCCC1)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
 7J3  7J3  '(2S)-2-amino-4-oxo-4-(piperidin-1-yl)butanoic acid'  peptide  29  14  .  2022-07-23  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_7J3
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
 7J3  C22  C  CH1    0  -0.211   2.1076  -0.5492   0.1246
 7J3  C23  C  CH2    0  -0.601   0.8525   0.2177  -0.2774
 7J3  C24  C  C      0   0.579  -0.3481  -0.6754  -0.5340
 7J3  C26  C  CH2    0  -0.314  -1.8332   1.3341  -0.4301
 7J3  C27  C  CH2    0  -0.427  -2.7624   1.5754   0.7533
 7J3  C28  C  CH2    0  -0.445  -4.0494   0.7717   0.5981
 7J3  C29  C  CH2    0  -0.432  -3.7402  -0.7012   0.3496
 7J3  C30  C  CH2    0  -0.308  -2.7679  -0.8699  -0.8118
 7J3  O01  O  O      0  -0.605   4.0529   0.5833   0.9564
 7J3  C02  C  C      0   0.386   3.3523   0.3615  -0.0496
 7J3  N25  N  NT     0  -0.459  -1.5643  -0.0846  -0.5909
 7J3  O31  O  O      0  -0.512  -0.2116  -1.8784  -0.7246
 7J3  N32  N  NH2    0  -0.785   1.9219  -1.1101   1.4529
 7J3  H4   H  HCH1   0   0.223   2.2305  -1.3826  -0.5736
 7J3  H6   H  HCH2   0   0.248   0.6336   0.9545   0.5006
 7J3  H7   H  HCH2   0   0.271   1.0481   0.7899  -1.1884
 7J3  H10  H  HCH2   0   0.222  -2.2496   1.2870   1.6760
 7J3  H11  H  HCH2   0   0.236  -2.9806   2.6430   0.8264
 7J3  H12  H  HCH2   0   0.236  -4.6795   0.8847   1.4827
 7J3  H13  H  HCH2   0   0.215  -4.6223   1.1701  -0.2462
 7J3  H14  H  HCH2   0   0.222  -3.3019  -1.1452   1.2485
 7J3  H15  H  HCH2   0   0.235  -4.6562  -1.2555   0.1326
 7J3  H23  H  HCH2   0   0.259  -2.4970  -1.9130  -0.9450
 7J3  H24  H  HCH2   0   0.228  -3.2403  -0.5337  -1.7426
 7J3  H33  H  HNH2   0   0.333   2.6970  -1.7304   1.6547
 7J3  OXT  O  OC    -1  -0.622   3.5524   0.7949  -1.2043
 7J3  H2   H  HNH2   0   0.322   2.0263  -0.3588   2.1260
 7J3  H8   H  HCH2   0   0.235  -2.3112   1.6994  -1.3462
 7J3  H9   H  HCH2   0   0.269  -0.9115   1.8968  -0.3195

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
 7J3  O01  C02  deloc   1.246  0.020  1.246
 7J3  C02  C22  single  1.552  0.020  1.552
 7J3  C29  C30  single  1.524  0.020  1.524
 7J3  C29  C28  single  1.525  0.020  1.525
 7J3  C30  N25  single  1.454  0.020  1.454
 7J3  C22  C23  single  1.525  0.020  1.525
 7J3  C22  N32  single  1.454  0.020  1.454
 7J3  C23  C24  single  1.518  0.020  1.518
 7J3  C28  C27  single  1.525  0.020  1.525
 7J3  N25  C24  single  1.353  0.020  1.353
 7J3  N25  C26  single  1.453  0.020  1.453
 7J3  C24  O31  double  1.226  0.020  1.226
 7J3  C27  C26  single  1.524  0.020  1.524
 7J3  C22  H4   single  0.970  0.020  1.090
 7J3  C23  H6   single  0.970  0.020  1.090
 7J3  C23  H7   single  0.970  0.020  1.090
 7J3  C26  H8   single  0.970  0.020  1.090
 7J3  C26  H9   single  0.970  0.020  1.090
 7J3  C27  H10  single  0.970  0.020  1.090
 7J3  C27  H11  single  0.970  0.020  1.090
 7J3  C28  H12  single  0.970  0.020  1.090
 7J3  C28  H13  single  0.970  0.020  1.090
 7J3  C29  H14  single  0.970  0.020  1.090
 7J3  C29  H15  single  0.970  0.020  1.090
 7J3  C30  H23  single  0.970  0.020  1.090
 7J3  C30  H24  single  0.970  0.020  1.090
 7J3  N32  H33  single  0.890  0.020  1.040
 7J3  C02  OXT  deloc   1.249  0.020  1.249
 7J3  N32  H2   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
 7J3  H4   C22  N32  107.67  3.000
 7J3  H4   C22  C02  106.57  3.000
 7J3  N32  C22  C02  115.56  3.000
 7J3  H4   C22  C23  107.89  3.000
 7J3  N32  C22  C23  109.25  3.000
 7J3  C02  C22  C23  109.60  3.000
 7J3  H7   C23  H6   106.02  3.000
 7J3  H7   C23  C24  107.97  3.000
 7J3  H6   C23  C24  111.00  3.000
 7J3  H7   C23  C22  109.61  3.000
 7J3  H6   C23  C22  108.42  3.000
 7J3  C24  C23  C22  113.56  3.000
 7J3  O31  C24  N25  121.47  3.000
 7J3  O31  C24  C23  121.04  3.000
 7J3  N25  C24  C23  117.45  3.000
 7J3  H9   C26  H8   106.42  3.000
 7J3  H9   C26  N25  111.11  3.000
 7J3  H8   C26  N25  108.28  3.000
 7J3  H9   C26  C27  110.89  3.000
 7J3  H8   C26  C27  109.30  3.000
 7J3  N25  C26  C27  110.70  3.000
 7J3  H11  C27  H10  107.15  3.000
 7J3  H11  C27  C28  110.68  3.000
 7J3  H10  C27  C28  110.02  3.000
 7J3  H11  C27  C26  109.18  3.000
 7J3  H10  C27  C26  109.11  3.000
 7J3  C28  C27  C26  110.61  3.000
 7J3  H13  C28  H12  106.57  3.000
 7J3  H13  C28  C29  109.36  3.000
 7J3  H12  C28  C29  110.42  3.000
 7J3  H13  C28  C27  109.15  3.000
 7J3  H12  C28  C27  110.48  3.000
 7J3  C29  C28  C27  110.75  3.000
 7J3  H15  C29  H14  107.04  3.000
 7J3  H15  C29  C30  109.11  3.000
 7J3  H14  C29  C30  109.00  3.000
 7J3  H15  C29  C28  110.63  3.000
 7J3  H14  C29  C28  109.83  3.000
 7J3  C30  C29  C28  111.12  3.000
 7J3  H24  C30  H23  107.33  3.000
 7J3  H24  C30  N25  108.66  3.000
 7J3  H23  C30  N25  109.33  3.000
 7J3  H24  C30  C29  109.75  3.000
 7J3  H23  C30  C29  111.04  3.000
 7J3  N25  C30  C29  110.64  3.000
 7J3  OXT  C02  O01  126.47  3.000
 7J3  OXT  C02  C22  115.83  3.000
 7J3  O01  C02  C22  117.70  3.000
 7J3  C30  N25  C26  113.01  3.000
 7J3  C26  N25  C24  126.02  3.000
 7J3  C30  N25  C24  120.97  3.000
 7J3  H2   N32  H33  104.05  3.000
 7J3  H2   N32  C22  107.91  3.000
 7J3  H33  N32  C22  108.69  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
 7J3  CONST_01  C30  N25  C24  C23  180.00   0.0  0
 7J3  CONST_02  C26  N25  C24  C23    0.00   0.0  0
 7J3  CONST_03  O31  C24  N25  C26  180.00   0.0  0
 7J3  CONST_04  O31  C24  N25  C30    0.00   0.0  0
 7J3  Var_01    C29  C30  N25  C26  -58.63  30.0  1
 7J3  Var_02    C29  C28  C27  C26   52.92  30.0  1
 7J3  Var_03    C30  C29  C28  C27  -52.57  30.0  1
 7J3  Var_04    C30  N25  C26  C27   59.31  30.0  1
 7J3  Var_05    N25  C30  C29  C28   54.61  30.0  1
 7J3  Var_06    N25  C26  C27  C28  -55.66  30.0  1
 7J3  Var_07    N25  C24  C23  C22  165.11  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
 7J3  chir_01  C22  C02  C23  N32  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
 7J3  plan-1  C23  0.020
 7J3  plan-1  C24  0.020
 7J3  plan-1  C26  0.020
 7J3  plan-1  C30  0.020
 7J3  plan-1  N25  0.020
 7J3  plan-1  O31  0.020
 7J3  plan-2  C22  0.020
 7J3  plan-2  O01  0.020
 7J3  plan-2  C02  0.020
 7J3  plan-2  OXT  0.020

