# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:49:18 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  30  14  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.205   2.1326  -0.5329   0.1499
 7J3  C23  C  CH2   0  -0.611   0.8943   0.2659  -0.2584
 7J3  C24  C  C     0   0.590  -0.2908  -0.6433  -0.5483
 7J3  C26  C  CH2   0  -0.317  -1.8083   1.3354  -0.3907
 7J3  C27  C  CH2   0  -0.428  -2.7586   1.5419   0.7822
 7J3  C28  C  CH2   0  -0.446  -4.0298   0.7212   0.5939
 7J3  C29  C  CH2   0  -0.433  -3.6927  -0.7426   0.3301
 7J3  C30  C  CH2   0  -0.309  -2.7027  -0.8808  -0.8199
 7J3  O01  O  O     0  -0.438   4.0348   0.7250   0.9644
 7J3  C02  C  C     0   0.523   3.3710   0.3476   0.0320
 7J3  N25  N  NT    0  -0.460  -1.5150  -0.0774  -0.5711
 7J3  O31  O  O     0  -0.505  -0.1182  -1.8322  -0.7856
 7J3  N32  N  NH2   0  -0.775   1.9407  -1.0874   1.4662
 7J3  H4   H  HCH1  0   0.279   2.2611  -1.3555  -0.5580
 7J3  H6   H  HCH2  0   0.271   0.6686   0.9803   0.5362
 7J3  H7   H  HCH2  0   0.294   1.0855   0.8611  -1.1558
 7J3  H9   H  HCH2  0   0.270  -0.8974   1.9111  -0.2571
 7J3  H10  H  HCH2  0   0.224  -2.2546   1.2459   1.7072
 7J3  H11  H  HCH2  0   0.239  -2.9936   2.6046   0.8696
 7J3  H12  H  HCH2  0   0.238  -4.6768   0.8119   1.4687
 7J3  H13  H  HCH2  0   0.217  -4.5944   1.1217  -0.2549
 7J3  H14  H  HCH2  0   0.223  -3.2609  -1.1927   1.2290
 7J3  H15  H  HCH2  0   0.237  -4.5958  -1.3083   0.0907
 7J3  H23  H  HCH2  0   0.262  -2.4126  -1.9176  -0.9611
 7J3  H24  H  HCH2  0   0.232  -3.1663  -0.5413  -1.7535
 7J3  H33  H  HNH2  0   0.355   2.6976  -1.7170   1.6990
 7J3  OXT  O  OH1   0  -0.593   3.6485   0.6517  -1.2310
 7J3  HXT  H  HOH1  0   0.482   4.4331   1.2189  -1.2741
 7J3  H2   H  HNH2  0   0.343   1.9597  -0.3518   2.1620
 7J3  H8   H  HCH2  0   0.240  -2.2772   1.7076  -1.3085

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  double  1.205  0.020  1.205
 7J3  C02  C22  single  1.524  0.020  1.524
 7J3  C29  C30  single  1.524  0.020  1.524
 7J3  C29  C28  single  1.525  0.020  1.525
 7J3  C30  N25  single  1.455  0.020  1.455
 7J3  C22  C23  single  1.529  0.020  1.529
 7J3  C22  N32  single  1.441  0.020  1.441
 7J3  C23  C24  single  1.522  0.020  1.522
 7J3  C28  C27  single  1.525  0.020  1.525
 7J3  N25  C24  single  1.349  0.020  1.349
 7J3  N25  C26  single  1.454  0.020  1.454
 7J3  C24  O31  double  1.225  0.020  1.225
 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  single  1.328  0.020  1.328
 7J3  OXT  HXT  single  0.850  0.020  0.980
 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  108.52  3.000
 7J3  H4   C22  C02  106.81  3.000
 7J3  N32  C22  C02  113.65  3.000
 7J3  H4   C22  C23  108.39  3.000
 7J3  N32  C22  C23  109.70  3.000
 7J3  C02  C22  C23  109.61  3.000
 7J3  H7   C23  H6   106.08  3.000
 7J3  H7   C23  C24  107.76  3.000
 7J3  H6   C23  C24  111.63  3.000
 7J3  H7   C23  C22  111.21  3.000
 7J3  H6   C23  C22  108.35  3.000
 7J3  C24  C23  C22  111.68  3.000
 7J3  O31  C24  N25  122.14  3.000
 7J3  O31  C24  C23  120.49  3.000
 7J3  N25  C24  C23  117.35  3.000
 7J3  H9   C26  H8   106.37  3.000
 7J3  H9   C26  N25  111.17  3.000
 7J3  H8   C26  N25  108.20  3.000
 7J3  H9   C26  C27  110.90  3.000
 7J3  H8   C26  C27  109.38  3.000
 7J3  N25  C26  C27  110.67  3.000
 7J3  H11  C27  H10  107.14  3.000
 7J3  H11  C27  C28  110.75  3.000
 7J3  H10  C27  C28  110.05  3.000
 7J3  H11  C27  C26  109.14  3.000
 7J3  H10  C27  C26  109.08  3.000
 7J3  C28  C27  C26  110.61  3.000
 7J3  H13  C28  H12  106.56  3.000
 7J3  H13  C28  C29  109.32  3.000
 7J3  H12  C28  C29  110.45  3.000
 7J3  H13  C28  C27  109.18  3.000
 7J3  H12  C28  C27  110.51  3.000
 7J3  C29  C28  C27  110.71  3.000
 7J3  H15  C29  H14  107.06  3.000
 7J3  H15  C29  C30  108.96  3.000
 7J3  H14  C29  C30  109.04  3.000
 7J3  H15  C29  C28  110.62  3.000
 7J3  H14  C29  C28  109.87  3.000
 7J3  C30  C29  C28  111.18  3.000
 7J3  H24  C30  H23  107.34  3.000
 7J3  H24  C30  N25  108.65  3.000
 7J3  H23  C30  N25  109.35  3.000
 7J3  H24  C30  C29  109.86  3.000
 7J3  H23  C30  C29  111.00  3.000
 7J3  N25  C30  C29  110.56  3.000
 7J3  OXT  C02  O01  123.29  3.000
 7J3  OXT  C02  C22  112.06  3.000
 7J3  O01  C02  C22  124.65  3.000
 7J3  C30  N25  C26  113.14  3.000
 7J3  C26  N25  C24  126.06  3.000
 7J3  C30  N25  C24  120.79  3.000
 7J3  H2   N32  H33  106.25  3.000
 7J3  H2   N32  C22  110.21  3.000
 7J3  H33  N32  C22  110.48  3.000
 7J3  HXT  OXT  C02  110.21  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  CONST_05  HXT  OXT  C02  C22  180.00   0.0  0
 7J3  Var_01    C29  C30  N25  C26  -58.42  30.0  1
 7J3  Var_02    C29  C28  C27  C26   53.10  30.0  1
 7J3  Var_03    C30  C29  C28  C27  -52.78  30.0  1
 7J3  Var_04    C30  N25  C26  C27   59.14  30.0  1
 7J3  Var_05    N25  C30  C29  C28   54.58  30.0  1
 7J3  Var_06    N25  C26  C27  C28  -55.63  30.0  1
 7J3  Var_07    N25  C24  C23  C22  162.91  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
 7J3  plan-2  HXT  0.020

