# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:38:56 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-2-amino-5-{[(E)-amino(methylamino)methylidene](hydroxy)azaniumyl}pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN\C(N)=[N+](O)/CCC[C@H](N)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
 J9Y  J9Y  (2S)-2-amino-5-{[(E)-amino(methylamino)methylidene](hydroxy)azaniumyl}pentanoate  L-peptide  30  14  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_J9Y
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
 J9Y  N    N  NH2    0  -0.807   -9.7360  22.3177  54.7743
 J9Y  CA   C  CH1    0  -0.223   -8.6054  23.1991  55.0260
 J9Y  CB   C  CH2    0  -0.404   -8.4503  23.4400  56.5270
 J9Y  C    C  C      0   0.409   -7.3097  22.6573  54.3684
 J9Y  O    O  O      0  -0.601   -7.4424  21.7941  53.4777
 J9Y  CG   C  CH2    0  -0.432   -8.1149  22.1875  57.3241
 J9Y  CD   C  CH2    0  -0.328   -8.1128  22.4753  58.8194
 J9Y  NE   N  N      1  -0.221   -7.6949  21.3432  59.6277
 J9Y  CZ   C  C      0   0.868   -8.4827  20.4500  60.2338
 J9Y  NH1  N  NH1    0  -0.649   -9.7939  20.4681  60.0191
 J9Y  NH2  N  NH2    0  -0.825   -7.9545  19.5692  61.0695
 J9Y  OXT  O  OC    -1  -0.607   -6.2399  23.1687  54.7551
 J9Y  C1   C  CH3    0  -0.549  -10.7281  19.6137  60.7233
 J9Y  O1   O  O      0  -0.534   -6.3510  21.2001  59.8184
 J9Y  H1   H  HNH2   0   0.328  -10.5987  22.8445  54.8165
 J9Y  H2   H  HNH2   0   0.332   -9.6540  21.9542  53.8345
 J9Y  H4   H  HCH1   0   0.205   -8.7585  24.1934  54.5700
 J9Y  H5   H  HCH2   0   0.213   -7.6787  24.1947  56.6912
 J9Y  H6   H  HCH2   0   0.209   -9.3824  23.8732  56.9085
 J9Y  H7   H  HCH2   0   0.228   -8.8370  21.4000  57.0966
 J9Y  H8   H  HCH2   0   0.230   -7.1302  21.8161  57.0290
 J9Y  H9   H  HCH2   0   0.281   -7.4265  23.2902  59.0561
 J9Y  H10  H  HCH2   0   0.261   -9.0960  22.8073  59.1593
 J9Y  H11  H  HNH1   0   0.440  -10.1518  20.9930  59.2385
 J9Y  H12  H  HNH2   0   0.444   -8.4952  18.8062  61.4402
 J9Y  H13  H  HNH2   0   0.434   -6.9751  19.5971  61.2982
 J9Y  H15  H  HCH3   0   0.284  -11.7313  19.9096  60.4351
 J9Y  H16  H  HCH3   0   0.259  -10.5969  18.5607  60.4677
 J9Y  H17  H  HCH3   0   0.264  -10.6347  19.7361  61.8018
 J9Y  H18  H  H      0   0.488   -6.0136  20.6933  59.0631

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
 J9Y  O    C    deloc   1.231  0.020  1.231
 J9Y  N    CA   single  1.458  0.019  1.458
 J9Y  C    OXT  deloc   1.247  0.020  1.247
 J9Y  C    CA   single  1.525  0.021  1.525
 J9Y  CA   CB   single  1.530  0.020  1.530
 J9Y  CB   CG   single  1.522  0.020  1.522
 J9Y  CG   CD   single  1.523  0.020  1.523
 J9Y  CD   NE   single  1.452  0.020  1.452
 J9Y  NE   O1   single  1.365  0.020  1.365
 J9Y  NE   CZ   double  1.336  0.020  1.336
 J9Y  NH1  CZ   single  1.329  0.020  1.329
 J9Y  NH1  C1   single  1.449  0.020  1.449
 J9Y  CZ   NH2  single  1.324  0.020  1.324
 J9Y  N    H1   single  0.890  0.020  1.040
 J9Y  N    H2   single  0.890  0.020  1.040
 J9Y  CA   H4   single  0.970  0.020  1.090
 J9Y  CB   H5   single  0.970  0.020  1.090
 J9Y  CB   H6   single  0.970  0.020  1.090
 J9Y  CG   H7   single  0.970  0.020  1.090
 J9Y  CG   H8   single  0.970  0.020  1.090
 J9Y  CD   H9   single  0.970  0.020  1.090
 J9Y  CD   H10  single  0.970  0.020  1.090
 J9Y  NH1  H11  single  0.860  0.020  1.020
 J9Y  NH2  H12  single  0.860  0.020  1.020
 J9Y  NH2  H13  single  0.860  0.020  1.020
 J9Y  C1   H15  single  0.970  0.020  1.090
 J9Y  C1   H16  single  0.970  0.020  1.090
 J9Y  C1   H17  single  0.970  0.020  1.090
 J9Y  O1   H18  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
 J9Y  H2   N    H1   107.16  3.000
 J9Y  H2   N    CA   108.39  3.000
 J9Y  H1   N    CA   109.87  3.000
 J9Y  H4   CA   C    104.79  3.000
 J9Y  H4   CA   CB   106.13  3.000
 J9Y  C    CA   CB   110.10  1.900
 J9Y  H4   CA   N    111.47  3.000
 J9Y  CB   CA   N    110.50  1.700
 J9Y  C    CA   N    111.00  2.800
 J9Y  H6   CB   H5   105.99  3.000
 J9Y  H6   CB   CG   109.29  3.000
 J9Y  H5   CB   CG   109.53  3.000
 J9Y  H6   CB   CA   108.53  3.000
 J9Y  H5   CB   CA   109.17  3.000
 J9Y  CG   CB   CA   114.02  3.000
 J9Y  OXT  C    O    126.61  3.000
 J9Y  OXT  C    CA   116.23  3.000
 J9Y  O    C    CA   120.80  1.700
 J9Y  H8   CG   H7   107.11  3.000
 J9Y  H8   CG   CD   109.16  3.000
 J9Y  H7   CG   CD   109.98  3.000
 J9Y  H8   CG   CB   109.68  3.000
 J9Y  H7   CG   CB   109.78  3.000
 J9Y  CD   CG   CB   111.04  3.000
 J9Y  H10  CD   H9   105.76  3.000
 J9Y  H10  CD   NE   108.83  3.000
 J9Y  H9   CD   NE   106.28  3.000
 J9Y  H10  CD   CG   111.22  3.000
 J9Y  H9   CD   CG   110.79  3.000
 J9Y  NE   CD   CG   113.55  3.000
 J9Y  O1   NE   CZ   116.55  3.000
 J9Y  CZ   NE   CD   127.14  3.000
 J9Y  O1   NE   CD   116.29  3.000
 J9Y  NH2  CZ   NH1  120.31  3.000
 J9Y  NH2  CZ   NE   119.72  3.000
 J9Y  NH1  CZ   NE   119.96  3.000
 J9Y  H11  NH1  C1   117.08  3.000
 J9Y  H11  NH1  CZ   118.91  3.000
 J9Y  C1   NH1  CZ   123.35  3.000
 J9Y  H13  NH2  H12  117.42  3.000
 J9Y  H13  NH2  CZ   120.89  3.000
 J9Y  H12  NH2  CZ   121.52  3.000
 J9Y  H17  C1   H16  109.27  3.000
 J9Y  H17  C1   H15  108.16  3.000
 J9Y  H16  C1   H15  108.19  3.000
 J9Y  H17  C1   NH1  111.08  3.000
 J9Y  H16  C1   NH1  112.18  3.000
 J9Y  H15  C1   NH1  107.83  3.000
 J9Y  H18  O1   NE   106.77  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
 J9Y  CONST_01  NH1  CZ   NE   CD      0.00   0.0  0
 J9Y  CONST_02  NH2  CZ   NE   CD    180.00   0.0  0
 J9Y  CONST_03  C1   NH1  CZ   NE    180.00   0.0  0
 J9Y  CONST_04  O1   NE   CZ   NH1   180.00   0.0  0
 J9Y  CONST_05  O1   NE   CZ   NH2     0.00   0.0  0
 J9Y  CONST_06  C1   NH1  CZ   NH2     0.00   0.0  0
 J9Y  CONST_08  H12  NH2  CZ   NE    180.00   0.0  0
 J9Y  CONST_09  H13  NH2  CZ   NE      0.00   0.0  0
 J9Y  Var_01    CD   CG   CB   CA   -174.34  30.0  3
 J9Y  Var_02    NE   CD   CG   CB   -175.37  30.0  3
 J9Y  Var_03    H15  C1   NH1  CZ    173.91  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
 J9Y  chir_01  CA  N  C  CB  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
 J9Y  plan-1  CD   0.020
 J9Y  plan-1  NE   0.020
 J9Y  plan-1  CZ   0.020
 J9Y  plan-1  NH1  0.020
 J9Y  plan-1  NH2  0.020
 J9Y  plan-1  C1   0.020
 J9Y  plan-1  O1   0.020
 J9Y  plan-1  H11  0.020
 J9Y  plan-1  H12  0.020
 J9Y  plan-1  H13  0.020
 J9Y  plan-2  CA   0.020
 J9Y  plan-2  C    0.020
 J9Y  plan-2  O    0.020
 J9Y  plan-2  OXT  0.020

