# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 21:49:31 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (3S)-3,6-bis(azanyl)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCC[C@H](N)CC(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
 KBE  KBE  '(3S)-3,6-bis(azanyl)hexanoic acid'  L-peptide  24  10  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KBE
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
 KBE  C     C  C     0   0.547  -2.8010   0.1831   0.1557
 KBE  N     N  NH2   0  -0.788  -0.2928  -1.3711  -0.7112
 KBE  O     O  O     0  -0.448  -2.9809  -0.7714   0.8727
 KBE  CA    C  CH2   0  -0.580  -1.4610   0.7802  -0.1735
 KBE  CB    C  CH1   0  -0.091  -0.2760  -0.1545   0.0855
 KBE  CE    C  CH2   0  -0.271   3.5498   0.6259  -0.0223
 KBE  CG    C  CH2   0  -0.413   1.0256   0.6103  -0.1479
 KBE  NZ    N  NH2   0  -0.801   4.7330  -0.1702   0.2725
 KBE  OXT   O  OH1   0  -0.594  -3.7983   0.8505  -0.4164
 KBE  HN    H  HNH2  0   0.346  -1.1156  -1.9193  -0.4978
 KBE  HNA   H  HNH2  0   0.334  -0.3524  -1.1370  -1.6959
 KBE  HA    H  HCH2  0   0.266  -1.4589   1.1169  -1.2144
 KBE  HAA   H  HCH2  0   0.282  -1.3668   1.6891   0.4327
 KBE  HB    H  HCH1  0   0.226  -0.3015  -0.4580   1.1368
 KBE  HD    H  HCH2  0   0.217   2.3181  -1.0718  -0.4906
 KBE  HDA   H  HCH2  0   0.207   2.2406  -0.5682   1.1864
 KBE  HE    H  HCH2  0   0.185   3.5527   1.0569  -1.0348
 KBE  HEA   H  HCH2  0   0.209   3.5323   1.4745   0.6678
 KBE  HG    H  HCH2  0   0.211   1.0553   0.9601  -1.1870
 KBE  HGA   H  HCH2  0   0.219   1.0128   1.5116   0.4734
 KBE  HNZ   H  HNH2  0   0.336   4.8351  -0.8913  -0.4314
 KBE  HNZA  H  HNH2  0   0.344   5.5595   0.4079   0.1893
 KBE  HXT   H  HOH1  0   0.478  -4.6478   0.4641  -0.1554
 KBE  CD    C  CH2   0  -0.418   2.2814  -0.1933   0.1587

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
 KBE  C    O     double  1.231  0.020  1.231
 KBE  C    CA    single  1.525  0.021  1.525
 KBE  C    OXT   single  1.329  0.020  1.329
 KBE  N    CB    single  1.454  0.020  1.454
 KBE  N    HN    single  0.890  0.020  1.040
 KBE  N    HNA   single  0.890  0.020  1.040
 KBE  CA   CB    single  1.530  0.020  1.530
 KBE  CA   HA    single  0.970  0.020  0.970
 KBE  CA   HAA   single  0.970  0.020  1.090
 KBE  CB   CG    single  1.528  0.020  1.528
 KBE  CB   HB    single  0.970  0.020  1.090
 KBE  CD   CE    single  1.521  0.020  1.521
 KBE  CD   CG    single  1.522  0.020  1.522
 KBE  CD   HD    single  0.970  0.020  1.090
 KBE  CD   HDA   single  0.970  0.020  1.090
 KBE  CE   NZ    single  1.456  0.020  1.456
 KBE  CE   HE    single  0.970  0.020  1.090
 KBE  CE   HEA   single  0.970  0.020  1.090
 KBE  CG   HG    single  0.970  0.020  1.090
 KBE  CG   HGA   single  0.970  0.020  1.090
 KBE  NZ   HNZ   single  0.890  0.020  1.040
 KBE  NZ   HNZA  single  0.890  0.020  1.040
 KBE  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
 KBE  OXT   C    CA   112.03  3.000
 KBE  OXT   C    O    122.73  3.000
 KBE  CA    C    O    120.80  1.700
 KBE  HNA   N    HN   106.40  3.000
 KBE  HNA   N    CB   109.86  3.000
 KBE  HN    N    CB   110.31  3.000
 KBE  HAA   CA   HA   105.70  3.000
 KBE  HAA   CA   CB   110.23  3.000
 KBE  HA    CA   CB   109.00  3.000
 KBE  HAA   CA   C    106.54  3.000
 KBE  HA    CA   C    109.00  3.000
 KBE  CB    CA   C    110.10  1.900
 KBE  HB    CB   CG   107.78  3.000
 KBE  HB    CB   CA   108.28  3.000
 KBE  CG    CB   CA   109.14  3.000
 KBE  HB    CB   N    107.10  3.000
 KBE  CG    CB   N    110.18  3.000
 KBE  CA    CB   N    110.50  1.700
 KBE  HEA   CE   HE   106.06  3.000
 KBE  HEA   CE   NZ   108.02  3.000
 KBE  HE    CE   NZ   113.47  3.000
 KBE  HEA   CE   CD   109.24  3.000
 KBE  HE    CE   CD   108.82  3.000
 KBE  NZ    CE   CD   111.04  3.000
 KBE  HGA   CG   HG   105.99  3.000
 KBE  HGA   CG   CD   109.27  3.000
 KBE  HG    CG   CD   109.69  3.000
 KBE  HGA   CG   CB   108.39  3.000
 KBE  HG    CG   CB   109.12  3.000
 KBE  CD    CG   CB   114.07  3.000
 KBE  HNZA  NZ   HNZ  105.50  3.000
 KBE  HNZA  NZ   CE   109.55  3.000
 KBE  HNZ   NZ   CE   109.30  3.000
 KBE  HXT   OXT  C    109.97  3.000
 KBE  HDA   CD   HD   106.48  3.000
 KBE  HDA   CD   CG   109.83  3.000
 KBE  HD    CD   CG   109.42  3.000
 KBE  HDA   CD   CE   109.10  3.000
 KBE  HD    CD   CE   109.52  3.000
 KBE  CG    CD   CE   112.32  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
 KBE  CONST_01  HXT  OXT  C   O      0.00   0.0  0
 KBE  Var_01    CB   CA   C   O     19.00  30.0  3
 KBE  Var_02    CE   CD   CG  CB  -177.23  30.0  1
 KBE  Var_03    NZ   CE   CD  CG  -179.77  30.0  3
 KBE  Var_04    HNZ  NZ   CE  CD    67.62  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
 KBE  chir_01  CB  N  CA  CG  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
 KBE  plan-1  C    0.020
 KBE  plan-1  O    0.020
 KBE  plan-1  CA   0.020
 KBE  plan-1  OXT  0.020
 KBE  plan-1  HXT  0.020

