# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:50:47 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  23  10  .  2022-03-22  2022-03-22
;
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   0.410  -2.8398   0.1701   0.0261
 KBE  N     N  NH2    0  -0.797  -0.2685  -1.3769  -0.7168
 KBE  O     O  O      0  -0.611  -2.9188  -0.8341   0.7654
 KBE  CA    C  CH2    0  -0.577  -1.4455   0.7748  -0.2177
 KBE  CB    C  CH1    0  -0.079  -0.2562  -0.1418   0.0625
 KBE  CE    C  CH2    0  -0.270   3.5808   0.6128  -0.0376
 KBE  CG    C  CH2    0  -0.408   1.0548   0.6082  -0.1649
 KBE  NZ    N  NH2    0  -0.801   4.7615  -0.1862   0.2627
 KBE  OXT   O  OC    -1  -0.625  -3.7983   0.7553  -0.5191
 KBE  HN    H  HNH2   0   0.338  -1.1432  -1.8510  -0.5283
 KBE  HNA   H  HNH2   0   0.322  -0.2894  -1.1423  -1.7042
 KBE  HA    H  HCH2   0   0.204  -1.3893   1.1392  -1.2503
 KBE  HAA   H  HCH2   0   0.221  -1.3687   1.6723   0.4103
 KBE  HB    H  HCH1   0   0.197  -0.2937  -0.4368   1.1167
 KBE  HD    H  HCH2   0   0.212   2.3396  -1.0815  -0.4942
 KBE  HDA   H  HCH2   0   0.203   2.2647  -0.5654   1.1790
 KBE  HE    H  HCH2   0   0.183   3.5866   1.0373  -1.0528
 KBE  HEA   H  HCH2   0   0.207   3.5672   1.4660   0.6471
 KBE  HG    H  HCH2   0   0.200   1.0931   0.9565  -1.2049
 KBE  HGA   H  HCH2   0   0.209   1.0446   1.5127   0.4526
 KBE  HNZ   H  HNH2   0   0.335   4.8493  -0.9231  -0.4267
 KBE  HNZA  H  HNH2   0   0.343   5.5917   0.3830   0.1557
 KBE  CD    C  CH2    0  -0.416   2.3079  -0.1978   0.1485

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     deloc   1.231  0.020  1.231
 KBE  C   CA    single  1.525  0.021  1.525
 KBE  C   OXT   deloc   1.248  0.020  1.248
 KBE  N   CB    single  1.460  0.020  1.460
 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  1.527  0.020  1.527
 KBE  CB  HB    single  0.970  0.020  1.090
 KBE  CD  CE    single  1.521  0.020  1.521
 KBE  CD  CG    single  1.523  0.020  1.523
 KBE  CD  HD    single  0.970  0.020  1.090
 KBE  CD  HDA   single  0.970  0.020  1.090
 KBE  CE  NZ    single  1.457  0.020  1.457
 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

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   116.24  3.000
 KBE  OXT   C   O    125.92  3.000
 KBE  CA    C   O    120.80  1.700
 KBE  HNA   N   HN   105.75  3.000
 KBE  HNA   N   CB   108.89  3.000
 KBE  HN    N   CB   107.69  3.000
 KBE  HAA   CA  HA   105.27  3.000
 KBE  HAA   CA  CB   109.34  3.000
 KBE  HA    CA  CB   109.00  3.000
 KBE  HAA   CA  C    107.09  3.000
 KBE  HA    CA  C    109.00  3.000
 KBE  CB    CA  C    110.10  1.900
 KBE  HB    CB  CG   107.75  3.000
 KBE  HB    CB  CA   108.15  3.000
 KBE  CG    CB  CA   110.26  3.000
 KBE  HB    CB  N    106.59  3.000
 KBE  CG    CB  N    110.06  3.000
 KBE  CA    CB  N    110.50  1.700
 KBE  HEA   CE  HE   106.05  3.000
 KBE  HEA   CE  NZ   107.99  3.000
 KBE  HE    CE  NZ   113.42  3.000
 KBE  HEA   CE  CD   109.19  3.000
 KBE  HE    CE  CD   108.84  3.000
 KBE  NZ    CE  CD   111.15  3.000
 KBE  HGA   CG  HG   105.82  3.000
 KBE  HGA   CG  CD   109.20  3.000
 KBE  HG    CG  CD   109.54  3.000
 KBE  HGA   CG  CB   108.28  3.000
 KBE  HG    CG  CB   109.08  3.000
 KBE  CD    CG  CB   114.57  3.000
 KBE  HNZA  NZ  HNZ  105.43  3.000
 KBE  HNZA  NZ  CE   109.54  3.000
 KBE  HNZ   NZ  CE   109.20  3.000
 KBE  HDA   CD  HD   106.44  3.000
 KBE  HDA   CD  CG   109.82  3.000
 KBE  HD    CD  CG   109.32  3.000
 KBE  HDA   CD  CE   109.10  3.000
 KBE  HD    CD  CE   109.55  3.000
 KBE  CG    CD  CE   112.43  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  Var_01  CB   CA  C   O     19.77  30.0  3
 KBE  Var_02  CE   CD  CG  CB  -177.56  30.0  1
 KBE  Var_03  NZ   CE  CD  CG  -179.71  30.0  3
 KBE  Var_04  HNZ  NZ  CE  CD    66.53  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

