# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:29:08 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: [(5~{S})-5-azanyl-6-(carboxyamino)hexyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCC[NH3+])CNC(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
 OUK  OUK  '[(5~{S})-5-azanyl-6-(carboxyamino)hexyl]azanium'  ligand  29  12  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OUK
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
 OUK  N    N  NH2    0  -0.794   0.3851   1.6720  -0.4137
 OUK  CA   C  CH1    0  -0.133   0.2916   0.3685   0.2348
 OUK  C    C  C      0   0.493   3.9963  -0.3060   0.0525
 OUK  O    O  O      0  -0.652   4.0551  -1.5377  -0.1547
 OUK  CB   C  CH2    0  -0.416  -0.9784  -0.4237  -0.0924
 OUK  CG   C  CH2    0  -0.433  -2.2659   0.3431   0.1812
 OUK  CD   C  CH2    0  -0.445  -3.5097  -0.5028  -0.0636
 OUK  CE   C  CH2    0  -0.302  -4.7672   0.3125   0.1556
 OUK  NZ   N  NT3    1  -0.777  -5.9891  -0.4979  -0.0938
 OUK  CM   C  CH2    0  -0.206   1.5297  -0.4532  -0.1148
 OUK  N2   N  NH1    0  -0.664   2.7260   0.2441   0.2775
 OUK  O1   O  OC    -1  -0.665   4.9597   0.4918   0.1119
 OUK  H2   H  HNH2   0   0.337   0.1896   1.5754  -1.4044
 OUK  H1   H  HNH2   0   0.352  -0.3191   2.3000  -0.0486
 OUK  HA   H  HCH1   0   0.219   0.3071   0.5519   1.3155
 OUK  HB2  H  HCH2   0   0.213  -0.9554  -0.7275  -1.1456
 OUK  HB3  H  HCH2   0   0.218  -0.9754  -1.3467   0.4962
 OUK  HG2  H  HCH2   0   0.226  -2.2672   0.7040   1.2149
 OUK  HG3  H  HCH2   0   0.221  -2.3086   1.2296  -0.4579
 OUK  HD2  H  HCH2   0   0.244  -3.4972  -0.8891  -1.0871
 OUK  HD3  H  HCH2   0   0.246  -3.5090  -1.3680   0.6056
 OUK  HE2  H  HCH2   0   0.290  -4.8382   0.6780   1.1779
 OUK  HE3  H  HCH2   0   0.289  -4.8159   1.1638  -0.5204
 OUK  HZ3  H  HNT3   0   0.469  -6.0561  -1.2926   0.5411
 OUK  HZ1  H  HNT3   0   0.477  -6.8369   0.0545   0.0301
 OUK  HZ2  H  HNT3   0   0.468  -6.0116  -0.8683  -1.0435
 OUK  HM3  H  HCH2   0   0.207   1.4706  -1.4150   0.3987
 OUK  HM2  H  HCH2   0   0.177   1.5017  -0.6789  -1.1936
 OUK  HN2  H  HNH1   0   0.340   2.6628   1.2391   0.1220

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
 OUK  N2  C    single  1.402  0.020  1.402
 OUK  N2  CM   single  1.439  0.020  1.439
 OUK  C   O    deloc   1.250  0.020  1.250
 OUK  N   CA   single  1.459  0.020  1.459
 OUK  CM  CA   single  1.527  0.020  1.527
 OUK  CA  CB   single  1.532  0.020  1.532
 OUK  CB  CG   single  1.523  0.020  1.523
 OUK  CG  CD   single  1.524  0.020  1.524
 OUK  CD  CE   single  1.515  0.020  1.515
 OUK  CE  NZ   single  1.487  0.020  1.487
 OUK  C   O1   deloc   1.252  0.020  1.252
 OUK  N   H2   single  0.890  0.020  1.040
 OUK  N   H1   single  0.890  0.020  1.040
 OUK  CA  HA   single  0.970  0.020  1.090
 OUK  CB  HB2  single  0.970  0.020  1.090
 OUK  CB  HB3  single  0.970  0.020  1.090
 OUK  CG  HG2  single  0.970  0.020  1.090
 OUK  CG  HG3  single  0.970  0.020  1.090
 OUK  CD  HD2  single  0.970  0.020  1.090
 OUK  CD  HD3  single  0.970  0.020  1.090
 OUK  CE  HE2  single  0.970  0.020  1.090
 OUK  CE  HE3  single  0.970  0.020  1.090
 OUK  NZ  HZ3  single  0.890  0.020  1.040
 OUK  NZ  HZ1  single  0.890  0.020  1.040
 OUK  NZ  HZ2  single  0.890  0.020  1.040
 OUK  CM  HM3  single  0.970  0.020  1.090
 OUK  CM  HM2  single  0.970  0.020  1.090
 OUK  N2  HN2  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
 OUK  H1   N   H2   106.10  3.000
 OUK  H1   N   CA   110.46  3.000
 OUK  H2   N   CA   109.68  3.000
 OUK  HA   CA  CM   107.72  3.000
 OUK  HA   CA  CB   107.99  3.000
 OUK  CM   CA  CB   110.19  3.000
 OUK  HA   CA  N    106.72  3.000
 OUK  CB   CA  N    114.85  3.000
 OUK  CM   CA  N    109.09  3.000
 OUK  O1   C   N2   116.06  3.000
 OUK  O1   C   O    126.82  3.000
 OUK  N2   C   O    117.10  3.000
 OUK  HB3  CB  HB2  106.43  3.000
 OUK  HB3  CB  CG   109.28  3.000
 OUK  HB2  CB  CG   109.25  3.000
 OUK  HB3  CB  CA   108.60  3.000
 OUK  HB2  CB  CA   109.33  3.000
 OUK  CG   CB  CA   113.70  3.000
 OUK  HG3  CG  HG2  106.53  3.000
 OUK  HG3  CG  CD   108.91  3.000
 OUK  HG2  CG  CD   109.49  3.000
 OUK  HG3  CG  CB   109.64  3.000
 OUK  HG2  CG  CB   109.66  3.000
 OUK  CD   CG  CB   112.43  3.000
 OUK  HD3  CD  HD2  107.04  3.000
 OUK  HD3  CD  CE   109.74  3.000
 OUK  HD2  CD  CE   109.57  3.000
 OUK  HD3  CD  CG   109.89  3.000
 OUK  HD2  CD  CG   109.69  3.000
 OUK  CE   CD  CG   110.83  3.000
 OUK  HE3  CE  HE2  108.54  3.000
 OUK  HE3  CE  NZ   106.58  3.000
 OUK  HE2  CE  NZ   106.68  3.000
 OUK  HE3  CE  CD   111.61  3.000
 OUK  HE2  CE  CD   111.77  3.000
 OUK  NZ   CE  CD   111.38  3.000
 OUK  HZ2  NZ  HZ1  106.96  3.000
 OUK  HZ2  NZ  HZ3  107.18  3.000
 OUK  HZ1  NZ  HZ3  106.98  3.000
 OUK  HZ2  NZ  CE   111.86  3.000
 OUK  HZ1  NZ  CE   111.57  3.000
 OUK  HZ3  NZ  CE   111.98  3.000
 OUK  HM2  CM  HM3  106.17  3.000
 OUK  HM2  CM  N2   112.77  3.000
 OUK  HM3  CM  N2   110.09  3.000
 OUK  HM2  CM  CA   108.28  3.000
 OUK  HM3  CM  CA   108.81  3.000
 OUK  N2   CM  CA   110.55  3.000
 OUK  HN2  N2  CM   112.55  3.000
 OUK  HN2  N2  C    114.76  3.000
 OUK  CM   N2  C    121.28  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
 OUK  Var_01  C    N2  CM  CA  -179.59  30.0  1
 OUK  Var_02  CD   CG  CB  CA  -176.10  30.0  3
 OUK  Var_03  CM   N2  C   O    -18.90  30.0  2
 OUK  Var_04  CE   CD  CG  CB  -177.33  30.0  3
 OUK  Var_05  NZ   CE  CD  CG   179.41  30.0  3
 OUK  Var_06  HZ3  NZ  CE  CD    61.55  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
 OUK  chir_01  CA  N  CM  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
 OUK  plan-1  C   0.020
 OUK  plan-1  O   0.020
 OUK  plan-1  N2  0.020
 OUK  plan-1  O1  0.020

