# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:04:34 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-2-azanyl-6-(2-hydroxy-2-oxoethylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNCC(O)=O)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
 6DN  6DN  '(2~{S})-2-azanyl-6-(2-hydroxy-2-oxoethylamino)hexanoic acid'  ligand  28  14  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6DN
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
 6DN  O1   O  OC    -1  -0.626  -10.6856  -29.3550  1.9460
 6DN  O2   O  O      0  -0.610  -12.0484  -28.7596  0.2845
 6DN  CB   C  CH2    0  -0.409  -14.6440  -23.1072  3.8778
 6DN  CA   C  CH1    0  -0.212  -14.8128  -21.6928  4.4419
 6DN  C    C  C      0   0.385  -16.1794  -21.5947  5.1631
 6DN  O    O  O      0  -0.610  -16.1726  -21.5566  6.4103
 6DN  N    N  NH2    0  -0.788  -13.6579  -21.3374  5.2550
 6DN  CG   C  CH2    0  -0.404  -13.4433  -23.2642  2.9555
 6DN  CD   C  CH2    0  -0.440  -13.2689  -24.6848  2.4330
 6DN  CE   C  CH2    0  -0.274  -12.1097  -24.8024  1.4420
 6DN  NZ   N  NH1    0  -0.596  -11.8448  -26.1184  0.8957
 6DN  CX1  C  CH2    0  -0.407  -11.3778  -27.0954  1.8553
 6DN  CX2  C  C      0   0.389  -11.3612  -28.5299  1.2987
 6DN  OXT  O  OC    -1  -0.625  -17.1893  -21.5920  4.4279
 6DN  HB2  H  HCH2   0   0.211  -15.5537  -23.3781  3.3358
 6DN  HB3  H  HCH2   0   0.200  -14.5620  -23.8170  4.7113
 6DN  HA   H  HCH1   0   0.203  -14.8384  -21.0036  3.5893
 6DN  H    H  HNH2   0   0.333  -13.6944  -20.3446  5.4533
 6DN  H2   H  HNH2   0   0.321  -13.7787  -21.7755  6.1619
 6DN  HG2  H  HCH2   0   0.210  -12.5389  -22.9533  3.4845
 6DN  HG3  H  HCH2   0   0.197  -13.5510  -22.5751  2.1089
 6DN  HD2  H  HCH2   0   0.202  -14.1915  -25.0134  1.9406
 6DN  HD3  H  HCH2   0   0.210  -13.1149  -25.3633  3.2783
 6DN  HE2  H  HCH2   0   0.201  -11.1915  -24.4429  1.9201
 6DN  HE3  H  HCH2   0   0.212  -12.2991  -24.1185  0.6076
 6DN  HZ1  H  HNH1   0   0.325  -12.6673  -26.4840  0.4336
 6DN  H16  H  HCH2   0   0.210  -10.3677  -26.8240  2.1801
 6DN  H17  H  HCH2   0   0.194  -11.9808  -27.1298  2.7793

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
 6DN  O2   CX2  deloc   1.246  0.020  1.246
 6DN  NZ   CE   single  1.449  0.020  1.449
 6DN  NZ   CX1  single  1.447  0.020  1.447
 6DN  CX2  O1   deloc   1.247  0.020  1.247
 6DN  CX2  CX1  single  1.539  0.020  1.539
 6DN  CE   CD   single  1.530  0.020  1.530
 6DN  CD   CG   single  1.524  0.020  1.524
 6DN  CG   CB   single  1.522  0.020  1.522
 6DN  CB   CA   single  1.532  0.020  1.532
 6DN  CA   C    single  1.548  0.020  1.548
 6DN  CA   N    single  1.457  0.020  1.457
 6DN  C    O    deloc   1.248  0.020  1.248
 6DN  C    OXT  deloc   1.249  0.020  1.249
 6DN  CB   HB2  single  0.970  0.020  1.090
 6DN  CB   HB3  single  0.970  0.020  1.090
 6DN  CA   HA   single  0.970  0.020  1.090
 6DN  N    H    single  0.860  0.020  1.020
 6DN  N    H2   single  0.890  0.020  1.040
 6DN  CG   HG2  single  0.970  0.020  1.090
 6DN  CG   HG3  single  0.970  0.020  1.090
 6DN  CD   HD2  single  0.970  0.020  1.090
 6DN  CD   HD3  single  0.970  0.020  1.090
 6DN  CE   HE2  single  0.970  0.020  1.090
 6DN  CE   HE3  single  0.970  0.020  1.090
 6DN  NZ   HZ1  single  0.890  0.020  1.040
 6DN  CX1  H16  single  0.970  0.020  1.090
 6DN  CX1  H17  single  0.970  0.020  1.090

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
 6DN  HB3  CB   HB2  106.17  3.000
 6DN  HB3  CB   CG   109.54  3.000
 6DN  HB2  CB   CG   109.29  3.000
 6DN  HB3  CB   CA   109.00  3.000
 6DN  HB2  CB   CA   108.64  3.000
 6DN  CG   CB   CA   113.91  3.000
 6DN  HA   CA   N    107.41  3.000
 6DN  HA   CA   C    107.56  3.000
 6DN  N    CA   C    115.11  3.000
 6DN  HA   CA   CB   107.25  3.000
 6DN  N    CA   CB   110.09  3.000
 6DN  C    CA   CB   109.10  3.000
 6DN  OXT  C    O    126.34  3.000
 6DN  OXT  C    CA   116.07  3.000
 6DN  O    C    CA   117.56  3.000
 6DN  H2   N    H    104.12  3.000
 6DN  H2   N    CA   107.41  3.000
 6DN  H    N    CA   108.65  3.000
 6DN  HG3  CG   HG2  106.03  3.000
 6DN  HG3  CG   CD   109.41  3.000
 6DN  HG2  CG   CD   109.66  3.000
 6DN  HG3  CG   CB   108.99  3.000
 6DN  HG2  CG   CB   109.28  3.000
 6DN  CD   CG   CB   113.22  3.000
 6DN  HD3  CD   HD2  106.23  3.000
 6DN  HD3  CD   CE   110.24  3.000
 6DN  HD2  CD   CE   108.89  3.000
 6DN  HD3  CD   CG   109.22  3.000
 6DN  HD2  CD   CG   109.70  3.000
 6DN  CE   CD   CG   112.37  3.000
 6DN  HE3  CE   HE2  105.80  3.000
 6DN  HE3  CE   NZ   108.14  3.000
 6DN  HE2  CE   NZ   108.01  3.000
 6DN  HE3  CE   CD   108.33  3.000
 6DN  HE2  CE   CD   109.10  3.000
 6DN  NZ   CE   CD   116.90  3.000
 6DN  HZ1  NZ   CX1  108.74  3.000
 6DN  HZ1  NZ   CE   110.60  3.000
 6DN  CX1  NZ   CE   114.97  3.000
 6DN  H17  CX1  H16  105.27  3.000
 6DN  H17  CX1  CX2  106.23  3.000
 6DN  H16  CX1  CX2  109.17  3.000
 6DN  H17  CX1  NZ   113.57  3.000
 6DN  H16  CX1  NZ   109.09  3.000
 6DN  CX2  CX1  NZ   113.15  3.000
 6DN  CX1  CX2  O2   117.40  3.000
 6DN  CX1  CX2  O1   115.77  3.000
 6DN  O2   CX2  O1   126.79  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
 6DN  Var_01  NZ   CX1  CX2  O1  163.67  30.0  3
 6DN  Var_02  CE   CD   CG   CB  176.49  30.0  1
 6DN  Var_03  CD   CG   CB   CA  178.47  30.0  1
 6DN  Var_04  NZ   CE   CD   CG  179.22  30.0  1
 6DN  Var_05  CX2  CX1  NZ   CE  169.23  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
 6DN  chir_01  CA  CB  C  N  negativ

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
 6DN  plan-1  CA   0.020
 6DN  plan-1  C    0.020
 6DN  plan-1  O    0.020
 6DN  plan-1  OXT  0.020
 6DN  plan-2  O1   0.020
 6DN  plan-2  O2   0.020
 6DN  plan-2  CX1  0.020
 6DN  plan-2  CX2  0.020

