# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 01:26:41 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  30  14  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  OH1   0  -0.597  -10.7808  -29.2705  2.1058
 6DN  O2   O  O     0  -0.440  -11.2852  -28.6288  0.0280
 6DN  CB   C  CH2   0  -0.429  -14.6105  -23.0003  3.8673
 6DN  CA   C  CH1   0  -0.207  -14.7289  -21.5802  4.4396
 6DN  C    C  C     0   0.521  -16.0538  -21.4501  5.1795
 6DN  O    O  O     0  -0.442  -16.1669  -21.3982  6.3790
 6DN  N    N  NH2   0  -0.776  -13.5816  -21.2636  5.2552
 6DN  CG   C  CH2   0  -0.409  -13.4087  -23.1780  2.9496
 6DN  CD   C  CH2   0  -0.447  -13.2897  -24.6037  2.4255
 6DN  CE   C  CH2   0  -0.286  -12.1395  -24.7608  1.4321
 6DN  NZ   N  NH1   0  -0.593  -11.9400  -26.0884  0.8783
 6DN  CX1  C  CH2   0  -0.393  -11.5540  -27.0745  1.8542
 6DN  CX2  C  C     0   0.523  -11.1978  -28.3873  1.2043
 6DN  OXT  O  OH1   0  -0.594  -17.0900  -21.4149  4.3484
 6DN  H1   H  HOH1  0   0.482  -10.5654  -30.1104  1.6738
 6DN  HB2  H  HCH2  0   0.239  -15.5200  -23.2476  3.3152
 6DN  HB3  H  HCH2  0   0.227  -14.5514  -23.7120  4.6990
 6DN  HA   H  HCH1  0   0.264  -14.7562  -20.8784  3.5989
 6DN  H    H  HNH2  0   0.353  -13.6431  -20.3151  5.6024
 6DN  H2   H  HNH2  0   0.342  -13.5573  -21.8637  6.0707
 6DN  HG2  H  HCH2  0   0.224  -12.4951  -22.9047  3.4821
 6DN  HG3  H  HCH2  0   0.213  -13.4937  -22.4819  2.1074
 6DN  HD2  H  HCH2  0   0.212  -14.2253  -24.8967  1.9358
 6DN  HD3  H  HCH2  0   0.222  -13.1575  -25.2868  3.2708
 6DN  HE2  H  HCH2  0   0.217  -11.2023  -24.4503  1.9057
 6DN  HE3  H  HCH2  0   0.229  -12.2992  -24.0739  0.5960
 6DN  HZ1  H  HNH1  0   0.345  -12.7799  -26.3866  0.3979
 6DN  H16  H  HCH2  0   0.271  -10.6698  -26.7162  2.3919
 6DN  H17  H  HCH2  0   0.249  -12.3048  -27.2838  2.6312
 6DN  HXT  H  HOH1  0   0.480  -17.9189  -21.3683  4.8483

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  double  1.204  0.020  1.204
 6DN  NZ   CE   single  1.452  0.020  1.452
 6DN  NZ   CX1  single  1.440  0.020  1.440
 6DN  CX2  O1   single  1.329  0.020  1.329
 6DN  CX2  CX1  single  1.508  0.020  1.508
 6DN  CE   CD   single  1.528  0.020  1.528
 6DN  CD   CG   single  1.524  0.020  1.524
 6DN  CG   CB   single  1.522  0.020  1.522
 6DN  CB   CA   single  1.536  0.020  1.536
 6DN  CA   C    single  1.523  0.020  1.523
 6DN  CA   N    single  1.443  0.020  1.443
 6DN  C    O    double  1.206  0.020  1.206
 6DN  C    OXT  single  1.329  0.020  1.329
 6DN  O1   H1   single  0.850  0.020  0.980
 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
 6DN  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
 6DN  H1   O1   CX2  110.08  3.000
 6DN  HB3  CB   HB2  106.34  3.000
 6DN  HB3  CB   CG   109.81  3.000
 6DN  HB2  CB   CG   109.03  3.000
 6DN  HB3  CB   CA   108.77  3.000
 6DN  HB2  CB   CA   109.48  3.000
 6DN  CG   CB   CA   113.17  3.000
 6DN  HA   CA   N    108.24  3.000
 6DN  HA   CA   C    107.24  3.000
 6DN  N    CA   C    113.47  3.000
 6DN  HA   CA   CB   107.96  3.000
 6DN  N    CA   CB   110.63  3.000
 6DN  C    CA   CB   109.10  3.000
 6DN  OXT  C    O    123.22  3.000
 6DN  OXT  C    CA   112.13  3.000
 6DN  O    C    CA   124.65  3.000
 6DN  H2   N    H    106.29  3.000
 6DN  H2   N    CA   110.13  3.000
 6DN  H    N    CA   110.57  3.000
 6DN  HG3  CG   HG2  106.29  3.000
 6DN  HG3  CG   CD   109.64  3.000
 6DN  HG2  CG   CD   109.67  3.000
 6DN  HG3  CG   CB   109.14  3.000
 6DN  HG2  CG   CB   109.71  3.000
 6DN  CD   CG   CB   112.22  3.000
 6DN  HD3  CD   HD2  106.34  3.000
 6DN  HD3  CD   CE   110.30  3.000
 6DN  HD2  CD   CE   108.94  3.000
 6DN  HD3  CD   CG   109.13  3.000
 6DN  HD2  CD   CG   109.71  3.000
 6DN  CE   CD   CG   112.25  3.000
 6DN  HE3  CE   HE2  106.11  3.000
 6DN  HE3  CE   NZ   107.62  3.000
 6DN  HE2  CE   NZ   107.86  3.000
 6DN  HE3  CE   CD   108.81  3.000
 6DN  HE2  CE   CD   109.50  3.000
 6DN  NZ   CE   CD   116.45  3.000
 6DN  HZ1  NZ   CX1  110.02  3.000
 6DN  HZ1  NZ   CE   109.64  3.000
 6DN  CX1  NZ   CE   113.85  3.000
 6DN  H17  CX1  H16  105.45  3.000
 6DN  H17  CX1  CX2  107.46  3.000
 6DN  H16  CX1  CX2  107.80  3.000
 6DN  H17  CX1  NZ   115.20  3.000
 6DN  H16  CX1  NZ   108.98  3.000
 6DN  CX2  CX1  NZ   111.56  3.000
 6DN  CX1  CX2  O2   125.36  3.000
 6DN  CX1  CX2  O1   111.12  3.000
 6DN  O2   CX2  O1   123.52  3.000
 6DN  HXT  OXT  C    110.22  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  CONST_01  H1   O1   CX2  O2     0.00   0.0  0
 6DN  CONST_02  HXT  OXT  C    CA   180.00   0.0  0
 6DN  Var_01    NZ   CX1  CX2  O1   176.96  30.0  3
 6DN  Var_02    CE   CD   CG   CB   176.20  30.0  1
 6DN  Var_03    CD   CG   CB   CA   178.39  30.0  1
 6DN  Var_04    NZ   CE   CD   CG   179.76  30.0  1
 6DN  Var_05    CX2  CX1  NZ   CE  -173.04  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-1  HXT  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
 6DN  plan-2  H1   0.020

