# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 19:30:49 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2~{S},3~{R},4~{S})-2,6-bis(azanyl)-3,4-bis(oxidanyl)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](O)[C@H](O)[C@H](N)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
 8RE  8RE  '(2~{S},3~{R},4~{S})-2,6-bis(azanyl)-3,4-bis(oxidanyl)hexanoic acid'  L-peptide  25  12  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8RE
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
 8RE  O    O  O      0  -0.591  5.2306  -21.2913  76.5749
 8RE  C    C  C      0   0.411  4.1952  -21.1884  77.2591
 8RE  CA   C  CH1    0  -0.244  4.1025  -22.0856  78.5303
 8RE  N    N  NH2    0  -0.823  3.0684  -21.5916  79.4411
 8RE  CB   C  CH1    0   0.068  3.8243  -23.5707  78.2022
 8RE  OH1  O  OH1    0  -0.671  3.2033  -23.6862  76.9383
 8RE  CG   C  CH1    0   0.009  5.0315  -24.5037  78.3380
 8RE  OH2  O  OH1    0  -0.683  4.4839  -25.8163  78.3115
 8RE  CD   C  CH2    0  -0.469  6.1224  -24.3195  77.2930
 8RE  CE   C  CH2    0  -0.279  7.3706  -25.1519  77.5561
 8RE  NZ   N  NH2    0  -0.794  8.3940  -24.8582  76.5617
 8RE  HA   H  HCH1   0   0.212  5.0872  -22.0417  79.0141
 8RE  H    H  HNH2   0   0.331  3.4386  -21.5071  80.3775
 8RE  H2   H  HNH2   0   0.334  2.7978  -20.6652  79.1392
 8RE  HB2  H  HCH1   0   0.199  3.1236  -23.8995  78.9840
 8RE  H7   H  HOH1   0   0.439  3.0086  -24.6188  76.7965
 8RE  HG2  H  HCH1   0   0.186  5.4689  -24.2998  79.3292
 8RE  H9   H  HOH1   0   0.445  5.2003  -26.4572  78.2997
 8RE  HD2  H  HCH2   0   0.244  6.4021  -23.2669  77.2615
 8RE  HD3  H  HCH2   0   0.207  5.7229  -24.5623  76.3026
 8RE  HE2  H  HCH2   0   0.178  7.1212  -26.2236  77.5952
 8RE  HE3  H  HCH2   0   0.213  7.7689  -24.8966  78.5426
 8RE  HZ1  H  HNH2   0   0.343  9.2130  -25.4240  76.7456
 8RE  HZ2  H  HNH2   0   0.336  8.0625  -25.1519  75.6505
 8RE  OXT  O  OC    -1  -0.599  3.2358  -20.4227  77.0440

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
 8RE  O    C    deloc   1.231  0.020  1.231
 8RE  C    CA   single  1.525  0.021  1.525
 8RE  NZ   CE   single  1.457  0.020  1.457
 8RE  OH2  CG   single  1.422  0.020  1.422
 8RE  CD   CE   single  1.523  0.020  1.523
 8RE  CD   CG   single  1.522  0.020  1.522
 8RE  OH1  CB   single  1.413  0.020  1.413
 8RE  CA   CB   single  1.530  0.020  1.530
 8RE  CA   N    single  1.458  0.019  1.458
 8RE  CG   CB   single  1.532  0.020  1.532
 8RE  CA   HA   single  0.970  0.020  0.970
 8RE  N    H    single  0.860  0.020  0.860
 8RE  N    H2   single  0.890  0.020  1.040
 8RE  CB   HB2  single  0.970  0.020  1.090
 8RE  OH1  H7   single  0.850  0.020  0.980
 8RE  CG   HG2  single  0.970  0.020  1.090
 8RE  OH2  H9   single  0.850  0.020  0.980
 8RE  CD   HD2  single  0.970  0.020  1.090
 8RE  CD   HD3  single  0.970  0.020  1.090
 8RE  CE   HE2  single  0.970  0.020  1.090
 8RE  CE   HE3  single  0.970  0.020  1.090
 8RE  NZ   HZ1  single  0.890  0.020  1.040
 8RE  NZ   HZ2  single  0.890  0.020  1.040
 8RE  C    OXT  deloc   1.246  0.020  1.246

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
 8RE  OXT  C    CA   116.66  3.000
 8RE  OXT  C    O    126.59  3.000
 8RE  CA   C    O    120.80  1.700
 8RE  HA   CA   CB   109.00  3.000
 8RE  HA   CA   N    110.00  3.000
 8RE  CB   CA   N    110.50  1.700
 8RE  HA   CA   C    109.00  3.000
 8RE  N    CA   C    111.00  2.800
 8RE  CB   CA   C    110.10  1.900
 8RE  H2   N    H    107.34  3.000
 8RE  H2   N    CA   108.21  3.000
 8RE  H    N    CA   114.00  3.000
 8RE  HB2  CB   CG   104.89  3.000
 8RE  HB2  CB   OH1  109.35  3.000
 8RE  CG   CB   OH1  112.08  3.000
 8RE  HB2  CB   CA   104.52  3.000
 8RE  CG   CB   CA   115.12  3.000
 8RE  OH1  CB   CA   110.33  3.000
 8RE  H7   OH1  CB   107.44  3.000
 8RE  HG2  CG   CD   108.09  3.000
 8RE  HG2  CG   OH2  109.88  3.000
 8RE  CD   CG   OH2  112.02  3.000
 8RE  HG2  CG   CB   106.24  3.000
 8RE  CD   CG   CB   115.49  3.000
 8RE  OH2  CG   CB   104.90  3.000
 8RE  H9   OH2  CG   109.19  3.000
 8RE  HD3  CD   HD2  106.36  3.000
 8RE  HD3  CD   CE   109.52  3.000
 8RE  HD2  CD   CE   108.82  3.000
 8RE  HD3  CD   CG   109.42  3.000
 8RE  HD2  CD   CG   108.71  3.000
 8RE  CE   CD   CG   113.75  3.000
 8RE  HE3  CE   HE2  106.12  3.000
 8RE  HE3  CE   NZ   108.22  3.000
 8RE  HE2  CE   NZ   112.31  3.000
 8RE  HE3  CE   CD   109.06  3.000
 8RE  HE2  CE   CD   110.63  3.000
 8RE  NZ   CE   CD   110.34  3.000
 8RE  HZ2  NZ   HZ1  105.43  3.000
 8RE  HZ2  NZ   CE   109.00  3.000
 8RE  HZ1  NZ   CE   109.37  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
 8RE  Var_01  NZ   CE  CD  CG  -176.51  30.0  3
 8RE  Var_02  HZ1  NZ  CE  CD  -179.54  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
 8RE  chir_01  CA  C    CB  N   positiv
 8RE  chir_02  CB  OH1  CA  CG  positiv
 8RE  chir_03  CG  OH2  CB  CD  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
 8RE  plan-1  O    0.020
 8RE  plan-1  C    0.020
 8RE  plan-1  CA   0.020
 8RE  plan-1  OXT  0.020

