# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 13:59:16 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,4S)-2,5-diamino-4-hydroxy-5-oxopentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@H](O)C(N)=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
 GHG  GHG  '(2S,4S)-2,5-diamino-4-hydroxy-5-oxopentanoic acid (non-preferred name)'  L-peptide  20  11  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_GHG
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
 GHG  N     N  NH2    0  -0.819  49.5714  37.2831  20.7157
 GHG  CA    C  CH1    0  -0.237  49.4808  38.4482  21.5851
 GHG  C     C  C      0   0.421  48.4939  39.4981  20.9909
 GHG  O     O  O      0  -0.598  47.6889  39.0825  20.1331
 GHG  CB    C  CH2    0  -0.438  50.8504  39.0638  21.8536
 GHG  CG    C  CH1    0  -0.035  51.7885  38.1871  22.6712
 GHG  OG1   O  OH1    0  -0.666  52.8861  38.9874  23.0558
 GHG  CD    C  C      0   0.485  52.3028  36.9856  21.8700
 GHG  OE1   O  O      0  -0.482  53.0049  37.1306  20.8820
 GHG  NE2   N  NH2    0  -0.806  51.9645  35.7838  22.3634
 GHG  H     H  HNH2   0   0.331  49.6318  36.4329  21.2580
 GHG  H2    H  HNH2   0   0.337  48.7054  37.2394  20.1925
 GHG  HA    H  HCH1   0   0.200  49.0478  38.1850  22.5663
 GHG  HB2   H  HCH2   0   0.212  51.3290  39.3261  20.9049
 GHG  HB3   H  HCH2   0   0.231  50.7098  39.9884  22.4145
 GHG  HG    H  HCH1   0   0.213  51.2415  37.8327  23.5579
 GHG  HG1   H  HOH1   0   0.449  53.4439  38.4847  23.6586
 GHG  HE21  H  HNH2   0   0.396  52.2357  34.9393  21.8855
 GHG  HE22  H  HNH2   0   0.404  51.3813  35.6858  23.1766
 GHG  OXT   O  OC    -1  -0.598  48.5600  40.6528  21.4518

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
 GHG  N    CA    single  1.458  0.019  1.458
 GHG  N    H     single  0.860  0.020  0.860
 GHG  N    H2    single  0.890  0.020  1.040
 GHG  CA   C     single  1.525  0.021  1.525
 GHG  CA   CB    single  1.530  0.020  1.530
 GHG  CA   HA    single  0.970  0.020  0.970
 GHG  C    O     deloc   1.231  0.020  1.231
 GHG  CB   CG    single  1.522  0.020  1.522
 GHG  CB   HB2   single  0.970  0.020  1.090
 GHG  CB   HB3   single  0.970  0.020  1.090
 GHG  CG   OG1   single  1.412  0.020  1.412
 GHG  CG   CD    single  1.533  0.020  1.533
 GHG  CG   HG    single  0.970  0.020  1.090
 GHG  OG1  HG1   single  0.850  0.020  0.980
 GHG  CD   OE1   double  1.221  0.020  1.221
 GHG  CD   NE2   single  1.342  0.020  1.342
 GHG  NE2  HE21  single  0.860  0.020  1.020
 GHG  NE2  HE22  single  0.860  0.020  1.020
 GHG  C    OXT   deloc   1.245  0.020  1.245

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
 GHG  H2    N    H     106.98  3.000
 GHG  H2    N    CA    106.85  3.000
 GHG  H     N    CA    114.00  3.000
 GHG  HA    CA   CB    109.00  3.000
 GHG  HA    CA   C     109.00  3.000
 GHG  CB    CA   C     110.10  1.900
 GHG  HA    CA   N     110.00  3.000
 GHG  CB    CA   N     110.50  1.700
 GHG  C     CA   N     111.00  2.800
 GHG  OXT   C    O     126.71  3.000
 GHG  OXT   C    CA    116.74  3.000
 GHG  O     C    CA    120.80  1.700
 GHG  HB3   CB   HB2   107.40  3.000
 GHG  HB3   CB   CG    106.95  3.000
 GHG  HB2   CB   CG    109.52  3.000
 GHG  HB3   CB   CA    108.48  3.000
 GHG  HB2   CB   CA    109.68  3.000
 GHG  CG    CB   CA    114.55  3.000
 GHG  HG    CG   CD    109.60  3.000
 GHG  HG    CG   OG1   110.46  3.000
 GHG  CD    CG   OG1   109.01  3.000
 GHG  HG    CG   CB    108.18  3.000
 GHG  CD    CG   CB    112.18  3.000
 GHG  OG1   CG   CB    107.39  3.000
 GHG  HG1   OG1  CG    108.96  3.000
 GHG  NE2   CD   OE1   123.28  3.000
 GHG  NE2   CD   CG    115.15  3.000
 GHG  OE1   CD   CG    121.53  3.000
 GHG  HE22  NE2  HE21  117.27  3.000
 GHG  HE22  NE2  CD    122.05  3.000
 GHG  HE21  NE2  CD    120.54  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
 GHG  CONST_01  HE21  NE2  CD  CG  180.00  0.0  0
 GHG  CONST_02  HE22  NE2  CD  CG    0.00  0.0  0

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
 GHG  chir_01  CA  N    C   CB  positiv
 GHG  chir_02  CG  OG1  CB  CD  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
 GHG  plan-1  CG    0.020
 GHG  plan-1  CD    0.020
 GHG  plan-1  OE1   0.020
 GHG  plan-1  NE2   0.020
 GHG  plan-1  HE21  0.020
 GHG  plan-1  HE22  0.020
 GHG  plan-2  CA    0.020
 GHG  plan-2  C     0.020
 GHG  plan-2  O     0.020
 GHG  plan-2  OXT   0.020

