# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:17:48 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (4S)-4-amino-5,5-dihydroxypentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(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
 GLK  GLK  '(4S)-4-amino-5,5-dihydroxypentanoic acid'  peptide  21  10  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GLK
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
 GLK  N    N  NH2   0  -0.789   1.2300   1.8318  -0.4241
 GLK  CA   C  CH1   0  -0.181   1.1311   0.5120   0.1786
 GLK  C    C  CH1   0   0.299   2.3713  -0.3026  -0.2048
 GLK  CB   C  CH2   0  -0.426  -0.1556  -0.2394  -0.1831
 GLK  CG   C  CH2   0  -0.584  -1.3918   0.5020   0.2973
 GLK  CD   C  C     0   0.552  -2.6821  -0.1861  -0.0485
 GLK  OE1  O  O     0  -0.445  -2.7870  -1.1769  -0.7278
 GLK  OE2  O  OH1   0  -0.598  -3.7299   0.4374   0.4845
 GLK  O    O  OH1   0  -0.663   3.4899   0.3739   0.2807
 GLK  H    H  HNH2  0   0.339   0.9692   1.7809  -1.4028
 GLK  H2   H  HNH2  0   0.353   0.5709   2.4660   0.0068
 GLK  HA   H  HCH1  0   0.231   1.1580   0.6473   1.2683
 GLK  HB2  H  HCH2  0   0.226  -0.1980  -0.3723  -1.2692
 GLK  HB3  H  HCH2  0   0.234  -0.1458  -1.2391   0.2524
 GLK  HG2  H  HCH2  0   0.277  -1.3567   0.6406   1.3825
 GLK  HG3  H  HCH2  0   0.272  -1.4375   1.5112  -0.1240
 GLK  HE2  H  HOH1  0   0.478  -4.5470  -0.0207   0.2382
 GLK  H1   H  HOH1  0   0.452   4.2801  -0.0427  -0.0794
 GLK  OXT  O  OH1   0  -0.663   2.3192  -1.6200   0.2666
 GLK  H10  H  HCH1  0   0.193   2.4135  -0.4019  -1.2984
 GLK  HXT  H  HOH1  0   0.445   2.1759  -1.6039   1.2211

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
 GLK  N    CA   single  1.458  0.019  1.458
 GLK  N    H    single  0.860  0.020  0.860
 GLK  N    H2   single  0.890  0.020  1.040
 GLK  CA   C    single  1.525  0.021  1.525
 GLK  CA   CB   single  1.530  0.020  1.530
 GLK  CA   HA   single  0.970  0.020  0.970
 GLK  C    O    single  1.231  0.020  1.231
 GLK  CB   CG   single  1.519  0.020  1.519
 GLK  CB   HB2  single  0.970  0.020  1.090
 GLK  CB   HB3  single  0.970  0.020  1.090
 GLK  CG   CD   single  1.503  0.020  1.503
 GLK  CG   HG2  single  0.970  0.020  1.090
 GLK  CG   HG3  single  0.970  0.020  1.090
 GLK  CD   OE1  double  1.206  0.020  1.206
 GLK  CD   OE2  single  1.331  0.020  1.331
 GLK  OE2  HE2  single  0.850  0.020  0.980
 GLK  O    H1   single  0.850  0.020  0.980
 GLK  C    OXT  single  1.400  0.020  1.400
 GLK  C    H10  single  0.970  0.020  1.090
 GLK  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
 GLK  H2   N    H    105.98  3.000
 GLK  H2   N    CA   110.38  3.000
 GLK  H    N    CA   114.00  3.000
 GLK  HA   CA   CB   109.00  3.000
 GLK  HA   CA   C    109.00  3.000
 GLK  CB   CA   C    110.10  1.900
 GLK  HA   CA   N    110.00  3.000
 GLK  CB   CA   N    110.50  1.700
 GLK  C    CA   N    111.00  2.800
 GLK  H10  C    OXT  104.56  3.000
 GLK  H10  C    O    111.07  3.000
 GLK  OXT  C    O    111.66  3.000
 GLK  H10  C    CA   109.15  3.000
 GLK  OXT  C    CA   112.69  3.000
 GLK  O    C    CA   120.80  1.700
 GLK  HB3  CB   HB2  106.57  3.000
 GLK  HB3  CB   CG   109.18  3.000
 GLK  HB2  CB   CG   109.96  3.000
 GLK  HB3  CB   CA   110.33  3.000
 GLK  HB2  CB   CA   109.02  3.000
 GLK  CG   CB   CA   111.66  3.000
 GLK  HG3  CG   HG2  105.44  3.000
 GLK  HG3  CG   CD   107.32  3.000
 GLK  HG2  CG   CD   108.28  3.000
 GLK  HG3  CG   CB   111.24  3.000
 GLK  HG2  CG   CB   110.44  3.000
 GLK  CD   CG   CB   113.73  3.000
 GLK  OE2  CD   OE1  122.83  3.000
 GLK  OE2  CD   CG   111.68  3.000
 GLK  OE1  CD   CG   125.49  3.000
 GLK  HE2  OE2  CD   109.92  3.000
 GLK  H1   O    C    108.55  3.000
 GLK  HXT  OXT  C    108.83  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
 GLK  CONST_01  HE2  OE2  CD  CG  180.00   0.0  0
 GLK  Var_01    CD   CG   CB  CA  179.27  30.0  3
 GLK  Var_02    OE1  CD   CG  CB   -5.53  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
 GLK  chir_01  CA  N  C  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
 GLK  plan-1  CG   0.020
 GLK  plan-1  CD   0.020
 GLK  plan-1  OE1  0.020
 GLK  plan-1  OE2  0.020
 GLK  plan-1  HE2  0.020

