# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:59:57 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  20  10  .  2022-03-18  2022-07-25
;
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  -0.788   1.2726   1.8056  -0.4155
 GLK  CA   C  CH1    0  -0.179   1.1386   0.4814   0.1779
 GLK  C    C  CH1    0   0.298   2.3495  -0.3663  -0.2230
 GLK  CB   C  CH2    0  -0.409  -0.1768  -0.2223  -0.1756
 GLK  CG   C  CH2    0  -0.586  -1.3993   0.5062   0.3601
 GLK  CD   C  C      0   0.413  -2.7614  -0.1117  -0.0054
 GLK  OE1  O  O      0  -0.609  -2.7804  -1.0174  -0.8619
 GLK  OE2  O  OC    -1  -0.633  -3.7535   0.3676   0.5839
 GLK  O    O  OH1    0  -0.664   3.5037   0.3003   0.1925
 GLK  H    H  HNH2   0   0.333   1.0585   1.7472  -1.4057
 GLK  H2   H  HNH2   0   0.347   0.5693   2.4203  -0.0267
 GLK  HA   H  HCH1   0   0.218   1.1843   0.6091   1.2689
 GLK  HB2  H  HCH2   0   0.202  -0.2452  -0.3109  -1.2653
 GLK  HB3  H  HCH2   0   0.210  -0.1745  -1.2431   0.2109
 GLK  HG2  H  HCH2   0   0.216  -1.3330   0.5811   1.4512
 GLK  HG3  H  HCH2   0   0.213  -1.4090   1.5439   0.0059
 GLK  H1   H  HOH1   0   0.450   4.2674  -0.1670  -0.1624
 GLK  OXT  O  OH1    0  -0.664   2.2911  -1.6651   0.2981
 GLK  H10  H  HCH1   0   0.187   2.3485  -0.5058  -1.3135
 GLK  HXT  H  HOH1   0   0.444   2.1495  -1.6095   1.2512

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  1.521  0.020  1.521
 GLK  CB   HB2  single  0.970  0.020  1.090
 GLK  CB   HB3  single  0.970  0.020  1.090
 GLK  CG   CD   single  1.540  0.020  1.540
 GLK  CG   HG2  single  0.970  0.020  1.090
 GLK  CG   HG3  single  0.970  0.020  1.090
 GLK  CD   OE1  deloc   1.247  0.020  1.247
 GLK  CD   OE2  deloc   1.250  0.020  1.250
 GLK  O    H1   single  0.850  0.020  0.980
 GLK  C    OXT  single  1.401  0.020  1.401
 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    105.26  3.000
 GLK  H2   N    CA   109.37  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  104.55  3.000
 GLK  H10  C    O    110.89  3.000
 GLK  OXT  C    O    111.50  3.000
 GLK  H10  C    CA   109.22  3.000
 GLK  OXT  C    CA   112.51  3.000
 GLK  O    C    CA   120.80  1.700
 GLK  HB3  CB   HB2  106.07  3.000
 GLK  HB3  CB   CG   108.97  3.000
 GLK  HB2  CB   CG   109.82  3.000
 GLK  HB3  CB   CA   110.23  3.000
 GLK  HB2  CB   CA   108.67  3.000
 GLK  CG   CB   CA   112.87  3.000
 GLK  HG3  CG   HG2  104.93  3.000
 GLK  HG3  CG   CD   107.17  3.000
 GLK  HG2  CG   CD   108.51  3.000
 GLK  HG3  CG   CB   110.28  3.000
 GLK  HG2  CG   CB   109.57  3.000
 GLK  CD   CG   CB   115.80  3.000
 GLK  OE2  CD   OE1  126.20  3.000
 GLK  OE2  CD   CG   115.88  3.000
 GLK  OE1  CD   CG   117.92  3.000
 GLK  H1   O    C    108.32  3.000
 GLK  HXT  OXT  C    108.67  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  Var_01  CD   CG  CB  CA  177.59  30.0  3
 GLK  Var_02  OE1  CD  CG  CB  -10.74  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

