# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 15:16:12 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: 5,5-dihydroxy-L-norvaline
#   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
 GLJ  GLJ  5,5-dihydroxy-L-norvaline  L-peptide  20  10  .  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_GLJ
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
 GLJ  N    N  NH2    0  -0.782  -8.0314  22.2921  35.8784
 GLJ  CA   C  CH1    0  -0.045  -7.5173  21.4562  34.7986
 GLJ  C    C  C      0   0.358  -8.6846  20.6568  34.1675
 GLJ  O    O  O      0  -0.504  -9.8308  21.0947  34.3386
 GLJ  CB   C  CH2    0  -0.397  -6.3592  20.5940  35.3407
 GLJ  CG   C  CH2    0  -0.397  -5.1060  20.5283  34.4675
 GLJ  CD   C  CH1    0   0.022  -5.3442  19.9786  33.0709
 GLJ  OE1  O  OH1    0  -0.767  -5.9861  18.7433  33.0976
 GLJ  H    H  HNH2   0   0.359  -7.3487  23.0069  36.0970
 GLJ  HA   H  HCH1   0   0.109  -7.1105  22.0700  33.9713
 GLJ  HB2  H  HCH2   0   0.142  -6.0514  21.0301  36.2940
 GLJ  HB3  H  HCH2   0   0.198  -6.7036  19.5879  35.5924
 GLJ  HG2  H  HCH2   0   0.221  -4.6801  21.5343  34.3868
 GLJ  HG3  H  HCH2   0   0.091  -4.3602  19.9035  34.9703
 GLJ  HD2  H  HCH1   0   0.327  -5.9669  20.7014  32.5107
 GLJ  OE2  O  OH1    0  -0.710  -4.1078  19.8598  32.4307
 GLJ  HE1  H  HOH1   0   0.410  -6.9427  18.9702  33.2620
 GLJ  H2   H  HNH2   0   0.357  -8.8641  22.7679  35.5593
 GLJ  OXT  O  OC    -1  -0.388  -8.4011  19.6418  33.4771
 GLJ  HE2  H  HOH1   0   0.396  -4.2669  19.5487  31.5331

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
 GLJ  N    CA   single  1.458  0.019  1.458
 GLJ  N    H    single  0.860  0.020  0.860
 GLJ  CA   C    single  1.525  0.021  1.525
 GLJ  CA   CB   single  1.530  0.020  1.530
 GLJ  CA   HA   single  0.970  0.020  0.970
 GLJ  C    O    deloc   1.231  0.020  1.231
 GLJ  CB   CG   single  1.529  0.020  1.529
 GLJ  CB   HB2  single  0.970  0.020  1.090
 GLJ  CB   HB3  single  0.970  0.020  1.090
 GLJ  CG   CD   single  1.520  0.020  1.520
 GLJ  CG   HG2  single  0.970  0.020  1.090
 GLJ  CG   HG3  single  0.970  0.020  1.090
 GLJ  CD   OE1  single  1.392  0.020  1.392
 GLJ  CD   HD2  single  0.970  0.020  1.090
 GLJ  CD   OE2  single  1.397  0.020  1.397
 GLJ  OE1  HE1  single  0.850  0.020  0.980
 GLJ  N    H2   single  0.890  0.020  1.040
 GLJ  C    OXT  deloc   1.260  0.020  1.260
 GLJ  OE2  HE2  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
 GLJ  H2   N    H    106.94  3.000
 GLJ  H2   N    CA   109.05  3.000
 GLJ  H    N    CA   114.00  3.000
 GLJ  HA   CA   CB   109.00  3.000
 GLJ  HA   CA   C    109.00  3.000
 GLJ  CB   CA   C    110.10  1.900
 GLJ  HA   CA   N    110.00  3.000
 GLJ  CB   CA   N    110.50  1.700
 GLJ  C    CA   N    111.00  2.800
 GLJ  OXT  C    O    124.65  3.000
 GLJ  OXT  C    CA   118.00  3.000
 GLJ  O    C    CA   120.80  1.700
 GLJ  HB3  CB   HB2  104.79  3.000
 GLJ  HB3  CB   CG   110.51  3.000
 GLJ  HB2  CB   CG   106.54  3.000
 GLJ  HB3  CB   CA   111.04  3.000
 GLJ  HB2  CB   CA   107.16  3.000
 GLJ  CG   CB   CA   116.03  3.000
 GLJ  HG3  CG   HG2  107.04  3.000
 GLJ  HG3  CG   CD   108.80  3.000
 GLJ  HG2  CG   CD   108.99  3.000
 GLJ  HG3  CG   CB   108.69  3.000
 GLJ  HG2  CG   CB   108.74  3.000
 GLJ  CD   CG   CB   114.33  3.000
 GLJ  OE2  CD   HD2  108.76  3.000
 GLJ  OE2  CD   OE1  109.96  3.000
 GLJ  HD2  CD   OE1  109.26  3.000
 GLJ  OE2  CD   CG   108.24  3.000
 GLJ  HD2  CD   CG   108.49  3.000
 GLJ  OE1  CD   CG   112.06  3.000
 GLJ  HE1  OE1  CD   104.10  3.000
 GLJ  HE2  OE2  CD   107.96  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
 GLJ  Var_01  CD   CG  CB  CA  -59.20  30.0  3
 GLJ  Var_02  OE1  CD  CG  CB  -53.23  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
 GLJ  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
 GLJ  plan-1  CA   0.020
 GLJ  plan-1  C    0.020
 GLJ  plan-1  O    0.020
 GLJ  plan-1  OXT  0.020

