# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 09:18:35 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (2R,3S)-2,3-dihydroxybutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]([C@@H](O)C(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
 SRT  SRT  '(2R,3S)-2,3-dihydroxybutanedioic acid'  ligand  16  10  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SRT
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
 SRT  O1   O  OH1   0  -0.573   2.4231  -1.0876   0.5633
 SRT  O11  O  O     0  -0.437   2.4819   0.6281  -0.8697
 SRT  C1   C  C     0   0.514   1.9193  -0.0209  -0.0244
 SRT  C2   C  CH1   0  -0.097   0.5185   0.3237   0.4604
 SRT  O2   O  OH1   0  -0.643   0.3363   1.7034   0.5334
 SRT  C3   C  CH1   0  -0.097  -0.5013  -0.3402  -0.4957
 SRT  O3   O  OH1   0  -0.642  -0.3326  -1.7215  -0.5623
 SRT  C4   C  C     0   0.515  -1.9002   0.0197  -0.0156
 SRT  O4   O  O     0  -0.437  -2.4594  -0.6032   0.8513
 SRT  O41  O  OH1   0  -0.574  -2.4077   1.0672  -0.6345
 SRT  H1   H  HOH1  0   0.488   3.2986  -1.2947   0.1998
 SRT  H2   H  HCH1  0   0.292   0.3687  -0.0727   1.4688
 SRT  HA   H  HOH1  0   0.455   0.5835   2.1034  -0.3092
 SRT  H3   H  HCH1  0   0.291  -0.3458   0.0496  -1.5057
 SRT  HB   H  HOH1  0   0.454  -0.5587  -2.1126   0.2904
 SRT  H41  H  HOH1  0   0.488  -3.2834   1.2828  -0.2765

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
 SRT  O1   C1   single  1.318  0.020  1.318
 SRT  O1   H1   single  0.850  0.020  0.980
 SRT  O11  C1   double  1.205  0.020  1.205
 SRT  C1   C2   single  1.522  0.020  1.522
 SRT  C2   O2   single  1.394  0.020  1.394
 SRT  C2   C3   single  1.548  0.020  1.548
 SRT  C2   H2   single  0.970  0.020  1.090
 SRT  O2   HA   single  0.850  0.020  0.980
 SRT  C3   O3   single  1.393  0.020  1.393
 SRT  C3   C4   single  1.522  0.020  1.522
 SRT  C3   H3   single  0.970  0.020  1.090
 SRT  O3   HB   single  0.850  0.020  0.980
 SRT  C4   O4   double  1.205  0.020  1.205
 SRT  C4   O41  single  1.318  0.020  1.318
 SRT  O41  H41  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
 SRT  H1   O1   C1   110.52  3.000
 SRT  C2   C1   O11  122.09  3.000
 SRT  C2   C1   O1   113.15  3.000
 SRT  O11  C1   O1   124.76  3.000
 SRT  H2   C2   C3   108.89  3.000
 SRT  H2   C2   O2   107.01  3.000
 SRT  C3   C2   O2   111.77  3.000
 SRT  H2   C2   C1   109.73  3.000
 SRT  C3   C2   C1   108.22  3.000
 SRT  O2   C2   C1   111.18  3.000
 SRT  HA   O2   C2   109.34  3.000
 SRT  H3   C3   C4   109.74  3.000
 SRT  H3   C3   O3   106.97  3.000
 SRT  C4   C3   O3   111.15  3.000
 SRT  H3   C3   C2   108.90  3.000
 SRT  C4   C3   C2   108.02  3.000
 SRT  O3   C3   C2   112.03  3.000
 SRT  HB   O3   C3   109.34  3.000
 SRT  O41  C4   O4   124.74  3.000
 SRT  O41  C4   C3   113.18  3.000
 SRT  O4   C4   C3   122.08  3.000
 SRT  H41  O41  C4   110.54  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
 SRT  CONST_01  H1   O1   C1  O11    0.00  0.0  0
 SRT  CONST_02  H41  O41  C4  C3   180.00  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
 SRT  chir_01  C2  C1  O2  C3  negativ
 SRT  chir_02  C3  O3  C2  C4  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
 SRT  plan-1  O1   0.020
 SRT  plan-1  O11  0.020
 SRT  plan-1  C1   0.020
 SRT  plan-1  C2   0.020
 SRT  plan-1  H1   0.020
 SRT  plan-2  C3   0.020
 SRT  plan-2  C4   0.020
 SRT  plan-2  O4   0.020
 SRT  plan-2  O41  0.020
 SRT  plan-2  H41  0.020

