# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:04:09 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-C-carboxy-2-deoxy-L-threo-pentaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](C(O)=O)[C@@](O)(CC(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
 7A2  7A2  '3-C-carboxy-2-deoxy-L-threo-pentaric acid'  ligand  22  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7A2
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
 7A2  C   C  C     0   0.567   2.6398  -0.2410  -0.0724
 7A2  O   O  O     0  -0.431   2.7637   0.8038   0.5157
 7A2  C1  C  CH2   0  -0.603   1.3404  -0.7781  -0.6068
 7A2  C2  C  CT    0   0.065   0.1123  -0.1646   0.0728
 7A2  C3  C  C     0   0.564   0.1365   1.3622  -0.0031
 7A2  C4  C  CH1   0  -0.059  -1.1614  -0.7213  -0.6454
 7A2  C5  C  C     0   0.524  -2.4228  -0.1847   0.0126
 7A2  O1  O  OH1   0  -0.590   3.6527  -1.0457  -0.3577
 7A2  O2  O  OH1   0  -0.652   0.0683  -0.4768   1.4317
 7A2  O3  O  OH1   0  -0.593   0.3566   1.7710  -1.2435
 7A2  O4  O  O     0  -0.424  -0.0610   2.0889   0.9299
 7A2  O5  O  OH1   0  -0.654  -1.1633  -2.1147  -0.5852
 7A2  O6  O  OH1   0  -0.576  -2.6686   1.0669  -0.3119
 7A2  O7  O  O     0  -0.429  -3.1063  -0.8568   0.7423
 7A2  H2  H  HCH2  0   0.312   1.3257  -0.6023  -1.6862
 7A2  H3  H  HCH2  0   0.307   1.3182  -1.8628  -0.4882
 7A2  H   H  HCH1  0   0.288  -1.1472  -0.4121  -1.6949
 7A2  H1  H  HOH1  0   0.484   4.4850  -0.6620  -0.0416
 7A2  H4  H  HOH1  0   0.457   0.1026  -1.4352   1.5324
 7A2  H5  H  HOH1  0   0.489   0.3328   2.7390  -1.2879
 7A2  H6  H  HOH1  0   0.457  -1.7754  -2.3935   0.1089
 7A2  H7  H  HOH1  0   0.496  -3.4467   1.4027   0.1606

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
 7A2  O   C   double  1.205  0.020  1.205
 7A2  O1  C   single  1.325  0.020  1.325
 7A2  O7  C5  double  1.205  0.020  1.205
 7A2  C   C1  single  1.504  0.020  1.504
 7A2  C1  C2  single  1.532  0.020  1.532
 7A2  C5  O6  single  1.316  0.020  1.316
 7A2  C5  C4  single  1.521  0.020  1.521
 7A2  O2  C2  single  1.395  0.020  1.395
 7A2  C2  C4  single  1.565  0.020  1.565
 7A2  C2  C3  single  1.529  0.020  1.529
 7A2  C4  O5  single  1.395  0.020  1.395
 7A2  C3  O4  double  1.199  0.020  1.199
 7A2  C3  O3  single  1.324  0.020  1.324
 7A2  C1  H2  single  0.970  0.020  1.090
 7A2  C1  H3  single  0.970  0.020  1.090
 7A2  C4  H   single  0.970  0.020  1.090
 7A2  O1  H1  single  0.850  0.020  0.980
 7A2  O2  H4  single  0.850  0.020  0.980
 7A2  O3  H5  single  0.850  0.020  0.980
 7A2  O5  H6  single  0.850  0.020  0.980
 7A2  O6  H7  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
 7A2  O1  C   C1  111.53  3.000
 7A2  C1  C   O   124.87  3.000
 7A2  O1  C   O   123.58  3.000
 7A2  H3  C1  H2  105.47  3.000
 7A2  H3  C1  C2  109.49  3.000
 7A2  H2  C1  C2  111.27  3.000
 7A2  H3  C1  C   109.50  3.000
 7A2  H2  C1  C   107.74  3.000
 7A2  C2  C1  C   113.07  3.000
 7A2  O2  C2  C4  109.99  3.000
 7A2  C4  C2  C3  110.21  3.000
 7A2  O2  C2  C3  105.81  3.000
 7A2  C3  C2  C1  111.42  3.000
 7A2  C4  C2  C1  107.85  3.000
 7A2  O2  C2  C1  111.58  3.000
 7A2  O4  C3  O3  124.69  3.000
 7A2  O3  C3  C2  110.94  3.000
 7A2  O4  C3  C2  124.33  3.000
 7A2  H   C4  O5  108.89  3.000
 7A2  H   C4  C5  109.04  3.000
 7A2  O5  C4  C5  109.44  3.000
 7A2  H   C4  C2  109.21  3.000
 7A2  O5  C4  C2  109.68  3.000
 7A2  C5  C4  C2  110.55  3.000
 7A2  O7  C5  O6  125.03  3.000
 7A2  O6  C5  C4  112.57  3.000
 7A2  O7  C5  C4  122.40  3.000
 7A2  H1  O1  C   110.23  3.000
 7A2  H4  O2  C2  108.85  3.000
 7A2  H5  O3  C3  110.31  3.000
 7A2  H6  O5  C4  108.66  3.000
 7A2  H7  O6  C5  111.03  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
 7A2  CONST_01  H1  O1  C   O     0.00   0.0  0
 7A2  CONST_02  H5  O3  C3  C2  180.00   0.0  0
 7A2  CONST_03  H7  O6  C5  C4  180.00   0.0  0
 7A2  Var_01    C2  C1  C   O   -20.87  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
 7A2  chir_01  C2  O2  C4  C3  negativ
 7A2  chir_02  C4  O5  C2  C5  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
 7A2  plan-1  C   0.020
 7A2  plan-1  O   0.020
 7A2  plan-1  C1  0.020
 7A2  plan-1  O1  0.020
 7A2  plan-1  H1  0.020
 7A2  plan-2  C2  0.020
 7A2  plan-2  C3  0.020
 7A2  plan-2  O3  0.020
 7A2  plan-2  O4  0.020
 7A2  plan-2  H5  0.020
 7A2  plan-3  C4  0.020
 7A2  plan-3  C5  0.020
 7A2  plan-3  O6  0.020
 7A2  plan-3  O7  0.020
 7A2  plan-3  H7  0.020

