# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:10:10 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@](O)(CC(=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
 7QD  7QD  '(2S)-2-hydroxy-4-oxobutane-1,2,4-tricarboxylic acid'  ligand  20  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7QD
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
 7QD  O01   O  O      0  -0.335   1.9871   1.0499   0.6471
 7QD  C02   C  C      0   0.238   2.0438  -0.0557   0.1586
 7QD  C03   C  C      0   0.232   3.4172  -0.7326  -0.0661
 7QD  O04   O  O      0  -0.299   3.4920  -1.4695  -1.0652
 7QD  O05   O  OC    -1  -0.818   4.2990  -0.4625   0.7633
 7QD  C06   C  CH2    0  -0.550   0.8273  -0.8122  -0.3006
 7QD  C07   C  CT     0   0.157  -0.5003  -0.2555   0.1927
 7QD  O08   O  OH1    0  -0.743  -0.5119  -0.3487   1.5954
 7QD  C09   C  C      0   0.447  -0.7335   1.1905  -0.3195
 7QD  O10   O  O      0  -0.623  -1.2623   2.0027   0.4597
 7QD  O11   O  OC    -1  -0.725  -0.4212   1.4050  -1.5118
 7QD  C12   C  CH2    0  -0.572  -1.6450  -1.1186  -0.3844
 7QD  C13   C  C      0   0.435  -3.0206  -0.7240   0.1677
 7QD  O14   O  OC    -1  -0.721  -3.1079  -0.6469   1.4248
 7QD  O15   O  O      0  -0.590  -3.9512  -0.5251  -0.6283
 7QD  H062  H  HCH2   0   0.257   0.8492  -0.8384  -1.3918
 7QD  H061  H  HCH2   0   0.284   0.9384  -1.8590   0.0064
 7QD  H081  H  HOH1   0   0.417  -1.4691  -0.3751   1.8156
 7QD  H121  H  HCH2   0   0.259  -1.6347  -1.0591  -1.4731
 7QD  H122  H  HCH2   0   0.250  -1.4565  -2.1660  -0.1189

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
 7QD  O04  C03   deloc   1.244  0.020  1.244
 7QD  O05  C03   deloc   1.240  0.020  1.240
 7QD  C03  C02   single  1.548  0.020  1.548
 7QD  C02  C06   single  1.504  0.020  1.504
 7QD  C02  O01   double  1.210  0.020  1.210
 7QD  C06  C07   single  1.522  0.020  1.522
 7QD  O08  C07   single  1.406  0.020  1.406
 7QD  C07  C12   single  1.545  0.020  1.545
 7QD  C07  C09   single  1.552  0.020  1.552
 7QD  C12  C13   single  1.534  0.020  1.534
 7QD  O15  C13   deloc   1.241  0.020  1.241
 7QD  C13  O14   deloc   1.263  0.020  1.263
 7QD  C09  O10   deloc   1.244  0.020  1.244
 7QD  C09  O11   deloc   1.251  0.020  1.251
 7QD  C06  H062  single  0.970  0.020  1.090
 7QD  C06  H061  single  0.970  0.020  1.090
 7QD  O08  H081  single  0.850  0.020  0.980
 7QD  C12  H121  single  0.970  0.020  1.090
 7QD  C12  H122  single  0.970  0.020  1.090

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
 7QD  C06   C02  C03   116.96  3.000
 7QD  C06   C02  O01   123.01  3.000
 7QD  C03   C02  O01   119.99  3.000
 7QD  O05   C03  O04   128.57  3.000
 7QD  O05   C03  C02   116.01  3.000
 7QD  O04   C03  C02   115.42  3.000
 7QD  H061  C06  H062  104.76  3.000
 7QD  H061  C06  C07   110.30  3.000
 7QD  H062  C06  C07   110.51  3.000
 7QD  H061  C06  C02   108.22  3.000
 7QD  H062  C06  C02   107.51  3.000
 7QD  C07   C06  C02   115.00  3.000
 7QD  C12   C07  C09   106.61  3.000
 7QD  C09   C07  O08   112.95  3.000
 7QD  C12   C07  O08   109.23  3.000
 7QD  C09   C07  C06   111.41  3.000
 7QD  C12   C07  C06   108.71  3.000
 7QD  O08   C07  C06   107.85  3.000
 7QD  H081  O08  C07   103.50  3.000
 7QD  O11   C09  O10   126.25  3.000
 7QD  O11   C09  C07   115.91  3.000
 7QD  O10   C09  C07   117.75  3.000
 7QD  H122  C12  H121  106.98  3.000
 7QD  H122  C12  C13   108.22  3.000
 7QD  H121  C12  C13   110.72  3.000
 7QD  H122  C12  C07   108.40  3.000
 7QD  H121  C12  C07   109.60  3.000
 7QD  C13   C12  C07   112.72  3.000
 7QD  O15   C13  O14   125.25  3.000
 7QD  O14   C13  C12   115.85  3.000
 7QD  O15   C13  C12   118.89  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
 7QD  Var_01  O04  C03  C02  O01  -146.71  30.0  2
 7QD  Var_02  C07  C06  C02  O01   -14.38  30.0  3
 7QD  Var_03  O15  C13  C12  C07   129.99  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
 7QD  chir_01  C07  O08  C12  C09  negativ

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
 7QD  plan-1  O01  0.020
 7QD  plan-1  C02  0.020
 7QD  plan-1  C03  0.020
 7QD  plan-1  C06  0.020
 7QD  plan-2  C02  0.020
 7QD  plan-2  C03  0.020
 7QD  plan-2  O04  0.020
 7QD  plan-2  O05  0.020
 7QD  plan-3  C07  0.020
 7QD  plan-3  C09  0.020
 7QD  plan-3  O10  0.020
 7QD  plan-3  O11  0.020
 7QD  plan-4  C12  0.020
 7QD  plan-4  C13  0.020
 7QD  plan-4  O14  0.020
 7QD  plan-4  O15  0.020

