# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 06:00:18 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{S})-2-ethyl-4-oxidanylidene-pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](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
 QVT  QVT  "4-ethyl-2-oxoglutarate"
  ligand  20  12  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QVT
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
 QVT  C01  C  C      0   0.421  17.4252  -25.3296  7.9383
 QVT  C02  C  C      0   0.336  22.4715  -25.3442  9.1420
 QVT  C04  C  CH2    0  -0.410  19.1446  -24.7724  6.1845
 QVT  C05  C  CH1    0  -0.360  18.8931  -25.5483  7.4841
 QVT  C06  C  CH2    0  -0.549  19.9204  -25.1868  8.5499
 QVT  C07  C  C      0   0.231  21.1916  -25.9949  8.5376
 QVT  O01  O  O      0  -0.617  16.5520  -25.6627  7.1097
 QVT  O02  O  OC    -1  -0.595  17.2184  -24.8481  9.0706
 QVT  O03  O  OC    -1  -0.577  22.2770  -24.3479  9.8608
 QVT  O04  O  O      0  -0.582  23.5436  -25.8940  8.8501
 QVT  O05  O  O      0  -0.407  21.2280  -27.1381  8.1364
 QVT  H04  H  HCH3   0   0.225  20.6130  -24.4114  4.6362
 QVT  H05  H  HCH3   0   0.214  21.3217  -24.5753  6.2304
 QVT  H03  H  HCH3   0   0.213  20.7454  -26.0043  5.3754
 QVT  H06  H  HCH2   0   0.200  18.9798  -23.7049  6.3728
 QVT  H07  H  HCH2   0   0.215  18.3961  -25.0709  5.4489
 QVT  H08  H  HCH1   0   0.212  18.9873  -26.6163  7.2528
 QVT  H10  H  HCH2   0   0.232  20.1586  -24.1218  8.5194
 QVT  H09  H  HCH2   0   0.264  19.4857  -25.3407  9.5442
 QVT  C03  C  CH3    0  -0.666  20.5308  -24.9541  5.5794

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
 QVT  C03  C04  single  1.523  0.020  1.523
 QVT  C04  C05  single  1.534  0.020  1.534
 QVT  O01  C01  deloc   1.249  0.020  1.249
 QVT  C05  C01  single  1.552  0.020  1.552
 QVT  C05  C06  single  1.524  0.020  1.524
 QVT  C01  O02  deloc   1.248  0.020  1.248
 QVT  O05  C07  double  1.212  0.020  1.212
 QVT  C07  C06  single  1.506  0.020  1.506
 QVT  C07  C02  single  1.558  0.020  1.558
 QVT  O04  C02  deloc   1.240  0.020  1.240
 QVT  C02  O03  deloc   1.244  0.020  1.244
 QVT  C03  H04  single  0.970  0.020  1.090
 QVT  C03  H05  single  0.970  0.020  1.090
 QVT  C03  H03  single  0.970  0.020  1.090
 QVT  C04  H06  single  0.970  0.020  1.090
 QVT  C04  H07  single  0.970  0.020  1.090
 QVT  C05  H08  single  0.970  0.020  1.090
 QVT  C06  H10  single  0.970  0.020  1.090
 QVT  C06  H09  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
 QVT  O02  C01  O01  126.10  3.000
 QVT  O02  C01  C05  118.47  3.000
 QVT  O01  C01  C05  115.43  3.000
 QVT  O04  C02  O03  128.80  3.000
 QVT  O03  C02  C07  115.48  3.000
 QVT  O04  C02  C07  115.71  3.000
 QVT  H07  C04  H06  106.20  3.000
 QVT  H07  C04  C05  108.68  3.000
 QVT  H06  C04  C05  108.80  3.000
 QVT  H07  C04  C03  108.89  3.000
 QVT  H06  C04  C03  108.73  3.000
 QVT  C05  C04  C03  115.17  3.000
 QVT  H08  C05  C06  108.70  3.000
 QVT  H08  C05  C04  107.44  3.000
 QVT  C06  C05  C04  111.22  3.000
 QVT  H08  C05  C01  106.27  3.000
 QVT  C06  C05  C01  113.55  3.000
 QVT  C04  C05  C01  109.37  3.000
 QVT  H09  C06  H10  104.41  3.000
 QVT  H09  C06  C07  105.47  3.000
 QVT  H10  C06  C07  109.81  3.000
 QVT  H09  C06  C05  109.50  3.000
 QVT  H10  C06  C05  111.04  3.000
 QVT  C07  C06  C05  115.84  3.000
 QVT  O05  C07  C06  122.27  3.000
 QVT  C06  C07  C02  117.78  3.000
 QVT  O05  C07  C02  119.85  3.000
 QVT  H03  C03  H05  107.63  3.000
 QVT  H03  C03  H04  107.59  3.000
 QVT  H05  C03  H04  106.74  3.000
 QVT  H03  C03  C04  111.60  3.000
 QVT  H05  C03  C04  112.39  3.000
 QVT  H04  C03  C04  110.64  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
 QVT  Var_01  C05  C06  C07  C02   154.92  30.0  3
 QVT  Var_02  O05  C07  C06  C05   -28.64  30.0  1
 QVT  Var_03  O04  C02  C07  C06  -164.31  30.0  2
 QVT  Var_04  O03  C02  C07  C06    16.19  30.0  2
 QVT  Var_05  O05  C07  C02  O03  -160.33  30.0  2
 QVT  Var_06  O05  C07  C02  O04    19.17  30.0  2
 QVT  Var_07  H10  C06  C07  C02    28.16  30.0  3
 QVT  Var_08  H09  C06  C07  C02   -83.82  30.0  3
 QVT  Var_09  H04  C03  C04  C05   177.23  30.0  3
 QVT  Var_10  H05  C03  C04  C05   -63.55  30.0  3
 QVT  Var_11  H03  C03  C04  C05    57.46  30.0  3
 QVT  Var_12  H10  C06  C07  O05  -155.41  30.0  3
 QVT  Var_13  H09  C06  C07  O05    92.62  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
 QVT  chir_01  C05  C04  C01  C06  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
 QVT  plan-1  C02  0.020
 QVT  plan-1  C06  0.020
 QVT  plan-1  C07  0.020
 QVT  plan-1  O05  0.020
 QVT  plan-2  C01  0.020
 QVT  plan-2  C05  0.020
 QVT  plan-2  O01  0.020
 QVT  plan-2  O02  0.020
 QVT  plan-3  C02  0.020
 QVT  plan-3  C07  0.020
 QVT  plan-3  O03  0.020
 QVT  plan-3  O04  0.020

