# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 15:43:21 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (3~{R})-3-ethyl-2-oxidanylidene-pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](CC(O)=O)C(=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
 QA8  QA8  '(3~{R})-3-ethyl-2-oxidanylidene-pentanedioic acid'  ligand  20  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QA8
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
 QA8  C10   C  C      0   0.336  56.3634  17.4956  16.5688
 QA8  C01   C  CH3    0  -0.666  59.9640  15.2075  15.5765
 QA8  C02   C  CH2    0  -0.406  59.7414  16.5085  14.8152
 QA8  C03   C  CH1    0  -0.327  58.3041  17.0109  14.8772
 QA8  C04   C  CH2    0  -0.580  58.0714  18.2080  13.9458
 QA8  C05   C  C      0   0.415  58.1214  17.8933  12.4309
 QA8  C08   C  C      0   0.258  57.8865  17.4496  16.2599
 QA8  O06   O  O      0  -0.612  58.3728  18.8658  11.6914
 QA8  O07   O  OC    -1  -0.600  57.8695  16.7263  12.0742
 QA8  O09   O  O      0  -0.410  58.6871  17.7865  17.1067
 QA8  O11   O  O      0  -0.579  55.6807  16.6235  16.0023
 QA8  O12   O  OC    -1  -0.584  55.9955  18.3750  17.3621
 QA8  H012  H  HCH3   0   0.222  60.9869  14.8485  15.4558
 QA8  H013  H  HCH3   0   0.218  59.7838  15.3234  16.6452
 QA8  H011  H  HCH3   0   0.212  59.2970  14.4231  15.2132
 QA8  H031  H  HCH1   0   0.228  57.6292  16.2158  14.5557
 QA8  H041  H  HCH2   0   0.214  58.7905  18.9996  14.1775
 QA8  H042  H  HCH2   0   0.237  57.0829  18.6443  14.1380
 QA8  H021  H  HCH2   0   0.221  60.0012  16.3507  13.7666
 QA8  H022  H  HCH2   0   0.203  60.4224  17.2799  15.1852

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
 QA8  O06  C05   deloc   1.247  0.020  1.247
 QA8  O07  C05   deloc   1.246  0.020  1.246
 QA8  C05  C04   single  1.548  0.020  1.548
 QA8  C04  C03   single  1.534  0.020  1.534
 QA8  C02  C03   single  1.524  0.020  1.524
 QA8  C02  C01   single  1.524  0.020  1.524
 QA8  C03  C08   single  1.510  0.020  1.510
 QA8  O11  C10   deloc   1.244  0.020  1.244
 QA8  C08  C10   single  1.555  0.020  1.555
 QA8  C08  O09   double  1.213  0.020  1.213
 QA8  C10  O12   deloc   1.240  0.020  1.240
 QA8  C01  H012  single  0.970  0.020  1.090
 QA8  C01  H013  single  0.970  0.020  1.090
 QA8  C01  H011  single  0.970  0.020  1.090
 QA8  C02  H021  single  0.970  0.020  1.090
 QA8  C02  H022  single  0.970  0.020  1.090
 QA8  C03  H031  single  0.970  0.020  1.090
 QA8  C04  H041  single  0.970  0.020  1.090
 QA8  C04  H042  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
 QA8  O12   C10  O11   128.73  3.000
 QA8  O12   C10  C08   116.02  3.000
 QA8  O11   C10  C08   115.24  3.000
 QA8  H011  C01  H013  107.56  3.000
 QA8  H011  C01  H012  107.43  3.000
 QA8  H013  C01  H012  107.37  3.000
 QA8  H011  C01  C02   110.97  3.000
 QA8  H013  C01  C02   112.02  3.000
 QA8  H012  C01  C02   111.27  3.000
 QA8  H022  C02  H021  106.18  3.000
 QA8  H022  C02  C03   109.94  3.000
 QA8  H021  C02  C03   108.13  3.000
 QA8  H022  C02  C01   110.02  3.000
 QA8  H021  C02  C01   108.77  3.000
 QA8  C03   C02  C01   113.52  3.000
 QA8  H031  C03  C08   108.09  3.000
 QA8  H031  C03  C04   107.21  3.000
 QA8  C08   C03  C04   106.70  3.000
 QA8  H031  C03  C02   109.33  3.000
 QA8  C08   C03  C02   113.20  3.000
 QA8  C04   C03  C02   112.06  3.000
 QA8  H042  C04  H041  105.50  3.000
 QA8  H042  C04  C05   106.33  3.000
 QA8  H041  C04  C05   109.45  3.000
 QA8  H042  C04  C03   109.91  3.000
 QA8  H041  C04  C03   109.65  3.000
 QA8  C05   C04  C03   115.50  3.000
 QA8  O07   C05  O06   126.96  3.000
 QA8  O07   C05  C04   117.64  3.000
 QA8  O06   C05  C04   115.36  3.000
 QA8  O09   C08  C03   122.52  3.000
 QA8  O09   C08  C10   119.97  3.000
 QA8  C03   C08  C10   117.49  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
 QA8  Var_01  O06   C05  C04  C03  -157.43  30.0  2
 QA8  Var_02  O11   C10  C08  C03    33.92  30.0  2
 QA8  Var_03  H012  C01  C02  C03   176.39  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
 QA8  chir_01  C03  C04  C02  C08  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
 QA8  plan-1  C10  0.020
 QA8  plan-1  C03  0.020
 QA8  plan-1  C08  0.020
 QA8  plan-1  O09  0.020
 QA8  plan-2  C10  0.020
 QA8  plan-2  C08  0.020
 QA8  plan-2  O11  0.020
 QA8  plan-2  O12  0.020
 QA8  plan-3  C04  0.020
 QA8  plan-3  C05  0.020
 QA8  plan-3  O06  0.020
 QA8  plan-3  O07  0.020

