# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 12:44:05 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: (4~{S})-2-oxidanylidene-4-(3-phenylpropyl)pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](CCCc1ccccc1)CC(=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
 QVN  QVN  "3-(3-phenylpropyl)-2-oxoglutarate"
  ligand  33  19  .  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_QVN
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
 QVN  C10  C  C1     0  -0.323  21.7773  27.6914  33.8810
 QVN  C13  C  C1     0  -0.237  24.0024  26.1389  33.3300
 QVN  C02  C  CH2    0  -0.557  19.5751  25.1151  28.3841
 QVN  C03  C  CH1    0  -0.388  18.5253  25.8870  29.1771
 QVN  C04  C  CH2    0  -0.402  18.7525  25.7525  30.6851
 QVN  C05  C  CH2    0  -0.424  20.1110  26.2275  31.1811
 QVN  C06  C  CH2    0  -0.496  20.2606  26.0604  32.6934
 QVN  C07  C  C      0   0.344  22.1443  24.9842  28.1016
 QVN  C08  C  C      0   0.431  17.0673  25.4992  28.7991
 QVN  C09  C  C      0   0.143  21.6122  26.4985  33.1826
 QVN  C11  C  C1     0  -0.237  23.0350  28.1065  34.3024
 QVN  C12  C  C1     0  -0.275  24.1530  27.3313  34.0282
 QVN  C14  C  C1     0  -0.307  22.7446  25.7296  32.9122
 QVN  O01  O  O      0  -0.431  20.9263  27.0401  27.9554
 QVN  O02  O  OC    -1  -0.584  23.0405  25.2612  28.9162
 QVN  O03  O  O      0  -0.589  22.1224  24.0991  27.2286
 QVN  O04  O  OC    -1  -0.608  16.1767  25.8998  29.5763
 QVN  O05  O  O      0  -0.595  16.8859  24.8543  27.7470
 QVN  H12  H  H      0   0.242  20.9101  28.3035  34.1018
 QVN  H15  H  H      0   0.248  24.8676  25.5250  33.1131
 QVN  H02  H  HCH2   0   0.270  19.1784  24.8857  27.3899
 QVN  H01  H  HCH2   0   0.230  19.7693  24.1424  28.8473
 QVN  H03  H  HCH1   0   0.222  18.6227  26.9504  28.9182
 QVN  H04  H  HCH2   0   0.216  17.9717  26.3070  31.2084
 QVN  H05  H  HCH2   0   0.198  18.6239  24.7010  30.9719
 QVN  H06  H  HCH2   0   0.219  20.9185  25.6723  30.6957
 QVN  H07  H  HCH2   0   0.214  20.2597  27.2787  30.9138
 QVN  H08  H  HCH2   0   0.234  19.4783  26.6282  33.2041
 QVN  H09  H  HCH2   0   0.232  20.0999  25.0086  32.9501
 QVN  H13  H  H      0   0.248  23.1394  29.0364  34.8472
 QVN  H14  H  H      0   0.249  25.1335  27.6511  34.3568
 QVN  H16  H  H      0   0.242  22.6388  24.7954  32.3718
 QVN  C01  C  C      0   0.271  20.8784  25.8418  28.1568

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
 QVN  O03  C07  deloc     1.243  0.020  1.243
 QVN  O02  C07  deloc     1.242  0.020  1.242
 QVN  C07  C01  single    1.530  0.020  1.530
 QVN  O05  C08  deloc     1.247  0.020  1.247
 QVN  C01  C02  single    1.509  0.020  1.509
 QVN  C01  O01  double    1.216  0.020  1.216
 QVN  C02  C03  single    1.525  0.020  1.525
 QVN  C08  C03  single    1.555  0.020  1.555
 QVN  C08  O04  deloc     1.248  0.020  1.248
 QVN  C03  C04  single    1.531  0.020  1.531
 QVN  C04  C05  single    1.522  0.020  1.522
 QVN  C05  C06  single    1.529  0.020  1.529
 QVN  C06  C09  single    1.503  0.020  1.503
 QVN  C09  C10  aromatic  1.392  0.020  1.392
 QVN  C09  C14  aromatic  1.395  0.020  1.395
 QVN  C10  C11  aromatic  1.390  0.020  1.390
 QVN  C14  C13  aromatic  1.387  0.020  1.387
 QVN  C11  C12  aromatic  1.388  0.020  1.388
 QVN  C13  C12  aromatic  1.390  0.020  1.390
 QVN  C10  H12  single    0.930  0.020  1.080
 QVN  C13  H15  single    0.930  0.020  1.080
 QVN  C02  H02  single    0.970  0.020  1.090
 QVN  C02  H01  single    0.970  0.020  1.090
 QVN  C03  H03  single    0.970  0.020  1.090
 QVN  C04  H04  single    0.970  0.020  1.090
 QVN  C04  H05  single    0.970  0.020  1.090
 QVN  C05  H06  single    0.970  0.020  1.090
 QVN  C05  H07  single    0.970  0.020  1.090
 QVN  C06  H08  single    0.970  0.020  1.090
 QVN  C06  H09  single    0.970  0.020  1.090
 QVN  C11  H13  single    0.930  0.020  1.080
 QVN  C12  H14  single    0.930  0.020  1.080
 QVN  C14  H16  single    0.930  0.020  1.080

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
 QVN  H12  C10  C11  119.57  3.000
 QVN  H12  C10  C09  119.41  3.000
 QVN  C11  C10  C09  121.02  3.000
 QVN  H15  C13  C14  119.80  3.000
 QVN  H15  C13  C12  120.03  3.000
 QVN  C14  C13  C12  120.17  3.000
 QVN  H01  C02  H02  105.21  3.000
 QVN  H01  C02  C03  110.60  3.000
 QVN  H02  C02  C03  109.20  3.000
 QVN  H01  C02  C01  109.77  3.000
 QVN  H02  C02  C01  106.08  3.000
 QVN  C03  C02  C01  115.40  3.000
 QVN  H03  C03  C08  105.50  3.000
 QVN  H03  C03  C04  107.70  3.000
 QVN  C08  C03  C04  110.89  3.000
 QVN  H03  C03  C02  107.83  3.000
 QVN  C04  C03  C02  111.44  3.000
 QVN  C08  C03  C02  113.12  3.000
 QVN  H05  C04  H04  106.12  3.000
 QVN  H05  C04  C05  108.57  3.000
 QVN  H04  C04  C05  108.89  3.000
 QVN  H05  C04  C03  108.91  3.000
 QVN  H04  C04  C03  108.75  3.000
 QVN  C05  C04  C03  115.21  3.000
 QVN  H07  C05  H06  106.19  3.000
 QVN  H07  C05  C06  109.46  3.000
 QVN  H06  C05  C06  108.14  3.000
 QVN  H07  C05  C04  109.95  3.000
 QVN  H06  C05  C04  110.85  3.000
 QVN  C06  C05  C04  112.05  3.000
 QVN  H09  C06  H08  106.53  3.000
 QVN  H09  C06  C09  109.62  3.000
 QVN  H08  C06  C09  109.88  3.000
 QVN  H09  C06  C05  108.83  3.000
 QVN  H08  C06  C05  109.59  3.000
 QVN  C09  C06  C05  112.22  3.000
 QVN  O03  C07  O02  129.18  3.000
 QVN  O02  C07  C01  116.63  3.000
 QVN  O03  C07  C01  114.19  3.000
 QVN  O05  C08  O04  125.98  3.000
 QVN  O04  C08  C03  115.95  3.000
 QVN  O05  C08  C03  118.05  3.000
 QVN  C14  C09  C06  120.41  3.000
 QVN  C14  C09  C10  118.24  3.000
 QVN  C06  C09  C10  121.32  3.000
 QVN  H13  C11  C12  120.09  3.000
 QVN  H13  C11  C10  119.76  3.000
 QVN  C12  C11  C10  120.15  3.000
 QVN  H14  C12  C11  120.32  3.000
 QVN  H14  C12  C13  120.27  3.000
 QVN  C11  C12  C13  119.42  3.000
 QVN  H16  C14  C09  119.49  3.000
 QVN  H16  C14  C13  119.52  3.000
 QVN  C09  C14  C13  121.00  3.000
 QVN  O01  C01  C07  120.91  3.000
 QVN  O01  C01  C02  122.23  3.000
 QVN  C07  C01  C02  116.74  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
 QVN  CONST_01  C13  C14  C09  C10     0.00   0.0  0
 QVN  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 QVN  CONST_03  C12  C11  C10  C09     0.00   0.0  0
 QVN  CONST_04  C12  C13  C14  C09     0.00   0.0  0
 QVN  CONST_05  C14  C09  C10  C11     0.00   0.0  0
 QVN  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 QVN  CONST_07  C06  C09  C14  C13   180.00   0.0  0
 QVN  CONST_08  C11  C10  C09  C06   180.00   0.0  0
 QVN  CONST_09  H16  C14  C09  C10   180.00   0.0  0
 QVN  CONST_10  H14  C12  C11  C10   180.00   0.0  0
 QVN  CONST_11  H13  C11  C12  C13   180.00   0.0  0
 QVN  CONST_12  H13  C11  C10  C09   180.00   0.0  0
 QVN  CONST_13  H15  C13  C14  C09   180.00   0.0  0
 QVN  CONST_14  H15  C13  C12  C11   180.00   0.0  0
 QVN  CONST_15  H12  C10  C11  C12   180.00   0.0  0
 QVN  CONST_16  H16  C14  C13  C12   180.00   0.0  0
 QVN  CONST_17  H12  C10  C09  C14   180.00   0.0  0
 QVN  CONST_18  H14  C12  C13  C14   180.00   0.0  0
 QVN  Var_01    C05  C06  C09  C10   105.97  30.0  2
 QVN  Var_02    C14  C09  C06  C05   -72.24  30.0  2
 QVN  Var_03    H08  C06  C09  C10   -16.23  30.0  2
 QVN  Var_04    H09  C06  C09  C10  -132.98  30.0  2
 QVN  Var_05    H08  C06  C09  C14   165.56  30.0  2
 QVN  Var_06    H09  C06  C09  C14    48.81  30.0  2
 QVN  Var_07    C09  C06  C05  C04   178.67  30.0  3
 QVN  Var_08    H06  C05  C06  C09    56.21  30.0  1
 QVN  Var_09    H07  C05  C06  C09   -59.07  30.0  1
 QVN  Var_10    O03  C07  C01  C02    57.59  30.0  2
 QVN  Var_11    O02  C07  C01  C02  -122.57  30.0  2
 QVN  Var_12    C07  C01  C02  C03   147.30  30.0  2
 QVN  Var_13    O01  C01  C02  C03   -36.51  30.0  2
 QVN  Var_14    C06  C05  C04  C03  -179.98  30.0  3
 QVN  Var_15    O03  C07  C01  O01  -118.66  30.0  2
 QVN  Var_16    O02  C07  C01  O01    61.18  30.0  2
 QVN  Var_17    H06  C05  C04  C03   -59.07  30.0  3
 QVN  Var_18    H07  C05  C04  C03    58.05  30.0  3
 QVN  Var_19    H08  C06  C05  C04   -58.96  30.0  3
 QVN  Var_20    H09  C06  C05  C04    57.17  30.0  3
 QVN  Var_21    H04  C04  C05  C06    57.56  30.0  1
 QVN  Var_22    H05  C04  C05  C06   -57.56  30.0  1
 QVN  Var_23    H02  C02  C01  C07   -91.66  30.0  3
 QVN  Var_24    H01  C02  C01  C07    21.53  30.0  3
 QVN  Var_25    H02  C02  C01  O01    84.54  30.0  3
 QVN  Var_26    H01  C02  C01  O01  -162.27  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
 QVN  chir_01  C03  C02  C08  C04  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
 QVN  plan-1  C10  0.020
 QVN  plan-1  C13  0.020
 QVN  plan-1  C06  0.020
 QVN  plan-1  C09  0.020
 QVN  plan-1  C11  0.020
 QVN  plan-1  C12  0.020
 QVN  plan-1  C14  0.020
 QVN  plan-1  H12  0.020
 QVN  plan-1  H15  0.020
 QVN  plan-1  H13  0.020
 QVN  plan-1  H14  0.020
 QVN  plan-1  H16  0.020
 QVN  plan-2  C02  0.020
 QVN  plan-2  C07  0.020
 QVN  plan-2  O01  0.020
 QVN  plan-2  C01  0.020
 QVN  plan-3  C07  0.020
 QVN  plan-3  O02  0.020
 QVN  plan-3  O03  0.020
 QVN  plan-3  C01  0.020
 QVN  plan-4  C03  0.020
 QVN  plan-4  C08  0.020
 QVN  plan-4  O04  0.020
 QVN  plan-4  O05  0.020

