# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 21:47:37 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-oxo-5-phenylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)CCCc1ccccc1
#
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
 KPV  KPV  '2-oxo-5-phenylpentanoic acid'  ligand  25  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KPV
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
 KPV  C1   C  CR6    0   0.138   2.3524  -0.5462   0.0086
 KPV  C2   C  CR16   0  -0.313   3.0083  -0.2393  -1.1821
 KPV  C3   C  CR16   0  -0.239   4.2721   0.3364  -1.1743
 KPV  C4   C  CR16   0  -0.275   4.9034   0.6175   0.0305
 KPV  C5   C  CR16   0  -0.240   4.2612   0.3150   1.2245
 KPV  C6   C  CR16   0  -0.313   2.9975  -0.2606   1.2104
 KPV  C7   C  CH2    0  -0.506   0.9639  -1.1214  -0.0023
 KPV  C8   C  CH2    0  -0.409  -0.1086  -0.0313   0.0056
 KPV  C9   C  CH2    0  -0.551  -1.5094  -0.6199   0.0026
 KPV  C10  C  C      0   0.234  -2.6142   0.4021   0.0117
 KPV  C11  C  C      0   0.345  -4.0802  -0.1251   0.0156
 KPV  O1   O  O      0  -0.578  -4.2044  -1.3616   0.0327
 KPV  O2   O  OC    -1  -0.584  -4.9631   0.7436   0.0022
 KPV  O3   O  O      0  -0.398  -2.3895   1.5904   0.0167
 KPV  H2   H  HCR6   0   0.244   2.5262  -0.4571  -2.1283
 KPV  H3   H  HCR6   0   0.252   4.7653   0.5622  -2.1113
 KPV  H4   H  HCR6   0   0.252   5.8884   1.0664   0.0390
 KPV  H5   H  HCR6   0   0.252   4.7457   0.5246   2.1697
 KPV  H6   H  HCR6   0   0.244   2.5066  -0.4945   2.1482
 KPV  H71  H  HCH2   0   0.238   0.8318  -1.7531  -0.8852
 KPV  H72  H  HCH2   0   0.238   0.8261  -1.7711   0.8666
 KPV  H81  H  HCH2   0   0.227   0.0292   0.6038   0.8849
 KPV  H82  H  HCH2   0   0.227   0.0292   0.6166  -0.8644
 KPV  H91  H  HCH2   0   0.258  -1.6544  -1.2709  -0.8667
 KPV  H92  H  HCH2   0   0.258  -1.6528  -1.2821   0.8632

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
 KPV  C1   C6   aromatic  1.394  0.020  1.394
 KPV  C1   C2   aromatic  1.394  0.020  1.394
 KPV  C1   C7   single    1.503  0.020  1.503
 KPV  C2   C3   aromatic  1.389  0.020  1.389
 KPV  C2   H2   single    0.930  0.020  1.080
 KPV  C3   C4   aromatic  1.389  0.020  1.389
 KPV  C3   H3   single    0.930  0.020  1.080
 KPV  C4   C5   aromatic  1.389  0.020  1.389
 KPV  C4   H4   single    0.930  0.020  1.080
 KPV  C5   C6   aromatic  1.389  0.020  1.389
 KPV  C5   H5   single    0.930  0.020  1.080
 KPV  C6   H6   single    0.930  0.020  1.080
 KPV  C7   C8   single    1.529  0.020  1.529
 KPV  C7   H71  single    0.970  0.020  1.090
 KPV  C7   H72  single    0.970  0.020  1.090
 KPV  C8   C9   single    1.519  0.020  1.519
 KPV  C8   H81  single    0.970  0.020  1.090
 KPV  C8   H82  single    0.970  0.020  1.090
 KPV  C9   C10  single    1.505  0.020  1.505
 KPV  C9   H91  single    0.970  0.020  1.090
 KPV  C9   H92  single    0.970  0.020  1.090
 KPV  C10  C11  single    1.558  0.020  1.558
 KPV  C10  O3   double    1.209  0.020  1.209
 KPV  C11  O1   deloc     1.243  0.020  1.243
 KPV  C11  O2   deloc     1.239  0.020  1.239

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
 KPV  C7   C1   C6   120.82  3.000
 KPV  C7   C1   C2   120.86  3.000
 KPV  C6   C1   C2   118.28  3.000
 KPV  H2   C2   C3   119.53  3.000
 KPV  H2   C2   C1   119.48  3.000
 KPV  C3   C2   C1   120.99  3.000
 KPV  H3   C3   C4   120.09  3.000
 KPV  H3   C3   C2   119.75  3.000
 KPV  C4   C3   C2   120.16  3.000
 KPV  H4   C4   C5   120.29  3.000
 KPV  H4   C4   C3   120.29  3.000
 KPV  C5   C4   C3   119.43  3.000
 KPV  H5   C5   C6   119.76  3.000
 KPV  H5   C5   C4   120.09  3.000
 KPV  C6   C5   C4   120.15  3.000
 KPV  H6   C6   C5   119.52  3.000
 KPV  H6   C6   C1   119.49  3.000
 KPV  C5   C6   C1   120.99  3.000
 KPV  H72  C7   H71  106.44  3.000
 KPV  H72  C7   C8   109.33  3.000
 KPV  H71  C7   C8   109.34  3.000
 KPV  H72  C7   C1   109.76  3.000
 KPV  H71  C7   C1   109.78  3.000
 KPV  C8   C7   C1   112.03  3.000
 KPV  H82  C8   H81  106.25  3.000
 KPV  H82  C8   C9   110.13  3.000
 KPV  H81  C8   C9   110.05  3.000
 KPV  H82  C8   C7   109.27  3.000
 KPV  H81  C8   C7   109.25  3.000
 KPV  C9   C8   C7   111.74  3.000
 KPV  H92  C9   H91  104.29  3.000
 KPV  H92  C9   C10  108.04  3.000
 KPV  H91  C9   C10  108.13  3.000
 KPV  H92  C9   C8   110.69  3.000
 KPV  H91  C9   C8   110.71  3.000
 KPV  C10  C9   C8   114.44  3.000
 KPV  O3   C10  C11  120.48  3.000
 KPV  O3   C10  C9   122.07  3.000
 KPV  C11  C10  C9   117.45  3.000
 KPV  O2   C11  O1   128.81  3.000
 KPV  O2   C11  C10  115.68  3.000
 KPV  O1   C11  C10  115.51  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
 KPV  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 KPV  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 KPV  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 KPV  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 KPV  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 KPV  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 KPV  CONST_07  C7   C1   C2   C3   180.00   0.0  0
 KPV  CONST_08  C7   C1   C6   C5   180.00   0.0  0
 KPV  CONST_09  H5   C5   C6   C1   180.00   0.0  0
 KPV  CONST_10  H3   C3   C2   C1   180.00   0.0  0
 KPV  CONST_11  H6   C6   C1   C2   180.00   0.0  0
 KPV  CONST_12  H4   C4   C3   C2   180.00   0.0  0
 KPV  CONST_13  H2   C2   C3   C4   180.00   0.0  0
 KPV  Var_01    C8   C7   C1   C2   -88.93  30.0  2
 KPV  Var_02    C9   C8   C7   C1  -179.67  30.0  3
 KPV  Var_03    C10  C9   C8   C7   179.93  30.0  3
 KPV  Var_04    C11  C10  C9   C8  -179.74  30.0  3
 KPV  Var_05    O1   C11  C10  C9     1.12  30.0  2

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
 KPV  plan-1  C1   0.020
 KPV  plan-1  C2   0.020
 KPV  plan-1  C3   0.020
 KPV  plan-1  C4   0.020
 KPV  plan-1  C5   0.020
 KPV  plan-1  C6   0.020
 KPV  plan-1  C7   0.020
 KPV  plan-1  H2   0.020
 KPV  plan-1  H3   0.020
 KPV  plan-1  H4   0.020
 KPV  plan-1  H5   0.020
 KPV  plan-1  H6   0.020
 KPV  plan-2  C9   0.020
 KPV  plan-2  C10  0.020
 KPV  plan-2  C11  0.020
 KPV  plan-2  O3   0.020
 KPV  plan-3  C10  0.020
 KPV  plan-3  C11  0.020
 KPV  plan-3  O1   0.020
 KPV  plan-3  O2   0.020

