# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 12:37:03 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2-oxo-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)Cc1ccccc1
#
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
 PPY  PPY  '2-oxo-3-phenylpropanoic acid'  ligand  20  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PPY
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
 PPY  C1   C  C     0   0.485  -0.1119  -0.0015   2.8402
 PPY  O1   O  O     0  -0.404  -1.2485  -0.0900   3.2203
 PPY  O2   O  OH1   0  -0.569   0.9510   0.1046   3.6042
 PPY  C2   C  C     0   0.306   0.2592  -0.0026   1.3481
 PPY  O3   O  O     0  -0.332   1.4129   0.0284   1.0194
 PPY  C3   C  CH2   0  -0.681  -0.9062  -0.0484   0.4012
 PPY  C1'  C  CR6   0   0.153  -0.4854  -0.0235  -1.0367
 PPY  C2'  C  CR16  0  -0.300  -0.2730  -1.2087  -1.7339
 PPY  C3'  C  CR16  0  -0.241   0.1400  -1.1866  -3.0596
 PPY  C4'  C  CR16  0  -0.267   0.3478   0.0257  -3.7038
 PPY  C5'  C  CR16  0  -0.242   0.1384   1.2138  -3.0152
 PPY  C6'  C  CR16  0  -0.296  -0.2743   1.1873  -1.6902
 PPY  HO2  H  HOH1  0   0.494   0.6975   0.1014   4.5403
 PPY  H31  H  HCH2  0   0.311  -1.4913  -0.9451   0.6292
 PPY  H32  H  HCH2  0   0.310  -1.5695   0.7901   0.6367
 PPY  H2'  H  HCR6  0   0.253  -0.4393  -2.1587  -1.2400
 PPY  H3'  H  HCR6  0   0.256   0.2976  -2.1175  -3.5889
 PPY  H4'  H  HCR6  0   0.256   0.6667   0.0452  -4.7379
 PPY  H5'  H  HCR6  0   0.256   0.2961   2.1629  -3.5112
 PPY  H6'  H  HCR6  0   0.252  -0.4411   2.1187  -1.1621

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
 PPY  C1   O1   double    1.202  0.020  1.202
 PPY  C1   O2   single    1.313  0.020  1.313
 PPY  C1   C2   single    1.538  0.020  1.538
 PPY  O2   HO2  single    0.850  0.020  0.980
 PPY  C2   O3   double    1.200  0.020  1.200
 PPY  C2   C3   single    1.502  0.020  1.502
 PPY  C3   C1'  single    1.498  0.020  1.498
 PPY  C3   H31  single    0.970  0.020  1.090
 PPY  C3   H32  single    0.970  0.020  1.090
 PPY  C1'  C2'  aromatic  1.391  0.020  1.391
 PPY  C1'  C6'  aromatic  1.392  0.020  1.392
 PPY  C2'  C3'  aromatic  1.389  0.020  1.389
 PPY  C2'  H2'  single    0.930  0.020  1.080
 PPY  C3'  C4'  aromatic  1.388  0.020  1.388
 PPY  C3'  H3'  single    0.930  0.020  1.080
 PPY  C4'  C5'  aromatic  1.389  0.020  1.389
 PPY  C4'  H4'  single    0.930  0.020  1.080
 PPY  C5'  C6'  aromatic  1.388  0.020  1.388
 PPY  C5'  H5'  single    0.930  0.020  1.080
 PPY  C6'  H6'  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
 PPY  C2   C1   O2   111.67  3.000
 PPY  C2   C1   O1   122.36  3.000
 PPY  O2   C1   O1   125.98  3.000
 PPY  HO2  O2   C1   110.46  3.000
 PPY  C3   C2   O3   125.03  3.000
 PPY  C3   C2   C1   115.11  3.000
 PPY  O3   C2   C1   119.86  3.000
 PPY  H32  C3   H31  105.00  3.000
 PPY  H32  C3   C1'  111.33  3.000
 PPY  H31  C3   C1'  111.31  3.000
 PPY  H32  C3   C2   108.13  3.000
 PPY  H31  C3   C2   107.96  3.000
 PPY  C1'  C3   C2   112.74  3.000
 PPY  C6'  C1'  C2'  118.85  3.000
 PPY  C6'  C1'  C3   120.50  3.000
 PPY  C2'  C1'  C3   120.64  3.000
 PPY  H2'  C2'  C3'  119.65  3.000
 PPY  H2'  C2'  C1'  119.67  3.000
 PPY  C3'  C2'  C1'  120.68  3.000
 PPY  H3'  C3'  C4'  120.15  3.000
 PPY  H3'  C3'  C2'  119.76  3.000
 PPY  C4'  C3'  C2'  120.08  3.000
 PPY  H4'  C4'  C5'  120.17  3.000
 PPY  H4'  C4'  C3'  120.20  3.000
 PPY  C5'  C4'  C3'  119.62  3.000
 PPY  H5'  C5'  C6'  119.83  3.000
 PPY  H5'  C5'  C4'  120.06  3.000
 PPY  C6'  C5'  C4'  120.11  3.000
 PPY  H6'  C6'  C5'  119.64  3.000
 PPY  H6'  C6'  C1'  119.70  3.000
 PPY  C5'  C6'  C1'  120.65  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
 PPY  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 PPY  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 PPY  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 PPY  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 PPY  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 PPY  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 PPY  CONST_07  C3'  C2'  C1'  C3    180.00   0.0  0
 PPY  CONST_08  C5'  C6'  C1'  C3    180.00   0.0  0
 PPY  CONST_09  H3'  C3'  C2'  C1'   180.00   0.0  0
 PPY  CONST_10  H5'  C5'  C6'  C1'   180.00   0.0  0
 PPY  CONST_11  H6'  C6'  C1'  C2'   180.00   0.0  0
 PPY  CONST_12  H4'  C4'  C3'  C2'   180.00   0.0  0
 PPY  CONST_13  H2'  C2'  C3'  C4'   180.00   0.0  0
 PPY  CONST_14  HO2  O2   C1   O1      0.00   0.0  0
 PPY  Var_01    C2'  C1'  C3   C2     91.90  30.0  2
 PPY  Var_02    C1'  C3   C2   C1    179.01  30.0  3
 PPY  Var_03    O3   C2   C1   O1   -176.70  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
 PPY  plan-1  C3   0.020
 PPY  plan-1  C1'  0.020
 PPY  plan-1  C2'  0.020
 PPY  plan-1  C3'  0.020
 PPY  plan-1  C4'  0.020
 PPY  plan-1  C5'  0.020
 PPY  plan-1  C6'  0.020
 PPY  plan-1  H2'  0.020
 PPY  plan-1  H3'  0.020
 PPY  plan-1  H4'  0.020
 PPY  plan-1  H5'  0.020
 PPY  plan-1  H6'  0.020
 PPY  plan-2  C1   0.020
 PPY  plan-2  C2   0.020
 PPY  plan-2  O3   0.020
 PPY  plan-2  C3   0.020
 PPY  plan-3  C1   0.020
 PPY  plan-3  O1   0.020
 PPY  plan-3  O2   0.020
 PPY  plan-3  C2   0.020
 PPY  plan-3  HO2  0.020

