# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 15:06:51 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-phenylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCc1ccccc1
#
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
 5PV  5PV  '5-phenylpentanoic acid   '  ligand  26  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5PV
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
 5PV  C1    C  CR6    0   0.141  -0.0222   0.4613  -2.1378
 5PV  C2    C  CR16   0  -0.314  -1.2120   0.1663  -2.8011
 5PV  C3    C  CR16   0  -0.240  -1.2031  -0.3628  -4.0851
 5PV  C4    C  CR16   0  -0.276   0.0022  -0.6088  -4.7301
 5PV  C5    C  CR16   0  -0.240   1.1953  -0.3193  -4.0805
 5PV  C6    C  CR16   0  -0.315   1.1800   0.2099  -2.7966
 5PV  C7    C  CH2    0  -0.504  -0.0341   0.9935  -0.7326
 5PV  C8    C  CH2    0  -0.407  -0.0231  -0.1182   0.3175
 5PV  C9    C  CH2    0  -0.406  -0.0223   0.4231   1.7419
 5PV  C10   C  CH2    0  -0.583  -0.0133  -0.6765   2.7894
 5PV  C11   C  C      0   0.411   0.0045  -0.2122   4.2568
 5PV  O1    O  OC    -1  -0.635   0.0022  -1.1196   5.1163
 5PV  O2    O  O      0  -0.609   0.0212   1.0141   4.4813
 5PV  H2    H  HCR6   0   0.243  -2.1587   0.3589  -2.3090
 5PV  H3    H  HCR6   0   0.251  -2.1396  -0.5791  -4.5836
 5PV  H4    H  HCR6   0   0.251   0.0119  -1.0191  -5.7318
 5PV  H5    H  HCR6   0   0.251   2.1410  -0.5020  -4.5750
 5PV  H6    H  HCR6   0   0.243   2.1168   0.4360  -2.3002
 5PV  H71   H  HCH2   0   0.234  -0.9184   1.6196  -0.5827
 5PV  H72   H  HCH2   0   0.233   0.8330   1.6418  -0.5771
 5PV  H81   H  HCH2   0   0.214   0.8567  -0.7529   0.1639
 5PV  H82   H  HCH2   0   0.214  -0.8930  -0.7670   0.1676
 5PV  H91   H  HCH2   0   0.203  -0.8973   1.0653   1.8824
 5PV  H92   H  HCH2   0   0.204   0.8477   1.0725   1.8775
 5PV  H101  H  HCH2   0   0.217   0.8527  -1.3303   2.6307
 5PV  H102  H  HCH2   0   0.217  -0.8838  -1.3284   2.6486

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
 5PV  C1   C2    aromatic  1.394  0.020  1.394
 5PV  C1   C6    aromatic  1.394  0.020  1.394
 5PV  C1   C7    single    1.503  0.020  1.503
 5PV  C2   C3    aromatic  1.389  0.020  1.389
 5PV  C2   H2    single    0.930  0.020  1.080
 5PV  C3   C4    aromatic  1.389  0.020  1.389
 5PV  C3   H3    single    0.930  0.020  1.080
 5PV  C4   C5    aromatic  1.389  0.020  1.389
 5PV  C4   H4    single    0.930  0.020  1.080
 5PV  C5   C6    aromatic  1.389  0.020  1.389
 5PV  C5   H5    single    0.930  0.020  1.080
 5PV  C6   H6    single    0.930  0.020  1.080
 5PV  C7   C8    single    1.529  0.020  1.529
 5PV  C7   H71   single    0.970  0.020  1.090
 5PV  C7   H72   single    0.970  0.020  1.090
 5PV  C8   C9    single    1.524  0.020  1.524
 5PV  C8   H81   single    0.970  0.020  1.090
 5PV  C8   H82   single    0.970  0.020  1.090
 5PV  C9   C10   single    1.519  0.020  1.519
 5PV  C9   H91   single    0.970  0.020  1.090
 5PV  C9   H92   single    0.970  0.020  1.090
 5PV  C10  C11   single    1.539  0.020  1.539
 5PV  C10  H101  single    0.970  0.020  1.090
 5PV  C10  H102  single    0.970  0.020  1.090
 5PV  C11  O1    deloc     1.250  0.020  1.250
 5PV  C11  O2    deloc     1.247  0.020  1.247

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
 5PV  C7    C1   C6    120.85  3.000
 5PV  C7    C1   C2    120.88  3.000
 5PV  C6    C1   C2    118.24  3.000
 5PV  H2    C2   C3    119.53  3.000
 5PV  H2    C2   C1    119.45  3.000
 5PV  C3    C2   C1    121.01  3.000
 5PV  H3    C3   C4    120.09  3.000
 5PV  H3    C3   C2    119.75  3.000
 5PV  C4    C3   C2    120.16  3.000
 5PV  H4    C4   C5    120.27  3.000
 5PV  H4    C4   C3    120.31  3.000
 5PV  C5    C4   C3    119.42  3.000
 5PV  H5    C5   C6    119.75  3.000
 5PV  H5    C5   C4    120.10  3.000
 5PV  C6    C5   C4    120.15  3.000
 5PV  H6    C6   C5    119.56  3.000
 5PV  H6    C6   C1    119.43  3.000
 5PV  C5    C6   C1    121.01  3.000
 5PV  H72   C7   H71   106.39  3.000
 5PV  H72   C7   C8    109.12  3.000
 5PV  H71   C7   C8    109.14  3.000
 5PV  H72   C7   C1    109.67  3.000
 5PV  H71   C7   C1    109.71  3.000
 5PV  C8    C7   C1    112.62  3.000
 5PV  H82   C8   H81   105.98  3.000
 5PV  H82   C8   C9    109.80  3.000
 5PV  H81   C8   C9    109.66  3.000
 5PV  H82   C8   C7    109.32  3.000
 5PV  H81   C8   C7    109.31  3.000
 5PV  C9    C8   C7    112.56  3.000
 5PV  H92   C9   H91   105.76  3.000
 5PV  H92   C9   C10   109.85  3.000
 5PV  H91   C9   C10   109.94  3.000
 5PV  H92   C9   C8    109.09  3.000
 5PV  H91   C9   C8    109.15  3.000
 5PV  C10   C9   C8    112.80  3.000
 5PV  H102  C10  H101  104.70  3.000
 5PV  H102  C10  C11   108.11  3.000
 5PV  H101  C10  C11   107.98  3.000
 5PV  H102  C10  C9    109.71  3.000
 5PV  H101  C10  C9    109.66  3.000
 5PV  C11   C10  C9    116.05  3.000
 5PV  O2    C11  O1    126.18  3.000
 5PV  O2    C11  C10   117.94  3.000
 5PV  O1    C11  C10   115.89  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
 5PV  CONST_01  C4   C3   C2   C1    0.00   0.0  0
 5PV  CONST_02  C4   C5   C6   C1    0.00   0.0  0
 5PV  CONST_03  C5   C6   C1   C2    0.00   0.0  0
 5PV  CONST_04  C5   C4   C3   C2    0.00   0.0  0
 5PV  CONST_05  C6   C1   C2   C3    0.00   0.0  0
 5PV  CONST_06  C6   C5   C4   C3    0.00   0.0  0
 5PV  CONST_07  C7   C1   C2   C3  180.00   0.0  0
 5PV  CONST_08  C7   C1   C6   C5  180.00   0.0  0
 5PV  CONST_09  H3   C3   C2   C1  180.00   0.0  0
 5PV  CONST_10  H5   C5   C6   C1  180.00   0.0  0
 5PV  CONST_11  H6   C6   C1   C2  180.00   0.0  0
 5PV  CONST_12  H4   C4   C3   C2  180.00   0.0  0
 5PV  CONST_13  H2   C2   C3   C4  180.00   0.0  0
 5PV  Var_01    C8   C7   C1   C2   88.68  30.0  2
 5PV  Var_02    C9   C8   C7   C1  179.48  30.0  3
 5PV  Var_03    C10  C9   C8   C7  179.92  30.0  3
 5PV  Var_04    C11  C10  C9   C8  179.31  30.0  3
 5PV  Var_05    O1   C11  C10  C9  179.50  30.0  3

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
 5PV  plan-1  C1   0.020
 5PV  plan-1  C2   0.020
 5PV  plan-1  C3   0.020
 5PV  plan-1  C4   0.020
 5PV  plan-1  C5   0.020
 5PV  plan-1  C6   0.020
 5PV  plan-1  C7   0.020
 5PV  plan-1  H2   0.020
 5PV  plan-1  H3   0.020
 5PV  plan-1  H4   0.020
 5PV  plan-1  H5   0.020
 5PV  plan-1  H6   0.020
 5PV  plan-2  C10  0.020
 5PV  plan-2  C11  0.020
 5PV  plan-2  O1   0.020
 5PV  plan-2  O2   0.020

