# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:49:29 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  27  13  .  2021-08-05  2021-08-05  
;
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   0.139   0.0105   0.4610  -2.1536
 5PV  C2    C  CR16  0  -0.314  -1.1898   0.1961  -2.8102
 5PV  C3    C  CR16  0  -0.240  -1.2007  -0.3499  -4.0870
 5PV  C4    C  CR16  0  -0.275  -0.0053  -0.6427  -4.7310
 5PV  C5    C  CR16  0  -0.239   1.1981  -0.3836  -4.0875
 5PV  C6    C  CR16  0  -0.313   1.2029   0.1623  -2.8105
 5PV  C7    C  CH2   0  -0.506   0.0187   1.0109  -0.7551
 5PV  C8    C  CH2   0  -0.412   0.0157  -0.0913   0.3039
 5PV  C9    C  CH2   0  -0.422   0.0191   0.4701   1.7200
 5PV  C10   C  CH2   0  -0.581   0.0167  -0.6341   2.7629
 5PV  C11   C  C     0   0.551   0.0159  -0.1325   4.1798
 5PV  O1    O  OH1   0  -0.598   0.0342  -1.1313   5.0587
 5PV  O2    O  O     0  -0.446  -0.0010   1.0280   4.5077
 5PV  H2    H  HCR6  0   0.244  -2.1287   0.4244  -2.3187
 5PV  H3    H  HCR6  0   0.252  -2.1445  -0.5427  -4.5812
 5PV  H4    H  HCR6  0   0.252  -0.0114  -1.0663  -5.7271
 5PV  H5    H  HCR6  0   0.252   2.1362  -0.6025  -4.5819
 5PV  H6    H  HCR6  0   0.244   2.1477   0.3646  -2.3192
 5PV  H71   H  HCH2  0   0.238  -0.8528   1.6547  -0.6061
 5PV  H72   H  HCH2  0   0.238   0.8989   1.6437  -0.6119
 5PV  H81   H  HCH2  0   0.225   0.8885  -0.7367   0.1601
 5PV  H82   H  HCH2  0   0.225  -0.8624  -0.7299   0.1623
 5PV  H91   H  HCH2  0   0.229  -0.8540   1.1141   1.8559
 5PV  H92   H  HCH2  0   0.229   0.8967   1.1084   1.8545
 5PV  H101  H  HCH2  0   0.276   0.8844  -1.2889   2.6337
 5PV  H102  H  HCH2  0   0.277  -0.8559  -1.2830   2.6340
 5PV  HO1   H  HOH1  0   0.478   0.0337  -0.7781   5.9608

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    1.523  0.020  1.523
 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    1.503  0.020  1.503
 5PV  C10  H101  single    0.970  0.020  1.090
 5PV  C10  H102  single    0.970  0.020  1.090
 5PV  C11  O1    single    1.331  0.020  1.331
 5PV  C11  O2    double    1.206  0.020  1.206
 5PV  O1   HO1   single    0.850  0.020  0.980

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    120.83  3.000
 5PV  C7    C1   C2    120.84  3.000
 5PV  C6    C1   C2    118.30  3.000
 5PV  H2    C2   C3    119.53  3.000
 5PV  H2    C2   C1    119.49  3.000
 5PV  C3    C2   C1    120.98  3.000
 5PV  H3    C3   C4    120.08  3.000
 5PV  H3    C3   C2    119.77  3.000
 5PV  C4    C3   C2    120.16  3.000
 5PV  H4    C4   C5    120.28  3.000
 5PV  H4    C4   C3    120.28  3.000
 5PV  C5    C4   C3    119.44  3.000
 5PV  H5    C5   C6    119.76  3.000
 5PV  H5    C5   C4    120.09  3.000
 5PV  C6    C5   C4    120.15  3.000
 5PV  H6    C6   C5    119.54  3.000
 5PV  H6    C6   C1    119.48  3.000
 5PV  C5    C6   C1    120.98  3.000
 5PV  H72   C7   H71   106.44  3.000
 5PV  H72   C7   C8    109.16  3.000
 5PV  H71   C7   C8    109.18  3.000
 5PV  H72   C7   C1    109.75  3.000
 5PV  H71   C7   C1    109.75  3.000
 5PV  C8    C7   C1    112.39  3.000
 5PV  H82   C8   H81   106.17  3.000
 5PV  H82   C8   C9    109.69  3.000
 5PV  H81   C8   C9    109.73  3.000
 5PV  H82   C8   C7    109.42  3.000
 5PV  H81   C8   C7    109.42  3.000
 5PV  C9    C8   C7    112.23  3.000
 5PV  H92   C9   H91   106.37  3.000
 5PV  H92   C9   C10   109.95  3.000
 5PV  H91   C9   C10   109.98  3.000
 5PV  H92   C9   C8    109.34  3.000
 5PV  H91   C9   C8    109.32  3.000
 5PV  C10   C9   C8    111.74  3.000
 5PV  H102  C10  H101  105.27  3.000
 5PV  H102  C10  C11   107.96  3.000
 5PV  H101  C10  C11   108.14  3.000
 5PV  H102  C10  C9    110.56  3.000
 5PV  H101  C10  C9    110.64  3.000
 5PV  C11   C10  C9    113.87  3.000
 5PV  O2    C11  O1    122.88  3.000
 5PV  O2    C11  C10   125.27  3.000
 5PV  O1    C11  C10   111.85  3.000
 5PV  HO1   O1   C11   109.96  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  CONST_14  HO1  O1   C11  C10   180.00   0.0  0
 5PV  Var_01    C8   C7   C1   C2     89.45  30.0  2
 5PV  Var_02    C9   C8   C7   C1   -179.80  30.0  3
 5PV  Var_03    C10  C9   C8   C7   -179.97  30.0  3
 5PV  Var_04    C11  C10  C9   C8   -179.83  30.0  3
 5PV  Var_05    O1   C11  C10  C9   -179.05  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
 5PV  plan-2  HO1  0.020

