# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:57:20 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-cyclopentylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC1CCCC1
#
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
 3PA  3PA  '3-cyclopentylpropanoic acid'  ligand  24  10  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3PA
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
 3PA  C1A  C  CH2   0  -0.444   0.4592  -0.4107  -3.3809
 3PA  C2A  C  CH2   0  -0.439   1.1479   0.3911  -2.2637
 3PA  C3A  C  CH1   0  -0.219   0.0950   0.5695  -1.1399
 3PA  C4A  C  CH2   0  -0.442  -1.1227  -0.2438  -1.6069
 3PA  C5A  C  CH2   0  -0.442  -1.0334  -0.2081  -3.1288
 3PA  C6A  C  CH2   0  -0.428   0.6168   0.1726   0.2354
 3PA  C7A  C  CH2   0  -0.585  -0.4343   0.3360   1.3218
 3PA  C8A  C  C     0   0.552   0.0682   0.0365   2.7063
 3PA  O9A  O  O     0  -0.446   1.1822  -0.3357   2.9805
 3PA  O10  O  OH1   0  -0.599  -0.8742   0.2300   3.6261
 3PA  H11  H  HCH2  0   0.227   0.7731  -0.1012  -4.3786
 3PA  H21  H  HCH2  0   0.218   0.6991  -1.4731  -3.2856
 3PA  H12  H  HCH2  0   0.226   1.4783   1.3637  -2.6319
 3PA  H22  H  HCH2  0   0.224   2.0413  -0.1210  -1.8990
 3PA  HC3  H  HCH1  0   0.224  -0.1978   1.6246  -1.0994
 3PA  H14  H  HCH2  0   0.213  -1.0337  -1.2801  -1.2605
 3PA  H24  H  HCH2  0   0.231  -2.0670   0.1453  -1.2216
 3PA  H15  H  HCH2  0   0.214  -1.3516   0.7706  -3.5005
 3PA  H25  H  HCH2  0   0.227  -1.6572  -0.9605  -3.6146
 3PA  H16  H  HCH2  0   0.233   1.4928   0.7792   0.4805
 3PA  H26  H  HCH2  0   0.222   0.9601  -0.8661   0.2018
 3PA  H17  H  HCH2  0   0.282  -1.2947  -0.3130   1.1315
 3PA  H27  H  HCH2  0   0.273  -0.8346   1.3554   1.3190
 3PA  H10  H  HOH1  0   0.477  -0.5229   0.0326   4.5070

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
 3PA  C1A  C2A  single  1.538  0.020  1.538
 3PA  C1A  C5A  single  1.527  0.020  1.527
 3PA  C1A  H11  single  0.970  0.020  1.090
 3PA  C1A  H21  single  0.970  0.020  1.090
 3PA  C2A  C3A  single  1.550  0.020  1.550
 3PA  C2A  H12  single  0.970  0.020  1.090
 3PA  C2A  H22  single  0.970  0.020  1.090
 3PA  C3A  C4A  single  1.537  0.020  1.537
 3PA  C3A  C6A  single  1.524  0.020  1.524
 3PA  C3A  HC3  single  0.970  0.020  1.090
 3PA  C4A  C5A  single  1.525  0.020  1.525
 3PA  C4A  H14  single  0.970  0.020  1.090
 3PA  C4A  H24  single  0.970  0.020  1.090
 3PA  C5A  H15  single  0.970  0.020  1.090
 3PA  C5A  H25  single  0.970  0.020  1.090
 3PA  C6A  C7A  single  1.520  0.020  1.520
 3PA  C6A  H16  single  0.970  0.020  1.090
 3PA  C6A  H26  single  0.970  0.020  1.090
 3PA  C7A  C8A  single  1.503  0.020  1.503
 3PA  C7A  H17  single  0.970  0.020  1.090
 3PA  C7A  H27  single  0.970  0.020  1.090
 3PA  C8A  O9A  double  1.206  0.020  1.206
 3PA  C8A  O10  single  1.331  0.020  1.331
 3PA  O10  H10  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
 3PA  H21  C1A  H11  107.00  3.000
 3PA  H21  C1A  C5A  109.21  3.000
 3PA  H11  C1A  C5A  113.24  3.000
 3PA  H21  C1A  C2A  110.18  3.000
 3PA  H11  C1A  C2A  112.81  3.000
 3PA  C5A  C1A  C2A  104.39  3.000
 3PA  H22  C2A  H12  106.43  3.000
 3PA  H22  C2A  C3A  111.56  3.000
 3PA  H12  C2A  C3A  110.34  3.000
 3PA  H22  C2A  C1A  111.37  3.000
 3PA  H12  C2A  C1A  110.80  3.000
 3PA  C3A  C2A  C1A  106.41  3.000
 3PA  HC3  C3A  C6A  107.99  3.000
 3PA  HC3  C3A  C4A  108.00  3.000
 3PA  C6A  C3A  C4A  114.07  3.000
 3PA  HC3  C3A  C2A  108.61  3.000
 3PA  C6A  C3A  C2A  113.06  3.000
 3PA  C4A  C3A  C2A  104.89  3.000
 3PA  H24  C4A  H14  107.19  3.000
 3PA  H24  C4A  C5A  113.24  3.000
 3PA  H14  C4A  C5A  109.43  3.000
 3PA  H24  C4A  C3A  112.93  3.000
 3PA  H14  C4A  C3A  109.87  3.000
 3PA  C5A  C4A  C3A  104.15  3.000
 3PA  H25  C5A  H15  107.41  3.000
 3PA  H25  C5A  C4A  113.24  3.000
 3PA  H15  C5A  C4A  110.05  3.000
 3PA  H25  C5A  C1A  113.18  3.000
 3PA  H15  C5A  C1A  110.29  3.000
 3PA  C4A  C5A  C1A  102.64  3.000
 3PA  H26  C6A  H16  106.39  3.000
 3PA  H26  C6A  C7A  109.92  3.000
 3PA  H16  C6A  C7A  109.52  3.000
 3PA  H26  C6A  C3A  109.08  3.000
 3PA  H16  C6A  C3A  109.41  3.000
 3PA  C7A  C6A  C3A  112.34  3.000
 3PA  H27  C7A  H17  105.32  3.000
 3PA  H27  C7A  C8A  108.06  3.000
 3PA  H17  C7A  C8A  107.75  3.000
 3PA  H27  C7A  C6A  110.55  3.000
 3PA  H17  C7A  C6A  110.83  3.000
 3PA  C8A  C7A  C6A  113.93  3.000
 3PA  O10  C8A  O9A  122.80  3.000
 3PA  O10  C8A  C7A  111.77  3.000
 3PA  O9A  C8A  C7A  125.43  3.000
 3PA  H10  O10  C8A  110.00  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
 3PA  CONST_01  H10  O10  C8A  C7A   180.00   0.0  0
 3PA  Var_01    C3A  C4A  C5A  C1A    41.61  30.0  1
 3PA  Var_02    C4A  C5A  C1A  C2A   -38.37  30.0  1
 3PA  Var_03    C5A  C1A  C2A  C3A    20.75  30.0  1
 3PA  Var_04    C8A  C7A  C6A  C3A  -176.37  30.0  3
 3PA  Var_05    O9A  C8A  C7A  C6A    -1.85  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
 3PA  chir_01  C3A  C2A  C4A  C6A  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
 3PA  plan-1  C7A  0.020
 3PA  plan-1  C8A  0.020
 3PA  plan-1  O9A  0.020
 3PA  plan-1  O10  0.020
 3PA  plan-1  H10  0.020

