# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:24:09 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (cyclopentyloxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COC1CCCC1
#
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
 01Y  01Y  '(cyclopentyloxy)acetic acid'  ligand  21  10  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_01Y
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
 01Y  O32   O  O      0  -0.600  -2.7730  -1.2529   0.0846
 01Y  C14   C  C      0   0.367  -2.6433  -0.0304  -0.0856
 01Y  C5    C  CH2    0  -0.285  -1.2243   0.5385  -0.2457
 01Y  O21   O  O2     0  -0.490  -0.2412  -0.4498  -0.0751
 01Y  C44   C  CH1    0   0.083   1.0504  -0.0344  -0.4327
 01Y  C49   C  CH2    0  -0.474   2.0263  -1.2161  -0.3468
 01Y  C48   C  CH2    0  -0.448   3.3951  -0.6104   0.0284
 01Y  C47   C  CH2    0  -0.454   3.1661   0.9073   0.1099
 01Y  C45   C  CH2    0  -0.477   1.6863   1.0416   0.4510
 01Y  H5    H  HCH2   0   0.197  -1.1459   0.9979  -1.2446
 01Y  H5A   H  HCH2   0   0.201  -1.0967   1.3594   0.4738
 01Y  H44   H  HCH1   0   0.187   1.0387   0.3498  -1.4665
 01Y  H49   H  HCH2   0   0.228   1.6843  -1.9078   0.4263
 01Y  H49A  H  HCH2   0   0.234   2.0590  -1.7776  -1.2814
 01Y  H48   H  HCH2   0   0.227   3.7218  -0.9911   0.9973
 01Y  H48A  H  HCH2   0   0.230   4.1759  -0.8667  -0.6882
 01Y  H47   H  HCH2   0   0.233   3.8177   1.3958   0.8351
 01Y  H47A  H  HCH2   0   0.222   3.3630   1.3719  -0.8601
 01Y  H45   H  HCH2   0   0.234   1.2980   2.0450   0.2675
 01Y  H45A  H  HCH2   0   0.218   1.5128   0.8012   1.5055
 01Y  OXT   O  OC    -1  -0.632  -3.5476   0.8278  -0.1518

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
 01Y  C14  O32   deloc   1.241  0.020  1.241
 01Y  C14  C5    single  1.537  0.020  1.537
 01Y  C5   O21   single  1.404  0.020  1.404
 01Y  O21  C44   single  1.403  0.020  1.403
 01Y  C45  C44   single  1.531  0.020  1.531
 01Y  C45  C47   single  1.525  0.020  1.525
 01Y  C44  C49   single  1.535  0.020  1.535
 01Y  C49  C48   single  1.543  0.020  1.543
 01Y  C47  C48   single  1.537  0.020  1.537
 01Y  C5   H5    single  0.970  0.020  1.090
 01Y  C5   H5A   single  0.970  0.020  1.090
 01Y  C44  H44   single  0.970  0.020  1.090
 01Y  C49  H49   single  0.970  0.020  1.090
 01Y  C49  H49A  single  0.970  0.020  1.090
 01Y  C48  H48   single  0.970  0.020  1.090
 01Y  C48  H48A  single  0.970  0.020  1.090
 01Y  C47  H47   single  0.970  0.020  1.090
 01Y  C47  H47A  single  0.970  0.020  1.090
 01Y  C45  H45   single  0.970  0.020  1.090
 01Y  C45  H45A  single  0.970  0.020  1.090
 01Y  C14  OXT   deloc   1.248  0.020  1.248

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
 01Y  OXT   C14  C5   114.12  3.000
 01Y  OXT   C14  O32  127.50  3.000
 01Y  C5    C14  O32  118.38  3.000
 01Y  H5A   C5   H5   105.89  3.000
 01Y  H5A   C5   O21  111.40  3.000
 01Y  H5    C5   O21  110.71  3.000
 01Y  H5A   C5   C14  108.38  3.000
 01Y  H5    C5   C14  108.32  3.000
 01Y  O21   C5   C14  111.91  3.000
 01Y  C44   O21  C5   113.89  3.000
 01Y  H44   C44  C45  107.49  3.000
 01Y  H44   C44  C49  109.11  3.000
 01Y  C45   C44  C49  104.17  3.000
 01Y  H44   C44  O21  109.41  3.000
 01Y  C49   C44  O21  110.07  3.000
 01Y  C45   C44  O21  116.32  3.000
 01Y  H49A  C49  H49  106.85  3.000
 01Y  H49A  C49  C48  112.57  3.000
 01Y  H49   C49  C48  110.74  3.000
 01Y  H49A  C49  C44  111.56  3.000
 01Y  H49   C49  C44  109.15  3.000
 01Y  C48   C49  C44  105.99  3.000
 01Y  H48A  C48  H48  106.69  3.000
 01Y  H48A  C48  C47  111.94  3.000
 01Y  H48   C48  C47  110.01  3.000
 01Y  H48A  C48  C49  112.52  3.000
 01Y  H48   C48  C49  110.15  3.000
 01Y  C47   C48  C49  105.56  3.000
 01Y  H47A  C47  H47  106.98  3.000
 01Y  H47A  C47  C45  109.63  3.000
 01Y  H47   C47  C45  113.06  3.000
 01Y  H47A  C47  C48  110.22  3.000
 01Y  H47   C47  C48  112.86  3.000
 01Y  C45   C47  C48  104.09  3.000
 01Y  H45A  C45  H45  107.90  3.000
 01Y  H45A  C45  C47  110.48  3.000
 01Y  H45   C45  C47  112.87  3.000
 01Y  H45A  C45  C44  109.61  3.000
 01Y  H45   C45  C44  113.66  3.000
 01Y  C47   C45  C44  102.25  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
 01Y  Var_01  C48  C47  C45  C44  -41.08  30.0  1
 01Y  Var_02  C47  C48  C49  C44   -1.43  30.0  1
 01Y  Var_03  C45  C47  C48  C49   26.34  30.0  1
 01Y  Var_04  H5   C5   O21  C44   48.83  30.0  1
 01Y  Var_05  O21  C5   C14  O32   -4.26  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
 01Y  chir_01  C44  O21  C45  C49  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
 01Y  plan-1  O32  0.020
 01Y  plan-1  C14  0.020
 01Y  plan-1  C5   0.020
 01Y  plan-1  OXT  0.020

