# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:08:51 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  22  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  -0.432  -2.7898  -1.2804   0.1147
 01Y  C14   C  C     0   0.497  -2.5932  -0.1219  -0.1377
 01Y  C5    C  CH2   0  -0.248  -1.2342   0.5151  -0.2874
 01Y  O21   O  O2    0  -0.486  -0.2593  -0.4508  -0.0539
 01Y  C44   C  CR15  0   0.065   1.0435  -0.0375  -0.3996
 01Y  C49   C  CH2   0  -0.473   2.0117  -1.2112  -0.2849
 01Y  C48   C  CH2   0  -0.448   3.4029  -0.5672  -0.1360
 01Y  C47   C  CH2   0  -0.459   3.1479   0.9327   0.1351
 01Y  C45   C  CH2   0  -0.476   1.6680   1.0261   0.5019
 01Y  H5    H  HCH2  0   0.249  -1.1622   0.9419  -1.2993
 01Y  H5A   H  HCH2  0   0.251  -1.1713   1.3627   0.4088
 01Y  H44   H  HCR5  0   0.204   1.0438   0.3403  -1.4345
 01Y  H49   H  HCH2  0   0.230   1.7592  -1.7838   0.6115
 01Y  H49A  H  HCH2  0   0.240   1.9448  -1.8919  -1.1341
 01Y  H48   H  HCH2  0   0.232   3.9524  -1.0280   0.6850
 01Y  H48A  H  HCH2  0   0.232   4.0101  -0.7046  -1.0310
 01Y  H47   H  HCH2  0   0.237   3.7961   1.3367   0.9126
 01Y  H47A  H  HCH2  0   0.229   3.3382   1.5156  -0.7687
 01Y  H45   H  HCH2  0   0.239   1.2619   2.0281   0.3533
 01Y  H45A  H  HCH2  0   0.225   1.5091   0.7485   1.5490
 01Y  OXT   O  OH1   0  -0.596  -3.5536   0.7749  -0.3239
 01Y  HXT   H  HOH1  0   0.486  -4.4234   0.3574  -0.2349

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   double  1.202  0.020  1.202
 01Y  C14  C5    single  1.508  0.020  1.508
 01Y  C5   O21   single  1.392  0.020  1.392
 01Y  O21  C44   single  1.410  0.020  1.410
 01Y  C45  C44   single  1.528  0.020  1.528
 01Y  C45  C47   single  1.528  0.020  1.528
 01Y  C44  C49   single  1.526  0.020  1.526
 01Y  C49  C48   single  1.540  0.020  1.540
 01Y  C47  C48   single  1.545  0.020  1.545
 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   single  1.327  0.020  1.327
 01Y  OXT  HXT   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
 01Y  OXT   C14  C5   110.65  3.000
 01Y  OXT   C14  O32  124.22  3.000
 01Y  C5    C14  O32  125.12  3.000
 01Y  H5A   C5   H5   106.24  3.000
 01Y  H5A   C5   O21  112.88  3.000
 01Y  H5    C5   O21  112.18  3.000
 01Y  H5A   C5   C14  108.33  3.000
 01Y  H5    C5   C14  108.30  3.000
 01Y  O21   C5   C14  108.74  3.000
 01Y  C44   O21  C5   113.74  3.000
 01Y  H44   C44  C45  108.39  3.000
 01Y  H44   C44  C49  109.52  3.000
 01Y  C45   C44  C49  103.40  3.000
 01Y  H44   C44  O21  109.34  3.000
 01Y  C49   C44  O21  110.03  3.000
 01Y  C45   C44  O21  115.92  3.000
 01Y  H49A  C49  H49  107.30  3.000
 01Y  H49A  C49  C48  113.06  3.000
 01Y  H49   C49  C48  110.38  3.000
 01Y  H49A  C49  C44  112.51  3.000
 01Y  H49   C49  C44  108.54  3.000
 01Y  C48   C49  C44  105.00  3.000
 01Y  H48A  C48  H48  106.51  3.000
 01Y  H48A  C48  C47  110.99  3.000
 01Y  H48   C48  C47  111.18  3.000
 01Y  H48A  C48  C49  111.78  3.000
 01Y  H48   C48  C49  110.57  3.000
 01Y  C47   C48  C49  105.89  3.000
 01Y  H47A  C47  H47  106.79  3.000
 01Y  H47A  C47  C45  109.57  3.000
 01Y  H47   C47  C45  112.47  3.000
 01Y  H47A  C47  C48  110.13  3.000
 01Y  H47   C47  C48  112.75  3.000
 01Y  C45   C47  C48  105.15  3.000
 01Y  H45A  C45  H45  108.00  3.000
 01Y  H45A  C45  C47  110.78  3.000
 01Y  H45   C45  C47  112.58  3.000
 01Y  H45A  C45  C44  109.18  3.000
 01Y  H45   C45  C44  114.00  3.000
 01Y  C47   C45  C44  102.23  3.000
 01Y  HXT   OXT  C14  110.21  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  CONST_01  HXT  OXT  C14  O32    0.00   0.0  0
 01Y  Var_01    C48  C47  C45  C44  -35.60  30.0  1
 01Y  Var_02    C47  C48  C49  C44   11.94  30.0  1
 01Y  Var_03    C45  C47  C48  C49   14.75  30.0  1
 01Y  Var_04    H5   C5   O21  C44   49.40  30.0  1
 01Y  Var_05    O21  C5   C14  O32   -1.40  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
 01Y  plan-1  HXT  0.020

