# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:48:48 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: [(1R,2S)-2-(benzenecarbonyl)cyclopentyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H]1CCC[C@@H]1C(=O)c2ccccc2
#
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
 KUG  KUG  '[(1R,2S)-2-(benzenecarbonyl)cyclopentyl]acetic acid'  ligand  33  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KUG
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
 KUG  C14  C  CH2   0  -0.438  -2.3684  -1.6421  -0.4888
 KUG  C12  C  CH2   0  -0.431  -0.0300  -2.1813   0.0084
 KUG  C13  C  CH2   0  -0.440  -1.4433  -2.7953  -0.0961
 KUG  C01  C  CR16  0  -0.238   3.9165  -0.1785  -1.4552
 KUG  C02  C  CR16  0  -0.248   4.8453   0.4105  -0.6089
 KUG  C03  C  CR16  0  -0.240   4.4408   0.9065   0.6255
 KUG  C04  C  CR16  0  -0.264   3.1142   0.8129   1.0092
 KUG  C05  C  CR6   0  -0.006   2.1704   0.2185   0.1675
 KUG  C06  C  CR16  0  -0.296   2.5874  -0.2749  -1.0692
 KUG  C07  C  C     0   0.399   0.7520   0.1370   0.6234
 KUG  C08  C  CH2   0  -0.582  -2.2098   0.9179  -0.3985
 KUG  C09  C  C     0   0.554  -3.6354   1.2210  -0.0265
 KUG  C10  C  CH1   0  -0.406  -0.2297  -0.6574  -0.2012
 KUG  C11  C  CH1   0  -0.210  -1.7042  -0.4133   0.1292
 KUG  O15  O  OH1   0  -0.596  -4.1502   2.1862  -0.7824
 KUG  O16  O  O     0  -0.396   0.4159   0.6701   1.6614
 KUG  O17  O  O     0  -0.444  -4.2495   0.6904   0.8658
 KUG  H1   H  HCH2  0   0.218  -2.3994  -1.5299  -1.5775
 KUG  H2   H  HCH2  0   0.242  -3.3935  -1.7914  -0.1493
 KUG  H3   H  HCH2  0   0.243   0.4048  -2.3859   0.9886
 KUG  H4   H  HCH2  0   0.245   0.6558  -2.5947  -0.7305
 KUG  H5   H  HCH2  0   0.232  -1.7448  -3.2028   0.8701
 KUG  H6   H  HCH2  0   0.238  -1.4806  -3.6158  -0.8126
 KUG  H8   H  HCR6  0   0.267   5.8826   0.4829  -0.9089
 KUG  H9   H  HCR6  0   0.264   5.1625   1.3654   1.2884
 KUG  H10  H  HCR6  0   0.261   2.8071   1.2004   1.9714
 KUG  H11  H  HCR6  0   0.262   1.8829  -0.7335  -1.7500
 KUG  H12  H  HCH2  0   0.268  -2.0983   0.9686  -1.4855
 KUG  H13  H  HCH2  0   0.294  -1.6090   1.7429   0.0008
 KUG  H14  H  HCH1  0   0.269  -0.0808  -0.4306  -1.2621
 KUG  H15  H  HCH1  0   0.239  -1.8347  -0.4495   1.2147
 KUG  H16  H  HOH1  0   0.478  -5.0514   2.3893  -0.4902
 KUG  H7   H  HCR6  0   0.266   4.2247  -0.5644  -2.4174

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
 KUG  O16  C07  double    1.214  0.020  1.214
 KUG  O17  C09  double    1.206  0.020  1.206
 KUG  C07  C10  single    1.508  0.020  1.508
 KUG  C07  C05  single    1.492  0.020  1.492
 KUG  C06  C05  aromatic  1.395  0.020  1.395
 KUG  C06  C01  aromatic  1.387  0.020  1.387
 KUG  C09  C08  single    1.504  0.020  1.504
 KUG  C09  O15  single    1.330  0.020  1.330
 KUG  C10  C11  single    1.531  0.020  1.531
 KUG  C10  C12  single    1.551  0.020  1.551
 KUG  C08  C11  single    1.519  0.020  1.519
 KUG  C05  C04  aromatic  1.397  0.020  1.397
 KUG  C01  C02  aromatic  1.388  0.020  1.388
 KUG  C11  C14  single    1.527  0.020  1.527
 KUG  C12  C13  single    1.544  0.020  1.544
 KUG  C14  C13  single    1.530  0.020  1.530
 KUG  C04  C03  aromatic  1.384  0.020  1.384
 KUG  C02  C03  aromatic  1.390  0.020  1.390
 KUG  C14  H1   single    0.970  0.020  1.090
 KUG  C14  H2   single    0.970  0.020  1.090
 KUG  C12  H3   single    0.970  0.020  1.090
 KUG  C12  H4   single    0.970  0.020  1.090
 KUG  C13  H5   single    0.970  0.020  1.090
 KUG  C13  H6   single    0.970  0.020  1.090
 KUG  C01  H7   single    0.930  0.020  1.080
 KUG  C02  H8   single    0.930  0.020  1.080
 KUG  C03  H9   single    0.930  0.020  1.080
 KUG  C04  H10  single    0.930  0.020  1.080
 KUG  C06  H11  single    0.930  0.020  1.080
 KUG  C08  H12  single    0.970  0.020  1.090
 KUG  C08  H13  single    0.970  0.020  1.090
 KUG  C10  H14  single    0.970  0.020  1.090
 KUG  C11  H15  single    0.970  0.020  1.090
 KUG  O15  H16  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
 KUG  H2   C14  H1   107.28  3.000
 KUG  H2   C14  C11  113.15  3.000
 KUG  H1   C14  C11  109.41  3.000
 KUG  H2   C14  C13  112.67  3.000
 KUG  H1   C14  C13  110.46  3.000
 KUG  C11  C14  C13  103.86  3.000
 KUG  H4   C12  H3   106.69  3.000
 KUG  H4   C12  C10  111.23  3.000
 KUG  H3   C12  C10  110.90  3.000
 KUG  H4   C12  C13  112.28  3.000
 KUG  H3   C12  C13  110.53  3.000
 KUG  C10  C12  C13  105.28  3.000
 KUG  H6   C13  H5   106.95  3.000
 KUG  H6   C13  C12  112.03  3.000
 KUG  H5   C13  C12  109.96  3.000
 KUG  H6   C13  C14  112.22  3.000
 KUG  H5   C13  C14  109.98  3.000
 KUG  C12  C13  C14  105.73  3.000
 KUG  H7   C01  C06  119.72  3.000
 KUG  H7   C01  C02  120.22  3.000
 KUG  C06  C01  C02  120.06  3.000
 KUG  H8   C02  C03  120.07  3.000
 KUG  H8   C02  C01  120.06  3.000
 KUG  C03  C02  C01  119.87  3.000
 KUG  H9   C03  C04  119.87  3.000
 KUG  H9   C03  C02  120.07  3.000
 KUG  C04  C03  C02  120.06  3.000
 KUG  H10  C04  C05  119.76  3.000
 KUG  H10  C04  C03  119.64  3.000
 KUG  C05  C04  C03  120.61  3.000
 KUG  C07  C05  C06  122.39  3.000
 KUG  C06  C05  C04  118.84  3.000
 KUG  C07  C05  C04  118.77  3.000
 KUG  H11  C06  C05  120.87  3.000
 KUG  H11  C06  C01  118.57  3.000
 KUG  C05  C06  C01  120.56  3.000
 KUG  O16  C07  C10  121.22  3.000
 KUG  C10  C07  C05  118.72  3.000
 KUG  O16  C07  C05  120.02  3.000
 KUG  H13  C08  H12  105.74  3.000
 KUG  H13  C08  C11  110.54  3.000
 KUG  H12  C08  C11  110.61  3.000
 KUG  H13  C08  C09  106.13  3.000
 KUG  H12  C08  C09  109.45  3.000
 KUG  C11  C08  C09  113.97  3.000
 KUG  O17  C09  O15  122.87  3.000
 KUG  O15  C09  C08  111.87  3.000
 KUG  O17  C09  C08  125.23  3.000
 KUG  H14  C10  C11  107.89  3.000
 KUG  H14  C10  C07  109.39  3.000
 KUG  C11  C10  C07  115.15  3.000
 KUG  H14  C10  C12  108.47  3.000
 KUG  C11  C10  C12  104.57  3.000
 KUG  C07  C10  C12  111.08  3.000
 KUG  H15  C11  C10  108.90  3.000
 KUG  H15  C11  C08  109.51  3.000
 KUG  C10  C11  C08  112.67  3.000
 KUG  H15  C11  C14  108.85  3.000
 KUG  C08  C11  C14  114.82  3.000
 KUG  C10  C11  C14  101.73  3.000
 KUG  H16  O15  C09  109.92  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
 KUG  CONST_01  C04  C05  C06  C01     0.00   0.0  0
 KUG  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 KUG  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 KUG  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 KUG  CONST_05  C06  C05  C04  C03     0.00   0.0  0
 KUG  CONST_06  C06  C01  C02  C03     0.00   0.0  0
 KUG  CONST_07  C07  C05  C06  C01   180.00   0.0  0
 KUG  CONST_08  C07  C05  C04  C03   180.00   0.0  0
 KUG  CONST_09  H9   C03  C02  C01   180.00   0.0  0
 KUG  CONST_10  H11  C06  C01  C02   180.00   0.0  0
 KUG  CONST_11  H10  C04  C03  C02   180.00   0.0  0
 KUG  CONST_12  H7   C01  C02  C03   180.00   0.0  0
 KUG  CONST_13  H8   C02  C03  C04   180.00   0.0  0
 KUG  CONST_14  H16  O15  C09  C08   180.00   0.0  0
 KUG  Var_01    C10  C12  C13  C14     5.23  30.0  1
 KUG  Var_02    C11  C14  C13  C12   -29.90  30.0  1
 KUG  Var_03    C10  C07  C05  C04  -172.27  30.0  2
 KUG  Var_04    O17  C09  C08  C11    18.58  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
 KUG  chir_01  C10  C07  C11  C12  positiv
 KUG  chir_02  C11  C10  C08  C14  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
 KUG  plan-1  C01  0.020
 KUG  plan-1  C02  0.020
 KUG  plan-1  C03  0.020
 KUG  plan-1  C04  0.020
 KUG  plan-1  C05  0.020
 KUG  plan-1  C06  0.020
 KUG  plan-1  C07  0.020
 KUG  plan-1  H8   0.020
 KUG  plan-1  H9   0.020
 KUG  plan-1  H10  0.020
 KUG  plan-1  H11  0.020
 KUG  plan-1  H7   0.020
 KUG  plan-2  C08  0.020
 KUG  plan-2  C09  0.020
 KUG  plan-2  O15  0.020
 KUG  plan-2  O17  0.020
 KUG  plan-2  H16  0.020
 KUG  plan-3  C05  0.020
 KUG  plan-3  C07  0.020
 KUG  plan-3  C10  0.020
 KUG  plan-3  O16  0.020

