# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 05:54:48 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: [(1S,2R)-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
 KUD  KUD  '[(1S,2R)-2-(benzenecarbonyl)cyclopentyl]acetic acid'  ligand  32  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_KUD
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
 KUD  C14  C  CH2    0  -0.436   2.3532   1.7675   0.1715
 KUD  O16  O  O      0  -0.399  -0.3940  -0.9933  -1.5103
 KUD  C13  C  CH2    0  -0.445   1.2669   2.8534   0.0174
 KUD  C12  C  CH2    0  -0.430   0.0009   2.1195  -0.4422
 KUD  C10  C  CH1    0  -0.404   0.2138   0.6821   0.0647
 KUD  C01  C  CR16   0  -0.239  -3.9401   0.3693   1.3625
 KUD  C02  C  CR16   0  -0.249  -4.8465  -0.3974   0.6441
 KUD  C03  C  CR16   0  -0.241  -4.4166  -1.1203  -0.4628
 KUD  C04  C  CR16   0  -0.266  -3.0876  -1.0739  -0.8478
 KUD  C05  C  CR6    0  -0.006  -2.1658  -0.3030  -0.1350
 KUD  C06  C  CR16   0  -0.296  -2.6087   0.4170   0.9749
 KUD  C07  C  C      0   0.405  -0.7435  -0.2775  -0.5932
 KUD  C08  C  CH2    0  -0.583   2.2603  -0.7674   0.5371
 KUD  C09  C  C      0   0.413   3.7544  -1.0558   0.3083
 KUD  C11  C  CH1    0  -0.180   1.6978   0.4298  -0.2099
 KUD  O15  O  O      0  -0.607   4.2795  -0.6078  -0.7303
 KUD  O17  O  OC    -1  -0.630   4.3206  -1.7522   1.1774
 KUD  H1   H  HCH2   0   0.231   3.2307   1.9618  -0.4432
 KUD  H2   H  HCH2   0   0.214   2.7035   1.7269   1.2066
 KUD  H3   H  HCH2   0   0.227   1.0841   3.3491   0.9721
 KUD  H4   H  HCH2   0   0.230   1.5510   3.6336  -0.6898
 KUD  H5   H  HCH2   0   0.243  -0.9162   2.5789  -0.0706
 KUD  H6   H  HCH2   0   0.231  -0.0633   2.1109  -1.5339
 KUD  H7   H  HCH1   0   0.253   0.0549   0.6723   1.1492
 KUD  H10  H  HCR6   0   0.263  -5.1192  -1.7215  -1.0246
 KUD  H11  H  HCR6   0   0.260  -2.7610  -1.6363  -1.7124
 KUD  H12  H  HCR6   0   0.261  -1.9227   1.0211   1.5525
 KUD  H13  H  HCH2   0   0.233   1.7110  -1.6720   0.2483
 KUD  H14  H  HCH2   0   0.205   2.0772  -0.6460   1.6107
 KUD  H15  H  HCH1   0   0.212   1.8240   0.2728  -1.2846
 KUD  H8   H  HCR6   0   0.264  -4.2682   0.9320   2.2264
 KUD  H9   H  HCR6   0   0.266  -5.8855  -0.4326   0.9450

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
 KUD  O15  C09  deloc     1.247  0.020  1.247
 KUD  O16  C07  double    1.215  0.020  1.215
 KUD  C06  C01  aromatic  1.387  0.020  1.387
 KUD  C06  C05  aromatic  1.395  0.020  1.395
 KUD  C09  C08  single    1.539  0.020  1.539
 KUD  C09  O17  deloc     1.249  0.020  1.249
 KUD  C07  C05  single    1.495  0.020  1.495
 KUD  C07  C10  single    1.507  0.020  1.507
 KUD  C11  C08  single    1.519  0.020  1.519
 KUD  C11  C10  single    1.530  0.020  1.530
 KUD  C11  C14  single    1.538  0.020  1.538
 KUD  C01  C02  aromatic  1.388  0.020  1.388
 KUD  C05  C04  aromatic  1.397  0.020  1.397
 KUD  C10  C12  single    1.539  0.020  1.539
 KUD  C14  C13  single    1.544  0.020  1.544
 KUD  C12  C13  single    1.534  0.020  1.534
 KUD  C02  C03  aromatic  1.390  0.020  1.390
 KUD  C04  C03  aromatic  1.384  0.020  1.384
 KUD  C14  H1   single    0.970  0.020  1.090
 KUD  C14  H2   single    0.970  0.020  1.090
 KUD  C13  H3   single    0.970  0.020  1.090
 KUD  C13  H4   single    0.970  0.020  1.090
 KUD  C12  H5   single    0.970  0.020  1.090
 KUD  C12  H6   single    0.970  0.020  1.090
 KUD  C10  H7   single    0.970  0.020  1.090
 KUD  C01  H8   single    0.930  0.020  1.080
 KUD  C02  H9   single    0.930  0.020  1.080
 KUD  C03  H10  single    0.930  0.020  1.080
 KUD  C04  H11  single    0.930  0.020  1.080
 KUD  C06  H12  single    0.930  0.020  1.080
 KUD  C08  H13  single    0.970  0.020  1.090
 KUD  C08  H14  single    0.970  0.020  1.090
 KUD  C11  H15  single    0.970  0.020  1.090

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
 KUD  H2   C14  H1   106.43  3.000
 KUD  H2   C14  C11  109.82  3.000
 KUD  H1   C14  C11  111.02  3.000
 KUD  H2   C14  C13  110.24  3.000
 KUD  H1   C14  C13  112.66  3.000
 KUD  C11  C14  C13  106.70  3.000
 KUD  H4   C13  H3   106.62  3.000
 KUD  H4   C13  C12  111.29  3.000
 KUD  H3   C13  C12  109.96  3.000
 KUD  H4   C13  C14  112.62  3.000
 KUD  H3   C13  C14  110.50  3.000
 KUD  C12  C13  C14  105.91  3.000
 KUD  H6   C12  H5   107.09  3.000
 KUD  H6   C12  C10  109.24  3.000
 KUD  H5   C12  C10  113.42  3.000
 KUD  H6   C12  C13  110.57  3.000
 KUD  H5   C12  C13  112.97  3.000
 KUD  C10  C12  C13  103.54  3.000
 KUD  H7   C10  C11  108.46  3.000
 KUD  H7   C10  C07  109.53  3.000
 KUD  C11  C10  C07  115.65  3.000
 KUD  H7   C10  C12  108.31  3.000
 KUD  C11  C10  C12  103.24  3.000
 KUD  C07  C10  C12  111.30  3.000
 KUD  H8   C01  C06  119.75  3.000
 KUD  H8   C01  C02  120.18  3.000
 KUD  C06  C01  C02  120.08  3.000
 KUD  H9   C02  C03  120.09  3.000
 KUD  H9   C02  C01  120.07  3.000
 KUD  C03  C02  C01  119.83  3.000
 KUD  H10  C03  C04  119.84  3.000
 KUD  H10  C03  C02  120.10  3.000
 KUD  C04  C03  C02  120.06  3.000
 KUD  H11  C04  C05  119.70  3.000
 KUD  H11  C04  C03  119.64  3.000
 KUD  C05  C04  C03  120.66  3.000
 KUD  C07  C05  C06  122.49  3.000
 KUD  C07  C05  C04  118.74  3.000
 KUD  C06  C05  C04  118.76  3.000
 KUD  H12  C06  C05  120.79  3.000
 KUD  H12  C06  C01  118.60  3.000
 KUD  C05  C06  C01  120.61  3.000
 KUD  C05  C07  C10  118.79  3.000
 KUD  C10  C07  O16  121.48  3.000
 KUD  C05  C07  O16  119.68  3.000
 KUD  H14  C08  H13  105.40  3.000
 KUD  H14  C08  C11  109.43  3.000
 KUD  H13  C08  C11  109.57  3.000
 KUD  H14  C08  C09  109.19  3.000
 KUD  H13  C08  C09  107.01  3.000
 KUD  C11  C08  C09  115.73  3.000
 KUD  O17  C09  O15  126.07  3.000
 KUD  O17  C09  C08  116.17  3.000
 KUD  O15  C09  C08  117.73  3.000
 KUD  H15  C11  C08  109.12  3.000
 KUD  H15  C11  C10  108.18  3.000
 KUD  C08  C11  C10  113.63  3.000
 KUD  H15  C11  C14  108.63  3.000
 KUD  C10  C11  C14  103.03  3.000
 KUD  C08  C11  C14  113.94  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
 KUD  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 KUD  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 KUD  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 KUD  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 KUD  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 KUD  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 KUD  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 KUD  CONST_08  C07  C05  C04  C03  180.00   0.0  0
 KUD  CONST_09  H10  C03  C02  C01  180.00   0.0  0
 KUD  CONST_10  H12  C06  C01  C02  180.00   0.0  0
 KUD  CONST_11  H11  C04  C03  C02  180.00   0.0  0
 KUD  CONST_12  H8   C01  C02  C03  180.00   0.0  0
 KUD  CONST_13  H9   C02  C03  C04  180.00   0.0  0
 KUD  Var_01    C10  C12  C13  C14   24.41  30.0  1
 KUD  Var_02    C11  C14  C13  C12    0.34  30.0  1
 KUD  Var_03    C06  C05  C07  C10   -7.32  30.0  2
 KUD  Var_04    O15  C09  C08  C11  -22.11  30.0  2

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
 KUD  chir_01  C10  C07  C11  C12  negativ
 KUD  chir_02  C11  C08  C10  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
 KUD  plan-1  C01  0.020
 KUD  plan-1  C02  0.020
 KUD  plan-1  C03  0.020
 KUD  plan-1  C04  0.020
 KUD  plan-1  C05  0.020
 KUD  plan-1  C06  0.020
 KUD  plan-1  C07  0.020
 KUD  plan-1  H10  0.020
 KUD  plan-1  H11  0.020
 KUD  plan-1  H12  0.020
 KUD  plan-1  H8   0.020
 KUD  plan-1  H9   0.020
 KUD  plan-2  C08  0.020
 KUD  plan-2  C09  0.020
 KUD  plan-2  O15  0.020
 KUD  plan-2  O17  0.020
 KUD  plan-3  O16  0.020
 KUD  plan-3  C10  0.020
 KUD  plan-3  C05  0.020
 KUD  plan-3  C07  0.020

