# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:37:09 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  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_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  -0.439   2.3922   1.7587   0.1354
 KUD  O16  O  O     0  -0.396  -0.3625  -1.0346  -1.4587
 KUD  C13  C  CH2   0  -0.445   1.2919   2.8380   0.0499
 KUD  C12  C  CH2   0  -0.430   0.0288   2.1134  -0.4240
 KUD  C10  C  CR15  0  -0.410   0.2342   0.6758   0.0817
 KUD  C01  C  CR16  0  -0.239  -3.9351   0.4093   1.3378
 KUD  C02  C  CR16  0  -0.248  -4.8471  -0.3242   0.5921
 KUD  C03  C  CR16  0  -0.240  -4.4166  -1.0391  -0.5198
 KUD  C04  C  CR16  0  -0.265  -3.0806  -1.0200  -0.8817
 KUD  C05  C  CR6   0  -0.005  -2.1537  -0.2815  -0.1416
 KUD  C06  C  CR16  0  -0.295  -2.5971   0.4326   0.9718
 KUD  C07  C  C     0   0.406  -0.7245  -0.2887  -0.5712
 KUD  C08  C  CH2   0  -0.588   2.2533  -0.7705   0.5743
 KUD  C09  C  C     0   0.553   3.6915  -1.0972   0.2843
 KUD  C11  C  CR15  0  -0.204   1.7146   0.4175  -0.2044
 KUD  O15  O  O     0  -0.442   4.3401  -0.6503  -0.6289
 KUD  O17  O  OH1   0  -0.598   4.1794  -1.9784   1.1535
 KUD  H1   H  HCH2  0   0.240   3.2195   1.9597  -0.5435
 KUD  H2   H  HCH2  0   0.227   2.8155   1.7270   1.1425
 KUD  H3   H  HCH2  0   0.233   1.1171   3.2787   1.0325
 KUD  H4   H  HCH2  0   0.237   1.5600   3.6564  -0.6187
 KUD  H5   H  HCH2  0   0.249  -0.8888   2.5728  -0.0548
 KUD  H6   H  HCH2  0   0.235  -0.0278   2.1090  -1.5161
 KUD  H7   H  HCR5  0   0.265   0.0801   0.6674   1.1668
 KUD  H9   H  HCR6  0   0.267  -5.8913  -0.3401   0.8761
 KUD  H10  H  HCR6  0   0.264  -5.1242  -1.6129  -1.1033
 KUD  H11  H  HCR6  0   0.261  -2.7534  -1.5770  -1.7496
 KUD  H12  H  HCR6  0   0.263  -1.9064   1.0099   1.5711
 KUD  H13  H  HCH2  0   0.292   1.6748  -1.6736   0.3504
 KUD  H14  H  HCH2  0   0.272   2.1370  -0.6061   1.6500
 KUD  H15  H  HCR5  0   0.241   1.8264   0.2247  -1.2746
 KUD  H16  H  HOH1  0   0.478   5.0947  -2.1974   0.9241
 KUD  H8   H  HCR6  0   0.266  -4.2639   0.9644   2.2062

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  double    1.206  0.020  1.206
 KUD  O16  C07  double    1.214  0.020  1.214
 KUD  C06  C01  aromatic  1.387  0.020  1.387
 KUD  C06  C05  aromatic  1.395  0.020  1.395
 KUD  C09  C08  single    1.503  0.020  1.503
 KUD  C09  O17  single    1.330  0.020  1.330
 KUD  C07  C05  single    1.492  0.020  1.492
 KUD  C07  C10  single    1.509  0.020  1.509
 KUD  C11  C08  single    1.519  0.020  1.519
 KUD  C11  C10  single    1.530  0.020  1.530
 KUD  C11  C14  single    1.541  0.020  1.541
 KUD  C01  C02  aromatic  1.388  0.020  1.388
 KUD  C05  C04  aromatic  1.397  0.020  1.397
 KUD  C10  C12  single    1.538  0.020  1.538
 KUD  C14  C13  single    1.544  0.020  1.544
 KUD  C12  C13  single    1.531  0.020  1.531
 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
 KUD  O17  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
 KUD  H2   C14  H1   106.60  3.000
 KUD  H2   C14  C11  110.39  3.000
 KUD  H1   C14  C11  110.94  3.000
 KUD  H2   C14  C13  110.32  3.000
 KUD  H1   C14  C13  112.20  3.000
 KUD  C11  C14  C13  106.44  3.000
 KUD  H4   C13  H3   106.77  3.000
 KUD  H4   C13  C12  111.61  3.000
 KUD  H3   C13  C12  109.73  3.000
 KUD  H4   C13  C14  112.56  3.000
 KUD  H3   C13  C14  110.29  3.000
 KUD  C12  C13  C14  105.92  3.000
 KUD  H6   C12  H5   107.23  3.000
 KUD  H6   C12  C10  109.36  3.000
 KUD  H5   C12  C10  113.25  3.000
 KUD  H6   C12  C13  110.71  3.000
 KUD  H5   C12  C13  112.95  3.000
 KUD  C10  C12  C13  103.32  3.000
 KUD  H7   C10  C11  108.65  3.000
 KUD  H7   C10  C07  109.52  3.000
 KUD  C11  C10  C07  115.22  3.000
 KUD  H7   C10  C12  108.30  3.000
 KUD  C11  C10  C12  103.04  3.000
 KUD  C07  C10  C12  111.75  3.000
 KUD  H8   C01  C06  119.75  3.000
 KUD  H8   C01  C02  120.18  3.000
 KUD  C06  C01  C02  120.06  3.000
 KUD  H9   C02  C03  120.08  3.000
 KUD  H9   C02  C01  120.06  3.000
 KUD  C03  C02  C01  119.87  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  119.76  3.000
 KUD  H11  C04  C03  119.64  3.000
 KUD  C05  C04  C03  120.60  3.000
 KUD  C07  C05  C06  122.45  3.000
 KUD  C07  C05  C04  118.70  3.000
 KUD  C06  C05  C04  118.85  3.000
 KUD  H12  C06  C05  120.83  3.000
 KUD  H12  C06  C01  118.60  3.000
 KUD  C05  C06  C01  120.56  3.000
 KUD  C05  C07  C10  118.75  3.000
 KUD  C10  C07  O16  121.30  3.000
 KUD  C05  C07  O16  119.92  3.000
 KUD  H14  C08  H13  105.58  3.000
 KUD  H14  C08  C11  110.40  3.000
 KUD  H13  C08  C11  110.65  3.000
 KUD  H14  C08  C09  108.90  3.000
 KUD  H13  C08  C09  106.66  3.000
 KUD  C11  C08  C09  114.23  3.000
 KUD  O17  C09  O15  122.89  3.000
 KUD  O17  C09  C08  111.64  3.000
 KUD  O15  C09  C08  125.46  3.000
 KUD  H15  C11  C08  109.13  3.000
 KUD  H15  C11  C10  108.17  3.000
 KUD  C08  C11  C10  112.30  3.000
 KUD  H15  C11  C14  108.93  3.000
 KUD  C10  C11  C14  103.73  3.000
 KUD  C08  C11  C14  114.32  3.000
 KUD  H16  O17  C09  109.97  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  CONST_14  H16  O17  C09  C08  180.00   0.0  0
 KUD  Var_01    C10  C12  C13  C14   27.47  30.0  1
 KUD  Var_02    C11  C14  C13  C12   -3.56  30.0  1
 KUD  Var_03    C06  C05  C07  C10   -9.92  30.0  2
 KUD  Var_04    O15  C09  C08  C11  -12.45  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  H9   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-2  C08  0.020
 KUD  plan-2  C09  0.020
 KUD  plan-2  O15  0.020
 KUD  plan-2  O17  0.020
 KUD  plan-2  H16  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

