# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 09:20:01 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H]1CCC[C@@H]1C(=O)c2ccccc2O
#
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
 KSP  KSP  '[(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid'  ligand  34  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KSP
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
 KSP  C01  C  CR16  0  -0.340   4.3269  -0.7243  -0.4594
 KSP  C02  C  CR16  0  -0.233   4.6051  -0.8134   0.8889
 KSP  C03  C  CR16  0  -0.270   3.6047  -0.6149   1.8407
 KSP  C04  C  CR16  0  -0.288   2.3254  -0.3240   1.4191
 KSP  C05  C  CR6   0  -0.164   2.0058  -0.2237   0.0577
 KSP  C06  C  CR6   0   0.368   3.0310  -0.4313  -0.8929
 KSP  C11  C  CR15  0  -0.402  -0.4238   0.4137   0.6153
 KSP  C12  C  CR15  0  -0.216  -1.8486   0.4529   0.0460
 KSP  C13  C  CH2   0  -0.436  -0.1917   1.8136   1.2641
 KSP  C14  C  CH2   0  -0.440  -1.5423   2.5374   1.1587
 KSP  C15  C  CH2   0  -0.435  -2.5635   1.4194   0.9878
 KSP  C07  C  C     0   0.466   0.6445   0.0957  -0.3988
 KSP  C08  C  CH2   0  -0.584  -2.4650  -0.9307  -0.0562
 KSP  C09  C  C     0   0.554  -3.8103  -0.9536  -0.7289
 KSP  O10  O  OH1   0  -0.624   2.8182  -0.3570  -2.2040
 KSP  O16  O  OH1   0  -0.597  -4.4461  -2.1032  -0.5223
 KSP  O17  O  O     0  -0.456   0.3934   0.1363  -1.6010
 KSP  O18  O  O     0  -0.443  -4.2690  -0.0649  -1.4031
 KSP  H1   H  HCR6  0   0.270   5.1042  -0.8802  -1.1968
 KSP  H2   H  HCR6  0   0.269   5.6138  -1.0438   1.2064
 KSP  H3   H  HCR6  0   0.262   3.8277  -0.6908   2.8958
 KSP  H4   H  HCR6  0   0.268   1.5551  -0.1776   2.1638
 KSP  H5   H  HCR5  0   0.281  -0.3855  -0.3434   1.4055
 KSP  H6   H  HCR5  0   0.245  -1.8182   0.9087  -0.9471
 KSP  H8   H  HCH2  0   0.247   0.6045   2.3747   0.7724
 KSP  H9   H  HCH2  0   0.240  -1.7367   3.1745   2.0220
 KSP  H10  H  HCH2  0   0.229  -1.5548   3.1782   0.2744
 KSP  H11  H  HCH2  0   0.243  -3.5177   1.7674   0.5918
 KSP  H12  H  HCH2  0   0.218  -2.7639   0.9313   1.9477
 KSP  H13  H  HCH2  0   0.293  -1.8174  -1.5985  -0.6362
 KSP  H14  H  HCH2  0   0.272  -2.5491  -1.3886   0.9338
 KSP  H15  H  HOH1  0   0.478   1.8625  -0.1586  -2.3354
 KSP  H16  H  HOH1  0   0.478  -5.2884  -2.1032  -1.0011
 KSP  H7   H  HCH2  0   0.247   0.1101   1.6929   2.3047

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
 KSP  O17  C07  double    1.229  0.020  1.229
 KSP  O10  C06  single    1.330  0.020  1.330
 KSP  O18  C09  double    1.206  0.020  1.206
 KSP  C07  C11  single    1.507  0.020  1.507
 KSP  C07  C05  single    1.471  0.020  1.471
 KSP  C09  C08  single    1.504  0.020  1.504
 KSP  C09  O16  single    1.330  0.020  1.330
 KSP  C08  C12  single    1.518  0.020  1.518
 KSP  C11  C12  single    1.535  0.020  1.535
 KSP  C11  C13  single    1.560  0.020  1.560
 KSP  C06  C05  aromatic  1.413  0.020  1.413
 KSP  C06  C01  aromatic  1.398  0.020  1.398
 KSP  C12  C15  single    1.527  0.020  1.527
 KSP  C05  C04  aromatic  1.402  0.020  1.402
 KSP  C13  C14  single    1.536  0.020  1.536
 KSP  C01  C02  aromatic  1.380  0.020  1.380
 KSP  C15  C14  single    1.524  0.020  1.524
 KSP  C04  C03  aromatic  1.378  0.020  1.378
 KSP  C02  C03  aromatic  1.395  0.020  1.395
 KSP  C01  H1   single    0.930  0.020  1.080
 KSP  C02  H2   single    0.930  0.020  1.080
 KSP  C03  H3   single    0.930  0.020  1.080
 KSP  C04  H4   single    0.930  0.020  1.080
 KSP  C11  H5   single    0.970  0.020  1.090
 KSP  C12  H6   single    0.970  0.020  1.090
 KSP  C13  H7   single    0.970  0.020  1.090
 KSP  C13  H8   single    0.970  0.020  1.090
 KSP  C14  H9   single    0.970  0.020  1.090
 KSP  C14  H10  single    0.970  0.020  1.090
 KSP  C15  H11  single    0.970  0.020  1.090
 KSP  C15  H12  single    0.970  0.020  1.090
 KSP  C08  H13  single    0.970  0.020  1.090
 KSP  C08  H14  single    0.970  0.020  1.090
 KSP  O10  H15  single    0.850  0.020  0.980
 KSP  O16  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
 KSP  H1   C01  C06  118.99  3.000
 KSP  H1   C01  C02  120.77  3.000
 KSP  C06  C01  C02  120.24  3.000
 KSP  H2   C02  C03  119.89  3.000
 KSP  H2   C02  C01  119.24  3.000
 KSP  C03  C02  C01  120.87  3.000
 KSP  H3   C03  C04  120.32  3.000
 KSP  H3   C03  C02  120.53  3.000
 KSP  C04  C03  C02  119.14  3.000
 KSP  H4   C04  C05  119.78  3.000
 KSP  H4   C04  C03  118.63  3.000
 KSP  C05  C04  C03  121.59  3.000
 KSP  C07  C05  C06  119.64  3.000
 KSP  C06  C05  C04  118.50  3.000
 KSP  C07  C05  C04  121.86  3.000
 KSP  O10  C06  C05  122.59  3.000
 KSP  C05  C06  C01  119.65  3.000
 KSP  O10  C06  C01  117.76  3.000
 KSP  H5   C11  C07  108.35  3.000
 KSP  H5   C11  C13  108.37  3.000
 KSP  C07  C11  C13  111.33  3.000
 KSP  H5   C11  C12  108.53  3.000
 KSP  C13  C11  C12  105.63  3.000
 KSP  C07  C11  C12  114.45  3.000
 KSP  H6   C12  C08  109.28  3.000
 KSP  H6   C12  C15  108.02  3.000
 KSP  C08  C12  C15  115.35  3.000
 KSP  H6   C12  C11  108.77  3.000
 KSP  C15  C12  C11  102.82  3.000
 KSP  C08  C12  C11  112.25  3.000
 KSP  H8   C13  H7   106.56  3.000
 KSP  H8   C13  C14  111.62  3.000
 KSP  H7   C13  C14  111.17  3.000
 KSP  H8   C13  C11  112.49  3.000
 KSP  H7   C13  C11  109.80  3.000
 KSP  C14  C13  C11  105.27  3.000
 KSP  H10  C14  H9   107.23  3.000
 KSP  H10  C14  C15  109.39  3.000
 KSP  H9   C14  C15  113.45  3.000
 KSP  H10  C14  C13  110.00  3.000
 KSP  H9   C14  C13  112.20  3.000
 KSP  C15  C14  C13  104.55  3.000
 KSP  H12  C15  H11  107.49  3.000
 KSP  H12  C15  C14  110.56  3.000
 KSP  H11  C15  C14  113.15  3.000
 KSP  H12  C15  C12  110.13  3.000
 KSP  H11  C15  C12  112.81  3.000
 KSP  C14  C15  C12  102.69  3.000
 KSP  O17  C07  C11  120.43  3.000
 KSP  C11  C07  C05  119.55  3.000
 KSP  O17  C07  C05  119.99  3.000
 KSP  H14  C08  H13  105.62  3.000
 KSP  H14  C08  C09  109.24  3.000
 KSP  H13  C08  C09  106.41  3.000
 KSP  H14  C08  C12  110.59  3.000
 KSP  H13  C08  C12  110.54  3.000
 KSP  C09  C08  C12  114.02  3.000
 KSP  O18  C09  O16  122.82  3.000
 KSP  O16  C09  C08  111.79  3.000
 KSP  O18  C09  C08  125.37  3.000
 KSP  H15  O10  C06  107.34  3.000
 KSP  H16  O16  C09  109.81  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
 KSP  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 KSP  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 KSP  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 KSP  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 KSP  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 KSP  CONST_06  C06  C01  C02  C03    0.00   0.0  0
 KSP  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 KSP  CONST_08  O10  C06  C01  C02  180.00   0.0  0
 KSP  CONST_09  C07  C05  C04  C03  180.00   0.0  0
 KSP  CONST_10  O10  C06  C05  C04  180.00   0.0  0
 KSP  CONST_11  H3   C03  C02  C01  180.00   0.0  0
 KSP  CONST_12  H4   C04  C03  C02  180.00   0.0  0
 KSP  CONST_13  H1   C01  C02  C03  180.00   0.0  0
 KSP  CONST_14  H2   C02  C03  C04  180.00   0.0  0
 KSP  CONST_15  H16  O16  C09  C08  180.00   0.0  0
 KSP  Var_01    C15  C14  C13  C11   21.16  30.0  1
 KSP  Var_02    C13  C14  C15  C12  -40.05  30.0  1
 KSP  Var_03    C11  C07  C05  C04    4.06  30.0  2
 KSP  Var_04    O18  C09  C08  C12   16.23  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
 KSP  chir_01  C11  C07  C12  C13  positiv
 KSP  chir_02  C12  C08  C11  C15  positiv

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
 KSP  plan-1  C01  0.020
 KSP  plan-1  C02  0.020
 KSP  plan-1  C03  0.020
 KSP  plan-1  C04  0.020
 KSP  plan-1  C05  0.020
 KSP  plan-1  C06  0.020
 KSP  plan-1  C07  0.020
 KSP  plan-1  O10  0.020
 KSP  plan-1  H1   0.020
 KSP  plan-1  H2   0.020
 KSP  plan-1  H3   0.020
 KSP  plan-1  H4   0.020
 KSP  plan-2  C08  0.020
 KSP  plan-2  C09  0.020
 KSP  plan-2  O16  0.020
 KSP  plan-2  O18  0.020
 KSP  plan-2  H16  0.020
 KSP  plan-3  C05  0.020
 KSP  plan-3  C11  0.020
 KSP  plan-3  C07  0.020
 KSP  plan-3  O17  0.020

