# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 03:05:10 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [(1S,2R)-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
 KSJ  KSJ  '[(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid'  ligand  33  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_KSJ
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
 KSJ  C11  C  CH1    0  -0.393   0.4122  -0.8670  -0.0177
 KSJ  C12  C  CH1    0  -0.189   1.8567  -0.4215   0.2274
 KSJ  C14  C  CH2    0  -0.440   1.7619  -2.7963   0.6894
 KSJ  C15  C  CH2    0  -0.438   2.6198  -1.7262   0.0089
 KSJ  C01  C  CR16   0  -0.341  -4.2927   0.8503  -0.0129
 KSJ  C02  C  CR16   0  -0.234  -4.5982   0.0159  -1.0685
 KSJ  C03  C  CR16   0  -0.269  -3.6304  -0.8235  -1.6204
 KSJ  C04  C  CR16   0  -0.295  -2.3541  -0.8095  -1.1009
 KSJ  C05  C  CR6    0  -0.165  -2.0053   0.0266  -0.0306
 KSJ  C06  C  CR6    0   0.371  -3.0014   0.8653   0.5208
 KSJ  C07  C  C      0   0.465  -0.6449   0.0512   0.5281
 KSJ  C08  C  CH2    0  -0.574   2.2933   0.7239  -0.6693
 KSJ  C09  C  C      0   0.412   3.7391   1.2093  -0.4661
 KSJ  C13  C  CH2    0  -0.431   0.3098  -2.2712   0.6311
 KSJ  O10  O  OH1    0  -0.625  -2.7594   1.6816   1.5424
 KSJ  O16  O  O      0  -0.607   4.2423   1.0611   0.6653
 KSJ  O17  O  O      0  -0.464  -0.3833   0.7971   1.4715
 KSJ  O18  O  OC    -1  -0.628   4.2852   1.7505  -1.4508
 KSJ  H1   H  HCH1   0   0.262   0.2803  -0.9760  -1.0977
 KSJ  H2   H  HCH1   0   0.216   1.9707  -0.1267   1.2749
 KSJ  H3   H  HCH2   0   0.232   1.8615  -3.7708   0.2107
 KSJ  H4   H  HCH2   0   0.228   2.0678  -2.9236   1.7288
 KSJ  H5   H  HCH2   0   0.207   2.6957  -1.9285  -1.0649
 KSJ  H6   H  HCH2   0   0.237   3.6357  -1.6771   0.4004
 KSJ  H9   H  HCR6   0   0.262  -3.8753  -1.4748  -2.4478
 KSJ  H10  H  HCR6   0   0.266  -1.6110  -1.4620  -1.5382
 KSJ  H11  H  HCH2   0   0.204   2.1469   0.4429  -1.7178
 KSJ  H12  H  HCH2   0   0.232   1.6371   1.5884  -0.5044
 KSJ  H13  H  HCH2   0   0.239  -0.1139  -2.2050   1.6349
 KSJ  H14  H  HCH2   0   0.242  -0.3483  -2.9218   0.0545
 KSJ  H15  H  HOH1   0   0.477  -1.8110   1.5626   1.7873
 KSJ  H7   H  HCR6   0   0.270  -5.0453   1.5009   0.4139
 KSJ  H8   H  HCR6   0   0.269  -5.6033   0.0178  -1.4700

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
 KSJ  O10  C06  single    1.330  0.020  1.330
 KSJ  O16  C09  deloc     1.247  0.020  1.247
 KSJ  O17  C07  double    1.231  0.020  1.231
 KSJ  C12  C15  single    1.527  0.020  1.527
 KSJ  C12  C08  single    1.519  0.020  1.519
 KSJ  C12  C11  single    1.531  0.020  1.531
 KSJ  C09  C08  single    1.539  0.020  1.539
 KSJ  C09  O18  deloc     1.249  0.020  1.249
 KSJ  C06  C01  aromatic  1.397  0.020  1.397
 KSJ  C06  C05  aromatic  1.414  0.020  1.414
 KSJ  C07  C05  single    1.471  0.020  1.471
 KSJ  C07  C11  single    1.503  0.020  1.503
 KSJ  C15  C14  single    1.531  0.020  1.531
 KSJ  C14  C13  single    1.545  0.020  1.545
 KSJ  C01  C02  aromatic  1.380  0.020  1.380
 KSJ  C05  C04  aromatic  1.402  0.020  1.402
 KSJ  C11  C13  single    1.550  0.020  1.550
 KSJ  C02  C03  aromatic  1.395  0.020  1.395
 KSJ  C04  C03  aromatic  1.378  0.020  1.378
 KSJ  C11  H1   single    0.970  0.020  1.090
 KSJ  C12  H2   single    0.970  0.020  1.090
 KSJ  C14  H3   single    0.970  0.020  1.090
 KSJ  C14  H4   single    0.970  0.020  1.090
 KSJ  C15  H5   single    0.970  0.020  1.090
 KSJ  C15  H6   single    0.970  0.020  1.090
 KSJ  C01  H7   single    0.930  0.020  1.080
 KSJ  C02  H8   single    0.930  0.020  1.080
 KSJ  C03  H9   single    0.930  0.020  1.080
 KSJ  C04  H10  single    0.930  0.020  1.080
 KSJ  C08  H11  single    0.970  0.020  1.090
 KSJ  C08  H12  single    0.970  0.020  1.090
 KSJ  C13  H13  single    0.970  0.020  1.090
 KSJ  C13  H14  single    0.970  0.020  1.090
 KSJ  O10  H15  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
 KSJ  H1   C11  C13  108.37  3.000
 KSJ  H1   C11  C07  109.56  3.000
 KSJ  C13  C11  C07  110.79  3.000
 KSJ  H1   C11  C12  107.51  3.000
 KSJ  C13  C11  C12  105.00  3.000
 KSJ  C07  C11  C12  115.32  3.000
 KSJ  H2   C12  C08  109.40  3.000
 KSJ  H2   C12  C15  108.36  3.000
 KSJ  C08  C12  C15  114.59  3.000
 KSJ  H2   C12  C11  109.26  3.000
 KSJ  C08  C12  C11  113.33  3.000
 KSJ  C15  C12  C11  101.53  3.000
 KSJ  H4   C14  H3   106.76  3.000
 KSJ  H4   C14  C13  109.82  3.000
 KSJ  H3   C14  C13  111.90  3.000
 KSJ  H4   C14  C15  110.36  3.000
 KSJ  H3   C14  C15  112.23  3.000
 KSJ  C13  C14  C15  105.81  3.000
 KSJ  H6   C15  H5   107.21  3.000
 KSJ  H6   C15  C14  113.22  3.000
 KSJ  H5   C15  C14  110.21  3.000
 KSJ  H6   C15  C12  112.08  3.000
 KSJ  H5   C15  C12  109.43  3.000
 KSJ  C14  C15  C12  104.68  3.000
 KSJ  H7   C01  C06  119.04  3.000
 KSJ  H7   C01  C02  120.74  3.000
 KSJ  C06  C01  C02  120.22  3.000
 KSJ  H8   C02  C03  119.90  3.000
 KSJ  H8   C02  C01  119.24  3.000
 KSJ  C03  C02  C01  120.86  3.000
 KSJ  H9   C03  C04  120.29  3.000
 KSJ  H9   C03  C02  120.54  3.000
 KSJ  C04  C03  C02  119.16  3.000
 KSJ  H10  C04  C05  119.84  3.000
 KSJ  H10  C04  C03  118.55  3.000
 KSJ  C05  C04  C03  121.62  3.000
 KSJ  C07  C05  C06  119.56  3.000
 KSJ  C07  C05  C04  122.01  3.000
 KSJ  C06  C05  C04  118.43  3.000
 KSJ  O10  C06  C05  122.38  3.000
 KSJ  C05  C06  C01  119.71  3.000
 KSJ  O10  C06  C01  117.92  3.000
 KSJ  O17  C07  C05  119.86  3.000
 KSJ  C05  C07  C11  120.16  3.000
 KSJ  O17  C07  C11  119.94  3.000
 KSJ  H12  C08  H11  105.42  3.000
 KSJ  H12  C08  C09  107.06  3.000
 KSJ  H11  C08  C09  109.45  3.000
 KSJ  H12  C08  C12  109.47  3.000
 KSJ  H11  C08  C12  109.47  3.000
 KSJ  C09  C08  C12  115.47  3.000
 KSJ  O18  C09  O16  126.17  3.000
 KSJ  O18  C09  C08  116.32  3.000
 KSJ  O16  C09  C08  117.48  3.000
 KSJ  H14  C13  H13  106.75  3.000
 KSJ  H14  C13  C14  112.61  3.000
 KSJ  H13  C13  C14  110.53  3.000
 KSJ  H14  C13  C11  111.04  3.000
 KSJ  H13  C13  C11  110.83  3.000
 KSJ  C14  C13  C11  105.16  3.000
 KSJ  H15  O10  C06  106.95  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
 KSJ  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 KSJ  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 KSJ  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 KSJ  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 KSJ  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 KSJ  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 KSJ  CONST_07  C07  C05  C06  C01  180.00   0.0  0
 KSJ  CONST_08  O10  C06  C01  C02  180.00   0.0  0
 KSJ  CONST_09  C07  C05  C04  C03  180.00   0.0  0
 KSJ  CONST_10  O10  C06  C05  C04  180.00   0.0  0
 KSJ  CONST_11  H9   C03  C02  C01  180.00   0.0  0
 KSJ  CONST_12  H10  C04  C03  C02  180.00   0.0  0
 KSJ  CONST_13  H7   C01  C02  C03  180.00   0.0  0
 KSJ  CONST_14  H8   C02  C03  C04  180.00   0.0  0
 KSJ  Var_01    C15  C14  C13  C11   -3.16  30.0  1
 KSJ  Var_02    C13  C14  C15  C12   27.78  30.0  1
 KSJ  Var_03    C06  C05  C07  C11  177.98  30.0  2
 KSJ  Var_04    O16  C09  C08  C12  -27.91  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
 KSJ  chir_01  C11  C12  C07  C13  positiv
 KSJ  chir_02  C12  C11  C08  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
 KSJ  plan-1  C01  0.020
 KSJ  plan-1  C02  0.020
 KSJ  plan-1  C03  0.020
 KSJ  plan-1  C04  0.020
 KSJ  plan-1  C05  0.020
 KSJ  plan-1  C06  0.020
 KSJ  plan-1  C07  0.020
 KSJ  plan-1  O10  0.020
 KSJ  plan-1  H9   0.020
 KSJ  plan-1  H10  0.020
 KSJ  plan-1  H7   0.020
 KSJ  plan-1  H8   0.020
 KSJ  plan-2  C08  0.020
 KSJ  plan-2  C09  0.020
 KSJ  plan-2  O16  0.020
 KSJ  plan-2  O18  0.020
 KSJ  plan-3  C11  0.020
 KSJ  plan-3  C05  0.020
 KSJ  plan-3  C07  0.020
 KSJ  plan-3  O17  0.020

