# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 08:27:12 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: {(1S,2R)-2-[4-(carboxymethyl)benzene-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)c2ccc(CC(O)=O)cc2
#
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
 L67  L67  '{(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetic acid'  ligand  37  21  .  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_L67
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
 L67  C13  C  CH2    0  -0.436   1.7240   2.1348   0.8014
 L67  C15  C  CH2    0  -0.430   3.9398   1.1859   0.9754
 L67  C17  C  C      0   0.411   4.8665  -1.6583  -0.1572
 L67  C01  C  CR16   0  -0.255  -1.6370   0.3659  -1.5527
 L67  C02  C  CR16   0  -0.296  -2.9990   0.4313  -1.3285
 L67  C03  C  CR6    0   0.185  -3.5123   0.6268  -0.0458
 L67  C04  C  CR16   0  -0.297  -2.6073   0.7568   1.0043
 L67  C05  C  CR16   0  -0.280  -1.2405   0.6891   0.7876
 L67  C06  C  CR6    0  -0.033  -0.7308   0.4918  -0.4960
 L67  C08  C  C      0   0.426  -5.6179  -0.7236   0.4556
 L67  C09  C  C      0   0.392   0.7294   0.4166  -0.7794
 L67  C11  C  CH1    0  -0.396   1.6952   0.6389   0.3605
 L67  C12  C  CH1    0  -0.191   3.1508   0.2635   0.0492
 L67  C14  C  CH2    0  -0.437   3.2116   2.5171   0.8337
 L67  C16  C  CH2    0  -0.575   3.4406  -1.2170   0.2193
 L67  O10  O  O      0  -0.405   1.1164   0.2063  -1.9123
 L67  O18  O  O      0  -0.595  -4.8687  -1.7134   0.4055
 L67  O19  O  OC    -1  -0.620  -6.8409  -0.7119   0.6905
 L67  O20  O  O      0  -0.610   5.4627  -0.9944  -1.0291
 L67  O21  O  OC    -1  -0.628   5.3034  -2.6774   0.4180
 L67  H1   H  HCH2   0   0.238   1.1536   2.7814   0.1321
 L67  H2   H  HCH2   0   0.238   1.2737   2.2412   1.7890
 L67  H3   H  HCH2   0   0.203   3.8756   0.8256   2.0085
 L67  H4   H  HCH2   0   0.231   4.9960   1.2398   0.7099
 L67  H5   H  HCR6   0   0.252  -1.2682   0.2171  -2.5591
 L67  H6   H  HCR6   0   0.247  -3.6811   0.3337  -2.1649
 L67  H7   H  HCR6   0   0.249  -2.9761   0.9153   2.0109
 L67  H8   H  HCR6   0   0.255  -0.5779   0.7905   1.6368
 L67  H9   H  HCH2   0   0.249  -5.2086   1.3145   1.0501
 L67  H10  H  HCH2   0   0.250  -5.4949   1.1187  -0.6623
 L67  H11  H  HCH1   0   0.260   1.3605   0.0368   1.2123
 L67  H13  H  HCH1   0   0.214   3.3784   0.5542  -0.9799
 L67  H15  H  HCH2   0   0.220   3.4989   2.9871  -0.1102
 L67  H16  H  HCH2   0   0.231   3.4382   3.2286   1.6291
 L67  H17  H  HCH2   0   0.231   2.7489  -1.7950  -0.4072
 L67  H18  H  HCH2   0   0.202   3.2236  -1.5197   1.2498
 L67  C07  C  CH2    0  -0.702  -4.9841   0.6706   0.1953

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
 L67  C13  C11  single    1.560  0.020  1.560
 L67  C13  C14  single    1.536  0.020  1.536
 L67  C15  C12  single    1.527  0.020  1.527
 L67  C15  C14  single    1.524  0.020  1.524
 L67  C17  C16  single    1.539  0.020  1.539
 L67  C17  O20  deloc     1.248  0.020  1.248
 L67  C17  O21  deloc     1.249  0.020  1.249
 L67  C01  C02  aromatic  1.382  0.020  1.382
 L67  C01  C06  aromatic  1.398  0.020  1.398
 L67  C02  C03  aromatic  1.395  0.020  1.395
 L67  C03  C04  aromatic  1.392  0.020  1.392
 L67  C03  C07  single    1.492  0.020  1.492
 L67  C04  C05  aromatic  1.386  0.020  1.386
 L67  C05  C06  aromatic  1.395  0.020  1.395
 L67  C06  C09  single    1.489  0.020  1.489
 L67  C07  C08  single    1.553  0.020  1.553
 L67  C08  O18  deloc     1.242  0.020  1.242
 L67  C08  O19  deloc     1.245  0.020  1.245
 L67  C09  C11  single    1.511  0.020  1.511
 L67  C09  O10  double    1.215  0.020  1.215
 L67  C12  C16  single    1.518  0.020  1.518
 L67  C13  H1   single    0.970  0.020  1.090
 L67  C13  H2   single    0.970  0.020  1.090
 L67  C15  H3   single    0.970  0.020  1.090
 L67  C15  H4   single    0.970  0.020  1.090
 L67  C01  H5   single    0.930  0.020  1.080
 L67  C02  H6   single    0.930  0.020  1.080
 L67  C04  H7   single    0.930  0.020  1.080
 L67  C05  H8   single    0.930  0.020  1.080
 L67  C07  H9   single    0.970  0.020  1.090
 L67  C07  H10  single    0.970  0.020  1.090
 L67  C11  H11  single    0.970  0.020  1.090
 L67  C12  H13  single    0.970  0.020  1.090
 L67  C14  H15  single    0.970  0.020  1.090
 L67  C14  H16  single    0.970  0.020  1.090
 L67  C16  H17  single    0.970  0.020  1.090
 L67  C16  H18  single    0.970  0.020  1.090
 L67  C12  C11  single    1.535  0.020  1.535

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
 L67  H2   C13  H1   106.37  3.000
 L67  H2   C13  C14  110.88  3.000
 L67  H1   C13  C14  111.81  3.000
 L67  H2   C13  C11  109.99  3.000
 L67  H1   C13  C11  112.65  3.000
 L67  C14  C13  C11  105.21  3.000
 L67  H4   C15  H3   107.61  3.000
 L67  H4   C15  C14  113.39  3.000
 L67  H3   C15  C14  110.29  3.000
 L67  H4   C15  C12  112.50  3.000
 L67  H3   C15  C12  110.06  3.000
 L67  C14  C15  C12  102.97  3.000
 L67  O21  C17  O20  126.07  3.000
 L67  O21  C17  C16  116.44  3.000
 L67  O20  C17  C16  117.46  3.000
 L67  H5   C01  C06  119.64  3.000
 L67  H5   C01  C02  119.56  3.000
 L67  C06  C01  C02  120.80  3.000
 L67  H6   C02  C03  119.38  3.000
 L67  H6   C02  C01  119.39  3.000
 L67  C03  C02  C01  121.22  3.000
 L67  C07  C03  C04  121.10  3.000
 L67  C07  C03  C02  121.03  3.000
 L67  C04  C03  C02  117.86  3.000
 L67  H7   C04  C05  119.22  3.000
 L67  H7   C04  C03  119.54  3.000
 L67  C05  C04  C03  121.24  3.000
 L67  H8   C05  C06  120.78  3.000
 L67  H8   C05  C04  118.47  3.000
 L67  C06  C05  C04  120.75  3.000
 L67  C09  C06  C05  122.71  3.000
 L67  C09  C06  C01  119.16  3.000
 L67  C05  C06  C01  118.13  3.000
 L67  O19  C08  O18  127.39  3.000
 L67  O19  C08  C07  115.08  3.000
 L67  O18  C08  C07  117.53  3.000
 L67  O10  C09  C11  121.69  3.000
 L67  O10  C09  C06  119.88  3.000
 L67  C11  C09  C06  118.41  3.000
 L67  H11  C11  C12  108.23  3.000
 L67  C12  C11  C09  114.66  3.000
 L67  H11  C11  C09  108.09  3.000
 L67  C12  C11  C13  105.93  3.000
 L67  H11  C11  C13  108.24  3.000
 L67  C09  C11  C13  111.48  3.000
 L67  H13  C12  C16  108.97  3.000
 L67  H13  C12  C11  108.86  3.000
 L67  C16  C12  C11  113.38  3.000
 L67  C11  C12  C15  102.66  3.000
 L67  H13  C12  C15  107.62  3.000
 L67  C16  C12  C15  115.00  3.000
 L67  H16  C14  H15  107.13  3.000
 L67  H16  C14  C15  113.74  3.000
 L67  H15  C14  C15  109.29  3.000
 L67  H16  C14  C13  112.26  3.000
 L67  H15  C14  C13  110.09  3.000
 L67  C15  C14  C13  104.32  3.000
 L67  H18  C16  H17  105.46  3.000
 L67  H18  C16  C12  109.69  3.000
 L67  H17  C16  C12  109.22  3.000
 L67  H18  C16  C17  109.53  3.000
 L67  H17  C16  C17  107.04  3.000
 L67  C12  C16  C17  115.40  3.000
 L67  H10  C07  H9   106.01  3.000
 L67  H10  C07  C08  107.96  3.000
 L67  H9   C07  C08  108.28  3.000
 L67  H10  C07  C03  110.24  3.000
 L67  H9   C07  C03  110.25  3.000
 L67  C08  C07  C03  113.77  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
 L67  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 L67  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 L67  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 L67  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 L67  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 L67  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 L67  CONST_07  C07  C03  C02  C01  180.00   0.0  0
 L67  CONST_08  C09  C06  C01  C02  180.00   0.0  0
 L67  CONST_09  C09  C06  C05  C04  180.00   0.0  0
 L67  CONST_10  C07  C03  C04  C05  180.00   0.0  0
 L67  CONST_11  H8   C05  C06  C01  180.00   0.0  0
 L67  CONST_12  H7   C04  C03  C02  180.00   0.0  0
 L67  CONST_13  H5   C01  C02  C03  180.00   0.0  0
 L67  CONST_14  H6   C02  C03  C04  180.00   0.0  0
 L67  Var_01    C12  C15  C14  C13   40.41  30.0  1
 L67  Var_02    C11  C13  C14  C15  -21.89  30.0  1
 L67  Var_03    C11  C09  C06  C01  176.32  30.0  2
 L67  Var_04    C08  C07  C03  C02   87.85  30.0  2
 L67  Var_05    O18  C08  C07  C03   -1.76  30.0  3
 L67  Var_06    O20  C17  C16  C12  -28.60  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
 L67  chir_01  C11  C13  C09  C12  negativ
 L67  chir_02  C12  C15  C16  C11  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
 L67  plan-1  C01  0.020
 L67  plan-1  C02  0.020
 L67  plan-1  C03  0.020
 L67  plan-1  C04  0.020
 L67  plan-1  C05  0.020
 L67  plan-1  C06  0.020
 L67  plan-1  C09  0.020
 L67  plan-1  H5   0.020
 L67  plan-1  H6   0.020
 L67  plan-1  H7   0.020
 L67  plan-1  H8   0.020
 L67  plan-1  C07  0.020
 L67  plan-2  C17  0.020
 L67  plan-2  C16  0.020
 L67  plan-2  O20  0.020
 L67  plan-2  O21  0.020
 L67  plan-3  C08  0.020
 L67  plan-3  O18  0.020
 L67  plan-3  O19  0.020
 L67  plan-3  C07  0.020
 L67  plan-4  C06  0.020
 L67  plan-4  C09  0.020
 L67  plan-4  C11  0.020
 L67  plan-4  O10  0.020

