# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:23:02 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: [(1R,2R)-2-(2-methoxybenzene-1-carbonyl)cyclopentyl]propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C(=O)[C@@H]2CCC[C@H]2C(C(O)=O)C(O)=O
#
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
 L6J  L6J  '[(1R,2R)-2-(2-methoxybenzene-1-carbonyl)cyclopentyl]propanedioic acid'  ligand  38  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L6J
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
 L6J  C10  C  CH1    0  -0.377   0.3940   1.3937  -0.0978
 L6J  C13  C  CH2    0  -0.451   1.9040   3.2548  -0.0905
 L6J  C15  C  CH1    0  -0.475   2.1673  -0.4406   0.2905
 L6J  C17  C  C      0   0.421   3.5532  -0.9626  -0.1085
 L6J  C22  C  CH3    0  -0.439  -3.5896  -2.3949  -1.4432
 L6J  C01  C  C      0   0.379  -3.0052  -0.4206  -0.2676
 L6J  C02  C  C1     0  -0.397  -4.2051  -0.4489   0.4437
 L6J  C03  C  C1     0  -0.242  -4.4784   0.5123   1.4073
 L6J  C04  C  C1     0  -0.274  -3.5582   1.5074   1.6882
 L6J  C05  C  C1     0  -0.298  -2.3569   1.5224   0.9942
 L6J  C06  C  C      0  -0.066  -2.0572   0.5862   0.0091
 L6J  C08  C  C      0   0.428  -0.7816   0.7029  -0.7551
 L6J  C11  C  CH1    0  -0.180   1.7638   0.8120  -0.4833
 L6J  C12  C  CH2    0  -0.429   0.5034   2.8595  -0.5473
 L6J  C14  C  CH2    0  -0.432   2.7515   1.9855  -0.2794
 L6J  C16  C  C      0   0.429   1.1127  -1.5619   0.1490
 L6J  O09  O  O      0  -0.422  -0.7182   0.3605  -1.9187
 L6J  O18  O  O      0  -0.620   3.9440  -0.7660  -1.2784
 L6J  O19  O  OC    -1  -0.640   4.1970  -1.5638   0.7810
 L6J  O20  O  O      0  -0.604   1.4120  -2.5607  -0.5346
 L6J  O21  O  OC    -1  -0.598   0.0253  -1.3731   0.7360
 L6J  H1   H  HCH1   0   0.235   0.2877   1.3623   0.9896
 L6J  H3   H  HCH2   0   0.227   2.2938   4.1150  -0.6372
 L6J  H4   H  HCH2   0   0.219   1.8739   3.5375   0.9645
 L6J  H5   H  HCH1   0   0.187   2.1967  -0.1620   1.3524
 L6J  H6   H  HCH3   0   0.258  -3.1317  -3.0061  -2.2174
 L6J  H7   H  HCH3   0   0.226  -3.7416  -3.0121  -0.5537
 L6J  H8   H  HCH3   0   0.226  -4.5630  -2.0495  -1.8019
 L6J  H10  H  H      0   0.260  -5.4212   0.4725   1.9377
 L6J  H11  H  H      0   0.252  -3.7643   2.2599   2.4372
 L6J  H12  H  H      0   0.261  -1.6392   2.2989   1.2217
 L6J  H13  H  HCH1   0   0.209   1.7348   0.5704  -1.5477
 L6J  H15  H  HCH2   0   0.222   0.4249   2.9155  -1.6372
 L6J  H16  H  HCH2   0   0.234  -0.2765   3.5030  -0.1340
 L6J  H17  H  HCH2   0   0.222   3.4205   2.0691  -1.1357
 L6J  H18  H  HCH2   0   0.214   3.3908   1.8142   0.5905
 L6J  O07  O  O2     0  -0.442  -2.6986  -1.3264  -1.2028
 L6J  H9   H  H      0   0.279  -4.9416  -1.2180   0.2569

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
 L6J  C10  C08  single    1.514  0.020  1.514
 L6J  C10  C12  single    1.537  0.020  1.537
 L6J  C13  C12  single    1.525  0.020  1.525
 L6J  C13  C14  single    1.538  0.020  1.538
 L6J  C15  C17  single    1.534  0.020  1.534
 L6J  C15  C11  single    1.527  0.020  1.527
 L6J  C15  C16  single    1.546  0.020  1.546
 L6J  C17  O18  deloc     1.249  0.020  1.249
 L6J  C17  O19  deloc     1.252  0.020  1.252
 L6J  C22  O07  single    1.412  0.020  1.412
 L6J  C01  C02  aromatic  1.395  0.020  1.395
 L6J  C01  C06  aromatic  1.410  0.020  1.410
 L6J  C01  O07  single    1.338  0.020  1.338
 L6J  C02  C03  aromatic  1.388  0.020  1.388
 L6J  C03  C04  aromatic  1.384  0.020  1.384
 L6J  C04  C05  aromatic  1.387  0.020  1.387
 L6J  C05  C06  aromatic  1.392  0.020  1.392
 L6J  C06  C08  single    1.492  0.020  1.492
 L6J  C08  O09  double    1.215  0.020  1.215
 L6J  C11  C14  single    1.547  0.020  1.547
 L6J  C16  O20  deloc     1.247  0.020  1.247
 L6J  C16  O21  deloc     1.250  0.020  1.250
 L6J  C10  H1   single    0.970  0.020  1.090
 L6J  C13  H3   single    0.970  0.020  1.090
 L6J  C13  H4   single    0.970  0.020  1.090
 L6J  C15  H5   single    0.970  0.020  1.090
 L6J  C22  H6   single    0.970  0.020  1.090
 L6J  C22  H7   single    0.970  0.020  1.090
 L6J  C22  H8   single    0.970  0.020  1.090
 L6J  C02  H9   single    0.930  0.020  1.080
 L6J  C03  H10  single    0.930  0.020  1.080
 L6J  C04  H11  single    0.930  0.020  1.080
 L6J  C05  H12  single    0.930  0.020  1.080
 L6J  C11  H13  single    0.970  0.020  1.090
 L6J  C12  H15  single    0.970  0.020  1.090
 L6J  C12  H16  single    0.970  0.020  1.090
 L6J  C14  H17  single    0.970  0.020  1.090
 L6J  C14  H18  single    0.970  0.020  1.090
 L6J  C10  C11  single    1.537  0.020  1.537

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
 L6J  H1   C10  C12  108.98  3.000
 L6J  H1   C10  C11  108.98  3.000
 L6J  C12  C10  C11  102.95  3.000
 L6J  C11  C10  C08  114.23  3.000
 L6J  H1   C10  C08  110.08  3.000
 L6J  C12  C10  C08  111.32  3.000
 L6J  H4   C13  H3   106.85  3.000
 L6J  H4   C13  C14  110.33  3.000
 L6J  H3   C13  C14  113.09  3.000
 L6J  H4   C13  C12  109.32  3.000
 L6J  H3   C13  C12  112.47  3.000
 L6J  C14  C13  C12  104.79  3.000
 L6J  H5   C15  C16  106.90  3.000
 L6J  H5   C15  C11  106.80  3.000
 L6J  C16  C15  C11  111.62  3.000
 L6J  H5   C15  C17  108.28  3.000
 L6J  C16  C15  C17  110.23  3.000
 L6J  C11  C15  C17  112.72  3.000
 L6J  O19  C17  O18  125.46  3.000
 L6J  O19  C17  C15  116.31  3.000
 L6J  O18  C17  C15  118.22  3.000
 L6J  H8   C22  H7   108.75  3.000
 L6J  H8   C22  H6   108.60  3.000
 L6J  H7   C22  H6   108.70  3.000
 L6J  H8   C22  O07  112.25  3.000
 L6J  H7   C22  O07  112.12  3.000
 L6J  H6   C22  O07  106.31  3.000
 L6J  O07  C01  C06  117.81  3.000
 L6J  O07  C01  C02  122.68  3.000
 L6J  C06  C01  C02  119.51  3.000
 L6J  H9   C02  C03  118.58  3.000
 L6J  H9   C02  C01  120.81  3.000
 L6J  C03  C02  C01  120.61  3.000
 L6J  H10  C03  C04  120.40  3.000
 L6J  H10  C03  C02  119.09  3.000
 L6J  C04  C03  C02  120.52  3.000
 L6J  H11  C04  C05  120.26  3.000
 L6J  H11  C04  C03  120.93  3.000
 L6J  C05  C04  C03  118.81  3.000
 L6J  H12  C05  C06  119.27  3.000
 L6J  H12  C05  C04  118.49  3.000
 L6J  C06  C05  C04  122.23  3.000
 L6J  C08  C06  C05  119.62  3.000
 L6J  C08  C06  C01  122.02  3.000
 L6J  C05  C06  C01  118.32  3.000
 L6J  O09  C08  C06  120.89  3.000
 L6J  O09  C08  C10  120.27  3.000
 L6J  C06  C08  C10  118.52  3.000
 L6J  H13  C11  C14  108.25  3.000
 L6J  H13  C11  C15  108.64  3.000
 L6J  C14  C11  C15  112.75  3.000
 L6J  H13  C11  C10  107.73  3.000
 L6J  C14  C11  C10  104.40  3.000
 L6J  C15  C11  C10  114.77  3.000
 L6J  H16  C12  H15  107.19  3.000
 L6J  H16  C12  C13  112.93  3.000
 L6J  H15  C12  C13  110.54  3.000
 L6J  H16  C12  C10  113.60  3.000
 L6J  H15  C12  C10  109.57  3.000
 L6J  C13  C12  C10  103.00  3.000
 L6J  H18  C14  H17  106.16  3.000
 L6J  H18  C14  C11  111.06  3.000
 L6J  H17  C14  C11  110.28  3.000
 L6J  H18  C14  C13  110.72  3.000
 L6J  H17  C14  C13  111.80  3.000
 L6J  C11  C14  C13  106.88  3.000
 L6J  O21  C16  O20  125.96  3.000
 L6J  O21  C16  C15  116.16  3.000
 L6J  O20  C16  C15  117.87  3.000
 L6J  C01  O07  C22  119.13  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
 L6J  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 L6J  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 L6J  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 L6J  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 L6J  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 L6J  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 L6J  CONST_07  C08  C06  C01  C02   180.00   0.0  0
 L6J  CONST_08  O07  C01  C02  C03   180.00   0.0  0
 L6J  CONST_09  C08  C06  C05  C04   180.00   0.0  0
 L6J  CONST_10  O07  C01  C06  C05   180.00   0.0  0
 L6J  CONST_11  H10  C03  C02  C01   180.00   0.0  0
 L6J  CONST_12  H12  C05  C06  C01   180.00   0.0  0
 L6J  CONST_13  H11  C04  C03  C02   180.00   0.0  0
 L6J  CONST_14  H9   C02  C03  C04   180.00   0.0  0
 L6J  Var_01    C14  C13  C12  C10    35.25  30.0  1
 L6J  Var_02    C12  C13  C14  C11   -14.37  30.0  1
 L6J  Var_03    C01  C06  C08  C10  -155.88  30.0  2
 L6J  Var_04    C02  C01  O07  C22    -3.11  30.0  1
 L6J  Var_05    O18  C17  C15  C11   -30.01  30.0  3
 L6J  Var_06    O20  C16  C15  C11   109.22  30.0  3
 L6J  Var_07    H6   C22  O07  C01  -178.88  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
 L6J  chir_01  C10  C08  C12  C11  positiv
 L6J  chir_02  C11  C10  C14  C15  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
 L6J  plan-1  C01  0.020
 L6J  plan-1  C02  0.020
 L6J  plan-1  C03  0.020
 L6J  plan-1  C04  0.020
 L6J  plan-1  C05  0.020
 L6J  plan-1  C06  0.020
 L6J  plan-1  C08  0.020
 L6J  plan-1  H10  0.020
 L6J  plan-1  H11  0.020
 L6J  plan-1  H12  0.020
 L6J  plan-1  O07  0.020
 L6J  plan-1  H9   0.020
 L6J  plan-2  C15  0.020
 L6J  plan-2  C17  0.020
 L6J  plan-2  O18  0.020
 L6J  plan-2  O19  0.020
 L6J  plan-3  C15  0.020
 L6J  plan-3  C16  0.020
 L6J  plan-3  O20  0.020
 L6J  plan-3  O21  0.020
 L6J  plan-4  C10  0.020
 L6J  plan-4  C06  0.020
 L6J  plan-4  C08  0.020
 L6J  plan-4  O09  0.020

