# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:27:19 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: {(1R,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1ccc(cc1)C(=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
 VJS  VJS  "{(1R,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}propanedioic acid"  ligand  39  24  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VJS
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
 VJS  C12  C  C      0   0.414  -1.6086  -33.0748  20.6699
 VJS  C15  C  CR6    0  -0.010   2.1145  -32.5902  21.8809
 VJS  C16  C  CR16   0  -0.293   2.2379  -32.7573  23.2600
 VJS  C17  C  CR16   0  -0.282   2.9404  -31.8423  24.0272
 VJS  C18  C  CR16   0  -0.260   2.7246  -31.4771  21.2981
 VJS  C19  C  CR16   0  -0.298   3.4162  -30.5599  22.0675
 VJS  C20  C  CR6    0   0.118   3.5415  -30.7261  23.4476
 VJS  C21  C  CH2    0  -0.612   4.2427  -29.7112  24.2946
 VJS  C22  C  C      0   0.402   3.2026  -28.6808  24.8276
 VJS  C02  C  C      0   0.410   1.3925  -33.5578  21.0065
 VJS  C03  C  CH1    0  -0.383   0.7295  -34.7603  21.6297
 VJS  C04  C  CH2    0  -0.434   1.7337  -35.9281  21.6737
 VJS  C05  C  CH2    0  -0.441   0.8674  -37.1866  21.8351
 VJS  C06  C  CH2    0  -0.436  -0.5577  -36.7703  21.4252
 VJS  C07  C  CH1    0  -0.180  -0.4674  -35.3407  20.8669
 VJS  C08  C  CH1    0  -0.454  -1.7763  -34.5693  21.0339
 VJS  C09  C  C      0   0.414  -2.9517  -35.1705  20.2423
 VJS  O10  O  OC    -1  -0.631  -4.0928  -34.9074  20.6832
 VJS  O11  O  O      0  -0.612  -2.7004  -35.8516  19.2254
 VJS  O13  O  O      0  -0.600  -1.9399  -32.7201  19.5214
 VJS  O14  O  OC    -1  -0.614  -1.1290  -32.3356  21.5587
 VJS  O23  O  OC    -1  -0.597   2.8660  -28.7967  26.0199
 VJS  O24  O  O      0  -0.598   2.7855  -27.8550  23.9951
 VJS  H1   H  HCR6   0   0.250   1.7906  -33.6092  23.7548
 VJS  H2   H  HCR6   0   0.245   3.0253  -31.9984  25.0961
 VJS  H3   H  HCR6   0   0.248   2.6518  -31.3281  20.2288
 VJS  H4   H  HCR6   0   0.241   3.8787  -29.7042  21.5906
 VJS  H5   H  HCH2   0   0.224   4.7485  -30.2071  25.1243
 VJS  H6   H  HCH2   0   0.231   4.9979  -29.1948  23.6981
 VJS  H7   H  HCH1   0   0.238   0.4064  -34.5331  22.6487
 VJS  H8   H  HCH2   0   0.226   2.2865  -35.9685  20.7316
 VJS  H9   H  HCH2   0   0.236   2.4710  -35.8128  22.4699
 VJS  H10  H  HCH2   0   0.223   0.8874  -37.5414  22.8665
 VJS  H11  H  HCH2   0   0.224   1.2502  -38.0023  21.2202
 VJS  H12  H  HCH2   0   0.208  -1.2120  -36.7711  22.3019
 VJS  H13  H  HCH2   0   0.225  -1.0055  -37.4504  20.7018
 VJS  H14  H  HCH1   0   0.202  -0.2106  -35.3913  19.8052
 VJS  H15  H  HCH1   0   0.175  -2.0313  -34.6123  22.1007
 VJS  O01  O  O      0  -0.420   1.4369  -33.4258  19.7979

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
 VJS  O11  C09  deloc     1.249  0.020  1.249
 VJS  O13  C12  deloc     1.247  0.020  1.247
 VJS  C09  O10  deloc     1.251  0.020  1.251
 VJS  C09  C08  single    1.539  0.020  1.539
 VJS  O01  C02  double    1.217  0.020  1.217
 VJS  C12  C08  single    1.547  0.020  1.547
 VJS  C12  O14  deloc     1.252  0.020  1.252
 VJS  C08  C07  single    1.529  0.020  1.529
 VJS  C07  C06  single    1.537  0.020  1.537
 VJS  C07  C03  single    1.533  0.020  1.533
 VJS  C02  C03  single    1.508  0.020  1.508
 VJS  C02  C15  single    1.491  0.020  1.491
 VJS  C18  C19  aromatic  1.383  0.020  1.383
 VJS  C18  C15  aromatic  1.397  0.020  1.397
 VJS  C06  C05  single    1.540  0.020  1.540
 VJS  C03  C04  single    1.541  0.020  1.541
 VJS  C19  C20  aromatic  1.396  0.020  1.396
 VJS  C15  C16  aromatic  1.395  0.020  1.395
 VJS  C05  C04  single    1.536  0.020  1.536
 VJS  C20  C21  single    1.496  0.020  1.496
 VJS  C20  C17  aromatic  1.394  0.020  1.394
 VJS  C16  C17  aromatic  1.385  0.020  1.385
 VJS  C21  C22  single    1.558  0.020  1.558
 VJS  O24  C22  deloc     1.245  0.020  1.245
 VJS  C22  O23  deloc     1.244  0.020  1.244
 VJS  C16  H1   single    0.930  0.020  1.080
 VJS  C17  H2   single    0.930  0.020  1.080
 VJS  C18  H3   single    0.930  0.020  1.080
 VJS  C19  H4   single    0.930  0.020  1.080
 VJS  C21  H5   single    0.970  0.020  1.090
 VJS  C21  H6   single    0.970  0.020  1.090
 VJS  C03  H7   single    0.970  0.020  1.090
 VJS  C04  H8   single    0.970  0.020  1.090
 VJS  C04  H9   single    0.970  0.020  1.090
 VJS  C05  H10  single    0.970  0.020  1.090
 VJS  C05  H11  single    0.970  0.020  1.090
 VJS  C06  H12  single    0.970  0.020  1.090
 VJS  C06  H13  single    0.970  0.020  1.090
 VJS  C07  H14  single    0.970  0.020  1.090
 VJS  C08  H15  single    0.970  0.020  1.090

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
 VJS  O14  C12  O13  126.01  3.000
 VJS  O14  C12  C08  116.42  3.000
 VJS  O13  C12  C08  117.56  3.000
 VJS  C02  C15  C18  118.96  3.000
 VJS  C18  C15  C16  118.00  3.000
 VJS  C02  C15  C16  123.03  3.000
 VJS  H1   C16  C17  118.45  3.000
 VJS  H1   C16  C15  120.66  3.000
 VJS  C17  C16  C15  120.89  3.000
 VJS  H2   C17  C20  119.46  3.000
 VJS  H2   C17  C16  119.39  3.000
 VJS  C20  C17  C16  121.15  3.000
 VJS  H3   C18  C19  119.48  3.000
 VJS  H3   C18  C15  119.52  3.000
 VJS  C19  C18  C15  121.00  3.000
 VJS  H4   C19  C20  119.41  3.000
 VJS  H4   C19  C18  119.51  3.000
 VJS  C20  C19  C18  121.07  3.000
 VJS  C21  C20  C19  121.40  3.000
 VJS  C21  C20  C17  120.65  3.000
 VJS  C19  C20  C17  117.89  3.000
 VJS  H6   C21  H5   108.04  3.000
 VJS  H6   C21  C22  109.62  3.000
 VJS  H5   C21  C22  110.48  3.000
 VJS  H6   C21  C20  109.61  3.000
 VJS  H5   C21  C20  109.84  3.000
 VJS  C22  C21  C20  109.23  3.000
 VJS  O24  C22  O23  127.74  3.000
 VJS  O23  C22  C21  116.54  3.000
 VJS  O24  C22  C21  115.70  3.000
 VJS  O01  C02  C03  120.87  3.000
 VJS  C03  C02  C15  119.22  3.000
 VJS  O01  C02  C15  119.64  3.000
 VJS  H7   C03  C07  108.16  3.000
 VJS  H7   C03  C04  108.88  3.000
 VJS  C07  C03  C04  103.66  3.000
 VJS  H7   C03  C02  110.46  3.000
 VJS  C04  C03  C02  109.25  3.000
 VJS  C07  C03  C02  116.07  3.000
 VJS  H9   C04  H8   106.92  3.000
 VJS  H9   C04  C05  113.01  3.000
 VJS  H8   C04  C05  110.21  3.000
 VJS  H9   C04  C03  112.40  3.000
 VJS  H8   C04  C03  109.45  3.000
 VJS  C05  C04  C03  104.85  3.000
 VJS  H11  C05  H10  106.46  3.000
 VJS  H11  C05  C06  112.14  3.000
 VJS  H10  C05  C06  110.89  3.000
 VJS  H11  C05  C04  110.82  3.000
 VJS  H10  C05  C04  110.81  3.000
 VJS  C06  C05  C04  105.81  3.000
 VJS  H13  C06  H12  106.61  3.000
 VJS  H13  C06  C07  111.32  3.000
 VJS  H12  C06  C07  109.07  3.000
 VJS  H13  C06  C05  112.85  3.000
 VJS  H12  C06  C05  109.88  3.000
 VJS  C07  C06  C05  107.08  3.000
 VJS  H14  C07  C08  109.30  3.000
 VJS  H14  C07  C06  108.86  3.000
 VJS  C08  C07  C06  112.29  3.000
 VJS  H14  C07  C03  108.49  3.000
 VJS  C06  C07  C03  102.54  3.000
 VJS  C08  C07  C03  115.03  3.000
 VJS  H15  C08  C09  107.88  3.000
 VJS  H15  C08  C07  106.57  3.000
 VJS  C09  C08  C07  113.62  3.000
 VJS  H15  C08  C12  106.96  3.000
 VJS  C07  C08  C12  111.65  3.000
 VJS  C09  C08  C12  109.82  3.000
 VJS  O11  C09  O10  125.79  3.000
 VJS  O10  C09  C08  115.66  3.000
 VJS  O11  C09  C08  118.54  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
 VJS  CONST_01  C20  C19  C18  C15     0.00   0.0  0
 VJS  CONST_02  C20  C17  C16  C15     0.00   0.0  0
 VJS  CONST_03  C19  C18  C15  C16     0.00   0.0  0
 VJS  CONST_04  C19  C20  C17  C16     0.00   0.0  0
 VJS  CONST_05  C18  C19  C20  C17     0.00   0.0  0
 VJS  CONST_06  C18  C15  C16  C17     0.00   0.0  0
 VJS  CONST_07  C21  C20  C17  C16   180.00   0.0  0
 VJS  CONST_08  C02  C15  C16  C17   180.00   0.0  0
 VJS  CONST_09  C21  C20  C19  C18   180.00   0.0  0
 VJS  CONST_10  C02  C15  C18  C19   180.00   0.0  0
 VJS  CONST_11  H4   C19  C18  C15   180.00   0.0  0
 VJS  CONST_12  H2   C17  C16  C15   180.00   0.0  0
 VJS  CONST_13  H3   C18  C15  C16   180.00   0.0  0
 VJS  CONST_14  H4   C19  C20  C17   180.00   0.0  0
 VJS  CONST_15  H1   C16  C15  C18   180.00   0.0  0
 VJS  CONST_16  H2   C17  C20  C19   180.00   0.0  0
 VJS  CONST_17  H3   C18  C19  C20   180.00   0.0  0
 VJS  CONST_18  H1   C16  C17  C20   180.00   0.0  0
 VJS  Var_01    C06  C05  C04  C03    17.84  30.0  1
 VJS  Var_02    C07  C06  C05  C04     6.98  30.0  1
 VJS  Var_03    C03  C02  C15  C16     1.59  30.0  2
 VJS  Var_04    C03  C02  C15  C18  -179.89  30.0  2
 VJS  Var_05    H10  C05  C04  C03  -102.43  30.0  1
 VJS  Var_06    H11  C05  C04  C03   139.62  30.0  1
 VJS  Var_07    H12  C06  C05  C04  -111.35  30.0  1
 VJS  Var_08    H13  C06  C05  C04   129.82  30.0  1
 VJS  Var_09    H8   C04  C05  C06   -99.85  30.0  1
 VJS  Var_10    H9   C04  C05  C06   140.59  30.0  1
 VJS  Var_11    H10  C05  C06  C07   127.20  30.0  1
 VJS  Var_12    H11  C05  C06  C07  -113.94  30.0  1
 VJS  Var_13    O01  C02  C15  C16  -172.56  30.0  2
 VJS  Var_14    C22  C21  C20  C17   -85.16  30.0  2
 VJS  Var_15    O01  C02  C15  C18     5.96  30.0  2
 VJS  Var_16    C22  C21  C20  C19    91.99  30.0  2
 VJS  Var_17    H5   C21  C20  C17    36.16  30.0  2
 VJS  Var_18    H6   C21  C20  C17   154.72  30.0  2
 VJS  Var_19    H5   C21  C20  C19  -146.68  30.0  2
 VJS  Var_20    H6   C21  C20  C19   -28.13  30.0  2
 VJS  Var_21    O24  C22  C21  C20   -74.43  30.0  3
 VJS  Var_22    O23  C22  C21  C20   104.06  30.0  3
 VJS  Var_23    O11  C09  C08  C07   -25.30  30.0  2
 VJS  Var_24    O10  C09  C08  C07   155.59  30.0  2
 VJS  Var_25    O13  C12  C08  C07    96.96  30.0  2
 VJS  Var_26    O14  C12  C08  C07   -81.95  30.0  2
 VJS  Var_27    O11  C09  C08  C12   100.55  30.0  2
 VJS  Var_28    O10  C09  C08  C12   -78.57  30.0  2
 VJS  Var_29    O13  C12  C08  C09   -30.00  30.0  2
 VJS  Var_30    O14  C12  C08  C09   151.10  30.0  2
 VJS  Var_31    H15  C08  C09  O10    37.67  30.0  3
 VJS  Var_32    H15  C08  C09  O11  -143.22  30.0  3
 VJS  Var_33    H15  C08  C12  O13  -146.82  30.0  3
 VJS  Var_34    H15  C08  C12  O14    34.28  30.0  3
 VJS  Var_35    H5   C21  C22  O23   -16.87  30.0  3
 VJS  Var_36    H6   C21  C22  O23  -135.82  30.0  3
 VJS  Var_37    H5   C21  C22  O24   164.64  30.0  3
 VJS  Var_38    H6   C21  C22  O24    45.69  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
 VJS  chir_01  C03  C07  C02  C04  positiv
 VJS  chir_02  C07  C03  C06  C08  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
 VJS  plan-1  C15  0.020
 VJS  plan-1  C16  0.020
 VJS  plan-1  C17  0.020
 VJS  plan-1  C18  0.020
 VJS  plan-1  C19  0.020
 VJS  plan-1  C20  0.020
 VJS  plan-1  C21  0.020
 VJS  plan-1  C02  0.020
 VJS  plan-1  H1   0.020
 VJS  plan-1  H2   0.020
 VJS  plan-1  H3   0.020
 VJS  plan-1  H4   0.020
 VJS  plan-2  C12  0.020
 VJS  plan-2  C08  0.020
 VJS  plan-2  O13  0.020
 VJS  plan-2  O14  0.020
 VJS  plan-3  C21  0.020
 VJS  plan-3  C22  0.020
 VJS  plan-3  O23  0.020
 VJS  plan-3  O24  0.020
 VJS  plan-4  C08  0.020
 VJS  plan-4  C09  0.020
 VJS  plan-4  O10  0.020
 VJS  plan-4  O11  0.020
 VJS  plan-5  C15  0.020
 VJS  plan-5  C02  0.020
 VJS  plan-5  C03  0.020
 VJS  plan-5  O01  0.020

