# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 04:09:43 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (3~{R},5~{R})-1-[2,4-bis(fluoranyl)phenyl]-5-oxidanyl-pyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@H](CN1c2ccc(F)cc2F)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
 Z24  Z24  '(3~{R},5~{R})-1-[2,4-bis(fluoranyl)phenyl]-5-oxidanyl-pyrrolidine-3-carboxylic acid'  ligand  28  17  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Z24
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
 Z24  OAB   O  OH1   0  -0.664   0.8356  -2.2505  -1.3607
 Z24  CAL   C  CH1   0   0.199   0.9851  -0.8447  -1.3932
 Z24  CAI   C  CH2   0  -0.487   2.4375  -0.3910  -1.2759
 Z24  CAP   C  CH1   0  -0.433   2.6486  -0.2974   0.2278
 Z24  CAK   C  C     0   0.561   3.8505   0.5016   0.6415
 Z24  OAC   O  O     0  -0.437   4.7267   0.8652  -0.1020
 Z24  OAA   O  OH1   0  -0.593   3.8511   0.7504   1.9461
 Z24  CAJ   C  CH2   0  -0.232   1.3167   0.2769   0.7156
 Z24  NAQ   N  NT    0  -0.560   0.3691  -0.3089  -0.2171
 Z24  CAO   C  CR6   0   0.173  -0.9782   0.0486  -0.1812
 Z24  CAN   C  CR6   0   0.520  -1.7714  -0.2993   0.9115
 Z24  FAE   F  F     0  -0.305  -1.2177  -0.9969   1.9114
 Z24  CAH   C  CR16  0  -0.565  -3.1049   0.0406   1.0191
 Z24  CAM   C  CR6   0   0.529  -3.6756   0.7345  -0.0301
 Z24  FAD   F  F     0  -0.312  -4.9734   1.0622   0.0484
 Z24  CAF   C  CR16  0  -0.420  -2.9513   1.0966  -1.1476
 Z24  CAG   C  CR16  0  -0.285  -1.6060   0.7625  -1.2022
 Z24  HAB1  H  HOH1  0   0.446   1.1372  -2.6011  -2.2059
 Z24  HAL1  H  HCH1  0   0.221   0.5331  -0.4542  -2.3125
 Z24  HAI1  H  HCH2  0   0.263   3.1283  -1.0674  -1.7784
 Z24  HAI2  H  HCH2  0   0.247   2.5452   0.5957  -1.7323
 Z24  HAP1  H  HCH1  0   0.306   2.7716  -1.3033   0.6462
 Z24  H1    H  HOH1  0   0.483   4.6413   1.2564   2.1889
 Z24  HAJ2  H  HCH2  0   0.250   1.1060   0.0020   1.7489
 Z24  HAJ1  H  HCH2  0   0.226   1.3130   1.3736   0.6538
 Z24  HAH1  H  HCR6  0   0.302  -3.6828  -0.2495   1.8872
 Z24  HAF1  H  HCR6  0   0.285  -3.4173   1.6451  -1.9549
 Z24  HAG1  H  HCR6  0   0.282  -1.0312   1.0690  -2.0663

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
 Z24  OAC  CAK   double    1.205  0.020  1.205
 Z24  FAE  CAN   single    1.339  0.020  1.339
 Z24  CAK  OAA   single    1.328  0.020  1.328
 Z24  CAK  CAP   single    1.501  0.020  1.501
 Z24  CAJ  CAP   single    1.530  0.020  1.530
 Z24  CAJ  NAQ   single    1.453  0.020  1.453
 Z24  CAN  CAH   aromatic  1.380  0.020  1.380
 Z24  CAN  CAO   aromatic  1.394  0.020  1.394
 Z24  CAH  CAM   aromatic  1.381  0.020  1.381
 Z24  CAP  CAI   single    1.521  0.020  1.521
 Z24  NAQ  CAO   single    1.394  0.020  1.394
 Z24  NAQ  CAL   single    1.432  0.020  1.432
 Z24  CAO  CAG   aromatic  1.395  0.020  1.395
 Z24  CAM  FAD   single    1.341  0.020  1.341
 Z24  CAM  CAF   aromatic  1.380  0.020  1.380
 Z24  CAI  CAL   single    1.526  0.020  1.526
 Z24  CAL  OAB   single    1.414  0.020  1.414
 Z24  CAG  CAF   aromatic  1.387  0.020  1.387
 Z24  OAB  HAB1  single    0.850  0.020  0.980
 Z24  CAL  HAL1  single    0.970  0.020  1.090
 Z24  CAI  HAI1  single    0.970  0.020  1.090
 Z24  CAI  HAI2  single    0.970  0.020  1.090
 Z24  CAP  HAP1  single    0.970  0.020  1.090
 Z24  OAA  H1    single    0.850  0.020  0.980
 Z24  CAJ  HAJ2  single    0.970  0.020  1.090
 Z24  CAJ  HAJ1  single    0.970  0.020  1.090
 Z24  CAH  HAH1  single    0.930  0.020  1.080
 Z24  CAF  HAF1  single    0.930  0.020  1.080
 Z24  CAG  HAG1  single    0.930  0.020  1.080

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
 Z24  HAB1  OAB  CAL   107.97  3.000
 Z24  HAL1  CAL  NAQ   112.22  3.000
 Z24  HAL1  CAL  CAI   110.55  3.000
 Z24  NAQ   CAL  CAI   103.60  3.000
 Z24  HAL1  CAL  OAB   109.26  3.000
 Z24  CAI   CAL  OAB   113.23  3.000
 Z24  NAQ   CAL  OAB   107.92  3.000
 Z24  HAI2  CAI  HAI1  107.79  3.000
 Z24  HAI2  CAI  CAP   110.10  3.000
 Z24  HAI1  CAI  CAP   113.96  3.000
 Z24  HAI2  CAI  CAL   109.28  3.000
 Z24  HAI1  CAI  CAL   112.54  3.000
 Z24  CAP   CAI  CAL   103.08  3.000
 Z24  HAP1  CAP  CAJ   108.69  3.000
 Z24  HAP1  CAP  CAK   107.06  3.000
 Z24  CAJ   CAP  CAK   114.15  3.000
 Z24  HAP1  CAP  CAI   109.65  3.000
 Z24  CAJ   CAP  CAI   102.56  3.000
 Z24  CAK   CAP  CAI   114.59  3.000
 Z24  OAA   CAK  OAC   123.30  3.000
 Z24  OAA   CAK  CAP   111.76  3.000
 Z24  OAC   CAK  CAP   124.92  3.000
 Z24  H1    OAA  CAK   110.13  3.000
 Z24  HAJ1  CAJ  HAJ2  107.74  3.000
 Z24  HAJ1  CAJ  NAQ   111.36  3.000
 Z24  HAJ2  CAJ  NAQ   112.38  3.000
 Z24  HAJ1  CAJ  CAP   111.08  3.000
 Z24  HAJ2  CAJ  CAP   112.08  3.000
 Z24  NAQ   CAJ  CAP   102.22  3.000
 Z24  CAO   NAQ  CAJ   120.68  3.000
 Z24  CAO   NAQ  CAL   122.19  3.000
 Z24  CAJ   NAQ  CAL   113.43  3.000
 Z24  CAG   CAO  CAN   116.44  3.000
 Z24  CAG   CAO  NAQ   123.17  3.000
 Z24  CAN   CAO  NAQ   120.39  3.000
 Z24  CAH   CAN  FAE   118.00  3.000
 Z24  CAH   CAN  CAO   123.31  3.000
 Z24  FAE   CAN  CAO   118.68  3.000
 Z24  HAH1  CAH  CAM   121.55  3.000
 Z24  HAH1  CAH  CAN   120.82  3.000
 Z24  CAM   CAH  CAN   117.62  3.000
 Z24  CAF   CAM  FAD   119.42  3.000
 Z24  CAF   CAM  CAH   122.01  3.000
 Z24  FAD   CAM  CAH   118.56  3.000
 Z24  HAF1  CAF  CAG   120.70  3.000
 Z24  HAF1  CAF  CAM   120.75  3.000
 Z24  CAG   CAF  CAM   118.53  3.000
 Z24  HAG1  CAG  CAF   118.58  3.000
 Z24  HAG1  CAG  CAO   119.36  3.000
 Z24  CAF   CAG  CAO   122.06  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
 Z24  CONST_01  CAM   CAH  CAN  CAO    0.00   0.0  0
 Z24  CONST_02  CAM   CAF  CAG  CAO    0.00   0.0  0
 Z24  CONST_03  CAF   CAM  CAH  CAN    0.00   0.0  0
 Z24  CONST_04  CAF   CAG  CAO  CAN    0.00   0.0  0
 Z24  CONST_05  CAG   CAO  CAN  CAH    0.00   0.0  0
 Z24  CONST_06  CAG   CAF  CAM  CAH    0.00   0.0  0
 Z24  CONST_07  CAH   CAN  CAO  NAQ  180.00   0.0  0
 Z24  CONST_08  CAF   CAG  CAO  NAQ  180.00   0.0  0
 Z24  CONST_09  FAE   CAN  CAO  NAQ    0.00   0.0  0
 Z24  CONST_10  FAD   CAM  CAH  CAN  180.00   0.0  0
 Z24  CONST_11  CAM   CAH  CAN  FAE  180.00   0.0  0
 Z24  CONST_12  CAG   CAO  CAN  FAE  180.00   0.0  0
 Z24  CONST_13  CAG   CAF  CAM  FAD  180.00   0.0  0
 Z24  CONST_14  HAG1  CAG  CAO  NAQ    0.00   0.0  0
 Z24  CONST_15  HAH1  CAH  CAN  CAO  180.00   0.0  0
 Z24  CONST_16  HAF1  CAF  CAG  CAO  180.00   0.0  0
 Z24  CONST_17  H1    OAA  CAK  CAP  180.00   0.0  0
 Z24  Var_01    CAP   CAJ  NAQ  CAL  -16.24  30.0  1
 Z24  Var_02    CAN   CAO  NAQ  CAL  136.06  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
 Z24  chir_01  CAL  NAQ  CAI  OAB  negativ
 Z24  chir_02  CAP  CAK  CAJ  CAI  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
 Z24  plan-1  NAQ   0.020
 Z24  plan-1  CAO   0.020
 Z24  plan-1  CAN   0.020
 Z24  plan-1  FAE   0.020
 Z24  plan-1  CAH   0.020
 Z24  plan-1  CAM   0.020
 Z24  plan-1  FAD   0.020
 Z24  plan-1  CAF   0.020
 Z24  plan-1  CAG   0.020
 Z24  plan-1  HAH1  0.020
 Z24  plan-1  HAF1  0.020
 Z24  plan-1  HAG1  0.020
 Z24  plan-2  CAP   0.020
 Z24  plan-2  CAK   0.020
 Z24  plan-2  OAC   0.020
 Z24  plan-2  OAA   0.020
 Z24  plan-2  H1    0.020

