# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 04:58:08 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5-bromo-2-{[(1S,3R)-3-carboxycyclohexyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCC[C@@H](C1)Nc2ccc(Br)cc2C(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
 AOD  AOD  '5-bromo-2-{[(1S,3R)-3-carboxycyclohexyl]amino}benzoic acid'  ligand  34  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AOD
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
 AOD  OAA   O   OC    -1  -0.580   2.0001   3.5297   0.4146
 AOD  OAC   O   O      0  -0.601  -0.1653   3.0489   0.4419
 AOD  OAD   O   O      0  -0.602  -5.8098   1.2679  -1.0096
 AOD  CAF   C   CR16   0  -0.229   2.1689  -1.4159  -0.1318
 AOD  CAG   C   CR16   0  -0.357   0.8285  -1.0876  -0.1071
 AOD  CAH   C   CR16   0  -0.261   2.7238   0.9011   0.1503
 AOD  CAI   C   CH2    0  -0.435  -3.3506  -2.0424   1.4136
 AOD  CAJ   C   CH2    0  -0.433  -2.1773  -1.0700   1.4308
 AOD  CAK   C   CH2    0  -0.416  -4.6431  -1.3426   1.0092
 AOD  CAL   C   CH2    0  -0.422  -3.3099   0.3293  -0.3115
 AOD  CAN   C   C      0   0.446   1.0481   2.7328   0.3587
 AOD  CAO   C   C      0   0.427  -5.8260   0.0484  -0.7481
 AOD  CAP   C   CR6    0  -0.138   3.1207  -0.4149  -0.0005
 AOD  CAQ   C   CR6    0   0.364   0.3901   0.2450   0.0449
 AOD  CAR   C   CR6    0  -0.221   1.3805   1.2595   0.1788
 AOD  CAS   C   CH1    0  -0.050  -2.0169  -0.3879   0.0699
 AOD  CAT   C   CH1    0  -0.383  -4.4994  -0.6239  -0.3355
 AOD  HAF   H   HCR6   0   0.267   2.4566  -2.4526  -0.2516
 AOD  HAG   H   HCR6   0   0.263   0.1090  -1.8878  -0.2094
 AOD  HAH   H   HCR6   0   0.259   3.4584   1.6886   0.2514
 AOD  HAI   H   HCH2   0   0.208  -3.1383  -2.8497   0.7033
 AOD  HAIA  H   HCH2   0   0.225  -3.4629  -2.5140   2.3931
 AOD  HAJ   H   HCH2   0   0.209  -2.3473  -0.2954   2.1871
 AOD  HAJA  H   HCH2   0   0.230  -1.2564  -1.5867   1.7132
 AOD  HAK   H   HCH2   0   0.222  -5.4637  -2.0589   0.9555
 AOD  HAKA  H   HCH2   0   0.201  -4.9113  -0.6116   1.7817
 AOD  HAL   H   HCH2   0   0.204  -3.4957   1.1305   0.4131
 AOD  HALA  H   HCH2   0   0.224  -3.1865   0.8070  -1.2861
 AOD  HNAM  H   HNH1   0   0.388  -1.1009   1.5401   0.2383
 AOD  HAS   H   HCH1   0   0.210  -1.8369  -1.1652  -0.6854
 AOD  HAT   H   HCH1   0   0.210  -4.2938  -1.3983  -1.0893
 AOD  NAM   N   NH1    0  -0.714  -0.9261   0.5573   0.0374
 AOD  BRAE  BR  BR     0  -0.094   4.9655  -0.8552  -0.0252
 AOD  OAB   O   OC    -1  -0.624  -6.8272  -0.6978  -0.7907

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
 AOD  OAA   CAN   deloc     1.243  0.020  1.243
 AOD  OAB   CAO   deloc     1.249  0.020  1.249
 AOD  OAC   CAN   deloc     1.257  0.020  1.257
 AOD  OAD   CAO   deloc     1.247  0.020  1.247
 AOD  BRAE  CAP   single    1.897  0.020  1.897
 AOD  CAF   CAG   aromatic  1.380  0.020  1.380
 AOD  CAF   CAP   aromatic  1.388  0.020  1.388
 AOD  CAF   HAF   single    0.930  0.020  1.080
 AOD  CAG   CAQ   aromatic  1.411  0.020  1.411
 AOD  CAG   HAG   single    0.930  0.020  1.080
 AOD  CAH   CAP   aromatic  1.383  0.020  1.383
 AOD  CAH   CAR   aromatic  1.391  0.020  1.391
 AOD  CAH   HAH   single    0.930  0.020  1.080
 AOD  CAI   CAJ   single    1.524  0.020  1.524
 AOD  CAI   CAK   single    1.524  0.020  1.524
 AOD  CAI   HAI   single    0.970  0.020  1.090
 AOD  CAI   HAIA  single    0.970  0.020  1.090
 AOD  CAJ   CAS   single    1.531  0.020  1.531
 AOD  CAJ   HAJ   single    0.970  0.020  1.090
 AOD  CAJ   HAJA  single    0.970  0.020  1.090
 AOD  CAK   CAT   single    1.531  0.020  1.531
 AOD  CAK   HAK   single    0.970  0.020  1.090
 AOD  CAK   HAKA  single    0.970  0.020  1.090
 AOD  CAL   CAS   single    1.527  0.020  1.527
 AOD  CAL   CAT   single    1.525  0.020  1.525
 AOD  CAL   HAL   single    0.970  0.020  1.090
 AOD  CAL   HALA  single    0.970  0.020  1.090
 AOD  NAM   CAQ   single    1.353  0.020  1.353
 AOD  NAM   CAS   single    1.444  0.020  1.444
 AOD  NAM   HNAM  single    0.860  0.020  1.020
 AOD  CAN   CAR   single    1.521  0.020  1.521
 AOD  CAO   CAT   single    1.543  0.020  1.543
 AOD  CAQ   CAR   aromatic  1.424  0.020  1.424
 AOD  CAS   HAS   single    0.970  0.020  1.090
 AOD  CAT   HAT   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
 AOD  HAF   CAF  CAP   121.26  3.000
 AOD  HAF   CAF  CAG   119.20  3.000
 AOD  CAP   CAF  CAG   119.54  3.000
 AOD  HAG   CAG  CAQ   120.17  3.000
 AOD  HAG   CAG  CAF   117.95  3.000
 AOD  CAQ   CAG  CAF   121.88  3.000
 AOD  HAH   CAH  CAR   117.80  3.000
 AOD  HAH   CAH  CAP   120.54  3.000
 AOD  CAR   CAH  CAP   121.66  3.000
 AOD  HAIA  CAI  HAI   106.43  3.000
 AOD  HAIA  CAI  CAK   110.41  3.000
 AOD  HAI   CAI  CAK   109.30  3.000
 AOD  HAIA  CAI  CAJ   110.14  3.000
 AOD  HAI   CAI  CAJ   109.16  3.000
 AOD  CAK   CAI  CAJ   111.28  3.000
 AOD  HAJA  CAJ  HAJ   106.65  3.000
 AOD  HAJA  CAJ  CAS   110.61  3.000
 AOD  HAJ   CAJ  CAS   108.36  3.000
 AOD  HAJA  CAJ  CAI   110.48  3.000
 AOD  HAJ   CAJ  CAI   109.84  3.000
 AOD  CAS   CAJ  CAI   110.79  3.000
 AOD  HAKA  CAK  HAK   106.76  3.000
 AOD  HAKA  CAK  CAT   109.18  3.000
 AOD  HAK   CAK  CAT   109.61  3.000
 AOD  HAKA  CAK  CAI   109.06  3.000
 AOD  HAK   CAK  CAI   110.46  3.000
 AOD  CAT   CAK  CAI   111.64  3.000
 AOD  HALA  CAL  HAL   106.82  3.000
 AOD  HALA  CAL  CAT   110.33  3.000
 AOD  HAL   CAL  CAT   109.58  3.000
 AOD  HALA  CAL  CAS   109.43  3.000
 AOD  HAL   CAL  CAS   108.77  3.000
 AOD  CAT   CAL  CAS   111.77  3.000
 AOD  CAR   CAN  OAC   117.55  3.000
 AOD  CAR   CAN  OAA   117.32  3.000
 AOD  OAC   CAN  OAA   125.13  3.000
 AOD  CAT   CAO  OAD   118.08  3.000
 AOD  CAT   CAO  OAB   115.96  3.000
 AOD  OAD   CAO  OAB   125.96  3.000
 AOD  CAH   CAP  CAF   120.00  3.000
 AOD  CAH   CAP  BRAE  120.10  3.000
 AOD  CAF   CAP  BRAE  119.90  3.000
 AOD  CAR   CAQ  NAM   120.85  3.000
 AOD  CAR   CAQ  CAG   117.83  3.000
 AOD  NAM   CAQ  CAG   121.31  3.000
 AOD  CAQ   CAR  CAN   123.31  3.000
 AOD  CAQ   CAR  CAH   119.10  3.000
 AOD  CAN   CAR  CAH   117.59  3.000
 AOD  HAS   CAS  NAM   108.90  3.000
 AOD  HAS   CAS  CAL   107.42  3.000
 AOD  NAM   CAS  CAL   109.07  3.000
 AOD  HAS   CAS  CAJ   108.24  3.000
 AOD  NAM   CAS  CAJ   113.01  3.000
 AOD  CAL   CAS  CAJ   110.04  3.000
 AOD  HAT   CAT  CAO   106.51  3.000
 AOD  HAT   CAT  CAL   107.76  3.000
 AOD  CAO   CAT  CAL   113.73  3.000
 AOD  HAT   CAT  CAK   106.79  3.000
 AOD  CAO   CAT  CAK   111.01  3.000
 AOD  CAL   CAT  CAK   110.66  3.000
 AOD  HNAM  NAM  CAS   119.85  3.000
 AOD  HNAM  NAM  CAQ   112.88  3.000
 AOD  CAS   NAM  CAQ   125.72  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
 AOD  CONST_01  CAR   CAQ  CAG  CAF     0.00   0.0  0
 AOD  CONST_02  CAR   CAH  CAP  CAF     0.00   0.0  0
 AOD  CONST_03  CAH   CAP  CAF  CAG     0.00   0.0  0
 AOD  CONST_04  CAH   CAR  CAQ  CAG     0.00   0.0  0
 AOD  CONST_05  CAQ   CAG  CAF  CAP     0.00   0.0  0
 AOD  CONST_06  CAQ   CAR  CAH  CAP     0.00   0.0  0
 AOD  CONST_07  CAG   CAF  CAP  BRAE  180.00   0.0  0
 AOD  CONST_08  CAR   CAH  CAP  BRAE  180.00   0.0  0
 AOD  CONST_09  NAM   CAQ  CAG  CAF   180.00   0.0  0
 AOD  CONST_10  CAN   CAR  CAQ  CAG   180.00   0.0  0
 AOD  CONST_11  NAM   CAQ  CAR  CAH   180.00   0.0  0
 AOD  CONST_12  CAP   CAH  CAR  CAN   180.00   0.0  0
 AOD  CONST_13  CAS   NAM  CAQ  CAG     0.00   0.0  0
 AOD  CONST_14  CAS   NAM  CAQ  CAR   180.00   0.0  0
 AOD  CONST_15  HAH   CAH  CAP  CAF   180.00   0.0  0
 AOD  CONST_16  HAF   CAF  CAP  CAH   180.00   0.0  0
 AOD  CONST_17  HAG   CAG  CAF  CAP   180.00   0.0  0
 AOD  CONST_18  HNAM  NAM  CAQ  CAG   180.00   0.0  0
 AOD  Var_01    CAT   CAK  CAI  CAJ    55.10  30.0  1
 AOD  Var_02    CAS   CAJ  CAI  CAK   -56.54  30.0  1
 AOD  Var_03    CAH   CAR  CAN  OAA     2.84  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
 AOD  chir_01  CAS  CAJ  CAL  NAM  negativ
 AOD  chir_02  CAT  CAO  CAL  CAK  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
 AOD  plan-1  CAF   0.020
 AOD  plan-1  CAG   0.020
 AOD  plan-1  CAH   0.020
 AOD  plan-1  CAN   0.020
 AOD  plan-1  CAP   0.020
 AOD  plan-1  CAQ   0.020
 AOD  plan-1  CAR   0.020
 AOD  plan-1  HAF   0.020
 AOD  plan-1  HAG   0.020
 AOD  plan-1  HAH   0.020
 AOD  plan-1  NAM   0.020
 AOD  plan-1  BRAE  0.020
 AOD  plan-2  CAQ   0.020
 AOD  plan-2  CAS   0.020
 AOD  plan-2  HNAM  0.020
 AOD  plan-2  NAM   0.020
 AOD  plan-3  OAA   0.020
 AOD  plan-3  OAC   0.020
 AOD  plan-3  CAN   0.020
 AOD  plan-3  CAR   0.020
 AOD  plan-4  OAD   0.020
 AOD  plan-4  CAO   0.020
 AOD  plan-4  CAT   0.020
 AOD  plan-4  OAB   0.020

