# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 02:46:10 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3,4-dihydroxy-2-(pentafluorobenzyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(O)c(O)c1Cc2c(F)c(F)c(F)c(F)c2F
#
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
 7HN  7HN  '3,4-dihydroxy-2-(pentafluorobenzyl)benzoic acid'  ligand  29  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7HN
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
 7HN  OAA   O  OC    -1  -0.593  -2.8812   3.2813  -0.0566
 7HN  CAM   C  C      0   0.375  -2.5100   2.3789  -0.8295
 7HN  OAB   O  O      0  -0.595  -2.1502   2.5258  -2.0163
 7HN  CAU   C  CR6    0  -0.142  -2.5571   0.9580  -0.2770
 7HN  CAK   C  CR16   0  -0.310  -3.5772   0.6607   0.6216
 7HN  CAJ   C  CR16   0  -0.376  -3.7506  -0.6159   1.1351
 7HN  CAN   C  CR6    0   0.248  -2.8778  -1.6244   0.7700
 7HN  OAC   O  OH1    0  -0.649  -2.9545  -2.9011   1.2164
 7HN  CAO   C  CR6    0   0.286  -1.8306  -1.3406  -0.1112
 7HN  OAD   O  OH1    0  -0.631  -0.9561  -2.3066  -0.4741
 7HN  CAV   C  CR6    0   0.006  -1.6643  -0.0626  -0.6427
 7HN  CAL   C  CH2    0  -0.566  -0.4716   0.1554  -1.5479
 7HN  CAW   C  CR6    0  -0.289   0.8337  -0.0181  -0.8176
 7HN  CAS   C  CR6    0   0.406   1.7460  -1.0127  -1.1308
 7HN  FAH   F  F      0  -0.294   1.5007  -1.8617  -2.1270
 7HN  CAQ   C  CR6    0   0.270   2.9389  -1.1623  -0.4467
 7HN  FAF   F  F      0  -0.295   3.7895  -2.1309  -0.7776
 7HN  CAP   C  CR6    0   0.267   3.2497  -0.2995   0.5854
 7HN  FAE   F  F      0  -0.290   4.3905  -0.4371   1.2513
 7HN  CAR   C  CR6    0   0.276   2.3674   0.7105   0.9177
 7HN  FAG   F  F      0  -0.294   2.6655   1.5533   1.9032
 7HN  CAT   C  CR6    0   0.444   1.1847   0.8392   0.2146
 7HN  FAI   F  F      0  -0.290   0.3635   1.8324   0.5525
 7HN  HAK   H  HCR6   0   0.244  -4.2607   1.4419   0.9242
 7HN  HAJ   H  HCR6   0   0.266  -4.5657  -0.8244   1.8192
 7HN  HAC   H  HOH1   0   0.481  -3.6983  -3.0072   1.8194
 7HN  HAD   H  HOH1   0   0.471  -1.1455  -3.1253  -0.0011
 7HN  HAL1  H  HCH2   0   0.273  -0.5097  -0.5372  -2.3890
 7HN  HAL2  H  HCH2   0   0.301  -0.5218   1.1533  -1.9756

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
 7HN  OAA  CAM   deloc     1.245  0.020  1.245
 7HN  CAM  OAB   deloc     1.249  0.020  1.249
 7HN  CAM  CAU   single    1.525  0.020  1.525
 7HN  CAU  CAK   aromatic  1.392  0.020  1.392
 7HN  CAU  CAV   aromatic  1.404  0.020  1.404
 7HN  CAK  CAJ   aromatic  1.387  0.020  1.387
 7HN  CAJ  CAN   aromatic  1.383  0.020  1.383
 7HN  CAN  OAC   single    1.355  0.020  1.355
 7HN  CAN  CAO   aromatic  1.398  0.020  1.398
 7HN  CAO  OAD   single    1.353  0.020  1.353
 7HN  CAO  CAV   aromatic  1.394  0.020  1.394
 7HN  CAV  CAL   single    1.513  0.020  1.513
 7HN  CAL  CAW   single    1.506  0.020  1.506
 7HN  CAW  CAS   aromatic  1.385  0.020  1.385
 7HN  CAW  CAT   aromatic  1.387  0.020  1.387
 7HN  CAS  FAH   single    1.332  0.020  1.332
 7HN  CAS  CAQ   aromatic  1.383  0.020  1.383
 7HN  CAQ  FAF   single    1.331  0.020  1.331
 7HN  CAQ  CAP   aromatic  1.381  0.020  1.381
 7HN  CAP  FAE   single    1.328  0.020  1.328
 7HN  CAP  CAR   aromatic  1.382  0.020  1.382
 7HN  CAR  FAG   single    1.331  0.020  1.331
 7HN  CAR  CAT   aromatic  1.382  0.020  1.382
 7HN  CAT  FAI   single    1.332  0.020  1.332
 7HN  CAK  HAK   single    0.930  0.020  1.080
 7HN  CAJ  HAJ   single    0.930  0.020  1.080
 7HN  OAC  HAC   single    0.850  0.020  0.980
 7HN  OAD  HAD   single    0.850  0.020  0.980
 7HN  CAL  HAL1  single    0.970  0.020  1.090
 7HN  CAL  HAL2  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
 7HN  CAU   CAM  OAB   117.56  3.000
 7HN  CAU   CAM  OAA   116.18  3.000
 7HN  OAB   CAM  OAA   126.21  3.000
 7HN  CAV   CAU  CAK   118.61  3.000
 7HN  CAV   CAU  CAM   124.26  3.000
 7HN  CAK   CAU  CAM   117.10  3.000
 7HN  HAK   CAK  CAJ   118.84  3.000
 7HN  HAK   CAK  CAU   119.33  3.000
 7HN  CAJ   CAK  CAU   121.83  3.000
 7HN  HAJ   CAJ  CAN   120.05  3.000
 7HN  HAJ   CAJ  CAK   120.30  3.000
 7HN  CAN   CAJ  CAK   119.65  3.000
 7HN  CAO   CAN  OAC   116.20  3.000
 7HN  CAO   CAN  CAJ   119.42  3.000
 7HN  OAC   CAN  CAJ   124.38  3.000
 7HN  HAC   OAC  CAN   110.72  3.000
 7HN  CAV   CAO  OAD   118.38  3.000
 7HN  CAV   CAO  CAN   121.06  3.000
 7HN  OAD   CAO  CAN   120.56  3.000
 7HN  HAD   OAD  CAO   110.35  3.000
 7HN  CAL   CAV  CAO   117.02  3.000
 7HN  CAL   CAV  CAU   123.51  3.000
 7HN  CAO   CAV  CAU   119.41  3.000
 7HN  HAL2  CAL  HAL1  106.15  3.000
 7HN  HAL2  CAL  CAW   109.67  3.000
 7HN  HAL1  CAL  CAW   109.34  3.000
 7HN  HAL2  CAL  CAV   109.35  3.000
 7HN  HAL1  CAL  CAV   110.03  3.000
 7HN  CAW   CAL  CAV   112.12  3.000
 7HN  CAT   CAW  CAS   116.44  3.000
 7HN  CAT   CAW  CAL   120.60  3.000
 7HN  CAS   CAW  CAL   122.95  3.000
 7HN  CAQ   CAS  FAH   117.37  3.000
 7HN  CAQ   CAS  CAW   122.26  3.000
 7HN  FAH   CAS  CAW   120.36  3.000
 7HN  CAP   CAQ  FAF   119.79  3.000
 7HN  CAP   CAQ  CAS   119.75  3.000
 7HN  FAF   CAQ  CAS   120.46  3.000
 7HN  CAR   CAP  FAE   120.24  3.000
 7HN  CAR   CAP  CAQ   119.53  3.000
 7HN  FAE   CAP  CAQ   120.23  3.000
 7HN  CAT   CAR  FAG   120.64  3.000
 7HN  CAT   CAR  CAP   119.48  3.000
 7HN  FAG   CAR  CAP   119.88  3.000
 7HN  FAI   CAT  CAR   117.89  3.000
 7HN  FAI   CAT  CAW   119.58  3.000
 7HN  CAR   CAT  CAW   122.53  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
 7HN  CONST_01  CAN  CAJ  CAK  CAU    0.00   0.0  0
 7HN  CONST_02  CAN  CAO  CAV  CAU    0.00   0.0  0
 7HN  CONST_03  CAO  CAV  CAU  CAK    0.00   0.0  0
 7HN  CONST_04  CAO  CAN  CAJ  CAK    0.00   0.0  0
 7HN  CONST_05  CAV  CAU  CAK  CAJ    0.00   0.0  0
 7HN  CONST_06  CAV  CAO  CAN  CAJ    0.00   0.0  0
 7HN  CONST_07  CAP  CAQ  CAS  CAW    0.00   0.0  0
 7HN  CONST_08  CAP  CAR  CAT  CAW    0.00   0.0  0
 7HN  CONST_09  CAR  CAT  CAW  CAS    0.00   0.0  0
 7HN  CONST_10  CAR  CAP  CAQ  CAS    0.00   0.0  0
 7HN  CONST_11  CAT  CAW  CAS  CAQ    0.00   0.0  0
 7HN  CONST_12  CAT  CAR  CAP  CAQ    0.00   0.0  0
 7HN  CONST_13  CAJ  CAK  CAU  CAM  180.00   0.0  0
 7HN  CONST_14  CAO  CAV  CAU  CAM  180.00   0.0  0
 7HN  CONST_15  OAD  CAO  CAV  CAU  180.00   0.0  0
 7HN  CONST_16  CAL  CAV  CAU  CAK  180.00   0.0  0
 7HN  CONST_17  OAC  CAN  CAJ  CAK  180.00   0.0  0
 7HN  CONST_18  OAD  CAO  CAN  CAJ  180.00   0.0  0
 7HN  CONST_19  CAL  CAV  CAO  CAN  180.00   0.0  0
 7HN  CONST_20  CAV  CAO  CAN  OAC  180.00   0.0  0
 7HN  CONST_21  CAQ  CAS  CAW  CAL  180.00   0.0  0
 7HN  CONST_22  CAR  CAT  CAW  CAL  180.00   0.0  0
 7HN  CONST_23  FAF  CAQ  CAS  CAW  180.00   0.0  0
 7HN  CONST_24  FAG  CAR  CAT  CAW  180.00   0.0  0
 7HN  CONST_25  FAI  CAT  CAW  CAS  180.00   0.0  0
 7HN  CONST_26  FAE  CAP  CAQ  CAS  180.00   0.0  0
 7HN  CONST_27  CAT  CAW  CAS  FAH  180.00   0.0  0
 7HN  CONST_28  CAP  CAQ  CAS  FAH  180.00   0.0  0
 7HN  CONST_29  FAG  CAR  CAP  CAQ  180.00   0.0  0
 7HN  CONST_30  CAR  CAP  CAQ  FAF  180.00   0.0  0
 7HN  CONST_31  FAI  CAT  CAR  CAP  180.00   0.0  0
 7HN  CONST_32  CAT  CAR  CAP  FAE  180.00   0.0  0
 7HN  CONST_33  HAJ  CAJ  CAK  CAU  180.00   0.0  0
 7HN  CONST_34  HAK  CAK  CAJ  CAN  180.00   0.0  0
 7HN  Var_01    CAW  CAL  CAV  CAU  112.90  30.0  2
 7HN  Var_02    CAS  CAW  CAL  CAV  116.43  30.0  2
 7HN  Var_03    CAK  CAU  CAM  OAA   33.56  30.0  2

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
 7HN  plan-1  CAM  0.020
 7HN  plan-1  CAU  0.020
 7HN  plan-1  CAK  0.020
 7HN  plan-1  CAJ  0.020
 7HN  plan-1  CAN  0.020
 7HN  plan-1  OAC  0.020
 7HN  plan-1  CAO  0.020
 7HN  plan-1  OAD  0.020
 7HN  plan-1  CAV  0.020
 7HN  plan-1  CAL  0.020
 7HN  plan-1  HAK  0.020
 7HN  plan-1  HAJ  0.020
 7HN  plan-2  CAL  0.020
 7HN  plan-2  CAW  0.020
 7HN  plan-2  CAS  0.020
 7HN  plan-2  FAH  0.020
 7HN  plan-2  CAQ  0.020
 7HN  plan-2  FAF  0.020
 7HN  plan-2  CAP  0.020
 7HN  plan-2  FAE  0.020
 7HN  plan-2  CAR  0.020
 7HN  plan-2  FAG  0.020
 7HN  plan-2  CAT  0.020
 7HN  plan-2  FAI  0.020
 7HN  plan-3  OAA  0.020
 7HN  plan-3  CAM  0.020
 7HN  plan-3  OAB  0.020
 7HN  plan-3  CAU  0.020

