# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 11:35:53 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-(3-chloro-4-fluorobenzyl)-4,5-dihydroxy-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2C(=O)N(Cc3ccc(F)c(Cl)c3)C(=O)c2c1O
#
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
 CIJ  CIJ  2-(3-chloro-4-fluorobenzyl)-4,5-dihydroxy-1H-isoindole-1,3(2H)-dione  ligand  31  22  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CIJ
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
 CIJ  CL    CL  CL    0  -0.091  -4.8826   1.5125  -0.3146
 CIJ  OAB   O   O     0  -0.424   1.5895  -2.1715   1.1762
 CIJ  OAC   O   OH1   0  -0.616   5.8174   0.0800  -1.4071
 CIJ  OAD   O   OH1   0  -0.611   4.2938  -1.8550  -0.2576
 CIJ  CAG   C   CR16  0  -0.352   4.2174   1.7154  -0.8842
 CIJ  CAH   C   CR16  0  -0.402  -2.9197  -1.9355  -0.6511
 CIJ  CAI   C   CR16  0  -0.271  -1.8920  -1.7838   0.2656
 CIJ  CAJ   C   CR16  0  -0.320   3.0001   2.1124  -0.3284
 CIJ  CAK   C   CR16  0  -0.248  -2.6910   0.4069   0.8321
 CIJ  CAM   C   CR6   0   0.334   4.6386   0.3922  -0.8557
 CIJ  CAN   C   CR6   0   0.604  -3.8273  -0.9087  -0.8164
 CIJ  CAO   C   CR6   0   0.239   3.8306  -0.6009  -0.2526
 CIJ  CAP   C   CR6   0  -0.216  -3.7239   0.2593  -0.0807
 CIJ  CAQ   C   CR6   0   0.123  -1.7668  -0.6145   1.0109
 CIJ  CAR   C   CR5   0   0.597   0.9095   1.2136   0.9175
 CIJ  CAS   C   CR5   0   0.614   1.5976  -0.9794   0.9648
 CIJ  CAT   C   CR56  0  -0.092   2.2241   1.1405   0.2540
 CIJ  CAU   C   CR56  0  -0.128   2.6360  -0.1879   0.2885
 CIJ  NAV   N   NR5   0  -0.594   0.6073  -0.0853   1.3219
 CIJ  HOAC  H   HOH1  0   0.484   6.0012  -0.8652  -1.3371
 CIJ  HOAD  H   HOH1  0   0.489   3.6693  -2.4621   0.1631
 CIJ  HAG   H   HCR6  0   0.287   4.8612   2.4479  -1.3541
 CIJ  HAH   H   HCR6  0   0.293  -3.0222  -2.8434  -1.2310
 CIJ  HAI   H   HCR6  0   0.271  -1.1833  -2.5906   0.4018
 CIJ  HAJ   H   HCR6  0   0.274   2.6936   3.1487  -0.3635
 CIJ  HAK   H   HCR6  0   0.285  -2.6161   1.3223   1.4042
 CIJ  HAL   H   HCH2  0   0.297  -0.8591   0.3147   2.7263
 CIJ  HALA  H   HCH2  0   0.297  -0.4518  -1.3780   2.5266
 CIJ  FAE   F   F     0  -0.293  -4.8235  -1.0392  -1.6941
 CIJ  CAL   C   CH2   0  -0.430  -0.6292  -0.4496   1.9850
 CIJ  OAA   O   O     0  -0.402   0.2011   2.1710   1.1032

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
 CIJ  CL   CAP   single    1.723  0.020  1.723
 CIJ  OAA  CAR   double    1.205  0.020  1.205
 CIJ  OAB  CAS   double    1.211  0.020  1.211
 CIJ  OAC  CAM   single    1.338  0.020  1.338
 CIJ  OAD  CAO   single    1.337  0.020  1.337
 CIJ  FAE  CAN   single    1.334  0.020  1.334
 CIJ  CAG  CAJ   aromatic  1.396  0.020  1.396
 CIJ  CAG  CAM   aromatic  1.389  0.020  1.389
 CIJ  CAH  CAI   aromatic  1.386  0.020  1.386
 CIJ  CAH  CAN   aromatic  1.380  0.020  1.380
 CIJ  CAI  CAQ   aromatic  1.392  0.020  1.392
 CIJ  CAJ  CAT   aromatic  1.373  0.020  1.373
 CIJ  CAK  CAP   aromatic  1.386  0.020  1.386
 CIJ  CAK  CAQ   aromatic  1.389  0.020  1.389
 CIJ  CAL  CAQ   single    1.507  0.020  1.507
 CIJ  CAL  NAV   single    1.450  0.020  1.450
 CIJ  CAM  CAO   aromatic  1.415  0.020  1.415
 CIJ  CAN  CAP   aromatic  1.384  0.020  1.384
 CIJ  CAO  CAU   aromatic  1.375  0.020  1.375
 CIJ  CAR  CAT   single    1.474  0.020  1.474
 CIJ  CAR  NAV   single    1.394  0.020  1.394
 CIJ  CAS  CAU   single    1.470  0.020  1.470
 CIJ  CAS  NAV   single    1.381  0.020  1.381
 CIJ  CAT  CAU   aromatic  1.391  0.020  1.391
 CIJ  OAC  HOAC  single    0.850  0.020  0.980
 CIJ  OAD  HOAD  single    0.850  0.020  0.980
 CIJ  CAG  HAG   single    0.930  0.020  1.080
 CIJ  CAH  HAH   single    0.930  0.020  1.080
 CIJ  CAI  HAI   single    0.930  0.020  1.080
 CIJ  CAJ  HAJ   single    0.930  0.020  1.080
 CIJ  CAK  HAK   single    0.930  0.020  1.080
 CIJ  CAL  HAL   single    0.970  0.020  1.090
 CIJ  CAL  HALA  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
 CIJ  HOAC  OAC  CAM  111.48  3.000
 CIJ  HOAD  OAD  CAO  111.31  3.000
 CIJ  HAG   CAG  CAM  118.24  3.000
 CIJ  HAG   CAG  CAJ  119.93  3.000
 CIJ  CAM   CAG  CAJ  121.82  3.000
 CIJ  HAH   CAH  CAN  119.84  3.000
 CIJ  HAH   CAH  CAI  121.11  3.000
 CIJ  CAN   CAH  CAI  119.05  3.000
 CIJ  HAI   CAI  CAQ  119.99  3.000
 CIJ  HAI   CAI  CAH  119.16  3.000
 CIJ  CAQ   CAI  CAH  120.85  3.000
 CIJ  HAJ   CAJ  CAT  122.13  3.000
 CIJ  HAJ   CAJ  CAG  120.46  3.000
 CIJ  CAT   CAJ  CAG  117.41  3.000
 CIJ  HAK   CAK  CAQ  120.53  3.000
 CIJ  HAK   CAK  CAP  119.33  3.000
 CIJ  CAQ   CAK  CAP  120.15  3.000
 CIJ  CAO   CAM  CAG  120.27  3.000
 CIJ  CAO   CAM  OAC  120.98  3.000
 CIJ  CAG   CAM  OAC  118.74  3.000
 CIJ  CAP   CAN  CAH  120.99  3.000
 CIJ  CAP   CAN  FAE  119.21  3.000
 CIJ  CAH   CAN  FAE  119.81  3.000
 CIJ  CAU   CAO  CAM  116.93  3.000
 CIJ  CAU   CAO  OAD  125.76  3.000
 CIJ  CAM   CAO  OAD  117.31  3.000
 CIJ  CAN   CAP  CAK  119.70  3.000
 CIJ  CAN   CAP  CL   119.43  3.000
 CIJ  CAK   CAP  CL   120.87  3.000
 CIJ  CAL   CAQ  CAK  120.34  3.000
 CIJ  CAL   CAQ  CAI  120.39  3.000
 CIJ  CAK   CAQ  CAI  119.26  3.000
 CIJ  NAV   CAR  CAT  106.13  3.000
 CIJ  NAV   CAR  OAA  124.62  3.000
 CIJ  CAT   CAR  OAA  129.25  3.000
 CIJ  NAV   CAS  CAU  106.07  3.000
 CIJ  NAV   CAS  OAB  125.97  3.000
 CIJ  CAU   CAS  OAB  127.96  3.000
 CIJ  CAU   CAT  CAR  107.47  3.000
 CIJ  CAU   CAT  CAJ  121.26  3.000
 CIJ  CAR   CAT  CAJ  131.27  3.000
 CIJ  CAT   CAU  CAS  108.44  3.000
 CIJ  CAT   CAU  CAO  122.30  3.000
 CIJ  CAS   CAU  CAO  129.26  3.000
 CIJ  CAS   NAV  CAR  111.89  3.000
 CIJ  CAS   NAV  CAL  124.55  3.000
 CIJ  CAR   NAV  CAL  123.51  3.000
 CIJ  HALA  CAL  HAL  107.10  3.000
 CIJ  HALA  CAL  NAV  107.62  3.000
 CIJ  HAL   CAL  NAV  108.36  3.000
 CIJ  HALA  CAL  CAQ  110.56  3.000
 CIJ  HAL   CAL  CAQ  110.94  3.000
 CIJ  NAV   CAL  CAQ  112.07  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
 CIJ  CONST_01  CAU  CAT  CAJ  CAG    0.00   0.0  0
 CIJ  CONST_02  CAU  CAO  CAM  CAG    0.00   0.0  0
 CIJ  CONST_03  CAK  CAQ  CAI  CAH    0.00   0.0  0
 CIJ  CONST_04  CAK  CAP  CAN  CAH    0.00   0.0  0
 CIJ  CONST_05  CAP  CAN  CAH  CAI    0.00   0.0  0
 CIJ  CONST_06  CAP  CAK  CAQ  CAI    0.00   0.0  0
 CIJ  CONST_07  CAO  CAM  CAG  CAJ    0.00   0.0  0
 CIJ  CONST_08  CAO  CAU  CAT  CAJ    0.00   0.0  0
 CIJ  CONST_09  CAT  CAJ  CAG  CAM    0.00   0.0  0
 CIJ  CONST_10  CAT  CAU  CAO  CAM    0.00   0.0  0
 CIJ  CONST_11  CAQ  CAI  CAH  CAN    0.00   0.0  0
 CIJ  CONST_12  CAQ  CAK  CAP  CAN    0.00   0.0  0
 CIJ  CONST_13  CAT  CAR  NAV  CAS    0.00   0.0  0
 CIJ  CONST_14  CAQ  CAK  CAP  CL   180.00   0.0  0
 CIJ  CONST_15  CAH  CAN  CAP  CL   180.00   0.0  0
 CIJ  CONST_16  CAJ  CAG  CAM  OAC  180.00   0.0  0
 CIJ  CONST_17  CAU  CAO  CAM  OAC  180.00   0.0  0
 CIJ  CONST_18  CAG  CAM  CAO  OAD  180.00   0.0  0
 CIJ  CONST_19  CAS  CAU  CAO  OAD    0.00   0.0  0
 CIJ  CONST_20  CAT  CAU  CAO  OAD  180.00   0.0  0
 CIJ  CONST_21  CAI  CAH  CAN  FAE  180.00   0.0  0
 CIJ  CONST_22  CAK  CAP  CAN  FAE  180.00   0.0  0
 CIJ  CONST_23  CAL  CAQ  CAI  CAH  180.00   0.0  0
 CIJ  CONST_24  CAP  CAK  CAQ  CAL  180.00   0.0  0
 CIJ  CONST_25  CAS  NAV  CAR  OAA  180.00   0.0  0
 CIJ  CONST_26  CAT  CAR  NAV  CAL  180.00   0.0  0
 CIJ  CONST_27  HAK  CAK  CAQ  CAI  180.00   0.0  0
 CIJ  CONST_28  HAI  CAI  CAQ  CAK  180.00   0.0  0
 CIJ  CONST_29  HAJ  CAJ  CAG  CAM  180.00   0.0  0
 CIJ  CONST_30  HAG  CAG  CAM  CAO  180.00   0.0  0
 CIJ  CONST_31  HAH  CAH  CAN  CAP  180.00   0.0  0
 CIJ  CONST_32  CAL  NAV  CAR  OAA    0.00   0.0  0
 CIJ  Var_01    NAV  CAL  CAQ  CAI   79.39  30.0  2
 CIJ  Var_02    CAR  NAV  CAL  CAQ   80.37  30.0  3

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
 CIJ  plan-1  CL   0.020
 CIJ  plan-1  CAH  0.020
 CIJ  plan-1  CAI  0.020
 CIJ  plan-1  CAK  0.020
 CIJ  plan-1  CAN  0.020
 CIJ  plan-1  CAP  0.020
 CIJ  plan-1  CAQ  0.020
 CIJ  plan-1  HAH  0.020
 CIJ  plan-1  HAI  0.020
 CIJ  plan-1  HAK  0.020
 CIJ  plan-1  FAE  0.020
 CIJ  plan-1  CAL  0.020
 CIJ  plan-2  OAB  0.020
 CIJ  plan-2  OAC  0.020
 CIJ  plan-2  OAD  0.020
 CIJ  plan-2  CAG  0.020
 CIJ  plan-2  CAJ  0.020
 CIJ  plan-2  CAM  0.020
 CIJ  plan-2  CAO  0.020
 CIJ  plan-2  CAR  0.020
 CIJ  plan-2  CAS  0.020
 CIJ  plan-2  CAT  0.020
 CIJ  plan-2  CAU  0.020
 CIJ  plan-2  NAV  0.020
 CIJ  plan-2  HAG  0.020
 CIJ  plan-2  HAJ  0.020
 CIJ  plan-2  CAL  0.020
 CIJ  plan-2  OAA  0.020

