# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 01:38:24 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2C(=O)N(c3ccc(cc3)C#N)C(=O)c12
#
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
 C16  C16  4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile  ligand  30  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C16
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
 C16  N41   N  NS    0  -0.246  -6.6103   0.2347   0.1337
 C16  C39   C  CSP   0   0.063  -5.4607   0.1706   0.0977
 C16  C32   C  CR6   0   0.006  -4.0360   0.0927   0.0524
 C16  C30   C  CR16  0  -0.240  -3.3232   0.9521  -0.7822
 C16  C28   C  CR16  0  -0.263  -1.9438   0.8704  -0.8295
 C16  C34   C  CR16  0  -0.240  -3.3693  -0.8412   0.8437
 C16  C36   C  CR16  0  -0.262  -1.9888  -0.9088   0.8045
 C16  C26   C  CR6   0   0.355  -1.2802  -0.0563  -0.0341
 C16  N19   N  NR5   0  -0.730   0.1263  -0.1342  -0.0781
 C16  C21   C  CR5   0   0.575   0.8341  -1.2836  -0.4269
 C16  O23   O  O     0  -0.386   0.3417  -2.3354  -0.7379
 C16  C6    C  CR56  0  -0.018   2.2623  -0.9139  -0.3367
 C16  C4    C  CR16  0  -0.322   3.3759  -1.6856  -0.5814
 C16  C2    C  CR16  0  -0.225   4.6120  -1.0671  -0.4124
 C16  C15   C  CR5   0   0.561   0.9792   0.9327   0.2269
 C16  O17   O  O     0  -0.386   0.6088   2.0262   0.5628
 C16  C8    C  CR56  0  -0.056   2.3526   0.4139   0.0554
 C16  C10   C  CR6   0   0.088   3.5726   1.0503   0.2316
 C16  C13   C  CH3   0  -0.729   3.7005   2.4804   0.6521
 C16  C1    C  CR16  0  -0.300   4.7021   0.2620  -0.0164
 C16  H30   H  HCR6  0   0.291  -3.8449   1.6728  -1.3963
 C16  H28   H  HCR6  0   0.289  -1.3905   1.5203  -1.4933
 C16  H34   H  HCR6  0   0.291  -3.9258  -1.5028   1.4929
 C16  H36   H  HCR6  0   0.290  -1.4690  -1.6172   1.4347
 C16  H4    H  HCR6  0   0.277   3.2992  -2.7203  -0.8867
 C16  H2    H  HCR6  0   0.279   5.5205  -1.6269  -0.5901
 C16  H13   H  HCH3  0   0.257   3.2152   2.6600   1.6113
 C16  H13A  H  HCH3  0   0.253   4.7476   2.7604   0.7462
 C16  H13B  H  HCH3  0   0.258   3.2353   3.1489  -0.0728
 C16  H1    H  HCR6  0   0.272   5.6829   0.7041   0.1069

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
 C16  C39  N41   triple    1.152  0.020  1.152
 C16  C39  C32   single    1.428  0.020  1.428
 C16  C34  C32   aromatic  1.394  0.020  1.394
 C16  C32  C30   aromatic  1.394  0.020  1.394
 C16  C30  C28   aromatic  1.383  0.020  1.383
 C16  C30  H30   single    0.930  0.020  1.080
 C16  C26  C28   aromatic  1.390  0.020  1.390
 C16  C28  H28   single    0.930  0.020  1.080
 C16  C34  C36   aromatic  1.383  0.020  1.383
 C16  C34  H34   single    0.930  0.020  1.080
 C16  C36  C26   aromatic  1.390  0.020  1.390
 C16  C36  H36   single    0.930  0.020  1.080
 C16  C26  N19   single    1.409  0.020  1.409
 C16  C21  N19   single    1.394  0.020  1.394
 C16  N19  C15   single    1.400  0.020  1.400
 C16  O23  C21   double    1.202  0.020  1.202
 C16  C21  C6    single    1.478  0.020  1.478
 C16  C6   C4    aromatic  1.377  0.020  1.377
 C16  C6   C8    aromatic  1.387  0.020  1.387
 C16  C4   C2    aromatic  1.393  0.020  1.393
 C16  C4   H4    single    0.930  0.020  1.080
 C16  C2   C1    aromatic  1.390  0.020  1.390
 C16  C2   H2    single    0.930  0.020  1.080
 C16  C15  O17   double    1.202  0.020  1.202
 C16  C15  C8    single    1.478  0.020  1.478
 C16  C8   C10   aromatic  1.387  0.020  1.387
 C16  C10  C1    aromatic  1.399  0.020  1.399
 C16  C10  C13   single    1.496  0.020  1.496
 C16  C13  H13   single    0.970  0.020  1.090
 C16  C13  H13A  single    0.970  0.020  1.090
 C16  C13  H13B  single    0.970  0.020  1.090
 C16  C1   H1    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
 C16  C32   C39  N41   180.00  3.000
 C16  C34   C32  C30   120.56  3.000
 C16  C30   C32  C39   119.71  3.000
 C16  C34   C32  C39   119.73  3.000
 C16  H30   C30  C28   120.10  3.000
 C16  H30   C30  C32   120.29  3.000
 C16  C28   C30  C32   119.61  3.000
 C16  H28   C28  C26   120.52  3.000
 C16  H28   C28  C30   119.73  3.000
 C16  C26   C28  C30   119.75  3.000
 C16  H34   C34  C36   120.07  3.000
 C16  H34   C34  C32   120.31  3.000
 C16  C36   C34  C32   119.61  3.000
 C16  H36   C36  C26   120.55  3.000
 C16  H36   C36  C34   119.70  3.000
 C16  C26   C36  C34   119.75  3.000
 C16  N19   C26  C36   119.59  3.000
 C16  N19   C26  C28   119.70  3.000
 C16  C36   C26  C28   120.71  3.000
 C16  C15   N19  C21   111.94  3.000
 C16  C15   N19  C26   124.00  3.000
 C16  C21   N19  C26   124.06  3.000
 C16  C6    C21  O23   129.07  3.000
 C16  C6    C21  N19   105.61  3.000
 C16  O23   C21  N19   125.31  3.000
 C16  C8    C6   C4    122.27  3.000
 C16  C8    C6   C21   108.63  3.000
 C16  C4    C6   C21   129.09  3.000
 C16  H4    C4   C2    121.47  3.000
 C16  H4    C4   C6    121.94  3.000
 C16  C2    C4   C6    116.59  3.000
 C16  H2    C2   C1    119.16  3.000
 C16  H2    C2   C4    119.72  3.000
 C16  C1    C2   C4    121.12  3.000
 C16  C8    C15  O17   129.63  3.000
 C16  C8    C15  N19   105.87  3.000
 C16  O17   C15  N19   124.50  3.000
 C16  C10   C8   C15   129.90  3.000
 C16  C10   C8   C6    122.15  3.000
 C16  C15   C8   C6    107.95  3.000
 C16  C1    C10  C13   121.28  3.000
 C16  C13   C10  C8    123.32  3.000
 C16  C1    C10  C8    115.40  3.000
 C16  H13B  C13  H13A  108.08  3.000
 C16  H13B  C13  H13   107.10  3.000
 C16  H13A  C13  H13   108.06  3.000
 C16  H13B  C13  C10   111.27  3.000
 C16  H13A  C13  C10   110.64  3.000
 C16  H13   C13  C10   111.52  3.000
 C16  H1    C1   C10   118.74  3.000
 C16  H1    C1   C2    118.79  3.000
 C16  C10   C1   C2    122.47  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
 C16  CONST_01  C26  C36  C34  C32     0.00   0.0  0
 C16  CONST_02  C26  C28  C30  C32     0.00   0.0  0
 C16  CONST_03  C36  C34  C32  C30     0.00   0.0  0
 C16  CONST_04  C36  C26  C28  C30     0.00   0.0  0
 C16  CONST_05  C34  C32  C30  C28     0.00   0.0  0
 C16  CONST_06  C34  C36  C26  C28     0.00   0.0  0
 C16  CONST_07  C1   C2   C4   C6      0.00   0.0  0
 C16  CONST_08  C1   C10  C8   C6      0.00   0.0  0
 C16  CONST_09  C10  C8   C6   C4      0.00   0.0  0
 C16  CONST_10  C10  C1   C2   C4      0.00   0.0  0
 C16  CONST_11  C8   C6   C4   C2      0.00   0.0  0
 C16  CONST_12  C8   C10  C1   C2      0.00   0.0  0
 C16  CONST_13  N19  C26  C28  C30   180.00   0.0  0
 C16  CONST_14  N19  C26  C36  C34   180.00   0.0  0
 C16  CONST_15  C6   C21  N19  C26   180.00   0.0  0
 C16  CONST_16  C15  N19  C21  C6      0.00   0.0  0
 C16  CONST_17  C36  C34  C32  C39   180.00   0.0  0
 C16  CONST_18  C28  C30  C32  C39   180.00   0.0  0
 C16  CONST_19  C13  C10  C8   C6    180.00   0.0  0
 C16  CONST_20  C13  C10  C1   C2    180.00   0.0  0
 C16  CONST_21  C13  C10  C8   C15     0.00   0.0  0
 C16  CONST_22  O23  C21  N19  C26     0.00   0.0  0
 C16  CONST_23  C15  N19  C21  O23   180.00   0.0  0
 C16  CONST_24  H36  C36  C34  C32   180.00   0.0  0
 C16  CONST_25  H28  C28  C30  C32   180.00   0.0  0
 C16  CONST_26  H34  C34  C32  C30   180.00   0.0  0
 C16  CONST_27  H30  C30  C32  C34   180.00   0.0  0
 C16  CONST_28  H4   C4   C6   C21     0.00   0.0  0
 C16  CONST_29  H2   C2   C4   C6    180.00   0.0  0
 C16  CONST_30  H1   C1   C2   C4    180.00   0.0  0
 C16  Var_01    C21  N19  C26  C28  -121.07  30.0  2
 C16  Var_02    H13  C13  C10  C8     58.54  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
 C16  plan-1  N41  0.020
 C16  plan-1  C39  0.020
 C16  plan-1  C32  0.020
 C16  plan-1  C30  0.020
 C16  plan-1  C28  0.020
 C16  plan-1  C34  0.020
 C16  plan-1  C36  0.020
 C16  plan-1  C26  0.020
 C16  plan-1  N19  0.020
 C16  plan-1  H30  0.020
 C16  plan-1  H28  0.020
 C16  plan-1  H34  0.020
 C16  plan-1  H36  0.020
 C16  plan-2  C26  0.020
 C16  plan-2  N19  0.020
 C16  plan-2  C21  0.020
 C16  plan-2  O23  0.020
 C16  plan-2  C6   0.020
 C16  plan-2  C4   0.020
 C16  plan-2  C2   0.020
 C16  plan-2  C15  0.020
 C16  plan-2  O17  0.020
 C16  plan-2  C8   0.020
 C16  plan-2  C10  0.020
 C16  plan-2  C13  0.020
 C16  plan-2  C1   0.020
 C16  plan-2  H4   0.020
 C16  plan-2  H2   0.020
 C16  plan-2  H1   0.020

