# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:55:50 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-iodo-N-phenyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1ccccc1C(=O)Nc2ccccc2
#
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
 BOL  BOL  2-iodo-N-phenyl-benzamide  ligand  26  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BOL
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
 BOL  I    I  I     0   0.074  -2.1371   1.1636  -0.7511
 BOL  N    N  NH1   0  -0.730   1.6364  -0.8600  -0.0846
 BOL  O    O  O     0  -0.439   0.4237   0.5187   1.2704
 BOL  C1   C  CR6   0  -0.255  -1.8887  -0.8513  -0.1892
 BOL  C2   C  CR6   0  -0.002  -0.6701  -1.3387   0.2783
 BOL  C3   C  CR16  0  -0.255  -0.5658  -2.6958   0.5796
 BOL  C4   C  CR16  0  -0.242  -1.6494  -3.5464   0.4279
 BOL  C5   C  CR16  0  -0.242  -2.8534  -3.0458  -0.0415
 BOL  C6   C  CR16  0  -0.222  -2.9741  -1.6994  -0.3580
 BOL  C7   C  C     0   0.483   0.5089  -0.4510   0.5422
 BOL  C8   C  CR6   0   0.375   2.9276  -0.3203  -0.0303
 BOL  C9   C  CR16  0  -0.315   3.2851   0.7944   0.7289
 BOL  C10  C  CR16  0  -0.244   4.5994   1.2443   0.7053
 BOL  C11  C  CR16  0  -0.270   5.5666   0.6082  -0.0579
 BOL  C12  C  CR16  0  -0.244   5.2068  -0.5017  -0.8118
 BOL  C13  C  CR16  0  -0.346   3.9021  -0.9624  -0.7987
 BOL  HN   H  HNH1  0   0.425   1.5361  -1.6509  -0.7040
 BOL  H3   H  HCR6  0   0.281   0.3712  -3.0875   0.9558
 BOL  H4   H  HCR6  0   0.274  -1.5510  -4.5941   0.6766
 BOL  H5   H  HCR6  0   0.276  -3.7055  -3.6998  -0.1698
 BOL  H6   H  HCR6  0   0.285  -3.9146  -1.3229  -0.7359
 BOL  H9   H  HCR6  0   0.282   2.5601   1.3121   1.3341
 BOL  H10  H  HCR6  0   0.260   4.8623   2.1116   1.2971
 BOL  H11  H  HCR6  0   0.257   6.5858   0.9703  -0.0662
 BOL  H12  H  HCR6  0   0.262   5.9432  -1.0148  -1.4161
 BOL  H13  H  HCR6  0   0.272   3.6340  -1.8316  -1.3880

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
 BOL  I    C1   single    2.106  0.020  2.106
 BOL  N    C7   single    1.353  0.020  1.353
 BOL  N    C8   single    1.401  0.020  1.401
 BOL  O    C7   double    1.216  0.020  1.216
 BOL  C1   C2   aromatic  1.393  0.020  1.393
 BOL  C1   C6   aromatic  1.388  0.020  1.388
 BOL  C2   C3   aromatic  1.394  0.020  1.394
 BOL  C2   C7   single    1.499  0.020  1.499
 BOL  C3   C4   aromatic  1.386  0.020  1.386
 BOL  C4   C5   aromatic  1.386  0.020  1.386
 BOL  C5   C6   aromatic  1.388  0.020  1.388
 BOL  C8   C9   aromatic  1.395  0.020  1.395
 BOL  C8   C13  aromatic  1.397  0.020  1.397
 BOL  C9   C10  aromatic  1.389  0.020  1.389
 BOL  C10  C11  aromatic  1.387  0.020  1.387
 BOL  C11  C12  aromatic  1.389  0.020  1.389
 BOL  C12  C13  aromatic  1.384  0.020  1.384
 BOL  N    HN   single    0.860  0.020  1.020
 BOL  C3   H3   single    0.930  0.020  1.080
 BOL  C4   H4   single    0.930  0.020  1.080
 BOL  C5   H5   single    0.930  0.020  1.080
 BOL  C6   H6   single    0.930  0.020  1.080
 BOL  C9   H9   single    0.930  0.020  1.080
 BOL  C10  H10  single    0.930  0.020  1.080
 BOL  C11  H11  single    0.930  0.020  1.080
 BOL  C12  H12  single    0.930  0.020  1.080
 BOL  C13  H13  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
 BOL  HN   N    C8   114.66  3.000
 BOL  HN   N    C7   115.98  3.000
 BOL  C8   N    C7   129.33  3.000
 BOL  C6   C1   C2   120.73  3.000
 BOL  C6   C1   I    117.38  3.000
 BOL  C2   C1   I    121.82  3.000
 BOL  C7   C2   C3   118.65  3.000
 BOL  C7   C2   C1   122.67  3.000
 BOL  C3   C2   C1   118.60  3.000
 BOL  H3   C3   C4   119.51  3.000
 BOL  H3   C3   C2   119.47  3.000
 BOL  C4   C3   C2   121.01  3.000
 BOL  H4   C4   C5   120.46  3.000
 BOL  H4   C4   C3   119.89  3.000
 BOL  C5   C4   C3   119.65  3.000
 BOL  H5   C5   C6   119.39  3.000
 BOL  H5   C5   C4   120.41  3.000
 BOL  C6   C5   C4   120.20  3.000
 BOL  H6   C6   C5   119.53  3.000
 BOL  H6   C6   C1   120.67  3.000
 BOL  C5   C6   C1   119.80  3.000
 BOL  C2   C7   O    121.51  3.000
 BOL  C2   C7   N    113.25  3.000
 BOL  O    C7   N    125.23  3.000
 BOL  C13  C8   C9   119.19  3.000
 BOL  C13  C8   N    116.40  3.000
 BOL  C9   C8   N    124.41  3.000
 BOL  H9   C9   C10  119.38  3.000
 BOL  H9   C9   C8   121.16  3.000
 BOL  C10  C9   C8   119.46  3.000
 BOL  H10  C10  C11  119.94  3.000
 BOL  H10  C10  C9   118.68  3.000
 BOL  C11  C10  C9   121.38  3.000
 BOL  H11  C11  C12  120.49  3.000
 BOL  H11  C11  C10  120.52  3.000
 BOL  C12  C11  C10  118.98  3.000
 BOL  H12  C12  C13  119.28  3.000
 BOL  H12  C12  C11  120.38  3.000
 BOL  C13  C12  C11  120.34  3.000
 BOL  H13  C13  C12  119.67  3.000
 BOL  H13  C13  C8   119.68  3.000
 BOL  C12  C13  C8   120.65  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
 BOL  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 BOL  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 BOL  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 BOL  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 BOL  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 BOL  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 BOL  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 BOL  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 BOL  CONST_09  C12  C13  C8   C9      0.00   0.0  0
 BOL  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 BOL  CONST_11  C13  C8   C9   C10     0.00   0.0  0
 BOL  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 BOL  CONST_13  C3   C2   C1   I     180.00   0.0  0
 BOL  CONST_14  C5   C6   C1   I     180.00   0.0  0
 BOL  CONST_15  C10  C9   C8   N     180.00   0.0  0
 BOL  CONST_16  C12  C13  C8   N     180.00   0.0  0
 BOL  CONST_17  C7   C2   C3   C4    180.00   0.0  0
 BOL  CONST_18  C7   C2   C1   C6    180.00   0.0  0
 BOL  CONST_19  H3   C3   C2   C1    180.00   0.0  0
 BOL  CONST_20  H5   C5   C6   C1    180.00   0.0  0
 BOL  CONST_21  H6   C6   C1   C2    180.00   0.0  0
 BOL  CONST_22  H4   C4   C3   C2    180.00   0.0  0
 BOL  CONST_23  H10  C10  C9   C8    180.00   0.0  0
 BOL  CONST_24  H12  C12  C13  C8    180.00   0.0  0
 BOL  CONST_25  H13  C13  C8   C9    180.00   0.0  0
 BOL  CONST_26  H11  C11  C10  C9    180.00   0.0  0
 BOL  CONST_27  H9   C9   C10  C11   180.00   0.0  0
 BOL  CONST_28  C8   N    C7   C2    180.00   0.0  0
 BOL  CONST_29  C9   C8   N    C7      0.00   0.0  0
 BOL  CONST_30  C13  C8   N    C7    180.00   0.0  0
 BOL  CONST_31  HN   N    C8   C9    180.00   0.0  0
 BOL  CONST_32  C8   N    C7   O       0.00   0.0  0
 BOL  Var_01    C1   C2   C7   N    -127.04  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
 BOL  plan-1  I    0.020
 BOL  plan-1  C1   0.020
 BOL  plan-1  C2   0.020
 BOL  plan-1  C3   0.020
 BOL  plan-1  C4   0.020
 BOL  plan-1  C5   0.020
 BOL  plan-1  C6   0.020
 BOL  plan-1  C7   0.020
 BOL  plan-1  H3   0.020
 BOL  plan-1  H4   0.020
 BOL  plan-1  H5   0.020
 BOL  plan-1  H6   0.020
 BOL  plan-2  N    0.020
 BOL  plan-2  C8   0.020
 BOL  plan-2  C9   0.020
 BOL  plan-2  C10  0.020
 BOL  plan-2  C11  0.020
 BOL  plan-2  C12  0.020
 BOL  plan-2  C13  0.020
 BOL  plan-2  H9   0.020
 BOL  plan-2  H10  0.020
 BOL  plan-2  H11  0.020
 BOL  plan-2  H12  0.020
 BOL  plan-2  H13  0.020
 BOL  plan-3  N    0.020
 BOL  plan-3  O    0.020
 BOL  plan-3  C2   0.020
 BOL  plan-3  C7   0.020
 BOL  plan-3  C8   0.020
 BOL  plan-3  HN   0.020

