# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:31:18 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-benzamido-4-chloranyl-~{N}-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(Cl)c(NC(=O)c2ccccc2)c1
#
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
 T61  T61  3-benzamido-4-chloranyl-~{N}-oxidanyl-benzamide  ligand  31  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T61
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
 T61  N    N   NH1   0  -0.382  -4.9651  -0.8762  -0.2789
 T61  C    C   C     0   0.505  -3.7329  -1.1952   0.1704
 T61  O    O   O     0  -0.456  -3.4422  -2.2830   0.6315
 T61  C1   C   CR6   0  -0.047  -2.7432  -0.0800   0.0725
 T61  C10  C   CR16  0  -0.248   5.8351  -0.8810  -0.2598
 T61  C11  C   CR16  0  -0.241   5.1830   0.3421  -0.3337
 T61  C12  C   CR16  0  -0.284   3.8099   0.4103  -0.1486
 T61  C13  C   CR16  0  -0.312  -1.4039  -0.4253  -0.0595
 T61  C2   C   CR16  0  -0.298  -3.1123   1.2611   0.1226
 T61  C3   C   CR16  0  -0.198  -2.1468   2.2476   0.0215
 T61  C4   C   CR6   0  -0.118  -0.8160   1.8934  -0.1140
 T61  C5   C   CR6   0   0.452  -0.4220   0.5534  -0.1565
 T61  C6   C   C     0   0.514   1.6073  -0.7257   0.3575
 T61  C7   C   CR6   0  -0.033   3.0797  -0.7468   0.1180
 T61  C8   C   CR16  0  -0.266   3.7433  -1.9686   0.2137
 T61  C9   C   CR16  0  -0.241   5.1128  -2.0360   0.0143
 T61  N1   N   NH1   0  -0.754   0.9301   0.2399  -0.3210
 T61  O1   O   OH1   0  -0.537  -5.9021  -1.8598  -0.3743
 T61  O2   O   O     0  -0.451   1.0663  -1.5231   1.1003
 T61  CL   CL  CL    0  -0.093   0.3783   3.1378  -0.2215
 T61  H1   H   HNH1  0   0.420  -5.1140  -0.1050  -0.9147
 T61  H3   H   HCR6  0   0.268   5.7426   1.2468  -0.5301
 T61  H4   H   HCR6  0   0.251   3.3291   1.3808  -0.1806
 T61  H5   H   HCR6  0   0.283  -1.1256  -1.4669  -0.1157
 T61  H6   H   HCR6  0   0.278  -4.1434   1.5568   0.2624
 T61  H7   H   HCR6  0   0.293  -2.4263   3.2910   0.0675
 T61  H8   H   HCR6  0   0.265   3.1862  -2.8696   0.4343
 T61  H9   H   HCR6  0   0.266   5.6183  -2.9907   0.0756
 T61  H10  H   HNH1  0   0.416   1.4541   0.8313  -0.9476
 T61  H11  H   HOH1  0   0.481  -6.4940  -1.7382   0.3791
 T61  H2   H   HCR6  0   0.267   6.9057  -0.9337  -0.4075

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
 T61  C3   C2   aromatic  1.384  0.020  1.384
 T61  C3   C4   aromatic  1.384  0.020  1.384
 T61  C2   C1   aromatic  1.392  0.020  1.392
 T61  CL   C4   single    1.728  0.020  1.728
 T61  C4   C5   aromatic  1.397  0.020  1.397
 T61  N    O1   single    1.362  0.020  1.362
 T61  N    C    single    1.350  0.020  1.350
 T61  C1   C    single    1.494  0.020  1.494
 T61  C1   C13  aromatic  1.389  0.020  1.389
 T61  C    O    double    1.217  0.020  1.217
 T61  C5   C13  aromatic  1.390  0.020  1.390
 T61  C5   N1   single    1.398  0.020  1.398
 T61  N1   C6   single    1.361  0.020  1.361
 T61  C6   O2   double    1.217  0.020  1.217
 T61  C6   C7   single    1.492  0.020  1.492
 T61  C7   C8   aromatic  1.394  0.020  1.394
 T61  C7   C12  aromatic  1.394  0.020  1.394
 T61  C8   C9   aromatic  1.386  0.020  1.386
 T61  C12  C11  aromatic  1.387  0.020  1.387
 T61  C9   C10  aromatic  1.390  0.020  1.390
 T61  C11  C10  aromatic  1.388  0.020  1.388
 T61  N    H1   single    0.890  0.020  1.040
 T61  C10  H2   single    0.930  0.020  1.080
 T61  C11  H3   single    0.930  0.020  1.080
 T61  C12  H4   single    0.930  0.020  1.080
 T61  C13  H5   single    0.930  0.020  1.080
 T61  C2   H6   single    0.930  0.020  1.080
 T61  C3   H7   single    0.930  0.020  1.080
 T61  C8   H8   single    0.930  0.020  1.080
 T61  C9   H9   single    0.930  0.020  1.080
 T61  N1   H10  single    0.860  0.020  1.020
 T61  O1   H11  single    0.850  0.020  0.980

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
 T61  H1   N    O1   113.94  3.000
 T61  H1   N    C    121.62  3.000
 T61  O1   N    C    118.74  3.000
 T61  C1   C    O    122.26  3.000
 T61  O    C    N    123.75  3.000
 T61  C1   C    N    113.98  3.000
 T61  C2   C1   C13  119.90  3.000
 T61  C13  C1   C    117.34  3.000
 T61  C2   C1   C    122.76  3.000
 T61  H2   C10  C9   120.05  3.000
 T61  H2   C10  C11  120.03  3.000
 T61  C9   C10  C11  119.92  3.000
 T61  H3   C11  C12  119.69  3.000
 T61  H3   C11  C10  120.23  3.000
 T61  C12  C11  C10  120.08  3.000
 T61  H4   C12  C7   121.11  3.000
 T61  H4   C12  C11  118.64  3.000
 T61  C7   C12  C11  120.22  3.000
 T61  H5   C13  C5   119.58  3.000
 T61  H5   C13  C1   119.55  3.000
 T61  C5   C13  C1   120.84  3.000
 T61  H6   C2   C3   118.65  3.000
 T61  H6   C2   C1   121.38  3.000
 T61  C3   C2   C1   119.95  3.000
 T61  H7   C3   C4   119.99  3.000
 T61  H7   C3   C2   120.29  3.000
 T61  C4   C3   C2   119.71  3.000
 T61  CL   C4   C5   119.59  3.000
 T61  C5   C4   C3   121.30  3.000
 T61  CL   C4   C3   119.11  3.000
 T61  N1   C5   C4   119.43  3.000
 T61  N1   C5   C13  122.26  3.000
 T61  C4   C5   C13  118.29  3.000
 T61  O2   C6   N1   123.25  3.000
 T61  O2   C6   C7   121.84  3.000
 T61  N1   C6   C7   114.91  3.000
 T61  C8   C7   C6   118.12  3.000
 T61  C8   C7   C12  119.43  3.000
 T61  C6   C7   C12  122.41  3.000
 T61  H8   C8   C9   119.85  3.000
 T61  H8   C8   C7   119.92  3.000
 T61  C9   C8   C7   120.23  3.000
 T61  H9   C9   C8   119.77  3.000
 T61  H9   C9   C10  120.11  3.000
 T61  C8   C9   C10  120.11  3.000
 T61  H10  N1   C6   117.87  3.000
 T61  H10  N1   C5   116.38  3.000
 T61  C6   N1   C5   125.58  3.000
 T61  H11  O1   N    106.03  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
 T61  CONST_01  C4  C3   C2   C1     0.00   0.0  0
 T61  CONST_02  C4  C5   C13  C1     0.00   0.0  0
 T61  CONST_03  C7  C8   C9   C10    0.00   0.0  0
 T61  CONST_04  C7  C12  C11  C10    0.00   0.0  0
 T61  CONST_05  C8  C7   C12  C11    0.00   0.0  0
 T61  CONST_06  C8  C9   C10  C11    0.00   0.0  0
 T61  CONST_07  C9  C8   C7   C12    0.00   0.0  0
 T61  CONST_08  C9  C10  C11  C12    0.00   0.0  0
 T61  CONST_09  C3  C2   C1   C13    0.00   0.0  0
 T61  CONST_10  C3  C4   C5   C13    0.00   0.0  0
 T61  CONST_11  C5  C4   C3   C2     0.00   0.0  0
 T61  CONST_12  C5  C13  C1   C2     0.00   0.0  0
 T61  CONST_13  C3  C2   C1   C    180.00   0.0  0
 T61  CONST_14  C5  C13  C1   C    180.00   0.0  0
 T61  CONST_15  N1  C5   C13  C1   180.00   0.0  0
 T61  CONST_16  C6  C7   C12  C11  180.00   0.0  0
 T61  CONST_17  CL  C4   C5   C13  180.00   0.0  0
 T61  CONST_18  CL  C4   C3   C2   180.00   0.0  0
 T61  CONST_19  N1  C5   C4   C3   180.00   0.0  0
 T61  CONST_20  C9  C8   C7   C6   180.00   0.0  0
 T61  CONST_21  H7  C3   C2   C1   180.00   0.0  0
 T61  CONST_22  H8  C8   C9   C10  180.00   0.0  0
 T61  CONST_23  H4  C12  C11  C10  180.00   0.0  0
 T61  CONST_24  H9  C9   C10  C11  180.00   0.0  0
 T61  CONST_25  H2  C10  C11  C12  180.00   0.0  0
 T61  CONST_26  H6  C2   C1   C13  180.00   0.0  0
 T61  CONST_27  H5  C13  C1   C2   180.00   0.0  0
 T61  CONST_28  H3  C11  C12  C7   180.00   0.0  0
 T61  CONST_29  C7  C6   N1   C5   180.00   0.0  0
 T61  CONST_33  O1  N    C    C1   180.00   0.0  0
 T61  CONST_34  O2  C6   N1   C5     0.00   0.0  0
 T61  CONST_36  O1  N    C    O      0.00   0.0  0
 T61  Var_01    C2  C1   C    N     28.10  30.0  2
 T61  Var_02    N1  C6   C7   C12   31.98  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
 T61  plan-1  C    0.020
 T61  plan-1  C1   0.020
 T61  plan-1  C13  0.020
 T61  plan-1  C2   0.020
 T61  plan-1  C3   0.020
 T61  plan-1  C4   0.020
 T61  plan-1  C5   0.020
 T61  plan-1  N1   0.020
 T61  plan-1  CL   0.020
 T61  plan-1  H5   0.020
 T61  plan-1  H6   0.020
 T61  plan-1  H7   0.020
 T61  plan-2  C10  0.020
 T61  plan-2  C11  0.020
 T61  plan-2  C12  0.020
 T61  plan-2  C6   0.020
 T61  plan-2  C7   0.020
 T61  plan-2  C8   0.020
 T61  plan-2  C9   0.020
 T61  plan-2  H3   0.020
 T61  plan-2  H4   0.020
 T61  plan-2  H8   0.020
 T61  plan-2  H9   0.020
 T61  plan-2  H2   0.020
 T61  plan-3  N    0.020
 T61  plan-3  C    0.020
 T61  plan-3  O    0.020
 T61  plan-3  C1   0.020
 T61  plan-3  O1   0.020
 T61  plan-3  H1   0.020
 T61  plan-4  C5   0.020
 T61  plan-4  C6   0.020
 T61  plan-4  C7   0.020
 T61  plan-4  N1   0.020
 T61  plan-4  O2   0.020
 T61  plan-4  H10  0.020

