# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:54:05 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-[(4-chlorophenyl)methyl]-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2ccccc2n1Cc3ccc(Cl)cc3
#
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
 QTS  QTS  1-[(4-chlorophenyl)methyl]-1H-benzimidazol-2-amine  ligand  30  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QTS
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
 QTS  N1   N   N     0  -0.525  36.1011  30.5259  23.6167
 QTS  C4   C   CR16  0  -0.286  33.1040  30.2367  26.4475
 QTS  C5   C   CR16  0  -0.317  32.9551  29.7177  25.1659
 QTS  C6   C   CR56  0   0.345  34.0247  29.8696  24.3009
 QTS  C8   C   CR6   0   0.132  32.6996  29.7573  21.0757
 QTS  C10  C   CR16  0  -0.196  31.6548  31.8512  20.4744
 QTS  C13  C   CR16  0  -0.319  32.6444  29.3654  19.7446
 QTS  C    C   CR5   0   0.629  35.4738  29.9123  22.6453
 QTS  C1   C   CR56  0   0.150  35.2164  30.5177  24.6693
 QTS  C11  C   CR6   0  -0.053  31.6081  31.4344  19.1517
 QTS  C12  C   CR16  0  -0.195  32.0984  30.1958  18.7750
 QTS  C2   C   CR16  0  -0.345  35.3472  31.0301  25.9556
 QTS  C3   C   CR16  0  -0.275  34.2816  30.8810  26.8344
 QTS  C9   C   CR16  0  -0.284  32.2003  31.0081  21.4288
 QTS  N2   N   NR5   0  -0.557  34.2218  29.4835  22.9897
 QTS  CL   CL  CL    0  -0.128  30.9306  32.4857  17.9517
 QTS  H1   H   HCR6  0   0.250  32.2919  30.1398  27.1559
 QTS  H2   H   HCR6  0   0.264  32.0394  29.2220  24.8682
 QTS  H3   H   HCH2  0   0.302  32.4741  28.4295  22.7456
 QTS  H4   H   HCH2  0   0.290  33.7383  27.9643  21.6469
 QTS  H5   H   HCR6  0   0.282  31.2692  32.8204  20.7598
 QTS  H6   H   HCR6  0   0.269  33.0341  28.3993  19.4479
 QTS  H7   H   HNH2  0   0.401  36.9473  29.8868  21.2948
 QTS  H8   H   HNH2  0   0.401  35.6070  28.9818  20.8396
 QTS  H9   H   HCR6  0   0.282  32.0660  29.8801  17.7412
 QTS  H10  H   HCR6  0   0.247  36.2564  31.5324  26.2613
 QTS  H11  H   HCR6  0   0.247  34.3633  31.2743  27.8396
 QTS  H12  H   HCR6  0   0.263  32.2319  31.3411  22.4594
 QTS  C7   C   CH2   0  -0.428  33.2721  28.8316  22.1200
 QTS  N    N   NH2   0  -0.850  35.9535  29.7515  21.3890

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
 QTS  CL   C11  single    1.733  0.020  1.733
 QTS  C12  C11  aromatic  1.384  0.020  1.384
 QTS  C12  C13  aromatic  1.388  0.020  1.388
 QTS  C11  C10  aromatic  1.388  0.020  1.388
 QTS  C13  C8   aromatic  1.389  0.020  1.389
 QTS  C10  C9   aromatic  1.385  0.020  1.385
 QTS  C8   C9   aromatic  1.392  0.020  1.392
 QTS  C8   C7   single    1.508  0.020  1.508
 QTS  N    C    single    1.354  0.020  1.354
 QTS  C7   N2   single    1.443  0.020  1.443
 QTS  C    N2   aromatic  1.367  0.020  1.367
 QTS  C    N1   aromatic  1.309  0.020  1.309
 QTS  N2   C6   aromatic  1.381  0.020  1.381
 QTS  N1   C1   aromatic  1.375  0.020  1.375
 QTS  C6   C1   aromatic  1.406  0.020  1.406
 QTS  C6   C5   aromatic  1.384  0.020  1.384
 QTS  C1   C2   aromatic  1.391  0.020  1.391
 QTS  C5   C4   aromatic  1.391  0.020  1.391
 QTS  C2   C3   aromatic  1.389  0.020  1.389
 QTS  C4   C3   aromatic  1.397  0.020  1.397
 QTS  C4   H1   single    0.930  0.020  1.080
 QTS  C5   H2   single    0.930  0.020  1.080
 QTS  C7   H3   single    0.970  0.020  1.090
 QTS  C7   H4   single    0.970  0.020  1.090
 QTS  C10  H5   single    0.930  0.020  1.080
 QTS  C13  H6   single    0.930  0.020  1.080
 QTS  N    H7   single    0.890  0.020  1.040
 QTS  N    H8   single    0.890  0.020  1.040
 QTS  C12  H9   single    0.930  0.020  1.080
 QTS  C2   H10  single    0.930  0.020  1.080
 QTS  C3   H11  single    0.930  0.020  1.080
 QTS  C9   H12  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
 QTS  C1   N1   C    104.88  3.000
 QTS  H1   C4   C3   119.52  3.000
 QTS  H1   C4   C5   119.32  3.000
 QTS  C3   C4   C5   121.17  3.000
 QTS  H2   C5   C6   122.13  3.000
 QTS  H2   C5   C4   120.98  3.000
 QTS  C6   C5   C4   116.89  3.000
 QTS  N2   C6   C1   104.88  3.000
 QTS  C1   C6   C5   122.82  3.000
 QTS  N2   C6   C5   132.30  3.000
 QTS  C9   C8   C13  118.84  3.000
 QTS  C9   C8   C7   120.79  3.000
 QTS  C13  C8   C7   120.37  3.000
 QTS  H5   C10  C9   120.27  3.000
 QTS  H5   C10  C11  120.58  3.000
 QTS  C9   C10  C11  119.15  3.000
 QTS  H6   C13  C12  118.93  3.000
 QTS  H6   C13  C8   119.99  3.000
 QTS  C12  C13  C8   121.08  3.000
 QTS  N2   C    N    121.38  3.000
 QTS  N2   C    N1   113.51  3.000
 QTS  N    C    N1   125.05  3.000
 QTS  C2   C1   C6   119.47  3.000
 QTS  C2   C1   N1   130.18  3.000
 QTS  C6   C1   N1   110.34  3.000
 QTS  CL   C11  C12  119.52  3.000
 QTS  C12  C11  C10  121.08  3.000
 QTS  CL   C11  C10  119.40  3.000
 QTS  H9   C12  C11  120.71  3.000
 QTS  H9   C12  C13  120.31  3.000
 QTS  C11  C12  C13  118.97  3.000
 QTS  H10  C2   C3   121.02  3.000
 QTS  H10  C2   C1   120.73  3.000
 QTS  C3   C2   C1   118.25  3.000
 QTS  H11  C3   C2   119.38  3.000
 QTS  H11  C3   C4   119.23  3.000
 QTS  C2   C3   C4   121.40  3.000
 QTS  H12  C9   C10  118.66  3.000
 QTS  H12  C9   C8   120.45  3.000
 QTS  C10  C9   C8   120.88  3.000
 QTS  C    N2   C7   126.32  3.000
 QTS  C    N2   C6   106.39  3.000
 QTS  C7   N2   C6   127.19  3.000
 QTS  H4   C7   H3   105.54  3.000
 QTS  H4   C7   N2   109.81  3.000
 QTS  H3   C7   N2   107.59  3.000
 QTS  H4   C7   C8   110.45  3.000
 QTS  H3   C7   C8   110.22  3.000
 QTS  N2   C7   C8   112.94  3.000
 QTS  H8   N    H7   113.02  3.000
 QTS  H8   N    C    118.36  3.000
 QTS  H7   N    C    114.85  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
 QTS  CONST_01  C6   N2   C    N1     0.00   0.0  0
 QTS  CONST_02  N2   C6   C1   N1     0.00   0.0  0
 QTS  CONST_03  C5   C6   C1   N1   180.00   0.0  0
 QTS  CONST_04  C3   C2   C1   N1   180.00   0.0  0
 QTS  CONST_05  N2   C6   C5   C4   180.00   0.0  0
 QTS  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 QTS  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 QTS  CONST_08  C    N2   C6   C5   180.00   0.0  0
 QTS  CONST_09  C2   C1   C6   C5     0.00   0.0  0
 QTS  CONST_10  C2   C3   C4   C5     0.00   0.0  0
 QTS  CONST_11  C    N1   C1   C6     0.00   0.0  0
 QTS  CONST_12  C3   C2   C1   C6     0.00   0.0  0
 QTS  CONST_13  C3   C4   C5   C6     0.00   0.0  0
 QTS  CONST_14  C11  C12  C13  C8     0.00   0.0  0
 QTS  CONST_15  C11  C10  C9   C8     0.00   0.0  0
 QTS  CONST_16  C13  C12  C11  C10    0.00   0.0  0
 QTS  CONST_17  C13  C8   C9   C10    0.00   0.0  0
 QTS  CONST_18  C1   C6   N2   C      0.00   0.0  0
 QTS  CONST_19  C2   C1   N1   C    180.00   0.0  0
 QTS  CONST_20  N2   C    N1   C1     0.00   0.0  0
 QTS  CONST_21  C9   C10  C11  C12    0.00   0.0  0
 QTS  CONST_22  C9   C8   C13  C12    0.00   0.0  0
 QTS  CONST_23  N2   C6   C1   C2   180.00   0.0  0
 QTS  CONST_24  C7   N2   C    N1   180.00   0.0  0
 QTS  CONST_25  C7   N2   C6   C5     0.00   0.0  0
 QTS  CONST_26  N    C    N2   C6   180.00   0.0  0
 QTS  CONST_27  C12  C13  C8   C7   180.00   0.0  0
 QTS  CONST_28  C10  C9   C8   C7   180.00   0.0  0
 QTS  CONST_29  C1   C6   N2   C7   180.00   0.0  0
 QTS  CONST_30  CL   C11  C12  C13  180.00   0.0  0
 QTS  CONST_31  C1   N1   C    N    180.00   0.0  0
 QTS  CONST_32  CL   C11  C10  C9   180.00   0.0  0
 QTS  CONST_33  H10  C2   C1   N1     0.00   0.0  0
 QTS  CONST_34  H11  C3   C4   C5   180.00   0.0  0
 QTS  CONST_35  H1   C4   C5   C6   180.00   0.0  0
 QTS  CONST_36  H9   C12  C13  C8   180.00   0.0  0
 QTS  CONST_37  H5   C10  C9   C8   180.00   0.0  0
 QTS  CONST_38  H12  C9   C8   C13  180.00   0.0  0
 QTS  CONST_39  H2   C5   C6   C1   180.00   0.0  0
 QTS  CONST_40  H6   C13  C12  C11  180.00   0.0  0
 QTS  Var_01    C8   C7   N2   C6   105.49  30.0  2
 QTS  Var_02    N2   C7   C8   C13  132.25  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
 QTS  plan-1  C8   0.020
 QTS  plan-1  C10  0.020
 QTS  plan-1  C13  0.020
 QTS  plan-1  C11  0.020
 QTS  plan-1  C12  0.020
 QTS  plan-1  C9   0.020
 QTS  plan-1  CL   0.020
 QTS  plan-1  H5   0.020
 QTS  plan-1  H6   0.020
 QTS  plan-1  H9   0.020
 QTS  plan-1  H12  0.020
 QTS  plan-1  C7   0.020
 QTS  plan-2  N1   0.020
 QTS  plan-2  C4   0.020
 QTS  plan-2  C5   0.020
 QTS  plan-2  C6   0.020
 QTS  plan-2  C    0.020
 QTS  plan-2  C1   0.020
 QTS  plan-2  C2   0.020
 QTS  plan-2  C3   0.020
 QTS  plan-2  N2   0.020
 QTS  plan-2  H1   0.020
 QTS  plan-2  H2   0.020
 QTS  plan-2  H10  0.020
 QTS  plan-2  H11  0.020
 QTS  plan-2  C7   0.020
 QTS  plan-2  N    0.020
 QTS  plan-3  C    0.020
 QTS  plan-3  H7   0.020
 QTS  plan-3  H8   0.020
 QTS  plan-3  N    0.020

