# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:09:50 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 2-pyridin-3-yl-1~{H}-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1c2ccccc2nc1c3cccnc3
#
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
 6SL  6SL  2-pyridin-3-yl-1~{H}-benzimidazole  ligand  24  15  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6SL
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
 6SL  C1   C  CR16  0  -0.269   4.1697   0.7661   0.0170
 6SL  C2   C  CR16  0  -0.276   4.2061  -0.6375  -0.0218
 6SL  C3   C  CR16  0  -0.312   3.0469  -1.3923  -0.0445
 6SL  C7   C  CR5   0   0.486  -0.2299   0.0328  -0.0056
 6SL  C8   C  CR6   0  -0.080  -1.6894   0.0131  -0.0028
 6SL  C9   C  CR16  0  -0.171  -2.3996   1.2126  -0.0328
 6SL  C10  C  CR16  0  -0.311  -3.7805   1.1748  -0.0274
 6SL  C11  C  CR16  0  -0.062  -4.4114  -0.0614   0.0068
 6SL  C12  C  CR16  0  -0.085  -2.4250  -1.1703   0.0324
 6SL  N3   N  N     0  -0.397  -3.7492  -1.2113   0.0365
 6SL  N2   N  NR15  0  -0.733   0.5392  -1.0896  -0.0381
 6SL  C4   C  CR56  0   0.335   1.8471  -0.6900  -0.0269
 6SL  N1   N  N     0  -0.481   0.4847   1.1278   0.0256
 6SL  C5   C  CR56  0   0.153   1.7907   0.7134   0.0124
 6SL  C6   C  CR16  0  -0.338   2.9722   1.4563   0.0343
 6SL  H1   H  HCR6  0   0.254   5.1017   1.3159   0.0338
 6SL  H2   H  HCR6  0   0.257   5.1642  -1.1406  -0.0341
 6SL  H3   H  HCR6  0   0.267   3.0773  -2.4734  -0.0733
 6SL  H4   H  HCR6  0   0.274  -1.8691   2.1550  -0.0609
 6SL  H5   H  HCR6  0   0.279  -4.3642   2.0843  -0.0510
 6SL  H6   H  HCR6  0   0.273  -5.4935  -0.1242   0.0108
 6SL  H7   H  HCR6  0   0.254  -1.9309  -2.1359   0.0615
 6SL  H8   H  HNR5  0   0.425   0.2217  -2.0450  -0.0732
 6SL  H10  H  HCR6  0   0.256   2.9473   2.5379   0.0637

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
 6SL  C10  C9   aromatic  1.381  0.020  1.381
 6SL  C10  C11  aromatic  1.388  0.020  1.388
 6SL  C9   C8   aromatic  1.394  0.020  1.394
 6SL  N1   C5   aromatic  1.370  0.020  1.370
 6SL  N1   C7   aromatic  1.308  0.020  1.308
 6SL  C6   C5   aromatic  1.396  0.020  1.396
 6SL  C6   C1   aromatic  1.382  0.020  1.382
 6SL  C11  N3   aromatic  1.327  0.020  1.327
 6SL  C5   C4   aromatic  1.405  0.020  1.405
 6SL  C8   C7   single    1.460  0.020  1.460
 6SL  C8   C12  aromatic  1.394  0.020  1.394
 6SL  C7   N2   aromatic  1.361  0.020  1.361
 6SL  C1   C2   aromatic  1.405  0.020  1.405
 6SL  N3   C12  aromatic  1.325  0.020  1.325
 6SL  C4   N2   aromatic  1.368  0.020  1.368
 6SL  C4   C3   aromatic  1.390  0.020  1.390
 6SL  C2   C3   aromatic  1.384  0.020  1.384
 6SL  C1   H1   single    0.930  0.020  1.080
 6SL  C2   H2   single    0.930  0.020  1.080
 6SL  C3   H3   single    0.930  0.020  1.080
 6SL  C9   H4   single    0.930  0.020  1.080
 6SL  C10  H5   single    0.930  0.020  1.080
 6SL  C11  H6   single    0.930  0.020  1.080
 6SL  C12  H7   single    0.930  0.020  1.080
 6SL  N2   H8   single    0.860  0.020  1.020
 6SL  C6   H10  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
 6SL  H1   C1   C6   119.48  3.000
 6SL  H1   C1   C2   119.06  3.000
 6SL  C6   C1   C2   121.45  3.000
 6SL  H2   C2   C3   119.21  3.000
 6SL  H2   C2   C1   119.20  3.000
 6SL  C3   C2   C1   121.59  3.000
 6SL  H3   C3   C4   121.96  3.000
 6SL  H3   C3   C2   121.47  3.000
 6SL  C4   C3   C2   116.57  3.000
 6SL  N1   C7   N2   112.47  3.000
 6SL  N2   C7   C8   123.64  3.000
 6SL  N1   C7   C8   123.89  3.000
 6SL  C12  C8   C9   117.52  3.000
 6SL  C12  C8   C7   122.63  3.000
 6SL  C9   C8   C7   119.85  3.000
 6SL  H4   C9   C10  120.94  3.000
 6SL  H4   C9   C8   120.01  3.000
 6SL  C10  C9   C8   119.05  3.000
 6SL  H5   C10  C11  120.29  3.000
 6SL  H5   C10  C9   121.11  3.000
 6SL  C11  C10  C9   118.60  3.000
 6SL  H6   C11  N3   116.61  3.000
 6SL  H6   C11  C10  120.35  3.000
 6SL  N3   C11  C10  123.04  3.000
 6SL  H7   C12  N3   115.31  3.000
 6SL  H7   C12  C8   121.06  3.000
 6SL  N3   C12  C8   123.63  3.000
 6SL  C12  N3   C11  118.16  3.000
 6SL  H8   N2   C4   125.36  3.000
 6SL  H8   N2   C7   127.22  3.000
 6SL  C4   N2   C7   107.41  3.000
 6SL  C5   C4   N2   104.69  3.000
 6SL  N2   C4   C3   132.66  3.000
 6SL  C5   C4   C3   122.65  3.000
 6SL  C5   N1   C7   105.50  3.000
 6SL  C6   C5   N1   130.21  3.000
 6SL  C6   C5   C4   119.87  3.000
 6SL  N1   C5   C4   109.92  3.000
 6SL  H10  C6   C5   120.85  3.000
 6SL  H10  C6   C1   121.29  3.000
 6SL  C5   C6   C1   117.86  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
 6SL  CONST_01  N1   C5   C6   C1   180.00  0.0  0
 6SL  CONST_02  C4   C5   C6   C1     0.00  0.0  0
 6SL  CONST_03  C4   C3   C2   C1     0.00  0.0  0
 6SL  CONST_04  C5   C6   C1   C2     0.00  0.0  0
 6SL  CONST_05  C5   C4   C3   C2     0.00  0.0  0
 6SL  CONST_06  N2   C4   C3   C2   180.00  0.0  0
 6SL  CONST_07  N1   C5   C4   C3   180.00  0.0  0
 6SL  CONST_08  C6   C5   C4   C3     0.00  0.0  0
 6SL  CONST_09  C7   N2   C4   C3   180.00  0.0  0
 6SL  CONST_10  C6   C1   C2   C3     0.00  0.0  0
 6SL  CONST_11  C6   C5   N1   C7   180.00  0.0  0
 6SL  CONST_12  C4   C5   N1   C7     0.00  0.0  0
 6SL  CONST_13  C10  C9   C8   C7   180.00  0.0  0
 6SL  CONST_14  N3   C12  C8   C7   180.00  0.0  0
 6SL  CONST_15  C5   C4   N2   C7     0.00  0.0  0
 6SL  CONST_16  C11  C10  C9   C8     0.00  0.0  0
 6SL  CONST_17  C5   N1   C7   C8   180.00  0.0  0
 6SL  CONST_18  C4   N2   C7   C8   180.00  0.0  0
 6SL  CONST_19  C11  N3   C12  C8     0.00  0.0  0
 6SL  CONST_20  N3   C11  C10  C9     0.00  0.0  0
 6SL  CONST_21  N1   C7   C8   C9     0.00  0.0  0
 6SL  CONST_22  N2   C7   C8   C9   180.00  0.0  0
 6SL  CONST_23  N3   C12  C8   C9     0.00  0.0  0
 6SL  CONST_24  C12  C8   C9   C10    0.00  0.0  0
 6SL  CONST_25  C12  N3   C11  C10    0.00  0.0  0
 6SL  CONST_26  N1   C7   C8   C12  180.00  0.0  0
 6SL  CONST_27  N2   C7   C8   C12    0.00  0.0  0
 6SL  CONST_28  C5   N1   C7   N2     0.00  0.0  0
 6SL  CONST_29  N1   C5   C4   N2     0.00  0.0  0
 6SL  CONST_30  C6   C5   C4   N2   180.00  0.0  0
 6SL  CONST_31  N1   C7   N2   C4     0.00  0.0  0
 6SL  CONST_32  H3   C3   C2   C1   180.00  0.0  0
 6SL  CONST_33  H10  C6   C1   C2   180.00  0.0  0
 6SL  CONST_34  H8   N2   C4   C3     0.00  0.0  0
 6SL  CONST_35  H1   C1   C2   C3   180.00  0.0  0
 6SL  CONST_36  H4   C9   C8   C7     0.00  0.0  0
 6SL  CONST_37  H7   C12  C8   C7     0.00  0.0  0
 6SL  CONST_38  H5   C10  C9   C8   180.00  0.0  0
 6SL  CONST_39  H6   C11  C10  C9   180.00  0.0  0
 6SL  CONST_40  H2   C2   C3   C4   180.00  0.0  0

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
 6SL  plan-1  C7   0.020
 6SL  plan-1  C8   0.020
 6SL  plan-1  C9   0.020
 6SL  plan-1  C10  0.020
 6SL  plan-1  C11  0.020
 6SL  plan-1  C12  0.020
 6SL  plan-1  N3   0.020
 6SL  plan-1  H4   0.020
 6SL  plan-1  H5   0.020
 6SL  plan-1  H6   0.020
 6SL  plan-1  H7   0.020
 6SL  plan-2  C1   0.020
 6SL  plan-2  C2   0.020
 6SL  plan-2  C3   0.020
 6SL  plan-2  C7   0.020
 6SL  plan-2  C8   0.020
 6SL  plan-2  N2   0.020
 6SL  plan-2  C4   0.020
 6SL  plan-2  N1   0.020
 6SL  plan-2  C5   0.020
 6SL  plan-2  C6   0.020
 6SL  plan-2  H1   0.020
 6SL  plan-2  H2   0.020
 6SL  plan-2  H3   0.020
 6SL  plan-2  H8   0.020
 6SL  plan-2  H10  0.020

