# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 19:13:47 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2-(difluoromethyl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)c1[nH]c2ccccc2n1
#
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
 56U  56U  2-(difluoromethyl)-1H-benzimidazole  ligand  18  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_56U
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
 56U  C1   C  CR16  0  -0.303   2.2180  -1.3986  -0.0433
 56U  C2   C  CR56  0   0.341   1.0269  -0.6856   0.0503
 56U  C3   C  CR56  0   0.136   0.9833   0.7182   0.0525
 56U  C4   C  CR16  0  -0.330   2.1667   1.4525  -0.0393
 56U  C5   C  CR16  0  -0.269   3.3542   0.7524  -0.1294
 56U  F12  F  F     0  -0.328  -3.0526   1.1062  -0.2249
 56U  F11  F  F     0  -0.339  -3.0078  -1.0866  -0.2295
 56U  C8   C  CR5   0   0.295  -1.0228   0.0563   0.2019
 56U  N7   N  NR15  0  -0.694  -0.2811  -1.0757   0.1502
 56U  N9   N  N     0  -0.457  -0.3186   1.1477   0.1523
 56U  C6   C  CR16  0  -0.275   3.3785  -0.6526  -0.1318
 56U  H1   H  HCR6  0   0.271   2.2390  -2.4801  -0.0463
 56U  H2   H  HCR6  0   0.259   2.1503   2.5344  -0.0391
 56U  H3   H  HCR6  0   0.256   4.2880   1.2943  -0.2015
 56U  H4   H  HCH1  0   0.231  -2.8148   0.0125   1.4225
 56U  H5   H  HNR5  0   0.427  -0.6220  -2.0246   0.1779
 56U  H7   H  HCR6  0   0.259   4.3298  -1.1630  -0.2062
 56U  C10  C  CH1   0   0.519  -2.5079   0.0240   0.3753

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
 56U  C1   C2   aromatic  1.391  0.020  1.391
 56U  C1   C6   aromatic  1.382  0.020  1.382
 56U  F11  C10  single    1.360  0.020  1.360
 56U  N7   C2   aromatic  1.369  0.020  1.369
 56U  N7   C8   aromatic  1.354  0.020  1.354
 56U  C2   C3   aromatic  1.405  0.020  1.405
 56U  C6   C5   aromatic  1.405  0.020  1.405
 56U  F12  C10  single    1.352  0.020  1.352
 56U  C10  C8   single    1.496  0.020  1.496
 56U  C8   N9   aromatic  1.300  0.020  1.300
 56U  C5   C4   aromatic  1.381  0.020  1.381
 56U  C3   N9   aromatic  1.375  0.020  1.375
 56U  C3   C4   aromatic  1.396  0.020  1.396
 56U  C1   H1   single    0.930  0.020  1.080
 56U  C4   H2   single    0.930  0.020  1.080
 56U  C5   H3   single    0.930  0.020  1.080
 56U  C10  H4   single    0.970  0.020  1.090
 56U  N7   H5   single    0.860  0.020  1.020
 56U  C6   H7   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
 56U  H1   C1   C6   121.54  3.000
 56U  H1   C1   C2   121.94  3.000
 56U  C6   C1   C2   116.51  3.000
 56U  N7   C2   C3   104.78  3.000
 56U  C3   C2   C1   122.61  3.000
 56U  N7   C2   C1   132.61  3.000
 56U  N9   C3   C4   130.05  3.000
 56U  C4   C3   C2   119.96  3.000
 56U  N9   C3   C2   109.99  3.000
 56U  H2   C4   C5   121.31  3.000
 56U  H2   C4   C3   120.88  3.000
 56U  C5   C4   C3   117.81  3.000
 56U  H3   C5   C6   119.05  3.000
 56U  H3   C5   C4   119.50  3.000
 56U  C6   C5   C4   121.45  3.000
 56U  N9   C8   N7   113.81  3.000
 56U  N9   C8   C10  124.09  3.000
 56U  N7   C8   C10  122.02  3.000
 56U  H5   N7   C8   126.88  3.000
 56U  H5   N7   C2   126.39  3.000
 56U  C8   N7   C2   106.73  3.000
 56U  C8   N9   C3   104.69  3.000
 56U  H7   C6   C5   119.14  3.000
 56U  H7   C6   C1   119.20  3.000
 56U  C5   C6   C1   121.66  3.000
 56U  H4   C10  C8   113.00  3.000
 56U  H4   C10  F11  108.34  3.000
 56U  C8   C10  F11  109.34  3.000
 56U  H4   C10  F12  108.73  3.000
 56U  C8   C10  F12  109.35  3.000
 56U  F11  C10  F12  107.95  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
 56U  CONST_01  C8   N7  C2   C1    180.00   0.0  0
 56U  CONST_02  N9   C3  C2   C1    180.00   0.0  0
 56U  CONST_03  C4   C3  C2   C1      0.00   0.0  0
 56U  CONST_04  C4   C5  C6   C1      0.00   0.0  0
 56U  CONST_05  C5   C6  C1   C2      0.00   0.0  0
 56U  CONST_06  N9   C8  N7   C2      0.00   0.0  0
 56U  CONST_07  C8   N9  C3   C2      0.00   0.0  0
 56U  CONST_08  C5   C4  C3   C2      0.00   0.0  0
 56U  CONST_09  C6   C1  C2   C3      0.00   0.0  0
 56U  CONST_10  C8   N7  C2   C3      0.00   0.0  0
 56U  CONST_11  N7   C8  N9   C3      0.00   0.0  0
 56U  CONST_12  C6   C5  C4   C3      0.00   0.0  0
 56U  CONST_13  N7   C2  C3   C4    180.00   0.0  0
 56U  CONST_14  C8   N9  C3   C4    180.00   0.0  0
 56U  CONST_15  N9   C3  C4   C5    180.00   0.0  0
 56U  CONST_16  C6   C1  C2   N7    180.00   0.0  0
 56U  CONST_17  N9   C3  C2   N7      0.00   0.0  0
 56U  CONST_18  C10  C8  N7   C2    180.00   0.0  0
 56U  CONST_19  C10  C8  N9   C3    180.00   0.0  0
 56U  CONST_20  H5   N7  C2   C1      0.00   0.0  0
 56U  CONST_21  H3   C5  C6   C1    180.00   0.0  0
 56U  CONST_22  H7   C6  C1   C2    180.00   0.0  0
 56U  CONST_23  H2   C4  C3   C2    180.00   0.0  0
 56U  CONST_24  H1   C1  C2   C3    180.00   0.0  0
 56U  Var_01    N7   C8  C10  F12  -150.61  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
 56U  plan-1  C1   0.020
 56U  plan-1  C2   0.020
 56U  plan-1  C3   0.020
 56U  plan-1  C4   0.020
 56U  plan-1  C5   0.020
 56U  plan-1  C8   0.020
 56U  plan-1  N7   0.020
 56U  plan-1  N9   0.020
 56U  plan-1  C6   0.020
 56U  plan-1  H1   0.020
 56U  plan-1  H2   0.020
 56U  plan-1  H3   0.020
 56U  plan-1  H5   0.020
 56U  plan-1  H7   0.020
 56U  plan-1  C10  0.020

