# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:49:28 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 4,5,6,7-tetrabromo-N,N-dimethyl-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1[nH]c2c(Br)c(Br)c(Br)c(Br)c2n1
#
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
 K25  K25  4,5,6,7-tetrabromo-N,N-dimethyl-1H-benzimidazol-2-amine  ligand  23  16  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K25
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
 K25  C2    C   CR6   0  -0.102  -0.9175  -0.6915   0.0304
 K25  C3    C   CR6   0  -0.137  -0.9534   0.7121   0.0155
 K25  C4    C   CR6   0  -0.170   0.2341   1.4477  -0.0216
 K25  C5    C   CR6   0  -0.239   0.2987  -1.3749   0.0097
 K25  N6    N   NR15  0  -0.755   2.7305   1.1557  -0.0768
 K25  C7    C   CR56  0   0.253   1.4825  -0.6502  -0.0262
 K25  C8    C   CR56  0   0.440   1.4240   0.7535  -0.0415
 K25  C13   C   CR5   0   0.768   3.4976   0.0219  -0.0888
 K25  N14   N   N     0  -0.509   2.7709  -1.0790  -0.0494
 K25  N15   N   NT    0  -0.513   4.8337   0.0581  -0.1536
 K25  C16   C   CH3   0  -0.552   5.5390   1.3114   0.0156
 K25  C17   C   CH3   0  -0.524   5.5660  -1.1792   0.0296
 K25  BR1   BR  BR    0   0.025  -2.5162  -1.6689   0.0786
 K25  BR9   BR  BR    0   0.026  -2.5895   1.6230   0.0458
 K25  BR10  BR  BR    0   0.028   0.2790   3.3173  -0.0460
 K25  BR11  BR  BR    0   0.011   0.4206  -3.2397   0.0271
 K25  HN6   H   HNR5  0   0.432   3.0569   2.1096  -0.0906
 K25  H161  H   HCH3  0   0.267   6.5795   1.1659  -0.2612
 K25  H162  H   HCH3  0   0.254   5.1400   2.0821  -0.6439
 K25  H163  H   HCH3  0   0.251   5.5073   1.6754   1.0460
 K25  H171  H   HCH3  0   0.240   5.6499  -1.4560   1.0835
 K25  H172  H   HCH3  0   0.259   5.0786  -1.9907  -0.5039
 K25  H173  H   HCH3  0   0.250   6.5675  -1.0551  -0.3757

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
 K25  C2   C3    aromatic  1.404  0.020  1.404
 K25  C2   C5    aromatic  1.395  0.020  1.395
 K25  C2   BR1   single    1.874  0.020  1.874
 K25  C3   C4    aromatic  1.397  0.020  1.397
 K25  C3   BR9   single    1.873  0.020  1.873
 K25  C4   C8    aromatic  1.378  0.020  1.378
 K25  C4   BR10  single    1.870  0.020  1.870
 K25  C5   C7    aromatic  1.388  0.020  1.388
 K25  C5   BR11  single    1.869  0.020  1.869
 K25  N6   C8    aromatic  1.367  0.020  1.367
 K25  N6   C13   aromatic  1.369  0.020  1.369
 K25  N6   HN6   single    0.860  0.020  1.020
 K25  C7   C8    aromatic  1.405  0.020  1.405
 K25  C7   N14   aromatic  1.358  0.020  1.358
 K25  C13  N14   aromatic  1.320  0.020  1.320
 K25  C13  N15   single    1.338  0.020  1.338
 K25  N15  C16   single    1.448  0.020  1.448
 K25  N15  C17   single    1.449  0.020  1.449
 K25  C16  H161  single    0.970  0.020  1.090
 K25  C16  H162  single    0.970  0.020  1.090
 K25  C16  H163  single    0.970  0.020  1.090
 K25  C17  H171  single    0.970  0.020  1.090
 K25  C17  H172  single    0.970  0.020  1.090
 K25  C17  H173  single    0.970  0.020  1.090

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
 K25  BR1   C2   C5    119.24  3.000
 K25  BR1   C2   C3    119.98  3.000
 K25  C5    C2   C3    120.79  3.000
 K25  BR9   C3   C4    119.13  3.000
 K25  BR9   C3   C2    120.56  3.000
 K25  C4    C3   C2    120.32  3.000
 K25  BR10  C4   C8    118.87  3.000
 K25  BR10  C4   C3    123.16  3.000
 K25  C8    C4   C3    117.97  3.000
 K25  BR11  C5   C7    117.74  3.000
 K25  BR11  C5   C2    123.06  3.000
 K25  C7    C5   C2    119.20  3.000
 K25  HN6   N6   C13   127.01  3.000
 K25  HN6   N6   C8    126.01  3.000
 K25  C13   N6   C8    106.98  3.000
 K25  N14   C7   C8    110.78  3.000
 K25  N14   C7   C5    130.13  3.000
 K25  C8    C7   C5    119.09  3.000
 K25  C7    C8   N6    104.73  3.000
 K25  C7    C8   C4    122.63  3.000
 K25  N6    C8   C4    132.64  3.000
 K25  N15   C13  N14   125.02  3.000
 K25  N15   C13  N6    122.52  3.000
 K25  N14   C13  N6    112.46  3.000
 K25  C13   N14  C7    105.04  3.000
 K25  C17   N15  C16   118.55  3.000
 K25  C17   N15  C13   118.38  3.000
 K25  C16   N15  C13   120.27  3.000
 K25  H163  C16  H162  108.92  3.000
 K25  H163  C16  H161  108.21  3.000
 K25  H162  C16  H161  106.92  3.000
 K25  H163  C16  N15   112.59  3.000
 K25  H162  C16  N15   111.28  3.000
 K25  H161  C16  N15   108.71  3.000
 K25  H173  C17  H172  108.38  3.000
 K25  H173  C17  H171  108.52  3.000
 K25  H172  C17  H171  108.58  3.000
 K25  H173  C17  N15   108.72  3.000
 K25  H172  C17  N15   110.42  3.000
 K25  H171  C17  N15   112.14  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
 K25  CONST_01  C8    C4   C3   C2      0.00   0.0  0
 K25  CONST_02  C8    C7   C5   C2      0.00   0.0  0
 K25  CONST_03  N14   C7   C5   C2    180.00   0.0  0
 K25  CONST_04  C7    C5   C2   C3      0.00   0.0  0
 K25  CONST_05  N6    C8   C4   C3    180.00   0.0  0
 K25  CONST_06  C7    C8   C4   C3      0.00   0.0  0
 K25  CONST_07  C5    C2   C3   C4      0.00   0.0  0
 K25  CONST_08  C13   N6   C8   C4    180.00   0.0  0
 K25  CONST_09  C5    C7   C8   C4      0.00   0.0  0
 K25  CONST_10  N14   C7   C8   C4    180.00   0.0  0
 K25  CONST_11  N6    C8   C7   C5    180.00   0.0  0
 K25  CONST_12  C13   N14  C7   C5    180.00   0.0  0
 K25  CONST_13  N14   C7   C8   N6      0.00   0.0  0
 K25  CONST_14  C7    N14  C13  N6      0.00   0.0  0
 K25  CONST_15  C13   N6   C8   C7      0.00   0.0  0
 K25  CONST_16  N14   C13  N6   C8      0.00   0.0  0
 K25  CONST_17  C13   N14  C7   C8      0.00   0.0  0
 K25  CONST_18  BR10  C4   C3   C2    180.00   0.0  0
 K25  CONST_19  BR11  C5   C2   C3    180.00   0.0  0
 K25  CONST_20  BR1   C2   C3   C4    180.00   0.0  0
 K25  CONST_21  BR9   C3   C2   C5    180.00   0.0  0
 K25  CONST_22  BR10  C4   C8   N6      0.00   0.0  0
 K25  CONST_23  BR1   C2   C5   C7    180.00   0.0  0
 K25  CONST_24  BR10  C4   C8   C7    180.00   0.0  0
 K25  CONST_25  N15   C13  N14  C7    180.00   0.0  0
 K25  CONST_26  BR9   C3   C4   C8    180.00   0.0  0
 K25  CONST_27  N15   C13  N6   C8    180.00   0.0  0
 K25  CONST_28  BR11  C5   C7   C8    180.00   0.0  0
 K25  CONST_29  BR11  C5   C7   N14     0.00   0.0  0
 K25  CONST_30  HN6   N6   C8   C4      0.00   0.0  0
 K25  CONST_31  C16   N15  C13  N6      0.00   0.0  0
 K25  CONST_32  C17   N15  C13  N6    180.00   0.0  0
 K25  CONST_33  C16   N15  C13  N14   180.00   0.0  0
 K25  CONST_34  C17   N15  C13  N14     0.00   0.0  0
 K25  Var_01    H161  C16  N15  C13  -169.08  30.0  3
 K25  Var_02    H171  C17  N15  C13   -78.96  30.0  3

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
 K25  plan-1  C2    0.020
 K25  plan-1  C3    0.020
 K25  plan-1  C4    0.020
 K25  plan-1  C5    0.020
 K25  plan-1  N6    0.020
 K25  plan-1  C7    0.020
 K25  plan-1  C8    0.020
 K25  plan-1  C13   0.020
 K25  plan-1  N14   0.020
 K25  plan-1  N15   0.020
 K25  plan-1  BR1   0.020
 K25  plan-1  BR9   0.020
 K25  plan-1  BR10  0.020
 K25  plan-1  BR11  0.020
 K25  plan-1  HN6   0.020
 K25  plan-2  C13   0.020
 K25  plan-2  N15   0.020
 K25  plan-2  C16   0.020
 K25  plan-2  C17   0.020

