# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 10:46:04 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 1,1'-dimethyl-4,4'-bipyridin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(cc1)c2cc[n+](C)cc2
#
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
 KHJ  KHJ  1,1'-dimethyl-4,4'-bipyridin-1-ium  ligand  28  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KHJ
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
 KHJ  C14  C  CH3   0  -0.533   4.9704   0.0088   0.0196
 KHJ  N2   N  NR6   1  -0.416   3.5028  -0.0106   0.0079
 KHJ  C12  C  CR16  0   0.114   2.8441   1.1031  -0.3385
 KHJ  C8   C  CR16  0  -0.381   1.4718   1.1383  -0.3374
 KHJ  C4   C  CR6   0   0.226   0.7558  -0.0002   0.0224
 KHJ  C6   C  CR16  0  -0.378   1.4659  -1.1425   0.3734
 KHJ  C10  C  CR16  0   0.101   2.8409  -1.1176   0.3599
 KHJ  C3   C  CR6   0   0.227  -0.7157   0.0077   0.0291
 KHJ  C5   C  CR16  0  -0.380  -1.4383  -1.1051  -0.3900
 KHJ  C9   C  CR16  0   0.110  -2.8113  -1.0662  -0.3759
 KHJ  C7   C  CR16  0  -0.379  -1.4195   1.1290   0.4549
 KHJ  C11  C  CR16  0   0.105  -2.7936   1.1092   0.4518
 KHJ  N1   N  NR6   1  -0.416  -3.4631   0.0267   0.0397
 KHJ  C13  C  CH3   0  -0.533  -4.9302   0.0469   0.0018
 KHJ  H1   H  HCH3  0   0.304   5.3088   0.6325   0.8424
 KHJ  H2   H  HCH3  0   0.290   5.3390  -1.0021   0.1493
 KHJ  H3   H  HCH3  0   0.299   5.3284   0.4094  -0.9234
 KHJ  H4   H  HCR6  0   0.360   3.4415   1.9582  -0.6171
 KHJ  H5   H  HCR6  0   0.326   0.9806   2.0513  -0.6409
 KHJ  H6   H  HCR6  0   0.327   0.9719  -2.0535   0.6783
 KHJ  H7   H  HCR6  0   0.361   3.4315  -1.9786   0.6331
 KHJ  H8   H  HCR6  0   0.326  -0.9527  -2.0015  -0.7466
 KHJ  H9   H  HCR6  0   0.360  -3.4126  -1.9023  -0.6995
 KHJ  H10  H  HCR6  0   0.327  -0.9194   2.0165   0.8139
 KHJ  H11  H  HCR6  0   0.360  -3.3791   1.9543   0.7797
 KHJ  H12  H  HCH3  0   0.305  -5.2541   0.3166  -0.9998
 KHJ  H13  H  HCH3  0   0.295  -5.3065  -0.9364   0.2625
 KHJ  H14  H  HCH3  0   0.292  -5.2953   0.7761   0.7163

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
 KHJ  C14  N2   single    1.468  0.020  1.468
 KHJ  C10  N2   aromatic  1.337  0.020  1.337
 KHJ  C10  C6   aromatic  1.375  0.020  1.375
 KHJ  N2   C12  aromatic  1.339  0.020  1.339
 KHJ  C6   C4   aromatic  1.390  0.020  1.390
 KHJ  C12  C8   aromatic  1.373  0.020  1.373
 KHJ  C7   C11  aromatic  1.374  0.020  1.374
 KHJ  C7   C3   aromatic  1.391  0.020  1.391
 KHJ  C4   C8   aromatic  1.392  0.020  1.392
 KHJ  C4   C3   single    1.472  0.020  1.472
 KHJ  C11  N1   aromatic  1.338  0.020  1.338
 KHJ  C3   C5   aromatic  1.391  0.020  1.391
 KHJ  N1   C13  single    1.468  0.020  1.468
 KHJ  N1   C9   aromatic  1.339  0.020  1.339
 KHJ  C5   C9   aromatic  1.374  0.020  1.374
 KHJ  C14  H1   single    0.970  0.020  1.090
 KHJ  C14  H2   single    0.970  0.020  1.090
 KHJ  C14  H3   single    0.970  0.020  1.090
 KHJ  C12  H4   single    0.930  0.020  1.080
 KHJ  C8   H5   single    0.930  0.020  1.080
 KHJ  C6   H6   single    0.930  0.020  1.080
 KHJ  C10  H7   single    0.930  0.020  1.080
 KHJ  C5   H8   single    0.930  0.020  1.080
 KHJ  C9   H9   single    0.930  0.020  1.080
 KHJ  C7   H10  single    0.930  0.020  1.080
 KHJ  C11  H11  single    0.930  0.020  1.080
 KHJ  C13  H12  single    0.970  0.020  1.090
 KHJ  C13  H13  single    0.970  0.020  1.090
 KHJ  C13  H14  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
 KHJ  H3   C14  H2   109.63  3.000
 KHJ  H3   C14  H1   110.08  3.000
 KHJ  H2   C14  H1   109.81  3.000
 KHJ  H3   C14  N2   109.13  3.000
 KHJ  H2   C14  N2   109.19  3.000
 KHJ  H1   C14  N2   108.97  3.000
 KHJ  C10  N2   C12  120.87  3.000
 KHJ  C12  N2   C14  118.86  3.000
 KHJ  C10  N2   C14  120.25  3.000
 KHJ  H4   C12  C8   122.21  3.000
 KHJ  H4   C12  N2   116.95  3.000
 KHJ  C8   C12  N2   120.84  3.000
 KHJ  H5   C8   C4   122.00  3.000
 KHJ  H5   C8   C12  118.43  3.000
 KHJ  C4   C8   C12  119.56  3.000
 KHJ  C3   C4   C6   120.93  3.000
 KHJ  C3   C4   C8   120.73  3.000
 KHJ  C6   C4   C8   118.33  3.000
 KHJ  H6   C6   C10  118.37  3.000
 KHJ  H6   C6   C4   122.05  3.000
 KHJ  C10  C6   C4   119.56  3.000
 KHJ  H7   C10  C6   122.02  3.000
 KHJ  H7   C10  N2   117.15  3.000
 KHJ  C6   C10  N2   120.83  3.000
 KHJ  C7   C3   C5   118.31  3.000
 KHJ  C5   C3   C4   120.91  3.000
 KHJ  C7   C3   C4   120.78  3.000
 KHJ  H8   C5   C9   118.45  3.000
 KHJ  H8   C5   C3   121.98  3.000
 KHJ  C9   C5   C3   119.56  3.000
 KHJ  H9   C9   N1   117.01  3.000
 KHJ  H9   C9   C5   122.12  3.000
 KHJ  N1   C9   C5   120.86  3.000
 KHJ  H10  C7   C11  118.40  3.000
 KHJ  H10  C7   C3   122.01  3.000
 KHJ  C11  C7   C3   119.58  3.000
 KHJ  H11  C11  N1   117.11  3.000
 KHJ  H11  C11  C7   122.04  3.000
 KHJ  N1   C11  C7   120.85  3.000
 KHJ  C13  N1   C11  119.80  3.000
 KHJ  C13  N1   C9   119.33  3.000
 KHJ  C11  N1   C9   120.84  3.000
 KHJ  H14  C13  H13  109.54  3.000
 KHJ  H14  C13  H12  109.88  3.000
 KHJ  H13  C13  H12  110.07  3.000
 KHJ  H14  C13  N1   109.20  3.000
 KHJ  H13  C13  N1   109.15  3.000
 KHJ  H12  C13  N1   108.98  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
 KHJ  CONST_01  C4   C6   C10  N2     0.00   0.0  0
 KHJ  CONST_02  C4   C8   C12  N2     0.00   0.0  0
 KHJ  CONST_03  C6   C10  N2   C12    0.00   0.0  0
 KHJ  CONST_04  C6   C4   C8   C12    0.00   0.0  0
 KHJ  CONST_05  C3   C4   C8   C12  180.00   0.0  0
 KHJ  CONST_06  C10  N2   C12  C8     0.00   0.0  0
 KHJ  CONST_07  C10  C6   C4   C8     0.00   0.0  0
 KHJ  CONST_10  C11  C7   C3   C4   180.00   0.0  0
 KHJ  CONST_11  C9   C5   C3   C4   180.00   0.0  0
 KHJ  CONST_14  C3   C4   C6   C10  180.00   0.0  0
 KHJ  CONST_15  N1   C11  C7   C3     0.00   0.0  0
 KHJ  CONST_16  N1   C9   C5   C3     0.00   0.0  0
 KHJ  CONST_17  C11  C7   C3   C5     0.00   0.0  0
 KHJ  CONST_18  C11  N1   C9   C5     0.00   0.0  0
 KHJ  CONST_19  C7   C11  N1   C9     0.00   0.0  0
 KHJ  CONST_20  C7   C3   C5   C9     0.00   0.0  0
 KHJ  CONST_21  C6   C10  N2   C14  180.00   0.0  0
 KHJ  CONST_22  C8   C12  N2   C14  180.00   0.0  0
 KHJ  CONST_23  C13  N1   C9   C5   180.00   0.0  0
 KHJ  CONST_24  C13  N1   C11  C7   180.00   0.0  0
 KHJ  CONST_25  H6   C6   C10  N2   180.00   0.0  0
 KHJ  CONST_26  H5   C8   C12  N2   180.00   0.0  0
 KHJ  CONST_27  H7   C10  N2   C12  180.00   0.0  0
 KHJ  CONST_28  H4   C12  C8   C4   180.00   0.0  0
 KHJ  CONST_29  H10  C7   C3   C4     0.00   0.0  0
 KHJ  CONST_30  H8   C5   C3   C4     0.00   0.0  0
 KHJ  CONST_31  H11  C11  C7   C3   180.00   0.0  0
 KHJ  CONST_32  H9   C9   C5   C3   180.00   0.0  0
 KHJ  Var_01    H1   C14  N2   C12   69.85  30.0  2
 KHJ  Var_02    H12  C13  N1   C9   -83.19  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
 KHJ  plan-1  C14  0.020
 KHJ  plan-1  N2   0.020
 KHJ  plan-1  C12  0.020
 KHJ  plan-1  C8   0.020
 KHJ  plan-1  C4   0.020
 KHJ  plan-1  C6   0.020
 KHJ  plan-1  C10  0.020
 KHJ  plan-1  C3   0.020
 KHJ  plan-1  H4   0.020
 KHJ  plan-1  H5   0.020
 KHJ  plan-1  H6   0.020
 KHJ  plan-1  H7   0.020
 KHJ  plan-2  C4   0.020
 KHJ  plan-2  C3   0.020
 KHJ  plan-2  C5   0.020
 KHJ  plan-2  C9   0.020
 KHJ  plan-2  C7   0.020
 KHJ  plan-2  C11  0.020
 KHJ  plan-2  N1   0.020
 KHJ  plan-2  C13  0.020
 KHJ  plan-2  H8   0.020
 KHJ  plan-2  H9   0.020
 KHJ  plan-2  H10  0.020
 KHJ  plan-2  H11  0.020

