# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:59:37 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-benzyl-4-(dimethylamino)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cc[n+](Cc2ccccc2)cc1
#
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
 G8V  G8V  1-benzyl-4-(dimethylamino)pyridinium  ligand  33  16  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G8V
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
 G8V  CAA   C  CH3   0  -0.553   4.5044   1.2932  -0.6681
 G8V  CAB   C  CH3   0  -0.552   4.3064  -1.1763  -1.0595
 G8V  CAG   C  CR16  0  -0.238  -3.9607  -1.3158  -0.7074
 G8V  CAH   C  CR16  0  -0.239  -3.6196   1.0046  -1.2353
 G8V  CAK   C  CR16  0  -0.304  -3.0421  -1.2121   0.3297
 G8V  CAL   C  CR16  0  -0.289  -2.7049   1.1069  -0.1982
 G8V  CAQ   C  CR16  0  -0.431   1.9243   1.2680   0.4649
 G8V  CAR   C  CR16  0  -0.429   1.7563  -1.1100   0.1368
 G8V  CAU   C  CR16  0   0.072   0.6824   1.2365   1.0201
 G8V  CAV   C  CR16  0   0.083   0.5221  -1.0592   0.7031
 G8V  CBC   C  CH2   0  -0.470  -1.3852   0.0991   1.6871
 G8V  CBF   C  CR16  0  -0.258  -4.2480  -0.2084  -1.4924
 G8V  CBH   C  CR6   0   0.151  -2.4066  -0.0027   0.5886
 G8V  CBJ   C  CR6   0   0.536   2.5259   0.0748  -0.0137
 G8V  NBM   N  NT    0  -0.478   3.7350   0.0651  -0.5662
 G8V  NBO   N  NR6   1  -0.432  -0.0174   0.0936   1.1456
 G8V  HAA   H  HCH3  0   0.261   4.0003   2.0311  -1.2939
 G8V  HAAA  H  HCH3  0   0.261   4.6842   1.7314   0.3145
 G8V  HAAB  H  HCH3  0   0.276   5.4668   1.0730  -1.1175
 G8V  HAB   H  HCH3  0   0.261   4.4831  -1.8871  -0.2504
 G8V  HABA  H  HCH3  0   0.262   3.6568  -1.6430  -1.8002
 G8V  HABB  H  HCH3  0   0.276   5.2573  -0.9646  -1.5360
 G8V  HAH   H  HCR6  0   0.263  -3.8467   1.8727  -1.8403
 G8V  HAK   H  HCR6  0   0.262  -2.8242  -2.0787   0.9430
 G8V  HAL   H  HCR6  0   0.256  -2.2265   2.0588   0.0011
 G8V  HAQ   H  HCR6  0   0.317   2.4212   2.2234   0.4027
 G8V  HAR   H  HCR6  0   0.318   2.1217  -2.0737  -0.1810
 G8V  HAU   H  HCR6  0   0.335   0.2107   2.1365   1.3863
 G8V  HAV   H  HCR6  0   0.333  -0.0741  -1.9518   0.8258
 G8V  HBC   H  HCH2  0   0.311  -1.5007   1.0175   2.2604
 G8V  HBCA  H  HCH2  0   0.316  -1.4718  -0.7314   2.3863
 G8V  HBF   H  HCR6  0   0.263  -4.9637  -0.2865  -2.3002
 G8V  HAG   H  HCR6  0   0.263  -4.4527  -2.2606  -0.8976

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
 G8V  CAA  NBM   single    1.453  0.020  1.453
 G8V  CAB  NBM   single    1.453  0.020  1.453
 G8V  CAG  CAK   aromatic  1.389  0.020  1.389
 G8V  CAG  CBF   aromatic  1.387  0.020  1.387
 G8V  CAH  CAL   aromatic  1.387  0.020  1.387
 G8V  CAH  CBF   aromatic  1.390  0.020  1.390
 G8V  CAK  CBH   aromatic  1.391  0.020  1.391
 G8V  CAL  CBH   aromatic  1.393  0.020  1.393
 G8V  CAQ  CAU   aromatic  1.361  0.020  1.361
 G8V  CAQ  CBJ   aromatic  1.419  0.020  1.419
 G8V  CAR  CAV   aromatic  1.359  0.020  1.359
 G8V  CAR  CBJ   aromatic  1.421  0.020  1.421
 G8V  CAU  NBO   aromatic  1.346  0.020  1.346
 G8V  CAV  NBO   aromatic  1.347  0.020  1.347
 G8V  CBC  CBH   single    1.503  0.020  1.503
 G8V  CBC  NBO   single    1.471  0.020  1.471
 G8V  CBJ  NBM   single    1.329  0.020  1.329
 G8V  CAA  HAA   single    0.970  0.020  1.090
 G8V  CAA  HAAA  single    0.970  0.020  1.090
 G8V  CAA  HAAB  single    0.970  0.020  1.090
 G8V  CAB  HAB   single    0.970  0.020  1.090
 G8V  CAB  HABA  single    0.970  0.020  1.090
 G8V  CAB  HABB  single    0.970  0.020  1.090
 G8V  CAG  HAG   single    0.930  0.020  1.080
 G8V  CAH  HAH   single    0.930  0.020  1.080
 G8V  CAK  HAK   single    0.930  0.020  1.080
 G8V  CAL  HAL   single    0.930  0.020  1.080
 G8V  CAQ  HAQ   single    0.930  0.020  1.080
 G8V  CAR  HAR   single    0.930  0.020  1.080
 G8V  CAU  HAU   single    0.930  0.020  1.080
 G8V  CAV  HAV   single    0.930  0.020  1.080
 G8V  CBC  HBC   single    0.970  0.020  1.090
 G8V  CBC  HBCA  single    0.970  0.020  1.090
 G8V  CBF  HBF   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
 G8V  HAAB  CAA  HAAA  107.97  3.000
 G8V  HAAB  CAA  HAA   108.03  3.000
 G8V  HAAA  CAA  HAA   108.73  3.000
 G8V  HAAB  CAA  NBM   109.11  3.000
 G8V  HAAA  CAA  NBM   111.33  3.000
 G8V  HAA   CAA  NBM   111.55  3.000
 G8V  HABB  CAB  HABA  107.91  3.000
 G8V  HABB  CAB  HAB   108.12  3.000
 G8V  HABA  CAB  HAB   108.75  3.000
 G8V  HABB  CAB  NBM   109.10  3.000
 G8V  HABA  CAB  NBM   111.23  3.000
 G8V  HAB   CAB  NBM   111.62  3.000
 G8V  HAG   CAG  CBF   120.21  3.000
 G8V  HAG   CAG  CAK   119.80  3.000
 G8V  CBF   CAG  CAK   119.98  3.000
 G8V  HAH   CAH  CBF   120.11  3.000
 G8V  HAH   CAH  CAL   119.83  3.000
 G8V  CBF   CAH  CAL   120.06  3.000
 G8V  HAK   CAK  CBH   119.89  3.000
 G8V  HAK   CAK  CAG   119.71  3.000
 G8V  CBH   CAK  CAG   120.40  3.000
 G8V  HAL   CAL  CBH   120.09  3.000
 G8V  HAL   CAL  CAH   119.57  3.000
 G8V  CBH   CAL  CAH   120.34  3.000
 G8V  HAQ   CAQ  CBJ   121.99  3.000
 G8V  HAQ   CAQ  CAU   117.68  3.000
 G8V  CBJ   CAQ  CAU   120.33  3.000
 G8V  HAR   CAR  CBJ   122.03  3.000
 G8V  HAR   CAR  CAV   117.64  3.000
 G8V  CBJ   CAR  CAV   120.33  3.000
 G8V  HAU   CAU  NBO   116.67  3.000
 G8V  HAU   CAU  CAQ   121.18  3.000
 G8V  NBO   CAU  CAQ   122.15  3.000
 G8V  HAV   CAV  NBO   116.65  3.000
 G8V  HAV   CAV  CAR   121.17  3.000
 G8V  NBO   CAV  CAR   122.17  3.000
 G8V  HBCA  CBC  HBC   107.27  3.000
 G8V  HBCA  CBC  NBO   107.90  3.000
 G8V  HBC   CBC  NBO   107.20  3.000
 G8V  HBCA  CBC  CBH   111.31  3.000
 G8V  HBC   CBC  CBH   111.70  3.000
 G8V  NBO   CBC  CBH   111.25  3.000
 G8V  HBF   CBF  CAH   120.00  3.000
 G8V  HBF   CBF  CAG   120.12  3.000
 G8V  CAH   CBF  CAG   119.88  3.000
 G8V  CBC   CBH  CAL   120.30  3.000
 G8V  CBC   CBH  CAK   120.36  3.000
 G8V  CAL   CBH  CAK   119.33  3.000
 G8V  NBM   CBJ  CAR   122.05  3.000
 G8V  NBM   CBJ  CAQ   122.13  3.000
 G8V  CAR   CBJ  CAQ   115.82  3.000
 G8V  CBJ   NBM  CAB   120.34  3.000
 G8V  CBJ   NBM  CAA   120.31  3.000
 G8V  CAB   NBM  CAA   119.35  3.000
 G8V  CBC   NBO  CAV   119.76  3.000
 G8V  CBC   NBO  CAU   120.97  3.000
 G8V  CAV   NBO  CAU   119.19  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
 G8V  CONST_01  CAL  CBH  CAK  CAG    0.00   0.0  0
 G8V  CONST_02  CAL  CAH  CBF  CAG    0.00   0.0  0
 G8V  CONST_03  CAK  CBH  CAL  CAH    0.00   0.0  0
 G8V  CONST_04  CAK  CAG  CBF  CAH    0.00   0.0  0
 G8V  CONST_05  CAV  NBO  CAU  CAQ    0.00   0.0  0
 G8V  CONST_06  CAV  CAR  CBJ  CAQ    0.00   0.0  0
 G8V  CONST_07  CAU  NBO  CAV  CAR    0.00   0.0  0
 G8V  CONST_08  CAU  CAQ  CBJ  CAR    0.00   0.0  0
 G8V  CONST_09  CBH  CAK  CAG  CBF    0.00   0.0  0
 G8V  CONST_10  CBH  CAL  CAH  CBF    0.00   0.0  0
 G8V  CONST_11  NBO  CAU  CAQ  CBJ    0.00   0.0  0
 G8V  CONST_12  NBO  CAV  CAR  CBJ    0.00   0.0  0
 G8V  CONST_13  CBC  CBH  CAK  CAG  180.00   0.0  0
 G8V  CONST_14  CBC  CBH  CAL  CAH  180.00   0.0  0
 G8V  CONST_15  CBC  NBO  CAU  CAQ  180.00   0.0  0
 G8V  CONST_16  CBC  NBO  CAV  CAR  180.00   0.0  0
 G8V  CONST_17  NBM  CBJ  CAQ  CAU  180.00   0.0  0
 G8V  CONST_18  NBM  CBJ  CAR  CAV  180.00   0.0  0
 G8V  CONST_19  HAH  CAH  CBF  CAG  180.00   0.0  0
 G8V  CONST_20  HAG  CAG  CBF  CAH  180.00   0.0  0
 G8V  CONST_21  HBF  CBF  CAG  CAK  180.00   0.0  0
 G8V  CONST_22  HAL  CAL  CBH  CAK  180.00   0.0  0
 G8V  CONST_23  HAK  CAK  CBH  CAL  180.00   0.0  0
 G8V  CONST_24  HAR  CAR  CBJ  CAQ  180.00   0.0  0
 G8V  CONST_25  HAQ  CAQ  CBJ  CAR  180.00   0.0  0
 G8V  CONST_26  HAV  CAV  NBO  CAU  180.00   0.0  0
 G8V  CONST_27  HAU  CAU  NBO  CAV  180.00   0.0  0
 G8V  CONST_28  CAQ  CBJ  NBM  CAA    0.00   0.0  0
 G8V  CONST_29  CAR  CBJ  NBM  CAA  180.00   0.0  0
 G8V  CONST_30  CAQ  CBJ  NBM  CAB  180.00   0.0  0
 G8V  CONST_31  CAR  CBJ  NBM  CAB    0.00   0.0  0
 G8V  Var_01    NBO  CBC  CBH  CAK  102.20  30.0  2
 G8V  Var_02    CBH  CBC  NBO  CAU  101.26  30.0  2
 G8V  Var_03    HAA  CAA  NBM  CBJ  -62.39  30.0  3
 G8V  Var_04    HAB  CAB  NBM  CBJ  -64.76  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
 G8V  plan-1  CAG  0.020
 G8V  plan-1  CAH  0.020
 G8V  plan-1  CAK  0.020
 G8V  plan-1  CAL  0.020
 G8V  plan-1  CBC  0.020
 G8V  plan-1  CBF  0.020
 G8V  plan-1  CBH  0.020
 G8V  plan-1  HAH  0.020
 G8V  plan-1  HAK  0.020
 G8V  plan-1  HAL  0.020
 G8V  plan-1  HBF  0.020
 G8V  plan-1  HAG  0.020
 G8V  plan-2  CAQ  0.020
 G8V  plan-2  CAR  0.020
 G8V  plan-2  CAU  0.020
 G8V  plan-2  CAV  0.020
 G8V  plan-2  CBC  0.020
 G8V  plan-2  CBJ  0.020
 G8V  plan-2  NBM  0.020
 G8V  plan-2  NBO  0.020
 G8V  plan-2  HAQ  0.020
 G8V  plan-2  HAR  0.020
 G8V  plan-2  HAU  0.020
 G8V  plan-2  HAV  0.020
 G8V  plan-3  CAA  0.020
 G8V  plan-3  CAB  0.020
 G8V  plan-3  CBJ  0.020
 G8V  plan-3  NBM  0.020

