# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:05:09 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 3,4-dihydro[1,2,4]triazolo[1,5-a][3,1]benzimidazol-9-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1cn[n+]2c1[nH]c3ccccc23
#
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
 VFB  VFB  3,4-dihydro[1,2,4]triazolo[1,5-a][3,1]benzimidazol-9-ium  ligand  19  12  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VFB
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
 VFB  N1    N  NR15  0  -0.718   0.2959  -1.6328  -0.0357
 VFB  CAB   C  CR16  0  -0.297  -2.1952  -1.2202  -0.0138
 VFB  CAC   C  CR16  0  -0.263  -2.7432   1.1510   0.0216
 VFB  CAD   C  CR56  0   0.287  -0.8597  -0.8543  -0.0179
 VFB  CAE   C  CR16  0  -0.278  -1.4091   1.5235   0.0174
 VFB  CAF   C  CR15  0   0.149   2.9685   0.5911  -0.0164
 VFB  CAG   C  CR55  0   0.903   1.3218  -0.7907  -0.0308
 VFB  NAH   N  NR15  0  -0.661   2.6529  -0.7433  -0.0366
 VFB  NAI   N  N     0  -0.232   1.9215   1.3514  -0.0001
 VFB  CAJ   C  CR16  0  -0.257  -3.1263  -0.1941   0.0065
 VFB  CAK   C  CR56  0   0.377  -0.4849   0.4960  -0.0019
 VFB  NAL   N  N     1  -0.430   0.8994   0.4722  -0.0097
 VFB  HN1   H  HNR5  0   0.459   0.3497  -2.6408  -0.0515
 VFB  HAB   H  HCR6  0   0.292  -2.4963  -2.2585  -0.0256
 VFB  HAC   H  HCR6  0   0.277  -3.5042   1.9184   0.0354
 VFB  HAE   H  HCR6  0   0.296  -1.1048   2.5605   0.0284
 VFB  HAF   H  HCR5  0   0.343   3.9860   0.9435  -0.0159
 VFB  HNAH  H  HNR5  0   0.474   3.2987  -1.5211  -0.0492
 VFB  HAJ   H  HCR6  0   0.277  -4.1789  -0.4415   0.0100

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
 VFB  N1   CAD   aromatic  1.394  0.020  1.394
 VFB  N1   CAG   aromatic  1.327  0.020  1.327
 VFB  CAB  CAD   aromatic  1.385  0.020  1.385
 VFB  CAB  CAJ   aromatic  1.386  0.020  1.386
 VFB  CAC  CAE   aromatic  1.385  0.020  1.385
 VFB  CAC  CAJ   aromatic  1.399  0.020  1.399
 VFB  CAD  CAK   aromatic  1.401  0.020  1.401
 VFB  CAE  CAK   aromatic  1.382  0.020  1.382
 VFB  CAF  NAH   aromatic  1.371  0.020  1.371
 VFB  CAF  NAI   aromatic  1.294  0.020  1.294
 VFB  CAG  NAH   aromatic  1.332  0.020  1.332
 VFB  CAG  NAL   aromatic  1.332  0.020  1.332
 VFB  NAI  NAL   aromatic  1.348  0.020  1.348
 VFB  CAK  NAL   aromatic  1.384  0.020  1.384
 VFB  N1   HN1   single    0.860  0.020  1.020
 VFB  CAB  HAB   single    0.930  0.020  1.080
 VFB  CAC  HAC   single    0.930  0.020  1.080
 VFB  CAE  HAE   single    0.930  0.020  1.080
 VFB  CAF  HAF   single    0.930  0.020  1.080
 VFB  NAH  HNAH  single    0.860  0.020  1.020
 VFB  CAJ  HAJ   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
 VFB  HN1   N1   CAG  126.33  3.000
 VFB  HN1   N1   CAD  127.02  3.000
 VFB  CAG   N1   CAD  106.65  3.000
 VFB  HAB   CAB  CAJ  121.61  3.000
 VFB  HAB   CAB  CAD  121.49  3.000
 VFB  CAJ   CAB  CAD  116.90  3.000
 VFB  HAC   CAC  CAJ  119.35  3.000
 VFB  HAC   CAC  CAE  119.16  3.000
 VFB  CAJ   CAC  CAE  121.49  3.000
 VFB  CAK   CAD  CAB  120.83  3.000
 VFB  CAK   CAD  N1   108.46  3.000
 VFB  CAB   CAD  N1   130.71  3.000
 VFB  HAE   CAE  CAK  121.68  3.000
 VFB  HAE   CAE  CAC  121.95  3.000
 VFB  CAK   CAE  CAC  116.37  3.000
 VFB  HAF   CAF  NAI  124.91  3.000
 VFB  HAF   CAF  NAH  122.41  3.000
 VFB  NAI   CAF  NAH  112.69  3.000
 VFB  NAL   CAG  NAH  106.46  3.000
 VFB  NAL   CAG  N1   110.89  3.000
 VFB  NAH   CAG  N1   142.65  3.000
 VFB  HNAH  NAH  CAG  127.67  3.000
 VFB  HNAH  NAH  CAF  126.99  3.000
 VFB  CAG   NAH  CAF  105.34  3.000
 VFB  NAL   NAI  CAF  103.30  3.000
 VFB  HAJ   CAJ  CAC  119.12  3.000
 VFB  HAJ   CAJ  CAB  118.99  3.000
 VFB  CAC   CAJ  CAB  121.89  3.000
 VFB  NAL   CAK  CAE  132.96  3.000
 VFB  NAL   CAK  CAD  104.52  3.000
 VFB  CAE   CAK  CAD  122.52  3.000
 VFB  CAK   NAL  NAI  138.30  3.000
 VFB  CAK   NAL  CAG  109.48  3.000
 VFB  NAI   NAL  CAG  112.21  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
 VFB  CONST_01  CAJ   CAB  CAD  N1   180.00  0.0  0
 VFB  CONST_02  CAE   CAK  CAD  N1   180.00  0.0  0
 VFB  CONST_03  NAL   CAK  CAD  N1     0.00  0.0  0
 VFB  CONST_04  CAF   NAH  CAG  N1   180.00  0.0  0
 VFB  CONST_05  NAI   NAL  CAG  N1   180.00  0.0  0
 VFB  CONST_06  CAK   NAL  CAG  N1     0.00  0.0  0
 VFB  CONST_07  CAG   N1   CAD  CAB  180.00  0.0  0
 VFB  CONST_08  CAE   CAK  CAD  CAB    0.00  0.0  0
 VFB  CONST_09  NAL   CAK  CAD  CAB  180.00  0.0  0
 VFB  CONST_10  CAE   CAC  CAJ  CAB    0.00  0.0  0
 VFB  CONST_11  CAD   CAK  CAE  CAC    0.00  0.0  0
 VFB  CONST_12  NAL   CAK  CAE  CAC  180.00  0.0  0
 VFB  CONST_13  CAD   CAB  CAJ  CAC    0.00  0.0  0
 VFB  CONST_14  NAH   CAG  N1   CAD  180.00  0.0  0
 VFB  CONST_15  NAL   CAG  N1   CAD    0.00  0.0  0
 VFB  CONST_16  CAG   NAL  CAK  CAD    0.00  0.0  0
 VFB  CONST_17  NAI   NAL  CAK  CAD  180.00  0.0  0
 VFB  CONST_18  CAG   NAL  CAK  CAE  180.00  0.0  0
 VFB  CONST_19  NAI   NAL  CAK  CAE    0.00  0.0  0
 VFB  CONST_20  NAL   CAG  NAH  CAF    0.00  0.0  0
 VFB  CONST_21  CAG   NAL  NAI  CAF    0.00  0.0  0
 VFB  CONST_22  CAK   NAL  NAI  CAF  180.00  0.0  0
 VFB  CONST_23  CAK   CAD  N1   CAG    0.00  0.0  0
 VFB  CONST_24  NAI   CAF  NAH  CAG    0.00  0.0  0
 VFB  CONST_25  NAL   NAI  CAF  NAH    0.00  0.0  0
 VFB  CONST_26  NAI   NAL  CAG  NAH    0.00  0.0  0
 VFB  CONST_27  CAK   NAL  CAG  NAH  180.00  0.0  0
 VFB  CONST_28  CAK   CAD  CAB  CAJ    0.00  0.0  0
 VFB  CONST_29  CAK   CAE  CAC  CAJ    0.00  0.0  0
 VFB  CONST_30  HAB   CAB  CAD  N1     0.00  0.0  0
 VFB  CONST_31  HNAH  NAH  CAG  N1     0.00  0.0  0
 VFB  CONST_32  HN1   N1   CAD  CAB    0.00  0.0  0
 VFB  CONST_33  HAC   CAC  CAJ  CAB  180.00  0.0  0
 VFB  CONST_34  HAJ   CAJ  CAB  CAD  180.00  0.0  0
 VFB  CONST_35  HAE   CAE  CAK  CAD  180.00  0.0  0
 VFB  CONST_36  HAF   CAF  NAH  CAG  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
 VFB  plan-1  N1    0.020
 VFB  plan-1  CAB   0.020
 VFB  plan-1  CAC   0.020
 VFB  plan-1  CAD   0.020
 VFB  plan-1  CAE   0.020
 VFB  plan-1  CAF   0.020
 VFB  plan-1  CAG   0.020
 VFB  plan-1  NAH   0.020
 VFB  plan-1  NAI   0.020
 VFB  plan-1  CAJ   0.020
 VFB  plan-1  CAK   0.020
 VFB  plan-1  NAL   0.020
 VFB  plan-1  HN1   0.020
 VFB  plan-1  HAB   0.020
 VFB  plan-1  HAC   0.020
 VFB  plan-1  HAE   0.020
 VFB  plan-1  HAF   0.020
 VFB  plan-1  HNAH  0.020
 VFB  plan-1  HAJ   0.020

