# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:30:13 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 6-chloro-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c2cc(Cl)ccc2n1
#
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
 VGD  VGD  6-chloro-1H-benzimidazol-2-amine  ligand  17  11  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VGD
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
 VGD  CLA   CL  CL    0  -0.145  -3.4257  -0.4869   0.0072
 VGD  CAH   C   CR6   0  -0.066  -1.7631   0.0249   0.0245
 VGD  CAC   C   CR16  0  -0.235  -1.4808   1.3896   0.0262
 VGD  CAD   C   CR16  0  -0.349  -0.1653   1.8337   0.0391
 VGD  CAK   C   CR56  0   0.168   0.8574   0.8930   0.0498
 VGD  CAJ   C   CR56  0   0.345   0.5311  -0.4766   0.0489
 VGD  CAE   C   CR16  0  -0.277  -0.7699  -0.9449   0.0360
 VGD  NAG   N   N     0  -0.519   2.2207   1.0596   0.0595
 VGD  CAI   C   CR5   0   0.612   2.7084  -0.1571   0.0671
 VGD  NAF   N   NR15  0  -0.721   1.7432  -1.1201   0.0610
 VGD  NAA   N   NH2   0  -0.846   4.0220  -0.4715   0.1351
 VGD  HAC   H   HCR6  0   0.270  -2.2909   2.1056   0.0173
 VGD  HAD   H   HCR6  0   0.258   0.0521   2.8939   0.0403
 VGD  HAE   H   HCR6  0   0.283  -1.0032  -2.0011   0.0337
 VGD  HNAF  H   HNR5  0   0.421   1.8954  -2.1162   0.0747
 VGD  HNAA  H   HNH2  0   0.400   4.6550   0.2686  -0.1208
 VGD  HNAB  H   HNH2  0   0.401   4.3045  -1.3780  -0.2002

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
 VGD  CLA  CAH   single    1.740  0.020  1.740
 VGD  CAH  CAC   aromatic  1.394  0.020  1.394
 VGD  CAH  CAE   aromatic  1.388  0.020  1.388
 VGD  CAC  CAD   aromatic  1.389  0.020  1.389
 VGD  CAD  CAK   aromatic  1.390  0.020  1.390
 VGD  CAK  CAJ   aromatic  1.408  0.020  1.408
 VGD  CAK  NAG   aromatic  1.373  0.020  1.373
 VGD  CAJ  CAE   aromatic  1.383  0.020  1.383
 VGD  CAJ  NAF   aromatic  1.372  0.020  1.372
 VGD  NAG  CAI   aromatic  1.311  0.020  1.311
 VGD  CAI  NAF   aromatic  1.363  0.020  1.363
 VGD  CAI  NAA   single    1.352  0.020  1.352
 VGD  CAC  HAC   single    0.930  0.020  1.080
 VGD  CAD  HAD   single    0.930  0.020  1.080
 VGD  CAE  HAE   single    0.930  0.020  1.080
 VGD  NAF  HNAF  single    0.860  0.020  1.020
 VGD  NAA  HNAA  single    0.890  0.020  1.040
 VGD  NAA  HNAB  single    0.890  0.020  1.040

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
 VGD  CAE   CAH  CAC   122.63  3.000
 VGD  CAE   CAH  CLA   118.58  3.000
 VGD  CAC   CAH  CLA   118.80  3.000
 VGD  HAC   CAC  CAD   119.87  3.000
 VGD  HAC   CAC  CAH   119.78  3.000
 VGD  CAD   CAC  CAH   120.34  3.000
 VGD  HAD   CAD  CAK   121.02  3.000
 VGD  HAD   CAD  CAC   120.24  3.000
 VGD  CAK   CAD  CAC   118.74  3.000
 VGD  NAG   CAK  CAJ   110.37  3.000
 VGD  NAG   CAK  CAD   130.42  3.000
 VGD  CAJ   CAK  CAD   119.21  3.000
 VGD  NAF   CAJ  CAE   132.24  3.000
 VGD  NAF   CAJ  CAK   104.56  3.000
 VGD  CAE   CAJ  CAK   123.20  3.000
 VGD  HAE   CAE  CAJ   122.25  3.000
 VGD  HAE   CAE  CAH   121.86  3.000
 VGD  CAJ   CAE  CAH   115.89  3.000
 VGD  CAI   NAG  CAK   104.88  3.000
 VGD  NAA   CAI  NAF   121.57  3.000
 VGD  NAA   CAI  NAG   125.27  3.000
 VGD  NAF   CAI  NAG   113.09  3.000
 VGD  HNAF  NAF  CAI   126.24  3.000
 VGD  HNAF  NAF  CAJ   126.65  3.000
 VGD  CAI   NAF  CAJ   107.10  3.000
 VGD  HNAB  NAA  HNAA  113.62  3.000
 VGD  HNAB  NAA  CAI   117.71  3.000
 VGD  HNAA  NAA  CAI   115.27  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
 VGD  CONST_01  CAK   CAD  CAC  CAH    0.00  0.0  0
 VGD  CONST_02  CAK   CAJ  CAE  CAH    0.00  0.0  0
 VGD  CONST_03  NAF   CAJ  CAE  CAH  180.00  0.0  0
 VGD  CONST_04  CAJ   CAE  CAH  CAC    0.00  0.0  0
 VGD  CONST_05  CAJ   CAK  CAD  CAC    0.00  0.0  0
 VGD  CONST_06  NAG   CAK  CAD  CAC  180.00  0.0  0
 VGD  CONST_07  CAE   CAH  CAC  CAD    0.00  0.0  0
 VGD  CONST_08  CAE   CAJ  CAK  CAD    0.00  0.0  0
 VGD  CONST_09  NAF   CAJ  CAK  CAD  180.00  0.0  0
 VGD  CONST_10  CAI   NAG  CAK  CAD  180.00  0.0  0
 VGD  CONST_11  CAI   NAF  CAJ  CAK    0.00  0.0  0
 VGD  CONST_12  NAF   CAI  NAG  CAK    0.00  0.0  0
 VGD  CONST_13  CAI   NAG  CAK  CAJ    0.00  0.0  0
 VGD  CONST_14  NAG   CAI  NAF  CAJ    0.00  0.0  0
 VGD  CONST_15  NAG   CAK  CAJ  CAE  180.00  0.0  0
 VGD  CONST_16  CAI   NAF  CAJ  CAE  180.00  0.0  0
 VGD  CONST_17  NAF   CAJ  CAK  NAG    0.00  0.0  0
 VGD  CONST_18  CAD   CAC  CAH  CLA  180.00  0.0  0
 VGD  CONST_19  CAJ   CAE  CAH  CLA  180.00  0.0  0
 VGD  CONST_20  NAA   CAI  NAG  CAK  180.00  0.0  0
 VGD  CONST_21  NAA   CAI  NAF  CAJ  180.00  0.0  0
 VGD  CONST_22  HAD   CAD  CAC  CAH  180.00  0.0  0
 VGD  CONST_23  HAE   CAE  CAH  CAC  180.00  0.0  0
 VGD  CONST_24  HAC   CAC  CAD  CAK  180.00  0.0  0
 VGD  CONST_25  HNAF  NAF  CAJ  CAK  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
 VGD  plan-1  CLA   0.020
 VGD  plan-1  CAH   0.020
 VGD  plan-1  CAC   0.020
 VGD  plan-1  CAD   0.020
 VGD  plan-1  CAK   0.020
 VGD  plan-1  CAJ   0.020
 VGD  plan-1  CAE   0.020
 VGD  plan-1  NAG   0.020
 VGD  plan-1  CAI   0.020
 VGD  plan-1  NAF   0.020
 VGD  plan-1  NAA   0.020
 VGD  plan-1  HAC   0.020
 VGD  plan-1  HAD   0.020
 VGD  plan-1  HAE   0.020
 VGD  plan-1  HNAF  0.020
 VGD  plan-2  CAI   0.020
 VGD  plan-2  NAA   0.020
 VGD  plan-2  HNAA  0.020
 VGD  plan-2  HNAB  0.020

