# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:48:24 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-(3,4-dichlorobenzyl)-7-phenyl-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2cccc(c3ccccc3)c2n1Cc4ccc(Cl)c(Cl)c4
#
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
 VGF  VGF  1-(3,4-dichlorobenzyl)-7-phenyl-1H-benzimidazol-2-amine  ligand  40  25  .  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_VGF
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
 VGF  CAN   C   CR16  0  -0.236  -1.4571   0.2516  -1.5783
 VGF  CAS   C   CR6   0   0.031  -2.5863   0.6101  -0.8636
 VGF  CLAC  CL  CL    0  -0.100  -3.6455   1.8061  -1.5062
 VGF  CAR   C   CR6   0  -0.018  -2.8409   0.0301   0.3728
 VGF  CLAB  CL  CL    0  -0.104  -4.2247   0.4882   1.2922
 VGF  CAK   C   CR16  0  -0.205  -1.9678  -0.9214   0.8758
 VGF  CAJ   C   CR16  0  -0.277  -0.8392  -1.2780   0.1574
 VGF  CAQ   C   CR6   0   0.085  -0.5685  -0.6844  -1.0687
 VGF  CAO   C   CH2   0  -0.362   0.6577  -1.0279  -1.8744
 VGF  NAY   N   NR5   0  -0.581   1.7779  -1.4455  -1.0632
 VGF  CAX   C   CR56  0   0.290   2.3595  -0.7693   0.0024
 VGF  CAU   C   CR5   0   0.607   2.3523  -2.6907  -1.0856
 VGF  NAA   N   NH2   0  -0.854   1.9696  -3.6423  -1.9779
 VGF  NAP   N   N     0  -0.517   3.2333  -2.8779  -0.1409
 VGF  CAW   C   CR56  0   0.162   3.2503  -1.7020   0.5676
 VGF  CAM   C   CR16  0  -0.354   3.9893  -1.3793   1.6989
 VGF  CAG   C   CR16  0  -0.260   3.8109  -0.1220   2.2541
 VGF  CAL   C   CR16  0  -0.340   2.9275   0.7941   1.6868
 VGF  CAV   C   CR6   0   0.076   2.1856   0.5062   0.5388
 VGF  CAT   C   CR6   0   0.037   1.2978   1.5446  -0.0271
 VGF  CAH   C   CR16  0  -0.265   0.2615   2.0755   0.7407
 VGF  CAE   C   CR16  0  -0.238  -0.5644   3.0630   0.2269
 VGF  CAD   C   CR16  0  -0.255  -0.3640   3.5403  -1.0618
 VGF  CAF   C   CR16  0  -0.247   0.6764   3.0318  -1.8273
 VGF  CAI   C   CR16  0  -0.300   1.5048   2.0446  -1.3113
 VGF  HAN   H   HCR6  0   0.280  -1.2532   0.7335  -2.5254
 VGF  HAK   H   HCR6  0   0.286  -2.1681  -1.3773   1.8357
 VGF  HAJ   H   HCR6  0   0.268  -0.1697  -2.0163   0.5792
 VGF  HAO1  H   HCH2  0   0.295   0.4145  -1.8412  -2.5575
 VGF  HAO2  H   HCH2  0   0.285   0.9388  -0.1816  -2.5014
 VGF  HAA1  H   HNH2  0   0.402   1.7773  -3.3464  -2.9222
 VGF  HAA2  H   HNH2  0   0.400   2.5534  -4.4639  -1.9556
 VGF  HAM   H   HCR6  0   0.249   4.6756  -2.0949   2.1328
 VGF  HAG   H   HCR6  0   0.249   4.3687   0.1602   3.1377
 VGF  HAL   H   HCR6  0   0.247   2.8244   1.7757   2.1323
 VGF  HAH   H   HCR6  0   0.245   0.0858   1.6928   1.7382
 VGF  HAI   H   HCR6  0   0.257   2.3227   1.6620  -1.9104
 VGF  HAE   H   HCR6  0   0.253  -1.3748   3.4526   0.8294
 VGF  HAD   H   HCR6  0   0.252  -1.0149   4.3038  -1.4674
 VGF  HAF   H   HCR6  0   0.255   0.8478   3.4050  -2.8288

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
 VGF  CAN  CAS   aromatic  1.384  0.020  1.384
 VGF  CAN  CAQ   aromatic  1.388  0.020  1.388
 VGF  CAS  CLAC  single    1.722  0.020  1.722
 VGF  CAS  CAR   aromatic  1.389  0.020  1.389
 VGF  CAR  CLAB  single    1.723  0.020  1.723
 VGF  CAR  CAK   aromatic  1.386  0.020  1.386
 VGF  CAK  CAJ   aromatic  1.385  0.020  1.385
 VGF  CAJ  CAQ   aromatic  1.389  0.020  1.389
 VGF  CAQ  CAO   single    1.507  0.020  1.507
 VGF  CAO  NAY   single    1.445  0.020  1.445
 VGF  NAY  CAX   aromatic  1.390  0.020  1.390
 VGF  NAY  CAU   aromatic  1.371  0.020  1.371
 VGF  CAX  CAW   aromatic  1.408  0.020  1.408
 VGF  CAX  CAV   aromatic  1.395  0.020  1.395
 VGF  CAU  NAA   single    1.359  0.020  1.359
 VGF  CAU  NAP   aromatic  1.305  0.020  1.305
 VGF  NAP  CAW   aromatic  1.373  0.020  1.373
 VGF  CAW  CAM   aromatic  1.389  0.020  1.389
 VGF  CAM  CAG   aromatic  1.386  0.020  1.386
 VGF  CAG  CAL   aromatic  1.393  0.020  1.393
 VGF  CAL  CAV   aromatic  1.397  0.020  1.397
 VGF  CAV  CAT   single    1.479  0.020  1.479
 VGF  CAT  CAH   aromatic  1.395  0.020  1.395
 VGF  CAT  CAI   aromatic  1.394  0.020  1.394
 VGF  CAH  CAE   aromatic  1.386  0.020  1.386
 VGF  CAE  CAD   aromatic  1.389  0.020  1.389
 VGF  CAD  CAF   aromatic  1.388  0.020  1.388
 VGF  CAF  CAI   aromatic  1.388  0.020  1.388
 VGF  CAN  HAN   single    0.930  0.020  1.080
 VGF  CAK  HAK   single    0.930  0.020  1.080
 VGF  CAJ  HAJ   single    0.930  0.020  1.080
 VGF  CAO  HAO1  single    0.970  0.020  1.090
 VGF  CAO  HAO2  single    0.970  0.020  1.090
 VGF  NAA  HAA1  single    0.890  0.020  1.040
 VGF  NAA  HAA2  single    0.890  0.020  1.040
 VGF  CAM  HAM   single    0.930  0.020  1.080
 VGF  CAG  HAG   single    0.930  0.020  1.080
 VGF  CAL  HAL   single    0.930  0.020  1.080
 VGF  CAH  HAH   single    0.930  0.020  1.080
 VGF  CAI  HAI   single    0.930  0.020  1.080
 VGF  CAE  HAE   single    0.930  0.020  1.080
 VGF  CAD  HAD   single    0.930  0.020  1.080
 VGF  CAF  HAF   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
 VGF  HAN   CAN  CAQ   120.08  3.000
 VGF  HAN   CAN  CAS   119.37  3.000
 VGF  CAQ   CAN  CAS   120.51  3.000
 VGF  CAR   CAS  CLAC  120.62  3.000
 VGF  CAR   CAS  CAN   120.07  3.000
 VGF  CLAC  CAS  CAN   119.29  3.000
 VGF  CAK   CAR  CLAB  119.65  3.000
 VGF  CAK   CAR  CAS   119.62  3.000
 VGF  CLAB  CAR  CAS   120.73  3.000
 VGF  HAK   CAK  CAJ   120.20  3.000
 VGF  HAK   CAK  CAR   119.66  3.000
 VGF  CAJ   CAK  CAR   120.14  3.000
 VGF  HAJ   CAJ  CAQ   121.00  3.000
 VGF  HAJ   CAJ  CAK   118.54  3.000
 VGF  CAQ   CAJ  CAK   120.45  3.000
 VGF  CAO   CAQ  CAJ   122.22  3.000
 VGF  CAO   CAQ  CAN   118.59  3.000
 VGF  CAJ   CAQ  CAN   119.19  3.000
 VGF  HAO2  CAO  HAO1  106.05  3.000
 VGF  HAO2  CAO  NAY   110.33  3.000
 VGF  HAO1  CAO  NAY   108.02  3.000
 VGF  HAO2  CAO  CAQ   109.90  3.000
 VGF  HAO1  CAO  CAQ   108.88  3.000
 VGF  NAY   CAO  CAQ   113.37  3.000
 VGF  CAU   NAY  CAX   106.20  3.000
 VGF  CAU   NAY  CAO   125.31  3.000
 VGF  CAX   NAY  CAO   127.91  3.000
 VGF  CAV   CAX  CAW   122.03  3.000
 VGF  CAV   CAX  NAY   133.46  3.000
 VGF  CAW   CAX  NAY   104.49  3.000
 VGF  NAP   CAU  NAA   124.38  3.000
 VGF  NAP   CAU  NAY   113.64  3.000
 VGF  NAA   CAU  NAY   121.89  3.000
 VGF  HAA2  NAA  HAA1  111.74  3.000
 VGF  HAA2  NAA  CAU   113.13  3.000
 VGF  HAA1  NAA  CAU   117.58  3.000
 VGF  CAW   NAP  CAU   105.02  3.000
 VGF  CAM   CAW  NAP   128.74  3.000
 VGF  CAM   CAW  CAX   120.63  3.000
 VGF  NAP   CAW  CAX   110.63  3.000
 VGF  HAM   CAM  CAG   121.38  3.000
 VGF  HAM   CAM  CAW   120.68  3.000
 VGF  CAG   CAM  CAW   117.93  3.000
 VGF  HAG   CAG  CAL   119.19  3.000
 VGF  HAG   CAG  CAM   119.82  3.000
 VGF  CAL   CAG  CAM   120.99  3.000
 VGF  HAL   CAL  CAV   118.32  3.000
 VGF  HAL   CAL  CAG   119.26  3.000
 VGF  CAV   CAL  CAG   122.40  3.000
 VGF  CAT   CAV  CAL   119.25  3.000
 VGF  CAT   CAV  CAX   124.74  3.000
 VGF  CAL   CAV  CAX   116.00  3.000
 VGF  CAI   CAT  CAH   118.76  3.000
 VGF  CAI   CAT  CAV   121.03  3.000
 VGF  CAH   CAT  CAV   120.18  3.000
 VGF  HAH   CAH  CAE   119.78  3.000
 VGF  HAH   CAH  CAT   119.55  3.000
 VGF  CAE   CAH  CAT   120.65  3.000
 VGF  HAE   CAE  CAD   120.06  3.000
 VGF  HAE   CAE  CAH   119.75  3.000
 VGF  CAD   CAE  CAH   120.19  3.000
 VGF  HAD   CAD  CAF   120.17  3.000
 VGF  HAD   CAD  CAE   120.23  3.000
 VGF  CAF   CAD  CAE   119.61  3.000
 VGF  HAF   CAF  CAI   119.64  3.000
 VGF  HAF   CAF  CAD   120.18  3.000
 VGF  CAI   CAF  CAD   120.18  3.000
 VGF  HAI   CAI  CAF   119.74  3.000
 VGF  HAI   CAI  CAT   119.66  3.000
 VGF  CAF   CAI  CAT   120.60  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
 VGF  CONST_01  CAK   CAR  CAS  CAN     0.00   0.0  0
 VGF  CONST_02  CAK   CAJ  CAQ  CAN     0.00   0.0  0
 VGF  CONST_03  CAJ   CAQ  CAN  CAS     0.00   0.0  0
 VGF  CONST_04  CAJ   CAK  CAR  CAS     0.00   0.0  0
 VGF  CONST_05  CAQ   CAN  CAS  CAR     0.00   0.0  0
 VGF  CONST_06  CAQ   CAJ  CAK  CAR     0.00   0.0  0
 VGF  CONST_07  NAP   CAW  CAX  NAY     0.00   0.0  0
 VGF  CONST_08  CAM   CAW  CAX  NAY   180.00   0.0  0
 VGF  CONST_09  CAL   CAV  CAX  NAY   180.00   0.0  0
 VGF  CONST_10  CAT   CAV  CAX  NAY     0.00   0.0  0
 VGF  CONST_11  CAW   NAP  CAU  NAY     0.00   0.0  0
 VGF  CONST_12  NAP   CAU  NAY  CAX     0.00   0.0  0
 VGF  CONST_13  CAU   NAP  CAW  CAX     0.00   0.0  0
 VGF  CONST_14  CAG   CAM  CAW  CAX     0.00   0.0  0
 VGF  CONST_15  CAG   CAL  CAV  CAX     0.00   0.0  0
 VGF  CONST_18  CAW   CAX  NAY  CAU     0.00   0.0  0
 VGF  CONST_19  CAV   CAX  NAY  CAU   180.00   0.0  0
 VGF  CONST_20  CAM   CAW  NAP  CAU   180.00   0.0  0
 VGF  CONST_21  CAV   CAX  CAW  NAP   180.00   0.0  0
 VGF  CONST_22  CAG   CAM  CAW  NAP   180.00   0.0  0
 VGF  CONST_23  CAL   CAV  CAX  CAW     0.00   0.0  0
 VGF  CONST_24  CAT   CAV  CAX  CAW   180.00   0.0  0
 VGF  CONST_25  CAL   CAG  CAM  CAW     0.00   0.0  0
 VGF  CONST_26  CAV   CAX  CAW  CAM     0.00   0.0  0
 VGF  CONST_27  CAV   CAL  CAG  CAM     0.00   0.0  0
 VGF  CONST_28  CAT   CAV  CAL  CAG   180.00   0.0  0
 VGF  CONST_31  CAE   CAH  CAT  CAV   180.00   0.0  0
 VGF  CONST_32  CAF   CAI  CAT  CAV   180.00   0.0  0
 VGF  CONST_33  CAD   CAE  CAH  CAT     0.00   0.0  0
 VGF  CONST_34  CAD   CAF  CAI  CAT     0.00   0.0  0
 VGF  CONST_35  CAF   CAI  CAT  CAH     0.00   0.0  0
 VGF  CONST_36  CAF   CAD  CAE  CAH     0.00   0.0  0
 VGF  CONST_37  CAI   CAT  CAH  CAE     0.00   0.0  0
 VGF  CONST_38  CAI   CAF  CAD  CAE     0.00   0.0  0
 VGF  CONST_39  CLAB  CAR  CAS  CAN   180.00   0.0  0
 VGF  CONST_40  CAO   CAQ  CAN  CAS   180.00   0.0  0
 VGF  CONST_41  CAQ   CAN  CAS  CLAC  180.00   0.0  0
 VGF  CONST_42  CAK   CAR  CAS  CLAC  180.00   0.0  0
 VGF  CONST_43  CAJ   CAK  CAR  CLAB  180.00   0.0  0
 VGF  CONST_44  CAO   CAQ  CAJ  CAK   180.00   0.0  0
 VGF  CONST_45  CAW   CAX  NAY  CAO   180.00   0.0  0
 VGF  CONST_46  CAV   CAX  NAY  CAO     0.00   0.0  0
 VGF  CONST_47  NAP   CAU  NAY  CAO   180.00   0.0  0
 VGF  CONST_48  NAA   CAU  NAY  CAX   180.00   0.0  0
 VGF  CONST_49  CAW   NAP  CAU  NAA   180.00   0.0  0
 VGF  CONST_50  HAJ   CAJ  CAQ  CAN   180.00   0.0  0
 VGF  CONST_51  HAK   CAK  CAR  CAS   180.00   0.0  0
 VGF  CONST_52  HAN   CAN  CAS  CAR   180.00   0.0  0
 VGF  CONST_53  HAM   CAM  CAW  CAX   180.00   0.0  0
 VGF  CONST_54  HAL   CAL  CAV  CAX   180.00   0.0  0
 VGF  CONST_55  HAG   CAG  CAM  CAW   180.00   0.0  0
 VGF  CONST_56  HAH   CAH  CAT  CAV     0.00   0.0  0
 VGF  CONST_57  HAI   CAI  CAT  CAV     0.00   0.0  0
 VGF  CONST_58  HAE   CAE  CAH  CAT   180.00   0.0  0
 VGF  CONST_59  HAF   CAF  CAI  CAT   180.00   0.0  0
 VGF  CONST_60  HAD   CAD  CAE  CAH   180.00   0.0  0
 VGF  CONST_62  HAA2  NAA  CAU  NAY   180.00   0.0  0
 VGF  Var_01    NAY   CAO  CAQ  CAN   151.44  30.0  2
 VGF  Var_02    CAX   NAY  CAO  CAQ   -54.17  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
 VGF  plan-1  CAN   0.020
 VGF  plan-1  CAS   0.020
 VGF  plan-1  CLAC  0.020
 VGF  plan-1  CAR   0.020
 VGF  plan-1  CLAB  0.020
 VGF  plan-1  CAK   0.020
 VGF  plan-1  CAJ   0.020
 VGF  plan-1  CAQ   0.020
 VGF  plan-1  CAO   0.020
 VGF  plan-1  HAN   0.020
 VGF  plan-1  HAK   0.020
 VGF  plan-1  HAJ   0.020
 VGF  plan-2  CAV   0.020
 VGF  plan-2  CAT   0.020
 VGF  plan-2  CAH   0.020
 VGF  plan-2  CAE   0.020
 VGF  plan-2  CAD   0.020
 VGF  plan-2  CAF   0.020
 VGF  plan-2  CAI   0.020
 VGF  plan-2  HAH   0.020
 VGF  plan-2  HAI   0.020
 VGF  plan-2  HAE   0.020
 VGF  plan-2  HAD   0.020
 VGF  plan-2  HAF   0.020
 VGF  plan-3  CAO   0.020
 VGF  plan-3  NAY   0.020
 VGF  plan-3  CAX   0.020
 VGF  plan-3  CAU   0.020
 VGF  plan-3  NAA   0.020
 VGF  plan-3  NAP   0.020
 VGF  plan-3  CAW   0.020
 VGF  plan-3  CAM   0.020
 VGF  plan-3  CAG   0.020
 VGF  plan-3  CAL   0.020
 VGF  plan-3  CAV   0.020
 VGF  plan-3  CAT   0.020
 VGF  plan-3  HAM   0.020
 VGF  plan-3  HAG   0.020
 VGF  plan-3  HAL   0.020
 VGF  plan-4  CAU   0.020
 VGF  plan-4  NAA   0.020
 VGF  plan-4  HAA1  0.020
 VGF  plan-4  HAA2  0.020

