# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 00:49:05 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(6-cyano-1H-indol-1-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1c(Cl)cc(CNC(=N)NC(=O)Cn2ccc3ccc(cc23)C#N)cc1Cl
#
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
 VSI  VSI  N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(6-cyano-1H-indol-1-yl)acetamide  ligand  49  31  .  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_VSI
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
 VSI  CBB  C   CH3   0  -0.785  -7.3978   2.0548  -1.1366
 VSI  CBA  C   C     0   0.503  -6.4966   1.0244  -0.5138
 VSI  OBC  O   O     0  -0.468  -6.9136   0.0108   0.0140
 VSI  NAZ  N   NH1   0  -0.726  -5.1704   1.3139  -0.5679
 VSI  CAU  C   CR6   0   0.456  -4.2063   0.4869   0.0224
 VSI  CAV  C   CR6   0  -0.073  -3.8245  -0.7214  -0.5623
 VSI  CLX  CL  CL    0  -0.093  -4.5475  -1.1965  -2.0530
 VSI  CAW  C   CR16  0  -0.250  -2.8696  -1.5371   0.0148
 VSI  CAT  C   CR6   0  -0.076  -3.5878   0.8413   1.2169
 VSI  CLY  CL  CL    0  -0.090  -4.0371   2.3203   1.9826
 VSI  CAS  C   CR16  0  -0.271  -2.6197   0.0418   1.8046
 VSI  CAR  C   CR6   0   0.059  -2.2636  -1.1578   1.2082
 VSI  CAQ  C   CH2   0  -0.310  -1.2121  -2.0382   1.8262
 VSI  NAO  N   NH1   0  -0.658  -0.0336  -2.0421   0.9921
 VSI  CAN  C   C     0   0.645   0.9397  -2.9609   1.1945
 VSI  NAP  N   N     0  -0.703   0.7862  -3.9419   1.9937
 VSI  NAL  N   NH1   0  -0.725   2.1177  -2.7841   0.4432
 VSI  C    C   C     0   0.557   2.4962  -1.7438  -0.3412
 VSI  O    O   O     0  -0.444   1.8474  -0.7367  -0.5364
 VSI  CA   C   CH2   0  -0.477   3.8580  -1.9583  -0.9922
 VSI  N    N   NR5   0  -0.520   4.3465  -0.7621  -1.6022
 VSI  CAD  C   CR56  0   0.403   4.8777   0.3073  -0.9349
 VSI  CAC  C   CR16  0  -0.298   5.1518   0.4652   0.4139
 VSI  CAB  C   CR6   0  -0.018   5.7133   1.6762   0.8025
 VSI  CBD  C   CSP   0   0.046   6.0127   1.8888   2.1792
 VSI  NBE  N   NS    0  -0.262   6.2564   2.0656   3.2925
 VSI  CAA  C   CR16  0  -0.262   5.9934   2.7004  -0.1260
 VSI  CAF  C   CR16  0  -0.331   5.7119   2.5265  -1.4618
 VSI  CAE  C   CR56  0   0.072   5.1425   1.3204  -1.8865
 VSI  CAI  C   CR15  0  -0.415   4.7272   0.8138  -3.1509
 VSI  CAH  C   CR15  0  -0.003   4.2444  -0.4422  -2.9274
 VSI  H1   H   HCH3  0   0.276  -7.9293   2.5869  -0.3466
 VSI  H2   H   HCH3  0   0.255  -6.8667   2.7871  -1.7408
 VSI  H3   H   HCH3  0   0.271  -8.1437   1.5610  -1.7571
 VSI  H4   H   HNH1  0   0.415  -4.8712   2.2013  -0.9427
 VSI  H5   H   HCR6  0   0.285  -2.5953  -2.4691  -0.4618
 VSI  H6   H   HCR6  0   0.287  -2.1532   0.3499   2.7309
 VSI  H7   H   HCH2  0   0.252  -0.9898  -1.6975   2.8428
 VSI  H8   H   HCH2  0   0.266  -1.5876  -3.0584   1.9126
 VSI  H9   H   HNH1  0   0.411   0.2273  -1.1775   0.5428
 VSI  H10  H   H     0   0.337   1.5868  -4.5610   1.9985
 VSI  H11  H   HNH1  0   0.429   2.7868  -3.5333   0.5482
 VSI  H12  H   HCH2  0   0.313   4.5765  -2.3336  -0.2596
 VSI  H13  H   HCH2  0   0.337   3.7619  -2.7346  -1.7537
 VSI  H14  H   HCR6  0   0.288   4.9476  -0.3068   1.1441
 VSI  H15  H   HCR6  0   0.273   6.4310   3.6256   0.2230
 VSI  H16  H   HCR6  0   0.264   5.9281   3.3147  -2.1707
 VSI  H17  H   HCR5  0   0.259   4.7873   1.3119  -4.1049
 VSI  H18  H   HCR5  0   0.299   3.8375  -1.1563  -3.6266

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
 VSI  NAP  CAN  double    1.275  0.020  1.275
 VSI  NAO  CAN  single    1.354  0.020  1.354
 VSI  NAO  CAQ  single    1.444  0.020  1.444
 VSI  CAN  NAL  single    1.408  0.020  1.408
 VSI  CAQ  CAR  single    1.504  0.020  1.504
 VSI  CAW  CAR  aromatic  1.391  0.020  1.391
 VSI  CAW  CAV  aromatic  1.382  0.020  1.382
 VSI  O    C    double    1.214  0.020  1.214
 VSI  CLX  CAV  single    1.723  0.020  1.723
 VSI  NAL  C    single    1.357  0.020  1.357
 VSI  CAR  CAS  aromatic  1.386  0.020  1.386
 VSI  CAV  CAU  aromatic  1.396  0.020  1.396
 VSI  C    CA   single    1.525  0.020  1.525
 VSI  CAS  CAT  aromatic  1.386  0.020  1.386
 VSI  CAU  CAT  aromatic  1.391  0.020  1.391
 VSI  CAU  NAZ  single    1.401  0.020  1.401
 VSI  CA   N    single    1.429  0.020  1.429
 VSI  CAH  N    aromatic  1.367  0.020  1.367
 VSI  CAH  CAI  aromatic  1.364  0.020  1.364
 VSI  N    CAD  aromatic  1.368  0.020  1.368
 VSI  CAT  CLY  single    1.725  0.020  1.725
 VSI  OBC  CBA  double    1.216  0.020  1.216
 VSI  NAZ  CBA  single    1.359  0.020  1.359
 VSI  CBA  CBB  single    1.504  0.020  1.504
 VSI  CAI  CAE  aromatic  1.424  0.020  1.424
 VSI  CAD  CAC  aromatic  1.385  0.020  1.385
 VSI  CAD  CAE  aromatic  1.415  0.020  1.415
 VSI  CAC  CAB  aromatic  1.390  0.020  1.390
 VSI  CAE  CAF  aromatic  1.400  0.020  1.400
 VSI  CAB  CAA  aromatic  1.411  0.020  1.411
 VSI  CAB  CBD  single    1.425  0.020  1.425
 VSI  CAF  CAA  aromatic  1.376  0.020  1.376
 VSI  CBD  NBE  triple    1.153  0.020  1.153
 VSI  CBB  H1   single    0.970  0.020  1.090
 VSI  CBB  H2   single    0.970  0.020  1.090
 VSI  CBB  H3   single    0.970  0.020  1.090
 VSI  NAZ  H4   single    0.860  0.020  1.020
 VSI  CAW  H5   single    0.930  0.020  1.080
 VSI  CAS  H6   single    0.930  0.020  1.080
 VSI  CAQ  H7   single    0.970  0.020  1.090
 VSI  CAQ  H8   single    0.970  0.020  1.090
 VSI  NAO  H9   single    0.890  0.020  1.040
 VSI  NAP  H10  single    0.890  0.020  1.040
 VSI  NAL  H11  single    0.860  0.020  1.020
 VSI  CA   H12  single    0.970  0.020  1.090
 VSI  CA   H13  single    0.970  0.020  1.090
 VSI  CAC  H14  single    0.930  0.020  1.080
 VSI  CAA  H15  single    0.930  0.020  1.080
 VSI  CAF  H16  single    0.930  0.020  1.080
 VSI  CAI  H17  single    0.930  0.020  1.080
 VSI  CAH  H18  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
 VSI  H3   CBB  H2   108.86  3.000
 VSI  H3   CBB  H1   107.47  3.000
 VSI  H2   CBB  H1   108.17  3.000
 VSI  H3   CBB  CBA  109.62  3.000
 VSI  H2   CBB  CBA  113.49  3.000
 VSI  H1   CBB  CBA  109.05  3.000
 VSI  NAZ  CBA  OBC  121.97  3.000
 VSI  NAZ  CBA  CBB  114.99  3.000
 VSI  OBC  CBA  CBB  123.03  3.000
 VSI  H4   NAZ  CAU  118.16  3.000
 VSI  H4   NAZ  CBA  119.46  3.000
 VSI  CAU  NAZ  CBA  121.96  3.000
 VSI  CAT  CAU  CAV  117.30  3.000
 VSI  CAT  CAU  NAZ  121.17  3.000
 VSI  CAV  CAU  NAZ  121.53  3.000
 VSI  CAW  CAV  CLX  119.23  3.000
 VSI  CLX  CAV  CAU  119.09  3.000
 VSI  CAW  CAV  CAU  121.67  3.000
 VSI  H5   CAW  CAR  120.14  3.000
 VSI  H5   CAW  CAV  119.97  3.000
 VSI  CAR  CAW  CAV  119.89  3.000
 VSI  CAS  CAT  CLY  119.22  3.000
 VSI  CLY  CAT  CAU  118.93  3.000
 VSI  CAS  CAT  CAU  121.85  3.000
 VSI  H6   CAS  CAR  120.27  3.000
 VSI  H6   CAS  CAT  119.99  3.000
 VSI  CAR  CAS  CAT  119.74  3.000
 VSI  CAQ  CAR  CAS  120.62  3.000
 VSI  CAS  CAR  CAW  119.54  3.000
 VSI  CAQ  CAR  CAW  119.83  3.000
 VSI  H8   CAQ  H7   106.71  3.000
 VSI  H8   CAQ  NAO  108.92  3.000
 VSI  H7   CAQ  NAO  111.80  3.000
 VSI  H8   CAQ  CAR  109.84  3.000
 VSI  H7   CAQ  CAR  109.95  3.000
 VSI  NAO  CAQ  CAR  109.56  3.000
 VSI  H9   NAO  CAN  117.54  3.000
 VSI  H9   NAO  CAQ  117.79  3.000
 VSI  CAN  NAO  CAQ  120.15  3.000
 VSI  NAL  CAN  NAP  122.13  3.000
 VSI  NAL  CAN  NAO  115.87  3.000
 VSI  NAP  CAN  NAO  121.97  3.000
 VSI  H10  NAP  CAN  112.24  3.000
 VSI  H11  NAL  C    116.36  3.000
 VSI  H11  NAL  CAN  113.93  3.000
 VSI  C    NAL  CAN  129.65  3.000
 VSI  CA   C    O    121.70  3.000
 VSI  CA   C    NAL  112.84  3.000
 VSI  O    C    NAL  125.45  3.000
 VSI  H13  CA   H12  106.34  3.000
 VSI  H13  CA   N    109.13  3.000
 VSI  H12  CA   N    110.43  3.000
 VSI  H13  CA   C    108.62  3.000
 VSI  H12  CA   C    110.45  3.000
 VSI  N    CA   C    111.71  3.000
 VSI  CAH  N    CAD  108.60  3.000
 VSI  CAD  N    CA   125.38  3.000
 VSI  CAH  N    CA   125.74  3.000
 VSI  CAE  CAD  CAC  122.42  3.000
 VSI  CAE  CAD  N    107.72  3.000
 VSI  CAC  CAD  N    129.86  3.000
 VSI  H14  CAC  CAB  120.60  3.000
 VSI  H14  CAC  CAD  122.57  3.000
 VSI  CAB  CAC  CAD  116.83  3.000
 VSI  CAA  CAB  CBD  119.08  3.000
 VSI  CBD  CAB  CAC  119.01  3.000
 VSI  CAA  CAB  CAC  121.92  3.000
 VSI  NBE  CBD  CAB  180.00  3.000
 VSI  H15  CAA  CAF  120.28  3.000
 VSI  H15  CAA  CAB  119.29  3.000
 VSI  CAF  CAA  CAB  120.44  3.000
 VSI  H16  CAF  CAE  120.68  3.000
 VSI  H16  CAF  CAA  120.20  3.000
 VSI  CAE  CAF  CAA  119.12  3.000
 VSI  CAI  CAE  CAF  133.99  3.000
 VSI  CAF  CAE  CAD  119.28  3.000
 VSI  CAI  CAE  CAD  106.73  3.000
 VSI  H17  CAI  CAH  126.17  3.000
 VSI  H17  CAI  CAE  127.25  3.000
 VSI  CAH  CAI  CAE  106.58  3.000
 VSI  H18  CAH  CAI  129.55  3.000
 VSI  H18  CAH  N    120.09  3.000
 VSI  CAI  CAH  N    110.35  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
 VSI  CONST_01  CAR  CAW  CAV  CAU     0.00   0.0  0
 VSI  CONST_02  CAR  CAS  CAT  CAU     0.00   0.0  0
 VSI  CONST_03  CAS  CAR  CAW  CAV     0.00   0.0  0
 VSI  CONST_04  CAS  CAT  CAU  CAV     0.00   0.0  0
 VSI  CONST_05  CAT  CAS  CAR  CAW     0.00   0.0  0
 VSI  CONST_06  CAT  CAU  CAV  CAW     0.00   0.0  0
 VSI  CONST_07  CAE  CAI  CAH  N       0.00   0.0  0
 VSI  CONST_08  CAB  CAC  CAD  N     180.00   0.0  0
 VSI  CONST_09  CAI  CAE  CAD  N       0.00   0.0  0
 VSI  CONST_10  CAF  CAE  CAD  N     180.00   0.0  0
 VSI  CONST_11  CAI  CAH  N    CAD     0.00   0.0  0
 VSI  CONST_12  CAA  CAB  CAC  CAD     0.00   0.0  0
 VSI  CONST_13  CAH  CAI  CAE  CAD     0.00   0.0  0
 VSI  CONST_14  CAA  CAF  CAE  CAD     0.00   0.0  0
 VSI  CONST_15  CAH  N    CAD  CAC   180.00   0.0  0
 VSI  CONST_16  CAI  CAE  CAD  CAC   180.00   0.0  0
 VSI  CONST_17  CAF  CAE  CAD  CAC     0.00   0.0  0
 VSI  CONST_18  CAF  CAA  CAB  CAC     0.00   0.0  0
 VSI  CONST_19  CAE  CAD  CAC  CAB     0.00   0.0  0
 VSI  CONST_20  CAE  CAF  CAA  CAB     0.00   0.0  0
 VSI  CONST_21  CAI  CAE  CAF  CAA   180.00   0.0  0
 VSI  CONST_22  CAH  CAI  CAE  CAF   180.00   0.0  0
 VSI  CONST_23  CAH  N    CAD  CAE     0.00   0.0  0
 VSI  CONST_24  CAW  CAV  CAU  NAZ   180.00   0.0  0
 VSI  CONST_25  CAS  CAT  CAU  NAZ   180.00   0.0  0
 VSI  CONST_26  CAQ  CAR  CAW  CAV   180.00   0.0  0
 VSI  CONST_27  CLY  CAT  CAU  CAV   180.00   0.0  0
 VSI  CONST_28  CAR  CAW  CAV  CLX   180.00   0.0  0
 VSI  CONST_29  CAT  CAU  CAV  CLX   180.00   0.0  0
 VSI  CONST_30  CAQ  CAR  CAS  CAT   180.00   0.0  0
 VSI  CONST_31  CAR  CAS  CAT  CLY   180.00   0.0  0
 VSI  CONST_32  CAI  CAH  N    CA    180.00   0.0  0
 VSI  CONST_33  CAC  CAD  N    CA      0.00   0.0  0
 VSI  CONST_34  CAE  CAD  N    CA    180.00   0.0  0
 VSI  CONST_35  CBD  CAB  CAC  CAD   180.00   0.0  0
 VSI  CONST_36  CAF  CAA  CAB  CBD   180.00   0.0  0
 VSI  CONST_37  H5   CAW  CAV  CAU   180.00   0.0  0
 VSI  CONST_38  H6   CAS  CAT  CAU   180.00   0.0  0
 VSI  CONST_39  H17  CAI  CAH  N     180.00   0.0  0
 VSI  CONST_40  H14  CAC  CAD  N       0.00   0.0  0
 VSI  CONST_41  H18  CAH  N    CAD   180.00   0.0  0
 VSI  CONST_42  H16  CAF  CAE  CAD   180.00   0.0  0
 VSI  CONST_43  H15  CAA  CAB  CAC   180.00   0.0  0
 VSI  CONST_47  CAU  NAZ  CBA  CBB   180.00   0.0  0
 VSI  CONST_48  CAU  NAZ  CBA  OBC     0.00   0.0  0
 VSI  CONST_49  O    C    NAL  CAN     0.00   0.0  0
 VSI  CONST_50  CA   C    NAL  CAN   180.00   0.0  0
 VSI  CONST_51  NAP  CAN  NAO  CAQ     0.00   0.0  0
 VSI  CONST_52  NAL  CAN  NAO  CAQ   180.00   0.0  0
 VSI  CONST_53  C    NAL  CAN  NAO     0.00   0.0  0
 VSI  CONST_54  C    NAL  CAN  NAP   180.00   0.0  0
 VSI  CONST_55  H11  NAL  C    O     180.00   0.0  0
 VSI  CONST_56  H10  NAP  CAN  NAO   180.00   0.0  0
 VSI  Var_01    NAO  CAQ  CAR  CAW    67.92  30.0  2
 VSI  Var_02    CAH  N    CA   C     -97.48  30.0  2
 VSI  Var_03    CAN  NAO  CAQ  CAR  -166.75  30.0  1
 VSI  Var_04    N    CA   C    NAL  -169.01  30.0  3
 VSI  Var_05    H1   CBB  CBA  OBC    71.40  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
 VSI  plan-1  NAZ  0.020
 VSI  plan-1  CAU  0.020
 VSI  plan-1  CAV  0.020
 VSI  plan-1  CLX  0.020
 VSI  plan-1  CAW  0.020
 VSI  plan-1  CAT  0.020
 VSI  plan-1  CLY  0.020
 VSI  plan-1  CAS  0.020
 VSI  plan-1  CAR  0.020
 VSI  plan-1  CAQ  0.020
 VSI  plan-1  H5   0.020
 VSI  plan-1  H6   0.020
 VSI  plan-2  CA   0.020
 VSI  plan-2  N    0.020
 VSI  plan-2  CAD  0.020
 VSI  plan-2  CAC  0.020
 VSI  plan-2  CAB  0.020
 VSI  plan-2  CBD  0.020
 VSI  plan-2  NBE  0.020
 VSI  plan-2  CAA  0.020
 VSI  plan-2  CAF  0.020
 VSI  plan-2  CAE  0.020
 VSI  plan-2  CAI  0.020
 VSI  plan-2  CAH  0.020
 VSI  plan-2  H14  0.020
 VSI  plan-2  H15  0.020
 VSI  plan-2  H16  0.020
 VSI  plan-2  H17  0.020
 VSI  plan-2  H18  0.020
 VSI  plan-3  CBB  0.020
 VSI  plan-3  CBA  0.020
 VSI  plan-3  OBC  0.020
 VSI  plan-3  NAZ  0.020
 VSI  plan-3  CAU  0.020
 VSI  plan-3  H4   0.020
 VSI  plan-4  CAQ  0.020
 VSI  plan-4  NAO  0.020
 VSI  plan-4  CAN  0.020
 VSI  plan-4  NAP  0.020
 VSI  plan-4  NAL  0.020
 VSI  plan-4  C    0.020
 VSI  plan-4  O    0.020
 VSI  plan-4  CA   0.020
 VSI  plan-4  H9   0.020
 VSI  plan-4  H10  0.020
 VSI  plan-4  H11  0.020

