# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 04:15:18 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(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)Cn2ccc3ccccc23)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
 VTI  VTI  N-{N-[4-(acetylamino)-3,5-dichlorobenzyl]carbamimidoyl}-2-(1H-indol-1-yl)acetamide  ligand  48  29  .  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_VTI
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
 VTI  CAA  C   CH3   0  -0.784  -7.7979   0.6543  -1.4662
 VTI  CAT  C   C     0   0.501  -6.4954   0.8074  -0.7295
 VTI  OAC  O   O     0  -0.469  -6.0640   1.8840  -0.3612
 VTI  NAS  N   NH1   0  -0.726  -5.8130  -0.3500  -0.5299
 VTI  CAZ  C   CR6   0   0.454  -4.5695  -0.3860   0.1130
 VTI  CAY  C   CR6   0  -0.085  -4.4344  -0.9070   1.3981
 VTI  CAN  C   CR16  0  -0.270  -3.2071  -0.9821   2.0322
 VTI  CLF  CL  CL    0  -0.095  -5.8416  -1.4900   2.2110
 VTI  CAX  C   CR6   0  -0.075  -3.4101   0.0770  -0.5058
 VTI  CLE  CL  CL    0  -0.098  -3.5062   0.6944  -2.1142
 VTI  CAM  C   CR16  0  -0.253  -2.1775   0.0322   0.1218
 VTI  CAW  C   CR6   0   0.086  -2.0685  -0.5047   1.3965
 VTI  CAO  C   CH2   0  -0.318  -0.7433  -0.5467   2.1229
 VTI  NAQ  N   NH1   0  -0.665   0.4022  -0.5100   1.2641
 VTI  CAU  C   C     0   0.638   0.7515  -1.5913   0.5330
 VTI  NAB  N   N     0  -0.691   0.0714  -2.6688   0.5687
 VTI  NAR  N   NH1   0  -0.725   1.8984  -1.4496  -0.2700
 VTI  C    C   C     0   0.556   2.7411  -0.3923  -0.3966
 VTI  O    O   O     0  -0.446   2.6489   0.6532   0.2133
 VTI  CA   C   CH2   0  -0.474   3.8432  -0.6326  -1.4216
 VTI  N    N   NR5   0  -0.514   4.8217   0.4052  -1.4075
 VTI  CBB  C   CR56  0   0.377   5.8462   0.5163  -0.5053
 VTI  CAJ  C   CR16  0  -0.310   6.2576  -0.3591   0.4976
 VTI  CAH  C   CR16  0  -0.281   7.3526   0.0115   1.2557
 VTI  CAG  C   CR16  0  -0.272   8.0229   1.2235   1.0256
 VTI  CAI  C   CR16  0  -0.346   7.6097   2.0887   0.0311
 VTI  CBA  C   CR56  0   0.054   6.5033   1.7413  -0.7518
 VTI  CAK  C   CR15  0  -0.422   5.8097   2.3700  -1.8334
 VTI  CAL  C   CR15  0  -0.019   4.7965   1.5325  -2.1876
 VTI  H1   H   HCH3  0   0.269  -8.5638   1.2653  -0.9924
 VTI  H2   H   HCH3  0   0.276  -7.6702   1.0195  -2.4864
 VTI  H3   H   HCH3  0   0.254  -8.1480  -0.3747  -1.5188
 VTI  H4   H   HNH1  0   0.413  -6.2475  -1.2274  -0.7717
 VTI  H5   H   HCR6  0   0.280  -3.1403  -1.4090   3.0247
 VTI  H6   H   HCR6  0   0.274  -1.2995   0.4022  -0.3905
 VTI  H7   H   HCH2  0   0.284  -0.6797   0.3194   2.7834
 VTI  H8   H   HCH2  0   0.257  -0.7168  -1.4332   2.7609
 VTI  H9   H   HNH1  0   0.418   0.9795   0.3138   1.2336
 VTI  H10  H   H     0   0.334   0.4654  -3.3863  -0.0269
 VTI  H11  H   HNH1  0   0.428   2.1043  -2.2582  -0.8399
 VTI  H12  H   HCH2  0   0.310   4.3148  -1.6020  -1.2457
 VTI  H13  H   HCH2  0   0.330   3.3893  -0.6904  -2.4135
 VTI  H14  H   HCR6  0   0.261   5.7508  -1.2977   0.6854
 VTI  H15  H   HCR6  0   0.251   7.7009  -0.6460   2.0417
 VTI  H16  H   HCR6  0   0.248   8.8770   1.4802   1.6390
 VTI  H17  H   HCR6  0   0.247   8.1315   3.0223  -0.1386
 VTI  H18  H   HCR5  0   0.249   6.0381   3.3198  -2.2900
 VTI  H19  H   HCR5  0   0.288   4.0480   1.6414  -2.9572

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
 VTI  CLE  CAX  single    1.725  0.020  1.725
 VTI  CAA  CAT  single    1.504  0.020  1.504
 VTI  CAI  CAG  aromatic  1.381  0.020  1.381
 VTI  CAI  CBA  aromatic  1.399  0.020  1.399
 VTI  CAG  CAH  aromatic  1.404  0.020  1.404
 VTI  CAT  OAC  double    1.217  0.020  1.217
 VTI  CAT  NAS  single    1.358  0.020  1.358
 VTI  CBA  CAK  aromatic  1.431  0.020  1.431
 VTI  CBA  CBB  aromatic  1.412  0.020  1.412
 VTI  CAK  CAL  aromatic  1.361  0.020  1.361
 VTI  CAH  CAJ  aromatic  1.382  0.020  1.382
 VTI  NAS  CAZ  single    1.400  0.020  1.400
 VTI  CAX  CAZ  aromatic  1.393  0.020  1.393
 VTI  CAX  CAM  aromatic  1.384  0.020  1.384
 VTI  CAZ  CAY  aromatic  1.393  0.020  1.393
 VTI  CAM  CAW  aromatic  1.387  0.020  1.387
 VTI  CBB  CAJ  aromatic  1.393  0.020  1.393
 VTI  CBB  N    aromatic  1.370  0.020  1.370
 VTI  CAL  N    aromatic  1.371  0.020  1.371
 VTI  N    CA   single    1.426  0.020  1.426
 VTI  O    C    double    1.214  0.020  1.214
 VTI  CAY  CAN  aromatic  1.383  0.020  1.383
 VTI  CAY  CLF  single    1.727  0.020  1.727
 VTI  CAW  CAN  aromatic  1.389  0.020  1.389
 VTI  CAW  CAO  single    1.512  0.020  1.512
 VTI  C    CA   single    1.524  0.020  1.524
 VTI  C    NAR  single    1.358  0.020  1.358
 VTI  NAQ  CAO  single    1.432  0.020  1.432
 VTI  NAQ  CAU  single    1.351  0.020  1.351
 VTI  NAR  CAU  single    1.407  0.020  1.407
 VTI  CAU  NAB  double    1.275  0.020  1.275
 VTI  CAA  H1   single    0.970  0.020  1.090
 VTI  CAA  H2   single    0.970  0.020  1.090
 VTI  CAA  H3   single    0.970  0.020  1.090
 VTI  NAS  H4   single    0.860  0.020  1.020
 VTI  CAN  H5   single    0.930  0.020  1.080
 VTI  CAM  H6   single    0.930  0.020  1.080
 VTI  CAO  H7   single    0.970  0.020  1.090
 VTI  CAO  H8   single    0.970  0.020  1.090
 VTI  NAQ  H9   single    0.860  0.020  1.020
 VTI  NAB  H10  single    0.890  0.020  1.040
 VTI  NAR  H11  single    0.860  0.020  1.020
 VTI  CA   H12  single    0.970  0.020  1.090
 VTI  CA   H13  single    0.970  0.020  1.090
 VTI  CAJ  H14  single    0.930  0.020  1.080
 VTI  CAH  H15  single    0.930  0.020  1.080
 VTI  CAG  H16  single    0.930  0.020  1.080
 VTI  CAI  H17  single    0.930  0.020  1.080
 VTI  CAK  H18  single    0.930  0.020  1.080
 VTI  CAL  H19  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
 VTI  H3   CAA  H2   107.99  3.000
 VTI  H3   CAA  H1   108.99  3.000
 VTI  H2   CAA  H1   107.54  3.000
 VTI  H3   CAA  CAT  113.49  3.000
 VTI  H2   CAA  CAT  108.82  3.000
 VTI  H1   CAA  CAT  109.82  3.000
 VTI  NAS  CAT  OAC  122.09  3.000
 VTI  NAS  CAT  CAA  114.85  3.000
 VTI  OAC  CAT  CAA  123.04  3.000
 VTI  H4   NAS  CAZ  118.05  3.000
 VTI  H4   NAS  CAT  119.32  3.000
 VTI  CAZ  NAS  CAT  122.38  3.000
 VTI  CAX  CAZ  CAY  116.95  3.000
 VTI  CAY  CAZ  NAS  121.28  3.000
 VTI  CAX  CAZ  NAS  121.77  3.000
 VTI  CLF  CAY  CAN  119.27  3.000
 VTI  CLF  CAY  CAZ  118.79  3.000
 VTI  CAN  CAY  CAZ  121.94  3.000
 VTI  H5   CAN  CAW  120.31  3.000
 VTI  H5   CAN  CAY  119.76  3.000
 VTI  CAW  CAN  CAY  119.93  3.000
 VTI  CAM  CAX  CLE  118.94  3.000
 VTI  CAM  CAX  CAZ  121.94  3.000
 VTI  CLE  CAX  CAZ  119.11  3.000
 VTI  H6   CAM  CAW  120.24  3.000
 VTI  H6   CAM  CAX  119.81  3.000
 VTI  CAW  CAM  CAX  119.94  3.000
 VTI  CAO  CAW  CAM  121.41  3.000
 VTI  CAO  CAW  CAN  119.29  3.000
 VTI  CAM  CAW  CAN  119.28  3.000
 VTI  H8   CAO  H7   106.81  3.000
 VTI  H8   CAO  NAQ  110.58  3.000
 VTI  H7   CAO  NAQ  107.22  3.000
 VTI  H8   CAO  CAW  108.93  3.000
 VTI  H7   CAO  CAW  108.66  3.000
 VTI  NAQ  CAO  CAW  114.35  3.000
 VTI  H9   NAQ  CAU  119.36  3.000
 VTI  H9   NAQ  CAO  119.87  3.000
 VTI  CAU  NAQ  CAO  120.71  3.000
 VTI  NAR  CAU  NAB  122.40  3.000
 VTI  NAB  CAU  NAQ  121.56  3.000
 VTI  NAR  CAU  NAQ  116.04  3.000
 VTI  H10  NAB  CAU  112.02  3.000
 VTI  H11  NAR  C    116.36  3.000
 VTI  H11  NAR  CAU  114.04  3.000
 VTI  C    NAR  CAU  129.59  3.000
 VTI  CA   C    O    121.91  3.000
 VTI  CA   C    NAR  112.87  3.000
 VTI  O    C    NAR  125.22  3.000
 VTI  H13  CA   H12  106.18  3.000
 VTI  H13  CA   N    109.42  3.000
 VTI  H12  CA   N    110.36  3.000
 VTI  H13  CA   C    108.58  3.000
 VTI  H12  CA   C    110.11  3.000
 VTI  N    CA   C    112.01  3.000
 VTI  CAL  N    CBB  108.77  3.000
 VTI  CAL  N    CA   125.45  3.000
 VTI  CBB  N    CA   125.35  3.000
 VTI  CBA  CBB  CAJ  122.23  3.000
 VTI  CAJ  CBB  N    130.10  3.000
 VTI  CBA  CBB  N    107.67  3.000
 VTI  H14  CAJ  CAH  120.52  3.000
 VTI  H14  CAJ  CBB  122.08  3.000
 VTI  CAH  CAJ  CBB  117.40  3.000
 VTI  H15  CAH  CAG  119.33  3.000
 VTI  H15  CAH  CAJ  119.35  3.000
 VTI  CAG  CAH  CAJ  121.31  3.000
 VTI  H16  CAG  CAI  119.70  3.000
 VTI  H16  CAG  CAH  119.24  3.000
 VTI  CAI  CAG  CAH  121.05  3.000
 VTI  H17  CAI  CBA  120.49  3.000
 VTI  H17  CAI  CAG  120.57  3.000
 VTI  CBA  CAI  CAG  118.94  3.000
 VTI  CAK  CBA  CAI  134.21  3.000
 VTI  CAK  CBA  CBB  106.72  3.000
 VTI  CAI  CBA  CBB  119.06  3.000
 VTI  H18  CAK  CAL  126.11  3.000
 VTI  H18  CAK  CBA  127.20  3.000
 VTI  CAL  CAK  CBA  106.68  3.000
 VTI  H19  CAL  CAK  129.77  3.000
 VTI  H19  CAL  N    120.10  3.000
 VTI  CAK  CAL  N    110.13  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
 VTI  CONST_01  CAW  CAM  CAX  CAZ     0.00   0.0  0
 VTI  CONST_02  CAW  CAN  CAY  CAZ     0.00   0.0  0
 VTI  CONST_03  CAM  CAX  CAZ  CAY     0.00   0.0  0
 VTI  CONST_04  CAM  CAW  CAN  CAY     0.00   0.0  0
 VTI  CONST_05  CAX  CAZ  CAY  CAN     0.00   0.0  0
 VTI  CONST_06  CAX  CAM  CAW  CAN     0.00   0.0  0
 VTI  CONST_07  CAI  CBA  CBB  N     180.00   0.0  0
 VTI  CONST_08  CAK  CBA  CBB  N       0.00   0.0  0
 VTI  CONST_09  CAH  CAJ  CBB  N     180.00   0.0  0
 VTI  CONST_10  CBA  CAK  CAL  N       0.00   0.0  0
 VTI  CONST_11  CAG  CAI  CBA  CBB     0.00   0.0  0
 VTI  CONST_12  CAL  CAK  CBA  CBB     0.00   0.0  0
 VTI  CONST_13  CAG  CAH  CAJ  CBB     0.00   0.0  0
 VTI  CONST_14  CAK  CAL  N    CBB     0.00   0.0  0
 VTI  CONST_15  CAI  CAG  CAH  CAJ     0.00   0.0  0
 VTI  CONST_16  CAI  CBA  CBB  CAJ     0.00   0.0  0
 VTI  CONST_17  CAK  CBA  CBB  CAJ   180.00   0.0  0
 VTI  CONST_18  CAL  N    CBB  CAJ   180.00   0.0  0
 VTI  CONST_19  CBA  CAI  CAG  CAH     0.00   0.0  0
 VTI  CONST_20  CBA  CBB  CAJ  CAH     0.00   0.0  0
 VTI  CONST_21  CAK  CBA  CAI  CAG   180.00   0.0  0
 VTI  CONST_22  CAL  CAK  CBA  CAI   180.00   0.0  0
 VTI  CONST_23  CAL  N    CBB  CBA     0.00   0.0  0
 VTI  CONST_24  CAM  CAX  CAZ  NAS   180.00   0.0  0
 VTI  CONST_25  CAN  CAY  CAZ  NAS   180.00   0.0  0
 VTI  CONST_26  CLE  CAX  CAZ  CAY   180.00   0.0  0
 VTI  CONST_27  CAO  CAW  CAN  CAY   180.00   0.0  0
 VTI  CONST_28  CAX  CAZ  CAY  CLF   180.00   0.0  0
 VTI  CONST_29  CAW  CAN  CAY  CLF   180.00   0.0  0
 VTI  CONST_30  CAO  CAW  CAM  CAX   180.00   0.0  0
 VTI  CONST_31  CAW  CAM  CAX  CLE   180.00   0.0  0
 VTI  CONST_32  CBA  CBB  N    CA    180.00   0.0  0
 VTI  CONST_33  CAJ  CBB  N    CA      0.00   0.0  0
 VTI  CONST_34  CAK  CAL  N    CA    180.00   0.0  0
 VTI  CONST_35  H6   CAM  CAX  CAZ   180.00   0.0  0
 VTI  CONST_36  H5   CAN  CAY  CAZ   180.00   0.0  0
 VTI  CONST_37  H14  CAJ  CBB  N       0.00   0.0  0
 VTI  CONST_38  H18  CAK  CAL  N     180.00   0.0  0
 VTI  CONST_39  H17  CAI  CBA  CBB   180.00   0.0  0
 VTI  CONST_40  H15  CAH  CAJ  CBB   180.00   0.0  0
 VTI  CONST_41  H19  CAL  N    CBB   180.00   0.0  0
 VTI  CONST_42  H16  CAG  CAH  CAJ   180.00   0.0  0
 VTI  CONST_46  CAZ  NAS  CAT  CAA   180.00   0.0  0
 VTI  CONST_47  CAZ  NAS  CAT  OAC     0.00   0.0  0
 VTI  CONST_48  O    C    NAR  CAU     0.00   0.0  0
 VTI  CONST_49  CA   C    NAR  CAU   180.00   0.0  0
 VTI  CONST_50  NAR  CAU  NAQ  CAO   180.00   0.0  0
 VTI  CONST_51  NAB  CAU  NAQ  CAO     0.00   0.0  0
 VTI  CONST_52  C    NAR  CAU  NAQ     0.00   0.0  0
 VTI  CONST_53  C    NAR  CAU  NAB   180.00   0.0  0
 VTI  CONST_54  H11  NAR  C    O     180.00   0.0  0
 VTI  CONST_55  H10  NAB  CAU  NAQ   180.00   0.0  0
 VTI  CONST_56  H9   NAQ  CAU  NAB   180.00   0.0  0
 VTI  Var_01    NAQ  CAO  CAW  CAN   158.14  30.0  2
 VTI  Var_02    CBB  N    CA   C      79.97  30.0  3
 VTI  Var_03    CAU  NAQ  CAO  CAW   -73.56  30.0  1
 VTI  Var_04    N    CA   C    NAR  -171.84  30.0  3
 VTI  Var_05    H1   CAA  CAT  OAC   -44.36  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
 VTI  plan-1  NAS  0.020
 VTI  plan-1  CAZ  0.020
 VTI  plan-1  CAY  0.020
 VTI  plan-1  CAN  0.020
 VTI  plan-1  CLF  0.020
 VTI  plan-1  CAX  0.020
 VTI  plan-1  CLE  0.020
 VTI  plan-1  CAM  0.020
 VTI  plan-1  CAW  0.020
 VTI  plan-1  CAO  0.020
 VTI  plan-1  H5   0.020
 VTI  plan-1  H6   0.020
 VTI  plan-2  CA   0.020
 VTI  plan-2  N    0.020
 VTI  plan-2  CBB  0.020
 VTI  plan-2  CAJ  0.020
 VTI  plan-2  CAH  0.020
 VTI  plan-2  CAG  0.020
 VTI  plan-2  CAI  0.020
 VTI  plan-2  CBA  0.020
 VTI  plan-2  CAK  0.020
 VTI  plan-2  CAL  0.020
 VTI  plan-2  H14  0.020
 VTI  plan-2  H15  0.020
 VTI  plan-2  H16  0.020
 VTI  plan-2  H17  0.020
 VTI  plan-2  H18  0.020
 VTI  plan-2  H19  0.020
 VTI  plan-3  CAA  0.020
 VTI  plan-3  CAT  0.020
 VTI  plan-3  OAC  0.020
 VTI  plan-3  NAS  0.020
 VTI  plan-3  CAZ  0.020
 VTI  plan-3  H4   0.020
 VTI  plan-4  CAO  0.020
 VTI  plan-4  NAQ  0.020
 VTI  plan-4  CAU  0.020
 VTI  plan-4  NAB  0.020
 VTI  plan-4  NAR  0.020
 VTI  plan-4  C    0.020
 VTI  plan-4  O    0.020
 VTI  plan-4  CA   0.020
 VTI  plan-4  H9   0.020
 VTI  plan-4  H10  0.020
 VTI  plan-4  H11  0.020

