# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 09:06:32 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-{4-[(1E)-N-carbamimidoylbutanehydrazonoyl]phenyl}-5-methoxy-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=N\NC(N)=N)/c1ccc(NC(=O)c2[nH]c3ccc(OC)cc3c2)cc1
#
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
 YIT  YIT  N-{4-[(1E)-N-carbamimidoylbutanehydrazonoyl]phenyl}-5-methoxy-1H-indole-2-carboxamide  ligand  53  29  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YIT
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
 YIT  NAA   N  NR15  0  -0.745   -3.6760  -0.5469  -0.4887
 YIT  CAI   C  CR56  0   0.333   -5.0338  -0.6270  -0.3623
 YIT  CAH   C  CR16  0  -0.293   -5.9381  -1.5516  -0.8736
 YIT  CAG   C  CR16  0  -0.395   -7.2761  -1.3874  -0.5729
 YIT  CAL   C  CR6   0   0.383   -7.7201  -0.3143   0.2290
 YIT  OBB   O  O2    0  -0.481   -9.0211  -0.1181   0.5492
 YIT  CAO   C  CH3   0  -0.435   -9.9866  -1.0324   0.0759
 YIT  CAK   C  CR16  0  -0.447   -6.8194   0.6078   0.7320
 YIT  CAJ   C  CR56  0   0.086   -5.4614   0.4592   0.4310
 YIT  CAN   C  CR15  0  -0.399   -4.2973   1.2123   0.7531
 YIT  CAM   C  CR5   0   0.209   -3.2350   0.5719   0.1713
 YIT  CAP   C  C     0   0.514   -1.8247   0.9926   0.2421
 YIT  OBC   O  O     0  -0.454   -1.5303   2.1406   0.5252
 YIT  NAB   N  NH1   0  -0.764   -0.9170   0.0142  -0.0218
 YIT  CAQ   C  CR6   0   0.368    0.4737   0.1452  -0.0889
 YIT  CAV   C  CR16  0  -0.325    1.2449  -1.0001   0.1291
 YIT  CAU   C  CR16  0  -0.275    2.6202  -0.9566   0.0372
 YIT  CAR   C  CR16  0  -0.285    1.1229   1.3345  -0.4055
 YIT  CAS   C  CR16  0  -0.324    2.5069   1.3636  -0.4974
 YIT  CAT   C  CR6   0   0.045    3.2898   0.2309  -0.2808
 YIT  CAW   C  C     0   0.227    4.7640   0.2749  -0.3706
 YIT  CAX   C  CH2   0  -0.595    5.4433   1.5188  -0.8789
 YIT  CAZ   C  CH2   0  -0.420    5.8401   2.4789   0.2493
 YIT  CBA   C  CH3   0  -0.662    6.5289   3.7273  -0.2810
 YIT  NAC   N  N     0  -0.210    5.3825  -0.7707   0.0317
 YIT  NAD   N  NH1   0  -0.522    6.7143  -0.8175  -0.0059
 YIT  CAY   C  C     0   0.561    7.3916  -1.9083   0.5030
 YIT  NAF   N  N     0  -0.679    6.7716  -2.8702   1.0650
 YIT  NAE   N  NH2   0  -0.843    8.7528  -1.7604   0.3686
 YIT  HAA   H  HNR5  0   0.415   -3.1333  -1.1017  -1.1307
 YIT  HAH   H  HCR6  0   0.269   -5.6145  -2.3825  -1.4869
 YIT  HAG   H  HCR6  0   0.279   -7.9788  -2.1070  -0.9697
 YIT  HAK   H  HCR6  0   0.255   -7.1672   1.4331   1.3413
 YIT  HAF   H  H     0   0.323    7.4265  -3.5959   1.3317
 YIT  HAO1  H  HCH3  0   0.257  -10.9460  -0.6944   0.4604
 YIT  HAO2  H  HCH3  0   0.225  -10.0371  -1.0524  -1.0164
 YIT  HAO3  H  HCH3  0   0.224   -9.8064  -2.0488   0.4368
 YIT  HAN   H  HCR5  0   0.260   -4.2421   2.1014   1.3607
 YIT  HAB   H  HNH1  0   0.417   -1.2528  -0.9380  -0.0220
 YIT  HAV   H  HCR6  0   0.270    0.7580  -1.9368   0.3742
 YIT  HAR   H  HCR6  0   0.274    0.5700   2.2402  -0.5968
 YIT  HAU   H  HCR6  0   0.258    3.1889  -1.8591   0.2150
 YIT  HAS   H  HCR6  0   0.251    2.9631   2.3110  -0.7495
 YIT  HAX1  H  HCH2  0   0.258    6.3294   1.2569  -1.4669
 YIT  HAX2  H  HCH2  0   0.265    4.7934   2.0371  -1.5851
 YIT  HAZ1  H  HCH2  0   0.234    4.9481   2.7612   0.8146
 YIT  HAZ2  H  HCH2  0   0.228    6.4980   1.9688   0.9585
 YIT  HBA1  H  HCH3  0   0.222    5.8768   4.2789  -0.9602
 YIT  HBA2  H  HCH3  0   0.234    6.8066   4.3990   0.5316
 YIT  HBA3  H  HCH3  0   0.222    7.4388   3.4737  -0.8274
 YIT  HAD   H  HNH1  0   0.401    7.2535  -0.0055  -0.2720
 YIT  HAE1  H  HNH2  0   0.390    9.0850  -1.2708  -0.4488
 YIT  HAE2  H  HNH2  0   0.393    9.2950  -2.5875   0.5585

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
 YIT  NAA  CAI   aromatic  1.366  0.020  1.366
 YIT  NAA  CAM   aromatic  1.372  0.020  1.372
 YIT  CAI  CAH   aromatic  1.391  0.020  1.391
 YIT  CAI  CAJ   aromatic  1.411  0.020  1.411
 YIT  CAH  CAG   aromatic  1.381  0.020  1.381
 YIT  CAG  CAL   aromatic  1.411  0.020  1.411
 YIT  CAL  OBB   single    1.354  0.020  1.354
 YIT  CAL  CAK   aromatic  1.384  0.020  1.384
 YIT  OBB  CAO   single    1.411  0.020  1.411
 YIT  CAK  CAJ   aromatic  1.399  0.020  1.399
 YIT  CAJ  CAN   aromatic  1.423  0.020  1.423
 YIT  CAN  CAM   aromatic  1.370  0.020  1.370
 YIT  CAM  CAP   single    1.473  0.020  1.473
 YIT  CAP  OBC   double    1.219  0.020  1.219
 YIT  CAP  NAB   single    1.360  0.020  1.360
 YIT  NAB  CAQ   single    1.398  0.020  1.398
 YIT  CAQ  CAV   aromatic  1.398  0.020  1.398
 YIT  CAQ  CAR   aromatic  1.392  0.020  1.392
 YIT  CAV  CAU   aromatic  1.379  0.020  1.379
 YIT  CAU  CAT   aromatic  1.400  0.020  1.400
 YIT  CAR  CAS   aromatic  1.387  0.020  1.387
 YIT  CAS  CAT   aromatic  1.394  0.020  1.394
 YIT  CAT  CAW   single    1.478  0.020  1.478
 YIT  CAW  CAX   single    1.506  0.020  1.506
 YIT  CAW  NAC   double    1.280  0.020  1.280
 YIT  CAX  CAZ   single    1.534  0.020  1.534
 YIT  CAZ  CBA   single    1.521  0.020  1.521
 YIT  NAC  NAD   single    1.333  0.020  1.333
 YIT  NAD  CAY   single    1.381  0.020  1.381
 YIT  CAY  NAF   double    1.275  0.020  1.275
 YIT  CAY  NAE   single    1.376  0.020  1.376
 YIT  NAA  HAA   single    0.860  0.020  1.020
 YIT  CAH  HAH   single    0.930  0.020  1.080
 YIT  CAG  HAG   single    0.930  0.020  1.080
 YIT  CAK  HAK   single    0.930  0.020  1.080
 YIT  CAO  HAO1  single    0.970  0.020  1.090
 YIT  CAO  HAO2  single    0.970  0.020  1.090
 YIT  CAO  HAO3  single    0.970  0.020  1.090
 YIT  CAN  HAN   single    0.930  0.020  1.080
 YIT  NAB  HAB   single    0.860  0.020  1.020
 YIT  CAV  HAV   single    0.930  0.020  1.080
 YIT  CAR  HAR   single    0.930  0.020  1.080
 YIT  CAU  HAU   single    0.930  0.020  1.080
 YIT  CAS  HAS   single    0.930  0.020  1.080
 YIT  CAX  HAX1  single    0.970  0.020  1.090
 YIT  CAX  HAX2  single    0.970  0.020  1.090
 YIT  CAZ  HAZ1  single    0.970  0.020  1.090
 YIT  CAZ  HAZ2  single    0.970  0.020  1.090
 YIT  CBA  HBA1  single    0.970  0.020  1.090
 YIT  CBA  HBA2  single    0.970  0.020  1.090
 YIT  CBA  HBA3  single    0.970  0.020  1.090
 YIT  NAD  HAD   single    0.860  0.020  1.020
 YIT  NAE  HAE1  single    0.890  0.020  1.040
 YIT  NAE  HAE2  single    0.890  0.020  1.040
 YIT  NAF  HAF   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
 YIT  HAA   NAA  CAM   125.64  3.000
 YIT  HAA   NAA  CAI   124.21  3.000
 YIT  CAM   NAA  CAI   108.84  3.000
 YIT  CAJ   CAI  CAH   121.42  3.000
 YIT  CAJ   CAI  NAA   107.94  3.000
 YIT  CAH   CAI  NAA   130.64  3.000
 YIT  HAH   CAH  CAG   120.28  3.000
 YIT  HAH   CAH  CAI   121.62  3.000
 YIT  CAG   CAH  CAI   118.09  3.000
 YIT  HAG   CAG  CAL   120.67  3.000
 YIT  HAG   CAG  CAH   118.07  3.000
 YIT  CAL   CAG  CAH   121.26  3.000
 YIT  CAK   CAL  OBB   116.29  3.000
 YIT  CAK   CAL  CAG   120.56  3.000
 YIT  OBB   CAL  CAG   123.15  3.000
 YIT  CAO   OBB  CAL   118.95  3.000
 YIT  HAO3  CAO  HAO2  108.68  3.000
 YIT  HAO3  CAO  HAO1  108.52  3.000
 YIT  HAO2  CAO  HAO1  108.54  3.000
 YIT  HAO3  CAO  OBB   112.25  3.000
 YIT  HAO2  CAO  OBB   112.24  3.000
 YIT  HAO1  CAO  OBB   106.47  3.000
 YIT  HAK   CAK  CAJ   120.90  3.000
 YIT  HAK   CAK  CAL   120.21  3.000
 YIT  CAJ   CAK  CAL   118.88  3.000
 YIT  CAN   CAJ  CAK   133.56  3.000
 YIT  CAN   CAJ  CAI   106.65  3.000
 YIT  CAK   CAJ  CAI   119.78  3.000
 YIT  HAN   CAN  CAM   125.81  3.000
 YIT  HAN   CAN  CAJ   127.27  3.000
 YIT  CAM   CAN  CAJ   106.90  3.000
 YIT  CAP   CAM  CAN   126.04  3.000
 YIT  CAP   CAM  NAA   124.31  3.000
 YIT  CAN   CAM  NAA   109.65  3.000
 YIT  NAB   CAP  OBC   124.16  3.000
 YIT  NAB   CAP  CAM   115.08  3.000
 YIT  OBC   CAP  CAM   120.75  3.000
 YIT  HAB   NAB  CAQ   114.77  3.000
 YIT  HAB   NAB  CAP   117.15  3.000
 YIT  CAQ   NAB  CAP   127.26  3.000
 YIT  CAR   CAQ  CAV   118.58  3.000
 YIT  CAR   CAQ  NAB   123.71  3.000
 YIT  CAV   CAQ  NAB   117.68  3.000
 YIT  HAV   CAV  CAU   119.37  3.000
 YIT  HAV   CAV  CAQ   119.70  3.000
 YIT  CAU   CAV  CAQ   120.93  3.000
 YIT  HAU   CAU  CAT   119.58  3.000
 YIT  HAU   CAU  CAV   119.15  3.000
 YIT  CAT   CAU  CAV   121.26  3.000
 YIT  HAR   CAR  CAS   118.83  3.000
 YIT  HAR   CAR  CAQ   121.27  3.000
 YIT  CAS   CAR  CAQ   119.90  3.000
 YIT  HAS   CAS  CAT   120.74  3.000
 YIT  HAS   CAS  CAR   117.05  3.000
 YIT  CAT   CAS  CAR   122.21  3.000
 YIT  CAW   CAT  CAS   121.79  3.000
 YIT  CAW   CAT  CAU   121.09  3.000
 YIT  CAS   CAT  CAU   117.12  3.000
 YIT  NAC   CAW  CAX   124.26  3.000
 YIT  NAC   CAW  CAT   116.03  3.000
 YIT  CAX   CAW  CAT   119.69  3.000
 YIT  HAX2  CAX  HAX1  104.36  3.000
 YIT  HAX2  CAX  CAZ   109.45  3.000
 YIT  HAX1  CAX  CAZ   109.59  3.000
 YIT  HAX2  CAX  CAW   110.01  3.000
 YIT  HAX1  CAX  CAW   110.41  3.000
 YIT  CAZ   CAX  CAW   112.68  3.000
 YIT  HAZ2  CAZ  HAZ1  106.02  3.000
 YIT  HAZ2  CAZ  CBA   109.66  3.000
 YIT  HAZ1  CAZ  CBA   109.75  3.000
 YIT  HAZ2  CAZ  CAX   109.92  3.000
 YIT  HAZ1  CAZ  CAX   109.33  3.000
 YIT  CBA   CAZ  CAX   111.99  3.000
 YIT  HBA3  CBA  HBA2  107.70  3.000
 YIT  HBA3  CBA  HBA1  107.70  3.000
 YIT  HBA2  CBA  HBA1  107.74  3.000
 YIT  HBA3  CBA  CAZ   111.18  3.000
 YIT  HBA2  CBA  CAZ   111.17  3.000
 YIT  HBA1  CBA  CAZ   111.17  3.000
 YIT  NAD   NAC  CAW   120.18  3.000
 YIT  HAD   NAD  CAY   118.04  3.000
 YIT  HAD   NAD  NAC   120.81  3.000
 YIT  CAY   NAD  NAC   120.48  3.000
 YIT  NAE   CAY  NAF   127.25  3.000
 YIT  NAE   CAY  NAD   111.36  3.000
 YIT  NAF   CAY  NAD   121.32  3.000
 YIT  HAF   NAF  CAY   110.01  3.000
 YIT  HAE2  NAE  HAE1  111.96  3.000
 YIT  HAE2  NAE  CAY   115.21  3.000
 YIT  HAE1  NAE  CAY   117.19  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
 YIT  CONST_01  CAG   CAH  CAI  NAA   180.00   0.0  0
 YIT  CONST_02  CAK   CAJ  CAI  NAA   180.00   0.0  0
 YIT  CONST_03  CAN   CAJ  CAI  NAA     0.00   0.0  0
 YIT  CONST_04  CAJ   CAN  CAM  NAA     0.00   0.0  0
 YIT  CONST_05  CAN   CAM  NAA  CAI     0.00   0.0  0
 YIT  CONST_06  CAL   CAG  CAH  CAI     0.00   0.0  0
 YIT  CONST_07  CAL   CAK  CAJ  CAI     0.00   0.0  0
 YIT  CONST_08  CAM   CAN  CAJ  CAI     0.00   0.0  0
 YIT  CONST_09  CAM   NAA  CAI  CAH   180.00   0.0  0
 YIT  CONST_10  CAK   CAJ  CAI  CAH     0.00   0.0  0
 YIT  CONST_11  CAN   CAJ  CAI  CAH   180.00   0.0  0
 YIT  CONST_12  CAK   CAL  CAG  CAH     0.00   0.0  0
 YIT  CONST_13  CAJ   CAI  CAH  CAG     0.00   0.0  0
 YIT  CONST_14  CAJ   CAK  CAL  CAG     0.00   0.0  0
 YIT  CONST_15  CAN   CAJ  CAK  CAL   180.00   0.0  0
 YIT  CONST_16  CAM   CAN  CAJ  CAK   180.00   0.0  0
 YIT  CONST_17  CAM   NAA  CAI  CAJ     0.00   0.0  0
 YIT  CONST_18  CAT   CAU  CAV  CAQ     0.00   0.0  0
 YIT  CONST_19  CAT   CAS  CAR  CAQ     0.00   0.0  0
 YIT  CONST_20  CAS   CAR  CAQ  CAV     0.00   0.0  0
 YIT  CONST_21  CAS   CAT  CAU  CAV     0.00   0.0  0
 YIT  CONST_22  CAR   CAQ  CAV  CAU     0.00   0.0  0
 YIT  CONST_23  CAR   CAS  CAT  CAU     0.00   0.0  0
 YIT  CONST_24  CAP   CAM  NAA  CAI   180.00   0.0  0
 YIT  CONST_25  OBB   CAL  CAG  CAH   180.00   0.0  0
 YIT  CONST_26  CAJ   CAK  CAL  OBB   180.00   0.0  0
 YIT  CONST_27  CAP   CAM  CAN  CAJ   180.00   0.0  0
 YIT  CONST_28  CAU   CAV  CAQ  NAB   180.00   0.0  0
 YIT  CONST_29  CAS   CAR  CAQ  NAB   180.00   0.0  0
 YIT  CONST_30  CAW   CAT  CAU  CAV   180.00   0.0  0
 YIT  CONST_31  CAW   CAT  CAS  CAR   180.00   0.0  0
 YIT  CONST_32  HAH   CAH  CAI  NAA     0.00   0.0  0
 YIT  CONST_33  HAN   CAN  CAM  NAA   180.00   0.0  0
 YIT  CONST_34  HAG   CAG  CAH  CAI   180.00   0.0  0
 YIT  CONST_35  HAK   CAK  CAJ  CAI   180.00   0.0  0
 YIT  CONST_36  HAA   NAA  CAI  CAH     0.00   0.0  0
 YIT  CONST_37  HAU   CAU  CAV  CAQ   180.00   0.0  0
 YIT  CONST_38  HAS   CAS  CAR  CAQ   180.00   0.0  0
 YIT  CONST_39  HAR   CAR  CAQ  CAV   180.00   0.0  0
 YIT  CONST_40  HAV   CAV  CAQ  CAR   180.00   0.0  0
 YIT  CONST_41  CAQ   NAB  CAP  CAM   180.00   0.0  0
 YIT  CONST_44  HAB   NAB  CAQ  CAV     0.00   0.0  0
 YIT  CONST_45  CAQ   NAB  CAP  OBC     0.00   0.0  0
 YIT  CONST_46  NAF   CAY  NAD  NAC     0.00   0.0  0
 YIT  CONST_47  NAE   CAY  NAD  NAC   180.00   0.0  0
 YIT  CONST_48  HAF   NAF  CAY  NAD   180.00   0.0  0
 YIT  CONST_50  HAE2  NAE  CAY  NAD   180.00   0.0  0
 YIT  CONST_51  HAD   NAD  CAY  NAF   180.00   0.0  0
 YIT  Var_01    OBC   CAP  CAM  NAA   160.62  30.0  2
 YIT  Var_02    CAK   CAL  OBB  CAO  -179.43  30.0  2
 YIT  Var_03    CAX   CAW  CAT  CAU   172.47  30.0  2
 YIT  Var_04    CAZ   CAX  CAW  CAT    92.94  30.0  3
 YIT  Var_05    HAO1  CAO  OBB  CAL   179.16  30.0  3
 YIT  Var_06    CBA   CAZ  CAX  CAW   179.81  30.0  3
 YIT  Var_07    CAY   NAD  NAC  CAW   175.97  30.0  3
 YIT  Var_08    HBA1  CBA  CAZ  CAX    60.08  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
 YIT  plan-1  NAB   0.020
 YIT  plan-1  CAQ   0.020
 YIT  plan-1  CAV   0.020
 YIT  plan-1  CAU   0.020
 YIT  plan-1  CAR   0.020
 YIT  plan-1  CAS   0.020
 YIT  plan-1  CAT   0.020
 YIT  plan-1  CAW   0.020
 YIT  plan-1  HAV   0.020
 YIT  plan-1  HAR   0.020
 YIT  plan-1  HAU   0.020
 YIT  plan-1  HAS   0.020
 YIT  plan-2  NAA   0.020
 YIT  plan-2  CAI   0.020
 YIT  plan-2  CAH   0.020
 YIT  plan-2  CAG   0.020
 YIT  plan-2  CAL   0.020
 YIT  plan-2  OBB   0.020
 YIT  plan-2  CAK   0.020
 YIT  plan-2  CAJ   0.020
 YIT  plan-2  CAN   0.020
 YIT  plan-2  CAM   0.020
 YIT  plan-2  CAP   0.020
 YIT  plan-2  HAA   0.020
 YIT  plan-2  HAH   0.020
 YIT  plan-2  HAG   0.020
 YIT  plan-2  HAK   0.020
 YIT  plan-2  HAN   0.020
 YIT  plan-3  CAM   0.020
 YIT  plan-3  CAP   0.020
 YIT  plan-3  OBC   0.020
 YIT  plan-3  NAB   0.020
 YIT  plan-3  CAQ   0.020
 YIT  plan-3  HAB   0.020
 YIT  plan-4  NAC   0.020
 YIT  plan-4  NAD   0.020
 YIT  plan-4  CAY   0.020
 YIT  plan-4  NAF   0.020
 YIT  plan-4  NAE   0.020
 YIT  plan-4  HAF   0.020
 YIT  plan-4  HAD   0.020
 YIT  plan-4  HAE1  0.020
 YIT  plan-4  HAE2  0.020
 YIT  plan-5  CAT   0.020
 YIT  plan-5  CAW   0.020
 YIT  plan-5  CAX   0.020
 YIT  plan-5  NAC   0.020
 YIT  plan-5  NAD   0.020

