# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:09:06 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(1H-indazol-5-yl)-N'-[2-(1H-indol-3-yl)ethyl]-6-methoxy-1,3,5-triazine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(NCCc2c[nH]c3ccccc23)nc(Nc4ccc5[nH]ncc5c4)n1
#
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
 NJD  NJD  N-(1H-indazol-5-yl)-N'-[2-(1H-indol-3-yl)ethyl]-6-methoxy-1,3,5-triazine-2,4-diamine  ligand  50  30  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NJD
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
 NJD  CAJ  C  CR16  0  -0.412  -5.1625   1.4018  -0.6221
 NJD  CBA  C  CR56  0  -0.075  -6.4849   0.9550  -0.7297
 NJD  CAH  C  CR15  0  -0.132  -7.6504   1.3805  -1.4222
 NJD  NAM  N  N     0  -0.227  -8.6526   0.5701  -1.1860
 NJD  NAT  N  NR15  0  -0.545  -8.1997  -0.3773  -0.3647
 NJD  CBB  C  CR56  0   0.409  -6.8948  -0.2017  -0.0490
 NJD  CAG  C  CR16  0  -0.291  -6.0153  -0.9213   0.7666
 NJD  CAD  C  CR16  0  -0.284  -4.7272  -0.4568   0.8779
 NJD  CAV  C  CR6   0   0.341  -4.2881   0.6943   0.1770
 NJD  NAR  N  NH1   0  -0.750  -2.9826   1.1916   0.3266
 NJD  CAY  C  CR6   0   0.593  -1.8224   0.5022   0.3829
 NJD  NAN  N  N     0  -0.526  -0.7168   1.2323   0.4498
 NJD  NAP  N  N     0  -0.526  -1.8665  -0.8322   0.3641
 NJD  CAZ  C  CR6   0   0.599  -0.6836  -1.4099   0.4306
 NJD  OAU  O  O2    0  -0.445  -0.6164  -2.7292   0.4276
 NJD  CAA  C  CH3   0  -0.414  -1.8297  -3.4711   0.3501
 NJD  NAO  N  N     0  -0.513   0.4910  -0.8102   0.5018
 NJD  CAX  C  CR6   0   0.607   0.4179   0.5255   0.5012
 NJD  NAQ  N  NH1   0  -0.659   1.5617   1.2113   0.5531
 NJD  CAK  C  CH2   0  -0.230   2.8706   0.6030   0.6446
 NJD  CAL  C  CH2   0  -0.583   3.9542   1.6765   0.6010
 NJD  CAW  C  CR5   0   0.009   5.3201   1.0793   0.6696
 NJD  CBD  C  CR56  0   0.028   5.9918   0.3554  -0.3698
 NJD  CAF  C  CR16  0  -0.375   5.6596   0.0240  -1.6888
 NJD  CAC  C  CR16  0  -0.269   6.5601  -0.7019  -2.4435
 NJD  CAB  C  CR16  0  -0.285   7.7931  -1.1079  -1.9054
 NJD  CAE  C  CR16  0  -0.306   8.1501  -0.7931  -0.6081
 NJD  CBC  C  CR56  0   0.355   7.2387  -0.0589   0.1501
 NJD  NAS  N  NR15  0  -0.687   7.3127   0.3937   1.4343
 NJD  CAI  C  CR15  0  -0.085   6.1659   1.0708   1.7423
 NJD  H1   H  HCR6  0   0.267  -4.8314   2.2857  -1.1540
 NJD  H2   H  HCR5  0   0.267  -7.7738   2.2360  -2.0686
 NJD  H4   H  HCR6  0   0.273  -6.3317  -1.8045   1.3053
 NJD  H5   H  HCR6  0   0.271  -4.0344  -0.9853   1.5141
 NJD  H6   H  HNH1  0   0.406  -2.8686   2.1891   0.2308
 NJD  H7   H  HCH3  0   0.235  -2.3816  -3.2457  -0.5618
 NJD  H8   H  HCH3  0   0.249  -1.5345  -4.5168   0.3470
 NJD  H9   H  HCH3  0   0.236  -2.4744  -3.2792   1.2078
 NJD  H10  H  HNH1  0   0.398   1.4859   2.2152   0.5828
 NJD  H11  H  HCH2  0   0.234   2.9630   0.0277   1.5700
 NJD  H12  H  HCH2  0   0.237   3.0104  -0.1005  -0.1793
 NJD  H13  H  HCH2  0   0.247   3.8446   2.2608  -0.3186
 NJD  H14  H  HCH2  0   0.256   3.8127   2.3721   1.4326
 NJD  H15  H  HCR6  0   0.241   4.7118   0.3340  -2.1137
 NJD  H16  H  HCR6  0   0.245   6.3164  -0.9666  -3.4642
 NJD  H17  H  HCR6  0   0.249   8.4776  -1.6790  -2.5193
 NJD  H18  H  HCR6  0   0.258   9.1019  -1.1063  -0.1979
 NJD  H19  H  HNR5  0   0.408   8.0820   0.2490   2.0659
 NJD  H20  H  HCR5  0   0.281   6.0337   1.5088   2.7196
 NJD  H3   H  HNR5  0   0.416  -8.8217  -1.1025  -0.0474

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
 NJD  CAA  OAU  single    1.424  0.020  1.424
 NJD  OAU  CAZ  single    1.321  0.020  1.321
 NJD  NAO  CAZ  aromatic  1.321  0.020  1.321
 NJD  NAO  CAX  aromatic  1.338  0.020  1.338
 NJD  CAZ  NAP  aromatic  1.318  0.020  1.318
 NJD  CAK  NAQ  single    1.446  0.020  1.446
 NJD  CAK  CAL  single    1.526  0.020  1.526
 NJD  NAQ  CAX  single    1.335  0.020  1.335
 NJD  CAX  NAN  aromatic  1.338  0.020  1.338
 NJD  CAL  CAW  single    1.492  0.020  1.492
 NJD  NAP  CAY  aromatic  1.335  0.020  1.335
 NJD  NAN  CAY  aromatic  1.327  0.020  1.327
 NJD  CAW  CAI  aromatic  1.366  0.020  1.366
 NJD  CAW  CBD  aromatic  1.434  0.020  1.434
 NJD  CAY  NAR  single    1.351  0.020  1.351
 NJD  CAF  CBD  aromatic  1.400  0.020  1.400
 NJD  CAF  CAC  aromatic  1.381  0.020  1.381
 NJD  CAI  NAS  aromatic  1.367  0.020  1.367
 NJD  CBD  CBC  aromatic  1.413  0.020  1.413
 NJD  NAR  CAV  single    1.405  0.020  1.405
 NJD  CAC  CAB  aromatic  1.405  0.020  1.405
 NJD  NAS  CBC  aromatic  1.364  0.020  1.364
 NJD  CBC  CAE  aromatic  1.394  0.020  1.394
 NJD  CAB  CAE  aromatic  1.382  0.020  1.382
 NJD  CAV  CAJ  aromatic  1.380  0.020  1.380
 NJD  CAV  CAD  aromatic  1.417  0.020  1.417
 NJD  CAJ  CBA  aromatic  1.400  0.020  1.400
 NJD  CAD  CAG  aromatic  1.374  0.020  1.374
 NJD  CBA  CAH  aromatic  1.421  0.020  1.421
 NJD  CBA  CBB  aromatic  1.403  0.020  1.403
 NJD  CAG  CBB  aromatic  1.399  0.020  1.399
 NJD  CAH  NAM  aromatic  1.310  0.020  1.310
 NJD  CBB  NAT  aromatic  1.354  0.020  1.354
 NJD  NAM  NAT  aromatic  1.333  0.020  1.333
 NJD  CAJ  H1   single    0.930  0.020  1.080
 NJD  CAH  H2   single    0.930  0.020  1.080
 NJD  CAG  H4   single    0.930  0.020  1.080
 NJD  CAD  H5   single    0.930  0.020  1.080
 NJD  NAR  H6   single    0.860  0.020  1.020
 NJD  CAA  H7   single    0.970  0.020  1.090
 NJD  CAA  H8   single    0.970  0.020  1.090
 NJD  CAA  H9   single    0.970  0.020  1.090
 NJD  NAQ  H10  single    0.860  0.020  1.020
 NJD  CAK  H11  single    0.970  0.020  1.090
 NJD  CAK  H12  single    0.970  0.020  1.090
 NJD  CAL  H13  single    0.970  0.020  1.090
 NJD  CAL  H14  single    0.970  0.020  1.090
 NJD  CAF  H15  single    0.930  0.020  1.080
 NJD  CAC  H16  single    0.930  0.020  1.080
 NJD  CAB  H17  single    0.930  0.020  1.080
 NJD  CAE  H18  single    0.930  0.020  1.080
 NJD  NAS  H19  single    0.860  0.020  1.020
 NJD  CAI  H20  single    0.930  0.020  1.080
 NJD  NAT  H3   single    0.860  0.020  1.020

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
 NJD  H1   CAJ  CAV  120.60  3.000
 NJD  H1   CAJ  CBA  120.75  3.000
 NJD  CAV  CAJ  CBA  118.65  3.000
 NJD  CBB  CBA  CAH  104.10  3.000
 NJD  CBB  CBA  CAJ  120.11  3.000
 NJD  CAH  CBA  CAJ  135.78  3.000
 NJD  H2   CAH  NAM  120.71  3.000
 NJD  H2   CAH  CBA  128.53  3.000
 NJD  NAM  CAH  CBA  110.75  3.000
 NJD  NAT  NAM  CAH  106.90  3.000
 NJD  H3   NAT  CBB  127.97  3.000
 NJD  H3   NAT  NAM  119.75  3.000
 NJD  CBB  NAT  NAM  112.27  3.000
 NJD  CAG  CBB  NAT  132.47  3.000
 NJD  NAT  CBB  CBA  105.98  3.000
 NJD  CAG  CBB  CBA  121.55  3.000
 NJD  H4   CAG  CAD  120.66  3.000
 NJD  H4   CAG  CBB  121.77  3.000
 NJD  CAD  CAG  CBB  117.57  3.000
 NJD  H5   CAD  CAV  119.37  3.000
 NJD  H5   CAD  CAG  118.96  3.000
 NJD  CAV  CAD  CAG  121.67  3.000
 NJD  NAR  CAV  CAD  121.51  3.000
 NJD  CAD  CAV  CAJ  120.43  3.000
 NJD  NAR  CAV  CAJ  117.97  3.000
 NJD  H6   NAR  CAY  114.31  3.000
 NJD  H6   NAR  CAV  116.42  3.000
 NJD  CAY  NAR  CAV  128.46  3.000
 NJD  NAP  CAY  NAN  125.32  3.000
 NJD  NAN  CAY  NAR  115.92  3.000
 NJD  NAP  CAY  NAR  118.76  3.000
 NJD  CAX  NAN  CAY  114.71  3.000
 NJD  CAZ  NAP  CAY  114.06  3.000
 NJD  NAO  CAZ  OAU  114.10  3.000
 NJD  NAO  CAZ  NAP  127.00  3.000
 NJD  OAU  CAZ  NAP  118.89  3.000
 NJD  CAA  OAU  CAZ  118.49  3.000
 NJD  H9   CAA  H8   109.41  3.000
 NJD  H9   CAA  H7   108.82  3.000
 NJD  H8   CAA  H7   109.53  3.000
 NJD  H9   CAA  OAU  111.68  3.000
 NJD  H8   CAA  OAU  105.67  3.000
 NJD  H7   CAA  OAU  111.67  3.000
 NJD  CAX  NAO  CAZ  113.87  3.000
 NJD  NAQ  CAX  NAO  117.79  3.000
 NJD  NAQ  CAX  NAN  117.18  3.000
 NJD  NAO  CAX  NAN  125.03  3.000
 NJD  H10  NAQ  CAK  119.04  3.000
 NJD  H10  NAQ  CAX  116.67  3.000
 NJD  CAK  NAQ  CAX  124.19  3.000
 NJD  H12  CAK  H11  106.78  3.000
 NJD  H12  CAK  CAL  109.92  3.000
 NJD  H11  CAK  CAL  109.52  3.000
 NJD  H12  CAK  NAQ  109.82  3.000
 NJD  H11  CAK  NAQ  110.57  3.000
 NJD  CAL  CAK  NAQ  110.18  3.000
 NJD  H14  CAL  H13  106.65  3.000
 NJD  H14  CAL  CAW  109.76  3.000
 NJD  H13  CAL  CAW  110.11  3.000
 NJD  H14  CAL  CAK  109.50  3.000
 NJD  H13  CAL  CAK  109.16  3.000
 NJD  CAW  CAL  CAK  111.54  3.000
 NJD  CAI  CAW  CBD  106.02  3.000
 NJD  CBD  CAW  CAL  126.70  3.000
 NJD  CAI  CAW  CAL  127.25  3.000
 NJD  CBC  CBD  CAF  119.12  3.000
 NJD  CBC  CBD  CAW  107.15  3.000
 NJD  CAF  CBD  CAW  133.73  3.000
 NJD  H15  CAF  CAC  120.42  3.000
 NJD  H15  CAF  CBD  120.61  3.000
 NJD  CAC  CAF  CBD  118.98  3.000
 NJD  H16  CAC  CAB  119.21  3.000
 NJD  H16  CAC  CAF  119.81  3.000
 NJD  CAB  CAC  CAF  120.98  3.000
 NJD  H17  CAB  CAE  119.30  3.000
 NJD  H17  CAB  CAC  119.35  3.000
 NJD  CAE  CAB  CAC  121.35  3.000
 NJD  H18  CAE  CBC  121.39  3.000
 NJD  H18  CAE  CAB  121.12  3.000
 NJD  CBC  CAE  CAB  117.49  3.000
 NJD  NAS  CBC  CAE  130.64  3.000
 NJD  CAE  CBC  CBD  122.08  3.000
 NJD  NAS  CBC  CBD  107.28  3.000
 NJD  H19  NAS  CAI  124.85  3.000
 NJD  H19  NAS  CBC  125.81  3.000
 NJD  CAI  NAS  CBC  109.34  3.000
 NJD  H20  CAI  NAS  120.52  3.000
 NJD  H20  CAI  CAW  129.26  3.000
 NJD  NAS  CAI  CAW  110.22  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
 NJD  CONST_01  CAG  CAD  CAV  CAJ     0.00   0.0  0
 NJD  CONST_02  NAM  CAH  CBA  CAJ   180.00   0.0  0
 NJD  CONST_03  CAG  CBB  CBA  CAJ     0.00   0.0  0
 NJD  CONST_04  NAT  CBB  CBA  CAJ   180.00   0.0  0
 NJD  CONST_05  CAD  CAV  CAJ  CBA     0.00   0.0  0
 NJD  CONST_06  NAT  NAM  CAH  CBA     0.00   0.0  0
 NJD  CONST_07  CAD  CAG  CBB  CBA     0.00   0.0  0
 NJD  CONST_08  NAM  NAT  CBB  CBA     0.00   0.0  0
 NJD  CONST_09  CAV  CAJ  CBA  CAH   180.00   0.0  0
 NJD  CONST_10  CAG  CBB  CBA  CAH   180.00   0.0  0
 NJD  CONST_11  NAT  CBB  CBA  CAH     0.00   0.0  0
 NJD  CONST_12  CBB  NAT  NAM  CAH     0.00   0.0  0
 NJD  CONST_13  CBB  CBA  CAH  NAM     0.00   0.0  0
 NJD  CONST_14  CAG  CBB  NAT  NAM   180.00   0.0  0
 NJD  CONST_15  CAD  CAG  CBB  NAT   180.00   0.0  0
 NJD  CONST_16  CAV  CAJ  CBA  CBB     0.00   0.0  0
 NJD  CONST_17  CAV  CAD  CAG  CBB     0.00   0.0  0
 NJD  CONST_18  NAO  CAZ  NAP  CAY     0.00   0.0  0
 NJD  CONST_19  NAO  CAX  NAN  CAY     0.00   0.0  0
 NJD  CONST_20  CAZ  NAO  CAX  NAN     0.00   0.0  0
 NJD  CONST_21  CAZ  NAP  CAY  NAN     0.00   0.0  0
 NJD  CONST_22  CAX  NAO  CAZ  NAP     0.00   0.0  0
 NJD  CONST_23  CAX  NAN  CAY  NAP     0.00   0.0  0
 NJD  CONST_24  CBC  NAS  CAI  CAW     0.00   0.0  0
 NJD  CONST_25  CAC  CAF  CBD  CAW   180.00   0.0  0
 NJD  CONST_26  NAS  CBC  CBD  CAW     0.00   0.0  0
 NJD  CONST_27  CAE  CBC  CBD  CAW   180.00   0.0  0
 NJD  CONST_28  NAS  CAI  CAW  CBD     0.00   0.0  0
 NJD  CONST_29  CAB  CAC  CAF  CBD     0.00   0.0  0
 NJD  CONST_30  CAI  NAS  CBC  CBD     0.00   0.0  0
 NJD  CONST_31  CAB  CAE  CBC  CBD     0.00   0.0  0
 NJD  CONST_32  CAI  CAW  CBD  CAF   180.00   0.0  0
 NJD  CONST_33  NAS  CBC  CBD  CAF   180.00   0.0  0
 NJD  CONST_34  CAE  CBC  CBD  CAF     0.00   0.0  0
 NJD  CONST_35  CAE  CAB  CAC  CAF     0.00   0.0  0
 NJD  CONST_36  CBC  CBD  CAF  CAC     0.00   0.0  0
 NJD  CONST_37  CBC  CAE  CAB  CAC     0.00   0.0  0
 NJD  CONST_38  NAS  CBC  CAE  CAB   180.00   0.0  0
 NJD  CONST_39  CAI  NAS  CBC  CAE   180.00   0.0  0
 NJD  CONST_40  CAI  CAW  CBD  CBC     0.00   0.0  0
 NJD  CONST_41  NAR  CAV  CAJ  CBA   180.00   0.0  0
 NJD  CONST_42  NAR  CAV  CAD  CAG   180.00   0.0  0
 NJD  CONST_43  CAZ  NAP  CAY  NAR   180.00   0.0  0
 NJD  CONST_44  CAX  NAN  CAY  NAR   180.00   0.0  0
 NJD  CONST_45  OAU  CAZ  NAP  CAY   180.00   0.0  0
 NJD  CONST_46  NAQ  CAX  NAN  CAY   180.00   0.0  0
 NJD  CONST_47  NAQ  CAX  NAO  CAZ   180.00   0.0  0
 NJD  CONST_48  CAX  NAO  CAZ  OAU   180.00   0.0  0
 NJD  CONST_49  NAS  CAI  CAW  CAL   180.00   0.0  0
 NJD  CONST_50  CAF  CBD  CAW  CAL     0.00   0.0  0
 NJD  CONST_51  CBC  CBD  CAW  CAL   180.00   0.0  0
 NJD  CONST_52  H5   CAD  CAV  CAJ   180.00   0.0  0
 NJD  CONST_53  H2   CAH  CBA  CAJ     0.00   0.0  0
 NJD  CONST_54  H4   CAG  CBB  CBA   180.00   0.0  0
 NJD  CONST_55  H3   NAT  CBB  CBA   180.00   0.0  0
 NJD  CONST_56  H1   CAJ  CBA  CAH     0.00   0.0  0
 NJD  CONST_57  H19  NAS  CAI  CAW   180.00   0.0  0
 NJD  CONST_58  H15  CAF  CBD  CAW     0.00   0.0  0
 NJD  CONST_59  H20  CAI  CAW  CBD   180.00   0.0  0
 NJD  CONST_60  H16  CAC  CAF  CBD   180.00   0.0  0
 NJD  CONST_61  H18  CAE  CBC  CBD   180.00   0.0  0
 NJD  CONST_62  H17  CAB  CAC  CAF   180.00   0.0  0
 NJD  CONST_63  CAK  NAQ  CAX  NAN   180.00   0.0  0
 NJD  CONST_64  CAK  NAQ  CAX  NAO     0.00   0.0  0
 NJD  CONST_65  H10  NAQ  CAX  NAN     0.00   0.0  0
 NJD  Var_01    CAY  NAR  CAV  CAJ  -141.14  30.0  2
 NJD  Var_02    NAP  CAY  NAR  CAV    -3.68  30.0  2
 NJD  Var_03    NAO  CAZ  OAU  CAA  -179.85  30.0  2
 NJD  Var_04    CAI  CAW  CAL  CAK  -104.93  30.0  2
 NJD  Var_05    CAL  CAK  NAQ  CAX   176.68  30.0  2
 NJD  Var_06    CAW  CAL  CAK  NAQ  -179.01  30.0  3
 NJD  Var_07    H7   CAA  OAU  CAZ    60.14  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
 NJD  plan-1  NAR  0.020
 NJD  plan-1  CAY  0.020
 NJD  plan-1  NAN  0.020
 NJD  plan-1  NAP  0.020
 NJD  plan-1  CAZ  0.020
 NJD  plan-1  OAU  0.020
 NJD  plan-1  NAO  0.020
 NJD  plan-1  CAX  0.020
 NJD  plan-1  NAQ  0.020
 NJD  plan-2  CAJ  0.020
 NJD  plan-2  CBA  0.020
 NJD  plan-2  CAH  0.020
 NJD  plan-2  NAM  0.020
 NJD  plan-2  NAT  0.020
 NJD  plan-2  CBB  0.020
 NJD  plan-2  CAG  0.020
 NJD  plan-2  CAD  0.020
 NJD  plan-2  CAV  0.020
 NJD  plan-2  NAR  0.020
 NJD  plan-2  H1   0.020
 NJD  plan-2  H2   0.020
 NJD  plan-2  H4   0.020
 NJD  plan-2  H5   0.020
 NJD  plan-2  H3   0.020
 NJD  plan-3  CAL  0.020
 NJD  plan-3  CAW  0.020
 NJD  plan-3  CBD  0.020
 NJD  plan-3  CAF  0.020
 NJD  plan-3  CAC  0.020
 NJD  plan-3  CAB  0.020
 NJD  plan-3  CAE  0.020
 NJD  plan-3  CBC  0.020
 NJD  plan-3  NAS  0.020
 NJD  plan-3  CAI  0.020
 NJD  plan-3  H15  0.020
 NJD  plan-3  H16  0.020
 NJD  plan-3  H17  0.020
 NJD  plan-3  H18  0.020
 NJD  plan-3  H19  0.020
 NJD  plan-3  H20  0.020
 NJD  plan-4  CAX  0.020
 NJD  plan-4  NAQ  0.020
 NJD  plan-4  CAK  0.020
 NJD  plan-4  H10  0.020

