# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 02:59:45 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-(difluoromethyl)-1-(4,6-dimorpholin-4-yl-1,3,5-triazin-2-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)c1nc2ccccc2n1c3nc(nc(n3)N4CCOCC4)N5CCOCC5
#
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
 ZS4  ZS4  2-(difluoromethyl)-1-(4,6-dimorpholin-4-yl-1,3,5-triazin-2-yl)-1H-benzimidazole  ligand  51  30  .  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_ZS4
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
 ZS4  CAQ   C  CH2   0  -0.342  -0.6381  -3.6930   0.7711
 ZS4  CAR   C  CH2   0  -0.182  -0.5924  -4.7070  -0.3599
 ZS4  OAW   O  O2    0  -0.482   0.5706  -5.5025  -0.2901
 ZS4  CBB   C  CH2   0  -0.181   1.7420  -4.7166  -0.3356
 ZS4  CBA   C  CH2   0  -0.342   1.7781  -3.7006   0.7949
 ZS4  NAV   N  NT    0  -0.497   0.5728  -2.8930   0.7458
 ZS4  CAU   C  CR6   0   0.679   0.5852  -1.5757   0.5032
 ZS4  NAP   N  N     0  -0.525  -0.6039  -0.9577   0.3633
 ZS4  NAT   N  N     0  -0.539   1.7580  -0.9535   0.4386
 ZS4  CAS   C  CR6   0   0.687   1.7192   0.3525   0.1894
 ZS4  NAY   N  NT    0  -0.503   2.8779   1.0208   0.1164
 ZS4  CAZ   C  CH2   0  -0.337   2.9612   2.4526  -0.1052
 ZS4  CAI   C  CH2   0  -0.180   3.9881   2.7421  -1.1867
 ZS4  OBD   O  O2    0  -0.482   5.2402   2.1695  -0.8859
 ZS4  CBC   C  CH2   0  -0.185   5.1373   0.7710  -0.7378
 ZS4  CAX   C  CH2   0  -0.329   4.1639   0.3941   0.3648
 ZS4  NAN   N  N     0  -0.545   0.5811   1.0453  -0.0110
 ZS4  CAO   C  CR6   0   0.634  -0.5072   0.3234   0.1074
 ZS4  NAJ   N  NR5   0  -0.665  -1.7203   1.0015  -0.0795
 ZS4  CAK   C  CR56  0   0.340  -2.9120   0.4541  -0.5347
 ZS4  CAL   C  CR16  0  -0.280  -3.2917  -0.8263  -0.9253
 ZS4  CAM   C  CR16  0  -0.267  -4.5928  -0.9813  -1.3710
 ZS4  CAH   C  CR16  0  -0.266  -5.4909   0.0932  -1.4306
 ZS4  CAG   C  CR16  0  -0.321  -5.1051   1.3637  -1.0498
 ZS4  CAF   C  CR56  0   0.128  -3.7980   1.5363  -0.6007
 ZS4  NAE   N  N     0  -0.444  -3.1742   2.6893  -0.1837
 ZS4  CAD   C  CR5   0   0.325  -1.9650   2.3457   0.1079
 ZS4  CAC   C  CH1   0   0.517  -0.9652   3.3183   0.6657
 ZS4  FA    F  F     0  -0.325  -1.5765   4.5145   0.8123
 ZS4  FB    F  F     0  -0.338  -0.5848   2.9079   1.9063
 ZS4  HAQ1  H  HCH2  0   0.280  -1.5152  -3.0585   0.6830
 ZS4  HAQ2  H  HCH2  0   0.255  -0.6932  -4.2098   1.7343
 ZS4  HAR1  H  HCH2  0   0.247  -1.4516  -5.3758  -0.2959
 ZS4  HAR2  H  HCH2  0   0.208  -0.6417  -4.1784  -1.3225
 ZS4  HBB1  H  HCH2  0   0.246   2.5934  -5.3934  -0.2549
 ZS4  HBB2  H  HCH2  0   0.210   1.8150  -4.1888  -1.2968
 ZS4  HBA1  H  HCH2  0   0.251   1.8179  -4.2134   1.7608
 ZS4  HBA2  H  HCH2  0   0.285   2.6580  -3.0693   0.7100
 ZS4  HAZ1  H  HCH2  0   0.285   1.9945   2.8399  -0.4122
 ZS4  HAZ2  H  HCH2  0   0.247   3.2463   2.9489   0.8289
 ZS4  HAX1  H  HCH2  0   0.246   4.5467   0.7303   1.3349
 ZS4  HAX2  H  HCH2  0   0.284   4.0496  -0.6852   0.4054
 ZS4  HAI1  H  HCH2  0   0.210   3.6139   2.3704  -2.1507
 ZS4  HAI2  H  HCH2  0   0.247   4.1318   3.8197  -1.2739
 ZS4  HBC1  H  HCH2  0   0.210   4.8184   0.3034  -1.6800
 ZS4  HBC2  H  HCH2  0   0.246   6.1306   0.3922  -0.4937
 ZS4  HAL   H  HCR6  0   0.276  -2.6124  -1.6623  -0.8854
 ZS4  HAM   H  HCR6  0   0.262  -4.9252  -1.9634  -1.6800
 ZS4  HAH   H  HCR6  0   0.260  -6.4987  -0.0792  -1.7843
 ZS4  HAG   H  HCR6  0   0.264  -5.7865   2.2025  -1.0992
 ZS4  HAC   H  HCH1  0   0.225  -0.0820   3.4445   0.0458

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
 ZS4  CAQ  CAR   single    1.520  0.020  1.520
 ZS4  CAQ  NAV   single    1.451  0.020  1.451
 ZS4  CAR  OAW   single    1.411  0.020  1.411
 ZS4  OAW  CBB   single    1.411  0.020  1.411
 ZS4  CBB  CBA   single    1.520  0.020  1.520
 ZS4  CBA  NAV   single    1.452  0.020  1.452
 ZS4  NAV  CAU   single    1.340  0.020  1.340
 ZS4  CAU  NAP   aromatic  1.347  0.020  1.347
 ZS4  CAU  NAT   aromatic  1.329  0.020  1.329
 ZS4  NAP  CAO   aromatic  1.310  0.020  1.310
 ZS4  NAT  CAS   aromatic  1.330  0.020  1.330
 ZS4  CAS  NAY   single    1.340  0.020  1.340
 ZS4  CAS  NAN   aromatic  1.347  0.020  1.347
 ZS4  NAY  CAZ   single    1.451  0.020  1.451
 ZS4  NAY  CAX   single    1.452  0.020  1.452
 ZS4  CAZ  CAI   single    1.519  0.020  1.519
 ZS4  CAI  OBD   single    1.409  0.020  1.409
 ZS4  OBD  CBC   single    1.410  0.020  1.410
 ZS4  CBC  CAX   single    1.518  0.020  1.518
 ZS4  NAN  CAO   aromatic  1.311  0.020  1.311
 ZS4  CAO  NAJ   single    1.402  0.020  1.402
 ZS4  NAJ  CAK   aromatic  1.388  0.020  1.388
 ZS4  NAJ  CAD   aromatic  1.379  0.020  1.379
 ZS4  CAK  CAL   aromatic  1.391  0.020  1.391
 ZS4  CAK  CAF   aromatic  1.400  0.020  1.400
 ZS4  CAL  CAM   aromatic  1.384  0.020  1.384
 ZS4  CAM  CAH   aromatic  1.402  0.020  1.402
 ZS4  CAH  CAG   aromatic  1.381  0.020  1.381
 ZS4  CAG  CAF   aromatic  1.393  0.020  1.393
 ZS4  CAF  NAE   aromatic  1.376  0.020  1.376
 ZS4  NAE  CAD   aromatic  1.291  0.020  1.291
 ZS4  CAD  CAC   single    1.502  0.020  1.502
 ZS4  CAC  FA    single    1.351  0.020  1.351
 ZS4  CAC  FB    single    1.361  0.020  1.361
 ZS4  CAQ  HAQ1  single    0.970  0.020  1.090
 ZS4  CAQ  HAQ2  single    0.970  0.020  1.090
 ZS4  CAR  HAR1  single    0.970  0.020  1.090
 ZS4  CAR  HAR2  single    0.970  0.020  1.090
 ZS4  CBB  HBB1  single    0.970  0.020  1.090
 ZS4  CBB  HBB2  single    0.970  0.020  1.090
 ZS4  CBA  HBA1  single    0.970  0.020  1.090
 ZS4  CBA  HBA2  single    0.970  0.020  1.090
 ZS4  CAZ  HAZ1  single    0.970  0.020  1.090
 ZS4  CAZ  HAZ2  single    0.970  0.020  1.090
 ZS4  CAX  HAX1  single    0.970  0.020  1.090
 ZS4  CAX  HAX2  single    0.970  0.020  1.090
 ZS4  CAI  HAI1  single    0.970  0.020  1.090
 ZS4  CAI  HAI2  single    0.970  0.020  1.090
 ZS4  CBC  HBC1  single    0.970  0.020  1.090
 ZS4  CBC  HBC2  single    0.970  0.020  1.090
 ZS4  CAL  HAL   single    0.930  0.020  1.080
 ZS4  CAM  HAM   single    0.930  0.020  1.080
 ZS4  CAH  HAH   single    0.930  0.020  1.080
 ZS4  CAG  HAG   single    0.930  0.020  1.080
 ZS4  CAC  HAC   single    0.970  0.020  1.090

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
 ZS4  HAQ2  CAQ  HAQ1  107.85  3.000
 ZS4  HAQ2  CAQ  NAV   108.52  3.000
 ZS4  HAQ1  CAQ  NAV   110.51  3.000
 ZS4  HAQ2  CAQ  CAR   109.96  3.000
 ZS4  HAQ1  CAQ  CAR   110.71  3.000
 ZS4  NAV   CAQ  CAR   109.25  3.000
 ZS4  HAR2  CAR  HAR1  108.11  3.000
 ZS4  HAR2  CAR  OAW   110.57  3.000
 ZS4  HAR1  CAR  OAW   107.50  3.000
 ZS4  HAR2  CAR  CAQ   109.23  3.000
 ZS4  HAR1  CAR  CAQ   109.99  3.000
 ZS4  OAW   CAR  CAQ   111.36  3.000
 ZS4  CBB   OAW  CAR   111.63  3.000
 ZS4  HBB2  CBB  HBB1  108.12  3.000
 ZS4  HBB2  CBB  CBA   109.14  3.000
 ZS4  HBB1  CBB  CBA   109.95  3.000
 ZS4  HBB2  CBB  OAW   110.53  3.000
 ZS4  HBB1  CBB  OAW   107.46  3.000
 ZS4  CBA   CBB  OAW   111.58  3.000
 ZS4  HBA2  CBA  HBA1  108.17  3.000
 ZS4  HBA2  CBA  NAV   110.28  3.000
 ZS4  HBA1  CBA  NAV   108.71  3.000
 ZS4  HBA2  CBA  CBB   110.45  3.000
 ZS4  HBA1  CBA  CBB   110.12  3.000
 ZS4  NAV   CBA  CBB   109.08  3.000
 ZS4  CAU   NAV  CBA   123.06  3.000
 ZS4  CAU   NAV  CAQ   123.57  3.000
 ZS4  CBA   NAV  CAQ   112.67  3.000
 ZS4  NAT   CAU  NAP   123.99  3.000
 ZS4  NAT   CAU  NAV   118.51  3.000
 ZS4  NAP   CAU  NAV   117.49  3.000
 ZS4  CAO   NAP  CAU   113.80  3.000
 ZS4  CAS   NAT  CAU   116.29  3.000
 ZS4  NAN   CAS  NAY   117.77  3.000
 ZS4  NAN   CAS  NAT   123.88  3.000
 ZS4  NAY   CAS  NAT   118.34  3.000
 ZS4  CAX   NAY  CAZ   113.65  3.000
 ZS4  CAX   NAY  CAS   122.78  3.000
 ZS4  CAZ   NAY  CAS   123.38  3.000
 ZS4  HAZ2  CAZ  HAZ1  108.14  3.000
 ZS4  HAZ2  CAZ  CAI   110.17  3.000
 ZS4  HAZ1  CAZ  CAI   109.43  3.000
 ZS4  HAZ2  CAZ  NAY   109.37  3.000
 ZS4  HAZ1  CAZ  NAY   110.12  3.000
 ZS4  CAI   CAZ  NAY   109.60  3.000
 ZS4  HAI2  CAI  HAI1  108.00  3.000
 ZS4  HAI2  CAI  OBD   107.55  3.000
 ZS4  HAI1  CAI  OBD   110.63  3.000
 ZS4  HAI2  CAI  CAZ   109.53  3.000
 ZS4  HAI1  CAI  CAZ   109.26  3.000
 ZS4  OBD   CAI  CAZ   111.79  3.000
 ZS4  CBC   OBD  CAI   111.14  3.000
 ZS4  HBC2  CBC  HBC1  107.96  3.000
 ZS4  HBC2  CBC  CAX   109.58  3.000
 ZS4  HBC1  CBC  CAX   109.33  3.000
 ZS4  HBC2  CBC  OBD   107.55  3.000
 ZS4  HBC1  CBC  OBD   110.67  3.000
 ZS4  CAX   CBC  OBD   111.67  3.000
 ZS4  HAX2  CAX  HAX1  107.97  3.000
 ZS4  HAX2  CAX  CBC   109.95  3.000
 ZS4  HAX1  CAX  CBC   110.05  3.000
 ZS4  HAX2  CAX  NAY   110.01  3.000
 ZS4  HAX1  CAX  NAY   109.17  3.000
 ZS4  CBC   CAX  NAY   109.66  3.000
 ZS4  CAO   NAN  CAS   113.86  3.000
 ZS4  NAJ   CAO  NAN   116.08  3.000
 ZS4  NAJ   CAO  NAP   115.79  3.000
 ZS4  NAN   CAO  NAP   128.12  3.000
 ZS4  CAD   NAJ  CAK   106.06  3.000
 ZS4  CAD   NAJ  CAO   127.35  3.000
 ZS4  CAK   NAJ  CAO   126.56  3.000
 ZS4  CAF   CAK  CAL   121.69  3.000
 ZS4  CAF   CAK  NAJ   104.71  3.000
 ZS4  CAL   CAK  NAJ   133.56  3.000
 ZS4  HAL   CAL  CAM   121.16  3.000
 ZS4  HAL   CAL  CAK   122.10  3.000
 ZS4  CAM   CAL  CAK   116.74  3.000
 ZS4  HAM   CAM  CAH   119.13  3.000
 ZS4  HAM   CAM  CAL   118.85  3.000
 ZS4  CAH   CAM  CAL   122.02  3.000
 ZS4  HAH   CAH  CAG   119.79  3.000
 ZS4  HAH   CAH  CAM   119.25  3.000
 ZS4  CAG   CAH  CAM   120.96  3.000
 ZS4  HAG   CAG  CAF   120.65  3.000
 ZS4  HAG   CAG  CAH   121.64  3.000
 ZS4  CAF   CAG  CAH   117.71  3.000
 ZS4  NAE   CAF  CAG   128.84  3.000
 ZS4  NAE   CAF  CAK   110.28  3.000
 ZS4  CAG   CAF  CAK   120.88  3.000
 ZS4  CAD   NAE  CAF   105.68  3.000
 ZS4  CAC   CAD  NAE   122.35  3.000
 ZS4  CAC   CAD  NAJ   124.30  3.000
 ZS4  NAE   CAD  NAJ   113.27  3.000
 ZS4  HAC   CAC  FB    109.14  3.000
 ZS4  HAC   CAC  FA    109.08  3.000
 ZS4  FB    CAC  FA    107.13  3.000
 ZS4  HAC   CAC  CAD   113.85  3.000
 ZS4  FB    CAC  CAD   109.22  3.000
 ZS4  FA    CAC  CAD   108.20  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
 ZS4  CONST_01  NAN   CAO  NAP  CAU     0.00   0.0  0
 ZS4  CONST_02  NAJ   CAO  NAP  CAU   180.00   0.0  0
 ZS4  CONST_03  NAN   CAS  NAT  CAU     0.00   0.0  0
 ZS4  CONST_04  CAS   NAT  CAU  NAP     0.00   0.0  0
 ZS4  CONST_05  CAS   NAN  CAO  NAP     0.00   0.0  0
 ZS4  CONST_08  CAO   NAP  CAU  NAT     0.00   0.0  0
 ZS4  CONST_09  CAO   NAN  CAS  NAT     0.00   0.0  0
 ZS4  CONST_10  NAJ   CAO  NAN  CAS   180.00   0.0  0
 ZS4  CONST_13  CAL   CAK  NAJ  CAO     0.00   0.0  0
 ZS4  CONST_14  CAF   CAK  NAJ  CAO   180.00   0.0  0
 ZS4  CONST_15  NAE   CAD  NAJ  CAO   180.00   0.0  0
 ZS4  CONST_16  CAM   CAL  CAK  NAJ   180.00   0.0  0
 ZS4  CONST_17  CAG   CAF  CAK  NAJ   180.00   0.0  0
 ZS4  CONST_18  NAE   CAF  CAK  NAJ     0.00   0.0  0
 ZS4  CONST_19  CAF   NAE  CAD  NAJ     0.00   0.0  0
 ZS4  CONST_20  NAE   CAD  NAJ  CAK     0.00   0.0  0
 ZS4  CONST_21  CAH   CAM  CAL  CAK     0.00   0.0  0
 ZS4  CONST_22  CAH   CAG  CAF  CAK     0.00   0.0  0
 ZS4  CONST_23  CAD   NAE  CAF  CAK     0.00   0.0  0
 ZS4  CONST_24  CAD   NAJ  CAK  CAL   180.00   0.0  0
 ZS4  CONST_25  CAG   CAF  CAK  CAL     0.00   0.0  0
 ZS4  CONST_26  NAE   CAF  CAK  CAL   180.00   0.0  0
 ZS4  CONST_27  CAG   CAH  CAM  CAL     0.00   0.0  0
 ZS4  CONST_28  CAF   CAK  CAL  CAM     0.00   0.0  0
 ZS4  CONST_29  CAF   CAG  CAH  CAM     0.00   0.0  0
 ZS4  CONST_30  NAE   CAF  CAG  CAH   180.00   0.0  0
 ZS4  CONST_31  CAD   NAE  CAF  CAG   180.00   0.0  0
 ZS4  CONST_32  CAD   NAJ  CAK  CAF     0.00   0.0  0
 ZS4  CONST_33  CAO   NAP  CAU  NAV   180.00   0.0  0
 ZS4  CONST_34  CAS   NAT  CAU  NAV   180.00   0.0  0
 ZS4  CONST_35  NAY   CAS  NAT  CAU   180.00   0.0  0
 ZS4  CONST_36  CAO   NAN  CAS  NAY   180.00   0.0  0
 ZS4  CONST_37  CAC   CAD  NAJ  CAO     0.00   0.0  0
 ZS4  CONST_38  CAC   CAD  NAJ  CAK   180.00   0.0  0
 ZS4  CONST_39  CAC   CAD  NAE  CAF   180.00   0.0  0
 ZS4  CONST_40  HAL   CAL  CAK  NAJ     0.00   0.0  0
 ZS4  CONST_41  HAM   CAM  CAL  CAK   180.00   0.0  0
 ZS4  CONST_42  HAG   CAG  CAF  CAK   180.00   0.0  0
 ZS4  CONST_43  HAH   CAH  CAM  CAL   180.00   0.0  0
 ZS4  Var_01    CBB   CBA  NAV  CAQ    54.93  30.0  1
 ZS4  Var_02    NAP   CAU  NAV  CAQ     4.46  30.0  2
 ZS4  Var_03    CBA   NAV  CAQ  CAR   -55.13  30.0  1
 ZS4  Var_04    CBA   CBB  OAW  CAR    58.15  30.0  1
 ZS4  Var_05    NAV   CAQ  CAR  OAW    55.64  30.0  1
 ZS4  Var_06    NAV   CBA  CBB  OAW   -55.44  30.0  1
 ZS4  Var_07    CAZ   NAY  CAS  NAT  -177.87  30.0  2
 ZS4  Var_08    CAI   CAZ  NAY  CAS  -132.75  30.0  1
 ZS4  Var_09    CBC   CAX  NAY  CAS   132.59  30.0  1
 ZS4  Var_10    OBD   CAI  CAZ  NAY   -54.57  30.0  1
 ZS4  Var_11    OBD   CBC  CAX  NAY    54.70  30.0  1
 ZS4  Var_12    CAX   CBC  OBD  CAI   -58.96  30.0  1
 ZS4  Var_13    HAR1  CAR  OAW  CBB  -178.69  30.0  1
 ZS4  Var_14    FA    CAC  CAD  NAJ  -175.00  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
 ZS4  plan-1  NAV  0.020
 ZS4  plan-1  CAU  0.020
 ZS4  plan-1  NAP  0.020
 ZS4  plan-1  NAT  0.020
 ZS4  plan-1  CAS  0.020
 ZS4  plan-1  NAY  0.020
 ZS4  plan-1  NAN  0.020
 ZS4  plan-1  CAO  0.020
 ZS4  plan-1  NAJ  0.020
 ZS4  plan-2  CAO  0.020
 ZS4  plan-2  NAJ  0.020
 ZS4  plan-2  CAK  0.020
 ZS4  plan-2  CAL  0.020
 ZS4  plan-2  CAM  0.020
 ZS4  plan-2  CAH  0.020
 ZS4  plan-2  CAG  0.020
 ZS4  plan-2  CAF  0.020
 ZS4  plan-2  NAE  0.020
 ZS4  plan-2  CAD  0.020
 ZS4  plan-2  CAC  0.020
 ZS4  plan-2  HAL  0.020
 ZS4  plan-2  HAM  0.020
 ZS4  plan-2  HAH  0.020
 ZS4  plan-2  HAG  0.020

