# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 06:16:07 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (4S)-4-(4-fluorophenyl)-N-(2H-indazol-5-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C([C@@H](NC(=O)N1)c2ccc(F)cc2)C(=O)Nc3ccc4n[nH]cc4c3
#
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
 KZQ  KZQ  (4S)-4-(4-fluorophenyl)-N-(2H-indazol-5-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxamide  ligand  43  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KZQ
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
 KZQ  CAA   C  CR15  0  -0.018  -5.2823  -0.4990   1.0360
 KZQ  NAB   N  NR15  0  -0.400  -6.3510   0.1131   0.5194
 KZQ  NAC   N  N     0  -0.314  -6.0934   1.1845  -0.2139
 KZQ  CAD   C  CR56  0   0.239  -4.7619   1.2828  -0.1774
 KZQ  CAE   C  CR56  0  -0.095  -4.1869   0.2416   0.6028
 KZQ  CAF   C  CR16  0  -0.294  -3.9313   2.2539  -0.7834
 KZQ  CAG   C  CR16  0  -0.291  -2.5838   2.1529  -0.6017
 KZQ  CAH   C  CR6   0   0.339  -2.0064   1.0962   0.1663
 KZQ  CAI   C  CR16  0  -0.389  -2.7883   0.1465   0.7643
 KZQ  NAJ   N  NH1   0  -0.742  -0.6094   1.0651   0.3535
 KZQ  CAK   C  C     0   0.516   0.2936   1.1047  -0.6582
 KZQ  OAL   O  O     0  -0.470  -0.0365   1.1144  -1.8341
 KZQ  CAM   C  C     0  -0.193   1.7177   1.0780  -0.2553
 KZQ  CAN   C  C     0   0.357   2.2611   1.8159   0.7272
 KZQ  NAO   N  NH1   0  -0.718   3.6145   1.7123   0.9872
 KZQ  CAP   C  C     0   0.643   4.5176   1.0798   0.1650
 KZQ  NAQ   N  NH1   0  -0.647   3.9706   0.4162  -0.8718
 KZQ  CAR   C  CH1   0  -0.177   2.5652   0.1243  -1.0586
 KZQ  CAS   C  CH3   0  -0.763   1.5606   2.8028   1.6066
 KZQ  OAT   O  O     0  -0.511   5.7202   1.1535   0.3660
 KZQ  CAU   C  CR6   0   0.166   2.2173  -1.3073  -0.6924
 KZQ  CAV   C  CR16  0  -0.281   2.5496  -1.8209   0.5586
 KZQ  CAW   C  CR16  0  -0.395   2.2037  -3.1143   0.9130
 KZQ  CAX   C  CR6   0   0.515   1.5119  -3.8879  -0.0020
 KZQ  CAY   C  CR16  0  -0.401   1.1636  -3.4130  -1.2490
 KZQ  CAZ   C  CR16  0  -0.305   1.5257  -2.1141  -1.5861
 KZQ  FBA   F  F     0  -0.317   1.1701  -5.1417   0.3383
 KZQ  HAA   H  HCR5  0   0.297  -5.3670  -1.3818   1.6474
 KZQ  HAF   H  HCR6  0   0.262  -4.3550   3.0645  -1.3617
 KZQ  HAG   H  HCR6  0   0.266  -1.9338   2.9020  -1.0327
 KZQ  HAI   H  HCR6  0   0.263  -2.3452  -0.6546   1.3433
 KZQ  HNAJ  H  HNH1  0   0.410  -0.2736   0.8136   1.2698
 KZQ  HNAO  H  HNH1  0   0.413   4.0135   2.2900   1.7111
 KZQ  HNAQ  H  HNH1  0   0.407   4.6197  -0.0771  -1.4651
 KZQ  HAR   H  HCH1  0   0.286   2.3393   0.2615  -2.1192
 KZQ  HAS   H  HCH3  0   0.273   1.4290   2.3964   2.6115
 KZQ  HASA  H  HCH3  0   0.268   2.1592   3.7096   1.6996
 KZQ  HASB  H  HCH3  0   0.271   0.5861   3.0834   1.2225
 KZQ  HAV   H  HCR6  0   0.260   3.0834  -1.2128   1.2792
 KZQ  HAW   H  HCR6  0   0.279   2.4656  -3.5142   1.8838
 KZQ  HAY   H  HCR6  0   0.284   0.6233  -4.0392  -1.9470
 KZQ  HAZ   H  HCR6  0   0.274   1.2595  -1.7301  -2.5633
 KZQ  HNAB  H  HNR5  0   0.434  -7.3101  -0.1764   0.6428

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
 KZQ  CAA  NAB   aromatic  1.336  0.020  1.336
 KZQ  CAA  CAE   aromatic  1.391  0.020  1.391
 KZQ  CAA  HAA   single    0.930  0.020  1.080
 KZQ  NAB  NAC   aromatic  1.324  0.020  1.324
 KZQ  NAC  CAD   aromatic  1.336  0.020  1.336
 KZQ  CAE  CAD   aromatic  1.422  0.020  1.422
 KZQ  CAD  CAF   aromatic  1.414  0.020  1.414
 KZQ  CAI  CAE   aromatic  1.411  0.020  1.411
 KZQ  CAG  CAF   aromatic  1.363  0.020  1.363
 KZQ  CAF  HAF   single    0.930  0.020  1.080
 KZQ  CAH  CAG   aromatic  1.428  0.020  1.428
 KZQ  CAG  HAG   single    0.930  0.020  1.080
 KZQ  CAI  CAH   aromatic  1.368  0.020  1.368
 KZQ  CAH  NAJ   single    1.410  0.020  1.410
 KZQ  CAI  HAI   single    0.930  0.020  1.080
 KZQ  NAJ  CAK   single    1.357  0.020  1.357
 KZQ  NAJ  HNAJ  single    0.860  0.020  1.020
 KZQ  CAM  CAK   single    1.480  0.020  1.480
 KZQ  CAK  OAL   double    1.221  0.020  1.221
 KZQ  CAR  CAM   single    1.508  0.020  1.508
 KZQ  CAM  CAN   double    1.344  0.020  1.344
 KZQ  NAO  HNAO  single    0.860  0.020  1.020
 KZQ  NAO  CAN   single    1.382  0.020  1.382
 KZQ  CAN  CAS   single    1.496  0.020  1.496
 KZQ  CAP  NAO   single    1.375  0.020  1.375
 KZQ  NAQ  CAP   single    1.347  0.020  1.347
 KZQ  OAT  CAP   double    1.222  0.020  1.222
 KZQ  CAR  NAQ   single    1.448  0.020  1.448
 KZQ  NAQ  HNAQ  single    0.860  0.020  1.020
 KZQ  CAU  CAR   single    1.518  0.020  1.518
 KZQ  CAR  HAR   single    0.970  0.020  1.090
 KZQ  CAS  HAS   single    0.970  0.020  1.090
 KZQ  CAS  HASA  single    0.970  0.020  1.090
 KZQ  CAS  HASB  single    0.970  0.020  1.090
 KZQ  CAV  CAU   aromatic  1.393  0.020  1.393
 KZQ  CAU  CAZ   aromatic  1.389  0.020  1.389
 KZQ  CAW  CAV   aromatic  1.385  0.020  1.385
 KZQ  CAV  HAV   single    0.930  0.020  1.080
 KZQ  CAW  CAX   aromatic  1.384  0.020  1.384
 KZQ  CAW  HAW   single    0.930  0.020  1.080
 KZQ  FBA  CAX   single    1.343  0.020  1.343
 KZQ  CAX  CAY   aromatic  1.379  0.020  1.379
 KZQ  CAY  CAZ   aromatic  1.390  0.020  1.390
 KZQ  CAY  HAY   single    0.930  0.020  1.080
 KZQ  CAZ  HAZ   single    0.930  0.020  1.080
 KZQ  NAB  HNAB  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
 KZQ  HAA   CAA  CAE   132.44  3.000
 KZQ  HAA   CAA  NAB   122.16  3.000
 KZQ  CAE   CAA  NAB   105.40  3.000
 KZQ  HNAB  NAB  NAC   119.00  3.000
 KZQ  HNAB  NAB  CAA   125.56  3.000
 KZQ  NAC   NAB  CAA   115.44  3.000
 KZQ  CAD   NAC  NAB   103.79  3.000
 KZQ  CAF   CAD  CAE   120.01  3.000
 KZQ  CAF   CAD  NAC   128.63  3.000
 KZQ  CAE   CAD  NAC   111.36  3.000
 KZQ  CAI   CAE  CAD   120.85  3.000
 KZQ  CAI   CAE  CAA   135.13  3.000
 KZQ  CAD   CAE  CAA   104.01  3.000
 KZQ  HAF   CAF  CAG   120.91  3.000
 KZQ  HAF   CAF  CAD   120.89  3.000
 KZQ  CAG   CAF  CAD   118.19  3.000
 KZQ  HAG   CAG  CAH   118.94  3.000
 KZQ  HAG   CAG  CAF   119.31  3.000
 KZQ  CAH   CAG  CAF   121.74  3.000
 KZQ  NAJ   CAH  CAI   119.54  3.000
 KZQ  NAJ   CAH  CAG   119.23  3.000
 KZQ  CAI   CAH  CAG   121.18  3.000
 KZQ  HAI   CAI  CAH   120.89  3.000
 KZQ  HAI   CAI  CAE   121.10  3.000
 KZQ  CAH   CAI  CAE   118.02  3.000
 KZQ  HNAJ  NAJ  CAK   117.61  3.000
 KZQ  HNAJ  NAJ  CAH   117.16  3.000
 KZQ  CAK   NAJ  CAH   124.05  3.000
 KZQ  CAM   CAK  OAL   121.48  3.000
 KZQ  OAL   CAK  NAJ   122.57  3.000
 KZQ  CAM   CAK  NAJ   115.91  3.000
 KZQ  CAR   CAM  CAN   120.65  3.000
 KZQ  CAN   CAM  CAK   125.32  3.000
 KZQ  CAR   CAM  CAK   114.03  3.000
 KZQ  CAS   CAN  NAO   113.42  3.000
 KZQ  CAS   CAN  CAM   127.08  3.000
 KZQ  NAO   CAN  CAM   119.50  3.000
 KZQ  HNAO  NAO  CAP   115.64  3.000
 KZQ  CAP   NAO  CAN   124.40  3.000
 KZQ  HNAO  NAO  CAN   118.66  3.000
 KZQ  OAT   CAP  NAQ   123.79  3.000
 KZQ  OAT   CAP  NAO   121.36  3.000
 KZQ  NAQ   CAP  NAO   114.84  3.000
 KZQ  HNAQ  NAQ  CAR   116.77  3.000
 KZQ  HNAQ  NAQ  CAP   115.63  3.000
 KZQ  CAR   NAQ  CAP   126.36  3.000
 KZQ  HAR   CAR  CAU   107.76  3.000
 KZQ  HAR   CAR  NAQ   107.49  3.000
 KZQ  CAU   CAR  NAQ   112.43  3.000
 KZQ  HAR   CAR  CAM   108.75  3.000
 KZQ  CAU   CAR  CAM   109.83  3.000
 KZQ  NAQ   CAR  CAM   110.45  3.000
 KZQ  HASB  CAS  HASA  107.96  3.000
 KZQ  HASB  CAS  HAS   108.30  3.000
 KZQ  HASA  CAS  HAS   107.29  3.000
 KZQ  HASB  CAS  CAN   112.53  3.000
 KZQ  HASA  CAS  CAN   109.98  3.000
 KZQ  HAS   CAS  CAN   110.60  3.000
 KZQ  CAZ   CAU  CAV   118.87  3.000
 KZQ  CAZ   CAU  CAR   120.45  3.000
 KZQ  CAV   CAU  CAR   120.65  3.000
 KZQ  HAV   CAV  CAW   118.49  3.000
 KZQ  HAV   CAV  CAU   120.53  3.000
 KZQ  CAW   CAV  CAU   120.98  3.000
 KZQ  HAW   CAW  CAX   120.51  3.000
 KZQ  HAW   CAW  CAV   120.95  3.000
 KZQ  CAX   CAW  CAV   118.54  3.000
 KZQ  FBA   CAX  CAY   119.09  3.000
 KZQ  CAY   CAX  CAW   122.13  3.000
 KZQ  FBA   CAX  CAW   118.78  3.000
 KZQ  HAY   CAY  CAZ   120.96  3.000
 KZQ  HAY   CAY  CAX   120.66  3.000
 KZQ  CAZ   CAY  CAX   118.38  3.000
 KZQ  HAZ   CAZ  CAY   119.08  3.000
 KZQ  HAZ   CAZ  CAU   119.81  3.000
 KZQ  CAY   CAZ  CAU   121.11  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
 KZQ  CONST_01  CAD   NAC  NAB  CAA    0.00   0.0  0
 KZQ  CONST_02  NAC   CAD  CAE  CAA    0.00   0.0  0
 KZQ  CONST_03  CAF   CAD  CAE  CAA  180.00   0.0  0
 KZQ  CONST_04  CAH   CAI  CAE  CAA  180.00   0.0  0
 KZQ  CONST_05  CAD   CAE  CAA  NAB    0.00   0.0  0
 KZQ  CONST_06  CAI   CAE  CAA  NAB  180.00   0.0  0
 KZQ  CONST_07  CAE   CAD  NAC  NAB    0.00   0.0  0
 KZQ  CONST_08  CAF   CAD  NAC  NAB  180.00   0.0  0
 KZQ  CONST_09  CAE   CAA  NAB  NAC    0.00   0.0  0
 KZQ  CONST_10  CAI   CAE  CAD  NAC  180.00   0.0  0
 KZQ  CONST_11  CAG   CAF  CAD  NAC  180.00   0.0  0
 KZQ  CONST_12  CAH   CAI  CAE  CAD    0.00   0.0  0
 KZQ  CONST_13  CAH   CAG  CAF  CAD    0.00   0.0  0
 KZQ  CONST_14  CAG   CAF  CAD  CAE    0.00   0.0  0
 KZQ  CONST_15  CAG   CAH  CAI  CAE    0.00   0.0  0
 KZQ  CONST_16  CAI   CAE  CAD  CAF    0.00   0.0  0
 KZQ  CONST_17  CAI   CAH  CAG  CAF    0.00   0.0  0
 KZQ  CONST_18  CAX   CAW  CAV  CAU    0.00   0.0  0
 KZQ  CONST_19  CAX   CAY  CAZ  CAU    0.00   0.0  0
 KZQ  CONST_20  CAY   CAZ  CAU  CAV    0.00   0.0  0
 KZQ  CONST_21  CAY   CAX  CAW  CAV    0.00   0.0  0
 KZQ  CONST_22  CAZ   CAU  CAV  CAW    0.00   0.0  0
 KZQ  CONST_23  CAZ   CAY  CAX  CAW    0.00   0.0  0
 KZQ  CONST_24  CAW   CAV  CAU  CAR  180.00   0.0  0
 KZQ  CONST_25  CAY   CAZ  CAU  CAR  180.00   0.0  0
 KZQ  CONST_26  NAQ   CAP  NAO  CAN    0.00   0.0  0
 KZQ  CONST_27  CAR   NAQ  CAP  NAO    0.00   0.0  0
 KZQ  CONST_28  NAJ   CAH  CAI  CAE  180.00   0.0  0
 KZQ  CONST_29  NAJ   CAH  CAG  CAF  180.00   0.0  0
 KZQ  CONST_30  FBA   CAX  CAW  CAV  180.00   0.0  0
 KZQ  CONST_31  FBA   CAX  CAY  CAZ  180.00   0.0  0
 KZQ  CONST_32  OAT   CAP  NAO  CAN  180.00   0.0  0
 KZQ  CONST_33  OAT   CAP  NAQ  CAR  180.00   0.0  0
 KZQ  CONST_34  HAI   CAI  CAE  CAA    0.00   0.0  0
 KZQ  CONST_35  HAA   CAA  NAB  NAC  180.00   0.0  0
 KZQ  CONST_36  HAF   CAF  CAD  NAC    0.00   0.0  0
 KZQ  CONST_37  HNAB  NAB  NAC  CAD  180.00   0.0  0
 KZQ  CONST_38  HAG   CAG  CAF  CAD  180.00   0.0  0
 KZQ  CONST_39  HAV   CAV  CAU  CAR    0.00   0.0  0
 KZQ  CONST_40  HAZ   CAZ  CAU  CAR    0.00   0.0  0
 KZQ  CONST_41  HAW   CAW  CAV  CAU  180.00   0.0  0
 KZQ  CONST_42  HAY   CAY  CAZ  CAU  180.00   0.0  0
 KZQ  CONST_43  HNAQ  NAQ  CAP  NAO  180.00   0.0  0
 KZQ  CONST_44  HNAO  NAO  CAP  NAQ  180.00   0.0  0
 KZQ  CONST_45  CAM   CAK  NAJ  CAH  180.00   0.0  0
 KZQ  CONST_49  OAL   CAK  NAJ  CAH    0.00   0.0  0
 KZQ  Var_01    CAP   NAO  CAN  CAM   11.99  30.0  1
 KZQ  Var_02    CAR   CAM  CAN  NAO    1.01  30.0  1
 KZQ  Var_03    HAS   CAS  CAN  CAM  106.15  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 KZQ  chir_01  CAR  CAM  NAQ  CAU  negativ

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
 KZQ  plan-1  CAR   0.020
 KZQ  plan-1  CAU   0.020
 KZQ  plan-1  CAV   0.020
 KZQ  plan-1  CAW   0.020
 KZQ  plan-1  CAX   0.020
 KZQ  plan-1  CAY   0.020
 KZQ  plan-1  CAZ   0.020
 KZQ  plan-1  FBA   0.020
 KZQ  plan-1  HAV   0.020
 KZQ  plan-1  HAW   0.020
 KZQ  plan-1  HAY   0.020
 KZQ  plan-1  HAZ   0.020
 KZQ  plan-2  CAA   0.020
 KZQ  plan-2  NAB   0.020
 KZQ  plan-2  NAC   0.020
 KZQ  plan-2  CAD   0.020
 KZQ  plan-2  CAE   0.020
 KZQ  plan-2  CAF   0.020
 KZQ  plan-2  CAG   0.020
 KZQ  plan-2  CAH   0.020
 KZQ  plan-2  CAI   0.020
 KZQ  plan-2  NAJ   0.020
 KZQ  plan-2  HAA   0.020
 KZQ  plan-2  HAF   0.020
 KZQ  plan-2  HAG   0.020
 KZQ  plan-2  HAI   0.020
 KZQ  plan-2  HNAB  0.020
 KZQ  plan-3  CAH   0.020
 KZQ  plan-3  NAJ   0.020
 KZQ  plan-3  CAK   0.020
 KZQ  plan-3  OAL   0.020
 KZQ  plan-3  CAM   0.020
 KZQ  plan-3  HNAJ  0.020
 KZQ  plan-4  CAN   0.020
 KZQ  plan-4  NAO   0.020
 KZQ  plan-4  CAP   0.020
 KZQ  plan-4  NAQ   0.020
 KZQ  plan-4  CAR   0.020
 KZQ  plan-4  OAT   0.020
 KZQ  plan-4  HNAO  0.020
 KZQ  plan-4  HNAQ  0.020

