# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:37:48 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[4-(pyridin-4-ylmethyl)piperazin-1-yl]-5,6,7,8-tetrahydro-3H-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=NC2=C1CCCC2)N3CCN(CC3)Cc4ccncc4
#
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
 JL9  JL9  2-[4-(pyridin-4-ylmethyl)piperazin-1-yl]-5,6,7,8-tetrahydro-3H-quinazolin-4-one  ligand  47  24  .  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_JL9
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
 JL9  CAA   C  CR16  0  -0.352  -4.9813  -0.2401  -0.9260
 JL9  CAB   C  CR16  0  -0.059  -6.1190   0.3730  -1.4251
 JL9  NAC   N  N     0  -0.412  -7.0924   0.8580  -0.6604
 JL9  CAD   C  CR16  0  -0.061  -6.9446   0.7410   0.6538
 JL9  CAE   C  CR16  0  -0.377  -5.8429   0.1477   1.2521
 JL9  CAF   C  CR6   0   0.166  -4.8296  -0.3642   0.4512
 JL9  CAG   C  CH2   0  -0.317  -3.6400  -1.0627   1.0528
 JL9  NAH   N  NT    0  -0.425  -2.4248  -0.8354   0.3034
 JL9  CAI   C  CH2   0  -0.288  -1.3803  -1.7784   0.6518
 JL9  CAJ   C  CH2   0  -0.304  -0.1715  -1.5829  -0.2401
 JL9  CAM   C  CH2   0  -0.279  -1.9345   0.5176   0.4675
 JL9  CAL   C  CH2   0  -0.325  -0.7323   0.7757  -0.4221
 JL9  NAK   N  NT    0  -0.515   0.3038  -0.2096  -0.1679
 JL9  CAN   C  CR6   0   0.780   1.6288   0.0484  -0.2033
 JL9  NAT   N  N     0  -0.540   2.4898  -0.9242  -0.0498
 JL9  CAS   C  CR6   0   0.266   3.8093  -0.6229  -0.0452
 JL9  CAU   C  CH2   0  -0.503   4.7185  -1.8023   0.1484
 JL9  CAV   C  CH2   0  -0.447   6.1668  -1.5092  -0.2149
 JL9  CAW   C  CH2   0  -0.447   6.6097  -0.1864   0.3923
 JL9  CAX   C  CH2   0  -0.473   5.7789   0.9642  -0.1616
 JL9  CAR   C  CR6   0  -0.184   4.3119   0.6425  -0.1861
 JL9  CAP   C  CR6   0   0.524   3.3833   1.7124  -0.3913
 JL9  OAQ   O  O     0  -0.494   3.6646   2.8928  -0.5683
 JL9  NAO   N  NR16  0  -0.741   2.0478   1.3268  -0.3868
 JL9  HAA   H  HCR6  0   0.261  -4.2179  -0.6066  -1.5991
 JL9  HAB   H  HCR6  0   0.261  -6.2497   0.4766  -2.4969
 JL9  HAD   H  HCR6  0   0.262  -7.7413   1.1452   1.2689
 JL9  HAE   H  HCR6  0   0.264  -5.7805   0.0935   2.3319
 JL9  HAG1  H  HCH2  0   0.225  -3.5399  -0.7737   2.1117
 JL9  HAG2  H  HCH2  0   0.269  -3.8449  -2.1380   1.0508
 JL9  HAI1  H  HCH2  0   0.206  -1.0748  -1.6834   1.7072
 JL9  HAI2  H  HCH2  0   0.251  -1.7509  -2.7954   0.5085
 JL9  HAM1  H  HCH2  0   0.256  -2.7142   1.2309   0.1946
 JL9  HAM2  H  HCH2  0   0.213  -1.6585   0.7196   1.5162
 JL9  HAJ1  H  HCH2  0   0.278   0.6252  -2.2545   0.0631
 JL9  HAJ2  H  HCH2  0   0.238  -0.4388  -1.8186  -1.2765
 JL9  HAL1  H  HCH2  0   0.251  -1.0325   0.7457  -1.4750
 JL9  HAL2  H  HCH2  0   0.260  -0.3873   1.7835  -0.2029
 JL9  HAO   H  HNR6  0   0.421   1.3875   2.0732  -0.5505
 JL9  HAU1  H  HCH2  0   0.252   4.6492  -2.1095   1.1980
 JL9  HAU2  H  HCH2  0   0.253   4.3274  -2.6417  -0.4311
 JL9  HAV1  H  HCH2  0   0.237   6.8036  -2.3272   0.1273
 JL9  HAV2  H  HCH2  0   0.223   6.2725  -1.4641  -1.3033
 JL9  HAW1  H  HCH2  0   0.221   6.4984  -0.2312   1.4803
 JL9  HAW2  H  HCH2  0   0.235   7.6681  -0.0060   0.1943
 JL9  HAX1  H  HCH2  0   0.239   5.9492   1.8656   0.4326
 JL9  HAX2  H  HCH2  0   0.231   6.1208   1.2094  -1.1737

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
 JL9  CAA  CAB   aromatic  1.385  0.020  1.385
 JL9  CAA  CAF   aromatic  1.391  0.020  1.391
 JL9  CAB  NAC   aromatic  1.329  0.020  1.329
 JL9  NAC  CAD   aromatic  1.328  0.020  1.328
 JL9  CAD  CAE   aromatic  1.387  0.020  1.387
 JL9  CAE  CAF   aromatic  1.389  0.020  1.389
 JL9  CAF  CAG   single    1.505  0.020  1.505
 JL9  CAG  NAH   single    1.446  0.020  1.446
 JL9  NAH  CAI   single    1.450  0.020  1.450
 JL9  NAH  CAM   single    1.448  0.020  1.448
 JL9  CAI  CAJ   single    1.515  0.020  1.515
 JL9  CAJ  NAK   single    1.455  0.020  1.455
 JL9  CAM  CAL   single    1.518  0.020  1.518
 JL9  CAL  NAK   single    1.452  0.020  1.452
 JL9  NAK  CAN   single    1.350  0.020  1.350
 JL9  CAN  NAT   double    1.308  0.020  1.308
 JL9  CAN  NAO   single    1.358  0.020  1.358
 JL9  NAT  CAS   single    1.353  0.020  1.353
 JL9  CAS  CAU   single    1.502  0.020  1.502
 JL9  CAS  CAR   double    1.369  0.020  1.369
 JL9  CAU  CAV   single    1.522  0.020  1.522
 JL9  CAV  CAW   single    1.521  0.020  1.521
 JL9  CAW  CAX   single    1.524  0.020  1.524
 JL9  CAX  CAR   single    1.502  0.020  1.502
 JL9  CAR  CAP   single    1.431  0.020  1.431
 JL9  CAP  OAQ   double    1.226  0.020  1.226
 JL9  CAP  NAO   single    1.390  0.020  1.390
 JL9  CAA  HAA   single    0.930  0.020  1.080
 JL9  CAB  HAB   single    0.930  0.020  1.080
 JL9  CAD  HAD   single    0.930  0.020  1.080
 JL9  CAE  HAE   single    0.930  0.020  1.080
 JL9  CAG  HAG1  single    0.970  0.020  1.090
 JL9  CAG  HAG2  single    0.970  0.020  1.090
 JL9  CAI  HAI1  single    0.970  0.020  1.090
 JL9  CAI  HAI2  single    0.970  0.020  1.090
 JL9  CAM  HAM1  single    0.970  0.020  1.090
 JL9  CAM  HAM2  single    0.970  0.020  1.090
 JL9  CAJ  HAJ1  single    0.970  0.020  1.090
 JL9  CAJ  HAJ2  single    0.970  0.020  1.090
 JL9  CAL  HAL1  single    0.970  0.020  1.090
 JL9  CAL  HAL2  single    0.970  0.020  1.090
 JL9  NAO  HAO   single    0.860  0.020  1.020
 JL9  CAU  HAU1  single    0.970  0.020  1.090
 JL9  CAU  HAU2  single    0.970  0.020  1.090
 JL9  CAV  HAV1  single    0.970  0.020  1.090
 JL9  CAV  HAV2  single    0.970  0.020  1.090
 JL9  CAW  HAW1  single    0.970  0.020  1.090
 JL9  CAW  HAW2  single    0.970  0.020  1.090
 JL9  CAX  HAX1  single    0.970  0.020  1.090
 JL9  CAX  HAX2  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
 JL9  HAA   CAA  CAF   120.59  3.000
 JL9  HAA   CAA  CAB   120.35  3.000
 JL9  CAF   CAA  CAB   119.06  3.000
 JL9  HAB   CAB  NAC   116.44  3.000
 JL9  HAB   CAB  CAA   119.81  3.000
 JL9  NAC   CAB  CAA   123.75  3.000
 JL9  CAD   NAC  CAB   117.11  3.000
 JL9  HAD   CAD  CAE   119.88  3.000
 JL9  HAD   CAD  NAC   116.54  3.000
 JL9  CAE   CAD  NAC   123.58  3.000
 JL9  HAE   CAE  CAF   120.95  3.000
 JL9  HAE   CAE  CAD   119.82  3.000
 JL9  CAF   CAE  CAD   119.22  3.000
 JL9  CAG   CAF  CAE   121.13  3.000
 JL9  CAG   CAF  CAA   121.56  3.000
 JL9  CAE   CAF  CAA   117.28  3.000
 JL9  HAG2  CAG  HAG1  106.04  3.000
 JL9  HAG2  CAG  NAH   108.12  3.000
 JL9  HAG1  CAG  NAH   112.36  3.000
 JL9  HAG2  CAG  CAF   107.90  3.000
 JL9  HAG1  CAG  CAF   109.52  3.000
 JL9  NAH   CAG  CAF   112.59  3.000
 JL9  CAM   NAH  CAI   109.66  3.000
 JL9  CAM   NAH  CAG   111.88  3.000
 JL9  CAI   NAH  CAG   112.25  3.000
 JL9  HAI2  CAI  HAI1  107.45  3.000
 JL9  HAI2  CAI  CAJ   108.29  3.000
 JL9  HAI1  CAI  CAJ   109.35  3.000
 JL9  HAI2  CAI  NAH   109.26  3.000
 JL9  HAI1  CAI  NAH   111.93  3.000
 JL9  CAJ   CAI  NAH   110.45  3.000
 JL9  HAJ2  CAJ  HAJ1  108.07  3.000
 JL9  HAJ2  CAJ  NAK   109.25  3.000
 JL9  HAJ1  CAJ  NAK   109.30  3.000
 JL9  HAJ2  CAJ  CAI   109.53  3.000
 JL9  HAJ1  CAJ  CAI   109.96  3.000
 JL9  NAK   CAJ  CAI   110.69  3.000
 JL9  HAM2  CAM  HAM1  107.26  3.000
 JL9  HAM2  CAM  CAL   109.14  3.000
 JL9  HAM1  CAM  CAL   107.95  3.000
 JL9  HAM2  CAM  NAH   111.32  3.000
 JL9  HAM1  CAM  NAH   109.90  3.000
 JL9  CAL   CAM  NAH   111.14  3.000
 JL9  HAL2  CAL  HAL1  107.82  3.000
 JL9  HAL2  CAL  NAK   111.54  3.000
 JL9  HAL1  CAL  NAK   110.20  3.000
 JL9  HAL2  CAL  CAM   106.91  3.000
 JL9  HAL1  CAL  CAM   109.98  3.000
 JL9  NAK   CAL  CAM   110.32  3.000
 JL9  CAN   NAK  CAL   124.47  3.000
 JL9  CAN   NAK  CAJ   119.97  3.000
 JL9  CAL   NAK  CAJ   113.49  3.000
 JL9  NAO   CAN  NAT   120.85  3.000
 JL9  NAO   CAN  NAK   119.09  3.000
 JL9  NAT   CAN  NAK   120.05  3.000
 JL9  CAS   NAT  CAN   118.47  3.000
 JL9  CAR   CAS  CAU   121.13  3.000
 JL9  CAR   CAS  NAT   124.29  3.000
 JL9  CAU   CAS  NAT   114.58  3.000
 JL9  HAU2  CAU  HAU1  105.67  3.000
 JL9  HAU2  CAU  CAV   111.23  3.000
 JL9  HAU1  CAU  CAV   110.05  3.000
 JL9  HAU2  CAU  CAS   108.56  3.000
 JL9  HAU1  CAU  CAS   107.78  3.000
 JL9  CAV   CAU  CAS   113.22  3.000
 JL9  HAV2  CAV  HAV1  106.63  3.000
 JL9  HAV2  CAV  CAW   109.44  3.000
 JL9  HAV1  CAV  CAW   110.89  3.000
 JL9  HAV2  CAV  CAU   109.71  3.000
 JL9  HAV1  CAV  CAU   109.64  3.000
 JL9  CAW   CAV  CAU   110.44  3.000
 JL9  HAW2  CAW  HAW1  106.60  3.000
 JL9  HAW2  CAW  CAX   109.75  3.000
 JL9  HAW1  CAW  CAX   109.68  3.000
 JL9  HAW2  CAW  CAV   110.70  3.000
 JL9  HAW1  CAW  CAV   109.36  3.000
 JL9  CAX   CAW  CAV   110.66  3.000
 JL9  HAX2  CAX  HAX1  105.60  3.000
 JL9  HAX2  CAX  CAR   109.73  3.000
 JL9  HAX1  CAX  CAR   109.74  3.000
 JL9  HAX2  CAX  CAW   109.54  3.000
 JL9  HAX1  CAX  CAW   109.89  3.000
 JL9  CAR   CAX  CAW   112.14  3.000
 JL9  CAP   CAR  CAX   118.41  3.000
 JL9  CAP   CAR  CAS   117.87  3.000
 JL9  CAX   CAR  CAS   123.70  3.000
 JL9  NAO   CAP  OAQ   119.20  3.000
 JL9  NAO   CAP  CAR   114.55  3.000
 JL9  OAQ   CAP  CAR   126.25  3.000
 JL9  HAO   NAO  CAP   115.00  3.000
 JL9  HAO   NAO  CAN   121.06  3.000
 JL9  CAP   NAO  CAN   123.92  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
 JL9  CONST_01  CAD  NAC  CAB  CAA     0.00   0.0  0
 JL9  CONST_02  CAD  CAE  CAF  CAA     0.00   0.0  0
 JL9  CONST_03  CAE  CAF  CAA  CAB     0.00   0.0  0
 JL9  CONST_04  CAE  CAD  NAC  CAB     0.00   0.0  0
 JL9  CONST_05  CAF  CAA  CAB  NAC     0.00   0.0  0
 JL9  CONST_06  CAF  CAE  CAD  NAC     0.00   0.0  0
 JL9  CONST_07  NAT  CAN  NAK  CAJ     0.00   0.0  0
 JL9  CONST_08  NAO  CAN  NAK  CAJ   180.00   0.0  0
 JL9  CONST_09  NAT  CAN  NAK  CAL   180.00   0.0  0
 JL9  CONST_10  NAO  CAN  NAK  CAL     0.00   0.0  0
 JL9  CONST_11  CAS  NAT  CAN  NAK   180.00   0.0  0
 JL9  CONST_12  CAP  NAO  CAN  NAK   180.00   0.0  0
 JL9  CONST_13  CAR  CAP  NAO  CAN     0.00   0.0  0
 JL9  CONST_14  CAP  NAO  CAN  NAT     0.00   0.0  0
 JL9  CONST_15  NAO  CAN  NAT  CAS     0.00   0.0  0
 JL9  CONST_16  CAG  CAF  CAA  CAB   180.00   0.0  0
 JL9  CONST_17  CAG  CAF  CAE  CAD   180.00   0.0  0
 JL9  CONST_18  OAQ  CAP  NAO  CAN   180.00   0.0  0
 JL9  CONST_19  HAE  CAE  CAF  CAA   180.00   0.0  0
 JL9  CONST_20  HAD  CAD  NAC  CAB   180.00   0.0  0
 JL9  CONST_21  HAA  CAA  CAB  NAC   180.00   0.0  0
 JL9  CONST_22  HAB  CAB  NAC  CAD   180.00   0.0  0
 JL9  CONST_23  HAO  NAO  CAN  NAK     0.00   0.0  0
 JL9  Var_01    NAK  CAJ  CAI  NAH    56.00  30.0  1
 JL9  Var_02    NAK  CAL  CAM  NAH   -55.32  30.0  1
 JL9  Var_03    CAL  CAM  NAH  CAI    59.89  30.0  1
 JL9  Var_04    CAL  NAK  CAJ  CAI   -52.73  30.0  1
 JL9  Var_05    CAM  NAH  CAI  CAJ   -59.97  30.0  1
 JL9  Var_06    CAM  CAL  NAK  CAJ    52.08  30.0  1
 JL9  Var_07    CAV  CAU  CAS  NAT   164.67  30.0  1
 JL9  Var_08    CAW  CAV  CAU  CAS    46.49  30.0  1
 JL9  Var_09    CAW  CAX  CAR  CAS   -14.96  30.0  1
 JL9  Var_10    CAX  CAW  CAV  CAU   -62.12  30.0  1
 JL9  Var_11    CAR  CAX  CAW  CAV    45.27  30.0  1
 JL9  Var_12    NAH  CAG  CAF  CAA    35.98  30.0  2
 JL9  Var_13    CAI  NAH  CAG  CAF  -164.15  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
 JL9  plan-1  CAA  0.020
 JL9  plan-1  CAB  0.020
 JL9  plan-1  NAC  0.020
 JL9  plan-1  CAD  0.020
 JL9  plan-1  CAE  0.020
 JL9  plan-1  CAF  0.020
 JL9  plan-1  CAG  0.020
 JL9  plan-1  HAA  0.020
 JL9  plan-1  HAB  0.020
 JL9  plan-1  HAD  0.020
 JL9  plan-1  HAE  0.020
 JL9  plan-2  CAJ  0.020
 JL9  plan-2  CAL  0.020
 JL9  plan-2  NAK  0.020
 JL9  plan-2  CAN  0.020
 JL9  plan-2  NAT  0.020
 JL9  plan-2  CAS  0.020
 JL9  plan-2  CAU  0.020
 JL9  plan-2  CAX  0.020
 JL9  plan-2  CAR  0.020
 JL9  plan-2  CAP  0.020
 JL9  plan-2  OAQ  0.020
 JL9  plan-2  NAO  0.020
 JL9  plan-2  HAO  0.020

