# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:33:37 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[4-(4-fluorophenyl)piperazin-1-yl]-6-methylpyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)NC(=N1)N2CCN(CC2)c3ccc(F)cc3
#
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
 NNF  NNF  2-[4-(4-fluorophenyl)piperazin-1-yl]-6-methylpyrimidin-4(3H)-one  ligand  38  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NNF
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
 NNF  CAA   C  CH3   0  -0.716   4.9549  -2.5039   0.8860
 NNF  OAB   O  O     0  -0.502   5.1154   2.3261   0.3123
 NNF  CAD   C  CR16  0  -0.398  -5.0316  -1.0432  -0.2278
 NNF  CAE   C  CR16  0  -0.400  -4.7749   1.0974   0.8390
 NNF  CAF   C  CR16  0  -0.302  -3.6873  -1.0361  -0.5543
 NNF  CAG   C  CR16  0  -0.336  -3.4211   1.0871   0.5228
 NNF  CAH   C  CR16  0  -0.524   5.1500  -0.0298   0.6312
 NNF  CAI   C  C     0  -0.300  -0.7400   1.2201  -0.3744
 NNF  CAJ   C  C     0  -0.303  -0.7395  -1.1749  -0.1664
 NNF  CAK   C  C     0  -0.331   0.5657   1.1483  -1.1512
 NNF  CAL   C  C     0  -0.314   0.5640  -1.2515  -0.9376
 NNF  NAM   N  N     0  -0.538   3.1342  -1.1852   0.0457
 NNF  NAN   N  NR16  0  -0.738   3.2714   1.1238  -0.2024
 NNF  CAO   C  CR6   0   0.294   4.4028  -1.1679   0.5053
 NNF  CAP   C  CR6   0   0.496  -5.5606   0.0303   0.4650
 NNF  CAQ   C  CR6   0   0.351  -2.8508   0.0255  -0.1842
 NNF  CAR   C  CR6   0   0.788   2.5852  -0.0439  -0.3001
 NNF  CAS   C  CR6   0   0.541   4.5826   1.2243   0.2623
 NNF  NAT   N  NR6   0  -0.520  -1.5010   0.0038  -0.5578
 NNF  NAU   N  NR6   0  -0.509   1.3246  -0.0259  -0.7664
 NNF  HAA   H  HCH3  0   0.255   4.3594  -2.9393   1.6898
 NNF  HAAA  H  HCH3  0   0.254   4.9001  -3.1902   0.0402
 NNF  HAAB  H  HCH3  0   0.246   5.9891  -2.4390   1.2169
 NNF  HAD   H  HCR6  0   0.277  -5.6622  -1.8703  -0.5268
 NNF  HAE   H  HCR6  0   0.277  -5.1999   1.9305   1.3837
 NNF  HAF   H  HCR6  0   0.272  -3.2912  -1.8663  -1.1244
 NNF  HAG   H  HCR6  0   0.278  -2.8207   1.9250   0.8489
 NNF  HAH   H  HCR6  0   0.259   6.1632  -0.0585   1.0051
 NNF  HAI   H  H     0   0.225  -0.5194   1.4222   0.6846
 NNF  HAIA  H  H     0   0.266  -1.3066   2.0678  -0.7615
 NNF  HAJ   H  H     0   0.265  -1.3101  -2.0777  -0.3761
 NNF  HAJA  H  H     0   0.226  -0.5259  -1.1647   0.9127
 NNF  HAK   H  H     0   0.263   0.3536   1.0975  -2.2232
 NNF  HAKA  H  H     0   0.266   1.1085   2.0739  -0.9795
 NNF  HAL   H  H     0   0.285   1.1499  -2.0960  -0.5909
 NNF  HALA  H  H     0   0.250   0.3557  -1.3910  -2.0029
 NNF  HNAN  H  HNR6  0   0.419   2.8503   1.9982  -0.4793
 NNF  FAC   F  F     0  -0.322  -6.8707   0.0303   0.7764

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
 NNF  CAA  CAO   single    1.495  0.020  1.495
 NNF  OAB  CAS   double    1.225  0.020  1.225
 NNF  FAC  CAP   single    1.347  0.020  1.347
 NNF  CAD  CAF   aromatic  1.383  0.020  1.383
 NNF  CAD  CAP   aromatic  1.383  0.020  1.383
 NNF  CAE  CAG   aromatic  1.390  0.020  1.390
 NNF  CAE  CAP   aromatic  1.377  0.020  1.377
 NNF  CAF  CAQ   aromatic  1.401  0.020  1.401
 NNF  CAG  CAQ   aromatic  1.397  0.020  1.397
 NNF  CAH  CAO   double    1.367  0.020  1.367
 NNF  CAH  CAS   single    1.425  0.020  1.425
 NNF  CAI  CAK   single    1.521  0.020  1.521
 NNF  CAI  NAT   single    1.446  0.020  1.446
 NNF  CAJ  CAL   single    1.516  0.020  1.516
 NNF  CAJ  NAT   single    1.457  0.020  1.457
 NNF  CAK  NAU   single    1.450  0.020  1.450
 NNF  CAL  NAU   single    1.453  0.020  1.453
 NNF  NAM  CAO   single    1.349  0.020  1.349
 NNF  NAM  CAR   double    1.313  0.020  1.313
 NNF  NAN  CAR   single    1.358  0.020  1.358
 NNF  NAN  CAS   single    1.395  0.020  1.395
 NNF  CAQ  NAT   single    1.401  0.020  1.401
 NNF  CAR  NAU   single    1.344  0.020  1.344
 NNF  CAA  HAA   single    0.970  0.020  1.090
 NNF  CAA  HAAA  single    0.970  0.020  1.090
 NNF  CAA  HAAB  single    0.970  0.020  1.090
 NNF  CAD  HAD   single    0.930  0.020  1.080
 NNF  CAE  HAE   single    0.930  0.020  1.080
 NNF  CAF  HAF   single    0.930  0.020  1.080
 NNF  CAG  HAG   single    0.930  0.020  1.080
 NNF  CAH  HAH   single    0.930  0.020  1.080
 NNF  CAI  HAI   single    0.970  0.020  1.090
 NNF  CAI  HAIA  single    0.970  0.020  1.090
 NNF  CAJ  HAJ   single    0.970  0.020  1.090
 NNF  CAJ  HAJA  single    0.970  0.020  1.090
 NNF  CAK  HAK   single    0.970  0.020  1.090
 NNF  CAK  HAKA  single    0.970  0.020  1.090
 NNF  CAL  HAL   single    0.970  0.020  1.090
 NNF  CAL  HALA  single    0.970  0.020  1.090
 NNF  NAN  HNAN  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
 NNF  HAAB  CAA  HAAA  108.74  3.000
 NNF  HAAB  CAA  HAA   108.58  3.000
 NNF  HAAA  CAA  HAA   107.02  3.000
 NNF  HAAB  CAA  CAO   112.04  3.000
 NNF  HAAA  CAA  CAO   110.27  3.000
 NNF  HAA   CAA  CAO   110.04  3.000
 NNF  HAD   CAD  CAP   120.58  3.000
 NNF  HAD   CAD  CAF   120.33  3.000
 NNF  CAP   CAD  CAF   119.08  3.000
 NNF  HAE   CAE  CAP   120.61  3.000
 NNF  HAE   CAE  CAG   120.17  3.000
 NNF  CAP   CAE  CAG   119.22  3.000
 NNF  HAF   CAF  CAQ   120.12  3.000
 NNF  HAF   CAF  CAD   118.43  3.000
 NNF  CAQ   CAF  CAD   121.44  3.000
 NNF  HAG   CAG  CAQ   120.99  3.000
 NNF  HAG   CAG  CAE   117.80  3.000
 NNF  CAQ   CAG  CAE   121.21  3.000
 NNF  HAH   CAH  CAS   119.10  3.000
 NNF  HAH   CAH  CAO   121.49  3.000
 NNF  CAS   CAH  CAO   119.41  3.000
 NNF  HAIA  CAI  HAI   107.63  3.000
 NNF  HAIA  CAI  NAT   109.59  3.000
 NNF  HAI   CAI  NAT   112.45  3.000
 NNF  HAIA  CAI  CAK   107.54  3.000
 NNF  HAI   CAI  CAK   109.15  3.000
 NNF  NAT   CAI  CAK   110.32  3.000
 NNF  HAJA  CAJ  HAJ   107.36  3.000
 NNF  HAJA  CAJ  NAT   110.95  3.000
 NNF  HAJ   CAJ  NAT   110.20  3.000
 NNF  HAJA  CAJ  CAL   109.42  3.000
 NNF  HAJ   CAJ  CAL   108.10  3.000
 NNF  NAT   CAJ  CAL   110.71  3.000
 NNF  HAKA  CAK  HAK   106.93  3.000
 NNF  HAKA  CAK  NAU   112.73  3.000
 NNF  HAK   CAK  NAU   108.90  3.000
 NNF  HAKA  CAK  CAI   107.94  3.000
 NNF  HAK   CAK  CAI   109.64  3.000
 NNF  NAU   CAK  CAI   110.61  3.000
 NNF  HALA  CAL  HAL   108.34  3.000
 NNF  HALA  CAL  NAU   108.78  3.000
 NNF  HAL   CAL  NAU   109.66  3.000
 NNF  HALA  CAL  CAJ   109.75  3.000
 NNF  HAL   CAL  CAJ   109.95  3.000
 NNF  NAU   CAL  CAJ   110.33  3.000
 NNF  CAR   NAM  CAO   118.15  3.000
 NNF  HNAN  NAN  CAS   114.91  3.000
 NNF  HNAN  NAN  CAR   120.96  3.000
 NNF  CAS   NAN  CAR   124.13  3.000
 NNF  NAM   CAO  CAH   123.77  3.000
 NNF  NAM   CAO  CAA   114.99  3.000
 NNF  CAH   CAO  CAA   121.24  3.000
 NNF  CAE   CAP  CAD   121.29  3.000
 NNF  CAE   CAP  FAC   119.49  3.000
 NNF  CAD   CAP  FAC   119.21  3.000
 NNF  NAT   CAQ  CAG   122.69  3.000
 NNF  NAT   CAQ  CAF   119.54  3.000
 NNF  CAG   CAQ  CAF   117.75  3.000
 NNF  NAU   CAR  NAN   119.17  3.000
 NNF  NAU   CAR  NAM   119.68  3.000
 NNF  NAN   CAR  NAM   121.15  3.000
 NNF  NAN   CAS  CAH   113.40  3.000
 NNF  NAN   CAS  OAB   119.17  3.000
 NNF  CAH   CAS  OAB   127.43  3.000
 NNF  CAQ   NAT  CAJ   116.40  3.000
 NNF  CAQ   NAT  CAI   117.40  3.000
 NNF  CAJ   NAT  CAI   111.79  3.000
 NNF  CAR   NAU  CAL   121.38  3.000
 NNF  CAR   NAU  CAK   126.42  3.000
 NNF  CAL   NAU  CAK   112.21  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
 NNF  CONST_01  CAG   CAQ  CAF  CAD    0.00   0.0  0
 NNF  CONST_02  CAG   CAE  CAP  CAD    0.00   0.0  0
 NNF  CONST_03  CAF   CAQ  CAG  CAE    0.00   0.0  0
 NNF  CONST_04  CAF   CAD  CAP  CAE    0.00   0.0  0
 NNF  CONST_05  CAQ   CAF  CAD  CAP    0.00   0.0  0
 NNF  CONST_06  CAQ   CAG  CAE  CAP    0.00   0.0  0
 NNF  CONST_07  NAT   CAQ  CAF  CAD  180.00   0.0  0
 NNF  CONST_08  NAT   CAQ  CAG  CAE  180.00   0.0  0
 NNF  CONST_09  CAR   NAN  CAS  CAH    0.00   0.0  0
 NNF  CONST_10  NAM   CAR  NAU  CAK  180.00   0.0  0
 NNF  CONST_11  NAN   CAR  NAU  CAK    0.00   0.0  0
 NNF  CONST_12  NAM   CAR  NAU  CAL    0.00   0.0  0
 NNF  CONST_13  NAN   CAR  NAU  CAL  180.00   0.0  0
 NNF  CONST_14  CAS   NAN  CAR  NAM    0.00   0.0  0
 NNF  CONST_15  CAO   NAM  CAR  NAN    0.00   0.0  0
 NNF  CONST_16  NAU   CAR  NAM  CAO  180.00   0.0  0
 NNF  CONST_17  NAU   CAR  NAN  CAS  180.00   0.0  0
 NNF  CONST_18  CAF   CAD  CAP  FAC  180.00   0.0  0
 NNF  CONST_19  CAG   CAE  CAP  FAC  180.00   0.0  0
 NNF  CONST_20  CAR   NAN  CAS  OAB  180.00   0.0  0
 NNF  CONST_21  HAE   CAE  CAP  CAD  180.00   0.0  0
 NNF  CONST_22  HAD   CAD  CAP  CAE  180.00   0.0  0
 NNF  CONST_23  HAG   CAG  CAQ  CAF  180.00   0.0  0
 NNF  CONST_24  HAF   CAF  CAQ  CAG  180.00   0.0  0
 NNF  CONST_25  HNAN  NAN  CAS  CAH  180.00   0.0  0
 NNF  Var_01    CAI   NAT  CAQ  CAF  168.80  30.0  2
 NNF  Var_02    CAL   NAU  CAK  CAI   56.16  30.0  1
 NNF  Var_03    CAL   CAJ  NAT  CAI  -56.73  30.0  1
 NNF  Var_04    CAK   NAU  CAL  CAJ  -55.87  30.0  1
 NNF  Var_05    CAK   CAI  NAT  CAJ   56.66  30.0  1
 NNF  Var_06    NAU   CAK  CAI  NAT  -55.74  30.0  1
 NNF  Var_07    NAU   CAL  CAJ  NAT   55.24  30.0  1
 NNF  Var_08    HAA   CAA  CAO  CAH  118.64  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
 NNF  plan-1  CAD   0.020
 NNF  plan-1  CAE   0.020
 NNF  plan-1  CAF   0.020
 NNF  plan-1  CAG   0.020
 NNF  plan-1  CAP   0.020
 NNF  plan-1  CAQ   0.020
 NNF  plan-1  NAT   0.020
 NNF  plan-1  HAD   0.020
 NNF  plan-1  HAE   0.020
 NNF  plan-1  HAF   0.020
 NNF  plan-1  HAG   0.020
 NNF  plan-1  FAC   0.020
 NNF  plan-2  CAA   0.020
 NNF  plan-2  OAB   0.020
 NNF  plan-2  CAH   0.020
 NNF  plan-2  CAK   0.020
 NNF  plan-2  CAL   0.020
 NNF  plan-2  NAM   0.020
 NNF  plan-2  NAN   0.020
 NNF  plan-2  CAO   0.020
 NNF  plan-2  CAR   0.020
 NNF  plan-2  CAS   0.020
 NNF  plan-2  NAU   0.020
 NNF  plan-2  HAH   0.020
 NNF  plan-2  HNAN  0.020

