# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:41:28 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C(=O)c1ccccc1)C2=C(N)N(Cc3ccccc3)C(=O)NC2=O
#
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
 N5Y  N5Y  N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzamide  ligand  44  26  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N5Y
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
 N5Y  CAY   C  CR16  0  -0.295  -3.8774  -1.8111   0.3795
 N5Y  CAZ   C  CR16  0  -0.241  -4.9196  -1.7923   1.2973
 N5Y  CBA   C  CR16  0  -0.262  -5.3543  -0.5870   1.8297
 N5Y  CAX   C  CR16  0  -0.239  -4.7437   0.5976   1.4371
 N5Y  CAW   C  CR16  0  -0.277  -3.7070   0.5790   0.5152
 N5Y  CAV   C  CR6   0   0.050  -3.2654  -0.6273  -0.0215
 N5Y  CAU   C  CH2   0  -0.406  -2.1670  -0.6788  -1.0543
 N5Y  NAN   N  NR6   0  -0.599  -1.1021   0.2946  -0.8293
 N5Y  CAO   C  CR6   0   0.687  -0.1994   0.1157   0.1937
 N5Y  NAP   N  NH2   0  -0.831  -0.3672  -0.9498   0.9875
 N5Y  CAM   C  CR6   0   0.723  -1.0256   1.3797  -1.6907
 N5Y  OAL   O  O     0  -0.473  -1.8372   1.5649  -2.5734
 N5Y  NAD   N  NR16  0  -0.738   0.0196   2.2226  -1.4763
 N5Y  CAE   C  CR6   0   0.567   1.0081   2.1092  -0.5090
 N5Y  OAA   O  O     0  -0.480   1.8940   2.9491  -0.4408
 N5Y  CAF   C  CR6   0  -0.082   0.8681   0.9774   0.3418
 N5Y  NAG   N  NT    0  -0.503   1.7811   0.8112   1.4016
 N5Y  OAC   O  O     0  -0.466   3.3847  -0.4347   2.3874
 N5Y  CA0   C  C     0   0.481   2.7390  -0.1520   1.3913
 N5Y  CAT   C  CR6   0  -0.049   2.9628  -0.8826   0.1063
 N5Y  CAS   C  CR16  0  -0.277   2.8959  -2.2725   0.1140
 N5Y  CAR   C  CR16  0  -0.247   3.1558  -2.9895  -1.0451
 N5Y  CAI   C  CR16  0  -0.255   3.5128  -2.3230  -2.2095
 N5Y  CAJ   C  CR16  0  -0.246   3.6064  -0.9368  -2.2124
 N5Y  CAA   C  CH3   0  -0.533   1.5949   1.6158   2.6024
 N5Y  CAK   C  CR16  0  -0.257   3.3247  -0.2166  -1.0611
 N5Y  HAW   H  HCR6  0   0.255  -3.2446   1.5140   0.2235
 N5Y  HAX   H  HCR6  0   0.262  -5.0758   1.5417   1.8489
 N5Y  HBA   H  HCR6  0   0.261  -6.1613  -0.5694   2.5500
 N5Y  HAZ   H  HCR6  0   0.262  -5.3855  -2.7214   1.5988
 N5Y  HAY   H  HCR6  0   0.264  -3.5360  -2.7566  -0.0264
 N5Y  HAU1  H  HCH2  0   0.294  -1.7274  -1.6767  -1.1056
 N5Y  HAU2  H  HCH2  0   0.318  -2.5785  -0.4780  -2.0404
 N5Y  HAP1  H  HNH2  0   0.429  -1.2605  -1.4060   1.0773
 N5Y  HAP2  H  HNH2  0   0.420   0.2120  -1.0230   1.8074
 N5Y  HAD   H  HNR6  0   0.426   0.0734   3.0205  -2.0967
 N5Y  HAA1  H  HCH3  0   0.244   0.9675   1.1088   3.3378
 N5Y  HAA2  H  HCH3  0   0.254   2.5532   1.8427   3.0630
 N5Y  HAA3  H  HCH3  0   0.254   1.1158   2.5508   2.3261
 N5Y  HAI   H  HCR6  0   0.260   3.7262  -2.8824  -3.1112
 N5Y  HAJ   H  HCR6  0   0.260   3.9004  -0.4148  -3.1135
 N5Y  HAR   H  HCR6  0   0.260   3.0864  -4.0693  -1.0363
 N5Y  HAK   H  HCR6  0   0.262   3.4095   0.8622  -1.0715
 N5Y  HAS   H  HCR6  0   0.260   2.6286  -2.7975   1.0226

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
 N5Y  CAW  CAX   aromatic  1.387  0.020  1.387
 N5Y  CAW  CAV   aromatic  1.392  0.020  1.392
 N5Y  CAX  CBA   aromatic  1.389  0.020  1.389
 N5Y  CBA  CAZ   aromatic  1.387  0.020  1.387
 N5Y  CAZ  CAY   aromatic  1.389  0.020  1.389
 N5Y  CAY  CAV   aromatic  1.392  0.020  1.392
 N5Y  CAV  CAU   single    1.509  0.020  1.509
 N5Y  CAU  NAN   single    1.460  0.020  1.460
 N5Y  NAN  CAO   single    1.376  0.020  1.376
 N5Y  NAN  CAM   single    1.388  0.020  1.388
 N5Y  CAO  NAP   single    1.339  0.020  1.339
 N5Y  CAO  CAF   double    1.380  0.020  1.380
 N5Y  CAM  OAL   double    1.213  0.020  1.213
 N5Y  CAM  NAD   single    1.360  0.020  1.360
 N5Y  NAD  CAE   single    1.388  0.020  1.388
 N5Y  CAE  OAA   double    1.223  0.020  1.223
 N5Y  CAE  CAF   single    1.423  0.020  1.423
 N5Y  CAF  NAG   single    1.409  0.020  1.409
 N5Y  NAG  CA0   single    1.358  0.020  1.358
 N5Y  NAG  CAA   single    1.457  0.020  1.457
 N5Y  OAC  CA0   double    1.220  0.020  1.220
 N5Y  CAI  CAJ   aromatic  1.389  0.020  1.389
 N5Y  CAI  CAR   aromatic  1.388  0.020  1.388
 N5Y  CAJ  CAK   aromatic  1.387  0.020  1.387
 N5Y  CA0  CAT   single    1.495  0.020  1.495
 N5Y  CAK  CAT   aromatic  1.392  0.020  1.392
 N5Y  CAT  CAS   aromatic  1.392  0.020  1.392
 N5Y  CAS  CAR   aromatic  1.388  0.020  1.388
 N5Y  CAW  HAW   single    0.930  0.020  1.080
 N5Y  CAX  HAX   single    0.930  0.020  1.080
 N5Y  CBA  HBA   single    0.930  0.020  1.080
 N5Y  CAZ  HAZ   single    0.930  0.020  1.080
 N5Y  CAY  HAY   single    0.930  0.020  1.080
 N5Y  CAU  HAU1  single    0.970  0.020  1.090
 N5Y  CAU  HAU2  single    0.970  0.020  1.090
 N5Y  NAP  HAP1  single    0.890  0.020  1.040
 N5Y  NAP  HAP2  single    0.890  0.020  1.040
 N5Y  NAD  HAD   single    0.860  0.020  1.020
 N5Y  CAA  HAA1  single    0.970  0.020  1.090
 N5Y  CAA  HAA2  single    0.970  0.020  1.090
 N5Y  CAA  HAA3  single    0.970  0.020  1.090
 N5Y  CAI  HAI   single    0.930  0.020  1.080
 N5Y  CAJ  HAJ   single    0.930  0.020  1.080
 N5Y  CAR  HAR   single    0.930  0.020  1.080
 N5Y  CAK  HAK   single    0.930  0.020  1.080
 N5Y  CAS  HAS   single    0.930  0.020  1.080

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
 N5Y  HAY   CAY  CAV   119.71  3.000
 N5Y  HAY   CAY  CAZ   119.70  3.000
 N5Y  CAV   CAY  CAZ   120.59  3.000
 N5Y  HAZ   CAZ  CBA   120.27  3.000
 N5Y  HAZ   CAZ  CAY   119.70  3.000
 N5Y  CBA   CAZ  CAY   120.03  3.000
 N5Y  HBA   CBA  CAX   120.14  3.000
 N5Y  HBA   CBA  CAZ   120.21  3.000
 N5Y  CAX   CBA  CAZ   119.64  3.000
 N5Y  HAX   CAX  CAW   119.60  3.000
 N5Y  HAX   CAX  CBA   120.10  3.000
 N5Y  CAW   CAX  CBA   120.31  3.000
 N5Y  HAW   CAW  CAV   120.59  3.000
 N5Y  HAW   CAW  CAX   119.09  3.000
 N5Y  CAV   CAW  CAX   120.32  3.000
 N5Y  CAU   CAV  CAW   121.63  3.000
 N5Y  CAU   CAV  CAY   119.24  3.000
 N5Y  CAW   CAV  CAY   119.11  3.000
 N5Y  HAU2  CAU  HAU1  106.18  3.000
 N5Y  HAU2  CAU  NAN   107.02  3.000
 N5Y  HAU1  CAU  NAN   108.84  3.000
 N5Y  HAU2  CAU  CAV   109.82  3.000
 N5Y  HAU1  CAU  CAV   110.89  3.000
 N5Y  NAN   CAU  CAV   113.75  3.000
 N5Y  CAM   NAN  CAO   121.81  3.000
 N5Y  CAM   NAN  CAU   117.76  3.000
 N5Y  CAO   NAN  CAU   120.42  3.000
 N5Y  CAF   CAO  NAP   122.01  3.000
 N5Y  CAF   CAO  NAN   120.41  3.000
 N5Y  NAP   CAO  NAN   117.51  3.000
 N5Y  HAP2  NAP  HAP1  113.88  3.000
 N5Y  HAP2  NAP  CAO   117.95  3.000
 N5Y  HAP1  NAP  CAO   121.63  3.000
 N5Y  NAD   CAM  OAL   122.29  3.000
 N5Y  NAD   CAM  NAN   115.42  3.000
 N5Y  OAL   CAM  NAN   122.29  3.000
 N5Y  HAD   NAD  CAE   116.99  3.000
 N5Y  HAD   NAD  CAM   115.65  3.000
 N5Y  CAE   NAD  CAM   127.36  3.000
 N5Y  CAF   CAE  OAA   125.76  3.000
 N5Y  CAF   CAE  NAD   114.32  3.000
 N5Y  OAA   CAE  NAD   119.93  3.000
 N5Y  NAG   CAF  CAE   118.68  3.000
 N5Y  NAG   CAF  CAO   120.56  3.000
 N5Y  CAE   CAF  CAO   120.58  3.000
 N5Y  CAA   NAG  CA0   119.19  3.000
 N5Y  CAA   NAG  CAF   118.16  3.000
 N5Y  CA0   NAG  CAF   122.34  3.000
 N5Y  CAT   CA0  OAC   120.61  3.000
 N5Y  CAT   CA0  NAG   117.29  3.000
 N5Y  OAC   CA0  NAG   122.09  3.000
 N5Y  CAK   CAT  CAS   119.68  3.000
 N5Y  CAS   CAT  CA0   118.43  3.000
 N5Y  CAK   CAT  CA0   121.74  3.000
 N5Y  HAS   CAS  CAR   119.78  3.000
 N5Y  HAS   CAS  CAT   120.06  3.000
 N5Y  CAR   CAS  CAT   120.16  3.000
 N5Y  HAR   CAR  CAI   120.16  3.000
 N5Y  HAR   CAR  CAS   119.79  3.000
 N5Y  CAI   CAR  CAS   120.05  3.000
 N5Y  HAI   CAI  CAJ   120.05  3.000
 N5Y  HAI   CAI  CAR   120.08  3.000
 N5Y  CAJ   CAI  CAR   119.87  3.000
 N5Y  HAJ   CAJ  CAK   119.73  3.000
 N5Y  HAJ   CAJ  CAI   120.09  3.000
 N5Y  CAK   CAJ  CAI   120.18  3.000
 N5Y  HAA3  CAA  HAA2  108.47  3.000
 N5Y  HAA3  CAA  HAA1  108.52  3.000
 N5Y  HAA2  CAA  HAA1  108.56  3.000
 N5Y  HAA3  CAA  NAG   108.78  3.000
 N5Y  HAA2  CAA  NAG   110.60  3.000
 N5Y  HAA1  CAA  NAG   111.84  3.000
 N5Y  HAK   CAK  CAJ   119.59  3.000
 N5Y  HAK   CAK  CAT   120.36  3.000
 N5Y  CAJ   CAK  CAT   120.04  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
 N5Y  CONST_01  CAX   CBA  CAZ  CAY     0.00   0.0  0
 N5Y  CONST_02  CAX   CAW  CAV  CAY     0.00   0.0  0
 N5Y  CONST_03  CAW   CAX  CBA  CAZ     0.00   0.0  0
 N5Y  CONST_04  CAW   CAV  CAY  CAZ     0.00   0.0  0
 N5Y  CONST_05  CAV   CAW  CAX  CBA     0.00   0.0  0
 N5Y  CONST_06  CAV   CAY  CAZ  CBA     0.00   0.0  0
 N5Y  CONST_07  CAI   CAJ  CAK  CAT     0.00   0.0  0
 N5Y  CONST_08  CAI   CAR  CAS  CAT     0.00   0.0  0
 N5Y  CONST_09  CAJ   CAK  CAT  CAS     0.00   0.0  0
 N5Y  CONST_10  CAJ   CAI  CAR  CAS     0.00   0.0  0
 N5Y  CONST_11  CAK   CAJ  CAI  CAR     0.00   0.0  0
 N5Y  CONST_12  CAK   CAT  CAS  CAR     0.00   0.0  0
 N5Y  CONST_13  CAE   NAD  CAM  NAN     0.00   0.0  0
 N5Y  CONST_14  NAD   CAM  NAN  CAO     0.00   0.0  0
 N5Y  CONST_15  CAF   CAO  NAN  CAM     0.00   0.0  0
 N5Y  CONST_16  CAF   CAE  NAD  CAM     0.00   0.0  0
 N5Y  CONST_17  CAU   CAV  CAY  CAZ   180.00   0.0  0
 N5Y  CONST_18  CAU   CAV  CAW  CAX   180.00   0.0  0
 N5Y  CONST_19  CAJ   CAK  CAT  CA0   180.00   0.0  0
 N5Y  CONST_20  CAR   CAS  CAT  CA0   180.00   0.0  0
 N5Y  CONST_21  CAF   CAO  NAN  CAU   180.00   0.0  0
 N5Y  CONST_22  NAD   CAM  NAN  CAU   180.00   0.0  0
 N5Y  CONST_23  OAL   CAM  NAN  CAO   180.00   0.0  0
 N5Y  CONST_24  CAM   NAN  CAO  NAP   180.00   0.0  0
 N5Y  CONST_25  OAA   CAE  NAD  CAM   180.00   0.0  0
 N5Y  CONST_26  CAE   NAD  CAM  OAL   180.00   0.0  0
 N5Y  CONST_27  HBA   CBA  CAZ  CAY   180.00   0.0  0
 N5Y  CONST_28  HAW   CAW  CAV  CAY   180.00   0.0  0
 N5Y  CONST_29  HAX   CAX  CBA  CAZ   180.00   0.0  0
 N5Y  CONST_30  HAY   CAY  CAZ  CBA   180.00   0.0  0
 N5Y  CONST_31  HAZ   CAZ  CBA  CAX   180.00   0.0  0
 N5Y  CONST_32  HAJ   CAJ  CAK  CAT   180.00   0.0  0
 N5Y  CONST_33  HAR   CAR  CAS  CAT   180.00   0.0  0
 N5Y  CONST_34  HAK   CAK  CAT  CAS   180.00   0.0  0
 N5Y  CONST_35  HAI   CAI  CAR  CAS   180.00   0.0  0
 N5Y  CONST_36  HAS   CAS  CAR  CAI   180.00   0.0  0
 N5Y  CONST_37  HAD   NAD  CAM  NAN   180.00   0.0  0
 N5Y  CONST_38  CAT   CA0  NAG  CAF     0.00   0.0  0
 N5Y  CONST_39  NAP   CAO  NAN  CAU     0.00   0.0  0
 N5Y  CONST_40  OAL   CAM  NAN  CAU     0.00   0.0  0
 N5Y  CONST_42  HAP2  NAP  CAO  NAN   180.00   0.0  0
 N5Y  CONST_43  OAC   CA0  NAG  CAF   180.00   0.0  0
 N5Y  CONST_44  CAA   NAG  CA0  CAT   180.00   0.0  0
 N5Y  CONST_45  CAA   NAG  CA0  OAC     0.00   0.0  0
 N5Y  Var_01    NAN   CAU  CAV  CAY  -144.06  30.0  2
 N5Y  Var_02    CAO   NAN  CAU  CAV    73.00  30.0  3
 N5Y  Var_03    CA0   NAG  CAF  CAO    76.48  30.0  2
 N5Y  Var_04    CAK   CAT  CA0  NAG    58.87  30.0  2
 N5Y  Var_05    HAA1  CAA  NAG  CAF    90.95  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
 N5Y  plan-1  CAY   0.020
 N5Y  plan-1  CAZ   0.020
 N5Y  plan-1  CBA   0.020
 N5Y  plan-1  CAX   0.020
 N5Y  plan-1  CAW   0.020
 N5Y  plan-1  CAV   0.020
 N5Y  plan-1  CAU   0.020
 N5Y  plan-1  HAW   0.020
 N5Y  plan-1  HAX   0.020
 N5Y  plan-1  HBA   0.020
 N5Y  plan-1  HAZ   0.020
 N5Y  plan-1  HAY   0.020
 N5Y  plan-2  CAU   0.020
 N5Y  plan-2  NAN   0.020
 N5Y  plan-2  CAO   0.020
 N5Y  plan-2  NAP   0.020
 N5Y  plan-2  CAM   0.020
 N5Y  plan-2  OAL   0.020
 N5Y  plan-2  NAD   0.020
 N5Y  plan-2  CAE   0.020
 N5Y  plan-2  OAA   0.020
 N5Y  plan-2  CAF   0.020
 N5Y  plan-2  NAG   0.020
 N5Y  plan-2  HAP1  0.020
 N5Y  plan-2  HAP2  0.020
 N5Y  plan-2  HAD   0.020
 N5Y  plan-3  CA0   0.020
 N5Y  plan-3  CAT   0.020
 N5Y  plan-3  CAS   0.020
 N5Y  plan-3  CAR   0.020
 N5Y  plan-3  CAI   0.020
 N5Y  plan-3  CAJ   0.020
 N5Y  plan-3  CAK   0.020
 N5Y  plan-3  HAI   0.020
 N5Y  plan-3  HAJ   0.020
 N5Y  plan-3  HAR   0.020
 N5Y  plan-3  HAK   0.020
 N5Y  plan-3  HAS   0.020
 N5Y  plan-4  CAF   0.020
 N5Y  plan-4  NAG   0.020
 N5Y  plan-4  OAC   0.020
 N5Y  plan-4  CA0   0.020
 N5Y  plan-4  CAT   0.020
 N5Y  plan-4  CAA   0.020

