# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:14:22 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1=C(N)N(Cc2ccccc2)C(=O)NC1=O)[S](=O)(=O)c3ccccc3
#
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
 N6A  N6A  N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzenesulfonamide  ligand  45  27  .  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_N6A
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
 N6A  CAW   C  CR16  0  -0.278  -4.4842   0.0164  -0.8508
 N6A  CAX   C  CR16  0  -0.239  -5.5672   0.7696  -1.2790
 N6A  CBA   C  CR16  0  -0.261  -6.3254   1.4909  -0.3644
 N6A  CAZ   C  CR16  0  -0.241  -5.9934   1.4557   0.9819
 N6A  CAY   C  CR16  0  -0.302  -4.9057   0.7047   1.4098
 N6A  CAV   C  CR6   0   0.061  -4.1435  -0.0208   0.4992
 N6A  CAU   C  CH2   0  -0.415  -2.9926  -0.8595   0.9973
 N6A  NAN   N  NR6   0  -0.596  -1.7984  -0.7757   0.1603
 N6A  CAO   C  CR6   0   0.683  -1.0067   0.3469   0.1904
 N6A  NAP   N  NH2   0  -0.818  -1.4127   1.3770   0.9326
 N6A  CAM   C  CR6   0   0.727  -1.4778  -1.8746  -0.6254
 N6A  OAL   O  O     0  -0.477  -2.1916  -2.8543  -0.6872
 N6A  NAD   N  NR16  0  -0.743  -0.3153  -1.7757  -1.3214
 N6A  CAE   C  CR6   0   0.576   0.5780  -0.7077  -1.3362
 N6A  OAA   O  O     0  -0.466   1.5714  -0.7606  -2.0427
 N6A  CAF   C  CR6   0  -0.083   0.1920   0.3807  -0.5034
 N6A  NAG   N  N     0  -0.634   0.9604   1.5628  -0.4548
 N6A  CAB   C  CH3   0  -0.530   1.1739   2.3165  -1.6909
 N6A  SAH   S  S     0   1.365   2.1682   1.6111   0.6949
 N6A  OAQ   O  OS    0  -0.654   2.6677   2.9772   0.7098
 N6A  OAC   O  OS    0  -0.647   1.6113   1.0343   1.9062
 N6A  CAI   C  CR6   0  -0.166   3.4696   0.5546   0.1314
 N6A  CAJ   C  CR16  0  -0.243   4.4264   1.0642  -0.7370
 N6A  CAK   C  CR16  0  -0.245   5.4210   0.2216  -1.2090
 N6A  CAT   C  CR16  0  -0.237   5.4569  -1.1077  -0.8088
 N6A  CAS   C  CR16  0  -0.244   4.5003  -1.6002   0.0694
 N6A  CAR   C  CR16  0  -0.223   3.4983  -0.7700   0.5457
 N6A  HAW   H  HCR6  0   0.257  -3.9100  -0.5436  -1.5787
 N6A  HAX   H  HCR6  0   0.262  -5.8219   0.7916  -2.3306
 N6A  HBA   H  HCR6  0   0.261  -7.1701   2.0772  -0.7015
 N6A  HAZ   H  HCR6  0   0.262  -6.5746   2.0180   1.7008
 N6A  HAY   H  HCR6  0   0.266  -4.6481   0.6848   2.4628
 N6A  HAU1  H  HCH2  0   0.295  -2.7242  -0.5804   2.0179
 N6A  HAU2  H  HCH2  0   0.316  -3.2857  -1.9058   1.0353
 N6A  HAP1  H  HNH2  0   0.427  -2.3699   1.4909   1.2196
 N6A  HAP2  H  HNH2  0   0.417  -0.8669   2.2222   0.8857
 N6A  HAD   H  HNR6  0   0.424  -0.0895  -2.5665  -1.9116
 N6A  HAB1  H  HCH3  0   0.262   1.3898   3.3578  -1.4688
 N6A  HAB2  H  HCH3  0   0.246   1.9727   1.9027  -2.3071
 N6A  HAB3  H  HCH3  0   0.266   0.2465   2.2781  -2.2570
 N6A  HAJ   H  HCR6  0   0.282   4.4092   2.1021  -1.0409
 N6A  HAR   H  HCR6  0   0.280   2.7555  -1.1561   1.2301
 N6A  HAK   H  HCR6  0   0.270   6.1729   0.6077  -1.8840
 N6A  HAT   H  HCR6  0   0.270   6.2364  -1.7606  -1.1786
 N6A  HAS   H  HCR6  0   0.270   4.5357  -2.6331   0.3884

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
 N6A  CAW  CAX   aromatic  1.387  0.020  1.387
 N6A  CAW  CAV   aromatic  1.393  0.020  1.393
 N6A  CAX  CBA   aromatic  1.390  0.020  1.390
 N6A  CBA  CAZ   aromatic  1.387  0.020  1.387
 N6A  CAZ  CAY   aromatic  1.389  0.020  1.389
 N6A  CAY  CAV   aromatic  1.392  0.020  1.392
 N6A  CAV  CAU   single    1.509  0.020  1.509
 N6A  CAU  NAN   single    1.461  0.020  1.461
 N6A  NAN  CAO   single    1.374  0.020  1.374
 N6A  NAN  CAM   single    1.388  0.020  1.388
 N6A  CAO  NAP   single    1.333  0.020  1.333
 N6A  CAO  CAF   double    1.385  0.020  1.385
 N6A  CAM  OAL   double    1.214  0.020  1.214
 N6A  CAM  NAD   single    1.359  0.020  1.359
 N6A  NAD  CAE   single    1.392  0.020  1.392
 N6A  CAE  OAA   double    1.220  0.020  1.220
 N6A  CAE  CAF   single    1.424  0.020  1.424
 N6A  CAF  NAG   single    1.411  0.020  1.411
 N6A  NAG  CAB   single    1.463  0.020  1.463
 N6A  NAG  SAH   single    1.668  0.020  1.668
 N6A  SAH  OAQ   double    1.455  0.020  1.455
 N6A  SAH  OAC   double    1.453  0.020  1.453
 N6A  SAH  CAI   single    1.768  0.020  1.768
 N6A  CAI  CAJ   aromatic  1.389  0.020  1.389
 N6A  CAI  CAR   aromatic  1.388  0.020  1.388
 N6A  CAJ  CAK   aromatic  1.386  0.020  1.386
 N6A  CAK  CAT   aromatic  1.389  0.020  1.389
 N6A  CAT  CAS   aromatic  1.389  0.020  1.389
 N6A  CAS  CAR   aromatic  1.386  0.020  1.386
 N6A  CAW  HAW   single    0.930  0.020  1.080
 N6A  CAX  HAX   single    0.930  0.020  1.080
 N6A  CBA  HBA   single    0.930  0.020  1.080
 N6A  CAZ  HAZ   single    0.930  0.020  1.080
 N6A  CAY  HAY   single    0.930  0.020  1.080
 N6A  CAU  HAU1  single    0.970  0.020  1.090
 N6A  CAU  HAU2  single    0.970  0.020  1.090
 N6A  NAP  HAP1  single    0.890  0.020  1.040
 N6A  NAP  HAP2  single    0.890  0.020  1.040
 N6A  NAD  HAD   single    0.860  0.020  1.020
 N6A  CAB  HAB1  single    0.970  0.020  1.090
 N6A  CAB  HAB2  single    0.970  0.020  1.090
 N6A  CAB  HAB3  single    0.970  0.020  1.090
 N6A  CAJ  HAJ   single    0.930  0.020  1.080
 N6A  CAR  HAR   single    0.930  0.020  1.080
 N6A  CAK  HAK   single    0.930  0.020  1.080
 N6A  CAT  HAT   single    0.930  0.020  1.080
 N6A  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
 N6A  HAW   CAW  CAV   120.53  3.000
 N6A  HAW   CAW  CAX   119.16  3.000
 N6A  CAV   CAW  CAX   120.31  3.000
 N6A  HAX   CAX  CBA   120.04  3.000
 N6A  HAX   CAX  CAW   119.66  3.000
 N6A  CBA   CAX  CAW   120.31  3.000
 N6A  HBA   CBA  CAZ   120.20  3.000
 N6A  HBA   CBA  CAX   120.13  3.000
 N6A  CAZ   CBA  CAX   119.67  3.000
 N6A  HAZ   CAZ  CAY   119.79  3.000
 N6A  HAZ   CAZ  CBA   120.20  3.000
 N6A  CAY   CAZ  CBA   120.00  3.000
 N6A  HAY   CAY  CAV   119.73  3.000
 N6A  HAY   CAY  CAZ   119.67  3.000
 N6A  CAV   CAY  CAZ   120.60  3.000
 N6A  CAU   CAV  CAY   119.45  3.000
 N6A  CAU   CAV  CAW   121.43  3.000
 N6A  CAY   CAV  CAW   119.10  3.000
 N6A  HAU2  CAU  HAU1  106.24  3.000
 N6A  HAU2  CAU  NAN   107.19  3.000
 N6A  HAU1  CAU  NAN   108.66  3.000
 N6A  HAU2  CAU  CAV   109.93  3.000
 N6A  HAU1  CAU  CAV   110.74  3.000
 N6A  NAN   CAU  CAV   113.74  3.000
 N6A  CAM   NAN  CAO   121.74  3.000
 N6A  CAM   NAN  CAU   117.88  3.000
 N6A  CAO   NAN  CAU   120.36  3.000
 N6A  CAF   CAO  NAP   121.57  3.000
 N6A  CAF   CAO  NAN   120.50  3.000
 N6A  NAP   CAO  NAN   117.91  3.000
 N6A  HAP2  NAP  HAP1  115.73  3.000
 N6A  HAP2  NAP  CAO   117.22  3.000
 N6A  HAP1  NAP  CAO   122.42  3.000
 N6A  NAD   CAM  OAL   122.41  3.000
 N6A  NAD   CAM  NAN   115.46  3.000
 N6A  OAL   CAM  NAN   122.13  3.000
 N6A  HAD   NAD  CAE   116.73  3.000
 N6A  HAD   NAD  CAM   115.64  3.000
 N6A  CAE   NAD  CAM   127.61  3.000
 N6A  CAF   CAE  OAA   126.34  3.000
 N6A  CAF   CAE  NAD   113.96  3.000
 N6A  OAA   CAE  NAD   119.68  3.000
 N6A  NAG   CAF  CAE   120.87  3.000
 N6A  NAG   CAF  CAO   118.32  3.000
 N6A  CAE   CAF  CAO   120.59  3.000
 N6A  SAH   NAG  CAB   117.49  3.000
 N6A  SAH   NAG  CAF   116.25  3.000
 N6A  CAB   NAG  CAF   118.81  3.000
 N6A  HAB3  CAB  HAB2  108.49  3.000
 N6A  HAB3  CAB  HAB1  108.05  3.000
 N6A  HAB2  CAB  HAB1  109.49  3.000
 N6A  HAB3  CAB  NAG   107.29  3.000
 N6A  HAB2  CAB  NAG   112.88  3.000
 N6A  HAB1  CAB  NAG   110.48  3.000
 N6A  CAI   SAH  OAC   108.10  3.000
 N6A  CAI   SAH  OAQ   108.16  3.000
 N6A  OAC   SAH  OAQ   119.73  3.000
 N6A  CAI   SAH  NAG   107.21  3.000
 N6A  OAC   SAH  NAG   106.59  3.000
 N6A  OAQ   SAH  NAG   106.43  3.000
 N6A  CAR   CAI  CAJ   121.50  3.000
 N6A  CAR   CAI  SAH   119.35  3.000
 N6A  CAJ   CAI  SAH   119.14  3.000
 N6A  HAJ   CAJ  CAK   119.93  3.000
 N6A  HAJ   CAJ  CAI   121.12  3.000
 N6A  CAK   CAJ  CAI   118.95  3.000
 N6A  HAK   CAK  CAT   120.24  3.000
 N6A  HAK   CAK  CAJ   119.61  3.000
 N6A  CAT   CAK  CAJ   120.15  3.000
 N6A  HAT   CAT  CAS   119.90  3.000
 N6A  HAT   CAT  CAK   119.84  3.000
 N6A  CAS   CAT  CAK   120.26  3.000
 N6A  HAS   CAS  CAR   119.63  3.000
 N6A  HAS   CAS  CAT   120.17  3.000
 N6A  CAR   CAS  CAT   120.20  3.000
 N6A  HAR   CAR  CAS   120.03  3.000
 N6A  HAR   CAR  CAI   121.02  3.000
 N6A  CAS   CAR  CAI   118.95  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
 N6A  CONST_01  CAZ   CBA  CAX  CAW     0.00   0.0  0
 N6A  CONST_02  CAZ   CAY  CAV  CAW     0.00   0.0  0
 N6A  CONST_03  CAY   CAV  CAW  CAX     0.00   0.0  0
 N6A  CONST_04  CAY   CAZ  CBA  CAX     0.00   0.0  0
 N6A  CONST_05  CAV   CAW  CAX  CBA     0.00   0.0  0
 N6A  CONST_06  CAV   CAY  CAZ  CBA     0.00   0.0  0
 N6A  CONST_07  CAT   CAK  CAJ  CAI     0.00   0.0  0
 N6A  CONST_08  CAT   CAS  CAR  CAI     0.00   0.0  0
 N6A  CONST_09  CAS   CAR  CAI  CAJ     0.00   0.0  0
 N6A  CONST_10  CAS   CAT  CAK  CAJ     0.00   0.0  0
 N6A  CONST_11  CAR   CAI  CAJ  CAK     0.00   0.0  0
 N6A  CONST_12  CAR   CAS  CAT  CAK     0.00   0.0  0
 N6A  CONST_13  CAE   NAD  CAM  NAN     0.00   0.0  0
 N6A  CONST_14  NAD   CAM  NAN  CAO     0.00   0.0  0
 N6A  CONST_15  CAF   CAO  NAN  CAM     0.00   0.0  0
 N6A  CONST_16  CAF   CAE  NAD  CAM     0.00   0.0  0
 N6A  CONST_17  CAU   CAV  CAW  CAX   180.00   0.0  0
 N6A  CONST_18  CAU   CAV  CAY  CAZ   180.00   0.0  0
 N6A  CONST_19  CAK   CAJ  CAI  SAH   180.00   0.0  0
 N6A  CONST_20  CAS   CAR  CAI  SAH   180.00   0.0  0
 N6A  CONST_21  CAF   CAO  NAN  CAU   180.00   0.0  0
 N6A  CONST_22  NAD   CAM  NAN  CAU   180.00   0.0  0
 N6A  CONST_23  OAL   CAM  NAN  CAO   180.00   0.0  0
 N6A  CONST_24  CAM   NAN  CAO  NAP   180.00   0.0  0
 N6A  CONST_25  OAA   CAE  NAD  CAM   180.00   0.0  0
 N6A  CONST_26  CAE   NAD  CAM  OAL   180.00   0.0  0
 N6A  CONST_27  HBA   CBA  CAX  CAW   180.00   0.0  0
 N6A  CONST_28  HAY   CAY  CAV  CAW   180.00   0.0  0
 N6A  CONST_29  HAZ   CAZ  CBA  CAX   180.00   0.0  0
 N6A  CONST_30  HAW   CAW  CAX  CBA   180.00   0.0  0
 N6A  CONST_31  HAX   CAX  CBA  CAZ   180.00   0.0  0
 N6A  CONST_32  HAK   CAK  CAJ  CAI   180.00   0.0  0
 N6A  CONST_33  HAS   CAS  CAR  CAI   180.00   0.0  0
 N6A  CONST_34  HAR   CAR  CAI  CAJ   180.00   0.0  0
 N6A  CONST_35  HAT   CAT  CAK  CAJ   180.00   0.0  0
 N6A  CONST_36  HAJ   CAJ  CAK  CAT   180.00   0.0  0
 N6A  CONST_37  HAD   NAD  CAM  NAN   180.00   0.0  0
 N6A  CONST_38  NAP   CAO  NAN  CAU     0.00   0.0  0
 N6A  CONST_39  OAL   CAM  NAN  CAU     0.00   0.0  0
 N6A  CONST_41  HAP2  NAP  CAO  NAN   180.00   0.0  0
 N6A  Var_01    NAN   CAU  CAV  CAW    43.47  30.0  2
 N6A  Var_02    CAO   NAN  CAU  CAV    74.51  30.0  3
 N6A  Var_03    CAB   NAG  CAF  CAO  -115.59  30.0  2
 N6A  Var_04    CAI   SAH  NAG  CAF    73.62  30.0  3
 N6A  Var_05    CAJ   CAI  SAH  NAG    85.49  30.0  2
 N6A  Var_06    HAB1  CAB  NAG  CAF   155.99  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
 N6A  plan-1  CAW   0.020
 N6A  plan-1  CAX   0.020
 N6A  plan-1  CBA   0.020
 N6A  plan-1  CAZ   0.020
 N6A  plan-1  CAY   0.020
 N6A  plan-1  CAV   0.020
 N6A  plan-1  CAU   0.020
 N6A  plan-1  HAW   0.020
 N6A  plan-1  HAX   0.020
 N6A  plan-1  HBA   0.020
 N6A  plan-1  HAZ   0.020
 N6A  plan-1  HAY   0.020
 N6A  plan-2  CAU   0.020
 N6A  plan-2  NAN   0.020
 N6A  plan-2  CAO   0.020
 N6A  plan-2  NAP   0.020
 N6A  plan-2  CAM   0.020
 N6A  plan-2  OAL   0.020
 N6A  plan-2  NAD   0.020
 N6A  plan-2  CAE   0.020
 N6A  plan-2  OAA   0.020
 N6A  plan-2  CAF   0.020
 N6A  plan-2  NAG   0.020
 N6A  plan-2  HAP1  0.020
 N6A  plan-2  HAP2  0.020
 N6A  plan-2  HAD   0.020
 N6A  plan-3  SAH   0.020
 N6A  plan-3  CAI   0.020
 N6A  plan-3  CAJ   0.020
 N6A  plan-3  CAK   0.020
 N6A  plan-3  CAT   0.020
 N6A  plan-3  CAS   0.020
 N6A  plan-3  CAR   0.020
 N6A  plan-3  HAJ   0.020
 N6A  plan-3  HAR   0.020
 N6A  plan-3  HAK   0.020
 N6A  plan-3  HAT   0.020
 N6A  plan-3  HAS   0.020

