# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:41:25 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(N[S](=O)(=O)c2ccccc2)C(=O)NC(=O)N1Cc3ccccc3
#
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
 Y46  Y46  N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)benzenesulfonamide  ligand  42  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y46
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
 Y46  CAW   C  CR16  0  -0.280  -4.5091  -0.3425   0.2929
 Y46  CAX   C  CR16  0  -0.239  -5.7378  -0.7041  -0.2393
 Y46  CBA   C  CR16  0  -0.262  -6.4012   0.1481  -1.1138
 Y46  CAZ   C  CR16  0  -0.241  -5.8272   1.3640  -1.4544
 Y46  CAY   C  CR16  0  -0.303  -4.5945   1.7238  -0.9241
 Y46  CAV   C  CR6   0   0.067  -3.9257   0.8754  -0.0470
 Y46  CAU   C  CH2   0  -0.417  -2.6059   1.3064   0.5439
 Y46  NAN   N  NR6   0  -0.594  -1.6116   0.2377   0.5969
 Y46  CAO   C  CR6   0   0.686  -0.9479  -0.1472  -0.5437
 Y46  NAP   N  NH2   0  -0.817  -1.3051   0.4181  -1.6966
 Y46  CAM   C  CR6   0   0.729  -1.3389  -0.3348   1.8320
 Y46  OAL   O  O     0  -0.476  -1.9400  -0.0163   2.8370
 Y46  NAD   N  NR16  0  -0.741  -0.3611  -1.2793   1.8389
 Y46  CAE   C  CR6   0   0.569   0.3937  -1.7195   0.7578
 Y46  OAA   O  O     0  -0.466   1.2101  -2.6142   0.9034
 Y46  CAF   C  CR6   0  -0.108   0.0852  -1.0656  -0.4700
 Y46  NAG   N  NC1   0  -0.777   0.7605  -1.4347  -1.6509
 Y46  SAH   S  S     0   1.367   2.1659  -0.6114  -2.0200
 Y46  OAC   O  OS    0  -0.658   2.7452  -1.3110  -3.1552
 Y46  OAQ   O  OS    0  -0.649   1.8011   0.7899  -2.1357
 Y46  CAI   C  CR6   0  -0.190   3.2428  -0.7716  -0.6278
 Y46  CAJ   C  CR16  0  -0.222   4.0847  -1.8725  -0.5481
 Y46  CAK   C  CR16  0  -0.246   4.8940  -2.0171   0.5665
 Y46  CAT   C  CR16  0  -0.236   4.8490  -1.0768   1.5885
 Y46  CAS   C  CR16  0  -0.242   4.0013   0.0183   1.4956
 Y46  CAR   C  CR16  0  -0.229   3.1924   0.1809   0.3807
 Y46  HAW   H  HCR6  0   0.257  -4.0102  -1.0197   0.9748
 Y46  HAX   H  HCR6  0   0.261  -6.1793  -1.6544   0.0316
 Y46  HBA   H  HCR6  0   0.261  -7.3594  -0.1364  -1.5283
 Y46  HAZ   H  HCR6  0   0.262  -6.3332   2.0328  -2.1382
 Y46  HAY   H  HCR6  0   0.265  -4.1501   2.6742  -1.1979
 Y46  HAU1  H  HCH2  0   0.295  -2.1874   2.1444  -0.0153
 Y46  HAU2  H  HCH2  0   0.316  -2.7512   1.6630   1.5608
 Y46  HAP1  H  HNH2  0   0.427  -2.2025   0.8532  -1.8268
 Y46  HAP2  H  HNH2  0   0.419  -0.8508   0.0899  -2.5332
 Y46  HAD   H  HNR6  0   0.426  -0.1836  -1.7202   2.7325
 Y46  HAG   H  HNC1  0   0.413   0.8526  -2.4329  -1.8135
 Y46  HAJ   H  HCR6  0   0.280   4.1179  -2.6092  -1.3394
 Y46  HAR   H  HCR6  0   0.283   2.5399   1.0398   0.3061
 Y46  HAK   H  HCR6  0   0.270   5.5605  -2.8659   0.6372
 Y46  HAT   H  HCR6  0   0.270   5.4813  -1.1966   2.4584
 Y46  HAS   H  HCR6  0   0.271   3.9697   0.7517   2.2898

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
 Y46  CAW  CAX   aromatic  1.387  0.020  1.387
 Y46  CAW  CAV   aromatic  1.393  0.020  1.393
 Y46  CAX  CBA   aromatic  1.390  0.020  1.390
 Y46  CBA  CAZ   aromatic  1.387  0.020  1.387
 Y46  CAZ  CAY   aromatic  1.389  0.020  1.389
 Y46  CAY  CAV   aromatic  1.392  0.020  1.392
 Y46  CAV  CAU   single    1.509  0.020  1.509
 Y46  CAU  NAN   single    1.461  0.020  1.461
 Y46  NAN  CAO   single    1.375  0.020  1.375
 Y46  NAN  CAM   single    1.388  0.020  1.388
 Y46  CAO  NAP   single    1.333  0.020  1.333
 Y46  CAO  CAF   double    1.384  0.020  1.384
 Y46  CAM  OAL   double    1.214  0.020  1.214
 Y46  CAM  NAD   single    1.359  0.020  1.359
 Y46  NAD  CAE   single    1.390  0.020  1.390
 Y46  CAE  OAA   double    1.220  0.020  1.220
 Y46  CAE  CAF   single    1.425  0.020  1.425
 Y46  CAF  NAG   single    1.410  0.020  1.410
 Y46  NAG  SAH   single    1.670  0.020  1.670
 Y46  SAH  OAQ   double    1.453  0.020  1.453
 Y46  SAH  OAC   double    1.454  0.020  1.454
 Y46  SAH  CAI   single    1.767  0.020  1.767
 Y46  CAI  CAJ   aromatic  1.388  0.020  1.388
 Y46  CAI  CAR   aromatic  1.388  0.020  1.388
 Y46  CAJ  CAK   aromatic  1.385  0.020  1.385
 Y46  CAK  CAT   aromatic  1.390  0.020  1.390
 Y46  CAT  CAS   aromatic  1.388  0.020  1.388
 Y46  CAS  CAR   aromatic  1.387  0.020  1.387
 Y46  CAW  HAW   single    0.930  0.020  1.080
 Y46  CAX  HAX   single    0.930  0.020  1.080
 Y46  CBA  HBA   single    0.930  0.020  1.080
 Y46  CAZ  HAZ   single    0.930  0.020  1.080
 Y46  CAY  HAY   single    0.930  0.020  1.080
 Y46  CAU  HAU1  single    0.970  0.020  1.090
 Y46  CAU  HAU2  single    0.970  0.020  1.090
 Y46  NAP  HAP1  single    0.890  0.020  1.040
 Y46  NAP  HAP2  single    0.890  0.020  1.040
 Y46  NAD  HAD   single    0.860  0.020  1.020
 Y46  NAG  HAG   single    0.890  0.020  1.040
 Y46  CAJ  HAJ   single    0.930  0.020  1.080
 Y46  CAR  HAR   single    0.930  0.020  1.080
 Y46  CAK  HAK   single    0.930  0.020  1.080
 Y46  CAT  HAT   single    0.930  0.020  1.080
 Y46  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
 Y46  HAW   CAW  CAV   120.51  3.000
 Y46  HAW   CAW  CAX   119.13  3.000
 Y46  CAV   CAW  CAX   120.36  3.000
 Y46  HAX   CAX  CBA   120.08  3.000
 Y46  HAX   CAX  CAW   119.62  3.000
 Y46  CBA   CAX  CAW   120.30  3.000
 Y46  HBA   CBA  CAZ   120.19  3.000
 Y46  HBA   CBA  CAX   120.17  3.000
 Y46  CAZ   CBA  CAX   119.64  3.000
 Y46  HAZ   CAZ  CAY   119.74  3.000
 Y46  HAZ   CAZ  CBA   120.23  3.000
 Y46  CAY   CAZ  CBA   120.03  3.000
 Y46  HAY   CAY  CAV   119.78  3.000
 Y46  HAY   CAY  CAZ   119.62  3.000
 Y46  CAV   CAY  CAZ   120.60  3.000
 Y46  CAU   CAV  CAY   119.54  3.000
 Y46  CAU   CAV  CAW   121.38  3.000
 Y46  CAY   CAV  CAW   119.06  3.000
 Y46  HAU2  CAU  HAU1  106.19  3.000
 Y46  HAU2  CAU  NAN   107.27  3.000
 Y46  HAU1  CAU  NAN   108.63  3.000
 Y46  HAU2  CAU  CAV   110.06  3.000
 Y46  HAU1  CAU  CAV   110.75  3.000
 Y46  NAN   CAU  CAV   113.62  3.000
 Y46  CAM   NAN  CAO   121.86  3.000
 Y46  CAM   NAN  CAU   117.89  3.000
 Y46  CAO   NAN  CAU   120.22  3.000
 Y46  CAF   CAO  NAP   121.84  3.000
 Y46  CAF   CAO  NAN   120.12  3.000
 Y46  NAP   CAO  NAN   118.01  3.000
 Y46  HAP2  NAP  HAP1  115.85  3.000
 Y46  HAP2  NAP  CAO   117.35  3.000
 Y46  HAP1  NAP  CAO   122.32  3.000
 Y46  NAD   CAM  OAL   122.30  3.000
 Y46  NAD   CAM  NAN   115.61  3.000
 Y46  OAL   CAM  NAN   122.09  3.000
 Y46  HAD   NAD  CAE   116.97  3.000
 Y46  HAD   NAD  CAM   115.67  3.000
 Y46  CAE   NAD  CAM   127.35  3.000
 Y46  CAF   CAE  OAA   125.76  3.000
 Y46  CAF   CAE  NAD   114.03  3.000
 Y46  OAA   CAE  NAD   120.19  3.000
 Y46  NAG   CAF  CAE   119.87  3.000
 Y46  NAG   CAF  CAO   119.12  3.000
 Y46  CAE   CAF  CAO   120.80  3.000
 Y46  HAG   NAG  SAH   111.89  3.000
 Y46  HAG   NAG  CAF   115.78  3.000
 Y46  SAH   NAG  CAF   117.35  3.000
 Y46  CAI   SAH  OAQ   107.65  3.000
 Y46  CAI   SAH  OAC   109.19  3.000
 Y46  OAQ   SAH  OAC   120.14  3.000
 Y46  CAI   SAH  NAG   107.09  3.000
 Y46  OAC   SAH  NAG   105.71  3.000
 Y46  OAQ   SAH  NAG   106.37  3.000
 Y46  CAR   CAI  CAJ   121.64  3.000
 Y46  CAR   CAI  SAH   119.21  3.000
 Y46  CAJ   CAI  SAH   119.12  3.000
 Y46  HAJ   CAJ  CAK   119.98  3.000
 Y46  HAJ   CAJ  CAI   121.12  3.000
 Y46  CAK   CAJ  CAI   118.91  3.000
 Y46  HAK   CAK  CAT   120.19  3.000
 Y46  HAK   CAK  CAJ   119.65  3.000
 Y46  CAT   CAK  CAJ   120.16  3.000
 Y46  HAT   CAT  CAS   119.87  3.000
 Y46  HAT   CAT  CAK   119.83  3.000
 Y46  CAS   CAT  CAK   120.30  3.000
 Y46  HAS   CAS  CAR   119.59  3.000
 Y46  HAS   CAS  CAT   120.25  3.000
 Y46  CAR   CAS  CAT   120.16  3.000
 Y46  HAR   CAR  CAS   120.03  3.000
 Y46  HAR   CAR  CAI   121.13  3.000
 Y46  CAS   CAR  CAI   118.84  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
 Y46  CONST_01  CAZ   CBA  CAX  CAW    0.00   0.0  0
 Y46  CONST_02  CAZ   CAY  CAV  CAW    0.00   0.0  0
 Y46  CONST_03  CAY   CAV  CAW  CAX    0.00   0.0  0
 Y46  CONST_04  CAY   CAZ  CBA  CAX    0.00   0.0  0
 Y46  CONST_05  CAV   CAW  CAX  CBA    0.00   0.0  0
 Y46  CONST_06  CAV   CAY  CAZ  CBA    0.00   0.0  0
 Y46  CONST_07  CAT   CAK  CAJ  CAI    0.00   0.0  0
 Y46  CONST_08  CAT   CAS  CAR  CAI    0.00   0.0  0
 Y46  CONST_09  CAS   CAR  CAI  CAJ    0.00   0.0  0
 Y46  CONST_10  CAS   CAT  CAK  CAJ    0.00   0.0  0
 Y46  CONST_11  CAR   CAI  CAJ  CAK    0.00   0.0  0
 Y46  CONST_12  CAR   CAS  CAT  CAK    0.00   0.0  0
 Y46  CONST_13  CAE   NAD  CAM  NAN    0.00   0.0  0
 Y46  CONST_14  NAD   CAM  NAN  CAO    0.00   0.0  0
 Y46  CONST_15  CAF   CAO  NAN  CAM    0.00   0.0  0
 Y46  CONST_16  CAF   CAE  NAD  CAM    0.00   0.0  0
 Y46  CONST_17  CAU   CAV  CAW  CAX  180.00   0.0  0
 Y46  CONST_18  CAU   CAV  CAY  CAZ  180.00   0.0  0
 Y46  CONST_19  CAK   CAJ  CAI  SAH  180.00   0.0  0
 Y46  CONST_20  CAS   CAR  CAI  SAH  180.00   0.0  0
 Y46  CONST_21  CAF   CAO  NAN  CAU  180.00   0.0  0
 Y46  CONST_22  NAD   CAM  NAN  CAU  180.00   0.0  0
 Y46  CONST_23  OAL   CAM  NAN  CAO  180.00   0.0  0
 Y46  CONST_24  CAM   NAN  CAO  NAP  180.00   0.0  0
 Y46  CONST_25  OAA   CAE  NAD  CAM  180.00   0.0  0
 Y46  CONST_26  CAE   NAD  CAM  OAL  180.00   0.0  0
 Y46  CONST_27  HBA   CBA  CAX  CAW  180.00   0.0  0
 Y46  CONST_28  HAY   CAY  CAV  CAW  180.00   0.0  0
 Y46  CONST_29  HAZ   CAZ  CBA  CAX  180.00   0.0  0
 Y46  CONST_30  HAW   CAW  CAX  CBA  180.00   0.0  0
 Y46  CONST_31  HAX   CAX  CBA  CAZ  180.00   0.0  0
 Y46  CONST_32  HAK   CAK  CAJ  CAI  180.00   0.0  0
 Y46  CONST_33  HAS   CAS  CAR  CAI  180.00   0.0  0
 Y46  CONST_34  HAR   CAR  CAI  CAJ  180.00   0.0  0
 Y46  CONST_35  HAT   CAT  CAK  CAJ  180.00   0.0  0
 Y46  CONST_36  HAJ   CAJ  CAK  CAT  180.00   0.0  0
 Y46  CONST_37  HAD   NAD  CAM  NAN  180.00   0.0  0
 Y46  CONST_38  NAP   CAO  NAN  CAU    0.00   0.0  0
 Y46  CONST_39  OAL   CAM  NAN  CAU    0.00   0.0  0
 Y46  CONST_41  HAP2  NAP  CAO  NAN  180.00   0.0  0
 Y46  Var_01    NAN   CAU  CAV  CAW   43.00  30.0  2
 Y46  Var_02    CAO   NAN  CAU  CAV   76.54  30.0  3
 Y46  Var_03    SAH   NAG  CAF  CAO   94.85  30.0  2
 Y46  Var_04    CAI   SAH  NAG  CAF   55.63  30.0  3
 Y46  Var_05    CAJ   CAI  SAH  NAG   87.51  30.0  2

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
 Y46  plan-1  CAW   0.020
 Y46  plan-1  CAX   0.020
 Y46  plan-1  CBA   0.020
 Y46  plan-1  CAZ   0.020
 Y46  plan-1  CAY   0.020
 Y46  plan-1  CAV   0.020
 Y46  plan-1  CAU   0.020
 Y46  plan-1  HAW   0.020
 Y46  plan-1  HAX   0.020
 Y46  plan-1  HBA   0.020
 Y46  plan-1  HAZ   0.020
 Y46  plan-1  HAY   0.020
 Y46  plan-2  CAU   0.020
 Y46  plan-2  NAN   0.020
 Y46  plan-2  CAO   0.020
 Y46  plan-2  NAP   0.020
 Y46  plan-2  CAM   0.020
 Y46  plan-2  OAL   0.020
 Y46  plan-2  NAD   0.020
 Y46  plan-2  CAE   0.020
 Y46  plan-2  OAA   0.020
 Y46  plan-2  CAF   0.020
 Y46  plan-2  NAG   0.020
 Y46  plan-2  HAP1  0.020
 Y46  plan-2  HAP2  0.020
 Y46  plan-2  HAD   0.020
 Y46  plan-3  SAH   0.020
 Y46  plan-3  CAI   0.020
 Y46  plan-3  CAJ   0.020
 Y46  plan-3  CAK   0.020
 Y46  plan-3  CAT   0.020
 Y46  plan-3  CAS   0.020
 Y46  plan-3  CAR   0.020
 Y46  plan-3  HAJ   0.020
 Y46  plan-3  HAR   0.020
 Y46  plan-3  HAK   0.020
 Y46  plan-3  HAT   0.020
 Y46  plan-3  HAS   0.020

