# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:37:43 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbutane-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[S](=O)(=O)N(C)C1=C(N)N(Cc2ccccc2)C(=O)NC1=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
 KKT  KKT  N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbutane-1-sulfonamide  ligand  47  25  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KKT
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
 KKT  CAW   C  CR16  0  -0.296  -4.7283   0.1900   1.5143
 KKT  CAX   C  CR16  0  -0.241  -5.8034   1.0602   1.3867
 KKT  CBA   C  CR16  0  -0.262  -6.1972   1.4968   0.1300
 KKT  CAZ   C  CR16  0  -0.239  -5.5120   1.0578  -0.9963
 KKT  CAY   C  CR16  0  -0.277  -4.4420   0.1839  -0.8687
 KKT  CAV   C  CR6   0   0.052  -4.0421  -0.2579   0.3895
 KKT  CAU   C  CH2   0  -0.405  -2.9114  -1.2415   0.5615
 KKT  NAN   N  NR6   0  -0.599  -1.7927  -1.0207  -0.3507
 KKT  CAO   C  CR6   0   0.678  -0.9356   0.0346  -0.1529
 KKT  NAP   N  NH2   0  -0.816  -1.2074   0.8835   0.8383
 KKT  CAM   C  CR6   0   0.725  -1.6031  -1.9319  -1.3804
 KKT  OAL   O  O     0  -0.473  -2.3729  -2.8472  -1.5847
 KKT  NAD   N  NR16  0  -0.740  -0.4965  -1.7285  -2.1431
 KKT  CAE   C  CR6   0   0.574   0.4559  -0.7260  -2.0034
 KKT  OAA   O  O     0  -0.481   1.4028  -0.6825  -2.7769
 KKT  CAF   C  CR6   0  -0.056   0.1948   0.1815  -0.9409
 KKT  NAG   N  N     0  -0.643   1.0170   1.3056  -0.7287
 KKT  CAB   C  CH3   0  -0.530   1.0746   2.3361  -1.7645
 KKT  SAH   S  S     0   1.341   2.3340   1.1198   0.2772
 KKT  OAC   O  OS    0  -0.672   2.7521   2.4575   0.6780
 KKT  OAQ   O  OS    0  -0.664   1.9342   0.1724   1.3077
 KKT  CAI   C  CH2   0  -0.609   3.6607   0.3880  -0.6739
 KKT  CAJ   C  CH2   0  -0.424   4.9312   0.2648   0.1572
 KKT  CAK   C  CH2   0  -0.422   6.0170  -0.4810  -0.6112
 KKT  CAT   C  CH3   0  -0.663   7.2919  -0.6316   0.2060
 KKT  HAW   H  HCR6  0   0.265  -4.4189  -0.1411   2.4992
 KKT  HAX   H  HCR6  0   0.262  -6.3276   1.3993   2.2706
 KKT  HBA   H  HCR6  0   0.261  -7.0317   2.1779   0.0276
 KKT  HAZ   H  HCR6  0   0.262  -5.8132   1.3946  -1.9796
 KKT  HAY   H  HCR6  0   0.255  -3.9208  -0.1461  -1.7589
 KKT  HAU1  H  HCH2  0   0.294  -2.5361  -1.2215   1.5862
 KKT  HAU2  H  HCH2  0   0.316  -3.2717  -2.2524   0.3878
 KKT  HAP1  H  HNH2  0   0.428  -2.1279   0.9745   1.2344
 KKT  HAP2  H  HNH2  0   0.416  -0.6120   1.6911   0.9261
 KKT  HAD   H  HNR6  0   0.425  -0.3565  -2.3909  -2.8950
 KKT  HAB1  H  HCH3  0   0.262   1.5248   3.2437  -1.3720
 KKT  HAB2  H  HCH3  0   0.245   1.6274   2.0133  -2.6471
 KKT  HAB3  H  HCH3  0   0.264   0.0538   2.5712  -2.0573
 KKT  HAI1  H  HCH2  0   0.294   3.3049  -0.5860  -1.0083
 KKT  HAI2  H  HCH2  0   0.291   3.8141   1.0136  -1.5549
 KKT  HAJ1  H  HCH2  0   0.244   5.2933   1.2563   0.4372
 KKT  HAJ2  H  HCH2  0   0.240   4.7157  -0.2712   1.0849
 KKT  HAK1  H  HCH2  0   0.224   5.6430  -1.4679  -0.8979
 KKT  HAK2  H  HCH2  0   0.224   6.2354   0.0475  -1.5433
 KKT  HAT1  H  HCH3  0   0.232   8.0550  -1.1790  -0.3475
 KKT  HAT2  H  HCH3  0   0.221   7.7084   0.3415   0.4718
 KKT  HAT3  H  HCH3  0   0.221   7.1018  -1.1740   1.1338

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
 KKT  CAW  CAX   aromatic  1.389  0.020  1.389
 KKT  CAW  CAV   aromatic  1.392  0.020  1.392
 KKT  CAX  CBA   aromatic  1.387  0.020  1.387
 KKT  CBA  CAZ   aromatic  1.390  0.020  1.390
 KKT  CAZ  CAY   aromatic  1.387  0.020  1.387
 KKT  CAY  CAV   aromatic  1.392  0.020  1.392
 KKT  CAV  CAU   single    1.509  0.020  1.509
 KKT  CAU  NAN   single    1.460  0.020  1.460
 KKT  NAN  CAO   single    1.374  0.020  1.374
 KKT  NAN  CAM   single    1.388  0.020  1.388
 KKT  CAO  NAP   single    1.333  0.020  1.333
 KKT  CAO  CAF   double    1.386  0.020  1.386
 KKT  CAM  OAL   double    1.213  0.020  1.213
 KKT  CAM  NAD   single    1.359  0.020  1.359
 KKT  NAD  CAE   single    1.390  0.020  1.390
 KKT  CAE  OAA   double    1.223  0.020  1.223
 KKT  CAE  CAF   single    1.422  0.020  1.422
 KKT  CAF  NAG   single    1.409  0.020  1.409
 KKT  NAG  CAB   single    1.462  0.020  1.462
 KKT  NAG  SAH   single    1.668  0.020  1.668
 KKT  SAH  OAQ   double    1.456  0.020  1.456
 KKT  SAH  OAC   double    1.458  0.020  1.458
 KKT  SAH  CAI   single    1.789  0.020  1.789
 KKT  CAI  CAJ   single    1.523  0.020  1.523
 KKT  CAJ  CAK   single    1.525  0.020  1.525
 KKT  CAK  CAT   single    1.522  0.020  1.522
 KKT  CAW  HAW   single    0.930  0.020  1.080
 KKT  CAX  HAX   single    0.930  0.020  1.080
 KKT  CBA  HBA   single    0.930  0.020  1.080
 KKT  CAZ  HAZ   single    0.930  0.020  1.080
 KKT  CAY  HAY   single    0.930  0.020  1.080
 KKT  CAU  HAU1  single    0.970  0.020  1.090
 KKT  CAU  HAU2  single    0.970  0.020  1.090
 KKT  NAP  HAP1  single    0.890  0.020  1.040
 KKT  NAP  HAP2  single    0.890  0.020  1.040
 KKT  NAD  HAD   single    0.860  0.020  1.020
 KKT  CAB  HAB1  single    0.970  0.020  1.090
 KKT  CAB  HAB2  single    0.970  0.020  1.090
 KKT  CAB  HAB3  single    0.970  0.020  1.090
 KKT  CAI  HAI1  single    0.970  0.020  1.090
 KKT  CAI  HAI2  single    0.970  0.020  1.090
 KKT  CAJ  HAJ1  single    0.970  0.020  1.090
 KKT  CAJ  HAJ2  single    0.970  0.020  1.090
 KKT  CAK  HAK1  single    0.970  0.020  1.090
 KKT  CAK  HAK2  single    0.970  0.020  1.090
 KKT  CAT  HAT1  single    0.970  0.020  1.090
 KKT  CAT  HAT2  single    0.970  0.020  1.090
 KKT  CAT  HAT3  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
 KKT  HAW   CAW  CAV   119.69  3.000
 KKT  HAW   CAW  CAX   119.71  3.000
 KKT  CAV   CAW  CAX   120.60  3.000
 KKT  HAX   CAX  CBA   120.24  3.000
 KKT  HAX   CAX  CAW   119.75  3.000
 KKT  CBA   CAX  CAW   120.01  3.000
 KKT  HBA   CBA  CAZ   120.16  3.000
 KKT  HBA   CBA  CAX   120.18  3.000
 KKT  CAZ   CBA  CAX   119.66  3.000
 KKT  HAZ   CAZ  CAY   119.62  3.000
 KKT  HAZ   CAZ  CBA   120.06  3.000
 KKT  CAY   CAZ  CBA   120.32  3.000
 KKT  HAY   CAY  CAV   120.53  3.000
 KKT  HAY   CAY  CAZ   119.17  3.000
 KKT  CAV   CAY  CAZ   120.30  3.000
 KKT  CAU   CAV  CAY   121.69  3.000
 KKT  CAU   CAV  CAW   119.16  3.000
 KKT  CAY   CAV  CAW   119.13  3.000
 KKT  HAU2  CAU  HAU1  106.32  3.000
 KKT  HAU2  CAU  NAN   107.14  3.000
 KKT  HAU1  CAU  NAN   108.68  3.000
 KKT  HAU2  CAU  CAV   109.86  3.000
 KKT  HAU1  CAU  CAV   110.66  3.000
 KKT  NAN   CAU  CAV   113.85  3.000
 KKT  CAM   NAN  CAO   121.72  3.000
 KKT  CAM   NAN  CAU   117.96  3.000
 KKT  CAO   NAN  CAU   120.28  3.000
 KKT  CAF   CAO  NAP   121.43  3.000
 KKT  CAF   CAO  NAN   120.57  3.000
 KKT  NAP   CAO  NAN   117.97  3.000
 KKT  HAP2  NAP  HAP1  115.72  3.000
 KKT  HAP2  NAP  CAO   117.07  3.000
 KKT  HAP1  NAP  CAO   122.46  3.000
 KKT  NAD   CAM  OAL   122.34  3.000
 KKT  NAD   CAM  NAN   115.42  3.000
 KKT  OAL   CAM  NAN   122.24  3.000
 KKT  HAD   NAD  CAE   116.88  3.000
 KKT  HAD   NAD  CAM   115.57  3.000
 KKT  CAE   NAD  CAM   127.55  3.000
 KKT  CAF   CAE  OAA   126.30  3.000
 KKT  CAF   CAE  NAD   114.19  3.000
 KKT  OAA   CAE  NAD   119.50  3.000
 KKT  NAG   CAF  CAE   120.99  3.000
 KKT  NAG   CAF  CAO   118.36  3.000
 KKT  CAE   CAF  CAO   120.47  3.000
 KKT  SAH   NAG  CAB   118.34  3.000
 KKT  SAH   NAG  CAF   117.58  3.000
 KKT  CAB   NAG  CAF   118.59  3.000
 KKT  HAB3  CAB  HAB2  108.78  3.000
 KKT  HAB3  CAB  HAB1  107.80  3.000
 KKT  HAB2  CAB  HAB1  109.25  3.000
 KKT  HAB3  CAB  NAG   107.82  3.000
 KKT  HAB2  CAB  NAG   112.63  3.000
 KKT  HAB1  CAB  NAG   110.43  3.000
 KKT  CAI   SAH  OAQ   108.29  3.000
 KKT  CAI   SAH  OAC   107.99  3.000
 KKT  OAQ   SAH  OAC   118.77  3.000
 KKT  CAI   SAH  NAG   108.09  3.000
 KKT  OAC   SAH  NAG   106.87  3.000
 KKT  OAQ   SAH  NAG   106.41  3.000
 KKT  HAI2  CAI  HAI1  108.09  3.000
 KKT  HAI2  CAI  CAJ   111.69  3.000
 KKT  HAI1  CAI  CAJ   111.57  3.000
 KKT  HAI2  CAI  SAH   107.39  3.000
 KKT  HAI1  CAI  SAH   106.66  3.000
 KKT  CAJ   CAI  SAH   111.20  3.000
 KKT  HAJ2  CAJ  HAJ1  107.04  3.000
 KKT  HAJ2  CAJ  CAK   109.16  3.000
 KKT  HAJ1  CAJ  CAK   109.70  3.000
 KKT  HAJ2  CAJ  CAI   109.78  3.000
 KKT  HAJ1  CAJ  CAI   110.06  3.000
 KKT  CAK   CAJ  CAI   111.01  3.000
 KKT  HAK2  CAK  HAK1  106.32  3.000
 KKT  HAK2  CAK  CAT   109.77  3.000
 KKT  HAK1  CAK  CAT   109.75  3.000
 KKT  HAK2  CAK  CAJ   109.59  3.000
 KKT  HAK1  CAK  CAJ   109.27  3.000
 KKT  CAT   CAK  CAJ   111.98  3.000
 KKT  HAT3  CAT  HAT2  107.61  3.000
 KKT  HAT3  CAT  HAT1  107.70  3.000
 KKT  HAT2  CAT  HAT1  107.72  3.000
 KKT  HAT3  CAT  CAK   111.08  3.000
 KKT  HAT2  CAT  CAK   111.24  3.000
 KKT  HAT1  CAT  CAK   111.32  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
 KKT  CONST_01  CAZ   CBA  CAX  CAW     0.00   0.0  0
 KKT  CONST_02  CAZ   CAY  CAV  CAW     0.00   0.0  0
 KKT  CONST_03  CAY   CAV  CAW  CAX     0.00   0.0  0
 KKT  CONST_04  CAY   CAZ  CBA  CAX     0.00   0.0  0
 KKT  CONST_05  CAV   CAW  CAX  CBA     0.00   0.0  0
 KKT  CONST_06  CAV   CAY  CAZ  CBA     0.00   0.0  0
 KKT  CONST_07  CAE   NAD  CAM  NAN     0.00   0.0  0
 KKT  CONST_08  NAD   CAM  NAN  CAO     0.00   0.0  0
 KKT  CONST_09  CAF   CAO  NAN  CAM     0.00   0.0  0
 KKT  CONST_10  CAF   CAE  NAD  CAM     0.00   0.0  0
 KKT  CONST_11  CAU   CAV  CAW  CAX   180.00   0.0  0
 KKT  CONST_12  CAU   CAV  CAY  CAZ   180.00   0.0  0
 KKT  CONST_13  CAF   CAO  NAN  CAU   180.00   0.0  0
 KKT  CONST_14  NAD   CAM  NAN  CAU   180.00   0.0  0
 KKT  CONST_15  OAL   CAM  NAN  CAO   180.00   0.0  0
 KKT  CONST_16  CAM   NAN  CAO  NAP   180.00   0.0  0
 KKT  CONST_17  OAA   CAE  NAD  CAM   180.00   0.0  0
 KKT  CONST_18  CAE   NAD  CAM  OAL   180.00   0.0  0
 KKT  CONST_19  HBA   CBA  CAX  CAW   180.00   0.0  0
 KKT  CONST_20  HAY   CAY  CAV  CAW   180.00   0.0  0
 KKT  CONST_21  HAZ   CAZ  CBA  CAX   180.00   0.0  0
 KKT  CONST_22  HAW   CAW  CAX  CBA   180.00   0.0  0
 KKT  CONST_23  HAX   CAX  CBA  CAZ   180.00   0.0  0
 KKT  CONST_24  HAD   NAD  CAM  NAN   180.00   0.0  0
 KKT  CONST_25  NAP   CAO  NAN  CAU     0.00   0.0  0
 KKT  CONST_26  OAL   CAM  NAN  CAU     0.00   0.0  0
 KKT  CONST_28  HAP2  NAP  CAO  NAN   180.00   0.0  0
 KKT  Var_01    NAN   CAU  CAV  CAW  -142.89  30.0  2
 KKT  Var_02    CAO   NAN  CAU  CAV    73.77  30.0  3
 KKT  Var_03    CAB   NAG  CAF  CAO  -111.43  30.0  2
 KKT  Var_04    OAQ   SAH  NAG  CAF   -34.14  30.0  3
 KKT  Var_05    HAB1  CAB  NAG  CAF   165.26  30.0  3
 KKT  Var_06    CAJ   CAI  SAH  NAG   176.51  30.0  3
 KKT  Var_07    CAK   CAJ  CAI  SAH   174.49  30.0  3
 KKT  Var_08    CAT   CAK  CAJ  CAI  -179.31  30.0  3
 KKT  Var_09    HAT1  CAT  CAK  CAJ   179.14  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
 KKT  plan-1  CAW   0.020
 KKT  plan-1  CAX   0.020
 KKT  plan-1  CBA   0.020
 KKT  plan-1  CAZ   0.020
 KKT  plan-1  CAY   0.020
 KKT  plan-1  CAV   0.020
 KKT  plan-1  CAU   0.020
 KKT  plan-1  HAW   0.020
 KKT  plan-1  HAX   0.020
 KKT  plan-1  HBA   0.020
 KKT  plan-1  HAZ   0.020
 KKT  plan-1  HAY   0.020
 KKT  plan-2  CAU   0.020
 KKT  plan-2  NAN   0.020
 KKT  plan-2  CAO   0.020
 KKT  plan-2  NAP   0.020
 KKT  plan-2  CAM   0.020
 KKT  plan-2  OAL   0.020
 KKT  plan-2  NAD   0.020
 KKT  plan-2  CAE   0.020
 KKT  plan-2  OAA   0.020
 KKT  plan-2  CAF   0.020
 KKT  plan-2  NAG   0.020
 KKT  plan-2  HAP1  0.020
 KKT  plan-2  HAP2  0.020
 KKT  plan-2  HAD   0.020

