# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:38:51 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N,3-dimethylbenzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1=C(N)N(Cc2ccccc2)C(=O)NC1=O)[S](=O)(=O)c3cccc(C)c3
#
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
 BBE  BBE  N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N,3-dimethylbenzenesulfonamide  ligand  48  28  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BBE
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
 BBE  CAY   C  CR16  0  -0.279  -4.4415  -0.3657  -0.8031
 BBE  CAZ   C  CR16  0  -0.239  -5.6287   0.1540  -1.2985
 BBE  CBA   C  CR16  0  -0.262  -6.4498   0.9251  -0.4850
 BBE  CAX   C  CR16  0  -0.242  -6.0751   1.1761   0.8271
 BBE  CAW   C  CR16  0  -0.297  -4.8837   0.6600   1.3208
 BBE  CAV   C  CR6   0   0.059  -4.0586  -0.1152   0.5117
 BBE  CAU   C  CH2   0  -0.410  -2.7920  -0.6971   1.0897
 BBE  NAN   N  NR6   0  -0.597  -1.6687  -0.6989   0.1574
 BBE  CAO   C  CR6   0   0.687  -1.0000   0.4692  -0.1230
 BBE  NAP   N  NH2   0  -0.817  -1.4668   1.5970   0.4106
 BBE  CAM   C  CR6   0   0.722  -1.2859  -1.9127  -0.3968
 BBE  OAL   O  O     0  -0.475  -1.8925  -2.9412  -0.1789
 BBE  NAD   N  NR16  0  -0.743  -0.1930  -1.8687  -1.2024
 BBE  CAE   C  CR6   0   0.586   0.5750  -0.7546  -1.5302
 BBE  OAA   O  O     0  -0.464   1.5054  -0.8701  -2.3103
 BBE  CAF   C  CR6   0  -0.101   0.1422   0.4524  -0.9071
 BBE  NAG   N  N     0  -0.632   0.7881   1.6757  -1.1887
 BBE  CAB   C  CH3   0  -0.522   0.8645   2.1351  -2.5765
 BBE  SAH   S  S     0   1.373   2.0488   2.0708  -0.1693
 BBE  OAQ   O  OS    0  -0.654   2.5838   3.3372  -0.6452
 BBE  OAC   O  OS    0  -0.649   1.5401   1.9764   1.1892
 BBE  CAI   C  CR6   0  -0.155   3.2769   0.8180  -0.3760
 BBE  CAJ   C  CR16  0  -0.256   4.2208   0.9569  -1.3848
 BBE  CAK   C  CR16  0  -0.231   5.1302  -0.0687  -1.5765
 BBE  CAT   C  CR16  0  -0.286   5.0872  -1.2039  -0.7770
 BBE  CAS   C  CR6   0   0.114   4.1460  -1.3381   0.2393
 BBE  CAR   C  CR16  0  -0.280   3.2359  -0.3035   0.4372
 BBE  CAL   C  CH3   0  -0.722   4.1101  -2.5542   1.1171
 BBE  HAY   H  HCR6  0   0.255  -3.8174  -0.9662  -1.4530
 BBE  HAZ   H  HCR6  0   0.261  -5.9126  -0.0452  -2.3236
 BBE  HBA   H  HCR6  0   0.261  -7.3744   1.3309  -0.8738
 BBE  HAX   H  HCR6  0   0.262  -6.7043   1.7805   1.4671
 BBE  HAW   H  HCR6  0   0.264  -4.5944   0.8645   2.3454
 BBE  HAU1  H  HCH2  0   0.294  -2.4953  -0.1601   1.9920
 BBE  HAU2  H  HCH2  0   0.316  -2.9620  -1.7276   1.3922
 BBE  HAP1  H  HNH2  0   0.427  -2.4098   1.6855   0.7490
 BBE  HAP2  H  HNH2  0   0.418  -1.0089   2.4553   0.1519
 BBE  HAD   H  HNR6  0   0.424   0.0731  -2.7473  -1.6286
 BBE  HAB1  H  HCH3  0   0.260   0.9257   3.2190  -2.6144
 BBE  HAB2  H  HCH3  0   0.243   1.7011   1.7027  -3.1263
 BBE  HAB3  H  HCH3  0   0.262  -0.0592   1.8331  -3.0636
 BBE  HAJ   H  HCR6  0   0.275   4.2521   1.8413  -2.0065
 BBE  HAR   H  HCR6  0   0.275   2.4993  -0.3842   1.2264
 BBE  HAK   H  HCR6  0   0.267   5.8779   0.0152  -2.3537
 BBE  HAT   H  HCR6  0   0.260   5.8046  -1.9979  -0.9454
 BBE  HAL1  H  HCH3  0   0.253   4.4414  -2.3164   2.1293
 BBE  HAL2  H  HCH3  0   0.248   3.0996  -2.9563   1.1959
 BBE  HAL3  H  HCH3  0   0.248   4.7567  -3.3423   0.7341

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
 BBE  CAY  CAZ   aromatic  1.387  0.020  1.387
 BBE  CAY  CAV   aromatic  1.392  0.020  1.392
 BBE  CAZ  CBA   aromatic  1.389  0.020  1.389
 BBE  CBA  CAX   aromatic  1.387  0.020  1.387
 BBE  CAX  CAW   aromatic  1.389  0.020  1.389
 BBE  CAW  CAV   aromatic  1.392  0.020  1.392
 BBE  CAV  CAU   single    1.509  0.020  1.509
 BBE  CAU  NAN   single    1.460  0.020  1.460
 BBE  NAN  CAO   single    1.375  0.020  1.375
 BBE  NAN  CAM   single    1.388  0.020  1.388
 BBE  CAO  NAP   single    1.332  0.020  1.332
 BBE  CAO  CAF   double    1.386  0.020  1.386
 BBE  CAM  OAL   double    1.214  0.020  1.214
 BBE  CAM  NAD   single    1.359  0.020  1.359
 BBE  NAD  CAE   single    1.392  0.020  1.392
 BBE  CAE  OAA   double    1.220  0.020  1.220
 BBE  CAE  CAF   single    1.426  0.020  1.426
 BBE  CAF  NAG   single    1.412  0.020  1.412
 BBE  NAG  CAB   single    1.464  0.020  1.464
 BBE  NAG  SAH   single    1.669  0.020  1.669
 BBE  SAH  OAC   double    1.454  0.020  1.454
 BBE  SAH  OAQ   double    1.455  0.020  1.455
 BBE  SAH  CAI   single    1.766  0.020  1.766
 BBE  CAI  CAJ   aromatic  1.389  0.020  1.389
 BBE  CAI  CAR   aromatic  1.386  0.020  1.386
 BBE  CAJ  CAK   aromatic  1.384  0.020  1.384
 BBE  CAK  CAT   aromatic  1.389  0.020  1.389
 BBE  CAT  CAS   aromatic  1.392  0.020  1.392
 BBE  CAS  CAR   aromatic  1.392  0.020  1.392
 BBE  CAS  CAL   single    1.500  0.020  1.500
 BBE  CAY  HAY   single    0.930  0.020  1.080
 BBE  CAZ  HAZ   single    0.930  0.020  1.080
 BBE  CBA  HBA   single    0.930  0.020  1.080
 BBE  CAX  HAX   single    0.930  0.020  1.080
 BBE  CAW  HAW   single    0.930  0.020  1.080
 BBE  CAU  HAU1  single    0.970  0.020  1.090
 BBE  CAU  HAU2  single    0.970  0.020  1.090
 BBE  NAP  HAP1  single    0.890  0.020  1.040
 BBE  NAP  HAP2  single    0.890  0.020  1.040
 BBE  NAD  HAD   single    0.860  0.020  1.020
 BBE  CAB  HAB1  single    0.970  0.020  1.090
 BBE  CAB  HAB2  single    0.970  0.020  1.090
 BBE  CAB  HAB3  single    0.970  0.020  1.090
 BBE  CAJ  HAJ   single    0.930  0.020  1.080
 BBE  CAR  HAR   single    0.930  0.020  1.080
 BBE  CAK  HAK   single    0.930  0.020  1.080
 BBE  CAT  HAT   single    0.930  0.020  1.080
 BBE  CAL  HAL1  single    0.970  0.020  1.090
 BBE  CAL  HAL2  single    0.970  0.020  1.090
 BBE  CAL  HAL3  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
 BBE  HAY   CAY  CAV   120.54  3.000
 BBE  HAY   CAY  CAZ   119.12  3.000
 BBE  CAV   CAY  CAZ   120.34  3.000
 BBE  HAZ   CAZ  CBA   120.11  3.000
 BBE  HAZ   CAZ  CAY   119.59  3.000
 BBE  CBA   CAZ  CAY   120.30  3.000
 BBE  HBA   CBA  CAX   120.18  3.000
 BBE  HBA   CBA  CAZ   120.18  3.000
 BBE  CAX   CBA  CAZ   119.64  3.000
 BBE  HAX   CAX  CAW   119.74  3.000
 BBE  HAX   CAX  CBA   120.22  3.000
 BBE  CAW   CAX  CBA   120.03  3.000
 BBE  HAW   CAW  CAV   119.76  3.000
 BBE  HAW   CAW  CAX   119.65  3.000
 BBE  CAV   CAW  CAX   120.59  3.000
 BBE  CAU   CAV  CAW   119.33  3.000
 BBE  CAU   CAV  CAY   121.55  3.000
 BBE  CAW   CAV  CAY   119.10  3.000
 BBE  HAU2  CAU  HAU1  106.19  3.000
 BBE  HAU2  CAU  NAN   107.27  3.000
 BBE  HAU1  CAU  NAN   108.63  3.000
 BBE  HAU2  CAU  CAV   109.93  3.000
 BBE  HAU1  CAU  CAV   110.80  3.000
 BBE  NAN   CAU  CAV   113.69  3.000
 BBE  CAM   NAN  CAO   121.83  3.000
 BBE  CAM   NAN  CAU   117.92  3.000
 BBE  CAO   NAN  CAU   120.23  3.000
 BBE  CAF   CAO  NAP   121.73  3.000
 BBE  CAF   CAO  NAN   120.40  3.000
 BBE  NAP   CAO  NAN   117.85  3.000
 BBE  HAP2  NAP  HAP1  115.97  3.000
 BBE  HAP2  NAP  CAO   117.35  3.000
 BBE  HAP1  NAP  CAO   122.54  3.000
 BBE  NAD   CAM  OAL   122.41  3.000
 BBE  NAD   CAM  NAN   115.48  3.000
 BBE  OAL   CAM  NAN   122.11  3.000
 BBE  HAD   NAD  CAE   116.78  3.000
 BBE  HAD   NAD  CAM   115.66  3.000
 BBE  CAE   NAD  CAM   127.54  3.000
 BBE  CAF   CAE  OAA   126.25  3.000
 BBE  CAF   CAE  NAD   114.02  3.000
 BBE  OAA   CAE  NAD   119.71  3.000
 BBE  NAG   CAF  CAE   120.50  3.000
 BBE  NAG   CAF  CAO   118.65  3.000
 BBE  CAE   CAF  CAO   120.52  3.000
 BBE  SAH   NAG  CAB   117.74  3.000
 BBE  SAH   NAG  CAF   115.40  3.000
 BBE  CAB   NAG  CAF   119.00  3.000
 BBE  HAB3  CAB  HAB2  108.41  3.000
 BBE  HAB3  CAB  HAB1  108.02  3.000
 BBE  HAB2  CAB  HAB1  109.56  3.000
 BBE  HAB3  CAB  NAG   107.06  3.000
 BBE  HAB2  CAB  NAG   113.18  3.000
 BBE  HAB1  CAB  NAG   110.43  3.000
 BBE  CAI   SAH  OAC   107.85  3.000
 BBE  CAI   SAH  OAQ   108.87  3.000
 BBE  OAC   SAH  OAQ   119.40  3.000
 BBE  CAI   SAH  NAG   106.61  3.000
 BBE  OAQ   SAH  NAG   106.51  3.000
 BBE  OAC   SAH  NAG   106.93  3.000
 BBE  CAR   CAI  CAJ   121.82  3.000
 BBE  CAR   CAI  SAH   119.00  3.000
 BBE  CAJ   CAI  SAH   119.12  3.000
 BBE  HAJ   CAJ  CAK   120.49  3.000
 BBE  HAJ   CAJ  CAI   121.27  3.000
 BBE  CAK   CAJ  CAI   118.24  3.000
 BBE  HAK   CAK  CAT   119.89  3.000
 BBE  HAK   CAK  CAJ   119.74  3.000
 BBE  CAT   CAK  CAJ   120.37  3.000
 BBE  HAT   CAT  CAS   119.39  3.000
 BBE  HAT   CAT  CAK   119.28  3.000
 BBE  CAS   CAT  CAK   121.33  3.000
 BBE  CAL   CAS  CAR   120.24  3.000
 BBE  CAL   CAS  CAT   121.44  3.000
 BBE  CAR   CAS  CAT   118.32  3.000
 BBE  HAR   CAR  CAS   119.55  3.000
 BBE  HAR   CAR  CAI   120.54  3.000
 BBE  CAS   CAR  CAI   119.92  3.000
 BBE  HAL3  CAL  HAL2  107.98  3.000
 BBE  HAL3  CAL  HAL1  107.68  3.000
 BBE  HAL2  CAL  HAL1  107.14  3.000
 BBE  HAL3  CAL  CAS   111.51  3.000
 BBE  HAL2  CAL  CAS   111.30  3.000
 BBE  HAL1  CAL  CAS   111.03  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
 BBE  CONST_01  CAX   CBA  CAZ  CAY     0.00   0.0  0
 BBE  CONST_02  CAX   CAW  CAV  CAY     0.00   0.0  0
 BBE  CONST_03  CAW   CAV  CAY  CAZ     0.00   0.0  0
 BBE  CONST_04  CAW   CAX  CBA  CAZ     0.00   0.0  0
 BBE  CONST_05  CAV   CAY  CAZ  CBA     0.00   0.0  0
 BBE  CONST_06  CAV   CAW  CAX  CBA     0.00   0.0  0
 BBE  CONST_07  CAT   CAK  CAJ  CAI     0.00   0.0  0
 BBE  CONST_08  CAT   CAS  CAR  CAI     0.00   0.0  0
 BBE  CONST_09  CAS   CAR  CAI  CAJ     0.00   0.0  0
 BBE  CONST_10  CAS   CAT  CAK  CAJ     0.00   0.0  0
 BBE  CONST_11  CAR   CAI  CAJ  CAK     0.00   0.0  0
 BBE  CONST_12  CAR   CAS  CAT  CAK     0.00   0.0  0
 BBE  CONST_13  CAE   NAD  CAM  NAN     0.00   0.0  0
 BBE  CONST_14  NAD   CAM  NAN  CAO     0.00   0.0  0
 BBE  CONST_15  CAF   CAO  NAN  CAM     0.00   0.0  0
 BBE  CONST_16  CAF   CAE  NAD  CAM     0.00   0.0  0
 BBE  CONST_17  CAU   CAV  CAY  CAZ   180.00   0.0  0
 BBE  CONST_18  CAU   CAV  CAW  CAX   180.00   0.0  0
 BBE  CONST_19  CAK   CAJ  CAI  SAH   180.00   0.0  0
 BBE  CONST_20  CAS   CAR  CAI  SAH   180.00   0.0  0
 BBE  CONST_21  CAL   CAS  CAR  CAI   180.00   0.0  0
 BBE  CONST_22  CAL   CAS  CAT  CAK   180.00   0.0  0
 BBE  CONST_23  CAF   CAO  NAN  CAU   180.00   0.0  0
 BBE  CONST_24  NAD   CAM  NAN  CAU   180.00   0.0  0
 BBE  CONST_25  OAL   CAM  NAN  CAO   180.00   0.0  0
 BBE  CONST_26  CAM   NAN  CAO  NAP   180.00   0.0  0
 BBE  CONST_27  OAA   CAE  NAD  CAM   180.00   0.0  0
 BBE  CONST_28  CAE   NAD  CAM  OAL   180.00   0.0  0
 BBE  CONST_29  HBA   CBA  CAZ  CAY   180.00   0.0  0
 BBE  CONST_30  HAW   CAW  CAV  CAY   180.00   0.0  0
 BBE  CONST_31  HAX   CAX  CBA  CAZ   180.00   0.0  0
 BBE  CONST_32  HAY   CAY  CAZ  CBA   180.00   0.0  0
 BBE  CONST_33  HAZ   CAZ  CBA  CAX   180.00   0.0  0
 BBE  CONST_34  HAK   CAK  CAJ  CAI   180.00   0.0  0
 BBE  CONST_35  HAR   CAR  CAI  CAJ   180.00   0.0  0
 BBE  CONST_36  HAT   CAT  CAK  CAJ   180.00   0.0  0
 BBE  CONST_37  HAJ   CAJ  CAK  CAT   180.00   0.0  0
 BBE  CONST_38  HAD   NAD  CAM  NAN   180.00   0.0  0
 BBE  CONST_39  NAP   CAO  NAN  CAU     0.00   0.0  0
 BBE  CONST_40  OAL   CAM  NAN  CAU     0.00   0.0  0
 BBE  CONST_42  HAP2  NAP  CAO  NAN   180.00   0.0  0
 BBE  Var_01    NAN   CAU  CAV  CAY    39.52  30.0  2
 BBE  Var_02    CAO   NAN  CAU  CAV    75.37  30.0  3
 BBE  Var_03    CAB   NAG  CAF  CAO  -116.57  30.0  2
 BBE  Var_04    CAI   SAH  NAG  CAF    62.79  30.0  3
 BBE  Var_05    CAJ   CAI  SAH  NAG    86.87  30.0  2
 BBE  Var_06    HAL1  CAL  CAS  CAT   109.35  30.0  2
 BBE  Var_07    HAB1  CAB  NAG  CAF   152.67  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
 BBE  plan-1  CAY   0.020
 BBE  plan-1  CAZ   0.020
 BBE  plan-1  CBA   0.020
 BBE  plan-1  CAX   0.020
 BBE  plan-1  CAW   0.020
 BBE  plan-1  CAV   0.020
 BBE  plan-1  CAU   0.020
 BBE  plan-1  HAY   0.020
 BBE  plan-1  HAZ   0.020
 BBE  plan-1  HBA   0.020
 BBE  plan-1  HAX   0.020
 BBE  plan-1  HAW   0.020
 BBE  plan-2  CAU   0.020
 BBE  plan-2  NAN   0.020
 BBE  plan-2  CAO   0.020
 BBE  plan-2  NAP   0.020
 BBE  plan-2  CAM   0.020
 BBE  plan-2  OAL   0.020
 BBE  plan-2  NAD   0.020
 BBE  plan-2  CAE   0.020
 BBE  plan-2  OAA   0.020
 BBE  plan-2  CAF   0.020
 BBE  plan-2  NAG   0.020
 BBE  plan-2  HAP1  0.020
 BBE  plan-2  HAP2  0.020
 BBE  plan-2  HAD   0.020
 BBE  plan-3  SAH   0.020
 BBE  plan-3  CAI   0.020
 BBE  plan-3  CAJ   0.020
 BBE  plan-3  CAK   0.020
 BBE  plan-3  CAT   0.020
 BBE  plan-3  CAS   0.020
 BBE  plan-3  CAR   0.020
 BBE  plan-3  CAL   0.020
 BBE  plan-3  HAJ   0.020
 BBE  plan-3  HAR   0.020
 BBE  plan-3  HAK   0.020
 BBE  plan-3  HAT   0.020

