# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 11:04:01 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-[6-amino-1-(3-bromobenzyl)-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(Cc2cccc(Br)c2)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
 HKX  HKX  N-[6-amino-1-(3-bromobenzyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl]-N-methylbenzenesulfonamide  ligand  45  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HKX
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
 HKX  OAA   O   O     0  -0.462  -3.5984   3.0660  -0.9760
 HKX  CAB   C   CH3   0  -0.517  -3.4587   0.4675  -2.8504
 HKX  OAC   O   OS    0  -0.635  -4.1416   0.5506   0.6635
 HKX  NAD   N   NR16  0  -0.741  -1.4697   3.6090  -0.4434
 HKX  CAE   C   CR6   0   0.574  -2.4400   2.7052  -0.8651
 HKX  CAF   C   CR6   0  -0.082  -1.9323   1.3985  -1.1347
 HKX  NAG   N   N     0  -0.656  -2.7974   0.3640  -1.5473
 HKX  SAH   S   S     0   1.375  -3.6163  -0.3987  -0.3038
 HKX  CAI   C   CR6   0  -0.202  -2.3008  -1.2866   0.4802
 HKX  CAJ   C   CR16  0  -0.231  -1.6603  -0.7323   1.5788
 HKX  CAK   C   CR16  0  -0.226  -0.5814  -1.4045   2.1347
 HKX  CAM   C   CR6   0   0.738  -0.1382   3.3838  -0.2899
 HKX  NAN   N   NR6   0  -0.590   0.3007   2.1165  -0.6498
 HKX  CAO   C   CR6   0   0.677  -0.5730   1.1473  -1.0794
 HKX  OAP   O   OS    0  -0.654  -4.5322  -1.3401  -0.9308
 HKX  CAQ   C   CR16  0  -0.247  -1.9004  -2.5043  -0.0577
 HKX  CAR   C   CR16  0  -0.245  -0.8227  -3.1661   0.5097
 HKX  CAS   C   CR16  0  -0.229  -0.1595  -2.6129   1.5987
 HKX  CAT   C   CH2   0  -0.455   1.7379   1.8499  -0.5876
 HKX  NAU   N   NH2   0  -0.822  -0.0630  -0.0220  -1.4858
 HKX  CAV   C   CR16  0  -0.309   2.7888  -0.1775   0.4488
 HKX  CAW   C   CR6   0   0.131   2.1335   1.0361   0.6200
 HKX  CAX   C   CR16  0  -0.278   1.8700   1.4946   1.9085
 HKX  CAY   C   CR6   0  -0.092   3.1589  -0.9229   1.5602
 HKX  CAZ   C   CR16  0  -0.237   2.9002  -0.4761   2.8442
 HKX  CBA   C   CR16  0  -0.236   2.2556   0.7444   3.0065
 HKX  BR1   BR  BR    0  -0.038   4.0225  -2.5823   1.3086
 HKX  HAB   H   HCH3  0   0.260  -3.7521  -0.5151  -3.2094
 HKX  HABA  H   HCH3  0   0.245  -4.3268   1.1261  -2.8383
 HKX  HABB  H   HCH3  0   0.261  -2.7251   0.8724  -3.5434
 HKX  HNAD  H   HNR6  0   0.426  -1.7857   4.5408  -0.2056
 HKX  HAJ   H   HCR6  0   0.286  -1.9833   0.2114   1.9965
 HKX  HAK   H   HCR6  0   0.272  -0.0692  -0.9796   2.9862
 HKX  HAQ   H   HCR6  0   0.289  -2.4146  -2.9342  -0.9075
 HKX  HAR   H   HCR6  0   0.275  -0.5017  -4.1141   0.0999
 HKX  HAS   H   HCR6  0   0.267   0.6852  -3.1308   2.0335
 HKX  HAT   H   HCH2  0   0.304   2.0424   1.3564  -1.5109
 HKX  HATA  H   HCH2  0   0.321   2.2473   2.8095  -0.5735
 HKX  HNAU  H   HNH2  0   0.422  -0.7320  -0.7319  -1.7384
 HKX  HNAA  H   HNH2  0   0.424   0.7993  -0.3794  -1.1119
 HKX  HAV   H   HCR6  0   0.293   3.0153  -0.5331  -0.5500
 HKX  HAX   H   HCR6  0   0.265   1.3779   2.4460   2.0627
 HKX  HAZ   H   HCR6  0   0.284   3.1892  -1.0566   3.7098
 HKX  HBA   H   HCR6  0   0.276   2.0535   1.1068   4.0055
 HKX  OAL   O   O     0  -0.478   0.6214   4.2354   0.1233

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
 HKX  OAA  CAE   double    1.218  0.020  1.218
 HKX  CAB  NAG   single    1.465  0.020  1.465
 HKX  OAC  SAH   double    1.454  0.020  1.454
 HKX  NAD  CAE   single    1.391  0.020  1.391
 HKX  NAD  CAM   single    1.359  0.020  1.359
 HKX  CAE  CAF   single    1.428  0.020  1.428
 HKX  CAF  NAG   single    1.410  0.020  1.410
 HKX  CAF  CAO   double    1.383  0.020  1.383
 HKX  NAG  SAH   single    1.673  0.020  1.673
 HKX  SAH  CAI   single    1.770  0.020  1.770
 HKX  SAH  OAP   double    1.455  0.020  1.455
 HKX  CAI  CAJ   aromatic  1.387  0.020  1.387
 HKX  CAI  CAQ   aromatic  1.390  0.020  1.390
 HKX  CAJ  CAK   aromatic  1.387  0.020  1.387
 HKX  CAK  CAS   aromatic  1.388  0.020  1.388
 HKX  OAL  CAM   double    1.214  0.020  1.214
 HKX  CAM  NAN   single    1.389  0.020  1.389
 HKX  NAN  CAO   single    1.374  0.020  1.374
 HKX  NAN  CAT   single    1.463  0.020  1.463
 HKX  CAO  NAU   single    1.339  0.020  1.339
 HKX  CAQ  CAR   aromatic  1.386  0.020  1.386
 HKX  CAR  CAS   aromatic  1.390  0.020  1.390
 HKX  CAT  CAW   single    1.509  0.020  1.509
 HKX  CAV  CAW   aromatic  1.390  0.020  1.390
 HKX  CAV  CAY   aromatic  1.388  0.020  1.388
 HKX  CAW  CAX   aromatic  1.393  0.020  1.393
 HKX  CAX  CBA   aromatic  1.385  0.020  1.385
 HKX  CAY  CAZ   aromatic  1.384  0.020  1.384
 HKX  CAY  BR1   single    1.888  0.020  1.888
 HKX  CAZ  CBA   aromatic  1.390  0.020  1.390
 HKX  CAB  HAB   single    0.970  0.020  1.090
 HKX  CAB  HABA  single    0.970  0.020  1.090
 HKX  CAB  HABB  single    0.970  0.020  1.090
 HKX  NAD  HNAD  single    0.860  0.020  1.020
 HKX  CAJ  HAJ   single    0.930  0.020  1.080
 HKX  CAK  HAK   single    0.930  0.020  1.080
 HKX  CAQ  HAQ   single    0.930  0.020  1.080
 HKX  CAR  HAR   single    0.930  0.020  1.080
 HKX  CAS  HAS   single    0.930  0.020  1.080
 HKX  CAT  HAT   single    0.970  0.020  1.090
 HKX  CAT  HATA  single    0.970  0.020  1.090
 HKX  NAU  HNAU  single    0.890  0.020  1.040
 HKX  NAU  HNAA  single    0.890  0.020  1.040
 HKX  CAV  HAV   single    0.930  0.020  1.080
 HKX  CAX  HAX   single    0.930  0.020  1.080
 HKX  CAZ  HAZ   single    0.930  0.020  1.080
 HKX  CBA  HBA   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
 HKX  HABB  CAB  HABA  108.63  3.000
 HKX  HABB  CAB  HAB   107.95  3.000
 HKX  HABA  CAB  HAB   109.58  3.000
 HKX  HABB  CAB  NAG   106.78  3.000
 HKX  HABA  CAB  NAG   113.11  3.000
 HKX  HAB   CAB  NAG   110.61  3.000
 HKX  HNAD  NAD  CAM   115.58  3.000
 HKX  HNAD  NAD  CAE   116.83  3.000
 HKX  CAM   NAD  CAE   127.58  3.000
 HKX  CAF   CAE  NAD   113.81  3.000
 HKX  CAF   CAE  OAA   126.30  3.000
 HKX  NAD   CAE  OAA   119.88  3.000
 HKX  CAO   CAF  NAG   118.77  3.000
 HKX  CAO   CAF  CAE   120.54  3.000
 HKX  NAG   CAF  CAE   120.57  3.000
 HKX  SAH   NAG  CAF   114.66  3.000
 HKX  SAH   NAG  CAB   118.19  3.000
 HKX  CAF   NAG  CAB   119.03  3.000
 HKX  OAP   SAH  CAI   109.51  3.000
 HKX  OAP   SAH  NAG   106.42  3.000
 HKX  CAI   SAH  NAG   101.20  3.000
 HKX  OAP   SAH  OAC   118.79  3.000
 HKX  CAI   SAH  OAC   107.54  3.000
 HKX  NAG   SAH  OAC   111.95  3.000
 HKX  CAQ   CAI  CAJ   121.56  3.000
 HKX  CAQ   CAI  SAH   118.82  3.000
 HKX  CAJ   CAI  SAH   119.56  3.000
 HKX  HAJ   CAJ  CAK   120.02  3.000
 HKX  HAJ   CAJ  CAI   121.11  3.000
 HKX  CAK   CAJ  CAI   118.86  3.000
 HKX  HAK   CAK  CAS   120.18  3.000
 HKX  HAK   CAK  CAJ   119.58  3.000
 HKX  CAS   CAK  CAJ   120.24  3.000
 HKX  NAN   CAM  OAL   122.06  3.000
 HKX  NAN   CAM  NAD   115.56  3.000
 HKX  OAL   CAM  NAD   122.37  3.000
 HKX  CAT   NAN  CAO   120.63  3.000
 HKX  CAT   NAN  CAM   117.76  3.000
 HKX  CAO   NAN  CAM   121.60  3.000
 HKX  NAU   CAO  NAN   117.96  3.000
 HKX  NAU   CAO  CAF   121.38  3.000
 HKX  NAN   CAO  CAF   120.61  3.000
 HKX  HAQ   CAQ  CAR   120.08  3.000
 HKX  HAQ   CAQ  CAI   120.99  3.000
 HKX  CAR   CAQ  CAI   118.93  3.000
 HKX  HAR   CAR  CAS   120.28  3.000
 HKX  HAR   CAR  CAQ   119.61  3.000
 HKX  CAS   CAR  CAQ   120.11  3.000
 HKX  HAS   CAS  CAR   119.79  3.000
 HKX  HAS   CAS  CAK   119.93  3.000
 HKX  CAR   CAS  CAK   120.28  3.000
 HKX  HATA  CAT  HAT   106.25  3.000
 HKX  HATA  CAT  CAW   110.06  3.000
 HKX  HAT   CAT  CAW   111.12  3.000
 HKX  HATA  CAT  NAN   107.47  3.000
 HKX  HAT   CAT  NAN   108.71  3.000
 HKX  CAW   CAT  NAN   112.94  3.000
 HKX  HNAA  NAU  HNAU  114.34  3.000
 HKX  HNAA  NAU  CAO   121.61  3.000
 HKX  HNAU  NAU  CAO   116.01  3.000
 HKX  HAV   CAV  CAY   120.38  3.000
 HKX  HAV   CAV  CAW   119.89  3.000
 HKX  CAY   CAV  CAW   119.73  3.000
 HKX  CAX   CAW  CAV   119.39  3.000
 HKX  CAX   CAW  CAT   120.87  3.000
 HKX  CAV   CAW  CAT   119.73  3.000
 HKX  HAX   CAX  CBA   119.34  3.000
 HKX  HAX   CAX  CAW   120.49  3.000
 HKX  CBA   CAX  CAW   120.17  3.000
 HKX  BR1   CAY  CAZ   119.54  3.000
 HKX  BR1   CAY  CAV   119.16  3.000
 HKX  CAZ   CAY  CAV   121.30  3.000
 HKX  HAZ   CAZ  CBA   120.12  3.000
 HKX  HAZ   CAZ  CAY   121.29  3.000
 HKX  CBA   CAZ  CAY   118.59  3.000
 HKX  HBA   CBA  CAZ   119.25  3.000
 HKX  HBA   CBA  CAX   119.92  3.000
 HKX  CAZ   CBA  CAX   120.82  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
 HKX  CONST_01  CAS   CAK  CAJ  CAI    0.00   0.0  0
 HKX  CONST_02  CAS   CAR  CAQ  CAI    0.00   0.0  0
 HKX  CONST_03  CAR   CAQ  CAI  CAJ    0.00   0.0  0
 HKX  CONST_04  CAR   CAS  CAK  CAJ    0.00   0.0  0
 HKX  CONST_05  CAQ   CAI  CAJ  CAK    0.00   0.0  0
 HKX  CONST_06  CAQ   CAR  CAS  CAK    0.00   0.0  0
 HKX  CONST_07  CBA   CAX  CAW  CAV    0.00   0.0  0
 HKX  CONST_08  CBA   CAZ  CAY  CAV    0.00   0.0  0
 HKX  CONST_09  CAZ   CAY  CAV  CAW    0.00   0.0  0
 HKX  CONST_10  CAZ   CBA  CAX  CAW    0.00   0.0  0
 HKX  CONST_11  CAY   CAV  CAW  CAX    0.00   0.0  0
 HKX  CONST_12  CAY   CAZ  CBA  CAX    0.00   0.0  0
 HKX  CONST_13  CAO   NAN  CAM  NAD    0.00   0.0  0
 HKX  CONST_14  NAN   CAM  NAD  CAE    0.00   0.0  0
 HKX  CONST_15  CAM   NAD  CAE  CAF    0.00   0.0  0
 HKX  CONST_16  CAM   NAN  CAO  CAF    0.00   0.0  0
 HKX  CONST_17  CAK   CAJ  CAI  SAH  180.00   0.0  0
 HKX  CONST_18  CAR   CAQ  CAI  SAH  180.00   0.0  0
 HKX  CONST_19  CAY   CAV  CAW  CAT  180.00   0.0  0
 HKX  CONST_20  CBA   CAX  CAW  CAT  180.00   0.0  0
 HKX  CONST_21  BR1   CAY  CAV  CAW  180.00   0.0  0
 HKX  CONST_22  BR1   CAY  CAZ  CBA  180.00   0.0  0
 HKX  CONST_23  CAM   NAD  CAE  OAA  180.00   0.0  0
 HKX  CONST_24  CAT   NAN  CAM  NAD  180.00   0.0  0
 HKX  CONST_25  OAL   CAM  NAD  CAE  180.00   0.0  0
 HKX  CONST_26  CAT   NAN  CAO  CAF  180.00   0.0  0
 HKX  CONST_27  CAO   NAN  CAM  OAL  180.00   0.0  0
 HKX  CONST_28  NAU   CAO  NAN  CAM  180.00   0.0  0
 HKX  CONST_29  HAK   CAK  CAJ  CAI  180.00   0.0  0
 HKX  CONST_30  HAR   CAR  CAQ  CAI  180.00   0.0  0
 HKX  CONST_31  HAQ   CAQ  CAI  CAJ  180.00   0.0  0
 HKX  CONST_32  HAS   CAS  CAK  CAJ  180.00   0.0  0
 HKX  CONST_33  HAJ   CAJ  CAI  CAQ  180.00   0.0  0
 HKX  CONST_34  HAX   CAX  CAW  CAV  180.00   0.0  0
 HKX  CONST_35  HAZ   CAZ  CAY  CAV  180.00   0.0  0
 HKX  CONST_36  HBA   CBA  CAX  CAW  180.00   0.0  0
 HKX  CONST_37  HAV   CAV  CAW  CAX  180.00   0.0  0
 HKX  CONST_38  HNAD  NAD  CAE  CAF  180.00   0.0  0
 HKX  CONST_39  CAT   NAN  CAM  OAL    0.00   0.0  0
 HKX  CONST_40  NAU   CAO  NAN  CAT    0.00   0.0  0
 HKX  CONST_41  HNAU  NAU  CAO  CAF    0.00   0.0  0
 HKX  Var_01    CAW   CAT  NAN  CAM  103.20  30.0  3
 HKX  Var_02    CAV   CAW  CAT  NAN  122.00  30.0  2
 HKX  Var_03    CAE   CAF  NAG  CAB   66.18  30.0  3
 HKX  Var_04    CAJ   CAI  SAH  OAC  -21.84  30.0  2
 HKX  Var_05    CAI   SAH  NAG  CAF  -70.44  30.0  3
 HKX  Var_06    HAB   CAB  NAG  CAF  157.28  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
 HKX  plan-1  OAA   0.020
 HKX  plan-1  NAD   0.020
 HKX  plan-1  CAE   0.020
 HKX  plan-1  CAF   0.020
 HKX  plan-1  NAG   0.020
 HKX  plan-1  CAM   0.020
 HKX  plan-1  NAN   0.020
 HKX  plan-1  CAO   0.020
 HKX  plan-1  CAT   0.020
 HKX  plan-1  NAU   0.020
 HKX  plan-1  HNAD  0.020
 HKX  plan-1  HNAU  0.020
 HKX  plan-1  HNAA  0.020
 HKX  plan-1  OAL   0.020
 HKX  plan-2  SAH   0.020
 HKX  plan-2  CAI   0.020
 HKX  plan-2  CAJ   0.020
 HKX  plan-2  CAK   0.020
 HKX  plan-2  CAQ   0.020
 HKX  plan-2  CAR   0.020
 HKX  plan-2  CAS   0.020
 HKX  plan-2  HAJ   0.020
 HKX  plan-2  HAK   0.020
 HKX  plan-2  HAQ   0.020
 HKX  plan-2  HAR   0.020
 HKX  plan-2  HAS   0.020
 HKX  plan-3  CAT   0.020
 HKX  plan-3  CAV   0.020
 HKX  plan-3  CAW   0.020
 HKX  plan-3  CAX   0.020
 HKX  plan-3  CAY   0.020
 HKX  plan-3  CAZ   0.020
 HKX  plan-3  CBA   0.020
 HKX  plan-3  BR1   0.020
 HKX  plan-3  HAV   0.020
 HKX  plan-3  HAX   0.020
 HKX  plan-3  HAZ   0.020
 HKX  plan-3  HBA   0.020

