# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 08:52:54 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-[6-azanyl-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-N-methyl-benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1=C(N)N(Cc2ccc(Br)cc2)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
 KDT  KDT  N-[6-azanyl-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-N-methyl-benzenesulfonamide  ligand  45  28  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KDT
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
 KDT  CAW   C   CR16  0  -0.295  -3.6230  -2.2836  -0.5259
 KDT  CAX   C   CR16  0  -0.214  -4.9278  -1.8105  -0.5267
 KDT  CBA   C   CR6   0  -0.123  -5.2454  -0.7149   0.2603
 KDT  BRBB  BR  BR    0  -0.044  -7.0131  -0.0520   0.2651
 KDT  CAZ   C   CR16  0  -0.210  -4.2826  -0.0957   1.0442
 KDT  CAY   C   CR16  0  -0.292  -2.9865  -0.5886   1.0375
 KDT  CAV   C   CR6   0   0.153  -2.6413  -1.6859   0.2538
 KDT  CAT   C   CH2   0  -0.445  -1.2386  -2.2358   0.2448
 KDT  NAN   N   NR6   0  -0.590  -0.2377  -1.2202  -0.0842
 KDT  CAO   C   CR6   0   0.686   0.5222  -0.5801   0.8645
 KDT  NAU   N   NH2   0  -0.827   0.3192  -0.8600   2.1517
 KDT  CAM   C   CR6   0   0.730  -0.1587  -0.8865  -1.4302
 KDT  OAL   O   O     0  -0.467  -0.8472  -1.4404  -2.2602
 KDT  NAD   N   NR16  0  -0.741   0.7273   0.0939  -1.7470
 KDT  CAE   C   CR6   0   0.584   1.5563   0.7926  -0.8761
 KDT  OAA   O   O     0  -0.465   2.2719   1.6844  -1.3013
 KDT  CAF   C   CR6   0  -0.096   1.4535   0.3736   0.4823
 KDT  NAG   N   N     0  -0.636   2.1972   1.0286   1.4862
 KDT  CAB   C   CH3   0  -0.521   1.9801   2.4578   1.7131
 KDT  SAH   S   S     0   1.375   3.7025   0.3941   1.8085
 KDT  OAP   O   OS    0  -0.654   4.2805   1.2148   2.8614
 KDT  OAC   O   OS    0  -0.650   3.5195  -1.0315   2.0287
 KDT  CAI   C   CR6   0  -0.172   4.6706   0.5884   0.3427
 KDT  CAJ   C   CR16  0  -0.233   5.3250   1.7924   0.1190
 KDT  CAK   C   CR16  0  -0.245   6.0413   1.9578  -1.0555
 KDT  CAS   C   CR16  0  -0.237   6.0983   0.9302  -1.9888
 KDT  CAR   C   CR16  0  -0.242   5.4461  -0.2712  -1.7475
 KDT  CAQ   C   CR16  0  -0.231   4.7272  -0.4509  -0.5756
 KDT  HAW   H   HCR6  0   0.267  -3.3748  -3.1338  -1.1486
 KDT  HAX   H   HCR6  0   0.282  -5.6730  -2.2915  -1.1456
 KDT  HAZ   H   HCR6  0   0.282  -4.5266   0.7594   1.6598
 KDT  HAY   H   HCR6  0   0.265  -2.2511  -0.0972   1.6626
 KDT  HAT1  H   HCH2  0   0.292  -0.9913  -2.6884   1.2021
 KDT  HAT2  H   HCH2  0   0.310  -1.1544  -3.0420  -0.4806
 KDT  HAU1  H   HNH2  0   0.428  -0.1951  -1.6624   2.4673
 KDT  HAU2  H   HNH2  0   0.418   0.9629  -0.4662   2.8178
 KDT  HAD   H   HNR6  0   0.424   0.7641   0.3539  -2.7242
 KDT  HAB1  H   HCH3  0   0.261   2.2008   2.7183   2.7443
 KDT  HAB2  H   HCH3  0   0.243   2.5626   3.0920   1.0448
 KDT  HAB3  H   HCH3  0   0.263   0.9249   2.6504   1.5356
 KDT  HAJ   H   HCR6  0   0.278   5.2902   2.5917   0.8466
 KDT  HAQ   H   HCR6  0   0.280   4.2262  -1.3899  -0.3848
 KDT  HAK   H   HCR6  0   0.270   6.5597   2.8893  -1.2398
 KDT  HAS   H   HCR6  0   0.269   6.6607   1.0642  -2.9036
 KDT  HAR   H   HCR6  0   0.270   5.4992  -1.0742  -2.4702

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
 KDT  CAW  CAX   aromatic  1.388  0.020  1.388
 KDT  CAW  CAV   aromatic  1.389  0.020  1.389
 KDT  CAX  CBA   aromatic  1.386  0.020  1.386
 KDT  CBA  BRBB  single    1.888  0.020  1.888
 KDT  CBA  CAZ   aromatic  1.387  0.020  1.387
 KDT  CAZ  CAY   aromatic  1.387  0.020  1.387
 KDT  CAY  CAV   aromatic  1.392  0.020  1.392
 KDT  CAV  CAT   single    1.507  0.020  1.507
 KDT  CAT  NAN   single    1.463  0.020  1.463
 KDT  NAN  CAO   single    1.374  0.020  1.374
 KDT  NAN  CAM   single    1.389  0.020  1.389
 KDT  CAO  NAU   single    1.333  0.020  1.333
 KDT  CAO  CAF   double    1.387  0.020  1.387
 KDT  CAM  OAL   double    1.212  0.020  1.212
 KDT  CAM  NAD   single    1.359  0.020  1.359
 KDT  NAD  CAE   single    1.391  0.020  1.391
 KDT  CAE  OAA   double    1.220  0.020  1.220
 KDT  CAE  CAF   single    1.425  0.020  1.425
 KDT  CAF  NAG   single    1.411  0.020  1.411
 KDT  NAG  CAB   single    1.463  0.020  1.463
 KDT  NAG  SAH   single    1.665  0.020  1.665
 KDT  SAH  OAP   double    1.455  0.020  1.455
 KDT  SAH  OAC   double    1.454  0.020  1.454
 KDT  SAH  CAI   single    1.767  0.020  1.767
 KDT  CAI  CAJ   aromatic  1.389  0.020  1.389
 KDT  CAI  CAQ   aromatic  1.388  0.020  1.388
 KDT  CAJ  CAK   aromatic  1.386  0.020  1.386
 KDT  CAK  CAS   aromatic  1.389  0.020  1.389
 KDT  CAS  CAR   aromatic  1.388  0.020  1.388
 KDT  CAR  CAQ   aromatic  1.387  0.020  1.387
 KDT  CAW  HAW   single    0.930  0.020  1.080
 KDT  CAX  HAX   single    0.930  0.020  1.080
 KDT  CAZ  HAZ   single    0.930  0.020  1.080
 KDT  CAY  HAY   single    0.930  0.020  1.080
 KDT  CAT  HAT1  single    0.970  0.020  1.090
 KDT  CAT  HAT2  single    0.970  0.020  1.090
 KDT  NAU  HAU1  single    0.890  0.020  1.040
 KDT  NAU  HAU2  single    0.890  0.020  1.040
 KDT  NAD  HAD   single    0.860  0.020  1.020
 KDT  CAB  HAB1  single    0.970  0.020  1.090
 KDT  CAB  HAB2  single    0.970  0.020  1.090
 KDT  CAB  HAB3  single    0.970  0.020  1.090
 KDT  CAJ  HAJ   single    0.930  0.020  1.080
 KDT  CAQ  HAQ   single    0.930  0.020  1.080
 KDT  CAK  HAK   single    0.930  0.020  1.080
 KDT  CAS  HAS   single    0.930  0.020  1.080
 KDT  CAR  HAR   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
 KDT  HAW   CAW  CAV   119.92  3.000
 KDT  HAW   CAW  CAX   118.87  3.000
 KDT  CAV   CAW  CAX   121.21  3.000
 KDT  HAX   CAX  CBA   121.24  3.000
 KDT  HAX   CAX  CAW   119.77  3.000
 KDT  CBA   CAX  CAW   118.99  3.000
 KDT  CAZ   CBA  BRBB  119.45  3.000
 KDT  CAZ   CBA  CAX   120.97  3.000
 KDT  BRBB  CBA  CAX   119.58  3.000
 KDT  HAZ   CAZ  CAY   119.65  3.000
 KDT  HAZ   CAZ  CBA   121.19  3.000
 KDT  CAY   CAZ  CBA   119.17  3.000
 KDT  HAY   CAY  CAV   120.94  3.000
 KDT  HAY   CAY  CAZ   118.08  3.000
 KDT  CAV   CAY  CAZ   120.98  3.000
 KDT  CAT   CAV  CAY   121.47  3.000
 KDT  CAT   CAV  CAW   119.85  3.000
 KDT  CAY   CAV  CAW   118.68  3.000
 KDT  HAT2  CAT  HAT1  105.12  3.000
 KDT  HAT2  CAT  NAN   108.15  3.000
 KDT  HAT1  CAT  NAN   109.35  3.000
 KDT  HAT2  CAT  CAV   110.27  3.000
 KDT  HAT1  CAT  CAV   111.00  3.000
 KDT  NAN   CAT  CAV   112.63  3.000
 KDT  CAM   NAN  CAO   121.73  3.000
 KDT  CAM   NAN  CAT   115.05  3.000
 KDT  CAO   NAN  CAT   123.12  3.000
 KDT  CAF   CAO  NAU   120.85  3.000
 KDT  CAF   CAO  NAN   120.11  3.000
 KDT  NAU   CAO  NAN   119.01  3.000
 KDT  HAU2  NAU  HAU1  115.61  3.000
 KDT  HAU2  NAU  CAO   117.36  3.000
 KDT  HAU1  NAU  CAO   123.33  3.000
 KDT  NAD   CAM  OAL   122.71  3.000
 KDT  NAD   CAM  NAN   115.86  3.000
 KDT  OAL   CAM  NAN   121.43  3.000
 KDT  HAD   NAD  CAE   117.00  3.000
 KDT  HAD   NAD  CAM   115.73  3.000
 KDT  CAE   NAD  CAM   127.25  3.000
 KDT  CAF   CAE  OAA   126.12  3.000
 KDT  CAF   CAE  NAD   113.96  3.000
 KDT  OAA   CAE  NAD   119.91  3.000
 KDT  NAG   CAF  CAE   120.24  3.000
 KDT  NAG   CAF  CAO   118.51  3.000
 KDT  CAE   CAF  CAO   120.88  3.000
 KDT  SAH   NAG  CAB   118.45  3.000
 KDT  SAH   NAG  CAF   115.94  3.000
 KDT  CAB   NAG  CAF   119.06  3.000
 KDT  HAB3  CAB  HAB2  108.39  3.000
 KDT  HAB3  CAB  HAB1  108.04  3.000
 KDT  HAB2  CAB  HAB1  109.51  3.000
 KDT  HAB3  CAB  NAG   106.96  3.000
 KDT  HAB2  CAB  NAG   113.20  3.000
 KDT  HAB1  CAB  NAG   110.57  3.000
 KDT  CAI   SAH  OAC   107.60  3.000
 KDT  CAI   SAH  OAP   108.70  3.000
 KDT  OAC   SAH  OAP   119.58  3.000
 KDT  CAI   SAH  NAG   107.02  3.000
 KDT  OAC   SAH  NAG   106.81  3.000
 KDT  OAP   SAH  NAG   106.52  3.000
 KDT  CAQ   CAI  CAJ   121.57  3.000
 KDT  CAQ   CAI  SAH   119.26  3.000
 KDT  CAJ   CAI  SAH   119.15  3.000
 KDT  HAJ   CAJ  CAK   119.92  3.000
 KDT  HAJ   CAJ  CAI   121.15  3.000
 KDT  CAK   CAJ  CAI   118.93  3.000
 KDT  HAK   CAK  CAS   120.18  3.000
 KDT  HAK   CAK  CAJ   119.67  3.000
 KDT  CAS   CAK  CAJ   120.15  3.000
 KDT  HAS   CAS  CAR   119.89  3.000
 KDT  HAS   CAS  CAK   119.84  3.000
 KDT  CAR   CAS  CAK   120.27  3.000
 KDT  HAR   CAR  CAQ   119.60  3.000
 KDT  HAR   CAR  CAS   120.22  3.000
 KDT  CAQ   CAR  CAS   120.18  3.000
 KDT  HAQ   CAQ  CAR   120.13  3.000
 KDT  HAQ   CAQ  CAI   120.97  3.000
 KDT  CAR   CAQ  CAI   118.90  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
 KDT  CONST_01  CAZ   CBA  CAX  CAW      0.00   0.0  0
 KDT  CONST_02  CAZ   CAY  CAV  CAW      0.00   0.0  0
 KDT  CONST_03  CAY   CAV  CAW  CAX      0.00   0.0  0
 KDT  CONST_04  CAY   CAZ  CBA  CAX      0.00   0.0  0
 KDT  CONST_05  CAV   CAW  CAX  CBA      0.00   0.0  0
 KDT  CONST_06  CAV   CAY  CAZ  CBA      0.00   0.0  0
 KDT  CONST_07  CAS   CAK  CAJ  CAI      0.00   0.0  0
 KDT  CONST_08  CAS   CAR  CAQ  CAI      0.00   0.0  0
 KDT  CONST_09  CAR   CAQ  CAI  CAJ      0.00   0.0  0
 KDT  CONST_10  CAR   CAS  CAK  CAJ      0.00   0.0  0
 KDT  CONST_11  CAQ   CAI  CAJ  CAK      0.00   0.0  0
 KDT  CONST_12  CAQ   CAR  CAS  CAK      0.00   0.0  0
 KDT  CONST_13  CAE   NAD  CAM  NAN      0.00   0.0  0
 KDT  CONST_14  NAD   CAM  NAN  CAO      0.00   0.0  0
 KDT  CONST_15  CAF   CAO  NAN  CAM      0.00   0.0  0
 KDT  CONST_16  CAF   CAE  NAD  CAM      0.00   0.0  0
 KDT  CONST_17  BRBB  CBA  CAX  CAW    180.00   0.0  0
 KDT  CONST_18  CAT   CAV  CAW  CAX    180.00   0.0  0
 KDT  CONST_19  CAY   CAZ  CBA  BRBB   180.00   0.0  0
 KDT  CONST_20  CAT   CAV  CAY  CAZ    180.00   0.0  0
 KDT  CONST_21  CAK   CAJ  CAI  SAH    180.00   0.0  0
 KDT  CONST_22  CAR   CAQ  CAI  SAH    180.00   0.0  0
 KDT  CONST_23  CAF   CAO  NAN  CAT    180.00   0.0  0
 KDT  CONST_24  NAD   CAM  NAN  CAT    180.00   0.0  0
 KDT  CONST_25  OAL   CAM  NAN  CAO    180.00   0.0  0
 KDT  CONST_26  CAM   NAN  CAO  NAU    180.00   0.0  0
 KDT  CONST_27  OAA   CAE  NAD  CAM    180.00   0.0  0
 KDT  CONST_28  CAE   NAD  CAM  OAL    180.00   0.0  0
 KDT  CONST_29  HAY   CAY  CAV  CAW    180.00   0.0  0
 KDT  CONST_30  HAZ   CAZ  CBA  CAX    180.00   0.0  0
 KDT  CONST_31  HAW   CAW  CAX  CBA    180.00   0.0  0
 KDT  CONST_32  HAX   CAX  CBA  CAZ    180.00   0.0  0
 KDT  CONST_33  HAK   CAK  CAJ  CAI    180.00   0.0  0
 KDT  CONST_34  HAR   CAR  CAQ  CAI    180.00   0.0  0
 KDT  CONST_35  HAQ   CAQ  CAI  CAJ    180.00   0.0  0
 KDT  CONST_36  HAS   CAS  CAK  CAJ    180.00   0.0  0
 KDT  CONST_37  HAJ   CAJ  CAK  CAS    180.00   0.0  0
 KDT  CONST_38  HAD   NAD  CAM  NAN    180.00   0.0  0
 KDT  CONST_39  NAU   CAO  NAN  CAT      0.00   0.0  0
 KDT  CONST_40  OAL   CAM  NAN  CAT      0.00   0.0  0
 KDT  CONST_42  HAU2  NAU  CAO  NAN    180.00   0.0  0
 KDT  Var_01    NAN   CAT  CAV  CAW    125.45  30.0  2
 KDT  Var_02    CAO   NAN  CAT  CAV     99.72  30.0  3
 KDT  Var_03    CAB   NAG  CAF  CAO   -112.79  30.0  2
 KDT  Var_04    CAI   SAH  NAG  CAF     63.89  30.0  3
 KDT  Var_05    CAJ   CAI  SAH  NAG     84.63  30.0  2
 KDT  Var_06    HAB1  CAB  NAG  CAF    152.12  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
 KDT  plan-1  CAW   0.020
 KDT  plan-1  CAX   0.020
 KDT  plan-1  CBA   0.020
 KDT  plan-1  BRBB  0.020
 KDT  plan-1  CAZ   0.020
 KDT  plan-1  CAY   0.020
 KDT  plan-1  CAV   0.020
 KDT  plan-1  CAT   0.020
 KDT  plan-1  HAW   0.020
 KDT  plan-1  HAX   0.020
 KDT  plan-1  HAZ   0.020
 KDT  plan-1  HAY   0.020
 KDT  plan-2  CAT   0.020
 KDT  plan-2  NAN   0.020
 KDT  plan-2  CAO   0.020
 KDT  plan-2  NAU   0.020
 KDT  plan-2  CAM   0.020
 KDT  plan-2  OAL   0.020
 KDT  plan-2  NAD   0.020
 KDT  plan-2  CAE   0.020
 KDT  plan-2  OAA   0.020
 KDT  plan-2  CAF   0.020
 KDT  plan-2  NAG   0.020
 KDT  plan-2  HAU1  0.020
 KDT  plan-2  HAU2  0.020
 KDT  plan-2  HAD   0.020
 KDT  plan-3  SAH   0.020
 KDT  plan-3  CAI   0.020
 KDT  plan-3  CAJ   0.020
 KDT  plan-3  CAK   0.020
 KDT  plan-3  CAS   0.020
 KDT  plan-3  CAR   0.020
 KDT  plan-3  CAQ   0.020
 KDT  plan-3  HAJ   0.020
 KDT  plan-3  HAQ   0.020
 KDT  plan-3  HAK   0.020
 KDT  plan-3  HAS   0.020
 KDT  plan-3  HAR   0.020

