# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 13:33:21 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5-bromo-6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1ccc(cc1C2=NC(=C(Br)C(=O)N2)CC)[S](=O)(=O)N3CCN(C)CC3
#
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
 5BO  5BO  5-bromo-6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one  ligand  57  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5BO
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
 5BO  CAA   C   CH3   0  -0.675  -1.2125   6.4235   0.4582
 5BO  CAB   C   CH3   0  -0.662  -3.0698  -0.7597   2.9876
 5BO  OAD   O   O     0  -0.451  -3.1890  -1.7582  -2.5229
 5BO  OAE   O   OS    0  -0.653   3.4040  -2.1021  -2.1451
 5BO  OAF   O   OS    0  -0.652   5.1193  -0.2610  -2.1488
 5BO  BRAG  BR  BR    0  -0.013  -5.1161  -1.6118  -0.1518
 5BO  CAH   C   CR16  0  -0.215   3.0102   1.6113  -1.2083
 5BO  CAI   C   CR16  0  -0.378   2.0152   2.5297  -0.9259
 5BO  CAJ   C   CR16  0  -0.237   1.3916  -0.1674  -1.1790
 5BO  CAK   C   CH2   0  -0.458  -1.3879   4.9357   0.1869
 5BO  CAL   C   CH2   0  -0.508  -3.4778   0.2742   1.9369
 5BO  CAM   C   CH2   0  -0.180  -0.0810   4.3067  -0.2460
 5BO  CAN   C   CH2   0  -0.281   2.8682  -1.4347   1.8491
 5BO  CAO   C   CH2   0  -0.283   4.5426   0.2600   1.8224
 5BO  CAP   C   CH2   0  -0.336   3.6247  -2.2353   0.8028
 5BO  CAQ   C   CH2   0  -0.333   5.3368  -0.5039   0.7773
 5BO  NAR   N   N     0  -0.422  -1.6070   0.4820   0.4399
 5BO  NAS   N   NR16  0  -0.675  -1.5198  -0.4842  -1.6644
 5BO  OAT   O   O2    0  -0.444  -0.3160   2.9177  -0.4686
 5BO  CAU   C   CR6   0  -0.222   2.7030   0.2635  -1.3225
 5BO  CAV   C   CR6   0   0.424   0.6980   2.1070  -0.7388
 5BO  CAW   C   CR6   0   0.314  -2.8549  -0.0361   0.6117
 5BO  CAX   C   CR6   0  -0.347  -3.4306  -0.8193  -0.3481
 5BO  CAY   C   CR6   0  -0.116   0.3924   0.7401  -0.8721
 5BO  CAZ   C   CR6   0   0.477  -0.9841   0.2483  -0.6671
 5BO  CBA   C   CR6   0   0.576  -2.7631  -1.0923  -1.5983
 5BO  NBB   N   NT    0  -0.411   3.7835  -0.6518   2.6560
 5BO  NBC   N   N     0  -0.557   4.4904  -1.3908  -0.0205
 5BO  HAA   H   HCH3  0   0.226  -0.8804   6.9558  -0.4346
 5BO  HAAA  H   HCH3  0   0.241  -2.1523   6.8725   0.7771
 5BO  HAAB  H   HCH3  0   0.226  -0.4777   6.6027   1.2447
 5BO  HAB   H   HCH3  0   0.234  -1.9859  -0.8026   3.0947
 5BO  HABA  H   HCH3  0   0.245  -3.4922  -0.4971   3.9568
 5BO  HABB  H   HCH3  0   0.233  -3.4244  -1.7563   2.7250
 5BO  HAC   H   HCH3  0   0.236   2.5520  -0.6518   4.3428
 5BO  HACA  H   HCH3  0   0.237   3.7954   0.5995   4.3284
 5BO  HACB  H   HCH3  0   0.194   2.3502   0.7803   3.3212
 5BO  HAH   H   HCR6  0   0.297   4.0243   1.9637  -1.3411
 5BO  HAI   H   HCR6  0   0.304   2.2800   3.5755  -0.8597
 5BO  HAJ   H   HCR6  0   0.303   1.1429  -1.2171  -1.2770
 5BO  HAK   H   HCH2  0   0.235  -1.7488   4.4306   1.0859
 5BO  HAKA  H   HCH2  0   0.236  -2.1405   4.7857  -0.5907
 5BO  HAL   H   HCH2  0   0.255  -4.5634   0.3228   1.8627
 5BO  HALA  H   HCH2  0   0.261  -3.1295   1.2614   2.2435
 5BO  HAM   H   HCH2  0   0.234   0.2891   4.7763  -1.1634
 5BO  HAMA  H   HCH2  0   0.233   0.6790   4.4371   0.5312
 5BO  HAN   H   HCH2  0   0.200   2.1085  -0.7966   1.3670
 5BO  HANA  H   HCH2  0   0.254   2.3297  -2.1345   2.4922
 5BO  HAO   H   HCH2  0   0.253   5.2446   0.8177   2.4462
 5BO  HAOA  H   HCH2  0   0.202   3.8888   1.0025   1.3347
 5BO  HAP   H   HCH2  0   0.265   4.2706  -2.9630   1.3002
 5BO  HAPA  H   HCH2  0   0.278   2.9368  -2.7983   0.1756
 5BO  HAQ   H   HCH2  0   0.278   5.8844   0.1786   0.1312
 5BO  HAQA  H   HCH2  0   0.262   6.0768  -1.1361   1.2743
 5BO  HNAS  H   HNR6  0   0.440  -1.0032  -0.5971  -2.5292
 5BO  SBD   S   S     0   1.378   3.9928  -0.9295  -1.5179
 5BO  CAC   C   CH3   0  -0.519   3.0846   0.0551   3.7054

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
 5BO  CAA   CAK   single    1.522  0.020  1.522
 5BO  CAB   CAL   single    1.530  0.020  1.530
 5BO  CAC   NBB   single    1.445  0.020  1.445
 5BO  OAD   CBA   double    1.216  0.020  1.216
 5BO  OAE   SBD   double    1.454  0.020  1.454
 5BO  OAF   SBD   double    1.454  0.020  1.454
 5BO  BRAG  CAX   single    1.873  0.020  1.873
 5BO  CAH   CAI   aromatic  1.383  0.020  1.383
 5BO  CAH   CAU   aromatic  1.387  0.020  1.387
 5BO  CAI   CAV   aromatic  1.396  0.020  1.396
 5BO  CAJ   CAU   aromatic  1.388  0.020  1.388
 5BO  CAJ   CAY   aromatic  1.384  0.020  1.384
 5BO  CAK   CAM   single    1.514  0.020  1.514
 5BO  CAL   CAW   single    1.497  0.020  1.497
 5BO  CAM   OAT   single    1.426  0.020  1.426
 5BO  CAN   CAP   single    1.519  0.020  1.519
 5BO  CAN   NBB   single    1.450  0.020  1.450
 5BO  CAO   CAQ   single    1.519  0.020  1.519
 5BO  CAO   NBB   single    1.450  0.020  1.450
 5BO  CAP   NBC   single    1.463  0.020  1.463
 5BO  CAQ   NBC   single    1.463  0.020  1.463
 5BO  NAR   CAW   single    1.362  0.020  1.362
 5BO  NAR   CAZ   double    1.292  0.020  1.292
 5BO  NAS   CAZ   single    1.348  0.020  1.348
 5BO  NAS   CBA   single    1.386  0.020  1.386
 5BO  OAT   CAV   single    1.326  0.020  1.326
 5BO  CAU   SBD   single    1.768  0.020  1.768
 5BO  CAV   CAY   aromatic  1.407  0.020  1.407
 5BO  CAW   CAX   double    1.366  0.020  1.366
 5BO  CAX   CBA   single    1.443  0.020  1.443
 5BO  CAY   CAZ   single    1.476  0.020  1.476
 5BO  NBC   SBD   single    1.644  0.020  1.644
 5BO  CAA   HAA   single    0.970  0.020  1.090
 5BO  CAA   HAAA  single    0.970  0.020  1.090
 5BO  CAA   HAAB  single    0.970  0.020  1.090
 5BO  CAB   HAB   single    0.970  0.020  1.090
 5BO  CAB   HABA  single    0.970  0.020  1.090
 5BO  CAB   HABB  single    0.970  0.020  1.090
 5BO  CAC   HAC   single    0.970  0.020  1.090
 5BO  CAC   HACA  single    0.970  0.020  1.090
 5BO  CAC   HACB  single    0.970  0.020  1.090
 5BO  CAH   HAH   single    0.930  0.020  1.080
 5BO  CAI   HAI   single    0.930  0.020  1.080
 5BO  CAJ   HAJ   single    0.930  0.020  1.080
 5BO  CAK   HAK   single    0.970  0.020  1.090
 5BO  CAK   HAKA  single    0.970  0.020  1.090
 5BO  CAL   HAL   single    0.970  0.020  1.090
 5BO  CAL   HALA  single    0.970  0.020  1.090
 5BO  CAM   HAM   single    0.970  0.020  1.090
 5BO  CAM   HAMA  single    0.970  0.020  1.090
 5BO  CAN   HAN   single    0.970  0.020  1.090
 5BO  CAN   HANA  single    0.970  0.020  1.090
 5BO  CAO   HAO   single    0.970  0.020  1.090
 5BO  CAO   HAOA  single    0.970  0.020  1.090
 5BO  CAP   HAP   single    0.970  0.020  1.090
 5BO  CAP   HAPA  single    0.970  0.020  1.090
 5BO  CAQ   HAQ   single    0.970  0.020  1.090
 5BO  CAQ   HAQA  single    0.970  0.020  1.090
 5BO  NAS   HNAS  single    0.860  0.020  1.020

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
 5BO  HAAB  CAA  HAAA  107.59  3.000
 5BO  HAAB  CAA  HAA   107.74  3.000
 5BO  HAAA  CAA  HAA   107.52  3.000
 5BO  HAAB  CAA  CAK   111.50  3.000
 5BO  HAAA  CAA  CAK   110.83  3.000
 5BO  HAA   CAA  CAK   111.47  3.000
 5BO  HABB  CAB  HABA  107.98  3.000
 5BO  HABB  CAB  HAB   108.13  3.000
 5BO  HABA  CAB  HAB   107.92  3.000
 5BO  HABB  CAB  CAL   111.45  3.000
 5BO  HABA  CAB  CAL   110.17  3.000
 5BO  HAB   CAB  CAL   111.06  3.000
 5BO  HAH   CAH  CAU   120.94  3.000
 5BO  HAH   CAH  CAI   118.89  3.000
 5BO  CAU   CAH  CAI   120.18  3.000
 5BO  HAI   CAI  CAV   121.07  3.000
 5BO  HAI   CAI  CAH   118.60  3.000
 5BO  CAV   CAI  CAH   120.34  3.000
 5BO  HAJ   CAJ  CAY   119.32  3.000
 5BO  HAJ   CAJ  CAU   120.56  3.000
 5BO  CAY   CAJ  CAU   120.10  3.000
 5BO  HAKA  CAK  HAK   107.13  3.000
 5BO  HAKA  CAK  CAM   109.53  3.000
 5BO  HAK   CAK  CAM   109.17  3.000
 5BO  HAKA  CAK  CAA   109.90  3.000
 5BO  HAK   CAK  CAA   110.07  3.000
 5BO  CAM   CAK  CAA   110.96  3.000
 5BO  HALA  CAL  HAL   107.28  3.000
 5BO  HALA  CAL  CAW   107.68  3.000
 5BO  HAL   CAL  CAW   111.33  3.000
 5BO  HALA  CAL  CAB   109.48  3.000
 5BO  HAL   CAL  CAB   110.05  3.000
 5BO  CAW   CAL  CAB   110.92  3.000
 5BO  HAMA  CAM  HAM   108.00  3.000
 5BO  HAMA  CAM  OAT   109.95  3.000
 5BO  HAM   CAM  OAT   110.04  3.000
 5BO  HAMA  CAM  CAK   110.30  3.000
 5BO  HAM   CAM  CAK   110.68  3.000
 5BO  OAT   CAM  CAK   107.88  3.000
 5BO  HANA  CAN  HAN   106.76  3.000
 5BO  HANA  CAN  NBB   109.24  3.000
 5BO  HAN   CAN  NBB   111.45  3.000
 5BO  HANA  CAN  CAP   108.26  3.000
 5BO  HAN   CAN  CAP   110.29  3.000
 5BO  NBB   CAN  CAP   110.70  3.000
 5BO  HAOA  CAO  HAO   106.84  3.000
 5BO  HAOA  CAO  NBB   111.54  3.000
 5BO  HAO   CAO  NBB   109.22  3.000
 5BO  HAOA  CAO  CAQ   110.14  3.000
 5BO  HAO   CAO  CAQ   108.29  3.000
 5BO  NBB   CAO  CAQ   110.68  3.000
 5BO  HAPA  CAP  HAP   106.95  3.000
 5BO  HAPA  CAP  NBC   110.39  3.000
 5BO  HAP   CAP  NBC   106.90  3.000
 5BO  HAPA  CAP  CAN   110.79  3.000
 5BO  HAP   CAP  CAN   109.38  3.000
 5BO  NBC   CAP  CAN   112.21  3.000
 5BO  HAQA  CAQ  HAQ   106.99  3.000
 5BO  HAQA  CAQ  NBC   106.80  3.000
 5BO  HAQ   CAQ  NBC   110.35  3.000
 5BO  HAQA  CAQ  CAO   109.40  3.000
 5BO  HAQ   CAQ  CAO   110.88  3.000
 5BO  NBC   CAQ  CAO   112.19  3.000
 5BO  CAZ   NAR  CAW   118.76  3.000
 5BO  HNAS  NAS  CBA   116.69  3.000
 5BO  HNAS  NAS  CAZ   119.27  3.000
 5BO  CBA   NAS  CAZ   124.03  3.000
 5BO  CAV   OAT  CAM   120.08  3.000
 5BO  SBD   CAU  CAJ   119.43  3.000
 5BO  SBD   CAU  CAH   120.22  3.000
 5BO  CAJ   CAU  CAH   120.16  3.000
 5BO  CAY   CAV  OAT   116.56  3.000
 5BO  CAY   CAV  CAI   119.11  3.000
 5BO  OAT   CAV  CAI   124.32  3.000
 5BO  CAX   CAW  NAR   121.04  3.000
 5BO  CAX   CAW  CAL   124.44  3.000
 5BO  NAR   CAW  CAL   114.46  3.000
 5BO  CBA   CAX  CAW   121.48  3.000
 5BO  CBA   CAX  BRAG  115.28  3.000
 5BO  CAW   CAX  BRAG  123.24  3.000
 5BO  CAZ   CAY  CAV   120.87  3.000
 5BO  CAZ   CAY  CAJ   119.04  3.000
 5BO  CAV   CAY  CAJ   120.07  3.000
 5BO  CAY   CAZ  NAS   116.67  3.000
 5BO  CAY   CAZ  NAR   120.56  3.000
 5BO  NAS   CAZ  NAR   122.73  3.000
 5BO  CAX   CBA  NAS   111.92  3.000
 5BO  CAX   CBA  OAD   126.87  3.000
 5BO  NAS   CBA  OAD   121.20  3.000
 5BO  CAO   NBB  CAN   110.50  3.000
 5BO  CAO   NBB  CAC   111.28  3.000
 5BO  CAN   NBB  CAC   111.28  3.000
 5BO  SBD   NBC  CAQ   120.12  3.000
 5BO  SBD   NBC  CAP   119.70  3.000
 5BO  CAQ   NBC  CAP   112.67  3.000
 5BO  NBC   SBD  CAU   108.03  3.000
 5BO  NBC   SBD  OAF   106.84  3.000
 5BO  CAU   SBD  OAF   107.64  3.000
 5BO  NBC   SBD  OAE   106.80  3.000
 5BO  CAU   SBD  OAE   107.24  3.000
 5BO  OAF   SBD  OAE   119.82  3.000
 5BO  HACB  CAC  HACA  107.77  3.000
 5BO  HACB  CAC  HAC   107.75  3.000
 5BO  HACA  CAC  HAC   107.93  3.000
 5BO  HACB  CAC  NBB   113.03  3.000
 5BO  HACA  CAC  NBB   110.10  3.000
 5BO  HAC   CAC  NBB   110.08  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
 5BO  CONST_01  CAY   CAV  CAI  CAH    0.00   0.0  0
 5BO  CONST_02  CAY   CAJ  CAU  CAH    0.00   0.0  0
 5BO  CONST_03  CAJ   CAU  CAH  CAI    0.00   0.0  0
 5BO  CONST_04  CAJ   CAY  CAV  CAI    0.00   0.0  0
 5BO  CONST_05  CAV   CAI  CAH  CAU    0.00   0.0  0
 5BO  CONST_06  CAV   CAY  CAJ  CAU    0.00   0.0  0
 5BO  CONST_07  CAZ   CAY  CAV  CAI  180.00   0.0  0
 5BO  CONST_08  CAZ   CAY  CAJ  CAU  180.00   0.0  0
 5BO  CONST_09  CBA   NAS  CAZ  NAR    0.00   0.0  0
 5BO  CONST_10  CAW   NAR  CAZ  NAS    0.00   0.0  0
 5BO  CONST_11  CAY   CAZ  NAR  CAW  180.00   0.0  0
 5BO  CONST_12  CAZ   NAS  CBA  CAX    0.00   0.0  0
 5BO  CONST_13  CBA   NAS  CAZ  CAY  180.00   0.0  0
 5BO  CONST_14  OAT   CAV  CAI  CAH  180.00   0.0  0
 5BO  CONST_15  SBD   CAU  CAH  CAI  180.00   0.0  0
 5BO  CONST_16  OAT   CAV  CAY  CAJ  180.00   0.0  0
 5BO  CONST_17  CAZ   CAY  CAV  OAT    0.00   0.0  0
 5BO  CONST_18  SBD   CAU  CAJ  CAY  180.00   0.0  0
 5BO  CONST_19  CAZ   NAS  CBA  OAD  180.00   0.0  0
 5BO  CONST_20  HAJ   CAJ  CAU  CAH  180.00   0.0  0
 5BO  CONST_21  HAH   CAH  CAU  CAJ  180.00   0.0  0
 5BO  CONST_22  HAI   CAI  CAH  CAU  180.00   0.0  0
 5BO  CONST_23  HNAS  NAS  CAZ  NAR  180.00   0.0  0
 5BO  Var_01    NAR   CAZ  CAY  CAJ  122.99  30.0  2
 5BO  Var_02    CAQ   NBC  CAP  CAN   49.68  30.0  1
 5BO  Var_03    CAQ   CAO  NBB  CAN  -59.25  30.0  1
 5BO  Var_04    CAP   NBC  CAQ  CAO  -49.75  30.0  1
 5BO  Var_05    CAP   CAN  NBB  CAO   59.17  30.0  1
 5BO  Var_06    NBC   CAP  CAN  NBB  -54.26  30.0  1
 5BO  Var_07    NBC   CAQ  CAO  NBB   54.42  30.0  1
 5BO  Var_08    NBC   SBD  CAU  CAH   88.24  30.0  2
 5BO  Var_09    CAU   SBD  NBC  CAP   71.82  30.0  3
 5BO  Var_10    NAR   CAW  CAL  CAB  -86.73  30.0  3
 5BO  Var_11    CAY   CAV  OAT  CAM  176.59  30.0  2
 5BO  Var_12    HAC   CAC  NBB  CAN   58.47  30.0  3
 5BO  Var_13    HAM   CAM  OAT  CAV   65.38  30.0  2
 5BO  Var_14    HAB   CAB  CAL  CAW   57.89  30.0  3
 5BO  Var_15    OAT   CAM  CAK  CAA  179.42  30.0  3
 5BO  Var_16    HAA   CAA  CAK  CAM   60.73  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
 5BO  plan-1  CAH   0.020
 5BO  plan-1  CAI   0.020
 5BO  plan-1  CAJ   0.020
 5BO  plan-1  OAT   0.020
 5BO  plan-1  CAU   0.020
 5BO  plan-1  CAV   0.020
 5BO  plan-1  CAY   0.020
 5BO  plan-1  CAZ   0.020
 5BO  plan-1  HAH   0.020
 5BO  plan-1  HAI   0.020
 5BO  plan-1  HAJ   0.020
 5BO  plan-1  SBD   0.020
 5BO  plan-2  OAD   0.020
 5BO  plan-2  BRAG  0.020
 5BO  plan-2  CAL   0.020
 5BO  plan-2  NAR   0.020
 5BO  plan-2  NAS   0.020
 5BO  plan-2  CAW   0.020
 5BO  plan-2  CAX   0.020
 5BO  plan-2  CAY   0.020
 5BO  plan-2  CAZ   0.020
 5BO  plan-2  CBA   0.020
 5BO  plan-2  HNAS  0.020

