# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:07:46 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5-chloro-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(Cl)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
 5CO  5CO  5-chloro-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_5CO
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
 5CO  CAA   C   CH3   0  -0.673  -3.3378   5.2497   2.0501
 5CO  CAB   C   CH3   0  -0.666  -5.9275   0.2426   0.2441
 5CO  OAD   O   O     0  -0.451  -2.0001  -3.3282   1.9261
 5CO  OAE   O   OS    0  -0.650   2.7303  -1.2038  -2.6782
 5CO  OAF   O   OS    0  -0.650   3.7639   1.0811  -2.8523
 5CO  CLAG  CL  CL    0  -0.091  -4.8562  -3.2137   1.1284
 5CO  CAH   C   CR16  0  -0.212   1.5948   2.1216  -1.0793
 5CO  CAI   C   CR16  0  -0.377   0.4854   2.6603  -0.4523
 5CO  CAJ   C   CR16  0  -0.237   0.5963  -0.0674  -0.9869
 5CO  CAK   C   CH2   0  -0.460  -3.1335   3.8098   1.6003
 5CO  CAL   C   CH2   0  -0.504  -5.1848  -0.7024  -0.7014
 5CO  CAM   C   CH2   0  -0.180  -1.7941   3.6362   0.9172
 5CO  CAN   C   CH2   0  -0.276   4.7666  -1.7849   1.0180
 5CO  CAO   C   CH2   0  -0.279   5.9031   0.2785   0.7285
 5CO  CAP   C   CH2   0  -0.319   3.6181  -1.3011   0.1544
 5CO  CAQ   C   CH2   0  -0.314   4.7785   0.8165  -0.1357
 5CO  NAR   N   N     0  -0.427  -2.8305  -0.2020  -0.4934
 5CO  NAS   N   NR16  0  -0.673  -1.3701  -1.4614   0.7938
 5CO  OAT   O   O2    0  -0.446  -1.6710   2.2651   0.5430
 5CO  CAU   C   CR6   0  -0.219   1.6541   0.7598  -1.3418
 5CO  CAV   C   CR6   0   0.428  -0.5836   1.8411  -0.0867
 5CO  CAW   C   CR6   0   0.332  -3.8377  -1.0549  -0.1560
 5CO  CAX   C   CR6   0  -0.275  -3.6112  -2.1251   0.6584
 5CO  CAY   C   CR6   0  -0.121  -0.5225   0.4650  -0.3716
 5CO  CAZ   C   CR6   0   0.472  -1.6507  -0.4195  -0.0162
 5CO  CBA   C   CR6   0   0.583  -2.3028  -2.4038   1.1961
 5CO  NBB   N   NT    0  -0.415   5.4007  -0.6745   1.6950
 5CO  NBC   N   N     0  -0.565   4.1170  -0.3080  -0.8001
 5CO  HAA   H   HCH3  0   0.226  -3.2828   5.9413   1.2083
 5CO  HAAA  H   HCH3  0   0.241  -4.3148   5.3725   2.5159
 5CO  HAAB  H   HCH3  0   0.226  -2.5844   5.5520   2.7790
 5CO  HAB   H   HCH3  0   0.234  -5.3539   1.1523   0.4237
 5CO  HABA  H   HCH3  0   0.245  -6.8851   0.5302  -0.1883
 5CO  HABB  H   HCH3  0   0.233  -6.1216  -0.2307   1.2063
 5CO  HAC   H   HCH3  0   0.196   7.2485  -1.6654   2.0990
 5CO  HACA  H   HCH3  0   0.236   6.8730  -0.2645   3.1160
 5CO  HACB  H   HCH3  0   0.236   6.0073  -1.7825   3.3559
 5CO  HAH   H   HCR6  0   0.297   2.4062   2.7784  -1.3630
 5CO  HAI   H   HCR6  0   0.304   0.4654   3.7222  -0.2532
 5CO  HAJ   H   HCR6  0   0.304   0.6269  -1.1259  -1.2132
 5CO  HAK   H   HCH2  0   0.236  -3.1935   3.1376   2.4594
 5CO  HAKA  H   HCH2  0   0.237  -3.9293   3.5193   0.9099
 5CO  HAL   H   HCH2  0   0.253  -5.7801  -1.5986  -0.8730
 5CO  HALA  H   HCH2  0   0.261  -5.0412  -0.2159  -1.6668
 5CO  HAM   H   HCH2  0   0.234  -1.7310   4.2758   0.0304
 5CO  HAMA  H   HCH2  0   0.234  -0.9762   3.9119   1.5917
 5CO  HAN   H   HCH2  0   0.251   4.3624  -2.4780   1.7588
 5CO  HANA  H   HCH2  0   0.206   5.4788  -2.3494   0.3930
 5CO  HAO   H   HCH2  0   0.205   6.6772  -0.1633   0.0784
 5CO  HAOA  H   HCH2  0   0.252   6.3609   1.1190   1.2539
 5CO  HAP   H   HCH2  0   0.276   3.1940  -2.1492  -0.3795
 5CO  HAPA  H   HCH2  0   0.237   2.8407  -0.8660   0.7956
 5CO  HAQ   H   HCH2  0   0.237   4.0707   1.3790   0.4864
 5CO  HAQA  H   HCH2  0   0.276   5.1994   1.4899  -0.8787
 5CO  HNAS  H   HNR6  0   0.435  -0.4328  -1.5624   1.1660
 5CO  SBD   S   S     0   1.378   3.1055   0.0568  -2.0593
 5CO  CAC   C   CH3   0  -0.520   6.4347  -1.1205   2.6014

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
 5CO  CAA   CAK   single    1.522  0.020  1.522
 5CO  CAB   CAL   single    1.529  0.020  1.529
 5CO  CAC   NBB   single    1.446  0.020  1.446
 5CO  OAD   CBA   double    1.216  0.020  1.216
 5CO  OAE   SBD   double    1.454  0.020  1.454
 5CO  OAF   SBD   double    1.453  0.020  1.453
 5CO  CLAG  CAX   single    1.719  0.020  1.719
 5CO  CAH   CAI   aromatic  1.384  0.020  1.384
 5CO  CAH   CAU   aromatic  1.388  0.020  1.388
 5CO  CAI   CAV   aromatic  1.396  0.020  1.396
 5CO  CAJ   CAU   aromatic  1.389  0.020  1.389
 5CO  CAJ   CAY   aromatic  1.383  0.020  1.383
 5CO  CAK   CAM   single    1.514  0.020  1.514
 5CO  CAL   CAW   single    1.495  0.020  1.495
 5CO  CAM   OAT   single    1.427  0.020  1.427
 5CO  CAN   CAP   single    1.516  0.020  1.516
 5CO  CAN   NBB   single    1.447  0.020  1.447
 5CO  CAO   CAQ   single    1.517  0.020  1.517
 5CO  CAO   NBB   single    1.447  0.020  1.447
 5CO  CAP   NBC   single    1.465  0.020  1.465
 5CO  CAQ   NBC   single    1.464  0.020  1.464
 5CO  NAR   CAW   single    1.362  0.020  1.362
 5CO  NAR   CAZ   double    1.291  0.020  1.291
 5CO  NAS   CAZ   single    1.349  0.020  1.349
 5CO  NAS   CBA   single    1.386  0.020  1.386
 5CO  OAT   CAV   single    1.326  0.020  1.326
 5CO  CAU   SBD   single    1.765  0.020  1.765
 5CO  CAV   CAY   aromatic  1.407  0.020  1.407
 5CO  CAW   CAX   double    1.364  0.020  1.364
 5CO  CAX   CBA   single    1.442  0.020  1.442
 5CO  CAY   CAZ   single    1.477  0.020  1.477
 5CO  NBC   SBD   single    1.656  0.020  1.656
 5CO  CAA   HAA   single    0.970  0.020  1.090
 5CO  CAA   HAAA  single    0.970  0.020  1.090
 5CO  CAA   HAAB  single    0.970  0.020  1.090
 5CO  CAB   HAB   single    0.970  0.020  1.090
 5CO  CAB   HABA  single    0.970  0.020  1.090
 5CO  CAB   HABB  single    0.970  0.020  1.090
 5CO  CAC   HAC   single    0.970  0.020  1.090
 5CO  CAC   HACA  single    0.970  0.020  1.090
 5CO  CAC   HACB  single    0.970  0.020  1.090
 5CO  CAH   HAH   single    0.930  0.020  1.080
 5CO  CAI   HAI   single    0.930  0.020  1.080
 5CO  CAJ   HAJ   single    0.930  0.020  1.080
 5CO  CAK   HAK   single    0.970  0.020  1.090
 5CO  CAK   HAKA  single    0.970  0.020  1.090
 5CO  CAL   HAL   single    0.970  0.020  1.090
 5CO  CAL   HALA  single    0.970  0.020  1.090
 5CO  CAM   HAM   single    0.970  0.020  1.090
 5CO  CAM   HAMA  single    0.970  0.020  1.090
 5CO  CAN   HAN   single    0.970  0.020  1.090
 5CO  CAN   HANA  single    0.970  0.020  1.090
 5CO  CAO   HAO   single    0.970  0.020  1.090
 5CO  CAO   HAOA  single    0.970  0.020  1.090
 5CO  CAP   HAP   single    0.970  0.020  1.090
 5CO  CAP   HAPA  single    0.970  0.020  1.090
 5CO  CAQ   HAQ   single    0.970  0.020  1.090
 5CO  CAQ   HAQA  single    0.970  0.020  1.090
 5CO  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
 5CO  HAAB  CAA  HAAA  107.60  3.000
 5CO  HAAB  CAA  HAA   107.76  3.000
 5CO  HAAA  CAA  HAA   107.68  3.000
 5CO  HAAB  CAA  CAK   111.52  3.000
 5CO  HAAA  CAA  CAK   110.70  3.000
 5CO  HAA   CAA  CAK   111.40  3.000
 5CO  HABB  CAB  HABA  107.97  3.000
 5CO  HABB  CAB  HAB   108.09  3.000
 5CO  HABA  CAB  HAB   107.91  3.000
 5CO  HABB  CAB  CAL   111.34  3.000
 5CO  HABA  CAB  CAL   110.16  3.000
 5CO  HAB   CAB  CAL   111.22  3.000
 5CO  HAH   CAH  CAU   120.93  3.000
 5CO  HAH   CAH  CAI   118.94  3.000
 5CO  CAU   CAH  CAI   120.13  3.000
 5CO  HAI   CAI  CAV   120.96  3.000
 5CO  HAI   CAI  CAH   118.75  3.000
 5CO  CAV   CAI  CAH   120.29  3.000
 5CO  HAJ   CAJ  CAY   119.48  3.000
 5CO  HAJ   CAJ  CAU   120.47  3.000
 5CO  CAY   CAJ  CAU   120.03  3.000
 5CO  HAKA  CAK  HAK   107.06  3.000
 5CO  HAKA  CAK  CAM   109.19  3.000
 5CO  HAK   CAK  CAM   109.45  3.000
 5CO  HAKA  CAK  CAA   109.90  3.000
 5CO  HAK   CAK  CAA   110.02  3.000
 5CO  CAM   CAK  CAA   111.14  3.000
 5CO  HALA  CAL  HAL   107.42  3.000
 5CO  HALA  CAL  CAW   108.02  3.000
 5CO  HAL   CAL  CAW   110.84  3.000
 5CO  HALA  CAL  CAB   109.61  3.000
 5CO  HAL   CAL  CAB   109.90  3.000
 5CO  CAW   CAL  CAB   110.96  3.000
 5CO  HAMA  CAM  HAM   107.97  3.000
 5CO  HAMA  CAM  OAT   109.82  3.000
 5CO  HAM   CAM  OAT   110.12  3.000
 5CO  HAMA  CAM  CAK   110.73  3.000
 5CO  HAM   CAM  CAK   110.45  3.000
 5CO  OAT   CAM  CAK   107.76  3.000
 5CO  HANA  CAN  HAN   107.37  3.000
 5CO  HANA  CAN  NBB   112.02  3.000
 5CO  HAN   CAN  NBB   109.38  3.000
 5CO  HANA  CAN  CAP   109.25  3.000
 5CO  HAN   CAN  CAP   107.97  3.000
 5CO  NBB   CAN  CAP   110.71  3.000
 5CO  HAOA  CAO  HAO   107.32  3.000
 5CO  HAOA  CAO  NBB   109.34  3.000
 5CO  HAO   CAO  NBB   111.93  3.000
 5CO  HAOA  CAO  CAQ   108.18  3.000
 5CO  HAO   CAO  CAQ   109.05  3.000
 5CO  NBB   CAO  CAQ   110.89  3.000
 5CO  HAPA  CAP  HAP   108.63  3.000
 5CO  HAPA  CAP  NBC   110.68  3.000
 5CO  HAP   CAP  NBC   109.97  3.000
 5CO  HAPA  CAP  CAN   109.28  3.000
 5CO  HAP   CAP  CAN   109.02  3.000
 5CO  NBC   CAP  CAN   109.23  3.000
 5CO  HAQA  CAQ  HAQ   108.63  3.000
 5CO  HAQA  CAQ  NBC   109.90  3.000
 5CO  HAQ   CAQ  NBC   111.07  3.000
 5CO  HAQA  CAQ  CAO   108.78  3.000
 5CO  HAQ   CAQ  CAO   109.69  3.000
 5CO  NBC   CAQ  CAO   108.73  3.000
 5CO  CAZ   NAR  CAW   118.60  3.000
 5CO  HNAS  NAS  CBA   116.62  3.000
 5CO  HNAS  NAS  CAZ   119.32  3.000
 5CO  CBA   NAS  CAZ   124.03  3.000
 5CO  CAV   OAT  CAM   120.17  3.000
 5CO  SBD   CAU  CAJ   119.53  3.000
 5CO  SBD   CAU  CAH   120.18  3.000
 5CO  CAJ   CAU  CAH   120.22  3.000
 5CO  CAY   CAV  OAT   116.40  3.000
 5CO  CAY   CAV  CAI   119.21  3.000
 5CO  OAT   CAV  CAI   124.39  3.000
 5CO  CAX   CAW  NAR   121.09  3.000
 5CO  CAX   CAW  CAL   123.53  3.000
 5CO  NAR   CAW  CAL   115.35  3.000
 5CO  CBA   CAX  CAW   121.68  3.000
 5CO  CBA   CAX  CLAG  115.64  3.000
 5CO  CAW   CAX  CLAG  122.67  3.000
 5CO  CAZ   CAY  CAV   120.26  3.000
 5CO  CAZ   CAY  CAJ   119.62  3.000
 5CO  CAV   CAY  CAJ   120.12  3.000
 5CO  CAY   CAZ  NAS   116.62  3.000
 5CO  CAY   CAZ  NAR   120.54  3.000
 5CO  NAS   CAZ  NAR   122.82  3.000
 5CO  CAX   CBA  NAS   111.78  3.000
 5CO  CAX   CBA  OAD   126.63  3.000
 5CO  NAS   CBA  OAD   121.58  3.000
 5CO  CAO   NBB  CAN   110.18  3.000
 5CO  CAO   NBB  CAC   111.93  3.000
 5CO  CAN   NBB  CAC   111.72  3.000
 5CO  SBD   NBC  CAQ   116.87  3.000
 5CO  SBD   NBC  CAP   115.90  3.000
 5CO  CAQ   NBC  CAP   112.27  3.000
 5CO  NBC   SBD  CAU   106.32  3.000
 5CO  NBC   SBD  OAF   107.07  3.000
 5CO  CAU   SBD  OAF   108.28  3.000
 5CO  NBC   SBD  OAE   106.88  3.000
 5CO  CAU   SBD  OAE   107.83  3.000
 5CO  OAF   SBD  OAE   119.73  3.000
 5CO  HACB  CAC  HACA  107.90  3.000
 5CO  HACB  CAC  HAC   107.75  3.000
 5CO  HACA  CAC  HAC   107.86  3.000
 5CO  HACB  CAC  NBB   109.91  3.000
 5CO  HACA  CAC  NBB   109.95  3.000
 5CO  HAC   CAC  NBB   113.29  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
 5CO  CONST_01  CAY   CAV  CAI  CAH     0.00   0.0  0
 5CO  CONST_02  CAY   CAJ  CAU  CAH     0.00   0.0  0
 5CO  CONST_03  CAJ   CAU  CAH  CAI     0.00   0.0  0
 5CO  CONST_04  CAJ   CAY  CAV  CAI     0.00   0.0  0
 5CO  CONST_05  CAV   CAI  CAH  CAU     0.00   0.0  0
 5CO  CONST_06  CAV   CAY  CAJ  CAU     0.00   0.0  0
 5CO  CONST_07  CAZ   CAY  CAV  CAI   180.00   0.0  0
 5CO  CONST_08  CAZ   CAY  CAJ  CAU   180.00   0.0  0
 5CO  CONST_09  CBA   NAS  CAZ  NAR     0.00   0.0  0
 5CO  CONST_10  CAW   NAR  CAZ  NAS     0.00   0.0  0
 5CO  CONST_11  CAY   CAZ  NAR  CAW   180.00   0.0  0
 5CO  CONST_12  CAZ   NAS  CBA  CAX     0.00   0.0  0
 5CO  CONST_13  CBA   NAS  CAZ  CAY   180.00   0.0  0
 5CO  CONST_14  OAT   CAV  CAI  CAH   180.00   0.0  0
 5CO  CONST_15  SBD   CAU  CAH  CAI   180.00   0.0  0
 5CO  CONST_16  OAT   CAV  CAY  CAJ   180.00   0.0  0
 5CO  CONST_17  CAZ   CAY  CAV  OAT     0.00   0.0  0
 5CO  CONST_18  SBD   CAU  CAJ  CAY   180.00   0.0  0
 5CO  CONST_19  CAZ   NAS  CBA  OAD   180.00   0.0  0
 5CO  CONST_20  HAJ   CAJ  CAU  CAH   180.00   0.0  0
 5CO  CONST_21  HAH   CAH  CAU  CAJ   180.00   0.0  0
 5CO  CONST_22  HAI   CAI  CAH  CAU   180.00   0.0  0
 5CO  CONST_23  HNAS  NAS  CAZ  NAR   180.00   0.0  0
 5CO  Var_01    NAR   CAZ  CAY  CAJ  -121.24  30.0  2
 5CO  Var_02    CAQ   NBC  CAP  CAN   -56.64  30.0  1
 5CO  Var_03    CAQ   CAO  NBB  CAN    59.70  30.0  1
 5CO  Var_04    CAP   NBC  CAQ  CAO    56.73  30.0  1
 5CO  Var_05    CAP   CAN  NBB  CAO   -59.20  30.0  1
 5CO  Var_06    NBC   CAP  CAN  NBB    56.99  30.0  1
 5CO  Var_07    NBC   CAQ  CAO  NBB   -57.60  30.0  1
 5CO  Var_08    NBC   SBD  CAU  CAH    87.04  30.0  2
 5CO  Var_09    CAU   SBD  NBC  CAP    62.58  30.0  3
 5CO  Var_10    NAR   CAW  CAL  CAB   -88.11  30.0  3
 5CO  Var_11    CAY   CAV  OAT  CAM   177.59  30.0  2
 5CO  Var_12    HAC   CAC  NBB  CAN    60.84  30.0  3
 5CO  Var_13    HAM   CAM  OAT  CAV    59.02  30.0  1
 5CO  Var_14    HAB   CAB  CAL  CAW    57.57  30.0  3
 5CO  Var_15    OAT   CAM  CAK  CAA   179.26  30.0  3
 5CO  Var_16    HAA   CAA  CAK  CAM    58.65  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
 5CO  plan-1  CAH   0.020
 5CO  plan-1  CAI   0.020
 5CO  plan-1  CAJ   0.020
 5CO  plan-1  OAT   0.020
 5CO  plan-1  CAU   0.020
 5CO  plan-1  CAV   0.020
 5CO  plan-1  CAY   0.020
 5CO  plan-1  CAZ   0.020
 5CO  plan-1  HAH   0.020
 5CO  plan-1  HAI   0.020
 5CO  plan-1  HAJ   0.020
 5CO  plan-1  SBD   0.020
 5CO  plan-2  OAD   0.020
 5CO  plan-2  CLAG  0.020
 5CO  plan-2  CAL   0.020
 5CO  plan-2  NAR   0.020
 5CO  plan-2  NAS   0.020
 5CO  plan-2  CAW   0.020
 5CO  plan-2  CAX   0.020
 5CO  plan-2  CAY   0.020
 5CO  plan-2  CAZ   0.020
 5CO  plan-2  CBA   0.020
 5CO  plan-2  HNAS  0.020

