# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 07:40:34 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-(2-chlorophenyl)-4-[(4-methoxyphenyl)carbonylamino]-N-pyrimidin-4-yl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C(=O)Nc2ccc(cc2)C(=O)N(c3ccncn3)c4ccccc4Cl
#
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
 8IR  8IR  N-(2-chlorophenyl)-4-[(4-methoxyphenyl)carbonylamino]-N-pyrimidin-4-yl-benzamide  ligand  52  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8IR
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
 8IR  CL    CL  CL    0  -0.088    3.5966  -2.0133  -1.7159
 8IR  CBB   C   CR6   0  -0.068    3.1155  -2.1099  -0.0603
 8IR  CBD   C   CR16  0  -0.215    2.7481  -3.3352   0.4705
 8IR  CBE   C   CR16  0  -0.256    2.3317  -3.4106   1.7914
 8IR  CBF   C   CR16  0  -0.244    2.2933  -2.2683   2.5781
 8IR  CBG   C   CR16  0  -0.259    2.6801  -1.0498   2.0449
 8IR  CBA   C   CR6   0   0.298    3.0834  -0.9547   0.7185
 8IR  NAT   N   NT    0  -0.632    3.4789   0.2955   0.1787
 8IR  C4    C   CR6   0   0.500    4.8253   0.4655  -0.1740
 8IR  N3    N   N     0  -0.406    5.0906   1.3225  -1.1468
 8IR  C2    C   CR16  0   0.057    6.3578   1.4585  -1.4975
 8IR  N1    N   N     0  -0.403    7.3946   0.8116  -0.9888
 8IR  C6    C   CR16  0  -0.025    7.1154  -0.0500  -0.0158
 8IR  C5    C   CR16  0  -0.359    5.8322  -0.2650   0.4474
 8IR  CAR   C   C     0   0.510    2.6438   1.4092   0.3031
 8IR  OAS   O   O     0  -0.406    3.0895   2.5249   0.4371
 8IR  CAO   C   CR6   0  -0.081    1.1878   1.1410   0.2660
 8IR  CAP   C   CR16  0  -0.257    0.3435   1.8977   1.0716
 8IR  CAQ   C   CR16  0  -0.302   -1.0296   1.7281   1.0396
 8IR  CAN   C   CR16  0  -0.227    0.6251   0.2149  -0.6097
 8IR  CAM   C   CR16  0  -0.346   -0.7428   0.0537  -0.6688
 8IR  CAL   C   CR6   0   0.396   -1.5905   0.7996   0.1581
 8IR  NAA   N   NH1   0  -0.766   -2.9525   0.5404   0.0485
 8IR  CAB   C   C     0   0.536   -4.0016   1.2592   0.5431
 8IR  OAC   O   O     0  -0.457   -3.8667   2.3111   1.1432
 8IR  CAD   C   CR6   0  -0.073   -5.3444   0.6791   0.2819
 8IR  CAE   C   CR16  0  -0.246   -6.4486   1.5359   0.2975
 8IR  CAF   C   CR16  0  -0.330   -7.7202   1.0589   0.0683
 8IR  CAG   C   CR6   0   0.393   -7.9304  -0.3044  -0.1671
 8IR  OAH   O   O2    0  -0.462   -9.1965  -0.6798  -0.3854
 8IR  CAI   C   CH3   0  -0.440   -9.4661  -2.0428  -0.6604
 8IR  CAJ   C   CR16  0  -0.370   -6.8412  -1.1745  -0.1583
 8IR  CAK   C   CR16  0  -0.277   -5.5656  -0.6769   0.0615
 8IR  HBD   H   HCR6  0   0.288    2.7806  -4.2221  -0.1473
 8IR  HBE   H   HCR6  0   0.276    2.0396  -4.3675   2.2018
 8IR  HBF   H   HCR6  0   0.274    1.9759  -2.3257   3.6101
 8IR  HBG   H   HCR6  0   0.284    2.6759  -0.1608   2.6628
 8IR  H5    H   HCR6  0   0.295    5.6425  -0.9641   1.2487
 8IR  H2    H   HCR6  0   0.267    6.5636   2.1665  -2.2929
 8IR  H6    H   HCR6  0   0.287    7.9485  -0.5892   0.4199
 8IR  HAP   H   HCR6  0   0.268    0.7619   2.6243   1.7561
 8IR  HAN   H   HCR6  0   0.255    1.2465  -0.3625  -1.2811
 8IR  HAQ   H   HCR6  0   0.285   -1.6471   2.3154   1.6975
 8IR  HAM   H   HCR6  0   0.278   -1.1649  -0.6568  -1.3691
 8IR  HAA   H   HNH1  0   0.425   -3.1814  -0.2286  -0.5627
 8IR  HAE   H   HCR6  0   0.264   -6.3080   2.5933   0.4772
 8IR  HAK   H   HCR6  0   0.266   -4.7490  -1.3878   0.0826
 8IR  HAF   H   HCR6  0   0.271   -8.5648   1.7359   0.0669
 8IR  HAJ   H   HCR6  0   0.289   -6.9637  -2.2374  -0.3133
 8IR  HAI1  H   HCH3  0   0.234   -8.9384  -2.3866  -1.5529
 8IR  HAI2  H   HCH3  0   0.234   -9.1994  -2.6872   0.1805
 8IR  HAI3  H   HCH3  0   0.264  -10.5363  -2.1155  -0.8339

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
 8IR  CL   CBB   single    1.727  0.020  1.727
 8IR  CBB  CBD   aromatic  1.385  0.020  1.385
 8IR  CBB  CBA   aromatic  1.394  0.020  1.394
 8IR  CBD  CBE   aromatic  1.387  0.020  1.387
 8IR  CBE  CBF   aromatic  1.387  0.020  1.387
 8IR  CBF  CBG   aromatic  1.385  0.020  1.385
 8IR  CBG  CBA   aromatic  1.390  0.020  1.390
 8IR  CBA  NAT   single    1.418  0.020  1.418
 8IR  NAT  C4    single    1.402  0.020  1.402
 8IR  NAT  CAR   single    1.398  0.020  1.398
 8IR  C4   N3    aromatic  1.323  0.020  1.323
 8IR  C4   C5    aromatic  1.391  0.020  1.391
 8IR  N3   C2    aromatic  1.322  0.020  1.322
 8IR  C2   N1    aromatic  1.324  0.020  1.324
 8IR  N1   C6    aromatic  1.329  0.020  1.329
 8IR  C6   C5    aromatic  1.381  0.020  1.381
 8IR  CAR  OAS   double    1.209  0.020  1.209
 8IR  CAR  CAO   single    1.481  0.020  1.481
 8IR  CAO  CAP   aromatic  1.391  0.020  1.391
 8IR  CAO  CAN   aromatic  1.393  0.020  1.393
 8IR  CAP  CAQ   aromatic  1.384  0.020  1.384
 8IR  CAQ  CAL   aromatic  1.398  0.020  1.398
 8IR  CAN  CAM   aromatic  1.379  0.020  1.379
 8IR  CAM  CAL   aromatic  1.400  0.020  1.400
 8IR  CAL  NAA   single    1.391  0.020  1.391
 8IR  NAA  CAB   single    1.364  0.020  1.364
 8IR  CAB  OAC   double    1.218  0.020  1.218
 8IR  CAB  CAD   single    1.486  0.020  1.486
 8IR  CAD  CAE   aromatic  1.398  0.020  1.398
 8IR  CAD  CAK   aromatic  1.391  0.020  1.391
 8IR  CAE  CAF   aromatic  1.377  0.020  1.377
 8IR  CAF  CAG   aromatic  1.399  0.020  1.399
 8IR  CAG  OAH   single    1.339  0.020  1.339
 8IR  CAG  CAJ   aromatic  1.394  0.020  1.394
 8IR  OAH  CAI   single    1.416  0.020  1.416
 8IR  CAJ  CAK   aromatic  1.387  0.020  1.387
 8IR  CBD  HBD   single    0.930  0.020  1.080
 8IR  CBE  HBE   single    0.930  0.020  1.080
 8IR  CBF  HBF   single    0.930  0.020  1.080
 8IR  CBG  HBG   single    0.930  0.020  1.080
 8IR  C5   H5    single    0.930  0.020  1.080
 8IR  C2   H2    single    0.930  0.020  1.080
 8IR  C6   H6    single    0.930  0.020  1.080
 8IR  CAP  HAP   single    0.930  0.020  1.080
 8IR  CAN  HAN   single    0.930  0.020  1.080
 8IR  CAQ  HAQ   single    0.930  0.020  1.080
 8IR  CAM  HAM   single    0.930  0.020  1.080
 8IR  NAA  HAA   single    0.860  0.020  1.020
 8IR  CAE  HAE   single    0.930  0.020  1.080
 8IR  CAK  HAK   single    0.930  0.020  1.080
 8IR  CAF  HAF   single    0.930  0.020  1.080
 8IR  CAJ  HAJ   single    0.930  0.020  1.080
 8IR  CAI  HAI1  single    0.970  0.020  1.090
 8IR  CAI  HAI2  single    0.970  0.020  1.090
 8IR  CAI  HAI3  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
 8IR  CBA   CBB  CBD   120.87  3.000
 8IR  CBA   CBB  CL    119.72  3.000
 8IR  CBD   CBB  CL    119.40  3.000
 8IR  HBD   CBD  CBE   120.57  3.000
 8IR  HBD   CBD  CBB   119.91  3.000
 8IR  CBE   CBD  CBB   119.52  3.000
 8IR  HBE   CBE  CBF   120.39  3.000
 8IR  HBE   CBE  CBD   119.38  3.000
 8IR  CBF   CBE  CBD   120.23  3.000
 8IR  HBF   CBF  CBG   119.74  3.000
 8IR  HBF   CBF  CBE   120.37  3.000
 8IR  CBG   CBF  CBE   119.88  3.000
 8IR  HBG   CBG  CBA   119.33  3.000
 8IR  HBG   CBG  CBF   120.10  3.000
 8IR  CBA   CBG  CBF   120.58  3.000
 8IR  NAT   CBA  CBG   120.30  3.000
 8IR  NAT   CBA  CBB   120.78  3.000
 8IR  CBG   CBA  CBB   118.90  3.000
 8IR  CAR   NAT  C4    119.97  3.000
 8IR  CAR   NAT  CBA   120.13  3.000
 8IR  C4    NAT  CBA   118.07  3.000
 8IR  C5    C4   N3    121.57  3.000
 8IR  C5    C4   NAT   121.27  3.000
 8IR  N3    C4   NAT   117.13  3.000
 8IR  C2    N3   C4    116.99  3.000
 8IR  H2    C2   N1    116.89  3.000
 8IR  H2    C2   N3    116.33  3.000
 8IR  N1    C2   N3    126.77  3.000
 8IR  C6    N1   C2    115.70  3.000
 8IR  H6    C6   C5    120.13  3.000
 8IR  H6    C6   N1    117.08  3.000
 8IR  C5    C6   N1    122.79  3.000
 8IR  H5    C5   C6    120.84  3.000
 8IR  H5    C5   C4    122.98  3.000
 8IR  C6    C5   C4    116.18  3.000
 8IR  CAO   CAR  OAS   122.17  3.000
 8IR  CAO   CAR  NAT   116.16  3.000
 8IR  OAS   CAR  NAT   121.67  3.000
 8IR  CAN   CAO  CAP   118.72  3.000
 8IR  CAN   CAO  CAR   122.23  3.000
 8IR  CAP   CAO  CAR   118.93  3.000
 8IR  HAP   CAP  CAQ   118.71  3.000
 8IR  HAP   CAP  CAO   119.79  3.000
 8IR  CAQ   CAP  CAO   121.48  3.000
 8IR  HAQ   CAQ  CAL   121.16  3.000
 8IR  HAQ   CAQ  CAP   119.22  3.000
 8IR  CAL   CAQ  CAP   119.62  3.000
 8IR  HAN   CAN  CAM   118.75  3.000
 8IR  HAN   CAN  CAO   120.85  3.000
 8IR  CAM   CAN  CAO   120.36  3.000
 8IR  HAM   CAM  CAL   119.70  3.000
 8IR  HAM   CAM  CAN   119.41  3.000
 8IR  CAL   CAM  CAN   120.89  3.000
 8IR  NAA   CAL  CAM   116.57  3.000
 8IR  NAA   CAL  CAQ   124.51  3.000
 8IR  CAM   CAL  CAQ   118.92  3.000
 8IR  HAA   NAA  CAB   116.54  3.000
 8IR  HAA   NAA  CAL   114.34  3.000
 8IR  CAB   NAA  CAL   128.77  3.000
 8IR  CAD   CAB  OAC   121.58  3.000
 8IR  CAD   CAB  NAA   115.17  3.000
 8IR  OAC   CAB  NAA   123.24  3.000
 8IR  CAK   CAD  CAE   118.26  3.000
 8IR  CAK   CAD  CAB   123.50  3.000
 8IR  CAE   CAD  CAB   118.21  3.000
 8IR  HAE   CAE  CAF   119.09  3.000
 8IR  HAE   CAE  CAD   119.89  3.000
 8IR  CAF   CAE  CAD   121.01  3.000
 8IR  HAF   CAF  CAG   119.47  3.000
 8IR  HAF   CAF  CAE   120.26  3.000
 8IR  CAG   CAF  CAE   120.27  3.000
 8IR  CAJ   CAG  OAH   124.40  3.000
 8IR  CAJ   CAG  CAF   119.32  3.000
 8IR  OAH   CAG  CAF   116.28  3.000
 8IR  CAI   OAH  CAG   118.79  3.000
 8IR  HAI3  CAI  HAI2  108.90  3.000
 8IR  HAI3  CAI  HAI1  108.92  3.000
 8IR  HAI2  CAI  HAI1  108.99  3.000
 8IR  HAI3  CAI  OAH   106.43  3.000
 8IR  HAI2  CAI  OAH   111.82  3.000
 8IR  HAI1  CAI  OAH   111.69  3.000
 8IR  HAJ   CAJ  CAK   118.67  3.000
 8IR  HAJ   CAJ  CAG   121.61  3.000
 8IR  CAK   CAJ  CAG   119.72  3.000
 8IR  HAK   CAK  CAJ   117.46  3.000
 8IR  HAK   CAK  CAD   121.12  3.000
 8IR  CAJ   CAK  CAD   121.40  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
 8IR  CONST_01  CBF   CBE  CBD  CBB     0.00   0.0  0
 8IR  CONST_02  CBF   CBG  CBA  CBB     0.00   0.0  0
 8IR  CONST_03  CBG   CBA  CBB  CBD     0.00   0.0  0
 8IR  CONST_04  CBG   CBF  CBE  CBD     0.00   0.0  0
 8IR  CONST_05  CBA   CBB  CBD  CBE     0.00   0.0  0
 8IR  CONST_06  CBA   CBG  CBF  CBE     0.00   0.0  0
 8IR  CONST_07  N1    C2   N3   C4      0.00   0.0  0
 8IR  CONST_08  N1    C6   C5   C4      0.00   0.0  0
 8IR  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 8IR  CONST_10  C6    N1   C2   N3      0.00   0.0  0
 8IR  CONST_11  C5    C4   N3   C2      0.00   0.0  0
 8IR  CONST_12  C5    C6   N1   C2      0.00   0.0  0
 8IR  CONST_13  CAL   CAQ  CAP  CAO     0.00   0.0  0
 8IR  CONST_14  CAL   CAM  CAN  CAO     0.00   0.0  0
 8IR  CONST_15  CAM   CAN  CAO  CAP     0.00   0.0  0
 8IR  CONST_16  CAM   CAL  CAQ  CAP     0.00   0.0  0
 8IR  CONST_17  CAN   CAO  CAP  CAQ     0.00   0.0  0
 8IR  CONST_18  CAN   CAM  CAL  CAQ     0.00   0.0  0
 8IR  CONST_19  CAG   CAF  CAE  CAD     0.00   0.0  0
 8IR  CONST_20  CAG   CAJ  CAK  CAD     0.00   0.0  0
 8IR  CONST_21  CAJ   CAK  CAD  CAE     0.00   0.0  0
 8IR  CONST_22  CAJ   CAG  CAF  CAE     0.00   0.0  0
 8IR  CONST_23  CAK   CAD  CAE  CAF     0.00   0.0  0
 8IR  CONST_24  CAK   CAJ  CAG  CAF     0.00   0.0  0
 8IR  CONST_25  CBE   CBD  CBB  CL    180.00   0.0  0
 8IR  CONST_26  CBG   CBA  CBB  CL    180.00   0.0  0
 8IR  CONST_27  NAT   CBA  CBB  CBD   180.00   0.0  0
 8IR  CONST_28  NAT   CBA  CBG  CBF   180.00   0.0  0
 8IR  CONST_29  C2    N3   C4   NAT   180.00   0.0  0
 8IR  CONST_30  C6    C5   C4   NAT   180.00   0.0  0
 8IR  CONST_31  CAQ   CAP  CAO  CAR   180.00   0.0  0
 8IR  CONST_32  CAM   CAN  CAO  CAR   180.00   0.0  0
 8IR  CONST_33  NAA   CAL  CAQ  CAP   180.00   0.0  0
 8IR  CONST_34  NAA   CAL  CAM  CAN   180.00   0.0  0
 8IR  CONST_35  CAF   CAE  CAD  CAB   180.00   0.0  0
 8IR  CONST_36  CAJ   CAK  CAD  CAB   180.00   0.0  0
 8IR  CONST_37  OAH   CAG  CAF  CAE   180.00   0.0  0
 8IR  CONST_38  CAK   CAJ  CAG  OAH   180.00   0.0  0
 8IR  CONST_39  HBE   CBE  CBD  CBB   180.00   0.0  0
 8IR  CONST_40  HBG   CBG  CBA  CBB   180.00   0.0  0
 8IR  CONST_41  HBF   CBF  CBE  CBD   180.00   0.0  0
 8IR  CONST_42  HBD   CBD  CBE  CBF   180.00   0.0  0
 8IR  CONST_43  H2    C2   N3   C4    180.00   0.0  0
 8IR  CONST_44  H6    C6   C5   C4    180.00   0.0  0
 8IR  CONST_45  H5    C5   C4   N3    180.00   0.0  0
 8IR  CONST_46  HAQ   CAQ  CAP  CAO   180.00   0.0  0
 8IR  CONST_47  HAM   CAM  CAN  CAO   180.00   0.0  0
 8IR  CONST_48  HAN   CAN  CAO  CAP   180.00   0.0  0
 8IR  CONST_49  HAP   CAP  CAO  CAN   180.00   0.0  0
 8IR  CONST_50  HAF   CAF  CAE  CAD   180.00   0.0  0
 8IR  CONST_51  HAJ   CAJ  CAK  CAD   180.00   0.0  0
 8IR  CONST_52  HAK   CAK  CAD  CAE   180.00   0.0  0
 8IR  CONST_53  HAE   CAE  CAF  CAG   180.00   0.0  0
 8IR  CONST_56  CAD   CAB  NAA  CAL   180.00   0.0  0
 8IR  CONST_57  CAB   NAA  CAL  CAQ     0.00   0.0  0
 8IR  CONST_58  CAB   NAA  CAL  CAM   180.00   0.0  0
 8IR  CONST_59  HAA   NAA  CAL  CAQ   180.00   0.0  0
 8IR  CONST_62  OAC   CAB  NAA  CAL     0.00   0.0  0
 8IR  Var_01    C4    NAT  CBA  CBB   -66.45  30.0  2
 8IR  Var_02    N3    C4   NAT  CBA   151.81  30.0  2
 8IR  Var_03    CAP   CAO  CAR  NAT   143.88  30.0  2
 8IR  Var_04    CAE   CAD  CAB  NAA  -156.85  30.0  2
 8IR  Var_05    CAJ   CAG  OAH  CAI    -1.63  30.0  3
 8IR  Var_06    HAI1  CAI  OAH  CAG   -59.50  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
 8IR  plan-1  CL   0.020
 8IR  plan-1  CBB  0.020
 8IR  plan-1  CBD  0.020
 8IR  plan-1  CBE  0.020
 8IR  plan-1  CBF  0.020
 8IR  plan-1  CBG  0.020
 8IR  plan-1  CBA  0.020
 8IR  plan-1  NAT  0.020
 8IR  plan-1  HBD  0.020
 8IR  plan-1  HBE  0.020
 8IR  plan-1  HBF  0.020
 8IR  plan-1  HBG  0.020
 8IR  plan-2  NAT  0.020
 8IR  plan-2  C4   0.020
 8IR  plan-2  N3   0.020
 8IR  plan-2  C2   0.020
 8IR  plan-2  N1   0.020
 8IR  plan-2  C6   0.020
 8IR  plan-2  C5   0.020
 8IR  plan-2  H5   0.020
 8IR  plan-2  H2   0.020
 8IR  plan-2  H6   0.020
 8IR  plan-3  CAR  0.020
 8IR  plan-3  CAO  0.020
 8IR  plan-3  CAP  0.020
 8IR  plan-3  CAQ  0.020
 8IR  plan-3  CAN  0.020
 8IR  plan-3  CAM  0.020
 8IR  plan-3  CAL  0.020
 8IR  plan-3  NAA  0.020
 8IR  plan-3  HAP  0.020
 8IR  plan-3  HAN  0.020
 8IR  plan-3  HAQ  0.020
 8IR  plan-3  HAM  0.020
 8IR  plan-4  CAB  0.020
 8IR  plan-4  CAD  0.020
 8IR  plan-4  CAE  0.020
 8IR  plan-4  CAF  0.020
 8IR  plan-4  CAG  0.020
 8IR  plan-4  OAH  0.020
 8IR  plan-4  CAJ  0.020
 8IR  plan-4  CAK  0.020
 8IR  plan-4  HAE  0.020
 8IR  plan-4  HAK  0.020
 8IR  plan-4  HAF  0.020
 8IR  plan-4  HAJ  0.020
 8IR  plan-5  CBA  0.020
 8IR  plan-5  NAT  0.020
 8IR  plan-5  C4   0.020
 8IR  plan-5  CAR  0.020
 8IR  plan-5  OAS  0.020
 8IR  plan-5  CAO  0.020
 8IR  plan-6  CAL  0.020
 8IR  plan-6  NAA  0.020
 8IR  plan-6  CAB  0.020
 8IR  plan-6  OAC  0.020
 8IR  plan-6  CAD  0.020
 8IR  plan-6  HAA  0.020

