# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 00:31:00 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-chloro-N-[4-({5-fluoro-2-[(4-hydroxyphenyl)amino]pyrimidin-4-yl}amino)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(Nc2ncc(F)c(Nc3ccc(NC(=O)c4ccccc4Cl)cc3)n2)cc1
#
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
 48B  48B  2-chloro-N-[4-({5-fluoro-2-[(4-hydroxyphenyl)amino]pyrimidin-4-yl}amino)phenyl]benzamide  ligand  49  32  .  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_48B
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
 48B  F23   F   F     0  -0.307   3.0711  -4.4948   0.0362
 48B  C17   C   CR6   0   0.303   3.3933  -3.1887   0.0552
 48B  C18   C   CR16  0  -0.141   4.6809  -2.7649  -0.0426
 48B  N19   N   N     0  -0.486   5.0063  -1.4678  -0.0271
 48B  C20   C   CR6   0   0.622   3.9973  -0.6198   0.0889
 48B  N24   N   NH1   0  -0.772   4.2271   0.7199   0.1196
 48B  C30   C   CR6   0   0.341   5.4095   1.4561   0.0367
 48B  C29   C   CR16  0  -0.342   5.3006   2.8393   0.2031
 48B  C28   C   CR16  0  -0.370   6.4065   3.6669   0.1217
 48B  C27   C   CR6   0   0.333   7.6666   3.1315  -0.1274
 48B  O31   O   OH1   0  -0.639   8.7833   3.8883  -0.2214
 48B  C26   C   CR16  0  -0.327   7.7852   1.7568  -0.2896
 48B  C25   C   CR16  0  -0.301   6.6771   0.9254  -0.2105
 48B  N21   N   N     0  -0.531   2.7002  -0.9447   0.1875
 48B  C22   C   CR6   0   0.450   2.3719  -2.2214   0.1720
 48B  N16   N   NH1   0  -0.778   1.0870  -2.6316   0.2625
 48B  C11   C   CR6   0   0.359  -0.1021  -1.9055   0.3293
 48B  C10   C   CR16  0  -0.353  -1.2854  -2.6462   0.3157
 48B  C12   C   CR16  0  -0.297  -0.1977  -0.5162   0.4125
 48B  C13   C   CR16  0  -0.336  -1.4426   0.0874   0.4624
 48B  C14   C   CR6   0   0.363  -2.6223  -0.6526   0.4376
 48B  C15   C   CR16  0  -0.298  -2.5282  -2.0425   0.3698
 48B  N9    N   NH1   0  -0.730  -3.8275   0.0594   0.4980
 48B  C7    C   C     0   0.496  -5.0832  -0.3847   0.2646
 48B  O8    O   O     0  -0.446  -5.3750  -1.5261  -0.0385
 48B  C4    C   CR6   0   0.014  -6.1298   0.6725   0.4384
 48B  C5    C   CR6   0  -0.084  -7.0496   0.9630  -0.5655
 48B  CL1   CL  CL    0  -0.116  -6.9333   0.1971  -2.1137
 48B  C6    C   CR16  0  -0.198  -8.0511   1.9003  -0.3690
 48B  C3    C   CR16  0  -0.277  -6.2391   1.3437   1.6537
 48B  C2    C   CR16  0  -0.232  -7.2460   2.2728   1.8666
 48B  C1    C   CR16  0  -0.260  -8.1515   2.5490   0.8533
 48B  H18   H   HCR6  0   0.289   5.4895  -3.4816  -0.1380
 48B  HN24  H   HNH1  0   0.408   3.3882   1.2667   0.2385
 48B  H29   H   HCR6  0   0.270   4.3315   3.2823   0.4016
 48B  H28   H   HCR6  0   0.272   6.2775   4.7352   0.2535
 48B  HO31  H   HOH1  0   0.472   8.5659   4.8193  -0.1041
 48B  H26   H   HCR6  0   0.261   8.7579   1.3225  -0.4856
 48B  H25   H   HCR6  0   0.285   6.8071  -0.1364  -0.3401
 48B  HN16  H   HNH1  0   0.421   0.9560  -3.6313   0.2397
 48B  H10   H   HCR6  0   0.274  -1.2404  -3.7278   0.2611
 48B  H12   H   HCR6  0   0.294   0.6855   0.0996   0.4343
 48B  H13   H   HCR6  0   0.273  -1.4890   1.1687   0.5200
 48B  H15   H   HCR6  0   0.284  -3.4062  -2.6664   0.3582
 48B  HN9   H   HNH1  0   0.424  -3.7260   1.0521   0.6498
 48B  H6    H   HCR6  0   0.286  -8.7467   2.1237  -1.1662
 48B  H3    H   HCR6  0   0.278  -5.5391   1.1224   2.4498
 48B  H2    H   HCR6  0   0.271  -7.3216   2.7761   2.8208
 48B  H1    H   HCR6  0   0.276  -8.9396   3.2741   1.0050

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
 48B  F23  C17   single    1.345  0.020  1.345
 48B  C17  C18   aromatic  1.359  0.020  1.359
 48B  C17  C22   aromatic  1.412  0.020  1.412
 48B  C18  N19   aromatic  1.337  0.020  1.337
 48B  N19  C20   aromatic  1.323  0.020  1.323
 48B  C20  N24   single    1.360  0.020  1.360
 48B  C20  N21   aromatic  1.341  0.020  1.341
 48B  N24  C30   single    1.395  0.020  1.395
 48B  C30  C29   aromatic  1.397  0.020  1.397
 48B  C30  C25   aromatic  1.396  0.020  1.396
 48B  C29  C28   aromatic  1.384  0.020  1.384
 48B  C28  C27   aromatic  1.392  0.020  1.392
 48B  C27  O31   single    1.352  0.020  1.352
 48B  C27  C26   aromatic  1.389  0.020  1.389
 48B  C26  C25   aromatic  1.388  0.020  1.388
 48B  N21  C22   aromatic  1.318  0.020  1.318
 48B  C22  N16   single    1.352  0.020  1.352
 48B  N16  C11   single    1.395  0.020  1.395
 48B  C11  C10   aromatic  1.396  0.020  1.396
 48B  C11  C12   aromatic  1.395  0.020  1.395
 48B  C10  C15   aromatic  1.383  0.020  1.383
 48B  C12  C13   aromatic  1.384  0.020  1.384
 48B  C13  C14   aromatic  1.393  0.020  1.393
 48B  C14  C15   aromatic  1.395  0.020  1.395
 48B  C14  N9    single    1.401  0.020  1.401
 48B  N9   C7    single    1.352  0.020  1.352
 48B  C7   O8    double    1.216  0.020  1.216
 48B  C7   C4    single    1.498  0.020  1.498
 48B  C4   C5    aromatic  1.392  0.020  1.392
 48B  C4   C3    aromatic  1.393  0.020  1.393
 48B  C5   CL1   single    1.731  0.020  1.731
 48B  C5   C6    aromatic  1.386  0.020  1.386
 48B  C6   C1    aromatic  1.387  0.020  1.387
 48B  C3   C2    aromatic  1.386  0.020  1.386
 48B  C2   C1    aromatic  1.387  0.020  1.387
 48B  C18  H18   single    0.930  0.020  1.080
 48B  N24  HN24  single    0.860  0.020  1.020
 48B  C29  H29   single    0.930  0.020  1.080
 48B  C28  H28   single    0.930  0.020  1.080
 48B  O31  HO31  single    0.850  0.020  0.980
 48B  C26  H26   single    0.930  0.020  1.080
 48B  C25  H25   single    0.930  0.020  1.080
 48B  N16  HN16  single    0.860  0.020  1.020
 48B  C10  H10   single    0.930  0.020  1.080
 48B  C12  H12   single    0.930  0.020  1.080
 48B  C13  H13   single    0.930  0.020  1.080
 48B  C15  H15   single    0.930  0.020  1.080
 48B  N9   HN9   single    0.860  0.020  1.020
 48B  C6   H6    single    0.930  0.020  1.080
 48B  C3   H3    single    0.930  0.020  1.080
 48B  C2   H2    single    0.930  0.020  1.080
 48B  C1   H1    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
 48B  C22   C17  C18  118.54  3.000
 48B  C22   C17  F23  119.55  3.000
 48B  C18   C17  F23  121.91  3.000
 48B  H18   C18  N19  117.42  3.000
 48B  H18   C18  C17  120.43  3.000
 48B  N19   C18  C17  122.15  3.000
 48B  C20   N19  C18  115.92  3.000
 48B  N21   C20  N24  113.62  3.000
 48B  N21   C20  N19  126.07  3.000
 48B  N24   C20  N19  120.31  3.000
 48B  HN24  N24  C30  115.20  3.000
 48B  HN24  N24  C20  113.35  3.000
 48B  C30   N24  C20  131.43  3.000
 48B  C25   C30  C29  117.91  3.000
 48B  C25   C30  N24  125.40  3.000
 48B  C29   C30  N24  116.69  3.000
 48B  H29   C29  C28  118.74  3.000
 48B  H29   C29  C30  119.74  3.000
 48B  C28   C29  C30  121.52  3.000
 48B  H28   C28  C27  120.57  3.000
 48B  H28   C28  C29  119.16  3.000
 48B  C27   C28  C29  120.27  3.000
 48B  C26   C27  O31  118.37  3.000
 48B  C26   C27  C28  118.61  3.000
 48B  O31   C27  C28  123.01  3.000
 48B  HO31  O31  C27  110.25  3.000
 48B  H26   C26  C25  119.16  3.000
 48B  H26   C26  C27  119.64  3.000
 48B  C25   C26  C27  121.20  3.000
 48B  H25   C25  C26  119.15  3.000
 48B  H25   C25  C30  120.36  3.000
 48B  C26   C25  C30  120.48  3.000
 48B  C22   N21  C20  118.34  3.000
 48B  N16   C22  N21  121.99  3.000
 48B  N16   C22  C17  119.04  3.000
 48B  N21   C22  C17  118.98  3.000
 48B  HN16  N16  C11  113.98  3.000
 48B  HN16  N16  C22  115.01  3.000
 48B  C11   N16  C22  130.96  3.000
 48B  C12   C11  C10  118.09  3.000
 48B  C12   C11  N16  125.43  3.000
 48B  C10   C11  N16  116.48  3.000
 48B  H10   C10  C15  118.36  3.000
 48B  H10   C10  C11  119.65  3.000
 48B  C15   C10  C11  121.99  3.000
 48B  H12   C12  C13  119.18  3.000
 48B  H12   C12  C11  120.96  3.000
 48B  C13   C12  C11  119.86  3.000
 48B  H13   C13  C14  119.65  3.000
 48B  H13   C13  C12  118.38  3.000
 48B  C14   C13  C12  121.97  3.000
 48B  N9    C14  C15  124.51  3.000
 48B  N9    C14  C13  117.25  3.000
 48B  C15   C14  C13  118.24  3.000
 48B  H15   C15  C14  121.52  3.000
 48B  H15   C15  C10  118.64  3.000
 48B  C14   C15  C10  119.84  3.000
 48B  HN9   N9   C7   116.26  3.000
 48B  HN9   N9   C14  114.82  3.000
 48B  C7    N9   C14  128.64  3.000
 48B  C4    C7   O8   121.57  3.000
 48B  C4    C7   N9   113.39  3.000
 48B  O8    C7   N9   125.03  3.000
 48B  C3    C4   C5   118.48  3.000
 48B  C3    C4   C7   119.75  3.000
 48B  C5    C4   C7   121.69  3.000
 48B  C6    C5   CL1  118.34  3.000
 48B  C6    C5   C4   121.09  3.000
 48B  CL1   C5   C4   120.54  3.000
 48B  H6    C6   C1   120.42  3.000
 48B  H6    C6   C5   120.01  3.000
 48B  C1    C6   C5   119.57  3.000
 48B  H3    C3   C2   119.57  3.000
 48B  H3    C3   C4   119.49  3.000
 48B  C2    C3   C4   120.93  3.000
 48B  H2    C2   C1   120.42  3.000
 48B  H2    C2   C3   119.88  3.000
 48B  C1    C2   C3   119.70  3.000
 48B  H1    C1   C2   120.45  3.000
 48B  H1    C1   C6   119.33  3.000
 48B  C2    C1   C6   120.22  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
 48B  CONST_01  C20  N19  C18  C17     0.00   0.0  0
 48B  CONST_02  C20  N21  C22  C17     0.00   0.0  0
 48B  CONST_03  N21  C22  C17  C18     0.00   0.0  0
 48B  CONST_04  N21  C20  N19  C18     0.00   0.0  0
 48B  CONST_05  C22  C17  C18  N19     0.00   0.0  0
 48B  CONST_06  C22  N21  C20  N19     0.00   0.0  0
 48B  CONST_07  C27  C28  C29  C30     0.00   0.0  0
 48B  CONST_08  C27  C26  C25  C30     0.00   0.0  0
 48B  CONST_09  C26  C25  C30  C29     0.00   0.0  0
 48B  CONST_10  C26  C27  C28  C29     0.00   0.0  0
 48B  CONST_11  C25  C30  C29  C28     0.00   0.0  0
 48B  CONST_12  C25  C26  C27  C28     0.00   0.0  0
 48B  CONST_13  C14  C15  C10  C11     0.00   0.0  0
 48B  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 48B  CONST_15  C13  C12  C11  C10     0.00   0.0  0
 48B  CONST_16  C13  C14  C15  C10     0.00   0.0  0
 48B  CONST_17  C15  C10  C11  C12     0.00   0.0  0
 48B  CONST_18  C15  C14  C13  C12     0.00   0.0  0
 48B  CONST_19  C1   C6   C5   C4      0.00   0.0  0
 48B  CONST_20  C1   C2   C3   C4      0.00   0.0  0
 48B  CONST_21  C2   C3   C4   C5      0.00   0.0  0
 48B  CONST_22  C2   C1   C6   C5      0.00   0.0  0
 48B  CONST_23  C3   C4   C5   C6      0.00   0.0  0
 48B  CONST_24  C3   C2   C1   C6      0.00   0.0  0
 48B  CONST_25  N19  C18  C17  F23   180.00   0.0  0
 48B  CONST_26  N21  C22  C17  F23   180.00   0.0  0
 48B  CONST_27  N16  C22  C17  C18   180.00   0.0  0
 48B  CONST_28  N24  C20  N19  C18   180.00   0.0  0
 48B  CONST_29  N16  C22  N21  C20   180.00   0.0  0
 48B  CONST_30  C22  N21  C20  N24   180.00   0.0  0
 48B  CONST_31  C28  C29  C30  N24   180.00   0.0  0
 48B  CONST_32  C26  C25  C30  N24   180.00   0.0  0
 48B  CONST_33  O31  C27  C28  C29   180.00   0.0  0
 48B  CONST_34  C25  C26  C27  O31   180.00   0.0  0
 48B  CONST_35  C15  C10  C11  N16   180.00   0.0  0
 48B  CONST_36  C13  C12  C11  N16   180.00   0.0  0
 48B  CONST_37  N9   C14  C15  C10   180.00   0.0  0
 48B  CONST_38  N9   C14  C13  C12   180.00   0.0  0
 48B  CONST_39  C6   C5   C4   C7    180.00   0.0  0
 48B  CONST_40  C2   C3   C4   C7    180.00   0.0  0
 48B  CONST_41  C3   C4   C5   CL1   180.00   0.0  0
 48B  CONST_42  C1   C6   C5   CL1   180.00   0.0  0
 48B  CONST_43  H18  C18  N19  C20   180.00   0.0  0
 48B  CONST_44  H28  C28  C29  C30   180.00   0.0  0
 48B  CONST_45  H26  C26  C25  C30   180.00   0.0  0
 48B  CONST_46  H25  C25  C30  C29   180.00   0.0  0
 48B  CONST_47  H29  C29  C28  C27   180.00   0.0  0
 48B  CONST_48  H15  C15  C10  C11   180.00   0.0  0
 48B  CONST_49  H13  C13  C12  C11   180.00   0.0  0
 48B  CONST_50  H12  C12  C11  C10   180.00   0.0  0
 48B  CONST_51  H10  C10  C11  C12   180.00   0.0  0
 48B  CONST_52  H6   C6   C5   C4    180.00   0.0  0
 48B  CONST_53  H2   C2   C3   C4    180.00   0.0  0
 48B  CONST_54  H3   C3   C4   C5    180.00   0.0  0
 48B  CONST_55  H1   C1   C6   C5    180.00   0.0  0
 48B  CONST_56  C4   C7   N9   C14   180.00   0.0  0
 48B  CONST_57  C7   N9   C14  C13   180.00   0.0  0
 48B  CONST_58  C7   N9   C14  C15     0.00   0.0  0
 48B  CONST_59  HN9  N9   C14  C13     0.00   0.0  0
 48B  CONST_60  O8   C7   N9   C14     0.00   0.0  0
 48B  Var_01    C11  N16  C22  C17  -177.01  30.0  2
 48B  Var_02    C30  N24  C20  N19     0.63  30.0  2
 48B  Var_03    C29  C30  N24  C20  -175.34  30.0  2
 48B  Var_04    C10  C11  N16  C22   175.31  30.0  2
 48B  Var_05    C5   C4   C7   N9    126.16  30.0  2

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
 48B  plan-1  F23  0.020
 48B  plan-1  C17  0.020
 48B  plan-1  C18  0.020
 48B  plan-1  N19  0.020
 48B  plan-1  C20  0.020
 48B  plan-1  N24  0.020
 48B  plan-1  N21  0.020
 48B  plan-1  C22  0.020
 48B  plan-1  N16  0.020
 48B  plan-1  H18  0.020
 48B  plan-2  N24  0.020
 48B  plan-2  C30  0.020
 48B  plan-2  C29  0.020
 48B  plan-2  C28  0.020
 48B  plan-2  C27  0.020
 48B  plan-2  O31  0.020
 48B  plan-2  C26  0.020
 48B  plan-2  C25  0.020
 48B  plan-2  H29  0.020
 48B  plan-2  H28  0.020
 48B  plan-2  H26  0.020
 48B  plan-2  H25  0.020
 48B  plan-3  N16  0.020
 48B  plan-3  C11  0.020
 48B  plan-3  C10  0.020
 48B  plan-3  C12  0.020
 48B  plan-3  C13  0.020
 48B  plan-3  C14  0.020
 48B  plan-3  C15  0.020
 48B  plan-3  N9   0.020
 48B  plan-3  H10  0.020
 48B  plan-3  H12  0.020
 48B  plan-3  H13  0.020
 48B  plan-3  H15  0.020
 48B  plan-4  C7   0.020
 48B  plan-4  C4   0.020
 48B  plan-4  C5   0.020
 48B  plan-4  CL1  0.020
 48B  plan-4  C6   0.020
 48B  plan-4  C3   0.020
 48B  plan-4  C2   0.020
 48B  plan-4  C1   0.020
 48B  plan-4  H6   0.020
 48B  plan-4  H3   0.020
 48B  plan-4  H2   0.020
 48B  plan-4  H1   0.020
 48B  plan-5  C14  0.020
 48B  plan-5  N9   0.020
 48B  plan-5  C7   0.020
 48B  plan-5  O8   0.020
 48B  plan-5  C4   0.020
 48B  plan-5  HN9  0.020

