# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 23:30:31 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 4-{[4-(biphenyl-2-ylamino)pyrimidin-2-yl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3c4ccccc4)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
 0C0  0C0  '4-{[4-(biphenyl-2-ylamino)pyrimidin-2-yl]amino}benzoic acid'  ligand  46  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0C0
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
 0C0  N01  N  N      0  -0.493  -1.2822  -1.7193  -0.9719
 0C0  N02  N  N      0  -0.518   0.2645   0.0275  -0.5254
 0C0  N03  N  NH1    0  -0.772   2.5190  -0.2103  -0.9962
 0C0  N04  N  NH1    0  -0.768  -1.9206   0.3224  -0.0461
 0C0  C05  C  CR16   0   0.003  -0.2633  -2.4540  -1.4263
 0C0  C06  C  CR6    0   0.604  -0.9598  -0.5087  -0.5406
 0C0  C07  C  CR6    0   0.551   1.2579  -0.7105  -0.9880
 0C0  C08  C  CR16   0  -0.460   1.0343  -2.0188  -1.4657
 0C0  C09  C  CR6    0   0.294   2.9579   1.0502  -0.5738
 0C0  C10  C  CR16   0  -0.272   2.2358   2.2088  -0.8602
 0C0  C11  C  CR16   0  -0.266   2.7332   3.4505  -0.5005
 0C0  C12  C  CR16   0  -0.256   3.9661   3.5584   0.1279
 0C0  C13  C  CR16   0  -0.299   4.6892   2.4094   0.4039
 0C0  C14  C  CR6    0   0.033   4.1976   1.1465   0.0778
 0C0  C15  C  CR6    0   0.025   4.9974  -0.0538   0.4154
 0C0  C16  C  CR6    0   0.352  -3.2953   0.1753   0.0875
 0C0  C17  C  CR16   0  -0.348  -3.9795   1.2347   0.6984
 0C0  C18  C  CR16   0  -0.281  -5.3501   1.1923   0.8675
 0C0  C19  C  CR6    0  -0.115  -6.1005   0.0992   0.4377
 0C0  C20  C  CR16   0  -0.281  -5.4122  -0.9474  -0.1657
 0C0  C21  C  CR16   0  -0.305  -4.0361  -0.9278  -0.3447
 0C0  C22  C  C      0   0.389  -7.6069   0.0546   0.6202
 0C0  C23  C  CR16   0  -0.291   4.4601  -1.0808   1.1945
 0C0  C24  C  CR16   0  -0.237   5.2286  -2.1834   1.5374
 0C0  C25  C  CR16   0  -0.264   6.5457  -2.2792   1.1059
 0C0  C26  C  CR16   0  -0.240   7.0894  -1.2642   0.3305
 0C0  C27  C  CR16   0  -0.291   6.3206  -0.1603  -0.0122
 0C0  O28  O  O      0  -0.598  -8.1942  -0.9590   0.1919
 0C0  O29  O  OC    -1  -0.599  -8.1337   1.0356   1.1824
 0C0  H1   H  HNH1   0   0.411   3.2430  -0.8741  -1.2253
 0C0  H2   H  HNH1   0   0.405  -1.5494   1.2027   0.2783
 0C0  H3   H  HCR6   0   0.268  -0.5136  -3.4483  -1.7788
 0C0  H4   H  HCR6   0   0.276   1.8338  -2.6397  -1.8444
 0C0  H5   H  HCR6   0   0.268   1.2908   2.1406  -1.3777
 0C0  H6   H  HCR6   0   0.259   2.1584   4.3386  -0.7286
 0C0  H7   H  HCR6   0   0.257   4.3616   4.5277   0.4003
 0C0  H8   H  HCR6   0   0.255   5.6457   2.4837   0.9066
 0C0  H9   H  HCR6   0   0.258  -3.4244   2.0997   1.0446
 0C0  H10  H  HCR6   0   0.242  -5.8470   2.0278   1.3427
 0C0  H11  H  HCR6   0   0.240  -5.9639  -1.8113  -0.5134
 0C0  H12  H  HCR6   0   0.277  -3.5432  -1.7623  -0.8148
 0C0  H13  H  HCR6   0   0.258   3.4407  -1.0080   1.5531
 0C0  H14  H  HCR6   0   0.259   4.7983  -2.9665   2.1480
 0C0  H15  H  HCR6   0   0.259   7.1452  -3.1391   1.3752
 0C0  H16  H  HCR6   0   0.259   8.1138  -1.3324  -0.0121
 0C0  H17  H  HCR6   0   0.255   6.7499   0.6236  -0.6240

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
 0C0  O28  C22  deloc     1.247  0.020  1.247
 0C0  O29  C22  deloc     1.247  0.020  1.247
 0C0  C22  C19  single    1.518  0.020  1.518
 0C0  C12  C11  aromatic  1.388  0.020  1.388
 0C0  C12  C13  aromatic  1.385  0.020  1.385
 0C0  C11  C10  aromatic  1.385  0.020  1.385
 0C0  C13  C14  aromatic  1.394  0.020  1.394
 0C0  C19  C20  aromatic  1.390  0.020  1.390
 0C0  C19  C18  aromatic  1.394  0.020  1.394
 0C0  C20  C21  aromatic  1.388  0.020  1.388
 0C0  C18  C17  aromatic  1.382  0.020  1.382
 0C0  C10  C09  aromatic  1.395  0.020  1.395
 0C0  C14  C09  aromatic  1.404  0.020  1.404
 0C0  C14  C15  single    1.481  0.020  1.481
 0C0  C21  C16  aromatic  1.397  0.020  1.397
 0C0  C09  N03  single    1.400  0.020  1.400
 0C0  C15  C27  aromatic  1.395  0.020  1.395
 0C0  C15  C23  aromatic  1.397  0.020  1.397
 0C0  C27  C26  aromatic  1.388  0.020  1.388
 0C0  C17  C16  aromatic  1.401  0.020  1.401
 0C0  C16  N04  single    1.389  0.020  1.389
 0C0  C23  C24  aromatic  1.387  0.020  1.387
 0C0  C26  C25  aromatic  1.388  0.020  1.388
 0C0  N03  C07  single    1.357  0.020  1.357
 0C0  C24  C25  aromatic  1.389  0.020  1.389
 0C0  N02  C07  aromatic  1.321  0.020  1.321
 0C0  N02  C06  aromatic  1.337  0.020  1.337
 0C0  N04  C06  single    1.363  0.020  1.363
 0C0  C07  C08  aromatic  1.411  0.020  1.411
 0C0  C06  N01  aromatic  1.325  0.020  1.325
 0C0  C08  C05  aromatic  1.369  0.020  1.369
 0C0  N01  C05  aromatic  1.336  0.020  1.336
 0C0  N03  H1   single    0.860  0.020  1.020
 0C0  N04  H2   single    0.860  0.020  1.020
 0C0  C05  H3   single    0.930  0.020  1.080
 0C0  C08  H4   single    0.930  0.020  1.080
 0C0  C10  H5   single    0.930  0.020  1.080
 0C0  C11  H6   single    0.930  0.020  1.080
 0C0  C12  H7   single    0.930  0.020  1.080
 0C0  C13  H8   single    0.930  0.020  1.080
 0C0  C17  H9   single    0.930  0.020  1.080
 0C0  C18  H10  single    0.930  0.020  1.080
 0C0  C20  H11  single    0.930  0.020  1.080
 0C0  C21  H12  single    0.930  0.020  1.080
 0C0  C23  H13  single    0.930  0.020  1.080
 0C0  C24  H14  single    0.930  0.020  1.080
 0C0  C25  H15  single    0.930  0.020  1.080
 0C0  C26  H16  single    0.930  0.020  1.080
 0C0  C27  H17  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
 0C0  C06  N01  C05  115.32  3.000
 0C0  C07  N02  C06  117.43  3.000
 0C0  H1   N03  C09  115.85  3.000
 0C0  H1   N03  C07  115.21  3.000
 0C0  C09  N03  C07  128.43  3.000
 0C0  H2   N04  C16  115.19  3.000
 0C0  H2   N04  C06  112.91  3.000
 0C0  C16  N04  C06  131.90  3.000
 0C0  H3   C05  C08  120.07  3.000
 0C0  H3   C05  N01  116.03  3.000
 0C0  C08  C05  N01  123.91  3.000
 0C0  N04  C06  N02  113.38  3.000
 0C0  N04  C06  N01  120.24  3.000
 0C0  N02  C06  N01  126.37  3.000
 0C0  C08  C07  N03  119.16  3.000
 0C0  C08  C07  N02  121.16  3.000
 0C0  N03  C07  N02  119.68  3.000
 0C0  H4   C08  C07  122.29  3.000
 0C0  H4   C08  C05  121.90  3.000
 0C0  C07  C08  C05  115.80  3.000
 0C0  C14  C09  C10  119.70  3.000
 0C0  C14  C09  N03  118.60  3.000
 0C0  C10  C09  N03  121.57  3.000
 0C0  H5   C10  C11  119.70  3.000
 0C0  H5   C10  C09  119.94  3.000
 0C0  C11  C10  C09  120.35  3.000
 0C0  H6   C11  C12  120.23  3.000
 0C0  H6   C11  C10  119.35  3.000
 0C0  C12  C11  C10  120.41  3.000
 0C0  H7   C12  C13  120.15  3.000
 0C0  H7   C12  C11  120.56  3.000
 0C0  C13  C12  C11  119.30  3.000
 0C0  H8   C13  C14  118.83  3.000
 0C0  H8   C13  C12  119.77  3.000
 0C0  C14  C13  C12  121.38  3.000
 0C0  C15  C14  C13  119.37  3.000
 0C0  C15  C14  C09  121.80  3.000
 0C0  C13  C14  C09  118.83  3.000
 0C0  C27  C15  C23  118.68  3.000
 0C0  C23  C15  C14  121.02  3.000
 0C0  C27  C15  C14  120.28  3.000
 0C0  C21  C16  C17  118.22  3.000
 0C0  C17  C16  N04  116.43  3.000
 0C0  C21  C16  N04  125.35  3.000
 0C0  H9   C17  C18  119.55  3.000
 0C0  H9   C17  C16  119.49  3.000
 0C0  C18  C17  C16  120.96  3.000
 0C0  H10  C18  C19  119.58  3.000
 0C0  H10  C18  C17  119.06  3.000
 0C0  C19  C18  C17  121.36  3.000
 0C0  C22  C19  C20  121.41  3.000
 0C0  C20  C19  C18  117.24  3.000
 0C0  C22  C19  C18  121.35  3.000
 0C0  H11  C20  C21  118.37  3.000
 0C0  H11  C20  C19  119.21  3.000
 0C0  C21  C20  C19  122.42  3.000
 0C0  H12  C21  C20  119.94  3.000
 0C0  H12  C21  C16  120.26  3.000
 0C0  C20  C21  C16  119.80  3.000
 0C0  O29  C22  O28  126.51  3.000
 0C0  O29  C22  C19  116.75  3.000
 0C0  O28  C22  C19  116.74  3.000
 0C0  H13  C23  C24  119.54  3.000
 0C0  H13  C23  C15  119.83  3.000
 0C0  C24  C23  C15  120.62  3.000
 0C0  H14  C24  C25  120.15  3.000
 0C0  H14  C24  C23  119.63  3.000
 0C0  C25  C24  C23  120.22  3.000
 0C0  H15  C25  C26  120.19  3.000
 0C0  H15  C25  C24  120.18  3.000
 0C0  C26  C25  C24  119.63  3.000
 0C0  H16  C26  C27  119.74  3.000
 0C0  H16  C26  C25  120.10  3.000
 0C0  C27  C26  C25  120.16  3.000
 0C0  H17  C27  C26  119.70  3.000
 0C0  H17  C27  C15  119.60  3.000
 0C0  C26  C27  C15  120.70  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
 0C0  CONST_01  C07  N02  C06  N01    0.00   0.0  0
 0C0  CONST_02  C07  C08  C05  N01    0.00   0.0  0
 0C0  CONST_03  C05  C08  C07  N02    0.00   0.0  0
 0C0  CONST_04  C05  N01  C06  N02    0.00   0.0  0
 0C0  CONST_05  C08  C07  N02  C06    0.00   0.0  0
 0C0  CONST_06  C08  C05  N01  C06    0.00   0.0  0
 0C0  CONST_07  C12  C11  C10  C09    0.00   0.0  0
 0C0  CONST_08  C12  C13  C14  C09    0.00   0.0  0
 0C0  CONST_11  C13  C12  C11  C10    0.00   0.0  0
 0C0  CONST_12  C13  C14  C09  C10    0.00   0.0  0
 0C0  CONST_13  C15  C14  C09  C10  180.00   0.0  0
 0C0  CONST_14  C14  C13  C12  C11    0.00   0.0  0
 0C0  CONST_15  C14  C09  C10  C11    0.00   0.0  0
 0C0  CONST_16  C15  C14  C13  C12  180.00   0.0  0
 0C0  CONST_19  C26  C27  C15  C14  180.00   0.0  0
 0C0  CONST_20  C24  C23  C15  C14  180.00   0.0  0
 0C0  CONST_21  C25  C26  C27  C15    0.00   0.0  0
 0C0  CONST_22  C25  C24  C23  C15    0.00   0.0  0
 0C0  CONST_23  C19  C20  C21  C16    0.00   0.0  0
 0C0  CONST_24  C19  C18  C17  C16    0.00   0.0  0
 0C0  CONST_25  C20  C19  C18  C17    0.00   0.0  0
 0C0  CONST_26  C20  C21  C16  C17    0.00   0.0  0
 0C0  CONST_27  C21  C20  C19  C18    0.00   0.0  0
 0C0  CONST_28  C21  C16  C17  C18    0.00   0.0  0
 0C0  CONST_29  C26  C27  C15  C23    0.00   0.0  0
 0C0  CONST_30  C26  C25  C24  C23    0.00   0.0  0
 0C0  CONST_31  C27  C15  C23  C24    0.00   0.0  0
 0C0  CONST_32  C27  C26  C25  C24    0.00   0.0  0
 0C0  CONST_33  C11  C10  C09  N03  180.00   0.0  0
 0C0  CONST_34  C13  C14  C09  N03  180.00   0.0  0
 0C0  CONST_35  C15  C14  C09  N03    0.00   0.0  0
 0C0  CONST_36  C06  N02  C07  N03  180.00   0.0  0
 0C0  CONST_37  C05  C08  C07  N03  180.00   0.0  0
 0C0  CONST_38  C20  C21  C16  N04  180.00   0.0  0
 0C0  CONST_39  C18  C17  C16  N04  180.00   0.0  0
 0C0  CONST_40  C07  N02  C06  N04  180.00   0.0  0
 0C0  CONST_41  C05  N01  C06  N04  180.00   0.0  0
 0C0  CONST_42  C22  C19  C18  C17  180.00   0.0  0
 0C0  CONST_43  C22  C19  C20  C21  180.00   0.0  0
 0C0  CONST_44  H4   C08  C05  N01  180.00   0.0  0
 0C0  CONST_45  H3   C05  N01  C06  180.00   0.0  0
 0C0  CONST_46  H6   C11  C10  C09  180.00   0.0  0
 0C0  CONST_47  H8   C13  C14  C09  180.00   0.0  0
 0C0  CONST_48  H7   C12  C11  C10  180.00   0.0  0
 0C0  CONST_49  H5   C10  C11  C12  180.00   0.0  0
 0C0  CONST_50  H17  C27  C15  C14    0.00   0.0  0
 0C0  CONST_51  H13  C23  C15  C14    0.00   0.0  0
 0C0  CONST_52  H16  C26  C27  C15  180.00   0.0  0
 0C0  CONST_53  H14  C24  C23  C15  180.00   0.0  0
 0C0  CONST_54  H11  C20  C21  C16  180.00   0.0  0
 0C0  CONST_55  H10  C18  C17  C16  180.00   0.0  0
 0C0  CONST_56  H12  C21  C16  C17  180.00   0.0  0
 0C0  CONST_57  H9   C17  C18  C19  180.00   0.0  0
 0C0  CONST_58  H15  C25  C24  C23  180.00   0.0  0
 0C0  Var_01    C16  N04  C06  N01   -1.94  30.0  1
 0C0  Var_02    C09  N03  C07  N02   -0.60  30.0  3
 0C0  Var_03    C21  C16  N04  C06   -2.95  30.0  2
 0C0  Var_04    C10  C09  N03  C07  -41.59  30.0  2
 0C0  Var_05    O28  C22  C19  C18  179.31  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
 0C0  plan-1  N01  0.020
 0C0  plan-1  N02  0.020
 0C0  plan-1  N03  0.020
 0C0  plan-1  N04  0.020
 0C0  plan-1  C05  0.020
 0C0  plan-1  C06  0.020
 0C0  plan-1  C07  0.020
 0C0  plan-1  C08  0.020
 0C0  plan-1  H3   0.020
 0C0  plan-1  H4   0.020
 0C0  plan-2  N03  0.020
 0C0  plan-2  C09  0.020
 0C0  plan-2  C10  0.020
 0C0  plan-2  C11  0.020
 0C0  plan-2  C12  0.020
 0C0  plan-2  C13  0.020
 0C0  plan-2  C14  0.020
 0C0  plan-2  C15  0.020
 0C0  plan-2  H5   0.020
 0C0  plan-2  H6   0.020
 0C0  plan-2  H7   0.020
 0C0  plan-2  H8   0.020
 0C0  plan-3  C14  0.020
 0C0  plan-3  C15  0.020
 0C0  plan-3  C23  0.020
 0C0  plan-3  C24  0.020
 0C0  plan-3  C25  0.020
 0C0  plan-3  C26  0.020
 0C0  plan-3  C27  0.020
 0C0  plan-3  H13  0.020
 0C0  plan-3  H14  0.020
 0C0  plan-3  H15  0.020
 0C0  plan-3  H16  0.020
 0C0  plan-3  H17  0.020
 0C0  plan-4  N04  0.020
 0C0  plan-4  C16  0.020
 0C0  plan-4  C17  0.020
 0C0  plan-4  C18  0.020
 0C0  plan-4  C19  0.020
 0C0  plan-4  C20  0.020
 0C0  plan-4  C21  0.020
 0C0  plan-4  C22  0.020
 0C0  plan-4  H9   0.020
 0C0  plan-4  H10  0.020
 0C0  plan-4  H11  0.020
 0C0  plan-4  H12  0.020
 0C0  plan-5  C19  0.020
 0C0  plan-5  C22  0.020
 0C0  plan-5  O28  0.020
 0C0  plan-5  O29  0.020

