# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:25:26 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-{[4-(phenylamino)pyrimidin-2-yl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3)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
 0BX  0BX  '4-{[4-(phenylamino)pyrimidin-2-yl]amino}benzoic acid'  ligand  37  23  .  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_0BX
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
 0BX  C06  C  CR6   0  -0.103  -4.7559   0.5258  -0.0324
 0BX  C11  C  C     0   0.524  -6.2135   0.7475  -0.0342
 0BX  C05  C  CR16  0  -0.245  -3.9065   1.6285  -0.1423
 0BX  C10  C  CR16  0  -0.347  -2.5401   1.4674  -0.1436
 0BX  C09  C  CR6   0   0.380  -1.9620   0.1919  -0.0369
 0BX  C08  C  CR16  0  -0.301  -2.8097  -0.9168   0.0719
 0BX  C07  C  CR16  0  -0.250  -4.1821  -0.7396   0.0745
 0BX  N01  N  NH1   0  -0.771  -0.5838   0.1423  -0.0433
 0BX  C12  C  CR6   0   0.625   0.2929  -0.9077   0.0089
 0BX  N03  N  N     0  -0.493  -0.1563  -2.1483   0.0598
 0BX  C15  C  CR16  0   0.005   0.7877  -3.0956   0.1019
 0BX  C14  C  CR16  0  -0.463   2.1296  -2.8314   0.0960
 0BX  C13  C  CR6   0   0.577   2.4937  -1.4679   0.0442
 0BX  N02  N  N     0  -0.533   1.5713  -0.5220  -0.0011
 0BX  N04  N  NH1   0  -0.777   3.8106  -1.1470   0.0449
 0BX  C16  C  CR6   0   0.361   4.4683   0.0821   0.0146
 0BX  C17  C  CR16  0  -0.358   5.8653   0.0347   0.0981
 0BX  C18  C  CR16  0  -0.243   6.6171   1.1952   0.0718
 0BX  C19  C  CR16  0  -0.277   5.9970   2.4342  -0.0369
 0BX  C20  C  CR16  0  -0.244   4.6140   2.4832  -0.1195
 0BX  C21  C  CR16  0  -0.314   3.8441   1.3269  -0.0956
 0BX  O22  O  OH1   0  -0.598  -6.9138  -0.3743   0.0937
 0BX  O23  O  O     0  -0.449  -6.7337   1.8351  -0.1396
 0BX  H1   H  HCR6  0   0.265  -4.3178   2.6253  -0.2286
 0BX  H2   H  HCR6  0   0.275  -1.9016   2.3384  -0.2301
 0BX  H3   H  HCR6  0   0.292  -2.3993  -1.9093   0.1538
 0BX  H4   H  HCR6  0   0.266  -4.8046  -1.6196   0.1626
 0BX  H5   H  HNH1  0   0.414  -0.1197   1.0367  -0.1002
 0BX  H6   H  HCR6  0   0.272   0.4346  -4.1197   0.1429
 0BX  H7   H  HCR6  0   0.283   2.8651  -3.6221   0.1313
 0BX  H8   H  HNH1  0   0.418   4.4293  -1.9419   0.0936
 0BX  H9   H  HCR6  0   0.268   6.3647  -0.9235   0.1877
 0BX  H10  H  HCR6  0   0.259   7.6952   1.1275   0.1365
 0BX  H11  H  HCR6  0   0.254   6.5841   3.3426  -0.0567
 0BX  H12  H  HCR6  0   0.256   4.1114   3.4383  -0.2060
 0BX  H13  H  HCR6  0   0.288   2.7714   1.3974  -0.1596
 0BX  H14  H  HOH1  0   0.485  -7.8606  -0.1718   0.0850

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
 0BX  C20  C19  aromatic  1.386  0.020  1.386
 0BX  C20  C21  aromatic  1.389  0.020  1.389
 0BX  C19  C18  aromatic  1.390  0.020  1.390
 0BX  C21  C16  aromatic  1.397  0.020  1.397
 0BX  C18  C17  aromatic  1.383  0.020  1.383
 0BX  C16  C17  aromatic  1.400  0.020  1.400
 0BX  C16  N04  single    1.394  0.020  1.394
 0BX  N04  C13  single    1.355  0.020  1.355
 0BX  C14  C13  aromatic  1.412  0.020  1.412
 0BX  C14  C15  aromatic  1.368  0.020  1.368
 0BX  C13  N02  aromatic  1.322  0.020  1.322
 0BX  C15  N03  aromatic  1.338  0.020  1.338
 0BX  N02  C12  aromatic  1.335  0.020  1.335
 0BX  C08  C07  aromatic  1.384  0.020  1.384
 0BX  C08  C09  aromatic  1.400  0.020  1.400
 0BX  C07  C06  aromatic  1.394  0.020  1.394
 0BX  C12  N03  aromatic  1.320  0.020  1.320
 0BX  C12  N01  single    1.369  0.020  1.369
 0BX  O23  C11  double    1.210  0.020  1.210
 0BX  C09  N01  single    1.379  0.020  1.379
 0BX  C09  C10  aromatic  1.404  0.020  1.404
 0BX  C06  C11  single    1.474  0.020  1.474
 0BX  C06  C05  aromatic  1.396  0.020  1.396
 0BX  C11  O22  single    1.329  0.020  1.329
 0BX  C10  C05  aromatic  1.376  0.020  1.376
 0BX  C05  H1   single    0.930  0.020  1.080
 0BX  C10  H2   single    0.930  0.020  1.080
 0BX  C08  H3   single    0.930  0.020  1.080
 0BX  C07  H4   single    0.930  0.020  1.080
 0BX  N01  H5   single    0.860  0.020  1.020
 0BX  C15  H6   single    0.930  0.020  1.080
 0BX  C14  H7   single    0.930  0.020  1.080
 0BX  N04  H8   single    0.860  0.020  1.020
 0BX  C17  H9   single    0.930  0.020  1.080
 0BX  C18  H10  single    0.930  0.020  1.080
 0BX  C19  H11  single    0.930  0.020  1.080
 0BX  C20  H12  single    0.930  0.020  1.080
 0BX  C21  H13  single    0.930  0.020  1.080
 0BX  O22  H14  single    0.850  0.020  0.980

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
 0BX  C07  C06  C05  118.21  3.000
 0BX  C05  C06  C11  118.86  3.000
 0BX  C07  C06  C11  122.94  3.000
 0BX  O23  C11  O22  122.73  3.000
 0BX  O22  C11  C06  113.20  3.000
 0BX  O23  C11  C06  124.07  3.000
 0BX  H1   C05  C10  119.04  3.000
 0BX  H1   C05  C06  120.18  3.000
 0BX  C10  C05  C06  120.78  3.000
 0BX  H2   C10  C09  119.58  3.000
 0BX  H2   C10  C05  119.42  3.000
 0BX  C09  C10  C05  121.00  3.000
 0BX  N01  C09  C08  125.24  3.000
 0BX  N01  C09  C10  116.34  3.000
 0BX  C08  C09  C10  118.42  3.000
 0BX  H3   C08  C07  119.71  3.000
 0BX  H3   C08  C09  120.33  3.000
 0BX  C07  C08  C09  119.95  3.000
 0BX  H4   C07  C08  117.83  3.000
 0BX  H4   C07  C06  120.53  3.000
 0BX  C08  C07  C06  121.64  3.000
 0BX  H5   N01  C12  112.79  3.000
 0BX  H5   N01  C09  115.34  3.000
 0BX  C12  N01  C09  131.87  3.000
 0BX  N02  C12  N03  126.68  3.000
 0BX  N03  C12  N01  120.28  3.000
 0BX  N02  C12  N01  113.04  3.000
 0BX  C15  N03  C12  115.24  3.000
 0BX  H6   C15  C14  120.15  3.000
 0BX  H6   C15  N03  116.12  3.000
 0BX  C14  C15  N03  123.73  3.000
 0BX  H7   C14  C13  122.16  3.000
 0BX  H7   C14  C15  121.76  3.000
 0BX  C13  C14  C15  116.08  3.000
 0BX  N04  C13  N02  120.56  3.000
 0BX  N02  C13  C14  120.81  3.000
 0BX  N04  C13  C14  118.62  3.000
 0BX  C13  N02  C12  117.45  3.000
 0BX  H8   N04  C16  113.99  3.000
 0BX  H8   N04  C13  114.17  3.000
 0BX  C16  N04  C13  131.83  3.000
 0BX  C21  C16  C17  118.73  3.000
 0BX  C17  C16  N04  116.07  3.000
 0BX  C21  C16  N04  125.21  3.000
 0BX  H9   C17  C18  119.52  3.000
 0BX  H9   C17  C16  119.63  3.000
 0BX  C18  C17  C16  120.85  3.000
 0BX  H10  C18  C19  120.33  3.000
 0BX  H10  C18  C17  119.21  3.000
 0BX  C19  C18  C17  120.47  3.000
 0BX  H11  C19  C20  120.70  3.000
 0BX  H11  C19  C18  120.53  3.000
 0BX  C20  C19  C18  118.77  3.000
 0BX  H12  C20  C21  118.57  3.000
 0BX  H12  C20  C19  119.94  3.000
 0BX  C21  C20  C19  121.49  3.000
 0BX  H13  C21  C20  119.77  3.000
 0BX  H13  C21  C16  120.54  3.000
 0BX  C20  C21  C16  119.70  3.000
 0BX  H14  O22  C11  109.75  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
 0BX  CONST_01  C09  C08  C07  C06     0.00   0.0  0
 0BX  CONST_02  C09  C10  C05  C06     0.00   0.0  0
 0BX  CONST_03  C08  C07  C06  C05     0.00   0.0  0
 0BX  CONST_04  C08  C09  C10  C05     0.00   0.0  0
 0BX  CONST_05  C07  C08  C09  C10     0.00   0.0  0
 0BX  CONST_06  C07  C06  C05  C10     0.00   0.0  0
 0BX  CONST_07  C14  C13  N02  C12     0.00   0.0  0
 0BX  CONST_08  C14  C15  N03  C12     0.00   0.0  0
 0BX  CONST_09  C13  C14  C15  N03     0.00   0.0  0
 0BX  CONST_10  C13  N02  C12  N03     0.00   0.0  0
 0BX  CONST_11  N02  C13  C14  C15     0.00   0.0  0
 0BX  CONST_12  N02  C12  N03  C15     0.00   0.0  0
 0BX  CONST_13  C19  C20  C21  C16     0.00   0.0  0
 0BX  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 0BX  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 0BX  CONST_16  C20  C21  C16  C17     0.00   0.0  0
 0BX  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 0BX  CONST_18  C21  C16  C17  C18     0.00   0.0  0
 0BX  CONST_19  C08  C07  C06  C11   180.00   0.0  0
 0BX  CONST_20  C10  C05  C06  C11   180.00   0.0  0
 0BX  CONST_21  N01  C09  C10  C05   180.00   0.0  0
 0BX  CONST_22  N01  C09  C08  C07   180.00   0.0  0
 0BX  CONST_23  C13  N02  C12  N01   180.00   0.0  0
 0BX  CONST_24  C15  N03  C12  N01   180.00   0.0  0
 0BX  CONST_25  N04  C13  N02  C12   180.00   0.0  0
 0BX  CONST_26  N04  C13  C14  C15   180.00   0.0  0
 0BX  CONST_27  C20  C21  C16  N04   180.00   0.0  0
 0BX  CONST_28  C18  C17  C16  N04   180.00   0.0  0
 0BX  CONST_29  H3   C08  C07  C06   180.00   0.0  0
 0BX  CONST_30  H2   C10  C05  C06   180.00   0.0  0
 0BX  CONST_31  H4   C07  C06  C05   180.00   0.0  0
 0BX  CONST_32  H1   C05  C10  C09   180.00   0.0  0
 0BX  CONST_33  H6   C15  N03  C12   180.00   0.0  0
 0BX  CONST_34  H7   C14  C15  N03   180.00   0.0  0
 0BX  CONST_35  H12  C20  C21  C16   180.00   0.0  0
 0BX  CONST_36  H10  C18  C17  C16   180.00   0.0  0
 0BX  CONST_37  H11  C19  C18  C17   180.00   0.0  0
 0BX  CONST_38  H13  C21  C16  C17   180.00   0.0  0
 0BX  CONST_39  H9   C17  C18  C19   180.00   0.0  0
 0BX  CONST_40  H14  O22  C11  C06   180.00   0.0  0
 0BX  Var_01    C12  N01  C09  C10  -178.18  30.0  2
 0BX  Var_02    N02  C12  N01  C09  -179.08  30.0  1
 0BX  Var_03    C16  N04  C13  C14  -179.28  30.0  2
 0BX  Var_04    C21  C16  N04  C13    -3.51  30.0  2
 0BX  Var_05    O23  C11  C06  C05     0.79  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
 0BX  plan-1  C06  0.020
 0BX  plan-1  C11  0.020
 0BX  plan-1  C05  0.020
 0BX  plan-1  C10  0.020
 0BX  plan-1  C09  0.020
 0BX  plan-1  C08  0.020
 0BX  plan-1  C07  0.020
 0BX  plan-1  N01  0.020
 0BX  plan-1  H1   0.020
 0BX  plan-1  H2   0.020
 0BX  plan-1  H3   0.020
 0BX  plan-1  H4   0.020
 0BX  plan-2  N01  0.020
 0BX  plan-2  C12  0.020
 0BX  plan-2  N03  0.020
 0BX  plan-2  C15  0.020
 0BX  plan-2  C14  0.020
 0BX  plan-2  C13  0.020
 0BX  plan-2  N02  0.020
 0BX  plan-2  N04  0.020
 0BX  plan-2  H6   0.020
 0BX  plan-2  H7   0.020
 0BX  plan-3  N04  0.020
 0BX  plan-3  C16  0.020
 0BX  plan-3  C17  0.020
 0BX  plan-3  C18  0.020
 0BX  plan-3  C19  0.020
 0BX  plan-3  C20  0.020
 0BX  plan-3  C21  0.020
 0BX  plan-3  H9   0.020
 0BX  plan-3  H10  0.020
 0BX  plan-3  H11  0.020
 0BX  plan-3  H12  0.020
 0BX  plan-3  H13  0.020
 0BX  plan-4  C06  0.020
 0BX  plan-4  C11  0.020
 0BX  plan-4  O22  0.020
 0BX  plan-4  O23  0.020
 0BX  plan-4  H14  0.020

