# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 10:34:29 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-({4-[(2-cyanophenyl)amino]pyrimidin-2-yl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3C#N)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
 0C5  0C5  '4-({4-[(2-cyanophenyl)amino]pyrimidin-2-yl}amino)benzoic acid'  ligand  38  25  .  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_0C5
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
 0C5  O01  O  O     0  -0.449  -7.2214   1.6972   0.4350
 0C5  C02  C  C     0   0.524  -6.6756   0.6385   0.2215
 0C5  C03  C  CR6   0  -0.103  -5.2134   0.4644   0.1416
 0C5  C04  C  CR16  0  -0.246  -4.3912   1.5763   0.3331
 0C5  C05  C  CR16  0  -0.346  -3.0218   1.4593   0.2663
 0C5  C06  C  CR16  0  -0.250  -4.6107  -0.7645  -0.1193
 0C5  C07  C  CR16  0  -0.300  -3.2350  -0.8969  -0.1889
 0C5  C08  C  CR6   0   0.380  -2.4150   0.2206   0.0041
 0C5  N09  N  NH1   0  -0.770  -1.0361   0.2143  -0.0466
 0C5  C10  C  CR6   0   0.623  -0.1345  -0.7959  -0.2354
 0C5  N11  N  N     0  -0.519   1.1333  -0.3784  -0.2187
 0C5  C12  C  CR6   0   0.572   2.0731  -1.2866  -0.3933
 0C5  N13  N  NH1   0  -0.790   3.3854  -0.9139  -0.3763
 0C5  C14  C  CR6   0   0.397   3.9332   0.3528  -0.2389
 0C5  C15  C  CR16  0  -0.284   3.2999   1.5209  -0.6657
 0C5  C16  C  CR16  0  -0.234   3.9311   2.7458  -0.5316
 0C5  C17  C  CR16  0  -0.263   5.2045   2.8523   0.0163
 0C5  C18  C  CR16  0  -0.245   5.8506   1.7076   0.4371
 0C5  C19  C  CR6   0  -0.071   5.2198   0.4679   0.3211
 0C5  C20  C  CSP   0   0.042   5.8951  -0.6941   0.7915
 0C5  N21  N  NS    0  -0.242   6.4365  -1.6393   1.1702
 0C5  C22  C  CR16  0  -0.457   1.7531  -2.6440  -0.5800
 0C5  C23  C  CR16  0   0.010   0.4165  -2.9468  -0.5744
 0C5  N24  N  N     0  -0.487  -0.5488  -2.0394  -0.4074
 0C5  O25  O  OH1   0  -0.598  -7.3479  -0.4918   0.0340
 0C5  H1   H  HCR6  0   0.266  -4.8259   2.5449   0.5401
 0C5  H2   H  HCR6  0   0.275  -2.4039   2.3359   0.4205
 0C5  H3   H  HCR6  0   0.266  -5.2122  -1.6495  -0.2767
 0C5  H4   H  HCR6  0   0.293  -2.8015  -1.8615  -0.3934
 0C5  H5   H  HNH1  0   0.413  -0.5945   1.1114   0.0918
 0C5  H6   H  HNH1  0   0.424   4.0381  -1.6821  -0.4203
 0C5  H7   H  HCR6  0   0.289   2.3191   1.4727  -1.1092
 0C5  H8   H  HCR6  0   0.276   3.4182   3.6350  -0.8736
 0C5  H9   H  HCR6  0   0.273   5.6856   3.8154   0.1119
 0C5  H10  H  HCR6  0   0.285   6.8413   1.7589   0.8680
 0C5  H11  H  HCR6  0   0.286   2.5094  -3.4035  -0.7157
 0C5  H12  H  HCR6  0   0.276   0.0904  -3.9712  -0.7127
 0C5  H13  H  HOH1  0   0.485  -8.2990  -0.3204   0.0928

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
 0C5  C16  C17  aromatic  1.390  0.020  1.390
 0C5  C16  C15  aromatic  1.385  0.020  1.385
 0C5  C17  C18  aromatic  1.380  0.020  1.380
 0C5  C15  C14  aromatic  1.396  0.020  1.396
 0C5  C18  C19  aromatic  1.396  0.020  1.396
 0C5  C14  C19  aromatic  1.408  0.020  1.408
 0C5  C14  N13  single    1.387  0.020  1.387
 0C5  C19  C20  single    1.424  0.020  1.424
 0C5  N13  C12  single    1.364  0.020  1.364
 0C5  C20  N21  triple    1.153  0.020  1.153
 0C5  C12  C22  aromatic  1.407  0.020  1.407
 0C5  C12  N11  aromatic  1.319  0.020  1.319
 0C5  C22  C23  aromatic  1.370  0.020  1.370
 0C5  O01  C02  double    1.210  0.020  1.210
 0C5  N11  C10  aromatic  1.335  0.020  1.335
 0C5  C06  C07  aromatic  1.384  0.020  1.384
 0C5  C06  C03  aromatic  1.393  0.020  1.393
 0C5  C23  N24  aromatic  1.335  0.020  1.335
 0C5  C07  C08  aromatic  1.400  0.020  1.400
 0C5  C02  C03  single    1.475  0.020  1.475
 0C5  C02  O25  single    1.328  0.020  1.328
 0C5  C03  C04  aromatic  1.396  0.020  1.396
 0C5  C10  N24  aromatic  1.322  0.020  1.322
 0C5  C10  N09  single    1.367  0.020  1.367
 0C5  C08  N09  single    1.380  0.020  1.380
 0C5  C08  C05  aromatic  1.404  0.020  1.404
 0C5  C04  C05  aromatic  1.376  0.020  1.376
 0C5  C04  H1   single    0.930  0.020  1.080
 0C5  C05  H2   single    0.930  0.020  1.080
 0C5  C06  H3   single    0.930  0.020  1.080
 0C5  C07  H4   single    0.930  0.020  1.080
 0C5  N09  H5   single    0.860  0.020  1.020
 0C5  N13  H6   single    0.860  0.020  1.020
 0C5  C15  H7   single    0.930  0.020  1.080
 0C5  C16  H8   single    0.930  0.020  1.080
 0C5  C17  H9   single    0.930  0.020  1.080
 0C5  C18  H10  single    0.930  0.020  1.080
 0C5  C22  H11  single    0.930  0.020  1.080
 0C5  C23  H12  single    0.930  0.020  1.080
 0C5  O25  H13  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
 0C5  O25  C02  C03  113.19  3.000
 0C5  O25  C02  O01  122.75  3.000
 0C5  C03  C02  O01  124.06  3.000
 0C5  C06  C03  C04  118.25  3.000
 0C5  C04  C03  C02  118.85  3.000
 0C5  C06  C03  C02  122.90  3.000
 0C5  H1   C04  C05  119.04  3.000
 0C5  H1   C04  C03  120.18  3.000
 0C5  C05  C04  C03  120.78  3.000
 0C5  H2   C05  C08  119.60  3.000
 0C5  H2   C05  C04  119.46  3.000
 0C5  C08  C05  C04  120.94  3.000
 0C5  H3   C06  C07  117.86  3.000
 0C5  H3   C06  C03  120.56  3.000
 0C5  C07  C06  C03  121.59  3.000
 0C5  H4   C07  C08  120.36  3.000
 0C5  H4   C07  C06  119.70  3.000
 0C5  C08  C07  C06  119.94  3.000
 0C5  N09  C08  C07  125.23  3.000
 0C5  N09  C08  C05  116.28  3.000
 0C5  C07  C08  C05  118.49  3.000
 0C5  H5   N09  C10  112.77  3.000
 0C5  H5   N09  C08  115.35  3.000
 0C5  C10  N09  C08  131.87  3.000
 0C5  N24  C10  N11  126.41  3.000
 0C5  N24  C10  N09  120.42  3.000
 0C5  N11  C10  N09  113.17  3.000
 0C5  C12  N11  C10  117.38  3.000
 0C5  C22  C12  N13  118.95  3.000
 0C5  C22  C12  N11  121.33  3.000
 0C5  N13  C12  N11  119.72  3.000
 0C5  H6   N13  C14  116.38  3.000
 0C5  H6   N13  C12  114.43  3.000
 0C5  C14  N13  C12  129.10  3.000
 0C5  C19  C14  C15  117.90  3.000
 0C5  C19  C14  N13  118.36  3.000
 0C5  C15  C14  N13  123.71  3.000
 0C5  H7   C15  C16  119.63  3.000
 0C5  H7   C15  C14  120.10  3.000
 0C5  C16  C15  C14  120.27  3.000
 0C5  H8   C16  C17  119.72  3.000
 0C5  H8   C16  C15  118.71  3.000
 0C5  C17  C16  C15  121.57  3.000
 0C5  H9   C17  C18  120.25  3.000
 0C5  H9   C17  C16  120.72  3.000
 0C5  C18  C17  C16  119.04  3.000
 0C5  H10  C18  C19  119.29  3.000
 0C5  H10  C18  C17  120.73  3.000
 0C5  C19  C18  C17  119.98  3.000
 0C5  C20  C19  C18  118.88  3.000
 0C5  C20  C19  C14  119.87  3.000
 0C5  C18  C19  C14  121.24  3.000
 0C5  N21  C20  C19  180.00  3.000
 0C5  H11  C22  C23  121.87  3.000
 0C5  H11  C22  C12  122.38  3.000
 0C5  C23  C22  C12  115.75  3.000
 0C5  H12  C23  N24  116.15  3.000
 0C5  H12  C23  C22  120.11  3.000
 0C5  N24  C23  C22  123.74  3.000
 0C5  C23  N24  C10  115.40  3.000
 0C5  H13  O25  C02  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
 0C5  CONST_01  C08  C07  C06  C03     0.00   0.0  0
 0C5  CONST_02  C08  C05  C04  C03     0.00   0.0  0
 0C5  CONST_03  C07  C06  C03  C04     0.00   0.0  0
 0C5  CONST_04  C07  C08  C05  C04     0.00   0.0  0
 0C5  CONST_05  C06  C07  C08  C05     0.00   0.0  0
 0C5  CONST_06  C06  C03  C04  C05     0.00   0.0  0
 0C5  CONST_07  C22  C12  N11  C10     0.00   0.0  0
 0C5  CONST_08  C22  C23  N24  C10     0.00   0.0  0
 0C5  CONST_09  C23  C22  C12  N11     0.00   0.0  0
 0C5  CONST_10  C23  N24  C10  N11     0.00   0.0  0
 0C5  CONST_11  N24  C23  C22  C12     0.00   0.0  0
 0C5  CONST_12  N24  C10  N11  C12     0.00   0.0  0
 0C5  CONST_13  C17  C16  C15  C14     0.00   0.0  0
 0C5  CONST_14  C17  C18  C19  C14     0.00   0.0  0
 0C5  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 0C5  CONST_16  C18  C19  C14  C15     0.00   0.0  0
 0C5  CONST_17  C19  C18  C17  C16     0.00   0.0  0
 0C5  CONST_18  C19  C14  C15  C16     0.00   0.0  0
 0C5  CONST_19  C07  C06  C03  C02   180.00   0.0  0
 0C5  CONST_20  C05  C04  C03  C02   180.00   0.0  0
 0C5  CONST_21  N09  C08  C05  C04   180.00   0.0  0
 0C5  CONST_22  N09  C08  C07  C06   180.00   0.0  0
 0C5  CONST_23  C12  N11  C10  N09   180.00   0.0  0
 0C5  CONST_24  C23  N24  C10  N09   180.00   0.0  0
 0C5  CONST_25  N13  C12  N11  C10   180.00   0.0  0
 0C5  CONST_26  C16  C15  C14  N13   180.00   0.0  0
 0C5  CONST_27  C18  C19  C14  N13   180.00   0.0  0
 0C5  CONST_28  C23  C22  C12  N13   180.00   0.0  0
 0C5  CONST_29  C20  C19  C14  C15   180.00   0.0  0
 0C5  CONST_30  C20  C19  C18  C17   180.00   0.0  0
 0C5  CONST_31  H4   C07  C06  C03   180.00   0.0  0
 0C5  CONST_32  H2   C05  C04  C03   180.00   0.0  0
 0C5  CONST_33  H3   C06  C03  C04   180.00   0.0  0
 0C5  CONST_34  H1   C04  C03  C06   180.00   0.0  0
 0C5  CONST_35  H12  C23  N24  C10   180.00   0.0  0
 0C5  CONST_36  H11  C22  C12  N11   180.00   0.0  0
 0C5  CONST_37  H8   C16  C15  C14   180.00   0.0  0
 0C5  CONST_38  H10  C18  C19  C14   180.00   0.0  0
 0C5  CONST_39  H9   C17  C16  C15   180.00   0.0  0
 0C5  CONST_40  H7   C15  C16  C17   180.00   0.0  0
 0C5  CONST_41  H13  O25  C02  C03   180.00   0.0  0
 0C5  Var_01    C10  N09  C08  C05   177.82  30.0  2
 0C5  Var_02    N11  C10  N09  C08   179.90  30.0  1
 0C5  Var_03    C14  N13  C12  N11    -2.43  30.0  2
 0C5  Var_04    C15  C14  N13  C12   -29.56  30.0  2
 0C5  Var_05    C06  C03  C02  O01  -179.32  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
 0C5  plan-1  C02  0.020
 0C5  plan-1  C03  0.020
 0C5  plan-1  C04  0.020
 0C5  plan-1  C05  0.020
 0C5  plan-1  C06  0.020
 0C5  plan-1  C07  0.020
 0C5  plan-1  C08  0.020
 0C5  plan-1  N09  0.020
 0C5  plan-1  H1   0.020
 0C5  plan-1  H2   0.020
 0C5  plan-1  H3   0.020
 0C5  plan-1  H4   0.020
 0C5  plan-2  N09  0.020
 0C5  plan-2  C10  0.020
 0C5  plan-2  N11  0.020
 0C5  plan-2  C12  0.020
 0C5  plan-2  N13  0.020
 0C5  plan-2  C22  0.020
 0C5  plan-2  C23  0.020
 0C5  plan-2  N24  0.020
 0C5  plan-2  H11  0.020
 0C5  plan-2  H12  0.020
 0C5  plan-3  N13  0.020
 0C5  plan-3  C14  0.020
 0C5  plan-3  C15  0.020
 0C5  plan-3  C16  0.020
 0C5  plan-3  C17  0.020
 0C5  plan-3  C18  0.020
 0C5  plan-3  C19  0.020
 0C5  plan-3  C20  0.020
 0C5  plan-3  N21  0.020
 0C5  plan-3  H7   0.020
 0C5  plan-3  H8   0.020
 0C5  plan-3  H9   0.020
 0C5  plan-3  H10  0.020
 0C5  plan-4  O01  0.020
 0C5  plan-4  C02  0.020
 0C5  plan-4  C03  0.020
 0C5  plan-4  O25  0.020
 0C5  plan-4  H13  0.020

