# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 19:35:14 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  37  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  -0.598  -7.2951   1.7166   0.2652
 0C5  C02  C  C      0   0.391  -6.8248   0.5739   0.0961
 0C5  C03  C  C      0  -0.115  -5.3112   0.4582   0.0569
 0C5  C04  C  C1     0  -0.280  -4.4963   1.5800   0.1975
 0C5  C05  C  C1     0  -0.347  -3.1192   1.4764   0.1595
 0C5  C06  C  C1     0  -0.282  -4.6822  -0.7688  -0.1233
 0C5  C07  C  C1     0  -0.303  -3.3007  -0.8973  -0.1642
 0C5  C08  C  C      0   0.354  -2.4955   0.2353  -0.0217
 0C5  N09  N  NH1    0  -0.770  -1.1052   0.2444  -0.0516
 0C5  C10  C  C      0   0.626  -0.1916  -0.7607  -0.1213
 0C5  N11  N  N      0  -0.534   1.0769  -0.3300  -0.1036
 0C5  C12  C  C      0   0.588   2.0280  -1.2390  -0.1607
 0C5  N13  N  NH1    0  -0.797   3.3446  -0.8700  -0.1450
 0C5  C14  C  C      0   0.404   3.9450   0.3728  -0.0979
 0C5  C15  C  C1     0  -0.308   3.2591   1.5906  -0.0676
 0C5  C16  C  C1     0  -0.227   3.9562   2.7865  -0.0268
 0C5  C17  C  C1     0  -0.267   5.3452   2.8264  -0.0139
 0C5  C18  C  C1     0  -0.244   6.0423   1.6359  -0.0424
 0C5  C19  C  C      0  -0.085   5.3567   0.4215  -0.0834
 0C5  C20  C  CSP    0   0.037   6.1131  -0.7834  -0.1120
 0C5  N21  N  NS     0  -0.244   6.7128  -1.7686  -0.1380
 0C5  C22  C  C1     0  -0.473   1.7265  -2.6120  -0.2371
 0C5  C23  C  C1     0   0.008   0.3931  -2.9283  -0.2505
 0C5  N24  N  N      0  -0.488  -0.5851  -2.0226  -0.1950
 0C5  O25  O  OC    -1  -0.598  -7.4720  -0.4825  -0.0464
 0C5  H1   H  H      0   0.243  -4.9467   2.5530   0.3433
 0C5  H2   H  H      0   0.260  -2.5114   2.3672   0.2742
 0C5  H3   H  H      0   0.241  -5.2875  -1.6589  -0.2381
 0C5  H4   H  H      0   0.277  -2.8551  -1.8682  -0.3062
 0C5  H5   H  HNH1   0   0.410  -0.6826   1.1575   0.0218
 0C5  H6   H  HNH1   0   0.426   3.9747  -1.6574  -0.1785
 0C5  H7   H  H      0   0.307   2.1830   1.5992  -0.0757
 0C5  H8   H  H      0   0.274   3.3919   3.7096  -0.0046
 0C5  H9   H  H      0   0.270   5.8736   3.7686   0.0182
 0C5  H10  H  H      0   0.284   7.1238   1.6297  -0.0340
 0C5  H11  H  H      0   0.285   2.4933  -3.3718  -0.2831
 0C5  H12  H  H      0   0.274   0.0818  -3.9650  -0.3095

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  1.398  0.020  1.398
 0C5  C18  C19  aromatic  1.395  0.020  1.395
 0C5  C14  C19  aromatic  1.413  0.020  1.413
 0C5  C14  N13  single    1.381  0.020  1.381
 0C5  C19  C20  single    1.423  0.020  1.423
 0C5  N13  C12  single    1.367  0.020  1.367
 0C5  C20  N21  triple    1.154  0.020  1.154
 0C5  C12  C22  aromatic  1.408  0.020  1.408
 0C5  C12  N11  aromatic  1.317  0.020  1.317
 0C5  C22  C23  aromatic  1.370  0.020  1.370
 0C5  O01  C02  deloc     1.247  0.020  1.247
 0C5  N11  C10  aromatic  1.340  0.020  1.340
 0C5  C06  C07  aromatic  1.388  0.020  1.388
 0C5  C06  C03  aromatic  1.391  0.020  1.391
 0C5  C23  N24  aromatic  1.334  0.020  1.334
 0C5  C07  C08  aromatic  1.397  0.020  1.397
 0C5  C02  C03  single    1.518  0.020  1.518
 0C5  C02  O25  deloc     1.247  0.020  1.247
 0C5  C03  C04  aromatic  1.394  0.020  1.394
 0C5  C10  N24  aromatic  1.324  0.020  1.324
 0C5  C10  N09  single    1.360  0.020  1.360
 0C5  C08  N09  single    1.391  0.020  1.391
 0C5  C08  C05  aromatic  1.401  0.020  1.401
 0C5  C04  C05  aromatic  1.381  0.020  1.381
 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

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  116.73  3.000
 0C5  O25  C02  O01  126.57  3.000
 0C5  C03  C02  O01  116.70  3.000
 0C5  C06  C03  C04  117.31  3.000
 0C5  C04  C03  C02  121.26  3.000
 0C5  C06  C03  C02  121.43  3.000
 0C5  H1   C04  C05  119.09  3.000
 0C5  H1   C04  C03  119.60  3.000
 0C5  C05  C04  C03  121.31  3.000
 0C5  H2   C05  C08  119.46  3.000
 0C5  H2   C05  C04  119.62  3.000
 0C5  C08  C05  C04  120.92  3.000
 0C5  H3   C06  C07  118.51  3.000
 0C5  H3   C06  C03  119.10  3.000
 0C5  C07  C06  C03  122.39  3.000
 0C5  H4   C07  C08  120.37  3.000
 0C5  H4   C07  C06  119.92  3.000
 0C5  C08  C07  C06  119.71  3.000
 0C5  N09  C08  C07  125.41  3.000
 0C5  N09  C08  C05  116.24  3.000
 0C5  C07  C08  C05  118.35  3.000
 0C5  H5   N09  C10  113.03  3.000
 0C5  H5   N09  C08  115.03  3.000
 0C5  C10  N09  C08  131.90  3.000
 0C5  N24  C10  N11  126.06  3.000
 0C5  N24  C10  N09  120.50  3.000
 0C5  N11  C10  N09  113.44  3.000
 0C5  C12  N11  C10  117.47  3.000
 0C5  C22  C12  N13  118.03  3.000
 0C5  C22  C12  N11  121.39  3.000
 0C5  N13  C12  N11  120.58  3.000
 0C5  H6   N13  C14  115.59  3.000
 0C5  H6   N13  C12  112.97  3.000
 0C5  C14  N13  C12  131.43  3.000
 0C5  C19  C14  C15  117.40  3.000
 0C5  C19  C14  N13  117.76  3.000
 0C5  C15  C14  N13  124.85  3.000
 0C5  H7   C15  C16  119.78  3.000
 0C5  H7   C15  C14  119.83  3.000
 0C5  C16  C15  C14  120.39  3.000
 0C5  H8   C16  C17  119.77  3.000
 0C5  H8   C16  C15  118.34  3.000
 0C5  C17  C16  C15  121.89  3.000
 0C5  H9   C17  C18  120.38  3.000
 0C5  H9   C17  C16  120.93  3.000
 0C5  C18  C17  C16  118.68  3.000
 0C5  H10  C18  C19  119.11  3.000
 0C5  H10  C18  C17  120.66  3.000
 0C5  C19  C18  C17  120.22  3.000
 0C5  C20  C19  C18  118.45  3.000
 0C5  C20  C19  C14  120.13  3.000
 0C5  C18  C19  C14  121.42  3.000
 0C5  N21  C20  C19  180.00  3.000
 0C5  H11  C22  C23  121.86  3.000
 0C5  H11  C22  C12  122.42  3.000
 0C5  C23  C22  C12  115.72  3.000
 0C5  H12  C23  N24  116.16  3.000
 0C5  H12  C23  C22  120.05  3.000
 0C5  N24  C23  C22  123.80  3.000
 0C5  C23  N24  C10  115.55  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  Var_01    C10  N09  C08  C05   175.16  30.0  2
 0C5  Var_02    N11  C10  N09  C08  -178.88  30.0  1
 0C5  Var_03    C14  N13  C12  N11    -1.24  30.0  2
 0C5  Var_04    C15  C14  N13  C12    -0.70  30.0  2
 0C5  Var_05    C06  C03  C02  O01   179.84  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

