# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:59:01 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-azanyl-6-[[(1~{S})-1-(4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ncnc(N)c1C#N)C2=Nn3cccc3C(=O)N2c4ccccc4
#
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
 7KA  7KA  4-azanyl-6-[[(1~{S})-1-(4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]pyrimidine-5-carbonitrile  ligand  44  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7KA
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
 7KA  N1   N  N     0  -0.359  -2.1270  -2.2588  -0.0451
 7KA  N2   N  N     0  -0.305  -0.9690  -1.6472  -0.3531
 7KA  C3   C  CR6   0   0.547  -0.9743  -0.3687  -0.3412
 7KA  N4   N  NR6   0  -0.678  -2.0789   0.3995  -0.0416
 7KA  C5   C  CR6   0   0.555  -3.3170  -0.1776   0.2735
 7KA  C6   C  CR56  0   0.237  -3.3007  -1.6102   0.2542
 7KA  C7   C  CR15  0  -0.383  -4.2585  -2.5714   0.5035
 7KA  C8   C  CR15  0  -0.337  -3.6309  -3.8184   0.3453
 7KA  C9   C  CR15  0  -0.035  -2.3106  -3.5939   0.0050
 7KA  O10  O  O     0  -0.435  -4.2815   0.5068   0.5406
 7KA  C11  C  CR6   0   0.245  -2.0032   1.8277   0.0341
 7KA  C12  C  CR16  0  -0.247  -2.4642   2.5964  -1.0235
 7KA  C13  C  CR16  0  -0.267  -2.4049   3.9799  -0.9372
 7KA  C14  C  CR16  0  -0.237  -1.8904   4.5859   0.2015
 7KA  C15  C  CR16  0  -0.261  -1.4372   3.8078   1.2585
 7KA  C16  C  CR16  0  -0.242  -1.4998   2.4238   1.1808
 7KA  C17  C  CH1   0  -0.181   0.3066   0.3161  -0.7632
 7KA  N19  N  NH1   0  -0.680   1.4163  -0.5521  -0.4451
 7KA  C20  C  CR6   0   0.608   2.6459  -0.1020  -0.1797
 7KA  N21  N  N     0  -0.493   2.8416   1.2189  -0.1327
 7KA  C22  C  CR16  0   0.085   4.0669   1.6247   0.1469
 7KA  N23  N  N     0  -0.475   5.1388   0.8975   0.3827
 7KA  C24  C  CR6   0   0.539   4.9802  -0.4340   0.3401
 7KA  C25  C  CR6   0  -0.244   3.7166  -0.9951   0.0553
 7KA  C26  C  CSP   0   0.013   3.5278  -2.3895   0.0109
 7KA  N27  N  NS    0  -0.253   3.3688  -3.5340  -0.0268
 7KA  N28  N  NH2   0  -0.818   6.0530  -1.1835   0.5770
 7KA  C29  C  CH3   0  -0.642   0.2612   0.6486  -2.2560
 7KA  H1   H  HCR5  0   0.268  -5.2869  -2.3853   0.7679
 7KA  H2   H  HCR5  0   0.264  -4.0853  -4.7883   0.4664
 7KA  H3   H  HCR5  0   0.298  -1.5028  -4.2754  -0.2036
 7KA  H4   H  HCR6  0   0.278  -2.8641   2.1184  -1.9084
 7KA  H5   H  HCR6  0   0.269  -2.7621   4.5823  -1.7616
 7KA  H6   H  HCR6  0   0.267  -1.8430   5.6649   0.2655
 7KA  H7   H  HCR6  0   0.270  -1.0366   4.2753   2.1478
 7KA  H8   H  HCR6  0   0.278  -1.1524   1.8117   2.0036
 7KA  H9   H  HCH1  0   0.299   0.4389   1.2372  -0.1985
 7KA  H10  H  HNH1  0   0.414   1.2586  -1.5440  -0.5492
 7KA  H11  H  HCR6  0   0.265   4.2084   2.7002   0.1840
 7KA  H12  H  HNH2  0   0.417   6.0332  -2.1884   0.5531
 7KA  H13  H  HNH2  0   0.412   6.9347  -0.7373   0.7647
 7KA  H14  H  HCH3  0   0.257   1.1881   1.1424  -2.5444
 7KA  H15  H  HCH3  0   0.243   0.1501  -0.2599  -2.8474
 7KA  H16  H  HCH3  0   0.246  -0.5612   1.3211  -2.4942

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
 7KA  C8   C9   aromatic  1.382  0.020  1.382
 7KA  C8   C7   aromatic  1.405  0.020  1.405
 7KA  C9   N1   aromatic  1.349  0.020  1.349
 7KA  C7   C6   aromatic  1.380  0.020  1.380
 7KA  N1   C6   aromatic  1.374  0.020  1.374
 7KA  N1   N2   single    1.345  0.020  1.345
 7KA  C6   C5   single    1.433  0.020  1.433
 7KA  N28  C24  single    1.330  0.020  1.330
 7KA  N27  C26  triple    1.156  0.020  1.156
 7KA  N2   C3   double    1.279  0.020  1.279
 7KA  C26  C25  single    1.408  0.020  1.408
 7KA  C24  C25  aromatic  1.412  0.020  1.412
 7KA  C24  N23  aromatic  1.342  0.020  1.342
 7KA  C5   O10  double    1.213  0.020  1.213
 7KA  C5   N4   single    1.402  0.020  1.402
 7KA  C25  C20  aromatic  1.414  0.020  1.414
 7KA  N23  C22  aromatic  1.317  0.020  1.317
 7KA  C22  N21  aromatic  1.321  0.020  1.321
 7KA  C20  N21  aromatic  1.336  0.020  1.336
 7KA  C20  N19  single    1.336  0.020  1.336
 7KA  C3   N4   single    1.378  0.020  1.378
 7KA  C3   C17  single    1.513  0.020  1.513
 7KA  N19  C17  single    1.444  0.020  1.444
 7KA  N4   C11  single    1.432  0.020  1.432
 7KA  C17  C29  single    1.530  0.020  1.530
 7KA  C11  C16  aromatic  1.387  0.020  1.387
 7KA  C11  C12  aromatic  1.386  0.020  1.386
 7KA  C16  C15  aromatic  1.388  0.020  1.388
 7KA  C12  C13  aromatic  1.387  0.020  1.387
 7KA  C15  C14  aromatic  1.389  0.020  1.389
 7KA  C13  C14  aromatic  1.389  0.020  1.389
 7KA  C7   H1   single    0.930  0.020  1.080
 7KA  C8   H2   single    0.930  0.020  1.080
 7KA  C9   H3   single    0.930  0.020  1.080
 7KA  C12  H4   single    0.930  0.020  1.080
 7KA  C13  H5   single    0.930  0.020  1.080
 7KA  C14  H6   single    0.930  0.020  1.080
 7KA  C15  H7   single    0.930  0.020  1.080
 7KA  C16  H8   single    0.930  0.020  1.080
 7KA  C17  H9   single    0.970  0.020  1.090
 7KA  N19  H10  single    0.860  0.020  1.020
 7KA  C22  H11  single    0.930  0.020  1.080
 7KA  N28  H12  single    0.860  0.020  1.020
 7KA  N28  H13  single    0.860  0.020  1.020
 7KA  C29  H14  single    0.970  0.020  1.090
 7KA  C29  H15  single    0.970  0.020  1.090
 7KA  C29  H16  single    0.970  0.020  1.090

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
 7KA  C9   N1   C6   110.06  3.000
 7KA  C6   N1   N2   124.79  3.000
 7KA  C9   N1   N2   125.15  3.000
 7KA  C3   N2   N1   116.67  3.000
 7KA  C17  C3   N4   119.14  3.000
 7KA  C17  C3   N2   116.52  3.000
 7KA  N4   C3   N2   124.24  3.000
 7KA  C11  N4   C5   116.44  3.000
 7KA  C11  N4   C3   121.66  3.000
 7KA  C5   N4   C3   121.81  3.000
 7KA  O10  C5   C6   125.20  3.000
 7KA  O10  C5   N4   121.31  3.000
 7KA  C6   C5   N4   113.49  3.000
 7KA  C7   C6   C5   133.33  3.000
 7KA  C5   C6   N1   118.99  3.000
 7KA  C7   C6   N1   107.67  3.000
 7KA  H1   C7   C8   127.38  3.000
 7KA  H1   C7   C6   125.89  3.000
 7KA  C8   C7   C6   106.73  3.000
 7KA  H2   C8   C9   125.21  3.000
 7KA  H2   C8   C7   126.71  3.000
 7KA  C9   C8   C7   108.08  3.000
 7KA  H3   C9   C8   131.40  3.000
 7KA  H3   C9   N1   121.14  3.000
 7KA  C8   C9   N1   107.46  3.000
 7KA  C16  C11  C12  120.87  3.000
 7KA  C12  C11  N4   119.67  3.000
 7KA  C16  C11  N4   119.44  3.000
 7KA  H4   C12  C13  120.47  3.000
 7KA  H4   C12  C11  120.11  3.000
 7KA  C13  C12  C11  119.42  3.000
 7KA  H5   C13  C14  120.28  3.000
 7KA  H5   C13  C12  119.59  3.000
 7KA  C14  C13  C12  120.13  3.000
 7KA  H6   C14  C15  119.97  3.000
 7KA  H6   C14  C13  119.99  3.000
 7KA  C15  C14  C13  120.04  3.000
 7KA  H7   C15  C16  119.60  3.000
 7KA  H7   C15  C14  120.30  3.000
 7KA  C16  C15  C14  120.10  3.000
 7KA  H8   C16  C15  120.45  3.000
 7KA  H8   C16  C11  120.11  3.000
 7KA  C15  C16  C11  119.43  3.000
 7KA  H9   C17  C29  109.01  3.000
 7KA  H9   C17  N19  107.52  3.000
 7KA  C29  C17  N19  111.61  3.000
 7KA  H9   C17  C3   109.96  3.000
 7KA  C29  C17  C3   110.21  3.000
 7KA  N19  C17  C3   108.49  3.000
 7KA  H10  N19  C20  119.68  3.000
 7KA  H10  N19  C17  116.60  3.000
 7KA  C20  N19  C17  123.25  3.000
 7KA  C25  C20  N21  120.51  3.000
 7KA  N21  C20  N19  118.35  3.000
 7KA  C25  C20  N19  121.14  3.000
 7KA  C22  N21  C20  116.56  3.000
 7KA  H11  C22  N23  115.79  3.000
 7KA  H11  C22  N21  115.64  3.000
 7KA  N23  C22  N21  128.57  3.000
 7KA  C24  N23  C22  116.51  3.000
 7KA  N28  C24  C25  122.28  3.000
 7KA  C25  C24  N23  120.44  3.000
 7KA  N28  C24  N23  117.28  3.000
 7KA  C26  C25  C24  121.34  3.000
 7KA  C24  C25  C20  117.41  3.000
 7KA  C26  C25  C20  121.25  3.000
 7KA  N27  C26  C25  180.00  3.000
 7KA  H13  N28  H12  117.71  3.000
 7KA  H13  N28  C24  119.36  3.000
 7KA  H12  N28  C24  122.90  3.000
 7KA  H16  C29  H15  108.61  3.000
 7KA  H16  C29  H14  107.75  3.000
 7KA  H15  C29  H14  108.73  3.000
 7KA  H16  C29  C17  111.72  3.000
 7KA  H15  C29  C17  110.57  3.000
 7KA  H14  C29  C17  109.37  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
 7KA  CONST_01  C7   C8   C9   N1     0.00   0.0  0
 7KA  CONST_02  C8   C7   C6   N1     0.00   0.0  0
 7KA  CONST_03  C9   C8   C7   C6     0.00   0.0  0
 7KA  CONST_04  C8   C9   N1   C6     0.00   0.0  0
 7KA  CONST_05  C9   N1   C6   C7     0.00   0.0  0
 7KA  CONST_06  C14  C15  C16  C11    0.00   0.0  0
 7KA  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 7KA  CONST_08  C15  C16  C11  C12    0.00   0.0  0
 7KA  CONST_09  C15  C14  C13  C12    0.00   0.0  0
 7KA  CONST_10  C16  C11  C12  C13    0.00   0.0  0
 7KA  CONST_11  C16  C15  C14  C13    0.00   0.0  0
 7KA  CONST_12  N23  C24  C25  C20    0.00   0.0  0
 7KA  CONST_13  N23  C22  N21  C20    0.00   0.0  0
 7KA  CONST_14  C24  N23  C22  N21    0.00   0.0  0
 7KA  CONST_15  C24  C25  C20  N21    0.00   0.0  0
 7KA  CONST_16  C25  C24  N23  C22    0.00   0.0  0
 7KA  CONST_17  C25  C20  N21  C22    0.00   0.0  0
 7KA  CONST_18  C15  C16  C11  N4   180.00   0.0  0
 7KA  CONST_19  C13  C12  C11  N4   180.00   0.0  0
 7KA  CONST_20  N4   C3   N2   N1     0.00   0.0  0
 7KA  CONST_21  C5   N4   C3   N2     0.00   0.0  0
 7KA  CONST_22  C11  N4   C3   N2   180.00   0.0  0
 7KA  CONST_23  C6   C5   N4   C3     0.00   0.0  0
 7KA  CONST_24  C11  N4   C5   C6   180.00   0.0  0
 7KA  CONST_25  C24  C25  C20  N19  180.00   0.0  0
 7KA  CONST_26  C22  N21  C20  N19  180.00   0.0  0
 7KA  CONST_27  N28  C24  C25  C20  180.00   0.0  0
 7KA  CONST_28  C26  C25  C20  N21  180.00   0.0  0
 7KA  CONST_29  N28  C24  N23  C22  180.00   0.0  0
 7KA  CONST_30  C26  C25  C24  N23  180.00   0.0  0
 7KA  CONST_31  C17  C3   N2   N1   180.00   0.0  0
 7KA  CONST_32  O10  C5   N4   C3   180.00   0.0  0
 7KA  CONST_33  C17  C3   N4   C5   180.00   0.0  0
 7KA  CONST_34  C11  N4   C5   O10    0.00   0.0  0
 7KA  CONST_35  C17  C3   N4   C11    0.00   0.0  0
 7KA  CONST_36  H2   C8   C9   N1   180.00   0.0  0
 7KA  CONST_37  H1   C7   C6   N1   180.00   0.0  0
 7KA  CONST_38  H3   C9   N1   N2     0.00   0.0  0
 7KA  CONST_39  H8   C16  C11  N4     0.00   0.0  0
 7KA  CONST_40  H4   C12  C11  N4     0.00   0.0  0
 7KA  CONST_41  H7   C15  C16  C11  180.00   0.0  0
 7KA  CONST_42  H5   C13  C12  C11  180.00   0.0  0
 7KA  CONST_43  H6   C14  C13  C12  180.00   0.0  0
 7KA  CONST_44  H11  C22  N21  C20  180.00   0.0  0
 7KA  CONST_45  C25  C20  N19  C17  180.00   0.0  0
 7KA  CONST_46  N21  C20  N19  C17    0.00   0.0  0
 7KA  CONST_47  H10  N19  C20  N21  180.00   0.0  0
 7KA  CONST_48  H12  N28  C24  N23  180.00   0.0  0
 7KA  CONST_49  H13  N28  C24  N23    0.00   0.0  0
 7KA  Var_01    C16  C11  N4   C3   -79.93  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7KA  chir_01  C17  C3  N19  C29  negativ

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
 7KA  plan-1  N4   0.020
 7KA  plan-1  C11  0.020
 7KA  plan-1  C12  0.020
 7KA  plan-1  C13  0.020
 7KA  plan-1  C14  0.020
 7KA  plan-1  C15  0.020
 7KA  plan-1  C16  0.020
 7KA  plan-1  H4   0.020
 7KA  plan-1  H5   0.020
 7KA  plan-1  H6   0.020
 7KA  plan-1  H7   0.020
 7KA  plan-1  H8   0.020
 7KA  plan-2  N19  0.020
 7KA  plan-2  C20  0.020
 7KA  plan-2  N21  0.020
 7KA  plan-2  C22  0.020
 7KA  plan-2  N23  0.020
 7KA  plan-2  C24  0.020
 7KA  plan-2  C25  0.020
 7KA  plan-2  C26  0.020
 7KA  plan-2  N27  0.020
 7KA  plan-2  N28  0.020
 7KA  plan-2  H11  0.020
 7KA  plan-3  N1   0.020
 7KA  plan-3  N2   0.020
 7KA  plan-3  C3   0.020
 7KA  plan-3  N4   0.020
 7KA  plan-3  C5   0.020
 7KA  plan-3  C6   0.020
 7KA  plan-3  C7   0.020
 7KA  plan-3  C8   0.020
 7KA  plan-3  C9   0.020
 7KA  plan-3  O10  0.020
 7KA  plan-3  C11  0.020
 7KA  plan-3  C17  0.020
 7KA  plan-3  H1   0.020
 7KA  plan-3  H2   0.020
 7KA  plan-3  H3   0.020
 7KA  plan-4  C17  0.020
 7KA  plan-4  N19  0.020
 7KA  plan-4  C20  0.020
 7KA  plan-4  H10  0.020
 7KA  plan-5  C24  0.020
 7KA  plan-5  N28  0.020
 7KA  plan-5  H12  0.020
 7KA  plan-5  H13  0.020

