# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:50:30 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2cc3nc(NCCc4ccc(cc4)C#N)[nH]c3cc2C(=O)N1
#
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
 2YX  2YX  4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzonitrile  ligand  41  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2YX
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
 2YX  O    O  O     0  -0.473   4.7211  -3.0620  -0.1831
 2YX  C17  C  CR6   0   0.543   4.9843  -1.8715  -0.1005
 2YX  N6   N  NR16  0  -0.719   6.2955  -1.4488  -0.0621
 2YX  C    C  CR6   0   0.639   6.6735  -0.1359   0.0247
 2YX  N    N  NH2   0  -0.834   8.0029   0.0968   0.0919
 2YX  C16  C  CR66  0  -0.157   4.0181  -0.7942  -0.0321
 2YX  C1   C  CR66  0   0.276   4.4891   0.5374   0.0658
 2YX  N1   N  N     0  -0.527   5.8285   0.8395   0.0856
 2YX  C15  C  CR16  0  -0.351   2.6462  -1.0896  -0.0649
 2YX  C14  C  CR56  0   0.355   1.7803  -0.0339   0.0047
 2YX  C3   C  CR56  0   0.197   2.2198   1.3112   0.1083
 2YX  C2   C  CR16  0  -0.453   3.5743   1.5948   0.1384
 2YX  N5   N  NR15  0  -0.749   0.4032   0.0546  -0.0046
 2YX  C4   C  CR5   0   0.694   0.0898   1.3749   0.0870
 2YX  N2   N  N     0  -0.541   1.1491   2.1580   0.1593
 2YX  N3   N  NH1   0  -0.690  -1.1746   1.8166   0.0760
 2YX  C5   C  CH2   0  -0.267  -2.3315   0.9514   0.1410
 2YX  C6   C  CH2   0  -0.554  -3.6006   1.7690  -0.0762
 2YX  C7   C  CR6   0   0.135  -4.8166   0.8898  -0.0452
 2YX  C13  C  CR16  0  -0.292  -5.4179   0.5536   1.1666
 2YX  C12  C  CR16  0  -0.223  -6.5237  -0.2764   1.2056
 2YX  C10  C  CR6   0  -0.012  -7.0422  -0.7846   0.0146
 2YX  C11  C  CSP   0   0.055  -8.1870  -1.6353   0.0440
 2YX  N4   N  NS    0  -0.254  -9.1123  -2.3221   0.0674
 2YX  C9   C  CR16  0  -0.222  -6.4503  -0.4602  -1.2056
 2YX  C8   C  CR16  0  -0.293  -5.3442   0.3704  -1.2254
 2YX  H1   H  HNR6  0   0.420   7.0046  -2.1698  -0.0910
 2YX  H2   H  HNH2  0   0.405   8.6461  -0.5918  -0.2623
 2YX  H3   H  HNH2  0   0.403   8.2902   1.0524  -0.0400
 2YX  H4   H  HCR6  0   0.268   2.3040  -2.1132  -0.1435
 2YX  H5   H  HCR6  0   0.245   3.9350   2.6127   0.2140
 2YX  H6   H  HNR5  0   0.426  -0.2411  -0.7183  -0.0428
 2YX  H8   H  HNH1  0   0.405  -1.2935   2.7908   0.3048
 2YX  H9   H  HCH2  0   0.253  -2.2610   0.1888  -0.6394
 2YX  H10  H  HCH2  0   0.250  -2.3863   0.4287   1.1029
 2YX  H11  H  HCH2  0   0.271  -3.6760   2.5327   0.7019
 2YX  H12  H  HCH2  0   0.271  -3.5359   2.2865  -1.0355
 2YX  H13  H  HCR6  0   0.268  -5.0219   0.9509   2.0929
 2YX  H14  H  HCR6  0   0.282  -6.9866  -0.5252   2.1509
 2YX  H15  H  HCR6  0   0.282  -6.8559  -0.8513  -2.1287
 2YX  H16  H  HCR6  0   0.268  -4.8893   0.6234  -2.1747

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
 2YX  N4   C11  triple    1.152  0.020  1.152
 2YX  C11  C10  single    1.427  0.020  1.427
 2YX  C10  C9   aromatic  1.394  0.020  1.394
 2YX  C10  C12  aromatic  1.395  0.020  1.395
 2YX  C9   C8   aromatic  1.383  0.020  1.383
 2YX  C12  C13  aromatic  1.383  0.020  1.383
 2YX  C8   C7   aromatic  1.393  0.020  1.393
 2YX  C13  C7   aromatic  1.394  0.020  1.394
 2YX  C7   C6   single    1.501  0.020  1.501
 2YX  C6   C5   single    1.525  0.020  1.525
 2YX  C5   N3   single    1.446  0.020  1.446
 2YX  N3   C4   single    1.339  0.020  1.339
 2YX  C4   N2   aromatic  1.319  0.020  1.319
 2YX  C4   N5   aromatic  1.360  0.020  1.360
 2YX  N2   C3   aromatic  1.366  0.020  1.366
 2YX  N5   C14  aromatic  1.380  0.020  1.380
 2YX  C3   C14  aromatic  1.419  0.020  1.419
 2YX  C3   C2   aromatic  1.384  0.020  1.384
 2YX  C14  C15  aromatic  1.367  0.020  1.367
 2YX  C2   C1   aromatic  1.400  0.020  1.400
 2YX  C15  C16  aromatic  1.404  0.020  1.404
 2YX  C1   C16  aromatic  1.416  0.020  1.416
 2YX  C1   N1   single    1.373  0.020  1.373
 2YX  C16  C17  single    1.449  0.020  1.449
 2YX  N1   C    double    1.292  0.020  1.292
 2YX  C17  O    double    1.222  0.020  1.222
 2YX  C17  N6   single    1.378  0.020  1.378
 2YX  C    N6   single    1.369  0.020  1.369
 2YX  C    N    single    1.351  0.020  1.351
 2YX  N6   H1   single    0.860  0.020  1.020
 2YX  N    H2   single    0.890  0.020  1.040
 2YX  N    H3   single    0.890  0.020  1.040
 2YX  C15  H4   single    0.930  0.020  1.080
 2YX  C2   H5   single    0.930  0.020  1.080
 2YX  N5   H6   single    0.860  0.020  1.020
 2YX  N3   H8   single    0.860  0.020  1.020
 2YX  C5   H9   single    0.970  0.020  1.090
 2YX  C5   H10  single    0.970  0.020  1.090
 2YX  C6   H11  single    0.970  0.020  1.090
 2YX  C6   H12  single    0.970  0.020  1.090
 2YX  C13  H13  single    0.930  0.020  1.080
 2YX  C12  H14  single    0.930  0.020  1.080
 2YX  C9   H15  single    0.930  0.020  1.080
 2YX  C8   H16  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
 2YX  C16  C17  N6   113.90  3.000
 2YX  N6   C17  O    120.37  3.000
 2YX  C16  C17  O    125.73  3.000
 2YX  H1   N6   C    119.45  3.000
 2YX  H1   N6   C17  116.58  3.000
 2YX  C    N6   C17  123.96  3.000
 2YX  N1   C    N    120.74  3.000
 2YX  N    C    N6   116.10  3.000
 2YX  N1   C    N6   123.13  3.000
 2YX  H3   N    H2   114.90  3.000
 2YX  H3   N    C    115.96  3.000
 2YX  H2   N    C    119.56  3.000
 2YX  C15  C16  C1   121.65  3.000
 2YX  C1   C16  C17  118.73  3.000
 2YX  C15  C16  C17  119.62  3.000
 2YX  C2   C1   N1   118.06  3.000
 2YX  N1   C1   C16  122.17  3.000
 2YX  C2   C1   C16  119.77  3.000
 2YX  C1   N1   C    118.11  3.000
 2YX  H4   C15  C14  122.27  3.000
 2YX  H4   C15  C16  120.65  3.000
 2YX  C14  C15  C16  117.08  3.000
 2YX  N5   C14  C3   104.40  3.000
 2YX  C3   C14  C15  122.66  3.000
 2YX  N5   C14  C15  132.94  3.000
 2YX  N2   C3   C2   129.73  3.000
 2YX  C2   C3   C14  119.93  3.000
 2YX  N2   C3   C14  110.35  3.000
 2YX  H5   C2   C3   121.35  3.000
 2YX  H5   C2   C1   119.74  3.000
 2YX  C3   C2   C1   118.92  3.000
 2YX  H6   N5   C4   126.88  3.000
 2YX  H6   N5   C14  126.12  3.000
 2YX  C4   N5   C14  106.97  3.000
 2YX  N3   C4   N2   124.24  3.000
 2YX  N2   C4   N5   113.26  3.000
 2YX  N3   C4   N5   122.49  3.000
 2YX  C4   N2   C3   105.02  3.000
 2YX  H8   N3   C5   118.28  3.000
 2YX  H8   N3   C4   115.36  3.000
 2YX  C5   N3   C4   123.89  3.000
 2YX  H10  C5   H9   107.27  3.000
 2YX  H10  C5   C6   109.82  3.000
 2YX  H9   C5   C6   109.02  3.000
 2YX  H10  C5   N3   111.39  3.000
 2YX  H9   C5   N3   109.49  3.000
 2YX  C6   C5   N3   109.79  3.000
 2YX  H12  C6   H11  107.36  3.000
 2YX  H12  C6   C7   110.10  3.000
 2YX  H11  C6   C7   109.80  3.000
 2YX  H12  C6   C5   109.26  3.000
 2YX  H11  C6   C5   109.31  3.000
 2YX  C7   C6   C5   110.93  3.000
 2YX  C8   C7   C13  118.89  3.000
 2YX  C13  C7   C6   120.58  3.000
 2YX  C8   C7   C6   120.51  3.000
 2YX  H13  C13  C12  119.23  3.000
 2YX  H13  C13  C7   119.82  3.000
 2YX  C12  C13  C7   120.94  3.000
 2YX  H14  C12  C10  120.23  3.000
 2YX  H14  C12  C13  120.33  3.000
 2YX  C10  C12  C13  119.45  3.000
 2YX  C9   C10  C11  119.83  3.000
 2YX  C9   C10  C12  120.31  3.000
 2YX  C11  C10  C12  119.86  3.000
 2YX  N4   C11  C10  180.00  3.000
 2YX  H15  C9   C8   120.31  3.000
 2YX  H15  C9   C10  120.24  3.000
 2YX  C8   C9   C10  119.44  3.000
 2YX  H16  C8   C9   119.26  3.000
 2YX  H16  C8   C7   119.78  3.000
 2YX  C9   C8   C7   120.97  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
 2YX  CONST_01  N5   C14  C15  C16   180.00   0.0  0
 2YX  CONST_02  C3   C14  C15  C16     0.00   0.0  0
 2YX  CONST_03  C3   C2   C1   C16     0.00   0.0  0
 2YX  CONST_04  N2   C3   C2   C1    180.00   0.0  0
 2YX  CONST_05  C14  C3   C2   C1      0.00   0.0  0
 2YX  CONST_06  C14  C15  C16  C1      0.00   0.0  0
 2YX  CONST_07  C4   N5   C14  C15   180.00   0.0  0
 2YX  CONST_08  N2   C3   C14  C15   180.00   0.0  0
 2YX  CONST_09  C2   C3   C14  C15     0.00   0.0  0
 2YX  CONST_10  C2   C1   C16  C15     0.00   0.0  0
 2YX  CONST_11  N2   C4   N5   C14     0.00   0.0  0
 2YX  CONST_12  C4   N2   C3   C14     0.00   0.0  0
 2YX  CONST_13  N5   C4   N2   C3      0.00   0.0  0
 2YX  CONST_14  C4   N5   C14  C3      0.00   0.0  0
 2YX  CONST_15  C4   N2   C3   C2    180.00   0.0  0
 2YX  CONST_16  N5   C14  C3   C2    180.00   0.0  0
 2YX  CONST_17  N2   C3   C14  N5      0.00   0.0  0
 2YX  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 2YX  CONST_19  C10  C12  C13  C7      0.00   0.0  0
 2YX  CONST_20  C9   C10  C12  C13     0.00   0.0  0
 2YX  CONST_21  C9   C8   C7   C13     0.00   0.0  0
 2YX  CONST_22  C8   C9   C10  C12     0.00   0.0  0
 2YX  CONST_23  C8   C7   C13  C12     0.00   0.0  0
 2YX  CONST_24  N1   C    N6   C17     0.00   0.0  0
 2YX  CONST_25  C1   N1   C    N6      0.00   0.0  0
 2YX  CONST_26  C16  C17  N6   C       0.00   0.0  0
 2YX  CONST_27  N3   C4   N5   C14   180.00   0.0  0
 2YX  CONST_28  N3   C4   N2   C3    180.00   0.0  0
 2YX  CONST_29  C9   C8   C7   C6    180.00   0.0  0
 2YX  CONST_30  C12  C13  C7   C6    180.00   0.0  0
 2YX  CONST_31  C11  C10  C12  C13   180.00   0.0  0
 2YX  CONST_32  C8   C9   C10  C11   180.00   0.0  0
 2YX  CONST_33  C    N6   C17  O     180.00   0.0  0
 2YX  CONST_34  N    C    N6   C17   180.00   0.0  0
 2YX  CONST_35  C1   N1   C    N     180.00   0.0  0
 2YX  CONST_36  H4   C15  C16  C17     0.00   0.0  0
 2YX  CONST_37  H5   C2   C1   C16   180.00   0.0  0
 2YX  CONST_38  H6   N5   C14  C15     0.00   0.0  0
 2YX  CONST_39  H15  C9   C8   C7    180.00   0.0  0
 2YX  CONST_40  H14  C12  C13  C7    180.00   0.0  0
 2YX  CONST_41  H16  C8   C7   C13   180.00   0.0  0
 2YX  CONST_42  H13  C13  C12  C10   180.00   0.0  0
 2YX  CONST_43  H1   N6   C17  C16   180.00   0.0  0
 2YX  CONST_44  C5   N3   C4   N5      0.00   0.0  0
 2YX  CONST_45  C5   N3   C4   N2    180.00   0.0  0
 2YX  CONST_46  H8   N3   C4   N5    180.00   0.0  0
 2YX  CONST_48  H3   N    C    N6    180.00   0.0  0
 2YX  Var_01    C8   C7   C6   C5    -93.89  30.0  2
 2YX  Var_02    C6   C5   N3   C4   -172.65  30.0  1
 2YX  Var_03    C7   C6   C5   N3    178.69  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
 2YX  plan-1  C6   0.020
 2YX  plan-1  C7   0.020
 2YX  plan-1  C13  0.020
 2YX  plan-1  C12  0.020
 2YX  plan-1  C10  0.020
 2YX  plan-1  C11  0.020
 2YX  plan-1  N4   0.020
 2YX  plan-1  C9   0.020
 2YX  plan-1  C8   0.020
 2YX  plan-1  H13  0.020
 2YX  plan-1  H14  0.020
 2YX  plan-1  H15  0.020
 2YX  plan-1  H16  0.020
 2YX  plan-2  O    0.020
 2YX  plan-2  C17  0.020
 2YX  plan-2  N6   0.020
 2YX  plan-2  C    0.020
 2YX  plan-2  N    0.020
 2YX  plan-2  C16  0.020
 2YX  plan-2  C1   0.020
 2YX  plan-2  N1   0.020
 2YX  plan-2  C15  0.020
 2YX  plan-2  C14  0.020
 2YX  plan-2  C3   0.020
 2YX  plan-2  C2   0.020
 2YX  plan-2  N5   0.020
 2YX  plan-2  C4   0.020
 2YX  plan-2  N2   0.020
 2YX  plan-2  N3   0.020
 2YX  plan-2  H1   0.020
 2YX  plan-2  H2   0.020
 2YX  plan-2  H3   0.020
 2YX  plan-2  H4   0.020
 2YX  plan-2  H5   0.020
 2YX  plan-2  H6   0.020
 2YX  plan-3  C4   0.020
 2YX  plan-3  N3   0.020
 2YX  plan-3  C5   0.020
 2YX  plan-3  H8   0.020

