# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 00:46:17 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2cc3C(=O)NC(=Nc3c(CCNCC4CCCCC4)c2n1)N
#
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
 PK2  PK2  6-amino-4-{2-[(cyclohexylmethyl)amino]ethyl}-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  54  27  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PK2
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
 PK2  C2    C  CR6   0   0.542  -3.5200   2.6908   0.5014
 PK2  O14   O  O     0  -0.477  -4.6356   2.9962   0.8982
 PK2  N3    N  NR16  0  -0.718  -2.5675   3.6634   0.2913
 PK2  C4    C  CR6   0   0.638  -1.3025   3.4032  -0.1610
 PK2  N15   N  NH2   0  -0.836  -0.4791   4.4707  -0.2709
 PK2  N5    N  N     0  -0.515  -0.8809   2.2134  -0.4296
 PK2  C6    C  CR66  0   0.224  -1.7390   1.1563  -0.2483
 PK2  C10   C  CR6   0  -0.076  -1.2623  -0.1355  -0.5424
 PK2  C18   C  CH2   0  -0.507   0.1404  -0.3653  -1.0144
 PK2  C19   C  CH2   0  -0.247   1.1282  -0.4708   0.1443
 PK2  N20   N  NH1   0  -0.599   2.4879  -0.5854  -0.3427
 PK2  C21   C  CH2   0  -0.237   3.4742  -0.6746   0.7151
 PK2  C22   C  CH1   0  -0.253   4.9000  -0.6465   0.1764
 PK2  C27   C  CH2   0  -0.417   5.9071  -0.8803   1.3025
 PK2  C26   C  CH2   0  -0.429   7.3462  -0.8427   0.7970
 PK2  C25   C  CH2   0  -0.428   7.6455   0.4646   0.0701
 PK2  C24   C  CH2   0  -0.432   6.6491   0.7019  -1.0606
 PK2  C23   C  CH2   0  -0.404   5.2123   0.6616  -0.5496
 PK2  C9    C  CR56  0   0.143  -2.1390  -1.1954  -0.3512
 PK2  N11   N  N     0  -0.537  -1.9259  -2.5306  -0.5566
 PK2  C12   C  CR5   0   0.690  -3.0668  -3.1137  -0.2405
 PK2  N16   N  NH1   0  -0.676  -3.2943  -4.4282  -0.3082
 PK2  C17   C  CH3   0  -0.544  -4.5329  -5.0533   0.0845
 PK2  N13   N  NR15  0  -0.750  -4.0226  -2.2340   0.1662
 PK2  C8    C  CR56  0   0.363  -3.4614  -0.9750   0.1098
 PK2  C7    C  CR16  0  -0.373  -3.9461   0.2700   0.3963
 PK2  C1    C  CR66  0  -0.155  -3.0646   1.3459   0.2132
 PK2  HN3   H  HNR6  0   0.419  -2.8400   4.6173   0.4892
 PK2  HN15  H  HNH2  0   0.404  -0.8752   5.3910  -0.3694
 PK2  HN1A  H  HNH2  0   0.401   0.3696   4.3182  -0.7901
 PK2  H18   H  HCH2  0   0.232   0.1779  -1.2853  -1.6039
 PK2  H18A  H  HCH2  0   0.231   0.4559   0.4505  -1.6660
 PK2  H19   H  HCH2  0   0.218   1.0605   0.4344   0.7546
 PK2  H19A  H  HCH2  0   0.186   0.8325  -1.3075   0.7975
 PK2  HN20  H  HNH1  0   0.334   2.5618  -1.4102  -0.9281
 PK2  H21   H  HCH2  0   0.206   3.3323   0.1812   1.3855
 PK2  H21A  H  HCH2  0   0.192   3.3425  -1.5731   1.3418
 PK2  H22   H  HCH1  0   0.205   5.0102  -1.4716  -0.5427
 PK2  H27   H  HCH2  0   0.204   5.7717  -0.1056   2.0673
 PK2  H27A  H  HCH2  0   0.221   5.7045  -1.8378   1.7910
 PK2  H26   H  HCH2  0   0.224   8.0412  -0.9831   1.6286
 PK2  H26A  H  HCH2  0   0.206   7.5089  -1.6809   0.1101
 PK2  H25   H  HCH2  0   0.206   7.5868   1.2958   0.7815
 PK2  H25A  H  HCH2  0   0.223   8.6677   0.4590  -0.3169
 PK2  H24   H  HCH2  0   0.222   6.8478   1.6611  -1.5455
 PK2  H24A  H  HCH2  0   0.206   6.7844  -0.0678  -1.8288
 PK2  H23   H  HCH2  0   0.224   4.5056   0.8078  -1.3683
 PK2  H23A  H  HCH2  0   0.197   5.0570   1.4934   0.1497
 PK2  HN16  H  HNH1  0   0.407  -2.5157  -5.0054  -0.5754
 PK2  H17   H  HCH3  0   0.244  -5.3759  -4.6934  -0.5090
 PK2  H17A  H  HCH3  0   0.270  -4.4442  -6.1222  -0.0827
 PK2  H17B  H  HCH3  0   0.243  -4.7596  -4.8960   1.1417
 PK2  HN13  H  HNR5  0   0.423  -4.9598  -2.4544   0.4612
 PK2  H7    H  HCR6  0   0.264  -4.9564   0.4346   0.7468

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
 PK2  C2   O14   double    1.223  0.020  1.223
 PK2  C2   N3    single    1.377  0.020  1.377
 PK2  C2   C1    single    1.449  0.020  1.449
 PK2  N3   C4    single    1.368  0.020  1.368
 PK2  C4   N15   single    1.353  0.020  1.353
 PK2  C4   N5    double    1.291  0.020  1.291
 PK2  N5   C6    single    1.374  0.020  1.374
 PK2  C6   C10   aromatic  1.408  0.020  1.408
 PK2  C6   C1    aromatic  1.416  0.020  1.416
 PK2  C10  C18   single    1.498  0.020  1.498
 PK2  C10  C9    aromatic  1.389  0.020  1.389
 PK2  C18  C19   single    1.526  0.020  1.526
 PK2  C19  N20   single    1.449  0.020  1.449
 PK2  N20  C21   single    1.449  0.020  1.449
 PK2  C21  C22   single    1.524  0.020  1.524
 PK2  C22  C27   single    1.529  0.020  1.529
 PK2  C22  C23   single    1.528  0.020  1.528
 PK2  C27  C26   single    1.526  0.020  1.526
 PK2  C26  C25   single    1.525  0.020  1.525
 PK2  C25  C24   single    1.526  0.020  1.526
 PK2  C24  C23   single    1.525  0.020  1.525
 PK2  C9   N11   aromatic  1.368  0.020  1.368
 PK2  C9   C8    aromatic  1.418  0.020  1.418
 PK2  N11  C12   aromatic  1.320  0.020  1.320
 PK2  C12  N16   single    1.336  0.020  1.336
 PK2  C12  N13   aromatic  1.361  0.020  1.361
 PK2  N16  C17   single    1.442  0.020  1.442
 PK2  N13  C8    aromatic  1.380  0.020  1.380
 PK2  C8   C7    aromatic  1.366  0.020  1.366
 PK2  C7   C1    aromatic  1.403  0.020  1.403
 PK2  N3   HN3   single    0.860  0.020  1.020
 PK2  N15  HN15  single    0.890  0.020  1.040
 PK2  N15  HN1A  single    0.890  0.020  1.040
 PK2  C18  H18   single    0.970  0.020  1.090
 PK2  C18  H18A  single    0.970  0.020  1.090
 PK2  C19  H19   single    0.970  0.020  1.090
 PK2  C19  H19A  single    0.970  0.020  1.090
 PK2  N20  HN20  single    0.890  0.020  1.040
 PK2  C21  H21   single    0.970  0.020  1.090
 PK2  C21  H21A  single    0.970  0.020  1.090
 PK2  C22  H22   single    0.970  0.020  1.090
 PK2  C27  H27   single    0.970  0.020  1.090
 PK2  C27  H27A  single    0.970  0.020  1.090
 PK2  C26  H26   single    0.970  0.020  1.090
 PK2  C26  H26A  single    0.970  0.020  1.090
 PK2  C25  H25   single    0.970  0.020  1.090
 PK2  C25  H25A  single    0.970  0.020  1.090
 PK2  C24  H24   single    0.970  0.020  1.090
 PK2  C24  H24A  single    0.970  0.020  1.090
 PK2  C23  H23   single    0.970  0.020  1.090
 PK2  C23  H23A  single    0.970  0.020  1.090
 PK2  N16  HN16  single    0.860  0.020  1.020
 PK2  C17  H17   single    0.970  0.020  1.090
 PK2  C17  H17A  single    0.970  0.020  1.090
 PK2  C17  H17B  single    0.970  0.020  1.090
 PK2  N13  HN13  single    0.860  0.020  1.020
 PK2  C7   H7    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
 PK2  C1    C2   N3    114.06  3.000
 PK2  C1    C2   O14   125.67  3.000
 PK2  N3    C2   O14   120.27  3.000
 PK2  HN3   N3   C4    119.54  3.000
 PK2  HN3   N3   C2    116.72  3.000
 PK2  C4    N3   C2    123.74  3.000
 PK2  N5    C4   N15   120.79  3.000
 PK2  N5    C4   N3    123.09  3.000
 PK2  N15   C4   N3    116.07  3.000
 PK2  HN1A  N15  HN15  114.82  3.000
 PK2  HN1A  N15  C4    115.82  3.000
 PK2  HN15  N15  C4    119.34  3.000
 PK2  C6    N5   C4    118.56  3.000
 PK2  C1    C6   C10   120.52  3.000
 PK2  C1    C6   N5    121.65  3.000
 PK2  C10   C6   N5    117.84  3.000
 PK2  C9    C10  C18   121.17  3.000
 PK2  C9    C10  C6    117.24  3.000
 PK2  C18   C10  C6    121.58  3.000
 PK2  H18A  C18  H18   107.31  3.000
 PK2  H18A  C18  C19   108.54  3.000
 PK2  H18   C18  C19   109.20  3.000
 PK2  H18A  C18  C10   110.15  3.000
 PK2  H18   C18  C10   109.33  3.000
 PK2  C19   C18  C10   112.18  3.000
 PK2  H19A  C19  H19   106.32  3.000
 PK2  H19A  C19  N20   113.02  3.000
 PK2  H19   C19  N20   108.13  3.000
 PK2  H19A  C19  C18   109.20  3.000
 PK2  H19   C19  C18   109.05  3.000
 PK2  N20   C19  C18   110.96  3.000
 PK2  HN20  N20  C21   108.77  3.000
 PK2  HN20  N20  C19   109.07  3.000
 PK2  C21   N20  C19   113.47  3.000
 PK2  H21A  C21  H21   105.84  3.000
 PK2  H21A  C21  C22   109.11  3.000
 PK2  H21   C21  C22   108.83  3.000
 PK2  H21A  C21  N20   112.55  3.000
 PK2  H21   C21  N20   108.08  3.000
 PK2  C22   C21  N20   112.18  3.000
 PK2  H22   C22  C23   108.12  3.000
 PK2  H22   C22  C27   107.51  3.000
 PK2  C23   C22  C27   110.25  3.000
 PK2  H22   C22  C21   108.11  3.000
 PK2  C23   C22  C21   112.01  3.000
 PK2  C27   C22  C21   110.67  3.000
 PK2  H27A  C27  H27   106.50  3.000
 PK2  H27A  C27  C26   110.13  3.000
 PK2  H27   C27  C26   109.27  3.000
 PK2  H27A  C27  C22   109.93  3.000
 PK2  H27   C27  C22   108.92  3.000
 PK2  C26   C27  C22   111.94  3.000
 PK2  H26A  C26  H26   106.52  3.000
 PK2  H26A  C26  C25   109.13  3.000
 PK2  H26   C26  C25   110.36  3.000
 PK2  H26A  C26  C27   109.20  3.000
 PK2  H26   C26  C27   110.16  3.000
 PK2  C25   C26  C27   111.35  3.000
 PK2  H25A  C25  H25   106.50  3.000
 PK2  H25A  C25  C24   110.44  3.000
 PK2  H25   C25  C24   109.16  3.000
 PK2  H25A  C25  C26   110.35  3.000
 PK2  H25   C25  C26   109.28  3.000
 PK2  C24   C25  C26   111.00  3.000
 PK2  H24A  C24  H24   106.44  3.000
 PK2  H24A  C24  C23   109.43  3.000
 PK2  H24   C24  C23   110.06  3.000
 PK2  H24A  C24  C25   109.25  3.000
 PK2  H24   C24  C25   110.27  3.000
 PK2  C23   C24  C25   111.27  3.000
 PK2  H23A  C23  H23   106.54  3.000
 PK2  H23A  C23  C24   109.07  3.000
 PK2  H23   C23  C24   110.80  3.000
 PK2  H23A  C23  C22   108.48  3.000
 PK2  H23   C23  C22   109.79  3.000
 PK2  C24   C23  C22   111.98  3.000
 PK2  C8    C9   N11   110.24  3.000
 PK2  C8    C9   C10   121.00  3.000
 PK2  N11   C9   C10   128.76  3.000
 PK2  C12   N11  C9    105.11  3.000
 PK2  N13   C12  N16   122.11  3.000
 PK2  N13   C12  N11   113.15  3.000
 PK2  N16   C12  N11   124.75  3.000
 PK2  HN16  N16  C17   119.26  3.000
 PK2  HN16  N16  C12   116.52  3.000
 PK2  C17   N16  C12   124.00  3.000
 PK2  H17B  C17  H17A  107.92  3.000
 PK2  H17B  C17  H17   108.56  3.000
 PK2  H17A  C17  H17   107.69  3.000
 PK2  H17B  C17  N16   112.29  3.000
 PK2  H17A  C17  N16   108.34  3.000
 PK2  H17   C17  N16   111.85  3.000
 PK2  HN13  N13  C8    126.18  3.000
 PK2  HN13  N13  C12   126.85  3.000
 PK2  C8    N13  C12   106.98  3.000
 PK2  C7    C8   N13   132.74  3.000
 PK2  C7    C8   C9    122.73  3.000
 PK2  N13   C8   C9    104.53  3.000
 PK2  H7    C7   C1    120.82  3.000
 PK2  H7    C7   C8    122.53  3.000
 PK2  C1    C7   C8    116.65  3.000
 PK2  C7    C1   C6    121.87  3.000
 PK2  C7    C1   C2    119.24  3.000
 PK2  C6    C1   C2    118.90  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
 PK2  CONST_01  N11   C9   C10  C6    180.00   0.0  0
 PK2  CONST_02  C8    C9   C10  C6      0.00   0.0  0
 PK2  CONST_03  C8    C7   C1   C6      0.00   0.0  0
 PK2  CONST_04  C7    C1   C6   C10     0.00   0.0  0
 PK2  CONST_05  C12   N11  C9   C10   180.00   0.0  0
 PK2  CONST_06  N13   C8   C9   C10   180.00   0.0  0
 PK2  CONST_07  C7    C8   C9   C10     0.00   0.0  0
 PK2  CONST_08  C1    C6   C10  C9      0.00   0.0  0
 PK2  CONST_09  N13   C12  N11  C9      0.00   0.0  0
 PK2  CONST_10  C12   N13  C8   C9      0.00   0.0  0
 PK2  CONST_11  C1    C7   C8   C9      0.00   0.0  0
 PK2  CONST_12  N13   C8   C9   N11     0.00   0.0  0
 PK2  CONST_13  C7    C8   C9   N11   180.00   0.0  0
 PK2  CONST_14  C8    N13  C12  N11     0.00   0.0  0
 PK2  CONST_15  C8    C9   N11  C12     0.00   0.0  0
 PK2  CONST_16  C7    C8   N13  C12   180.00   0.0  0
 PK2  CONST_17  C1    C7   C8   N13   180.00   0.0  0
 PK2  CONST_18  N5    C4   N3   C2      0.00   0.0  0
 PK2  CONST_19  C6    N5   C4   N3      0.00   0.0  0
 PK2  CONST_20  C1    C2   N3   C4      0.00   0.0  0
 PK2  CONST_21  C18   C10  C6   N5      0.00   0.0  0
 PK2  CONST_22  C1    C6   C10  C18   180.00   0.0  0
 PK2  CONST_23  N11   C9   C10  C18     0.00   0.0  0
 PK2  CONST_24  C8    C9   C10  C18   180.00   0.0  0
 PK2  CONST_25  N16   C12  N11  C9    180.00   0.0  0
 PK2  CONST_26  C8    N13  C12  N16   180.00   0.0  0
 PK2  CONST_27  N15   C4   N3   C2    180.00   0.0  0
 PK2  CONST_28  C4    N3   C2   O14   180.00   0.0  0
 PK2  CONST_29  C6    N5   C4   N15   180.00   0.0  0
 PK2  CONST_30  H7    C7   C1   C2      0.00   0.0  0
 PK2  CONST_31  HN13  N13  C8   C9    180.00   0.0  0
 PK2  CONST_32  HN3   N3   C4   N5    180.00   0.0  0
 PK2  CONST_33  C17   N16  C12  N11   180.00   0.0  0
 PK2  CONST_34  N13   C12  N16  C17     0.00   0.0  0
 PK2  CONST_35  HN16  N16  C12  N11     0.00   0.0  0
 PK2  CONST_37  HN1A  N15  C4   N3    180.00   0.0  0
 PK2  Var_01    C25   C26  C27  C22    55.54  30.0  1
 PK2  Var_02    C25   C24  C23  C22   -55.66  30.0  1
 PK2  Var_03    C24   C25  C26  C27   -55.14  30.0  1
 PK2  Var_04    C23   C24  C25  C26    55.16  30.0  1
 PK2  Var_05    C19   C18  C10  C6     84.64  30.0  2
 PK2  Var_06    N20   C19  C18  C10  -175.43  30.0  3
 PK2  Var_07    C22   C21  N20  C19  -174.00  30.0  3
 PK2  Var_08    H17   C17  N16  C12    60.97  30.0  3
 PK2  Var_09    C21   N20  C19  C18   179.37  30.0  3

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
 PK2  chir_01  C22  C21  C27  C23  positiv

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
 PK2  plan-1  C2    0.020
 PK2  plan-1  O14   0.020
 PK2  plan-1  N3    0.020
 PK2  plan-1  C4    0.020
 PK2  plan-1  N15   0.020
 PK2  plan-1  N5    0.020
 PK2  plan-1  C6    0.020
 PK2  plan-1  C10   0.020
 PK2  plan-1  C18   0.020
 PK2  plan-1  C9    0.020
 PK2  plan-1  N11   0.020
 PK2  plan-1  C12   0.020
 PK2  plan-1  N16   0.020
 PK2  plan-1  N13   0.020
 PK2  plan-1  C8    0.020
 PK2  plan-1  C7    0.020
 PK2  plan-1  C1    0.020
 PK2  plan-1  HN3   0.020
 PK2  plan-1  HN15  0.020
 PK2  plan-1  HN1A  0.020
 PK2  plan-1  HN13  0.020
 PK2  plan-1  H7    0.020
 PK2  plan-2  C12   0.020
 PK2  plan-2  N16   0.020
 PK2  plan-2  C17   0.020
 PK2  plan-2  HN16  0.020

