# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:46:06 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 6-amino-2-{[2-(piperidin-1-yl)ethyl]amino}-3,5-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2cc3nc(NCCN4CCCCC4)[nH]c3cc2N1
#
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
 2YM  2YM  6-amino-2-{[2-(piperidin-1-yl)ethyl]amino}-3,5-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  45  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2YM
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
 2YM  O    O  O     0  -0.492   5.6580  -1.8916  -1.0129
 2YM  C1   C  CR6   0   0.434   5.3342  -0.8099  -0.5295
 2YM  N1   N  N     0  -0.535   6.2772   0.1216  -0.2245
 2YM  C2   C  CR66  0  -0.173   3.9191  -0.4887  -0.2695
 2YM  C15  C  CR66  0   0.419   3.6057   0.7615   0.2822
 2YM  N6   N  NR16  0  -0.751   4.6518   1.6215   0.5533
 2YM  C    C  CR6   0   0.658   5.9287   1.2739   0.2939
 2YM  N    N  NH2   0  -0.826   6.8797   2.1602   0.6190
 2YM  C14  C  CR16  0  -0.407   2.2932   1.1424   0.5543
 2YM  C13  C  CR56  0   0.375   1.3188   0.2169   0.2498
 2YM  C4   C  CR56  0   0.180   1.5959  -1.0537  -0.3059
 2YM  C3   C  CR16  0  -0.409   2.9050  -1.4040  -0.5656
 2YM  N5   N  NR15  0  -0.745  -0.0436   0.2501   0.3748
 2YM  C5   C  CR5   0   0.676  -0.5211  -0.9482  -0.0857
 2YM  N2   N  N     0  -0.533   0.4257  -1.7510  -0.5029
 2YM  N3   N  NH1   0  -0.688  -1.8345  -1.2464  -0.0663
 2YM  C6   C  CH2   0  -0.294  -2.8666  -0.2359   0.0583
 2YM  C7   C  CH2   0  -0.297  -4.2253  -0.9164   0.1670
 2YM  N4   N  NT    0  -0.422  -5.3076   0.0453   0.1951
 2YM  C12  C  CH2   0  -0.280  -6.4902  -0.4995   0.8461
 2YM  C11  C  CH2   0  -0.439  -7.5862   0.5479   0.9679
 2YM  C10  C  CH2   0  -0.440  -7.9485   1.1179  -0.3974
 2YM  C9   C  CH2   0  -0.435  -6.6904   1.6233  -1.0909
 2YM  C8   C  CH2   0  -0.289  -5.6303   0.5342  -1.1377
 2YM  H1   H  HNR6  0   0.425   4.4478   2.5210   0.9628
 2YM  H2   H  HNH2  0   0.412   6.6546   3.1145   0.8433
 2YM  H3   H  HNH2  0   0.409   7.8180   1.9742   0.3100
 2YM  H4   H  HCR6  0   0.283   2.0597   2.1107   0.9784
 2YM  H5   H  HCR6  0   0.254   3.1554  -2.3663  -0.9919
 2YM  H6   H  HNR5  0   0.425  -0.5844   1.0154   0.7443
 2YM  H8   H  HNH1  0   0.396  -2.0724  -2.0633  -0.6086
 2YM  H9   H  HCH2  0   0.241  -2.7074   0.3469   0.9681
 2YM  H10  H  HCH2  0   0.241  -2.8402   0.4619  -0.7856
 2YM  H11  H  HCH2  0   0.205  -4.3450  -1.6424  -0.6559
 2YM  H12  H  HCH2  0   0.248  -4.2398  -1.4938   1.0943
 2YM  H14  H  HCH2  0   0.185  -6.8819  -1.3735   0.2955
 2YM  H15  H  HCH2  0   0.235  -6.2064  -0.8547   1.8394
 2YM  H16  H  HCH2  0   0.231  -8.4585   0.1013   1.4500
 2YM  H17  H  HCH2  0   0.215  -7.2378   1.3545   1.6205
 2YM  H18  H  HCH2  0   0.210  -8.4118   0.3364  -1.0092
 2YM  H19  H  HCH2  0   0.231  -8.6858   1.9176  -0.2989
 2YM  H20  H  HCH2  0   0.230  -6.9111   1.9536  -2.1082
 2YM  H21  H  HCH2  0   0.216  -6.2950   2.4894  -0.5518
 2YM  H22  H  HCH2  0   0.236  -4.7274   0.9265  -1.6092
 2YM  H23  H  HCH2  0   0.188  -5.9851  -0.2927  -1.7797

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
 2YM  C10  C11  single    1.523  0.020  1.523
 2YM  C10  C9   single    1.523  0.020  1.523
 2YM  C11  C12  single    1.521  0.020  1.521
 2YM  C9   C8   single    1.521  0.020  1.521
 2YM  C12  N4   single    1.456  0.020  1.456
 2YM  C8   N4   single    1.456  0.020  1.456
 2YM  N4   C7   single    1.448  0.020  1.448
 2YM  C7   C6   single    1.524  0.020  1.524
 2YM  C6   N3   single    1.450  0.020  1.450
 2YM  N3   C5   single    1.347  0.020  1.347
 2YM  C5   N5   aromatic  1.370  0.020  1.370
 2YM  C5   N2   aromatic  1.310  0.020  1.310
 2YM  N5   C13  aromatic  1.369  0.020  1.369
 2YM  N2   C4   aromatic  1.376  0.020  1.376
 2YM  C13  C4   aromatic  1.414  0.020  1.414
 2YM  C13  C14  aromatic  1.378  0.020  1.378
 2YM  C4   C3   aromatic  1.380  0.020  1.380
 2YM  C14  C15  aromatic  1.394  0.020  1.394
 2YM  C3   C2   aromatic  1.398  0.020  1.398
 2YM  C15  C2   aromatic  1.402  0.020  1.402
 2YM  C15  N6   single    1.381  0.020  1.381
 2YM  C2   C1   single    1.474  0.020  1.474
 2YM  N6   C    single    1.349  0.020  1.349
 2YM  C1   O    double    1.228  0.020  1.228
 2YM  C1   N1   single    1.360  0.020  1.360
 2YM  C    N1   double    1.311  0.020  1.311
 2YM  C    N    single    1.340  0.020  1.340
 2YM  N6   H1   single    0.860  0.020  1.020
 2YM  N    H2   single    0.890  0.020  1.040
 2YM  N    H3   single    0.890  0.020  1.040
 2YM  C14  H4   single    0.930  0.020  1.080
 2YM  C3   H5   single    0.930  0.020  1.080
 2YM  N5   H6   single    0.860  0.020  1.020
 2YM  N3   H8   single    0.890  0.020  1.040
 2YM  C6   H9   single    0.970  0.020  1.090
 2YM  C6   H10  single    0.970  0.020  1.090
 2YM  C7   H11  single    0.970  0.020  1.090
 2YM  C7   H12  single    0.970  0.020  1.090
 2YM  C12  H14  single    0.970  0.020  1.090
 2YM  C12  H15  single    0.970  0.020  1.090
 2YM  C11  H16  single    0.970  0.020  1.090
 2YM  C11  H17  single    0.970  0.020  1.090
 2YM  C10  H18  single    0.970  0.020  1.090
 2YM  C10  H19  single    0.970  0.020  1.090
 2YM  C9   H20  single    0.970  0.020  1.090
 2YM  C9   H21  single    0.970  0.020  1.090
 2YM  C8   H22  single    0.970  0.020  1.090
 2YM  C8   H23  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
 2YM  C2   C1   N1   118.48  3.000
 2YM  N1   C1   O    120.57  3.000
 2YM  C2   C1   O    120.96  3.000
 2YM  C    N1   C1   120.43  3.000
 2YM  C3   C2   C15  120.34  3.000
 2YM  C15  C2   C1   118.57  3.000
 2YM  C3   C2   C1   121.09  3.000
 2YM  C14  C15  N6   120.32  3.000
 2YM  N6   C15  C2   117.60  3.000
 2YM  C14  C15  C2   122.08  3.000
 2YM  H1   N6   C    119.95  3.000
 2YM  H1   N6   C15  118.79  3.000
 2YM  C    N6   C15  121.26  3.000
 2YM  N    C    N6   117.05  3.000
 2YM  N    C    N1   119.26  3.000
 2YM  N6   C    N1   123.67  3.000
 2YM  H3   N    H2   116.93  3.000
 2YM  H3   N    C    117.74  3.000
 2YM  H2   N    C    121.53  3.000
 2YM  H4   C14  C13  122.33  3.000
 2YM  H4   C14  C15  121.61  3.000
 2YM  C13  C14  C15  116.06  3.000
 2YM  N5   C13  C4   104.64  3.000
 2YM  C4   C13  C14  123.49  3.000
 2YM  N5   C13  C14  131.88  3.000
 2YM  N2   C4   C3   130.62  3.000
 2YM  C3   C4   C13  119.21  3.000
 2YM  N2   C4   C13  110.17  3.000
 2YM  H5   C3   C4   121.31  3.000
 2YM  H5   C3   C2   119.87  3.000
 2YM  C4   C3   C2   118.83  3.000
 2YM  H6   N5   C5   126.93  3.000
 2YM  H6   N5   C13  125.90  3.000
 2YM  C5   N5   C13  107.17  3.000
 2YM  N3   C5   N2   125.02  3.000
 2YM  N2   C5   N5   113.04  3.000
 2YM  N3   C5   N5   121.92  3.000
 2YM  C5   N2   C4   104.98  3.000
 2YM  H8   N3   C6   116.28  3.000
 2YM  H8   N3   C5   113.66  3.000
 2YM  C6   N3   C5   122.75  3.000
 2YM  H10  C6   H9   107.36  3.000
 2YM  H10  C6   C7   111.16  3.000
 2YM  H9   C6   C7   107.99  3.000
 2YM  H10  C6   N3   111.14  3.000
 2YM  H9   C6   N3   109.87  3.000
 2YM  C7   C6   N3   109.25  3.000
 2YM  H12  C7   H11  106.48  3.000
 2YM  H12  C7   N4   108.94  3.000
 2YM  H11  C7   N4   111.73  3.000
 2YM  H12  C7   C6   107.96  3.000
 2YM  H11  C7   C6   109.71  3.000
 2YM  N4   C7   C6   111.80  3.000
 2YM  C8   N4   C12  110.79  3.000
 2YM  C8   N4   C7   111.77  3.000
 2YM  C12  N4   C7   111.55  3.000
 2YM  H15  C12  H14  106.74  3.000
 2YM  H15  C12  C11  109.77  3.000
 2YM  H14  C12  C11  109.22  3.000
 2YM  H15  C12  N4   108.50  3.000
 2YM  H14  C12  N4   111.18  3.000
 2YM  C11  C12  N4   111.32  3.000
 2YM  H17  C11  H16  107.00  3.000
 2YM  H17  C11  C10  109.53  3.000
 2YM  H16  C11  C10  111.02  3.000
 2YM  H17  C11  C12  109.03  3.000
 2YM  H16  C11  C12  109.22  3.000
 2YM  C10  C11  C12  110.93  3.000
 2YM  H19  C10  H18  106.69  3.000
 2YM  H19  C10  C9   110.84  3.000
 2YM  H18  C10  C9   109.38  3.000
 2YM  H19  C10  C11  110.72  3.000
 2YM  H18  C10  C11  109.53  3.000
 2YM  C9   C10  C11  109.63  3.000
 2YM  H21  C9   H20  107.01  3.000
 2YM  H21  C9   C8   109.28  3.000
 2YM  H20  C9   C8   109.20  3.000
 2YM  H21  C9   C10  109.68  3.000
 2YM  H20  C9   C10  110.95  3.000
 2YM  C8   C9   C10  110.63  3.000
 2YM  H23  C8   H22  106.47  3.000
 2YM  H23  C8   C9   109.27  3.000
 2YM  H22  C8   C9   109.43  3.000
 2YM  H23  C8   N4   110.59  3.000
 2YM  H22  C8   N4   109.44  3.000
 2YM  C9   C8   N4   111.52  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
 2YM  CONST_01  N2   C4   C3   C2    180.00   0.0  0
 2YM  CONST_02  C13  C4   C3   C2      0.00   0.0  0
 2YM  CONST_03  C13  C14  C15  C2      0.00   0.0  0
 2YM  CONST_04  N5   C13  C14  C15   180.00   0.0  0
 2YM  CONST_05  C4   C13  C14  C15     0.00   0.0  0
 2YM  CONST_06  C4   C3   C2   C15     0.00   0.0  0
 2YM  CONST_07  C5   N5   C13  C14   180.00   0.0  0
 2YM  CONST_08  N2   C4   C13  C14   180.00   0.0  0
 2YM  CONST_09  C3   C4   C13  C14     0.00   0.0  0
 2YM  CONST_10  C3   C2   C15  C14     0.00   0.0  0
 2YM  CONST_11  N2   C5   N5   C13     0.00   0.0  0
 2YM  CONST_12  C5   N2   C4   C13     0.00   0.0  0
 2YM  CONST_13  N5   C5   N2   C4      0.00   0.0  0
 2YM  CONST_14  C5   N5   C13  C4      0.00   0.0  0
 2YM  CONST_15  C5   N2   C4   C3    180.00   0.0  0
 2YM  CONST_16  N5   C13  C4   C3    180.00   0.0  0
 2YM  CONST_17  N2   C4   C13  N5      0.00   0.0  0
 2YM  CONST_18  N6   C    N1   C1      0.00   0.0  0
 2YM  CONST_19  C15  N6   C    N1      0.00   0.0  0
 2YM  CONST_20  N3   C5   N5   C13   180.00   0.0  0
 2YM  CONST_21  N3   C5   N2   C4    180.00   0.0  0
 2YM  CONST_22  N    C    N1   C1    180.00   0.0  0
 2YM  CONST_23  N    C    N6   C15   180.00   0.0  0
 2YM  CONST_24  H5   C3   C2   C1      0.00   0.0  0
 2YM  CONST_25  H4   C14  C15  C2    180.00   0.0  0
 2YM  CONST_26  H6   N5   C13  C14     0.00   0.0  0
 2YM  CONST_27  H1   N6   C    N1    180.00   0.0  0
 2YM  CONST_30  H8   N3   C5   N5    180.00   0.0  0
 2YM  CONST_31  H2   N    C    N1    180.00   0.0  0
 2YM  CONST_32  H3   N    C    N1      0.00   0.0  0
 2YM  Var_01    C10  C11  C12  N4     56.71  30.0  1
 2YM  Var_02    C10  C9   C8   N4    -56.97  30.0  1
 2YM  Var_03    C9   C10  C11  C12   -53.50  30.0  1
 2YM  Var_04    C9   C8   N4   C12    59.43  30.0  1
 2YM  Var_05    C8   C9   C10  C11    53.48  30.0  1
 2YM  Var_06    C8   N4   C12  C11   -59.14  30.0  1
 2YM  Var_07    C12  N4   C7   C6   -155.72  30.0  2
 2YM  Var_08    C7   C6   N3   C5   -175.19  30.0  1
 2YM  Var_09    N4   C7   C6   N3   -175.76  30.0  1

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
 2YM  plan-1  O    0.020
 2YM  plan-1  C1   0.020
 2YM  plan-1  N1   0.020
 2YM  plan-1  C2   0.020
 2YM  plan-1  C15  0.020
 2YM  plan-1  N6   0.020
 2YM  plan-1  C    0.020
 2YM  plan-1  N    0.020
 2YM  plan-1  C14  0.020
 2YM  plan-1  C13  0.020
 2YM  plan-1  C4   0.020
 2YM  plan-1  C3   0.020
 2YM  plan-1  N5   0.020
 2YM  plan-1  C5   0.020
 2YM  plan-1  N2   0.020
 2YM  plan-1  N3   0.020
 2YM  plan-1  H1   0.020
 2YM  plan-1  H2   0.020
 2YM  plan-1  H3   0.020
 2YM  plan-1  H4   0.020
 2YM  plan-1  H5   0.020
 2YM  plan-1  H6   0.020
 2YM  plan-2  C5   0.020
 2YM  plan-2  N3   0.020
 2YM  plan-2  C6   0.020
 2YM  plan-2  H8   0.020

