# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:34:29 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 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: O=C1N=CNc2cc3[nH]c(NCCN4CCCCC4)nc3cc12
#
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
 2YO  2YO  2-{[2-(piperidin-1-yl)ethyl]amino}-3,5-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  43  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2YO
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
 2YO  O    O  O     0  -0.472   6.0917  -1.7767   0.2246
 2YO  C1   C  CR6   0   0.444   5.6850  -0.6240   0.1656
 2YO  N1   N  N     0  -0.485   6.5807   0.4235   0.1479
 2YO  C2   C  CR66  0  -0.170   4.2517  -0.3072   0.1115
 2YO  C15  C  CR66  0   0.410   3.8527   1.0387   0.0435
 2YO  N6   N  NR16  0  -0.679   4.8512   1.9890   0.0335
 2YO  C    C  CR16  0   0.139   6.1359   1.6368   0.0852
 2YO  C14  C  CR16  0  -0.396   2.5108   1.4160  -0.0131
 2YO  C13  C  CR56  0   0.379   1.5957   0.3894   0.0042
 2YO  C4   C  CR56  0   0.189   1.9576  -0.9800   0.0743
 2YO  C3   C  CR16  0  -0.405   3.2911  -1.3252   0.1267
 2YO  N5   N  NR15  0  -0.747   0.2289   0.3823  -0.0349
 2YO  C5   C  CR5   0   0.687  -0.1708  -0.9273   0.0100
 2YO  N2   N  N     0  -0.533   0.8331  -1.7681   0.0778
 2YO  N3   N  NH1   0  -0.689  -1.4663  -1.2776  -0.0406
 2YO  C6   C  CH2   0  -0.293  -2.5507  -0.3346   0.1419
 2YO  C7   C  CH2   0  -0.289  -3.8787  -1.0279  -0.1382
 2YO  N4   N  NT    0  -0.424  -5.0099  -0.1792   0.1654
 2YO  C12  C  CH2   0  -0.279  -6.2342  -0.9531   0.3006
 2YO  C11  C  CH2   0  -0.436  -7.3905  -0.0813   0.7661
 2YO  C10  C  CH2   0  -0.440  -7.6031   1.0888  -0.1860
 2YO  C9   C  CH2   0  -0.434  -6.2946   1.8437  -0.3772
 2YO  C8   C  CH2   0  -0.286  -5.1782   0.8995  -0.7975
 2YO  H1   H  HNR6  0   0.435   4.6127   2.9687  -0.0129
 2YO  H2   H  HCR6  0   0.297   6.8384   2.4617   0.0716
 2YO  H3   H  HCR6  0   0.288   2.2187   2.4570  -0.0677
 2YO  H4   H  HCR6  0   0.257   3.5997  -2.3606   0.1798
 2YO  H5   H  HNR5  0   0.429  -0.3669   1.1936  -0.0750
 2YO  H7   H  HNH1  0   0.400  -1.6458  -2.2423   0.1925
 2YO  H8   H  HCH2  0   0.241  -2.5679   0.0773   1.1568
 2YO  H9   H  HCH2  0   0.240  -2.4095   0.4967  -0.5514
 2YO  H10  H  HCH2  0   0.207  -3.8879  -1.3945  -1.1780
 2YO  H11  H  HCH2  0   0.241  -3.9384  -1.9101   0.5061
 2YO  H13  H  HCH2  0   0.185  -6.5111  -1.4376  -0.6531
 2YO  H14  H  HCH2  0   0.235  -6.0618  -1.7535   1.0240
 2YO  H15  H  HCH2  0   0.230  -8.2934  -0.6916   0.8403
 2YO  H16  H  HCH2  0   0.215  -7.1744   0.2941   1.7708
 2YO  H17  H  HCH2  0   0.210  -7.9483   0.7104  -1.1542
 2YO  H18  H  HCH2  0   0.231  -8.3829   1.7554   0.1885
 2YO  H19  H  HCH2  0   0.230  -6.4028   2.6275  -1.1300
 2YO  H20  H  HCH2  0   0.215  -6.0111   2.3349   0.5583
 2YO  H21  H  HCH2  0   0.236  -4.2471   1.4633  -0.8779
 2YO  H22  H  HCH2  0   0.187  -5.3945   0.5004  -1.8051

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
 2YO  C10  C11  single    1.523  0.020  1.523
 2YO  C10  C9   single    1.523  0.020  1.523
 2YO  C11  C12  single    1.521  0.020  1.521
 2YO  C9   C8   single    1.521  0.020  1.521
 2YO  C12  N4   single    1.455  0.020  1.455
 2YO  C8   N4   single    1.456  0.020  1.456
 2YO  N4   C7   single    1.446  0.020  1.446
 2YO  C7   C6   single    1.524  0.020  1.524
 2YO  C6   N3   single    1.449  0.020  1.449
 2YO  N3   C5   single    1.343  0.020  1.343
 2YO  C5   N5   aromatic  1.370  0.020  1.370
 2YO  C5   N2   aromatic  1.311  0.020  1.311
 2YO  N5   C13  aromatic  1.367  0.020  1.367
 2YO  N2   C4   aromatic  1.373  0.020  1.373
 2YO  C13  C4   aromatic  1.418  0.020  1.418
 2YO  C13  C14  aromatic  1.375  0.020  1.375
 2YO  C4   C3   aromatic  1.379  0.020  1.379
 2YO  C14  C15  aromatic  1.395  0.020  1.395
 2YO  C3   C2   aromatic  1.400  0.020  1.400
 2YO  C15  C2   aromatic  1.405  0.020  1.405
 2YO  C15  N6   single    1.379  0.020  1.379
 2YO  C2   C1   single    1.469  0.020  1.469
 2YO  N6   C    single    1.333  0.020  1.333
 2YO  C1   O    double    1.224  0.020  1.224
 2YO  C1   N1   single    1.378  0.020  1.378
 2YO  C    N1   double    1.294  0.020  1.294
 2YO  N6   H1   single    0.860  0.020  1.020
 2YO  C    H2   single    0.930  0.020  1.080
 2YO  C14  H3   single    0.930  0.020  1.080
 2YO  C3   H4   single    0.930  0.020  1.080
 2YO  N5   H5   single    0.860  0.020  1.020
 2YO  N3   H7   single    0.890  0.020  1.040
 2YO  C6   H8   single    0.970  0.020  1.090
 2YO  C6   H9   single    0.970  0.020  1.090
 2YO  C7   H10  single    0.970  0.020  1.090
 2YO  C7   H11  single    0.970  0.020  1.090
 2YO  C12  H13  single    0.970  0.020  1.090
 2YO  C12  H14  single    0.970  0.020  1.090
 2YO  C11  H15  single    0.970  0.020  1.090
 2YO  C11  H16  single    0.970  0.020  1.090
 2YO  C10  H17  single    0.970  0.020  1.090
 2YO  C10  H18  single    0.970  0.020  1.090
 2YO  C9   H19  single    0.970  0.020  1.090
 2YO  C9   H20  single    0.970  0.020  1.090
 2YO  C8   H21  single    0.970  0.020  1.090
 2YO  C8   H22  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
 2YO  C2   C1   N1   118.02  3.000
 2YO  N1   C1   O    120.04  3.000
 2YO  C2   C1   O    121.94  3.000
 2YO  C    N1   C1   119.34  3.000
 2YO  C3   C2   C15  120.14  3.000
 2YO  C15  C2   C1   119.03  3.000
 2YO  C3   C2   C1   120.82  3.000
 2YO  C14  C15  N6   120.66  3.000
 2YO  N6   C15  C2   117.06  3.000
 2YO  C14  C15  C2   122.28  3.000
 2YO  H1   N6   C    119.08  3.000
 2YO  H1   N6   C15  119.89  3.000
 2YO  C    N6   C15  121.04  3.000
 2YO  H2   C    N6   115.03  3.000
 2YO  H2   C    N1   119.45  3.000
 2YO  N6   C    N1   125.52  3.000
 2YO  H3   C14  C13  122.61  3.000
 2YO  H3   C14  C15  121.44  3.000
 2YO  C13  C14  C15  115.95  3.000
 2YO  N5   C13  C4   104.57  3.000
 2YO  C4   C13  C14  123.48  3.000
 2YO  N5   C13  C14  131.95  3.000
 2YO  N2   C4   C3   130.42  3.000
 2YO  C3   C4   C13  119.38  3.000
 2YO  N2   C4   C13  110.20  3.000
 2YO  H4   C3   C4   121.16  3.000
 2YO  H4   C3   C2   120.06  3.000
 2YO  C4   C3   C2   118.77  3.000
 2YO  H5   N5   C5   126.77  3.000
 2YO  H5   N5   C13  126.03  3.000
 2YO  C5   N5   C13  107.19  3.000
 2YO  N3   C5   N2   124.97  3.000
 2YO  N2   C5   N5   113.04  3.000
 2YO  N3   C5   N5   121.98  3.000
 2YO  C5   N2   C4   105.00  3.000
 2YO  H7   N3   C6   117.41  3.000
 2YO  H7   N3   C5   114.36  3.000
 2YO  C6   N3   C5   123.20  3.000
 2YO  H9   C6   H8   107.70  3.000
 2YO  H9   C6   C7   110.02  3.000
 2YO  H8   C6   C7   109.13  3.000
 2YO  H9   C6   N3   108.60  3.000
 2YO  H8   C6   N3   111.92  3.000
 2YO  C7   C6   N3   109.45  3.000
 2YO  H11  C7   H10  106.66  3.000
 2YO  H11  C7   N4   107.87  3.000
 2YO  H10  C7   N4   112.74  3.000
 2YO  H11  C7   C6   107.83  3.000
 2YO  H10  C7   C6   109.38  3.000
 2YO  N4   C7   C6   112.09  3.000
 2YO  C8   N4   C12  111.01  3.000
 2YO  C8   N4   C7   112.73  3.000
 2YO  C12  N4   C7   111.44  3.000
 2YO  H14  C12  H13  106.84  3.000
 2YO  H14  C12  C11  109.71  3.000
 2YO  H13  C12  C11  108.96  3.000
 2YO  H14  C12  N4   108.58  3.000
 2YO  H13  C12  N4   111.35  3.000
 2YO  C11  C12  N4   111.31  3.000
 2YO  H16  C11  H15  107.01  3.000
 2YO  H16  C11  C10  109.75  3.000
 2YO  H15  C11  C10  110.87  3.000
 2YO  H16  C11  C12  109.11  3.000
 2YO  H15  C11  C12  109.21  3.000
 2YO  C10  C11  C12  110.80  3.000
 2YO  H18  C10  H17  106.80  3.000
 2YO  H18  C10  C9   110.73  3.000
 2YO  H17  C10  C9   109.33  3.000
 2YO  H18  C10  C11  110.74  3.000
 2YO  H17  C10  C11  109.33  3.000
 2YO  C9   C10  C11  109.84  3.000
 2YO  H20  C9   H19  107.03  3.000
 2YO  H20  C9   C8   108.95  3.000
 2YO  H19  C9   C8   109.13  3.000
 2YO  H20  C9   C10  109.75  3.000
 2YO  H19  C9   C10  110.93  3.000
 2YO  C8   C9   C10  110.95  3.000
 2YO  H22  C8   H21  106.64  3.000
 2YO  H22  C8   C9   109.41  3.000
 2YO  H21  C8   C9   109.01  3.000
 2YO  H22  C8   N4   110.98  3.000
 2YO  H21  C8   N4   109.45  3.000
 2YO  C9   C8   N4   111.22  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
 2YO  CONST_01  N2   C4   C3   C2    180.00   0.0  0
 2YO  CONST_02  C13  C4   C3   C2      0.00   0.0  0
 2YO  CONST_03  C13  C14  C15  C2      0.00   0.0  0
 2YO  CONST_04  N5   C13  C14  C15   180.00   0.0  0
 2YO  CONST_05  C4   C13  C14  C15     0.00   0.0  0
 2YO  CONST_06  C4   C3   C2   C15     0.00   0.0  0
 2YO  CONST_07  C5   N5   C13  C14   180.00   0.0  0
 2YO  CONST_08  N2   C4   C13  C14   180.00   0.0  0
 2YO  CONST_09  C3   C4   C13  C14     0.00   0.0  0
 2YO  CONST_10  C3   C2   C15  C14     0.00   0.0  0
 2YO  CONST_11  N2   C5   N5   C13     0.00   0.0  0
 2YO  CONST_12  C5   N2   C4   C13     0.00   0.0  0
 2YO  CONST_13  N5   C5   N2   C4      0.00   0.0  0
 2YO  CONST_14  C5   N5   C13  C4      0.00   0.0  0
 2YO  CONST_15  C5   N2   C4   C3    180.00   0.0  0
 2YO  CONST_16  N5   C13  C4   C3    180.00   0.0  0
 2YO  CONST_17  N2   C4   C13  N5      0.00   0.0  0
 2YO  CONST_18  N6   C    N1   C1      0.00   0.0  0
 2YO  CONST_19  C15  N6   C    N1      0.00   0.0  0
 2YO  CONST_20  N3   C5   N5   C13   180.00   0.0  0
 2YO  CONST_21  N3   C5   N2   C4    180.00   0.0  0
 2YO  CONST_22  H4   C3   C2   C1      0.00   0.0  0
 2YO  CONST_23  H3   C14  C15  C2    180.00   0.0  0
 2YO  CONST_24  H5   N5   C13  C14     0.00   0.0  0
 2YO  CONST_25  H2   C    N1   C1    180.00   0.0  0
 2YO  CONST_26  H1   N6   C    N1    180.00   0.0  0
 2YO  CONST_27  C6   N3   C5   N5      0.00   0.0  0
 2YO  CONST_28  C6   N3   C5   N2    180.00   0.0  0
 2YO  CONST_29  H7   N3   C5   N5    180.00   0.0  0
 2YO  Var_01    C10  C11  C12  N4     56.69  30.0  1
 2YO  Var_02    C10  C9   C8   N4    -56.49  30.0  1
 2YO  Var_03    C9   C10  C11  C12   -53.09  30.0  1
 2YO  Var_04    C9   C8   N4   C12    59.41  30.0  1
 2YO  Var_05    C8   C9   C10  C11    53.07  30.0  1
 2YO  Var_06    C8   N4   C12  C11   -59.58  30.0  1
 2YO  Var_07    C12  N4   C7   C6   -162.12  30.0  2
 2YO  Var_08    C7   C6   N3   C5    173.42  30.0  1
 2YO  Var_09    N4   C7   C6   N3    173.81  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
 2YO  plan-1  O    0.020
 2YO  plan-1  C1   0.020
 2YO  plan-1  N1   0.020
 2YO  plan-1  C2   0.020
 2YO  plan-1  C15  0.020
 2YO  plan-1  N6   0.020
 2YO  plan-1  C    0.020
 2YO  plan-1  C14  0.020
 2YO  plan-1  C13  0.020
 2YO  plan-1  C4   0.020
 2YO  plan-1  C3   0.020
 2YO  plan-1  N5   0.020
 2YO  plan-1  C5   0.020
 2YO  plan-1  N2   0.020
 2YO  plan-1  N3   0.020
 2YO  plan-1  H1   0.020
 2YO  plan-1  H2   0.020
 2YO  plan-1  H3   0.020
 2YO  plan-1  H4   0.020
 2YO  plan-1  H5   0.020
 2YO  plan-2  C5   0.020
 2YO  plan-2  N3   0.020
 2YO  plan-2  C6   0.020
 2YO  plan-2  H7   0.020

