# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:55:21 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 4-{2-[(cyclopentylmethyl)amino]ethyl}-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2c(CCNCC3CCCC3)c4N=CNC(=O)c4cc2n1
#
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
 AEK  AEK  4-{2-[(cyclopentylmethyl)amino]ethyl}-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  49  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AEK
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
 AEK  N1    N  NH1   0  -0.678   1.6780   4.4923   0.2790
 AEK  N3    N  NH1   0  -0.598  -2.6054  -0.7213  -0.4657
 AEK  C4    C  CR6   0   0.001   1.1303  -0.1870  -0.6217
 AEK  C5    C  CH2   0  -0.530  -0.2698  -0.3731  -1.1230
 AEK  C6    C  CH2   0  -0.245  -1.2493  -0.6074   0.0267
 AEK  C7    C  CH2   0  -0.258  -3.5864  -0.8674   0.5907
 AEK  C8    C  CH1   0  -0.246  -4.9939  -1.0031   0.0330
 AEK  C10   C  CH2   0  -0.441  -7.0492   0.0304   0.9185
 AEK  C13   C  CR66  0   0.174   2.0174  -1.2650  -0.4361
 AEK  C15   C  CR6   0   0.551   4.2034  -2.1914   0.2637
 AEK  C17   C  CR16  0  -0.420   3.7722   0.2261   0.4305
 AEK  C1    C  CH3   0  -0.545   0.4042   5.0803  -0.0546
 AEK  C2    C  CR5   0   0.682   1.9485   3.1877   0.1869
 AEK  N2    N  NR15  0  -0.757   1.0269   2.2926  -0.2862
 AEK  C3    C  CR56  0   0.344   1.6132   1.0513  -0.2565
 AEK  C9    C  CH2   0  -0.447  -6.0625  -1.1227   1.1497
 AEK  C11   C  CH2   0  -0.444  -6.9313   0.3208  -0.5754
 AEK  C12   C  CH2   0  -0.424  -5.4304   0.1985  -0.8220
 AEK  N4    N  N     0  -0.449   1.5731  -2.5271  -0.7705
 AEK  C14   C  CR16  0   0.127   2.3755  -3.5068  -0.5960
 AEK  N5    N  NR16  0  -0.663   3.6366  -3.3895  -0.1042
 AEK  C16   C  CR66  0  -0.120   3.3175  -1.0489   0.0817
 AEK  C18   C  CR56  0   0.182   2.9108   1.2890   0.2604
 AEK  N6    N  N     0  -0.536   3.0869   2.6232   0.5231
 AEK  HN3   H  HNH1  0   0.336  -2.6659  -1.5253  -1.0810
 AEK  H5    H  HCH2  0   0.236  -0.5921   0.5064  -1.6869
 AEK  H5A   H  HCH2  0   0.254  -0.3078  -1.2184  -1.8112
 AEK  H6    H  HCH2  0   0.220  -1.2042   0.2421   0.7160
 AEK  H6A   H  HCH2  0   0.198  -0.9213  -1.4883   0.5998
 AEK  H7    H  HCH2  0   0.195  -3.3744  -1.7244   1.2517
 AEK  H7A   H  HCH2  0   0.210  -3.5405   0.0252   1.2261
 AEK  H8    H  HCH1  0   0.224  -5.0277  -1.9065  -0.5867
 AEK  H10   H  HCH2  0   0.227  -8.0645  -0.2113   1.2366
 AEK  H10A  H  HCH2  0   0.216  -6.7351   0.9130   1.4826
 AEK  H17   H  HCR6  0   0.255   4.7687   0.3686   0.8265
 AEK  H1    H  HCH3  0   0.244  -0.4058   4.6898   0.5656
 AEK  H1A   H  HCH3  0   0.272   0.4673   6.1504   0.1160
 AEK  H9    H  HCH2  0   0.227  -6.5775  -2.0828   1.0819
 AEK  H9A   H  HCH2  0   0.226  -5.6163  -1.0816   2.1467
 AEK  H11   H  HCH2  0   0.212  -7.4730  -0.4367  -1.1502
 AEK  H11A  H  HCH2  0   0.225  -7.3354   1.2938  -0.8608
 AEK  H12   H  HCH2  0   0.210  -4.9294   1.1054  -0.4669
 AEK  H12A  H  HCH2  0   0.226  -5.1729   0.0838  -1.8754
 AEK  H14   H  HCR6  0   0.291   2.0692  -4.5156  -0.8435
 AEK  HN5   H  HNR6  0   0.426   4.1923  -4.2272   0.0052
 AEK  HN2   H  HNR5  0   0.426   0.0948   2.5063  -0.6034
 AEK  H23   H  HNH1  0   0.408   2.4051   5.0762   0.6550
 AEK  H24   H  HCH3  0   0.245   0.1446   4.9256  -1.1040
 AEK  O1    O  O     0  -0.470   5.3432  -2.1415   0.6993

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
 AEK  N1   C2    single    1.336  0.020  1.336
 AEK  N3   C7    single    1.449  0.020  1.449
 AEK  N3   C6    single    1.447  0.020  1.447
 AEK  N3   HN3   single    0.890  0.020  1.040
 AEK  C4   C13   aromatic  1.408  0.020  1.408
 AEK  C5   C4    single    1.499  0.020  1.499
 AEK  C5   H5    single    0.970  0.020  1.090
 AEK  C5   H5A   single    0.970  0.020  1.090
 AEK  C6   C5    single    1.528  0.020  1.528
 AEK  C6   H6    single    0.970  0.020  1.090
 AEK  C6   H6A   single    0.970  0.020  1.090
 AEK  C7   H7    single    0.970  0.020  1.090
 AEK  C7   H7A   single    0.970  0.020  1.090
 AEK  C8   C7    single    1.520  0.020  1.520
 AEK  C8   C9    single    1.550  0.020  1.550
 AEK  C8   H8    single    0.970  0.020  1.090
 AEK  C10  C9    single    1.535  0.020  1.535
 AEK  C10  H10   single    0.970  0.020  1.090
 AEK  C10  H10A  single    0.970  0.020  1.090
 AEK  C13  C16   aromatic  1.416  0.020  1.416
 AEK  C13  N4    single    1.379  0.020  1.379
 AEK  C15  O1    double    1.221  0.020  1.221
 AEK  C15  N5    single    1.375  0.020  1.375
 AEK  C17  C16   aromatic  1.398  0.020  1.398
 AEK  C17  H17   single    0.930  0.020  1.080
 AEK  C1   N1    single    1.442  0.020  1.442
 AEK  C1   H1    single    0.970  0.020  1.090
 AEK  C1   H1A   single    0.970  0.020  1.090
 AEK  C2   N2    aromatic  1.369  0.020  1.369
 AEK  C2   N6    aromatic  1.314  0.020  1.314
 AEK  N2   C3    aromatic  1.373  0.020  1.373
 AEK  N2   HN2   single    0.860  0.020  1.020
 AEK  C3   C4    aromatic  1.378  0.020  1.378
 AEK  C3   C18   aromatic  1.417  0.020  1.417
 AEK  C9   H9    single    0.970  0.020  1.090
 AEK  C9   H9A   single    0.970  0.020  1.090
 AEK  C11  C10   single    1.526  0.020  1.526
 AEK  C11  C12   single    1.526  0.020  1.526
 AEK  C11  H11   single    0.970  0.020  1.090
 AEK  C11  H11A  single    0.970  0.020  1.090
 AEK  C12  C8    single    1.538  0.020  1.538
 AEK  C12  H12   single    0.970  0.020  1.090
 AEK  C12  H12A  single    0.970  0.020  1.090
 AEK  N4   C14   double    1.278  0.020  1.278
 AEK  C14  N5    single    1.359  0.020  1.359
 AEK  C14  H14   single    0.930  0.020  1.080
 AEK  N5   HN5   single    0.860  0.020  1.020
 AEK  C16  C15   single    1.457  0.020  1.457
 AEK  C18  C17   aromatic  1.379  0.020  1.379
 AEK  N6   C18   aromatic  1.371  0.020  1.371
 AEK  N1   H23   single    0.860  0.020  1.020
 AEK  C1   H24   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
 AEK  H23   N1   C2   116.53  3.000
 AEK  H23   N1   C1   119.24  3.000
 AEK  C2    N1   C1   124.14  3.000
 AEK  HN3   N3   C7   108.79  3.000
 AEK  HN3   N3   C6   108.95  3.000
 AEK  C7    N3   C6   113.22  3.000
 AEK  C3    C4   C13  115.59  3.000
 AEK  C3    C4   C5   121.84  3.000
 AEK  C13   C4   C5   122.51  3.000
 AEK  H5A   C5   H5   106.72  3.000
 AEK  H5A   C5   C6   109.48  3.000
 AEK  H5    C5   C6   108.81  3.000
 AEK  C6    C5   C4   111.48  3.000
 AEK  H5A   C5   C4   109.87  3.000
 AEK  H5    C5   C4   110.37  3.000
 AEK  H6A   C6   H6   106.31  3.000
 AEK  H6A   C6   C5   108.87  3.000
 AEK  H6    C6   C5   109.16  3.000
 AEK  H6A   C6   N3   113.16  3.000
 AEK  H6    C6   N3   108.29  3.000
 AEK  C5    C6   N3   110.90  3.000
 AEK  H7A   C7   H7   106.10  3.000
 AEK  H7A   C7   C8   108.90  3.000
 AEK  H7    C7   C8   109.18  3.000
 AEK  C8    C7   N3   111.62  3.000
 AEK  H7A   C7   N3   108.18  3.000
 AEK  H7    C7   N3   112.65  3.000
 AEK  H8    C8   C12  108.71  3.000
 AEK  C12   C8   C9   105.37  3.000
 AEK  H8    C8   C9   108.81  3.000
 AEK  C12   C8   C7   113.39  3.000
 AEK  H8    C8   C7   108.03  3.000
 AEK  C9    C8   C7   112.39  3.000
 AEK  H10A  C10  H10  107.20  3.000
 AEK  H10A  C10  C11  109.22  3.000
 AEK  H10   C10  C11  113.55  3.000
 AEK  C11   C10  C9   103.93  3.000
 AEK  H10A  C10  C9   110.11  3.000
 AEK  H10   C10  C9   112.81  3.000
 AEK  C16   C13  N4   121.60  3.000
 AEK  N4    C13  C4   117.75  3.000
 AEK  C16   C13  C4   120.65  3.000
 AEK  C16   C15  O1   125.45  3.000
 AEK  C16   C15  N5   113.52  3.000
 AEK  O1    C15  N5   121.04  3.000
 AEK  H17   C17  C18  121.28  3.000
 AEK  C18   C17  C16  117.98  3.000
 AEK  H17   C17  C16  120.74  3.000
 AEK  H24   C1   H1A  107.73  3.000
 AEK  H24   C1   H1   108.59  3.000
 AEK  H1A   C1   H1   107.84  3.000
 AEK  H24   C1   N1   112.00  3.000
 AEK  H1A   C1   N1   108.31  3.000
 AEK  H1    C1   N1   112.20  3.000
 AEK  N6    C2   N2   112.99  3.000
 AEK  N6    C2   N1   125.26  3.000
 AEK  N2    C2   N1   121.75  3.000
 AEK  HN2   N2   C3   126.41  3.000
 AEK  HN2   N2   C2   126.36  3.000
 AEK  C3    N2   C2   107.23  3.000
 AEK  C18   C3   N2   104.32  3.000
 AEK  C18   C3   C4   124.63  3.000
 AEK  N2    C3   C4   131.05  3.000
 AEK  H9A   C9   H9   106.39  3.000
 AEK  H9A   C9   C10  111.81  3.000
 AEK  H9    C9   C10  110.37  3.000
 AEK  H9A   C9   C8   111.89  3.000
 AEK  H9    C9   C8   110.38  3.000
 AEK  C10   C9   C8   106.06  3.000
 AEK  H11A  C11  H11  107.24  3.000
 AEK  H11A  C11  C12  113.16  3.000
 AEK  H11   C11  C12  110.28  3.000
 AEK  H11A  C11  C10  113.39  3.000
 AEK  H11   C11  C10  110.13  3.000
 AEK  C12   C11  C10  102.65  3.000
 AEK  H12A  C12  H12  106.99  3.000
 AEK  H12A  C12  C11  113.38  3.000
 AEK  H12   C12  C11  109.34  3.000
 AEK  H12A  C12  C8   112.82  3.000
 AEK  H12   C12  C8   109.69  3.000
 AEK  C11   C12  C8   104.59  3.000
 AEK  C14   N4   C13  117.78  3.000
 AEK  H14   C14  N5   115.19  3.000
 AEK  H14   C14  N4   120.35  3.000
 AEK  N5    C14  N4   124.46  3.000
 AEK  HN5   N5   C14  118.54  3.000
 AEK  HN5   N5   C15  117.78  3.000
 AEK  C14   N5   C15  123.68  3.000
 AEK  C17   C16  C15  119.09  3.000
 AEK  C15   C16  C13  118.96  3.000
 AEK  C17   C16  C13  121.94  3.000
 AEK  N6    C18  C3   110.53  3.000
 AEK  N6    C18  C17  130.26  3.000
 AEK  C3    C18  C17  119.20  3.000
 AEK  C18   N6   C2   104.93  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
 AEK  CONST_01  C17  C16  C13  C4      0.00   0.0  0
 AEK  CONST_02  C2   N2   C3   C4    180.00   0.0  0
 AEK  CONST_03  C17  C18  C3   C4      0.00   0.0  0
 AEK  CONST_04  N6   C18  C3   C4    180.00   0.0  0
 AEK  CONST_05  N2   C3   C4   C13   180.00   0.0  0
 AEK  CONST_06  C18  C3   C4   C13     0.00   0.0  0
 AEK  CONST_07  C18  C17  C16  C13     0.00   0.0  0
 AEK  CONST_08  N2   C3   C18  C17   180.00   0.0  0
 AEK  CONST_09  C2   N6   C18  C17   180.00   0.0  0
 AEK  CONST_10  C18  C3   N2   C2      0.00   0.0  0
 AEK  CONST_11  C3   C18  N6   C2      0.00   0.0  0
 AEK  CONST_12  C18  N6   C2   N2      0.00   0.0  0
 AEK  CONST_13  N6   C18  C3   N2      0.00   0.0  0
 AEK  CONST_14  N6   C2   N2   C3      0.00   0.0  0
 AEK  CONST_15  C16  C13  C4   C3      0.00   0.0  0
 AEK  CONST_16  C16  C17  C18  C3      0.00   0.0  0
 AEK  CONST_17  N6   C18  C17  C16   180.00   0.0  0
 AEK  CONST_18  N5   C14  N4   C13     0.00   0.0  0
 AEK  CONST_19  N4   C14  N5   C15     0.00   0.0  0
 AEK  CONST_20  C16  C15  N5   C14     0.00   0.0  0
 AEK  CONST_21  C3   N2   C2   N1    180.00   0.0  0
 AEK  CONST_22  C18  N6   C2   N1    180.00   0.0  0
 AEK  CONST_23  C16  C13  C4   C5    180.00   0.0  0
 AEK  CONST_24  N4   C13  C4   C5      0.00   0.0  0
 AEK  CONST_25  N2   C3   C4   C5      0.00   0.0  0
 AEK  CONST_26  C18  C3   C4   C5    180.00   0.0  0
 AEK  CONST_27  O1   C15  N5   C14   180.00   0.0  0
 AEK  CONST_28  HN2  N2   C3   C4      0.00   0.0  0
 AEK  CONST_29  H17  C17  C16  C13   180.00   0.0  0
 AEK  CONST_30  H14  C14  N4   C13   180.00   0.0  0
 AEK  CONST_31  HN5  N5   C14  N4    180.00   0.0  0
 AEK  CONST_32  N2   C2   N1   C1      0.00   0.0  0
 AEK  CONST_33  N6   C2   N1   C1    180.00   0.0  0
 AEK  CONST_34  H23  N1   C2   N2    180.00   0.0  0
 AEK  Var_01    C11  C10  C9   C8     25.83  30.0  1
 AEK  Var_02    C10  C11  C12  C8     39.75  30.0  1
 AEK  Var_03    C12  C11  C10  C9    -40.44  30.0  1
 AEK  Var_04    C13  C4   C5   C6     89.30  30.0  2
 AEK  Var_05    C4   C5   C6   N3    177.25  30.0  3
 AEK  Var_06    C8   C7   N3   C6   -179.21  30.0  3
 AEK  Var_07    H1   C1   N1   C2     60.96  30.0  3
 AEK  Var_08    C7   N3   C6   C5   -176.64  30.0  1

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
 AEK  chir_01  C8  C7  C9  C12  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
 AEK  plan-1  N1   0.020
 AEK  plan-1  C4   0.020
 AEK  plan-1  C5   0.020
 AEK  plan-1  C13  0.020
 AEK  plan-1  C15  0.020
 AEK  plan-1  C17  0.020
 AEK  plan-1  C2   0.020
 AEK  plan-1  N2   0.020
 AEK  plan-1  C3   0.020
 AEK  plan-1  N4   0.020
 AEK  plan-1  C14  0.020
 AEK  plan-1  N5   0.020
 AEK  plan-1  C16  0.020
 AEK  plan-1  C18  0.020
 AEK  plan-1  N6   0.020
 AEK  plan-1  H17  0.020
 AEK  plan-1  H14  0.020
 AEK  plan-1  HN5  0.020
 AEK  plan-1  HN2  0.020
 AEK  plan-1  O1   0.020
 AEK  plan-2  N1   0.020
 AEK  plan-2  C1   0.020
 AEK  plan-2  C2   0.020
 AEK  plan-2  H23  0.020

