# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:57:47 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 6-amino-2-[(naphthalen-1-ylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2cc3[nH]c(NCc4cccc5ccccc45)nc3cc2C(=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
 S79  S79  6-amino-2-[(naphthalen-1-ylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  43  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S79
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
 S79  N1    N  NH2   0  -0.834  -7.3682  -0.2560   1.7544
 S79  C8    C  CR6   0   0.639  -6.2449  -0.1082   1.0186
 S79  N2    N  N     0  -0.526  -5.1049  -0.5283   1.4578
 S79  C4    C  CR66  0   0.260  -3.9936  -0.2985   0.6870
 S79  C5    C  CR16  0  -0.409  -2.7555  -0.7519   1.1651
 S79  C6    C  CR56  0   0.384  -1.6503  -0.5224   0.3794
 S79  N3    N  NR15  0  -0.751  -0.3264  -0.8337   0.5475
 S79  C9    C  CR5   0   0.688   0.3426  -0.3670  -0.5528
 S79  N4    N  NH1   0  -0.681   1.6786  -0.4825  -0.6797
 S79  C17   C  CH2   0  -0.398   2.4799  -1.3775   0.1338
 S79  C18   C  CR6   0   0.068   3.9436  -1.1528  -0.1275
 S79  C20   C  CR66  0   0.100   4.5866   0.0486   0.2898
 S79  C26   C  CR16  0  -0.327   3.9049   1.0842   0.9745
 S79  C25   C  CR16  0  -0.248   4.5624   2.2180   1.3692
 S79  C24   C  CR16  0  -0.260   5.9355   2.3817   1.0981
 S79  C23   C  CR16  0  -0.310   6.6222   1.4006   0.4380
 S79  C21   C  CR66  0   0.113   5.9717   0.2156   0.0206
 S79  C22   C  CR16  0  -0.324   6.6792  -0.8061  -0.6567
 S79  C27   C  CR16  0  -0.246   6.0415  -1.9480  -1.0483
 S79  C19   C  CR16  0  -0.321   4.6675  -2.1155  -0.7808
 S79  N5    N  N     0  -0.533  -0.4419   0.2152  -1.4237
 S79  C1    C  CR56  0   0.175  -1.7010   0.1400  -0.8719
 S79  C2    C  CR16  0  -0.396  -2.9146   0.5885  -1.3420
 S79  C3    C  CR66  0  -0.138  -4.0558   0.3672  -0.5601
 S79  C7    C  CR6   0   0.547  -5.3496   0.8274  -1.0327
 S79  O1    O  O     0  -0.469  -5.5552   1.4162  -2.0827
 S79  N6    N  NR16  0  -0.719  -6.3901   0.5460  -0.1757
 S79  HN11  H  HNH2  0   0.406  -8.2662  -0.2264   1.3013
 S79  HN12  H  HNH2  0   0.403  -7.3061  -0.8882   2.5350
 S79  H5    H  HCR6  0   0.263  -2.6969  -1.2631   2.1171
 S79  HN3   H  HNR5  0   0.425   0.0713  -1.3044   1.3440
 S79  HN4   H  HNH1  0   0.402   2.0303  -0.2695  -1.6004
 S79  H171  H  HCH2  0   0.258   2.2689  -1.1943   1.1914
 S79  H172  H  HCH2  0   0.275   2.2340  -2.4262  -0.0614
 S79  H26   H  HCR6  0   0.254   2.8491   0.9863   1.1870
 S79  H25   H  HCR6  0   0.260   4.0242   2.9977   1.8922
 S79  H24   H  HCR6  0   0.260   6.4418   3.2842   1.4143
 S79  H23   H  HCR6  0   0.257   7.6780   1.5189   0.2253
 S79  H22   H  HCR6  0   0.258   7.7344  -0.6680  -0.8594
 S79  H27   H  HCR6  0   0.261   6.5822  -2.7291  -1.5658
 S79  H19   H  HCR6  0   0.259   4.1761  -3.0265  -1.1002
 S79  H2    H  HCR6  0   0.255  -2.9923   1.0995  -2.2930
 S79  HN6   H  HNR6  0   0.421  -7.3087   0.8603  -0.4600

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
 S79  C27  C22   aromatic  1.365  0.020  1.365
 S79  C27  C19   aromatic  1.410  0.020  1.410
 S79  C22  C21   aromatic  1.415  0.020  1.415
 S79  C19  C18   aromatic  1.370  0.020  1.370
 S79  C21  C23   aromatic  1.415  0.020  1.415
 S79  C21  C20   aromatic  1.421  0.020  1.421
 S79  C23  C24   aromatic  1.367  0.020  1.367
 S79  C18  C20   aromatic  1.425  0.020  1.425
 S79  C18  C17   single    1.504  0.020  1.504
 S79  C20  C26   aromatic  1.416  0.020  1.416
 S79  C24  C25   aromatic  1.409  0.020  1.409
 S79  C26  C25   aromatic  1.369  0.020  1.369
 S79  C17  N4    single    1.451  0.020  1.451
 S79  N4   C9    single    1.347  0.020  1.347
 S79  C9   N3    aromatic  1.370  0.020  1.370
 S79  C9   N5    aromatic  1.309  0.020  1.309
 S79  N3   C6    aromatic  1.370  0.020  1.370
 S79  N5   C1    aromatic  1.377  0.020  1.377
 S79  C6   C1    aromatic  1.417  0.020  1.417
 S79  C6   C5    aromatic  1.375  0.020  1.375
 S79  C1   C2    aromatic  1.377  0.020  1.377
 S79  C5   C4    aromatic  1.402  0.020  1.402
 S79  C2   C3    aromatic  1.401  0.020  1.401
 S79  C4   C3    aromatic  1.415  0.020  1.415
 S79  C4   N2    single    1.372  0.020  1.372
 S79  C3   C7    single    1.452  0.020  1.452
 S79  N2   C8    double    1.292  0.020  1.292
 S79  C7   O1    double    1.221  0.020  1.221
 S79  C7   N6    single    1.377  0.020  1.377
 S79  C8   N6    single    1.369  0.020  1.369
 S79  C8   N1    single    1.351  0.020  1.351
 S79  N1   HN11  single    0.890  0.020  1.040
 S79  N1   HN12  single    0.890  0.020  1.040
 S79  C5   H5    single    0.930  0.020  1.080
 S79  N3   HN3   single    0.860  0.020  1.020
 S79  N4   HN4   single    0.890  0.020  1.040
 S79  C17  H171  single    0.970  0.020  1.090
 S79  C17  H172  single    0.970  0.020  1.090
 S79  C26  H26   single    0.930  0.020  1.080
 S79  C25  H25   single    0.930  0.020  1.080
 S79  C24  H24   single    0.930  0.020  1.080
 S79  C23  H23   single    0.930  0.020  1.080
 S79  C22  H22   single    0.930  0.020  1.080
 S79  C27  H27   single    0.930  0.020  1.080
 S79  C19  H19   single    0.930  0.020  1.080
 S79  C2   H2    single    0.930  0.020  1.080
 S79  N6   HN6   single    0.860  0.020  1.020

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
 S79  HN12  N1   HN11  115.01  3.000
 S79  HN12  N1   C8    116.10  3.000
 S79  HN11  N1   C8    119.57  3.000
 S79  N6    C8   N2    123.05  3.000
 S79  N6    C8   N1    116.05  3.000
 S79  N2    C8   N1    120.86  3.000
 S79  C4    N2   C8    117.99  3.000
 S79  C3    C4   C5    119.43  3.000
 S79  C3    C4   N2    122.57  3.000
 S79  C5    C4   N2    118.00  3.000
 S79  H5    C5   C6    122.54  3.000
 S79  H5    C5   C4    120.03  3.000
 S79  C6    C5   C4    117.43  3.000
 S79  C1    C6   N3    104.42  3.000
 S79  C1    C6   C5    123.63  3.000
 S79  N3    C6   C5    131.94  3.000
 S79  HN3   N3   C9    126.99  3.000
 S79  HN3   N3   C6    125.78  3.000
 S79  C9    N3   C6    107.22  3.000
 S79  N5    C9   N4    124.75  3.000
 S79  N5    C9   N3    113.16  3.000
 S79  N4    C9   N3    122.07  3.000
 S79  HN4   N4   C17   116.72  3.000
 S79  HN4   N4   C9    114.45  3.000
 S79  C17   N4   C9    123.22  3.000
 S79  H172  C17  H171  106.83  3.000
 S79  H172  C17  C18   109.31  3.000
 S79  H171  C17  C18   109.31  3.000
 S79  H172  C17  N4    111.52  3.000
 S79  H171  C17  N4    109.41  3.000
 S79  C18   C17  N4    110.37  3.000
 S79  C19   C18  C20   119.58  3.000
 S79  C20   C18  C17   120.94  3.000
 S79  C19   C18  C17   119.48  3.000
 S79  C21   C20  C26   118.35  3.000
 S79  C26   C20  C18   122.74  3.000
 S79  C21   C20  C18   118.91  3.000
 S79  H26   C26  C25   119.16  3.000
 S79  H26   C26  C20   119.92  3.000
 S79  C25   C26  C20   120.92  3.000
 S79  H25   C25  C24   119.60  3.000
 S79  H25   C25  C26   119.82  3.000
 S79  C24   C25  C26   120.58  3.000
 S79  H24   C24  C23   120.30  3.000
 S79  H24   C24  C25   119.77  3.000
 S79  C23   C24  C25   119.93  3.000
 S79  H23   C23  C21   118.79  3.000
 S79  H23   C23  C24   120.38  3.000
 S79  C21   C23  C24   120.83  3.000
 S79  C22   C21  C23   121.06  3.000
 S79  C23   C21  C20   119.39  3.000
 S79  C22   C21  C20   119.55  3.000
 S79  H22   C22  C27   120.53  3.000
 S79  H22   C22  C21   118.97  3.000
 S79  C27   C22  C21   120.50  3.000
 S79  H27   C27  C19   119.48  3.000
 S79  H27   C27  C22   120.51  3.000
 S79  C19   C27  C22   120.01  3.000
 S79  H19   C19  C27   119.09  3.000
 S79  H19   C19  C18   119.46  3.000
 S79  C27   C19  C18   121.46  3.000
 S79  C1    N5   C9    104.90  3.000
 S79  C2    C1   N5    130.66  3.000
 S79  C2    C1   C6    119.05  3.000
 S79  N5    C1   C6    110.30  3.000
 S79  H2    C2   C3    120.43  3.000
 S79  H2    C2   C1    121.15  3.000
 S79  C3    C2   C1    118.42  3.000
 S79  C7    C3   C2    119.61  3.000
 S79  C7    C3   C4    118.36  3.000
 S79  C2    C3   C4    122.03  3.000
 S79  N6    C7   O1    120.43  3.000
 S79  N6    C7   C3    113.95  3.000
 S79  O1    C7   C3    125.63  3.000
 S79  HN6   N6   C7    116.60  3.000
 S79  HN6   N6   C8    119.32  3.000
 S79  C7    N6   C8    124.08  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
 S79  CONST_01  N3    C6   C5   C4    180.00   0.0  0
 S79  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 S79  CONST_03  C1    C2   C3   C4      0.00   0.0  0
 S79  CONST_04  C9    N3   C6   C5    180.00   0.0  0
 S79  CONST_05  N5    C1   C6   C5    180.00   0.0  0
 S79  CONST_06  C2    C1   C6   C5      0.00   0.0  0
 S79  CONST_07  C2    C3   C4   C5      0.00   0.0  0
 S79  CONST_08  N5    C9   N3   C6      0.00   0.0  0
 S79  CONST_09  C9    N5   C1   C6      0.00   0.0  0
 S79  CONST_10  C3    C2   C1   C6      0.00   0.0  0
 S79  CONST_11  C3    C4   C5   C6      0.00   0.0  0
 S79  CONST_12  C1    N5   C9   N3      0.00   0.0  0
 S79  CONST_13  N5    C1   C6   N3      0.00   0.0  0
 S79  CONST_14  C2    C1   C6   N3    180.00   0.0  0
 S79  CONST_15  C1    C6   N3   C9      0.00   0.0  0
 S79  CONST_16  C2    C1   N5   C9    180.00   0.0  0
 S79  CONST_17  C22   C27  C19  C18     0.00   0.0  0
 S79  CONST_18  C22   C21  C20  C18     0.00   0.0  0
 S79  CONST_19  C23   C21  C20  C18   180.00   0.0  0
 S79  CONST_20  C25   C26  C20  C18   180.00   0.0  0
 S79  CONST_21  C27   C22  C21  C20     0.00   0.0  0
 S79  CONST_22  C24   C23  C21  C20     0.00   0.0  0
 S79  CONST_23  C27   C19  C18  C20     0.00   0.0  0
 S79  CONST_24  C24   C25  C26  C20     0.00   0.0  0
 S79  CONST_25  C22   C21  C20  C26   180.00   0.0  0
 S79  CONST_26  C23   C21  C20  C26     0.00   0.0  0
 S79  CONST_27  C19   C18  C20  C26   180.00   0.0  0
 S79  CONST_28  C23   C24  C25  C26     0.00   0.0  0
 S79  CONST_29  C21   C23  C24  C25     0.00   0.0  0
 S79  CONST_30  C21   C20  C26  C25     0.00   0.0  0
 S79  CONST_31  C22   C21  C23  C24   180.00   0.0  0
 S79  CONST_32  C27   C22  C21  C23   180.00   0.0  0
 S79  CONST_33  C19   C27  C22  C21     0.00   0.0  0
 S79  CONST_34  C19   C18  C20  C21     0.00   0.0  0
 S79  CONST_35  C3    C2   C1   N5    180.00   0.0  0
 S79  CONST_36  C3    C7   N6   C8      0.00   0.0  0
 S79  CONST_37  C7    N6   C8   N2      0.00   0.0  0
 S79  CONST_38  N6    C8   N2   C4      0.00   0.0  0
 S79  CONST_39  N4    C9   N3   C6    180.00   0.0  0
 S79  CONST_40  C1    N5   C9   N4    180.00   0.0  0
 S79  CONST_41  C27   C19  C18  C17   180.00   0.0  0
 S79  CONST_42  C21   C20  C18  C17   180.00   0.0  0
 S79  CONST_43  C26   C20  C18  C17     0.00   0.0  0
 S79  CONST_44  C4    N2   C8   N1    180.00   0.0  0
 S79  CONST_45  C7    N6   C8   N1    180.00   0.0  0
 S79  CONST_46  O1    C7   N6   C8    180.00   0.0  0
 S79  CONST_47  H5    C5   C4   N2      0.00   0.0  0
 S79  CONST_48  H2    C2   C3   C4    180.00   0.0  0
 S79  CONST_49  HN3   N3   C6   C5      0.00   0.0  0
 S79  CONST_50  H27   C27  C19  C18   180.00   0.0  0
 S79  CONST_51  H26   C26  C20  C18     0.00   0.0  0
 S79  CONST_52  H22   C22  C21  C20   180.00   0.0  0
 S79  CONST_53  H23   C23  C21  C20   180.00   0.0  0
 S79  CONST_54  H19   C19  C18  C20   180.00   0.0  0
 S79  CONST_55  H25   C25  C26  C20   180.00   0.0  0
 S79  CONST_56  H24   C24  C25  C26   180.00   0.0  0
 S79  CONST_57  HN6   N6   C8   N2    180.00   0.0  0
 S79  CONST_59  N5    C9   N4   C17   180.00   0.0  0
 S79  CONST_60  HN4   N4   C9   N3    180.00   0.0  0
 S79  CONST_62  HN12  N1   C8   N2      0.00   0.0  0
 S79  Var_01    C18   C17  N4   C9   -172.96  30.0  1
 S79  Var_02    C19   C18  C17  N4   -110.56  30.0  3

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
 S79  plan-1  C17   0.020
 S79  plan-1  C18   0.020
 S79  plan-1  C20   0.020
 S79  plan-1  C26   0.020
 S79  plan-1  C25   0.020
 S79  plan-1  C24   0.020
 S79  plan-1  C23   0.020
 S79  plan-1  C21   0.020
 S79  plan-1  C22   0.020
 S79  plan-1  C27   0.020
 S79  plan-1  C19   0.020
 S79  plan-1  H26   0.020
 S79  plan-1  H25   0.020
 S79  plan-1  H24   0.020
 S79  plan-1  H23   0.020
 S79  plan-1  H22   0.020
 S79  plan-1  H27   0.020
 S79  plan-1  H19   0.020
 S79  plan-2  N1    0.020
 S79  plan-2  C8    0.020
 S79  plan-2  N2    0.020
 S79  plan-2  C4    0.020
 S79  plan-2  C5    0.020
 S79  plan-2  C6    0.020
 S79  plan-2  N3    0.020
 S79  plan-2  C9    0.020
 S79  plan-2  N4    0.020
 S79  plan-2  N5    0.020
 S79  plan-2  C1    0.020
 S79  plan-2  C2    0.020
 S79  plan-2  C3    0.020
 S79  plan-2  C7    0.020
 S79  plan-2  O1    0.020
 S79  plan-2  N6    0.020
 S79  plan-2  HN11  0.020
 S79  plan-2  HN12  0.020
 S79  plan-2  H5    0.020
 S79  plan-2  HN3   0.020
 S79  plan-2  H2    0.020
 S79  plan-2  HN6   0.020
 S79  plan-3  C9    0.020
 S79  plan-3  N4    0.020
 S79  plan-3  C17   0.020
 S79  plan-3  HN4   0.020

