# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:54:36 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-[(thiophen-2-ylmethyl)amino]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Nc2cc3nc(NCc4sccc4)[nH]c3cc12
#
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
 SAQ  SAQ  2-[(thiophen-2-ylmethyl)amino]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  32  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SAQ
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
 SAQ  N1    N  NR16  0  -0.665   5.9412  -0.4339   0.3710
 SAQ  N3    N  N     0  -0.461   4.8492   1.6271   0.2334
 SAQ  C4    C  CR66  0   0.251   3.6490   0.9513   0.1198
 SAQ  C5    C  CR66  0  -0.140   3.5894  -0.4632   0.1307
 SAQ  C6    C  CR6   0   0.550   4.8194  -1.2258   0.2672
 SAQ  C7    C  CR16  0  -0.349   2.3682  -1.1402   0.0141
 SAQ  C8    C  CR56  0   0.367   1.2421  -0.3715  -0.1112
 SAQ  C10   C  CR16  0  -0.433   2.4816   1.7082  -0.0080
 SAQ  N12   N  NR15  0  -0.748  -0.0904  -0.6876  -0.2499
 SAQ  C13   C  CR5   0   0.703  -0.7712   0.4880  -0.3377
 SAQ  C2    C  CR16  0   0.131   5.9110   0.9243   0.3503
 SAQ  C9    C  CR56  0   0.198   1.2724   1.0461  -0.1260
 SAQ  N14   N  N     0  -0.533   0.0094   1.5459  -0.2686
 SAQ  N15   N  NH1   0  -0.688  -2.1092   0.5544  -0.4518
 SAQ  O16   O  O     0  -0.468   4.9010  -2.4436   0.2934
 SAQ  C25   C  CH2   0  -0.338  -2.9452  -0.5793  -0.7870
 SAQ  C11   C  CR5   0  -0.182  -4.3722  -0.2914  -0.4639
 SAQ  S1    S  S2    0   0.218  -4.8293   0.2894   1.0937
 SAQ  C12   C  CR15  0  -0.465  -6.4902   0.2996   0.6673
 SAQ  C131  C  CR15  0  -0.182  -6.6824  -0.1238  -0.6108
 SAQ  C14   C  CR15  0  -0.225  -5.4626  -0.4597  -1.2619
 SAQ  HN1   H  HNR6  0   0.427   6.8355  -0.8946   0.4722
 SAQ  H7    H  HCR6  0   0.274   2.3299  -2.2213   0.0233
 SAQ  H10   H  HCR6  0   0.256   2.5398   2.7887  -0.0157
 SAQ  HN12  H  HNR5  0   0.427  -0.4693  -1.6191  -0.3052
 SAQ  H2    H  HCR6  0   0.293   6.8763   1.4066   0.4433
 SAQ  HN15  H  HNH1  0   0.407  -2.4576   1.4652  -0.7101
 SAQ  H25   H  HCH2  0   0.272  -2.8717  -0.8491  -1.8452
 SAQ  H25A  H  HCH2  0   0.269  -2.6144  -1.4466  -0.2104
 SAQ  H9    H  HCR5  0   0.297  -7.2326   0.6267   1.3789
 SAQ  H101  H  HCR5  0   0.268  -7.6544  -0.1898  -1.0778
 SAQ  H11   H  HCR5  0   0.268  -5.3981  -0.8120  -2.2824

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
 SAQ  N1    C6    single    1.377  0.020  1.377
 SAQ  N1    C2    single    1.359  0.020  1.359
 SAQ  N3    C4    single    1.382  0.020  1.382
 SAQ  N3    C2    double    1.279  0.020  1.279
 SAQ  C4    C5    aromatic  1.416  0.020  1.416
 SAQ  C4    C10   aromatic  1.397  0.020  1.397
 SAQ  C5    C6    single    1.454  0.020  1.454
 SAQ  C5    C7    aromatic  1.401  0.020  1.401
 SAQ  C6    O16   double    1.221  0.020  1.221
 SAQ  C7    C8    aromatic  1.369  0.020  1.369
 SAQ  C8    N12   aromatic  1.376  0.020  1.376
 SAQ  C8    C9    aromatic  1.418  0.020  1.418
 SAQ  C10   C9    aromatic  1.384  0.020  1.384
 SAQ  N12   C13   aromatic  1.361  0.020  1.361
 SAQ  C13   N14   aromatic  1.317  0.020  1.317
 SAQ  C13   N15   single    1.345  0.020  1.345
 SAQ  C9    N14   aromatic  1.366  0.020  1.366
 SAQ  N15   C25   single    1.448  0.020  1.448
 SAQ  C25   C11   single    1.491  0.020  1.491
 SAQ  C14   C11   aromatic  1.362  0.020  1.362
 SAQ  S1    C11   aromatic  1.724  0.020  1.724
 SAQ  S1    C12   aromatic  1.715  0.020  1.715
 SAQ  C12   C131  aromatic  1.360  0.020  1.360
 SAQ  C131  C14   aromatic  1.423  0.020  1.423
 SAQ  N1    HN1   single    0.860  0.020  1.020
 SAQ  C7    H7    single    0.930  0.020  1.080
 SAQ  C10   H10   single    0.930  0.020  1.080
 SAQ  N12   HN12  single    0.860  0.020  1.020
 SAQ  C2    H2    single    0.930  0.020  1.080
 SAQ  N15   HN15  single    0.890  0.020  1.040
 SAQ  C25   H25   single    0.970  0.020  1.090
 SAQ  C25   H25A  single    0.970  0.020  1.090
 SAQ  C12   H9    single    0.930  0.020  1.080
 SAQ  C131  H101  single    0.930  0.020  1.080
 SAQ  C14   H11   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
 SAQ  HN1   N1    C2    118.48  3.000
 SAQ  HN1   N1    C6    117.78  3.000
 SAQ  C2    N1    C6    123.75  3.000
 SAQ  C2    N3    C4    117.38  3.000
 SAQ  C10   C4    C5    120.45  3.000
 SAQ  C10   C4    N3    117.92  3.000
 SAQ  C5    C4    N3    121.63  3.000
 SAQ  C7    C5    C6    119.46  3.000
 SAQ  C7    C5    C4    121.25  3.000
 SAQ  C6    C5    C4    119.29  3.000
 SAQ  O16   C6    C5    125.58  3.000
 SAQ  O16   C6    N1    121.17  3.000
 SAQ  C5    C6    N1    113.25  3.000
 SAQ  H7    C7    C8    122.20  3.000
 SAQ  H7    C7    C5    120.86  3.000
 SAQ  C8    C7    C5    116.94  3.000
 SAQ  C9    C8    N12   104.43  3.000
 SAQ  C9    C8    C7    123.00  3.000
 SAQ  N12   C8    C7    132.57  3.000
 SAQ  H10   C10   C9    121.61  3.000
 SAQ  H10   C10   C4    119.78  3.000
 SAQ  C9    C10   C4    118.60  3.000
 SAQ  HN12  N12   C13   127.37  3.000
 SAQ  HN12  N12   C8    125.60  3.000
 SAQ  C13   N12   C8    107.00  3.000
 SAQ  N15   C13   N14   123.70  3.000
 SAQ  N15   C13   N12   123.08  3.000
 SAQ  N14   C13   N12   113.20  3.000
 SAQ  H2    C2    N3    120.21  3.000
 SAQ  H2    C2    N1    115.09  3.000
 SAQ  N3    C2    N1    124.71  3.000
 SAQ  N14   C9    C10   129.94  3.000
 SAQ  N14   C9    C8    110.31  3.000
 SAQ  C10   C9    C8    119.75  3.000
 SAQ  C9    N14   C13   105.05  3.000
 SAQ  HN15  N15   C25   116.63  3.000
 SAQ  HN15  N15   C13   114.20  3.000
 SAQ  C25   N15   C13   123.75  3.000
 SAQ  H25A  C25   H25   107.11  3.000
 SAQ  H25A  C25   C11   109.18  3.000
 SAQ  H25   C25   C11   108.75  3.000
 SAQ  H25A  C25   N15   108.93  3.000
 SAQ  H25   C25   N15   112.21  3.000
 SAQ  C11   C25   N15   110.56  3.000
 SAQ  C14   C11   S1    111.03  3.000
 SAQ  S1    C11   C25   120.96  3.000
 SAQ  C14   C11   C25   127.99  3.000
 SAQ  C12   S1    C11    91.96  3.000
 SAQ  H9    C12   C131  128.09  3.000
 SAQ  H9    C12   S1    120.28  3.000
 SAQ  C131  C12   S1    111.63  3.000
 SAQ  H101  C131  C14   123.99  3.000
 SAQ  H101  C131  C12   123.53  3.000
 SAQ  C14   C131  C12   112.48  3.000
 SAQ  H11   C14   C131  124.04  3.000
 SAQ  H11   C14   C11   123.06  3.000
 SAQ  C131  C14   C11   112.90  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
 SAQ  CONST_01  C8    C7    C5   C4     0.00   0.0  0
 SAQ  CONST_02  C8    C9    C10  C4     0.00   0.0  0
 SAQ  CONST_03  N14   C9    C10  C4   180.00   0.0  0
 SAQ  CONST_04  C9    C10   C4   C5     0.00   0.0  0
 SAQ  CONST_05  N12   C8    C7   C5   180.00   0.0  0
 SAQ  CONST_06  C9    C8    C7   C5     0.00   0.0  0
 SAQ  CONST_07  C10   C4    C5   C7     0.00   0.0  0
 SAQ  CONST_08  C13   N12   C8   C7   180.00   0.0  0
 SAQ  CONST_09  C10   C9    C8   C7     0.00   0.0  0
 SAQ  CONST_10  N14   C9    C8   C7   180.00   0.0  0
 SAQ  CONST_11  N14   C13   N12  C8     0.00   0.0  0
 SAQ  CONST_12  C13   N14   C9   C8     0.00   0.0  0
 SAQ  CONST_13  N12   C8    C9   C10  180.00   0.0  0
 SAQ  CONST_14  C13   N14   C9   C10  180.00   0.0  0
 SAQ  CONST_15  N14   C9    C8   N12    0.00   0.0  0
 SAQ  CONST_16  C9    N14   C13  N12    0.00   0.0  0
 SAQ  CONST_17  C9    C8    N12  C13    0.00   0.0  0
 SAQ  CONST_18  C12   C131  C14  C11    0.00   0.0  0
 SAQ  CONST_19  C131  C12   S1   C11    0.00   0.0  0
 SAQ  CONST_20  C131  C14   C11  S1     0.00   0.0  0
 SAQ  CONST_21  C14   C131  C12  S1     0.00   0.0  0
 SAQ  CONST_22  C14   C11   S1   C12    0.00   0.0  0
 SAQ  CONST_23  C4    N3    C2   N1     0.00   0.0  0
 SAQ  CONST_24  C6    N1    C2   N3     0.00   0.0  0
 SAQ  CONST_25  C2    N1    C6   C5     0.00   0.0  0
 SAQ  CONST_26  N15   C13   N12  C8   180.00   0.0  0
 SAQ  CONST_27  N15   C13   N14  C9   180.00   0.0  0
 SAQ  CONST_28  C131  C14   C11  C25  180.00   0.0  0
 SAQ  CONST_29  C12   S1    C11  C25  180.00   0.0  0
 SAQ  CONST_30  O16   C6    N1   C2   180.00   0.0  0
 SAQ  CONST_31  H10   C10   C4   N3     0.00   0.0  0
 SAQ  CONST_32  H7    C7    C5   C4   180.00   0.0  0
 SAQ  CONST_33  HN12  N12   C8   C7     0.00   0.0  0
 SAQ  CONST_34  H101  C131  C14  C11  180.00   0.0  0
 SAQ  CONST_35  H9    C12   S1   C11  180.00   0.0  0
 SAQ  CONST_36  H11   C14   C11  S1   180.00   0.0  0
 SAQ  CONST_37  HN1   N1    C2   N3   180.00   0.0  0
 SAQ  CONST_38  H2    C2    N3   C4   180.00   0.0  0
 SAQ  CONST_39  C25   N15   C13  N12    0.00   0.0  0
 SAQ  CONST_40  C25   N15   C13  N14  180.00   0.0  0
 SAQ  CONST_41  HN15  N15   C13  N12  180.00   0.0  0
 SAQ  Var_01    C11   C25   N15  C13  164.01  30.0  3
 SAQ  Var_02    C14   C11   C25  N15  130.44  30.0  2

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
 SAQ  plan-1  C25   0.020
 SAQ  plan-1  C11   0.020
 SAQ  plan-1  S1    0.020
 SAQ  plan-1  C12   0.020
 SAQ  plan-1  C131  0.020
 SAQ  plan-1  C14   0.020
 SAQ  plan-1  H9    0.020
 SAQ  plan-1  H101  0.020
 SAQ  plan-1  H11   0.020
 SAQ  plan-2  N1    0.020
 SAQ  plan-2  N3    0.020
 SAQ  plan-2  C4    0.020
 SAQ  plan-2  C5    0.020
 SAQ  plan-2  C6    0.020
 SAQ  plan-2  C7    0.020
 SAQ  plan-2  C8    0.020
 SAQ  plan-2  C10   0.020
 SAQ  plan-2  N12   0.020
 SAQ  plan-2  C13   0.020
 SAQ  plan-2  C2    0.020
 SAQ  plan-2  C9    0.020
 SAQ  plan-2  N14   0.020
 SAQ  plan-2  N15   0.020
 SAQ  plan-2  O16   0.020
 SAQ  plan-2  HN1   0.020
 SAQ  plan-2  H7    0.020
 SAQ  plan-2  H10   0.020
 SAQ  plan-2  HN12  0.020
 SAQ  plan-2  H2    0.020
 SAQ  plan-3  C13   0.020
 SAQ  plan-3  N15   0.020
 SAQ  plan-3  C25   0.020
 SAQ  plan-3  HN15  0.020

