# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:13:29 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 6-amino-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: NC1=Nc2cc3nc(NCc4sccc4)[nH]c3cc2C(=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
 S98  S98  6-amino-2-[(thiophen-2-ylmethyl)amino]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one  ligand  34  22  .  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_S98
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
 S98  N2    N  NR15  0  -0.748   0.4823  -0.7659   0.2750
 S98  C3    C  CR56  0   0.354  -0.8631  -0.4843   0.1531
 S98  C12   C  CR56  0   0.198  -0.9332   0.9310   0.1900
 S98  N13   N  N     0  -0.538   0.3187   1.4632   0.3267
 S98  C1    C  CR5   0   0.699   1.1291   0.4258   0.3707
 S98  N14   N  NH1   0  -0.688   2.4678   0.5297   0.4680
 S98  C15   C  CH2   0  -0.337   3.3358  -0.5843   0.7868
 S98  C16   C  CR5   0  -0.181   4.7515  -0.2588   0.4493
 S98  C11   C  CR16  0  -0.452  -2.1598   1.5651   0.0942
 S98  C10   C  CR66  0   0.277  -3.3155   0.7858  -0.0366
 S98  C5    C  CR66  0  -0.156  -3.2107  -0.6261  -0.0710
 S98  C6    C  CR6   0   0.544  -4.4208  -1.4114  -0.2122
 S98  O21   O  O     0  -0.472  -4.4776  -2.6309  -0.2610
 S98  N7    N  NR16  0  -0.719  -5.5695  -0.6557  -0.2915
 S98  C8    C  CR6   0   0.640  -5.5902   0.7126  -0.2483
 S98  N22   N  NH2   0  -0.834  -6.8124   1.2869  -0.2869
 S98  N9    N  N     0  -0.527  -4.5235   1.4320  -0.1319
 S98  C4    C  CR16  0  -0.350  -1.9709  -1.2756   0.0247
 S98  C121  C  CR15  0  -0.226   5.8561  -0.4144   1.2300
 S98  C13   C  CR15  0  -0.182   7.0595  -0.0431   0.5675
 S98  C14   C  CR15  0  -0.466   6.8407   0.3936  -0.7019
 S98  S1    S  S2    0   0.218   5.1745   0.3536  -1.1058
 S98  HN2   H  HNR5  0   0.425   0.8901  -1.6862   0.3020
 S98  HN14  H  HNH1  0   0.406   2.7917   1.4454   0.7409
 S98  H15   H  HCH2  0   0.271   3.2819  -0.8638   1.8436
 S98  H15A  H  HCH2  0   0.268   3.0206  -1.4556   0.2075
 S98  H11   H  HCR6  0   0.247  -2.2403   2.6441   0.1199
 S98  HN7   H  HNR6  0   0.420  -6.4405  -1.1626  -0.3818
 S98  HN22  H  HNH2  0   0.406  -7.5848   0.7816  -0.6887
 S98  HN2A  H  HNH2  0   0.403  -6.8298   2.2815  -0.4396
 S98  H4    H  HCR6  0   0.270  -1.9087  -2.3555  -0.0032
 S98  H111  H  HCR5  0   0.267   5.8131  -0.7823   2.2461
 S98  H13   H  HCR5  0   0.268   8.0391  -0.0939   1.0205
 S98  H151  H  HCR5  0   0.297   7.5662   0.7464  -1.4189

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
 S98  N2    C3    aromatic  1.380  0.020  1.380
 S98  N2    C1    aromatic  1.359  0.020  1.359
 S98  C3    C12   aromatic  1.417  0.020  1.417
 S98  C3    C4    aromatic  1.367  0.020  1.367
 S98  C12   N13   aromatic  1.367  0.020  1.367
 S98  C12   C11   aromatic  1.384  0.020  1.384
 S98  N13   C1    aromatic  1.317  0.020  1.317
 S98  C1    N14   single    1.346  0.020  1.346
 S98  N14   C15   single    1.448  0.020  1.448
 S98  C15   C16   single    1.491  0.020  1.491
 S98  C16   C121  aromatic  1.362  0.020  1.362
 S98  C16   S1    aromatic  1.724  0.020  1.724
 S98  C11   C10   aromatic  1.400  0.020  1.400
 S98  C10   C5    aromatic  1.416  0.020  1.416
 S98  C10   N9    single    1.373  0.020  1.373
 S98  C5    C6    single    1.449  0.020  1.449
 S98  C5    C4    aromatic  1.403  0.020  1.403
 S98  C6    O21   double    1.222  0.020  1.222
 S98  C6    N7    single    1.377  0.020  1.377
 S98  N7    C8    single    1.369  0.020  1.369
 S98  C8    N22   single    1.351  0.020  1.351
 S98  C8    N9    double    1.292  0.020  1.292
 S98  C121  C13   aromatic  1.423  0.020  1.423
 S98  C13   C14   aromatic  1.360  0.020  1.360
 S98  C14   S1    aromatic  1.715  0.020  1.715
 S98  N2    HN2   single    0.860  0.020  1.020
 S98  N14   HN14  single    0.890  0.020  1.040
 S98  C15   H15   single    0.970  0.020  1.090
 S98  C15   H15A  single    0.970  0.020  1.090
 S98  C11   H11   single    0.930  0.020  1.080
 S98  N7    HN7   single    0.860  0.020  1.020
 S98  N22   HN22  single    0.890  0.020  1.040
 S98  N22   HN2A  single    0.890  0.020  1.040
 S98  C4    H4    single    0.930  0.020  1.080
 S98  C121  H111  single    0.930  0.020  1.080
 S98  C13   H13   single    0.930  0.020  1.080
 S98  C14   H151  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
 S98  HN2   N2    C1    127.35  3.000
 S98  HN2   N2    C3    125.71  3.000
 S98  C1    N2    C3    106.93  3.000
 S98  C4    C3    C12   122.70  3.000
 S98  C4    C3    N2    132.85  3.000
 S98  C12   C3    N2    104.46  3.000
 S98  C11   C12   N13   129.79  3.000
 S98  C11   C12   C3    119.96  3.000
 S98  N13   C12   C3    110.24  3.000
 S98  C1    N13   C12   105.08  3.000
 S98  N14   C1    N13   123.61  3.000
 S98  N14   C1    N2    123.09  3.000
 S98  N13   C1    N2    113.29  3.000
 S98  HN14  N14   C15   116.51  3.000
 S98  HN14  N14   C1    114.13  3.000
 S98  C15   N14   C1    123.56  3.000
 S98  H15A  C15   H15   107.09  3.000
 S98  H15A  C15   C16   109.14  3.000
 S98  H15   C15   C16   108.72  3.000
 S98  H15A  C15   N14   108.90  3.000
 S98  H15   C15   N14   112.31  3.000
 S98  C16   C15   N14   110.57  3.000
 S98  S1    C16   C121  111.03  3.000
 S98  S1    C16   C15   120.97  3.000
 S98  C121  C16   C15   127.98  3.000
 S98  H11   C11   C10   119.72  3.000
 S98  H11   C11   C12   121.40  3.000
 S98  C10   C11   C12   118.88  3.000
 S98  N9    C10   C5    122.18  3.000
 S98  N9    C10   C11   118.08  3.000
 S98  C5    C10   C11   119.74  3.000
 S98  C4    C5    C6    119.58  3.000
 S98  C4    C5    C10   121.69  3.000
 S98  C6    C5    C10   118.73  3.000
 S98  N7    C6    O21   120.43  3.000
 S98  N7    C6    C5    113.87  3.000
 S98  O21   C6    C5    125.70  3.000
 S98  HN7   N7    C8    119.38  3.000
 S98  HN7   N7    C6    116.63  3.000
 S98  C8    N7    C6    123.99  3.000
 S98  N9    C8    N22   120.86  3.000
 S98  N9    C8    N7    123.15  3.000
 S98  N22   C8    N7    115.95  3.000
 S98  HN2A  N22   HN22  114.97  3.000
 S98  HN2A  N22   C8    116.11  3.000
 S98  HN22  N22   C8    119.49  3.000
 S98  C8    N9    C10   118.07  3.000
 S98  H4    C4    C5    120.74  3.000
 S98  H4    C4    C3    122.23  3.000
 S98  C5    C4    C3    117.02  3.000
 S98  H111  C121  C13   124.05  3.000
 S98  H111  C121  C16   123.04  3.000
 S98  C13   C121  C16   112.91  3.000
 S98  H13   C13   C14   123.52  3.000
 S98  H13   C13   C121  124.00  3.000
 S98  C14   C13   C121  112.48  3.000
 S98  H151  C14   S1    120.28  3.000
 S98  H151  C14   C13   128.09  3.000
 S98  S1    C14   C13   111.63  3.000
 S98  C14   S1    C16    91.96  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
 S98  CONST_01  N13   C12   C3    N2      0.00   0.0  0
 S98  CONST_02  C11   C12   C3    N2    180.00   0.0  0
 S98  CONST_03  C5    C4    C3    N2    180.00   0.0  0
 S98  CONST_04  C12   N13   C1    N2      0.00   0.0  0
 S98  CONST_05  N13   C1    N2    C3      0.00   0.0  0
 S98  CONST_06  C1    N13   C12   C3      0.00   0.0  0
 S98  CONST_07  C10   C11   C12   C3      0.00   0.0  0
 S98  CONST_08  C10   C5    C4    C3      0.00   0.0  0
 S98  CONST_09  C1    N2    C3    C12     0.00   0.0  0
 S98  CONST_10  C5    C4    C3    C12     0.00   0.0  0
 S98  CONST_11  C5    C10   C11   C12     0.00   0.0  0
 S98  CONST_12  C4    C3    C12   N13   180.00   0.0  0
 S98  CONST_13  C10   C11   C12   N13   180.00   0.0  0
 S98  CONST_14  C4    C3    N2    C1    180.00   0.0  0
 S98  CONST_15  C11   C12   N13   C1    180.00   0.0  0
 S98  CONST_16  C14   C13   C121  C16     0.00   0.0  0
 S98  CONST_17  C13   C14   S1    C16     0.00   0.0  0
 S98  CONST_18  C4    C3    C12   C11     0.00   0.0  0
 S98  CONST_19  C4    C5    C10   C11     0.00   0.0  0
 S98  CONST_20  C14   S1    C16   C121    0.00   0.0  0
 S98  CONST_21  S1    C14   C13   C121    0.00   0.0  0
 S98  CONST_22  S1    C16   C121  C13     0.00   0.0  0
 S98  CONST_23  N7    C8    N9    C10     0.00   0.0  0
 S98  CONST_24  C8    N7    C6    C5      0.00   0.0  0
 S98  CONST_25  N9    C8    N7    C6      0.00   0.0  0
 S98  CONST_26  N14   C1    N2    C3    180.00   0.0  0
 S98  CONST_27  N14   C1    N13   C12   180.00   0.0  0
 S98  CONST_28  C13   C121  C16   C15   180.00   0.0  0
 S98  CONST_29  C14   S1    C16   C15   180.00   0.0  0
 S98  CONST_30  N22   C8    N9    C10   180.00   0.0  0
 S98  CONST_31  N22   C8    N7    C6    180.00   0.0  0
 S98  CONST_32  C8    N7    C6    O21   180.00   0.0  0
 S98  CONST_33  H4    C4    C3    N2      0.00   0.0  0
 S98  CONST_34  H11   C11   C12   C3    180.00   0.0  0
 S98  CONST_35  HN2   N2    C3    C12   180.00   0.0  0
 S98  CONST_36  H13   C13   C121  C16   180.00   0.0  0
 S98  CONST_37  H151  C14   S1    C16   180.00   0.0  0
 S98  CONST_38  H111  C121  C13   C14   180.00   0.0  0
 S98  CONST_39  HN7   N7    C6    C5    180.00   0.0  0
 S98  CONST_40  C15   N14   C1    N2      0.00   0.0  0
 S98  CONST_41  C15   N14   C1    N13   180.00   0.0  0
 S98  CONST_42  HN14  N14   C1    N2    180.00   0.0  0
 S98  CONST_44  HN2A  N22   C8    N7    180.00   0.0  0
 S98  Var_01    C16   C15   N14   C1    164.07  30.0  3
 S98  Var_02    C121  C16   C15   N14   131.02  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
 S98  plan-1  C15   0.020
 S98  plan-1  C16   0.020
 S98  plan-1  C121  0.020
 S98  plan-1  C13   0.020
 S98  plan-1  C14   0.020
 S98  plan-1  S1    0.020
 S98  plan-1  H111  0.020
 S98  plan-1  H13   0.020
 S98  plan-1  H151  0.020
 S98  plan-2  N2    0.020
 S98  plan-2  C3    0.020
 S98  plan-2  C12   0.020
 S98  plan-2  N13   0.020
 S98  plan-2  C1    0.020
 S98  plan-2  N14   0.020
 S98  plan-2  C11   0.020
 S98  plan-2  C10   0.020
 S98  plan-2  C5    0.020
 S98  plan-2  C6    0.020
 S98  plan-2  O21   0.020
 S98  plan-2  N7    0.020
 S98  plan-2  C8    0.020
 S98  plan-2  N22   0.020
 S98  plan-2  N9    0.020
 S98  plan-2  C4    0.020
 S98  plan-2  HN2   0.020
 S98  plan-2  H11   0.020
 S98  plan-2  HN7   0.020
 S98  plan-2  HN22  0.020
 S98  plan-2  HN2A  0.020
 S98  plan-2  H4    0.020
 S98  plan-3  C1    0.020
 S98  plan-3  N14   0.020
 S98  plan-3  C15   0.020
 S98  plan-3  HN14  0.020

