# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 11:39:34 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 7-[5,6-dimethoxy-2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]quinazoline-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2nc(n(c3ccc4c(N)nc(N)nc4c3)c2cc1OC)c5sccn5
#
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
 1DN  1DN  7-[5,6-dimethoxy-2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]quinazoline-2,4-diamine  ligand  47  30  .  2021-08-03  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1DN
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
 1DN  N12  N  NH2   0  -0.821   5.1152  -2.2655  -2.5789
 1DN  C3   C  CR6   0   0.526   4.3888  -1.9228  -1.4969
 1DN  N2   N  N     0  -0.507   4.9137  -2.2918  -0.3101
 1DN  N4   N  N     0  -0.532   3.2452  -1.2965  -1.6959
 1DN  C5   C  CR66  0   0.278   2.5275  -1.0093  -0.5913
 1DN  C10  C  CR16  0  -0.323   1.2888  -0.3473  -0.7346
 1DN  C9   C  CR6   0   0.193   0.5446  -0.0387   0.3742
 1DN  C8   C  CR16  0  -0.252   0.9656  -0.3779   1.6685
 1DN  C7   C  CR16  0  -0.298   2.1684  -1.0205   1.8240
 1DN  C6   C  CR66  0  -0.037   2.9587  -1.3402   0.7113
 1DN  C1   C  CR6   0   0.494   4.2344  -2.0148   0.7805
 1DN  N11  N  NH2   0  -0.823   4.7613  -2.3744   1.9510
 1DN  N13  N  NR5   0  -0.657  -0.6944   0.6333   0.2121
 1DN  C17  C  CR5   0   0.470  -0.9477   1.9806   0.2512
 1DN  C22  C  CR5   0  -0.056   0.0658   3.0051   0.4403
 1DN  N26  N  N     0  -0.376  -0.2478   4.2666   0.4968
 1DN  C25  C  CR15  0  -0.017   0.8506   5.0421   0.6759
 1DN  C24  C  CR15  0  -0.495   2.0331   4.3753   0.7595
 1DN  S23  S  S2    0   0.269   1.7625   2.6965   0.6072
 1DN  N16  N  N     0  -0.452  -2.2170   2.2545   0.0951
 1DN  C15  C  CR56  0   0.139  -2.8358   1.0464  -0.0515
 1DN  C21  C  CR16  0  -0.484  -4.1925   0.7487  -0.2473
 1DN  C20  C  CR6   0   0.309  -4.5580  -0.5739  -0.3654
 1DN  O29  O  O2    0  -0.465  -5.8183  -1.0081  -0.5573
 1DN  C30  C  CH3   0  -0.438  -6.8465  -0.0422  -0.6207
 1DN  C19  C  CR6   0   0.317  -3.5812  -1.6181  -0.2905
 1DN  C18  C  CR16  0  -0.460  -2.2448  -1.3314  -0.0972
 1DN  C14  C  CR56  0   0.360  -1.9030   0.0148   0.0186
 1DN  O27  O  O2    0  -0.460  -4.0794  -2.8583  -0.4223
 1DN  C28  C  CH3   0  -0.441  -3.1776  -3.9453  -0.3726
 1DN  H1   H  HNH2  0   0.394   6.0642  -2.5704  -2.4509
 1DN  H2   H  HNH2  0   0.393   4.8793  -1.8598  -3.4678
 1DN  H3   H  HCR6  0   0.275   0.9445  -0.0789  -1.7251
 1DN  H4   H  HCR6  0   0.278   0.3532  -0.1262   2.5234
 1DN  H5   H  HCR6  0   0.261   2.4887  -1.2708   2.8268
 1DN  H6   H  HNH2  0   0.407   5.6445  -2.8557   1.9696
 1DN  H7   H  HNH2  0   0.419   4.3056  -2.2129   2.8302
 1DN  H8   H  HCR5  0   0.276   0.7435   6.1151   0.7422
 1DN  H9   H  HCR5  0   0.315   3.0242   4.7762   0.9000
 1DN  H10  H  HCR6  0   0.284  -4.9148   1.5514  -0.2975
 1DN  H11  H  HCH3  0   0.228  -6.9238   0.5318   0.3068
 1DN  H12  H  HCH3  0   0.228  -6.7028   0.6534  -1.4523
 1DN  H13  H  HCH3  0   0.262  -7.7748  -0.5868  -0.7743
 1DN  H14  H  HCR6  0   0.295  -1.4916  -2.1049  -0.0392
 1DN  H15  H  HCH3  0   0.230  -2.4317  -3.8918  -1.1702
 1DN  H16  H  HCH3  0   0.230  -2.6613  -4.0013   0.5893
 1DN  H17  H  HCH3  0   0.264  -3.7711  -4.8463  -0.5047

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
 1DN  C24  S23  aromatic  1.707  0.020  1.707
 1DN  C24  C25  aromatic  1.360  0.020  1.360
 1DN  S23  C22  aromatic  1.733  0.020  1.733
 1DN  C25  N26  aromatic  1.356  0.020  1.356
 1DN  N26  C22  aromatic  1.301  0.020  1.301
 1DN  C22  C17  single    1.454  0.020  1.454
 1DN  N16  C17  aromatic  1.308  0.020  1.308
 1DN  N16  C15  aromatic  1.365  0.020  1.365
 1DN  C17  N13  aromatic  1.371  0.020  1.371
 1DN  C15  C21  aromatic  1.403  0.020  1.403
 1DN  C15  C14  aromatic  1.393  0.020  1.393
 1DN  C21  C20  aromatic  1.377  0.020  1.377
 1DN  N13  C14  aromatic  1.371  0.020  1.371
 1DN  N13  C9   single    1.419  0.020  1.419
 1DN  C14  C18  aromatic  1.394  0.020  1.394
 1DN  C10  C9   aromatic  1.371  0.020  1.371
 1DN  C10  C5   aromatic  1.412  0.020  1.412
 1DN  C9   C8   aromatic  1.403  0.020  1.403
 1DN  C30  O29  single    1.412  0.020  1.412
 1DN  C20  O29  single    1.347  0.020  1.347
 1DN  C20  C19  aromatic  1.432  0.020  1.432
 1DN  N4   C5   aromatic  1.348  0.020  1.348
 1DN  N4   C3   aromatic  1.319  0.020  1.319
 1DN  C5   C6   aromatic  1.411  0.020  1.411
 1DN  C8   C7   aromatic  1.373  0.020  1.373
 1DN  C18  C19  aromatic  1.380  0.020  1.380
 1DN  N12  C3   single    1.348  0.020  1.348
 1DN  C3   N2   aromatic  1.349  0.020  1.349
 1DN  C19  O27  single    1.343  0.020  1.343
 1DN  C6   C7   aromatic  1.402  0.020  1.402
 1DN  C6   C1   aromatic  1.445  0.020  1.445
 1DN  N2   C1   aromatic  1.314  0.020  1.314
 1DN  C1   N11  single    1.333  0.020  1.333
 1DN  O27  C28  single    1.413  0.020  1.413
 1DN  N12  H1   single    0.890  0.020  1.040
 1DN  N12  H2   single    0.890  0.020  1.040
 1DN  C10  H3   single    0.930  0.020  1.080
 1DN  C8   H4   single    0.930  0.020  1.080
 1DN  C7   H5   single    0.930  0.020  1.080
 1DN  N11  H6   single    0.860  0.020  1.020
 1DN  N11  H7   single    0.860  0.020  1.020
 1DN  C25  H8   single    0.930  0.020  1.080
 1DN  C24  H9   single    0.930  0.020  1.080
 1DN  C21  H10  single    0.930  0.020  1.080
 1DN  C30  H11  single    0.970  0.020  1.090
 1DN  C30  H12  single    0.970  0.020  1.090
 1DN  C30  H13  single    0.970  0.020  1.090
 1DN  C18  H14  single    0.930  0.020  1.080
 1DN  C28  H15  single    0.970  0.020  1.090
 1DN  C28  H16  single    0.970  0.020  1.090
 1DN  C28  H17  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
 1DN  H2   N12  H1   117.17  3.000
 1DN  H2   N12  C3   118.74  3.000
 1DN  H1   N12  C3   118.94  3.000
 1DN  N4   C3   N2   126.87  3.000
 1DN  N2   C3   N12  115.28  3.000
 1DN  N4   C3   N12  117.83  3.000
 1DN  C1   N2   C3   118.11  3.000
 1DN  C5   N4   C3   116.04  3.000
 1DN  C6   C5   C10  118.14  3.000
 1DN  C6   C5   N4   122.92  3.000
 1DN  C10  C5   N4   118.93  3.000
 1DN  H3   C10  C9   120.78  3.000
 1DN  H3   C10  C5   119.23  3.000
 1DN  C9   C10  C5   119.99  3.000
 1DN  N13  C9   C8   118.82  3.000
 1DN  C8   C9   C10  121.94  3.000
 1DN  N13  C9   C10  119.24  3.000
 1DN  H4   C8   C7   121.04  3.000
 1DN  H4   C8   C9   120.22  3.000
 1DN  C7   C8   C9   118.74  3.000
 1DN  H5   C7   C6   121.06  3.000
 1DN  H5   C7   C8   118.22  3.000
 1DN  C6   C7   C8   120.72  3.000
 1DN  C1   C6   C7   124.49  3.000
 1DN  C1   C6   C5   115.05  3.000
 1DN  C7   C6   C5   120.45  3.000
 1DN  N11  C1   C6   121.13  3.000
 1DN  N11  C1   N2   117.87  3.000
 1DN  C6   C1   N2   121.00  3.000
 1DN  H7   N11  H6   117.36  3.000
 1DN  H7   N11  C1   123.13  3.000
 1DN  H6   N11  C1   119.49  3.000
 1DN  C14  N13  C17  106.52  3.000
 1DN  C14  N13  C9   124.90  3.000
 1DN  C17  N13  C9   128.56  3.000
 1DN  N16  C17  C22  123.00  3.000
 1DN  N16  C17  N13  112.43  3.000
 1DN  C22  C17  N13  124.57  3.000
 1DN  S23  C22  N26  113.86  3.000
 1DN  N26  C22  C17  121.40  3.000
 1DN  S23  C22  C17  124.74  3.000
 1DN  C25  N26  C22  111.39  3.000
 1DN  H8   C25  C24  124.70  3.000
 1DN  H8   C25  N26  119.71  3.000
 1DN  C24  C25  N26  115.59  3.000
 1DN  H9   C24  S23  121.53  3.000
 1DN  H9   C24  C25  128.67  3.000
 1DN  S23  C24  C25  109.80  3.000
 1DN  C24  S23  C22   89.35  3.000
 1DN  C15  N16  C17  105.51  3.000
 1DN  C14  C15  C21  119.85  3.000
 1DN  C14  C15  N16  110.28  3.000
 1DN  C21  C15  N16  129.88  3.000
 1DN  H10  C21  C20  122.12  3.000
 1DN  H10  C21  C15  119.68  3.000
 1DN  C20  C21  C15  118.20  3.000
 1DN  C19  C20  O29  114.25  3.000
 1DN  C19  C20  C21  120.98  3.000
 1DN  O29  C20  C21  124.77  3.000
 1DN  C30  O29  C20  117.85  3.000
 1DN  H13  C30  H12  108.86  3.000
 1DN  H13  C30  H11  108.81  3.000
 1DN  H12  C30  H11  108.69  3.000
 1DN  H13  C30  O29  106.58  3.000
 1DN  H12  C30  O29  111.93  3.000
 1DN  H11  C30  O29  111.87  3.000
 1DN  O27  C19  C18  124.38  3.000
 1DN  O27  C19  C20  114.53  3.000
 1DN  C18  C19  C20  121.09  3.000
 1DN  H14  C18  C14  121.05  3.000
 1DN  H14  C18  C19  122.23  3.000
 1DN  C14  C18  C19  116.72  3.000
 1DN  C18  C14  C15  123.17  3.000
 1DN  C18  C14  N13  131.56  3.000
 1DN  C15  C14  N13  105.27  3.000
 1DN  C28  O27  C19  118.04  3.000
 1DN  H17  C28  H16  108.81  3.000
 1DN  H17  C28  H15  108.93  3.000
 1DN  H16  C28  H15  108.79  3.000
 1DN  H17  C28  O27  106.55  3.000
 1DN  H16  C28  O27  111.82  3.000
 1DN  H15  C28  O27  111.84  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
 1DN  CONST_01  C10  C5   N4   C3   180.00   0.0  0
 1DN  CONST_02  C6   C5   N4   C3     0.00   0.0  0
 1DN  CONST_03  C6   C1   N2   C3     0.00   0.0  0
 1DN  CONST_04  C5   N4   C3   N2     0.00   0.0  0
 1DN  CONST_05  C5   C6   C1   N2     0.00   0.0  0
 1DN  CONST_06  C7   C6   C1   N2   180.00   0.0  0
 1DN  CONST_07  C9   C10  C5   N4   180.00   0.0  0
 1DN  CONST_08  C7   C6   C5   N4   180.00   0.0  0
 1DN  CONST_09  C1   C6   C5   N4     0.00   0.0  0
 1DN  CONST_10  C1   N2   C3   N4     0.00   0.0  0
 1DN  CONST_11  N13  C9   C10  C5   180.00   0.0  0
 1DN  CONST_12  C8   C9   C10  C5     0.00   0.0  0
 1DN  CONST_13  C8   C7   C6   C5     0.00   0.0  0
 1DN  CONST_16  C7   C8   C9   C10    0.00   0.0  0
 1DN  CONST_17  C7   C6   C5   C10    0.00   0.0  0
 1DN  CONST_18  C1   C6   C5   C10  180.00   0.0  0
 1DN  CONST_19  C22  C17  N13  C9     0.00   0.0  0
 1DN  CONST_20  N16  C17  N13  C9   180.00   0.0  0
 1DN  CONST_21  C15  C14  N13  C9   180.00   0.0  0
 1DN  CONST_22  C18  C14  N13  C9     0.00   0.0  0
 1DN  CONST_23  C6   C5   C10  C9     0.00   0.0  0
 1DN  CONST_24  C6   C7   C8   C9     0.00   0.0  0
 1DN  CONST_27  C1   C6   C7   C8   180.00   0.0  0
 1DN  CONST_28  N13  C9   C8   C7   180.00   0.0  0
 1DN  CONST_29  S23  C22  C17  N13    0.00   0.0  0
 1DN  CONST_30  N26  C22  C17  N13  180.00   0.0  0
 1DN  CONST_31  C15  N16  C17  N13    0.00   0.0  0
 1DN  CONST_32  N16  C15  C14  N13    0.00   0.0  0
 1DN  CONST_33  C21  C15  C14  N13  180.00   0.0  0
 1DN  CONST_34  C19  C18  C14  N13  180.00   0.0  0
 1DN  CONST_35  C24  S23  C22  C17  180.00   0.0  0
 1DN  CONST_36  C25  N26  C22  C17  180.00   0.0  0
 1DN  CONST_37  C21  C15  N16  C17  180.00   0.0  0
 1DN  CONST_38  C14  C15  N16  C17    0.00   0.0  0
 1DN  CONST_39  C15  C14  N13  C17    0.00   0.0  0
 1DN  CONST_40  C18  C14  N13  C17  180.00   0.0  0
 1DN  CONST_41  C25  C24  S23  C22    0.00   0.0  0
 1DN  CONST_42  C24  C25  N26  C22    0.00   0.0  0
 1DN  CONST_43  C15  N16  C17  C22  180.00   0.0  0
 1DN  CONST_44  C14  N13  C17  C22  180.00   0.0  0
 1DN  CONST_45  S23  C24  C25  N26    0.00   0.0  0
 1DN  CONST_46  C24  S23  C22  N26    0.00   0.0  0
 1DN  CONST_47  N16  C17  C22  N26    0.00   0.0  0
 1DN  CONST_48  S23  C22  N26  C25    0.00   0.0  0
 1DN  CONST_49  N16  C17  C22  S23  180.00   0.0  0
 1DN  CONST_50  C14  N13  C17  N16    0.00   0.0  0
 1DN  CONST_51  C20  C21  C15  N16  180.00   0.0  0
 1DN  CONST_52  C18  C14  C15  N16  180.00   0.0  0
 1DN  CONST_53  C19  C20  C21  C15    0.00   0.0  0
 1DN  CONST_54  C19  C18  C14  C15    0.00   0.0  0
 1DN  CONST_55  C18  C14  C15  C21    0.00   0.0  0
 1DN  CONST_56  C18  C19  C20  C21    0.00   0.0  0
 1DN  CONST_57  C14  C15  C21  C20    0.00   0.0  0
 1DN  CONST_58  C14  C18  C19  C20    0.00   0.0  0
 1DN  CONST_59  C5   N4   C3   N12  180.00   0.0  0
 1DN  CONST_60  C1   N2   C3   N12  180.00   0.0  0
 1DN  CONST_61  N11  C1   N2   C3   180.00   0.0  0
 1DN  CONST_62  N11  C1   C6   C5   180.00   0.0  0
 1DN  CONST_63  N11  C1   C6   C7     0.00   0.0  0
 1DN  CONST_64  O29  C20  C21  C15  180.00   0.0  0
 1DN  CONST_65  O27  C19  C20  C21  180.00   0.0  0
 1DN  CONST_66  C18  C19  C20  O29  180.00   0.0  0
 1DN  CONST_67  O27  C19  C18  C14  180.00   0.0  0
 1DN  CONST_68  H3   C10  C5   N4     0.00   0.0  0
 1DN  CONST_69  H5   C7   C6   C5   180.00   0.0  0
 1DN  CONST_70  H4   C8   C9   C10  180.00   0.0  0
 1DN  CONST_71  H14  C18  C14  N13    0.00   0.0  0
 1DN  CONST_72  H9   C24  S23  C22  180.00   0.0  0
 1DN  CONST_73  H8   C25  N26  C22  180.00   0.0  0
 1DN  CONST_74  H10  C21  C15  N16    0.00   0.0  0
 1DN  CONST_75  H1   N12  C3   N2     0.00   0.0  0
 1DN  CONST_76  H2   N12  C3   N2   180.00   0.0  0
 1DN  CONST_77  H6   N11  C1   N2     0.00   0.0  0
 1DN  CONST_78  H7   N11  C1   N2   180.00   0.0  0
 1DN  Var_01    C19  C20  O29  C30  178.97  30.0  2
 1DN  Var_02    H11  C30  O29  C20  -60.98  30.0  3
 1DN  Var_03    H15  C28  O27  C19  -60.65  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
 1DN  plan-1  C17  0.020
 1DN  plan-1  C22  0.020
 1DN  plan-1  N26  0.020
 1DN  plan-1  C25  0.020
 1DN  plan-1  C24  0.020
 1DN  plan-1  S23  0.020
 1DN  plan-1  H8   0.020
 1DN  plan-1  H9   0.020
 1DN  plan-2  C9   0.020
 1DN  plan-2  N13  0.020
 1DN  plan-2  C17  0.020
 1DN  plan-2  C22  0.020
 1DN  plan-2  N16  0.020
 1DN  plan-2  C15  0.020
 1DN  plan-2  C21  0.020
 1DN  plan-2  C20  0.020
 1DN  plan-2  O29  0.020
 1DN  plan-2  C19  0.020
 1DN  plan-2  C18  0.020
 1DN  plan-2  C14  0.020
 1DN  plan-2  O27  0.020
 1DN  plan-2  H10  0.020
 1DN  plan-2  H14  0.020
 1DN  plan-3  N12  0.020
 1DN  plan-3  C3   0.020
 1DN  plan-3  N2   0.020
 1DN  plan-3  N4   0.020
 1DN  plan-3  C5   0.020
 1DN  plan-3  C10  0.020
 1DN  plan-3  C9   0.020
 1DN  plan-3  C8   0.020
 1DN  plan-3  C7   0.020
 1DN  plan-3  C6   0.020
 1DN  plan-3  C1   0.020
 1DN  plan-3  N11  0.020
 1DN  plan-3  N13  0.020
 1DN  plan-3  H3   0.020
 1DN  plan-3  H4   0.020
 1DN  plan-3  H5   0.020
 1DN  plan-4  N12  0.020
 1DN  plan-4  C3   0.020
 1DN  plan-4  H1   0.020
 1DN  plan-4  H2   0.020
 1DN  plan-5  C1   0.020
 1DN  plan-5  N11  0.020
 1DN  plan-5  H6   0.020
 1DN  plan-5  H7   0.020

