# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:42:46 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 7-[5,6-dimethyl-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: Cc1cc2nc(n(c3ccc4c(N)nc(N)nc4c3)c2cc1C)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
 1VM  1VM  7-[5,6-dimethyl-2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]quinazoline-2,4-diamine  ligand  45  28  .  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_1VM
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
 1VM  N11  N  NH2   0  -0.822  -4.5404  -2.0871   1.9735
 1VM  C1   C  CR6   0   0.494  -3.9744  -1.8144   0.7979
 1VM  N2   N  N     0  -0.507  -4.6707  -2.0571  -0.2900
 1VM  C6   C  CR66  0  -0.038  -2.6387  -1.2685   0.7209
 1VM  C5   C  CR66  0   0.277  -2.1682  -1.0248  -0.5873
 1VM  N4   N  N     0  -0.533  -2.9013  -1.2796  -1.6898
 1VM  C3   C  CR6   0   0.527  -4.1034  -1.7815  -1.4826
 1VM  N12  N  NH2   0  -0.821  -4.8525  -2.0847  -2.5603
 1VM  C7   C  CR16  0  -0.297  -1.8290  -0.9886   1.8307
 1VM  C8   C  CR16  0  -0.253  -0.5698  -0.4675   1.6668
 1VM  C9   C  CR6   0   0.196  -0.1108  -0.2092   0.3670
 1VM  C10  C  CR16  0  -0.325  -0.8734  -0.4831  -0.7386
 1VM  N13  N  NR5   0  -0.660   1.1828   0.3467   0.1934
 1VM  C14  C  CR56  0   0.349   2.3264  -0.3762  -0.0428
 1VM  C18  C  CR16  0  -0.362   2.5567  -1.7375  -0.1936
 1VM  C19  C  CR6   0   0.057   3.8581  -2.1471  -0.4323
 1VM  C22  C  CH3   0  -0.737   4.1554  -3.6072  -0.6100
 1VM  C20  C  CR6   0   0.064   4.9139  -1.1981  -0.5169
 1VM  C23  C  CH3   0  -0.736   6.3125  -1.6686  -0.7952
 1VM  C21  C  CR16  0  -0.389   4.6591   0.1516  -0.3561
 1VM  C15  C  CR56  0   0.141   3.3495   0.5729  -0.1159
 1VM  N16  N  N     0  -0.452   2.8425   1.8299   0.0699
 1VM  C17  C  CR5   0   0.475   1.5596   1.6641   0.2502
 1VM  C24  C  CR5   0  -0.055   0.6423   2.7718   0.4728
 1VM  N25  N  N     0  -0.372   1.0721   3.9935   0.5929
 1VM  C26  C  CR15  0  -0.017   0.0470   4.8628   0.7729
 1VM  C27  C  CR15  0  -0.493  -1.1955   4.3087   0.7915
 1VM  S28  S  S2    0   0.274  -1.0801   2.6204   0.5755
 1VM  H1   H  HNH2  0   0.407  -5.4643  -2.4843   1.9977
 1VM  H2   H  HNH2  0   0.419  -4.0770  -1.9427   2.8513
 1VM  H3   H  HNH2  0   0.393  -4.5611  -1.7508  -3.4623
 1VM  H4   H  HNH2  0   0.394  -5.8299  -2.2822  -2.4358
 1VM  H5   H  HCR6  0   0.262  -2.1770  -1.1774   2.8379
 1VM  H6   H  HCR6  0   0.278   0.0582  -0.2488   2.5195
 1VM  H7   H  HCR6  0   0.275  -0.5023  -0.2743  -1.7337
 1VM  H8   H  HCR6  0   0.264   1.7515  -2.4592  -0.1338
 1VM  H9   H  HCH3  0   0.246   4.5547  -3.8165  -1.6046
 1VM  H10  H  HCH3  0   0.244   4.9012  -3.9576   0.1064
 1VM  H11  H  HCH3  0   0.253   3.2600  -4.2128  -0.4795
 1VM  H12  H  HCH3  0   0.244   6.3876  -2.1416  -1.7769
 1VM  H13  H  HCH3  0   0.252   7.0187  -0.8404  -0.7725
 1VM  H14  H  HCH3  0   0.241   6.6451  -2.4095  -0.0657
 1VM  H15  H  HCR6  0   0.250   5.4619   0.8763  -0.4169
 1VM  H16  H  HCR5  0   0.277   0.2521   5.9171   0.8892
 1VM  H17  H  HCR5  0   0.316  -2.1483   4.7968   0.9218

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
 1VM  C27  S28  aromatic  1.706  0.020  1.706
 1VM  C27  C26  aromatic  1.361  0.020  1.361
 1VM  S28  C24  aromatic  1.732  0.020  1.732
 1VM  C26  N25  aromatic  1.356  0.020  1.356
 1VM  C24  N25  aromatic  1.301  0.020  1.301
 1VM  C24  C17  single    1.455  0.020  1.455
 1VM  N16  C17  aromatic  1.306  0.020  1.306
 1VM  N16  C15  aromatic  1.368  0.020  1.368
 1VM  C17  N13  aromatic  1.371  0.020  1.371
 1VM  C15  C21  aromatic  1.397  0.020  1.397
 1VM  C15  C14  aromatic  1.397  0.020  1.397
 1VM  C21  C20  aromatic  1.383  0.020  1.383
 1VM  N13  C14  aromatic  1.373  0.020  1.373
 1VM  N13  C9   single    1.419  0.020  1.419
 1VM  C14  C18  aromatic  1.389  0.020  1.389
 1VM  C10  C9   aromatic  1.371  0.020  1.371
 1VM  C10  C5   aromatic  1.412  0.020  1.412
 1VM  C9   C8   aromatic  1.403  0.020  1.403
 1VM  C20  C23  single    1.502  0.020  1.502
 1VM  C20  C19  aromatic  1.422  0.020  1.422
 1VM  N4   C5   aromatic  1.348  0.020  1.348
 1VM  N4   C3   aromatic  1.319  0.020  1.319
 1VM  C5   C6   aromatic  1.411  0.020  1.411
 1VM  C8   C7   aromatic  1.373  0.020  1.373
 1VM  C18  C19  aromatic  1.385  0.020  1.385
 1VM  N12  C3   single    1.347  0.020  1.347
 1VM  C3   N2   aromatic  1.349  0.020  1.349
 1VM  C19  C22  single    1.501  0.020  1.501
 1VM  C6   C7   aromatic  1.402  0.020  1.402
 1VM  C6   C1   aromatic  1.445  0.020  1.445
 1VM  N2   C1   aromatic  1.314  0.020  1.314
 1VM  C1   N11  single    1.333  0.020  1.333
 1VM  N11  H1   single    0.860  0.020  1.020
 1VM  N11  H2   single    0.860  0.020  1.020
 1VM  N12  H3   single    0.890  0.020  1.040
 1VM  N12  H4   single    0.890  0.020  1.040
 1VM  C7   H5   single    0.930  0.020  1.080
 1VM  C8   H6   single    0.930  0.020  1.080
 1VM  C10  H7   single    0.930  0.020  1.080
 1VM  C18  H8   single    0.930  0.020  1.080
 1VM  C22  H9   single    0.970  0.020  1.090
 1VM  C22  H10  single    0.970  0.020  1.090
 1VM  C22  H11  single    0.970  0.020  1.090
 1VM  C23  H12  single    0.970  0.020  1.090
 1VM  C23  H13  single    0.970  0.020  1.090
 1VM  C23  H14  single    0.970  0.020  1.090
 1VM  C21  H15  single    0.930  0.020  1.080
 1VM  C26  H16  single    0.930  0.020  1.080
 1VM  C27  H17  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
 1VM  H2   N11  H1   117.39  3.000
 1VM  H2   N11  C1   123.11  3.000
 1VM  H1   N11  C1   119.47  3.000
 1VM  C6   C1   N2   121.02  3.000
 1VM  N2   C1   N11  117.86  3.000
 1VM  C6   C1   N11  121.12  3.000
 1VM  C3   N2   C1   118.11  3.000
 1VM  C7   C6   C5   120.44  3.000
 1VM  C7   C6   C1   124.55  3.000
 1VM  C5   C6   C1   115.01  3.000
 1VM  C10  C5   N4   118.92  3.000
 1VM  N4   C5   C6   122.96  3.000
 1VM  C10  C5   C6   118.12  3.000
 1VM  C3   N4   C5   116.04  3.000
 1VM  N12  C3   N4   117.82  3.000
 1VM  N12  C3   N2   115.30  3.000
 1VM  N4   C3   N2   126.86  3.000
 1VM  H4   N12  H3   117.30  3.000
 1VM  H4   N12  C3   119.08  3.000
 1VM  H3   N12  C3   118.82  3.000
 1VM  H5   C7   C8   118.19  3.000
 1VM  H5   C7   C6   121.07  3.000
 1VM  C8   C7   C6   120.74  3.000
 1VM  H6   C8   C9   120.23  3.000
 1VM  H6   C8   C7   121.03  3.000
 1VM  C9   C8   C7   118.74  3.000
 1VM  N13  C9   C10  119.14  3.000
 1VM  C10  C9   C8   121.91  3.000
 1VM  N13  C9   C8   118.94  3.000
 1VM  H7   C10  C9   120.81  3.000
 1VM  H7   C10  C5   119.15  3.000
 1VM  C9   C10  C5   120.04  3.000
 1VM  C17  N13  C14  106.49  3.000
 1VM  C14  N13  C9   125.03  3.000
 1VM  C17  N13  C9   128.46  3.000
 1VM  C15  C14  C18  122.59  3.000
 1VM  C18  C14  N13  132.28  3.000
 1VM  C15  C14  N13  105.14  3.000
 1VM  H8   C18  C19  120.73  3.000
 1VM  H8   C18  C14  121.59  3.000
 1VM  C19  C18  C14  117.67  3.000
 1VM  C20  C19  C22  119.68  3.000
 1VM  C22  C19  C18  119.62  3.000
 1VM  C20  C19  C18  120.69  3.000
 1VM  H11  C22  H10  107.74  3.000
 1VM  H11  C22  H9   107.66  3.000
 1VM  H10  C22  H9   106.63  3.000
 1VM  H11  C22  C19  111.35  3.000
 1VM  H10  C22  C19  111.71  3.000
 1VM  H9   C22  C19  111.52  3.000
 1VM  C21  C20  C23  119.93  3.000
 1VM  C23  C20  C19  119.56  3.000
 1VM  C21  C20  C19  120.50  3.000
 1VM  H14  C23  H13  107.74  3.000
 1VM  H14  C23  H12  106.60  3.000
 1VM  H13  C23  H12  107.68  3.000
 1VM  H14  C23  C20  111.88  3.000
 1VM  H13  C23  C20  111.22  3.000
 1VM  H12  C23  C20  111.49  3.000
 1VM  H15  C21  C15  120.19  3.000
 1VM  H15  C21  C20  120.65  3.000
 1VM  C15  C21  C20  119.16  3.000
 1VM  N16  C15  C21  130.40  3.000
 1VM  C21  C15  C14  119.38  3.000
 1VM  N16  C15  C14  110.22  3.000
 1VM  C17  N16  C15  105.43  3.000
 1VM  C24  C17  N16  122.93  3.000
 1VM  N16  C17  N13  112.71  3.000
 1VM  C24  C17  N13  124.35  3.000
 1VM  S28  C24  N25  113.91  3.000
 1VM  N25  C24  C17  121.38  3.000
 1VM  S28  C24  C17  124.70  3.000
 1VM  C26  N25  C24  111.38  3.000
 1VM  H16  C26  C27  124.70  3.000
 1VM  H16  C26  N25  119.76  3.000
 1VM  C27  C26  N25  115.54  3.000
 1VM  H17  C27  S28  121.53  3.000
 1VM  H17  C27  C26  128.62  3.000
 1VM  S28  C27  C26  109.85  3.000
 1VM  C27  S28  C24   89.33  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
 1VM  CONST_01  C10  C5   C6   C1   180.00   0.0  0
 1VM  CONST_02  N4   C5   C6   C1     0.00   0.0  0
 1VM  CONST_03  C8   C7   C6   C1   180.00   0.0  0
 1VM  CONST_04  N4   C3   N2   C1     0.00   0.0  0
 1VM  CONST_05  C5   N4   C3   N2     0.00   0.0  0
 1VM  CONST_06  C5   C6   C1   N2     0.00   0.0  0
 1VM  CONST_07  C7   C6   C1   N2   180.00   0.0  0
 1VM  CONST_08  C9   C10  C5   C6     0.00   0.0  0
 1VM  CONST_09  C3   N4   C5   C6     0.00   0.0  0
 1VM  CONST_10  C9   C8   C7   C6     0.00   0.0  0
 1VM  CONST_11  C3   N2   C1   C6     0.00   0.0  0
 1VM  CONST_12  N13  C9   C10  C5   180.00   0.0  0
 1VM  CONST_13  C8   C9   C10  C5     0.00   0.0  0
 1VM  CONST_14  C8   C7   C6   C5     0.00   0.0  0
 1VM  CONST_15  C9   C10  C5   N4   180.00   0.0  0
 1VM  CONST_16  C7   C6   C5   N4   180.00   0.0  0
 1VM  CONST_17  C10  C5   N4   C3   180.00   0.0  0
 1VM  CONST_18  N13  C9   C8   C7   180.00   0.0  0
 1VM  CONST_19  C10  C9   C8   C7     0.00   0.0  0
 1VM  CONST_20  C10  C5   C6   C7     0.00   0.0  0
 1VM  CONST_23  C24  C17  N13  C9     0.00   0.0  0
 1VM  CONST_24  N16  C17  N13  C9   180.00   0.0  0
 1VM  CONST_25  C15  C14  N13  C9   180.00   0.0  0
 1VM  CONST_26  C18  C14  N13  C9     0.00   0.0  0
 1VM  CONST_29  S28  C24  C17  N13    0.00   0.0  0
 1VM  CONST_30  N25  C24  C17  N13  180.00   0.0  0
 1VM  CONST_31  C15  N16  C17  N13    0.00   0.0  0
 1VM  CONST_32  N16  C15  C14  N13    0.00   0.0  0
 1VM  CONST_33  C21  C15  C14  N13  180.00   0.0  0
 1VM  CONST_34  C19  C18  C14  N13  180.00   0.0  0
 1VM  CONST_35  C17  N16  C15  C14    0.00   0.0  0
 1VM  CONST_36  C20  C21  C15  C14    0.00   0.0  0
 1VM  CONST_37  C24  C17  N13  C14  180.00   0.0  0
 1VM  CONST_38  N16  C17  N13  C14    0.00   0.0  0
 1VM  CONST_39  C20  C19  C18  C14    0.00   0.0  0
 1VM  CONST_40  N16  C15  C14  C18  180.00   0.0  0
 1VM  CONST_41  C21  C15  C14  C18    0.00   0.0  0
 1VM  CONST_42  C17  N13  C14  C18  180.00   0.0  0
 1VM  CONST_43  C21  C20  C19  C18    0.00   0.0  0
 1VM  CONST_44  C15  C21  C20  C19    0.00   0.0  0
 1VM  CONST_45  C15  C14  C18  C19    0.00   0.0  0
 1VM  CONST_46  N16  C15  C21  C20  180.00   0.0  0
 1VM  CONST_47  C17  N16  C15  C21  180.00   0.0  0
 1VM  CONST_48  C24  C17  N16  C15  180.00   0.0  0
 1VM  CONST_49  C17  N13  C14  C15    0.00   0.0  0
 1VM  CONST_50  S28  C24  C17  N16  180.00   0.0  0
 1VM  CONST_51  N25  C24  C17  N16    0.00   0.0  0
 1VM  CONST_52  C27  S28  C24  C17  180.00   0.0  0
 1VM  CONST_53  C26  N25  C24  C17  180.00   0.0  0
 1VM  CONST_54  C26  C27  S28  C24    0.00   0.0  0
 1VM  CONST_55  C27  C26  N25  C24    0.00   0.0  0
 1VM  CONST_56  S28  C27  C26  N25    0.00   0.0  0
 1VM  CONST_57  C27  S28  C24  N25    0.00   0.0  0
 1VM  CONST_58  S28  C24  N25  C26    0.00   0.0  0
 1VM  CONST_59  C5   C6   C1   N11  180.00   0.0  0
 1VM  CONST_60  C7   C6   C1   N11    0.00   0.0  0
 1VM  CONST_61  C3   N2   C1   N11  180.00   0.0  0
 1VM  CONST_62  N12  C3   N2   C1   180.00   0.0  0
 1VM  CONST_63  N12  C3   N4   C5   180.00   0.0  0
 1VM  CONST_64  C22  C19  C18  C14  180.00   0.0  0
 1VM  CONST_65  C23  C20  C19  C18  180.00   0.0  0
 1VM  CONST_66  C21  C20  C19  C22  180.00   0.0  0
 1VM  CONST_67  C15  C21  C20  C23  180.00   0.0  0
 1VM  CONST_68  H5   C7   C6   C1     0.00   0.0  0
 1VM  CONST_69  H7   C10  C5   C6   180.00   0.0  0
 1VM  CONST_70  H6   C8   C7   C6   180.00   0.0  0
 1VM  CONST_71  H8   C18  C14  N13    0.00   0.0  0
 1VM  CONST_72  H15  C21  C15  C14  180.00   0.0  0
 1VM  CONST_73  H17  C27  S28  C24  180.00   0.0  0
 1VM  CONST_74  H16  C26  N25  C24  180.00   0.0  0
 1VM  CONST_75  H3   N12  C3   N2   180.00   0.0  0
 1VM  CONST_76  H4   N12  C3   N2     0.00   0.0  0
 1VM  CONST_77  H1   N11  C1   N2     0.00   0.0  0
 1VM  CONST_78  H2   N11  C1   N2   180.00   0.0  0
 1VM  Var_01    H9   C22  C19  C18  117.70  30.0  2
 1VM  Var_02    H12  C23  C20  C19   63.18  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
 1VM  plan-1  C17  0.020
 1VM  plan-1  C24  0.020
 1VM  plan-1  N25  0.020
 1VM  plan-1  C26  0.020
 1VM  plan-1  C27  0.020
 1VM  plan-1  S28  0.020
 1VM  plan-1  H16  0.020
 1VM  plan-1  H17  0.020
 1VM  plan-2  C9   0.020
 1VM  plan-2  N13  0.020
 1VM  plan-2  C14  0.020
 1VM  plan-2  C18  0.020
 1VM  plan-2  C19  0.020
 1VM  plan-2  C22  0.020
 1VM  plan-2  C20  0.020
 1VM  plan-2  C23  0.020
 1VM  plan-2  C21  0.020
 1VM  plan-2  C15  0.020
 1VM  plan-2  N16  0.020
 1VM  plan-2  C17  0.020
 1VM  plan-2  C24  0.020
 1VM  plan-2  H8   0.020
 1VM  plan-2  H15  0.020
 1VM  plan-3  N11  0.020
 1VM  plan-3  C1   0.020
 1VM  plan-3  N2   0.020
 1VM  plan-3  C6   0.020
 1VM  plan-3  C5   0.020
 1VM  plan-3  N4   0.020
 1VM  plan-3  C3   0.020
 1VM  plan-3  N12  0.020
 1VM  plan-3  C7   0.020
 1VM  plan-3  C8   0.020
 1VM  plan-3  C9   0.020
 1VM  plan-3  C10  0.020
 1VM  plan-3  N13  0.020
 1VM  plan-3  H5   0.020
 1VM  plan-3  H6   0.020
 1VM  plan-3  H7   0.020
 1VM  plan-4  N11  0.020
 1VM  plan-4  C1   0.020
 1VM  plan-4  H1   0.020
 1VM  plan-4  H2   0.020
 1VM  plan-5  C3   0.020
 1VM  plan-5  N12  0.020
 1VM  plan-5  H3   0.020
 1VM  plan-5  H4   0.020

