# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:14:25 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 7-[5,6-dimethyl-2-(1,3-thiazol-4-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)c5cscn5
#
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
 1VO  1VO  7-[5,6-dimethyl-2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]quinazoline-2,4-diamine  ligand  45  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1VO
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
 1VO  N12  N  NH2   0  -0.823   5.3771  -0.8679  -2.2184
 1VO  C3   C  CR6   0   0.522   4.4232  -1.1106  -1.2962
 1VO  N2   N  N     0  -0.509   4.8046  -1.8970  -0.2686
 1VO  N4   N  N     0  -0.535   3.2439  -0.5479  -1.4683
 1VO  C5   C  CR66  0   0.279   2.3314  -0.7741  -0.4994
 1VO  C10  C  CR16  0  -0.350   1.0476  -0.2054  -0.6258
 1VO  C9   C  CR6   0   0.319   0.1091  -0.3968   0.3545
 1VO  C8   C  CR16  0  -0.296   0.3793  -1.1813   1.4860
 1VO  C7   C  CR16  0  -0.299   1.6152  -1.7644   1.6113
 1VO  C6   C  CR66  0  -0.046   2.6027  -1.5700   0.6346
 1VO  C1   C  CR6   0   0.491   3.9291  -2.1366   0.6831
 1VO  N11  N  NH2   0  -0.824   4.3091  -2.9187   1.6950
 1VO  N13  N  NR5   0  -0.656  -1.1743   0.1835   0.2189
 1VO  C17  C  CR5   0   0.441  -1.4913   1.5047   0.0299
 1VO  C22  C  CR5   0   0.237  -0.5179   2.5838   0.1324
 1VO  N26  N  N     0  -0.353   0.5464   2.4921   0.9841
 1VO  C25  C  CR15  0  -0.229   1.2606   3.5661   0.9428
 1VO  S24  S  S2    0   0.247   0.6890   4.7742  -0.1406
 1VO  C23  C  CR15  0  -0.527  -0.6093   3.7532  -0.5635
 1VO  N16  N  N     0  -0.469  -2.7576   1.6932  -0.2176
 1VO  C15  C  CR56  0   0.145  -3.3231   0.4432  -0.2007
 1VO  C21  C  CR16  0  -0.394  -4.6449   0.0499  -0.4077
 1VO  C20  C  CR6   0   0.061  -4.9682  -1.2944  -0.3408
 1VO  C28  C  CH3   0  -0.735  -6.3866  -1.7355  -0.5641
 1VO  C19  C  CR6   0   0.057  -3.9658  -2.2611  -0.0667
 1VO  C27  C  CH3   0  -0.736  -4.3312  -3.7156   0.0022
 1VO  C18  C  CR16  0  -0.354  -2.6501  -1.8762   0.1407
 1VO  C14  C  CR56  0   0.332  -2.3512  -0.5211   0.0768
 1VO  H1   H  HNH2  0   0.392   6.2066  -1.4348  -2.2200
 1VO  H2   H  HNH2  0   0.392   5.1116  -0.4393  -3.0878
 1VO  H3   H  HCR6  0   0.266   0.8234   0.3887  -1.5026
 1VO  H4   H  HCR6  0   0.277  -0.3733  -1.3119   2.2515
 1VO  H5   H  HCR6  0   0.257   1.8098  -2.3672   2.4888
 1VO  H6   H  HNH2  0   0.405   5.2322  -3.3184   1.6922
 1VO  H7   H  HNH2  0   0.418   3.6966  -3.1766   2.4465
 1VO  H8   H  HCR5  0   0.305   2.1510   3.7243   1.5348
 1VO  H9   H  HCR5  0   0.312  -1.3552   4.0411  -1.2869
 1VO  H10  H  HCR6  0   0.248  -5.4077   0.7901  -0.6191
 1VO  H11  H  HCH3  0   0.241  -6.4671  -2.4194  -1.4123
 1VO  H12  H  HCH3  0   0.241  -6.7885  -2.2632   0.3031
 1VO  H13  H  HCH3  0   0.251  -7.0364  -0.8846  -0.7633
 1VO  H14  H  HCH3  0   0.243  -4.7669  -4.0662  -0.9354
 1VO  H15  H  HCH3  0   0.252  -3.4592  -4.3330   0.2128
 1VO  H16  H  HCH3  0   0.243  -5.0710  -3.9083   0.7825
 1VO  H17  H  HCR6  0   0.262  -1.8880  -2.6189   0.3413

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
 1VO  S24  C23  aromatic  1.705  0.020  1.705
 1VO  S24  C25  aromatic  1.720  0.020  1.720
 1VO  C23  C22  aromatic  1.364  0.020  1.364
 1VO  C25  N26  aromatic  1.290  0.020  1.290
 1VO  C22  N26  aromatic  1.366  0.020  1.366
 1VO  C22  C17  single    1.457  0.020  1.457
 1VO  N16  C17  aromatic  1.304  0.020  1.304
 1VO  N16  C15  aromatic  1.372  0.020  1.372
 1VO  C17  N13  aromatic  1.372  0.020  1.372
 1VO  C15  C21  aromatic  1.394  0.020  1.394
 1VO  C15  C14  aromatic  1.397  0.020  1.397
 1VO  C21  C20  aromatic  1.384  0.020  1.384
 1VO  N13  C14  aromatic  1.379  0.020  1.379
 1VO  N13  C9   single    1.415  0.020  1.415
 1VO  C14  C18  aromatic  1.389  0.020  1.389
 1VO  C10  C9   aromatic  1.371  0.020  1.371
 1VO  C10  C5   aromatic  1.410  0.020  1.410
 1VO  C9   C8   aromatic  1.403  0.020  1.403
 1VO  C20  C28  single    1.502  0.020  1.502
 1VO  C20  C19  aromatic  1.419  0.020  1.419
 1VO  N4   C5   aromatic  1.350  0.020  1.350
 1VO  N4   C3   aromatic  1.318  0.020  1.318
 1VO  C5   C6   aromatic  1.412  0.020  1.412
 1VO  C8   C7   aromatic  1.372  0.020  1.372
 1VO  C18  C19  aromatic  1.386  0.020  1.386
 1VO  N12  C3   single    1.349  0.020  1.349
 1VO  C3   N2   aromatic  1.349  0.020  1.349
 1VO  C19  C27  single    1.501  0.020  1.501
 1VO  C6   C7   aromatic  1.402  0.020  1.402
 1VO  C6   C1   aromatic  1.443  0.020  1.443
 1VO  N2   C1   aromatic  1.315  0.020  1.315
 1VO  C1   N11  single    1.334  0.020  1.334
 1VO  N12  H1   single    0.890  0.020  1.040
 1VO  N12  H2   single    0.890  0.020  1.040
 1VO  C10  H3   single    0.930  0.020  1.080
 1VO  C8   H4   single    0.930  0.020  1.080
 1VO  C7   H5   single    0.930  0.020  1.080
 1VO  N11  H6   single    0.860  0.020  1.020
 1VO  N11  H7   single    0.860  0.020  1.020
 1VO  C25  H8   single    0.930  0.020  1.080
 1VO  C23  H9   single    0.930  0.020  1.080
 1VO  C21  H10  single    0.930  0.020  1.080
 1VO  C28  H11  single    0.970  0.020  1.090
 1VO  C28  H12  single    0.970  0.020  1.090
 1VO  C28  H13  single    0.970  0.020  1.090
 1VO  C27  H14  single    0.970  0.020  1.090
 1VO  C27  H15  single    0.970  0.020  1.090
 1VO  C27  H16  single    0.970  0.020  1.090
 1VO  C18  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
 1VO  H2   N12  H1   117.22  3.000
 1VO  H2   N12  C3   118.77  3.000
 1VO  H1   N12  C3   118.91  3.000
 1VO  N4   C3   N2   126.96  3.000
 1VO  N2   C3   N12  115.20  3.000
 1VO  N4   C3   N12  117.82  3.000
 1VO  C1   N2   C3   117.99  3.000
 1VO  C5   N4   C3   116.07  3.000
 1VO  C6   C5   C10  118.32  3.000
 1VO  C6   C5   N4   122.76  3.000
 1VO  C10  C5   N4   118.92  3.000
 1VO  H3   C10  C9   120.94  3.000
 1VO  H3   C10  C5   118.85  3.000
 1VO  C9   C10  C5   120.21  3.000
 1VO  N13  C9   C8   118.77  3.000
 1VO  C8   C9   C10  121.53  3.000
 1VO  N13  C9   C10  119.69  3.000
 1VO  H4   C8   C7   120.72  3.000
 1VO  H4   C8   C9   120.29  3.000
 1VO  C7   C8   C9   118.99  3.000
 1VO  H5   C7   C6   121.02  3.000
 1VO  H5   C7   C8   118.21  3.000
 1VO  C6   C7   C8   120.77  3.000
 1VO  C1   C6   C7   124.70  3.000
 1VO  C1   C6   C5   115.14  3.000
 1VO  C7   C6   C5   120.15  3.000
 1VO  N11  C1   C6   121.16  3.000
 1VO  N11  C1   N2   117.78  3.000
 1VO  C6   C1   N2   121.06  3.000
 1VO  H7   N11  H6   117.39  3.000
 1VO  H7   N11  C1   123.02  3.000
 1VO  H6   N11  C1   119.49  3.000
 1VO  C14  N13  C17  106.30  3.000
 1VO  C14  N13  C9   125.06  3.000
 1VO  C17  N13  C9   128.15  3.000
 1VO  N16  C17  C22  123.72  3.000
 1VO  N16  C17  N13  112.94  3.000
 1VO  C22  C17  N13  123.32  3.000
 1VO  C23  C22  N26  115.33  3.000
 1VO  N26  C22  C17  120.98  3.000
 1VO  C23  C22  C17  123.67  3.000
 1VO  C25  N26  C22  110.81  3.000
 1VO  H8   C25  S24  121.05  3.000
 1VO  H8   C25  N26  124.07  3.000
 1VO  S24  C25  N26  114.88  3.000
 1VO  C23  S24  C25   89.35  3.000
 1VO  H9   C23  S24  122.23  3.000
 1VO  H9   C23  C22  128.14  3.000
 1VO  S24  C23  C22  109.63  3.000
 1VO  C15  N16  C17  105.44  3.000
 1VO  C14  C15  C21  119.62  3.000
 1VO  C14  C15  N16  110.15  3.000
 1VO  C21  C15  N16  130.23  3.000
 1VO  H10  C21  C20  120.55  3.000
 1VO  H10  C21  C15  120.23  3.000
 1VO  C20  C21  C15  119.22  3.000
 1VO  C19  C20  C28  119.71  3.000
 1VO  C19  C20  C21  120.38  3.000
 1VO  C28  C20  C21  119.91  3.000
 1VO  H13  C28  H12  107.65  3.000
 1VO  H13  C28  H11  107.64  3.000
 1VO  H12  C28  H11  106.68  3.000
 1VO  H13  C28  C20  111.17  3.000
 1VO  H12  C28  C20  111.81  3.000
 1VO  H11  C28  C20  111.65  3.000
 1VO  C18  C19  C27  119.54  3.000
 1VO  C27  C19  C20  119.79  3.000
 1VO  C18  C19  C20  120.67  3.000
 1VO  H16  C27  H15  107.71  3.000
 1VO  H16  C27  H14  106.65  3.000
 1VO  H15  C27  H14  107.68  3.000
 1VO  H16  C27  C19  111.63  3.000
 1VO  H15  C27  C19  111.30  3.000
 1VO  H14  C27  C19  111.64  3.000
 1VO  H17  C18  C14  121.74  3.000
 1VO  H17  C18  C19  120.34  3.000
 1VO  C14  C18  C19  117.91  3.000
 1VO  C18  C14  C15  122.19  3.000
 1VO  C18  C14  N13  132.63  3.000
 1VO  C15  C14  N13  105.17  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
 1VO  CONST_01  C10  C5   N4   C3   180.00   0.0  0
 1VO  CONST_02  C6   C5   N4   C3     0.00   0.0  0
 1VO  CONST_03  C6   C1   N2   C3     0.00   0.0  0
 1VO  CONST_04  C5   N4   C3   N2     0.00   0.0  0
 1VO  CONST_05  C5   C6   C1   N2     0.00   0.0  0
 1VO  CONST_06  C7   C6   C1   N2   180.00   0.0  0
 1VO  CONST_07  C9   C10  C5   N4   180.00   0.0  0
 1VO  CONST_08  C7   C6   C5   N4   180.00   0.0  0
 1VO  CONST_09  C1   C6   C5   N4     0.00   0.0  0
 1VO  CONST_10  C1   N2   C3   N4     0.00   0.0  0
 1VO  CONST_11  N13  C9   C10  C5   180.00   0.0  0
 1VO  CONST_12  C8   C9   C10  C5     0.00   0.0  0
 1VO  CONST_13  C8   C7   C6   C5     0.00   0.0  0
 1VO  CONST_16  C7   C8   C9   C10    0.00   0.0  0
 1VO  CONST_17  C7   C6   C5   C10    0.00   0.0  0
 1VO  CONST_18  C1   C6   C5   C10  180.00   0.0  0
 1VO  CONST_19  C22  C17  N13  C9     0.00   0.0  0
 1VO  CONST_20  N16  C17  N13  C9   180.00   0.0  0
 1VO  CONST_21  C15  C14  N13  C9   180.00   0.0  0
 1VO  CONST_22  C18  C14  N13  C9     0.00   0.0  0
 1VO  CONST_23  C6   C5   C10  C9     0.00   0.0  0
 1VO  CONST_24  C6   C7   C8   C9     0.00   0.0  0
 1VO  CONST_27  C1   C6   C7   C8   180.00   0.0  0
 1VO  CONST_28  N13  C9   C8   C7   180.00   0.0  0
 1VO  CONST_31  C15  N16  C17  N13    0.00   0.0  0
 1VO  CONST_32  N16  C15  C14  N13    0.00   0.0  0
 1VO  CONST_33  C21  C15  C14  N13  180.00   0.0  0
 1VO  CONST_34  C19  C18  C14  N13  180.00   0.0  0
 1VO  CONST_35  S24  C23  C22  C17  180.00   0.0  0
 1VO  CONST_36  C25  N26  C22  C17  180.00   0.0  0
 1VO  CONST_37  C21  C15  N16  C17  180.00   0.0  0
 1VO  CONST_38  C14  C15  N16  C17    0.00   0.0  0
 1VO  CONST_39  C15  C14  N13  C17    0.00   0.0  0
 1VO  CONST_40  C18  C14  N13  C17  180.00   0.0  0
 1VO  CONST_41  C25  S24  C23  C22    0.00   0.0  0
 1VO  CONST_42  S24  C25  N26  C22    0.00   0.0  0
 1VO  CONST_43  C15  N16  C17  C22  180.00   0.0  0
 1VO  CONST_44  C14  N13  C17  C22  180.00   0.0  0
 1VO  CONST_45  C23  S24  C25  N26    0.00   0.0  0
 1VO  CONST_46  S24  C23  C22  N26    0.00   0.0  0
 1VO  CONST_48  C23  C22  N26  C25    0.00   0.0  0
 1VO  CONST_50  C14  N13  C17  N16    0.00   0.0  0
 1VO  CONST_51  C20  C21  C15  N16  180.00   0.0  0
 1VO  CONST_52  C18  C14  C15  N16  180.00   0.0  0
 1VO  CONST_53  C19  C20  C21  C15    0.00   0.0  0
 1VO  CONST_54  C19  C18  C14  C15    0.00   0.0  0
 1VO  CONST_55  C18  C14  C15  C21    0.00   0.0  0
 1VO  CONST_56  C18  C19  C20  C21    0.00   0.0  0
 1VO  CONST_57  C14  C15  C21  C20    0.00   0.0  0
 1VO  CONST_58  C14  C18  C19  C20    0.00   0.0  0
 1VO  CONST_59  C5   N4   C3   N12  180.00   0.0  0
 1VO  CONST_60  C1   N2   C3   N12  180.00   0.0  0
 1VO  CONST_61  N11  C1   N2   C3   180.00   0.0  0
 1VO  CONST_62  N11  C1   C6   C5   180.00   0.0  0
 1VO  CONST_63  N11  C1   C6   C7     0.00   0.0  0
 1VO  CONST_64  C28  C20  C21  C15  180.00   0.0  0
 1VO  CONST_65  C27  C19  C20  C21  180.00   0.0  0
 1VO  CONST_66  C18  C19  C20  C28  180.00   0.0  0
 1VO  CONST_67  C14  C18  C19  C27  180.00   0.0  0
 1VO  CONST_68  H3   C10  C5   N4     0.00   0.0  0
 1VO  CONST_69  H5   C7   C6   C5   180.00   0.0  0
 1VO  CONST_70  H4   C8   C9   C10  180.00   0.0  0
 1VO  CONST_71  H17  C18  C14  N13    0.00   0.0  0
 1VO  CONST_72  H9   C23  C22  C17    0.00   0.0  0
 1VO  CONST_73  H8   C25  N26  C22  180.00   0.0  0
 1VO  CONST_74  H10  C21  C15  N16    0.00   0.0  0
 1VO  CONST_75  H1   N12  C3   N2     0.00   0.0  0
 1VO  CONST_76  H2   N12  C3   N2   180.00   0.0  0
 1VO  CONST_77  H6   N11  C1   N2     0.00   0.0  0
 1VO  CONST_78  H7   N11  C1   N2   180.00   0.0  0
 1VO  Var_01    H11  C28  C20  C21  120.06  30.0  2
 1VO  Var_02    H14  C27  C19  C20   59.27  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
 1VO  plan-1  C17  0.020
 1VO  plan-1  C22  0.020
 1VO  plan-1  N26  0.020
 1VO  plan-1  C25  0.020
 1VO  plan-1  S24  0.020
 1VO  plan-1  C23  0.020
 1VO  plan-1  H8   0.020
 1VO  plan-1  H9   0.020
 1VO  plan-2  C9   0.020
 1VO  plan-2  N13  0.020
 1VO  plan-2  C17  0.020
 1VO  plan-2  C22  0.020
 1VO  plan-2  N16  0.020
 1VO  plan-2  C15  0.020
 1VO  plan-2  C21  0.020
 1VO  plan-2  C20  0.020
 1VO  plan-2  C28  0.020
 1VO  plan-2  C19  0.020
 1VO  plan-2  C27  0.020
 1VO  plan-2  C18  0.020
 1VO  plan-2  C14  0.020
 1VO  plan-2  H10  0.020
 1VO  plan-2  H17  0.020
 1VO  plan-3  N12  0.020
 1VO  plan-3  C3   0.020
 1VO  plan-3  N2   0.020
 1VO  plan-3  N4   0.020
 1VO  plan-3  C5   0.020
 1VO  plan-3  C10  0.020
 1VO  plan-3  C9   0.020
 1VO  plan-3  C8   0.020
 1VO  plan-3  C7   0.020
 1VO  plan-3  C6   0.020
 1VO  plan-3  C1   0.020
 1VO  plan-3  N11  0.020
 1VO  plan-3  N13  0.020
 1VO  plan-3  H3   0.020
 1VO  plan-3  H4   0.020
 1VO  plan-3  H5   0.020
 1VO  plan-4  N12  0.020
 1VO  plan-4  C3   0.020
 1VO  plan-4  H1   0.020
 1VO  plan-4  H2   0.020
 1VO  plan-5  C1   0.020
 1VO  plan-5  N11  0.020
 1VO  plan-5  H6   0.020
 1VO  plan-5  H7   0.020

