# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:35:59 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 6-chloro-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(c3cc4nc(N)nc(N)c4cc3Cl)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
 1VN  1VN  6-chloro-7-[5,6-dimethyl-2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]quinazoline-2,4-diamine  ligand  45  29  .  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_1VN
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
 1VN  CL1  CL  CL    0  -0.094  -0.3646   0.4414   2.6600
 1VN  C8   C   CR6   0  -0.060   0.6568  -0.1351   1.3968
 1VN  C7   C   CR16  0  -0.263   1.9375  -0.5455   1.6606
 1VN  C6   C   CR66  0  -0.040   2.7596  -0.9917   0.6182
 1VN  C1   C   CR6   0   0.501   4.1233  -1.4395   0.7943
 1VN  N11  N   NH2   0  -0.822   4.6936  -1.4598   1.9984
 1VN  C9   C   CR6   0   0.262   0.1746  -0.1518   0.0742
 1VN  C10  C   CR16  0  -0.332   0.9652  -0.5932  -0.9528
 1VN  C5   C   CR66  0   0.282   2.2880  -1.0229  -0.7110
 1VN  N4   N   N     0  -0.530   3.0405  -1.4313  -1.7491
 1VN  C3   C   CR6   0   0.533   4.2719  -1.8077  -1.4574
 1VN  N12  N   NH2   0  -0.820   5.0509  -2.2448  -2.4623
 1VN  N2   N   N     0  -0.504   4.8411  -1.8289  -0.2342
 1VN  N14  N   NR5   0  -0.653  -1.1408   0.2819  -0.1949
 1VN  C18  C   CR5   0   0.475  -1.5947   1.5652  -0.3740
 1VN  C25  C   CR5   0  -0.055  -0.7424   2.7439  -0.3715
 1VN  N29  N   N     0  -0.371  -1.2414   3.9409  -0.4679
 1VN  C28  C   CR15  0  -0.016  -0.2682   4.8849  -0.4493
 1VN  C27  C   CR15  0  -0.490   1.0034   4.4143  -0.3365
 1VN  S26  S   S2    0   0.271   0.9848   2.7108  -0.2513
 1VN  N17  N   N     0  -0.449  -2.8854   1.6201  -0.5514
 1VN  C16  C   CR56  0   0.144  -3.3210   0.3244  -0.4782
 1VN  C22  C   CR16  0  -0.388  -4.6068  -0.2049  -0.5974
 1VN  C21  C   CR6   0   0.065  -4.7866  -1.5708  -0.4741
 1VN  C24  C   CH3   0  -0.735  -6.1632  -2.1566  -0.6034
 1VN  C20  C   CR6   0   0.056  -3.6788  -2.4260  -0.2242
 1VN  C23  C   CH3   0  -0.737  -3.8988  -3.9037  -0.0794
 1VN  C19  C   CR16  0  -0.356  -2.3980  -1.9086  -0.1132
 1VN  C15  C   CR56  0   0.348  -2.2449  -0.5355  -0.2473
 1VN  H1   H   HCR6  0   0.279   2.2906  -0.5114   2.6826
 1VN  H2   H   HNH2  0   0.421   4.1952  -1.2556   2.8448
 1VN  H3   H   HNH2  0   0.409   5.6290  -1.8180   2.0931
 1VN  H4   H   HCR6  0   0.284   0.5852  -0.5978  -1.9661
 1VN  H5   H   HNH2  0   0.396   4.7441  -2.1181  -3.4108
 1VN  H6   H   HNH2  0   0.397   6.0354  -2.3673  -2.3036
 1VN  H7   H   HCR5  0   0.279  -0.5325   5.9299  -0.5200
 1VN  H8   H   HCR5  0   0.317   1.9263   4.9707  -0.3001
 1VN  H9   H   HCR6  0   0.251  -5.4515   0.4480  -0.7815
 1VN  H10  H   HCH3  0   0.242  -6.2198  -2.8836  -1.4165
 1VN  H11  H   HCH3  0   0.242  -6.4678  -2.6774   0.3066
 1VN  H12  H   HCH3  0   0.252  -6.9021  -1.3816  -0.8019
 1VN  H13  H   HCH3  0   0.245  -4.2989  -4.3427  -0.9959
 1VN  H14  H   HCH3  0   0.253  -2.9696  -4.4209   0.1554
 1VN  H15  H   HCH3  0   0.244  -4.6148  -4.1279   0.7139
 1VN  H16  H   HCR6  0   0.264  -1.5514  -2.5589   0.0707

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
 1VN  C27  S26  aromatic  1.706  0.020  1.706
 1VN  C27  C28  aromatic  1.361  0.020  1.361
 1VN  S26  C25  aromatic  1.732  0.020  1.732
 1VN  C28  N29  aromatic  1.356  0.020  1.356
 1VN  C25  N29  aromatic  1.300  0.020  1.300
 1VN  C25  C18  single    1.455  0.020  1.455
 1VN  N17  C18  aromatic  1.304  0.020  1.304
 1VN  N17  C16  aromatic  1.369  0.020  1.369
 1VN  C18  N14  aromatic  1.373  0.020  1.373
 1VN  C16  C22  aromatic  1.396  0.020  1.396
 1VN  C16  C15  aromatic  1.397  0.020  1.397
 1VN  C22  C21  aromatic  1.383  0.020  1.383
 1VN  N14  C15  aromatic  1.375  0.020  1.375
 1VN  N14  C9   single    1.411  0.020  1.411
 1VN  C15  C19  aromatic  1.388  0.020  1.388
 1VN  C9   C10  aromatic  1.369  0.020  1.369
 1VN  C9   C8   aromatic  1.408  0.020  1.408
 1VN  C10  C5   aromatic  1.412  0.020  1.412
 1VN  C21  C24  single    1.502  0.020  1.502
 1VN  C21  C20  aromatic  1.422  0.020  1.422
 1VN  C5   N4   aromatic  1.346  0.020  1.346
 1VN  C5   C6   aromatic  1.411  0.020  1.411
 1VN  C8   CL1  single    1.724  0.020  1.724
 1VN  C8   C7   aromatic  1.371  0.020  1.371
 1VN  N4   C3   aromatic  1.320  0.020  1.320
 1VN  C19  C20  aromatic  1.386  0.020  1.386
 1VN  C20  C23  single    1.501  0.020  1.501
 1VN  N12  C3   single    1.345  0.020  1.345
 1VN  C3   N2   aromatic  1.349  0.020  1.349
 1VN  C7   C6   aromatic  1.401  0.020  1.401
 1VN  C6   C1   aromatic  1.446  0.020  1.446
 1VN  N2   C1   aromatic  1.313  0.020  1.313
 1VN  C1   N11  single    1.333  0.020  1.333
 1VN  C7   H1   single    0.930  0.020  1.080
 1VN  N11  H2   single    0.860  0.020  1.020
 1VN  N11  H3   single    0.860  0.020  1.020
 1VN  C10  H4   single    0.930  0.020  1.080
 1VN  N12  H5   single    0.890  0.020  1.040
 1VN  N12  H6   single    0.890  0.020  1.040
 1VN  C28  H7   single    0.930  0.020  1.080
 1VN  C27  H8   single    0.930  0.020  1.080
 1VN  C22  H9   single    0.930  0.020  1.080
 1VN  C24  H10  single    0.970  0.020  1.090
 1VN  C24  H11  single    0.970  0.020  1.090
 1VN  C24  H12  single    0.970  0.020  1.090
 1VN  C23  H13  single    0.970  0.020  1.090
 1VN  C23  H14  single    0.970  0.020  1.090
 1VN  C23  H15  single    0.970  0.020  1.090
 1VN  C19  H16  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
 1VN  C9   C8   C7   119.83  3.000
 1VN  C7   C8   CL1  120.85  3.000
 1VN  C9   C8   CL1  119.31  3.000
 1VN  H1   C7   C6   121.43  3.000
 1VN  H1   C7   C8   118.52  3.000
 1VN  C6   C7   C8   120.04  3.000
 1VN  C5   C6   C1   115.03  3.000
 1VN  C1   C6   C7   124.17  3.000
 1VN  C5   C6   C7   120.80  3.000
 1VN  N2   C1   N11  117.99  3.000
 1VN  N11  C1   C6   121.22  3.000
 1VN  N2   C1   C6   120.79  3.000
 1VN  H3   N11  H2   117.07  3.000
 1VN  H3   N11  C1   119.23  3.000
 1VN  H2   N11  C1   123.14  3.000
 1VN  N14  C9   C10  119.63  3.000
 1VN  C10  C9   C8   120.71  3.000
 1VN  N14  C9   C8   119.66  3.000
 1VN  H4   C10  C5   119.22  3.000
 1VN  H4   C10  C9   120.06  3.000
 1VN  C5   C10  C9   120.72  3.000
 1VN  N4   C5   C10  118.97  3.000
 1VN  N4   C5   C6   123.13  3.000
 1VN  C10  C5   C6   117.90  3.000
 1VN  C3   N4   C5   115.96  3.000
 1VN  N2   C3   N12  115.34  3.000
 1VN  N2   C3   N4   126.74  3.000
 1VN  N12  C3   N4   117.90  3.000
 1VN  H6   N12  H5   117.62  3.000
 1VN  H6   N12  C3   119.29  3.000
 1VN  H5   N12  C3   119.18  3.000
 1VN  C3   N2   C1   118.34  3.000
 1VN  C15  N14  C18  106.58  3.000
 1VN  C15  N14  C9   124.98  3.000
 1VN  C18  N14  C9   128.34  3.000
 1VN  N17  C18  C25  123.10  3.000
 1VN  N17  C18  N14  112.60  3.000
 1VN  C25  C18  N14  124.30  3.000
 1VN  S26  C25  N29  113.92  3.000
 1VN  N29  C25  C18  121.39  3.000
 1VN  S26  C25  C18  124.68  3.000
 1VN  C28  N29  C25  111.37  3.000
 1VN  H7   C28  C27  124.66  3.000
 1VN  H7   C28  N29  119.80  3.000
 1VN  C27  C28  N29  115.54  3.000
 1VN  H8   C27  S26  121.54  3.000
 1VN  H8   C27  C28  128.63  3.000
 1VN  S26  C27  C28  109.84  3.000
 1VN  C27  S26  C25   89.33  3.000
 1VN  C16  N17  C18  105.54  3.000
 1VN  C15  C16  C22  119.37  3.000
 1VN  C15  C16  N17  110.27  3.000
 1VN  C22  C16  N17  130.36  3.000
 1VN  H9   C22  C21  120.60  3.000
 1VN  H9   C22  C16  120.28  3.000
 1VN  C21  C22  C16  119.12  3.000
 1VN  C20  C21  C24  119.66  3.000
 1VN  C20  C21  C22  120.56  3.000
 1VN  C24  C21  C22  119.79  3.000
 1VN  H12  C24  H11  107.58  3.000
 1VN  H12  C24  H10  107.62  3.000
 1VN  H11  C24  H10  106.77  3.000
 1VN  H12  C24  C21  111.10  3.000
 1VN  H11  C24  C21  111.72  3.000
 1VN  H10  C24  C21  111.80  3.000
 1VN  C19  C20  C23  119.69  3.000
 1VN  C23  C20  C21  119.67  3.000
 1VN  C19  C20  C21  120.65  3.000
 1VN  H15  C23  H14  107.78  3.000
 1VN  H15  C23  H13  106.67  3.000
 1VN  H14  C23  H13  107.62  3.000
 1VN  H15  C23  C20  111.61  3.000
 1VN  H14  C23  C20  111.30  3.000
 1VN  H13  C23  C20  111.62  3.000
 1VN  H16  C19  C15  121.60  3.000
 1VN  H16  C19  C20  120.79  3.000
 1VN  C15  C19  C20  117.61  3.000
 1VN  C19  C15  C16  122.69  3.000
 1VN  C19  C15  N14  132.30  3.000
 1VN  C16  C15  N14  105.01  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
 1VN  CONST_03  C5   C10  C9   C8     0.00   0.0  0
 1VN  CONST_04  C5   C6   C7   C8     0.00   0.0  0
 1VN  CONST_05  C1   C6   C7   C8   180.00   0.0  0
 1VN  CONST_06  N14  C9   C8   C7   180.00   0.0  0
 1VN  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 1VN  CONST_08  C10  C5   C6   C7     0.00   0.0  0
 1VN  CONST_09  N4   C5   C6   C7   180.00   0.0  0
 1VN  CONST_10  N2   C1   C6   C7   180.00   0.0  0
 1VN  CONST_11  C9   C10  C5   C6     0.00   0.0  0
 1VN  CONST_12  C3   N4   C5   C6     0.00   0.0  0
 1VN  CONST_13  C9   C8   C7   C6     0.00   0.0  0
 1VN  CONST_14  C3   N2   C1   C6     0.00   0.0  0
 1VN  CONST_15  C10  C5   C6   C1   180.00   0.0  0
 1VN  CONST_16  N4   C5   C6   C1     0.00   0.0  0
 1VN  CONST_17  N4   C3   N2   C1     0.00   0.0  0
 1VN  CONST_18  C25  C18  N14  C9     0.00   0.0  0
 1VN  CONST_19  N17  C18  N14  C9   180.00   0.0  0
 1VN  CONST_20  C16  C15  N14  C9   180.00   0.0  0
 1VN  CONST_21  C19  C15  N14  C9     0.00   0.0  0
 1VN  CONST_22  N4   C5   C10  C9   180.00   0.0  0
 1VN  CONST_25  C3   N4   C5   C10  180.00   0.0  0
 1VN  CONST_26  N14  C9   C10  C5   180.00   0.0  0
 1VN  CONST_27  N2   C3   N4   C5     0.00   0.0  0
 1VN  CONST_28  N2   C1   C6   C5     0.00   0.0  0
 1VN  CONST_29  S26  C25  C18  N14    0.00   0.0  0
 1VN  CONST_30  N29  C25  C18  N14  180.00   0.0  0
 1VN  CONST_31  C16  N17  C18  N14    0.00   0.0  0
 1VN  CONST_32  N17  C16  C15  N14    0.00   0.0  0
 1VN  CONST_33  C22  C16  C15  N14  180.00   0.0  0
 1VN  CONST_34  C20  C19  C15  N14  180.00   0.0  0
 1VN  CONST_35  C27  S26  C25  C18  180.00   0.0  0
 1VN  CONST_36  C28  N29  C25  C18  180.00   0.0  0
 1VN  CONST_37  C22  C16  N17  C18  180.00   0.0  0
 1VN  CONST_38  C15  C16  N17  C18    0.00   0.0  0
 1VN  CONST_39  C16  C15  N14  C18    0.00   0.0  0
 1VN  CONST_40  C19  C15  N14  C18  180.00   0.0  0
 1VN  CONST_41  C28  C27  S26  C25    0.00   0.0  0
 1VN  CONST_42  C27  C28  N29  C25    0.00   0.0  0
 1VN  CONST_43  C16  N17  C18  C25  180.00   0.0  0
 1VN  CONST_44  C15  N14  C18  C25  180.00   0.0  0
 1VN  CONST_45  S26  C27  C28  N29    0.00   0.0  0
 1VN  CONST_46  C27  S26  C25  N29    0.00   0.0  0
 1VN  CONST_47  N17  C18  C25  N29    0.00   0.0  0
 1VN  CONST_48  S26  C25  N29  C28    0.00   0.0  0
 1VN  CONST_49  N17  C18  C25  S26  180.00   0.0  0
 1VN  CONST_50  C15  N14  C18  N17    0.00   0.0  0
 1VN  CONST_51  C21  C22  C16  N17  180.00   0.0  0
 1VN  CONST_52  C19  C15  C16  N17  180.00   0.0  0
 1VN  CONST_53  C20  C21  C22  C16    0.00   0.0  0
 1VN  CONST_54  C20  C19  C15  C16    0.00   0.0  0
 1VN  CONST_55  C19  C15  C16  C22    0.00   0.0  0
 1VN  CONST_56  C19  C20  C21  C22    0.00   0.0  0
 1VN  CONST_57  C15  C16  C22  C21    0.00   0.0  0
 1VN  CONST_58  C15  C19  C20  C21    0.00   0.0  0
 1VN  CONST_59  N14  C9   C8   CL1    0.00   0.0  0
 1VN  CONST_60  C10  C9   C8   CL1  180.00   0.0  0
 1VN  CONST_61  C6   C7   C8   CL1  180.00   0.0  0
 1VN  CONST_62  N11  C1   C6   C7     0.00   0.0  0
 1VN  CONST_63  N12  C3   N2   C1   180.00   0.0  0
 1VN  CONST_64  C5   C6   C1   N11  180.00   0.0  0
 1VN  CONST_65  C3   N2   C1   N11  180.00   0.0  0
 1VN  CONST_66  N12  C3   N4   C5   180.00   0.0  0
 1VN  CONST_67  C24  C21  C22  C16  180.00   0.0  0
 1VN  CONST_68  C23  C20  C21  C22  180.00   0.0  0
 1VN  CONST_69  C19  C20  C21  C24  180.00   0.0  0
 1VN  CONST_70  C15  C19  C20  C23  180.00   0.0  0
 1VN  CONST_71  H4   C10  C9   C8   180.00   0.0  0
 1VN  CONST_72  H1   C7   C6   C1     0.00   0.0  0
 1VN  CONST_73  H16  C19  C15  N14    0.00   0.0  0
 1VN  CONST_74  H8   C27  S26  C25  180.00   0.0  0
 1VN  CONST_75  H7   C28  N29  C25  180.00   0.0  0
 1VN  CONST_76  H9   C22  C16  N17    0.00   0.0  0
 1VN  CONST_77  H2   N11  C1   C6     0.00   0.0  0
 1VN  CONST_78  H3   N11  C1   C6   180.00   0.0  0
 1VN  CONST_79  H5   N12  C3   N4     0.00   0.0  0
 1VN  CONST_80  H6   N12  C3   N4   180.00   0.0  0
 1VN  Var_01    H10  C24  C21  C22  120.85  30.0  2
 1VN  Var_02    H13  C23  C20  C21   62.45  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
 1VN  plan-1  C18  0.020
 1VN  plan-1  C25  0.020
 1VN  plan-1  N29  0.020
 1VN  plan-1  C28  0.020
 1VN  plan-1  C27  0.020
 1VN  plan-1  S26  0.020
 1VN  plan-1  H7   0.020
 1VN  plan-1  H8   0.020
 1VN  plan-2  C9   0.020
 1VN  plan-2  N14  0.020
 1VN  plan-2  C18  0.020
 1VN  plan-2  C25  0.020
 1VN  plan-2  N17  0.020
 1VN  plan-2  C16  0.020
 1VN  plan-2  C22  0.020
 1VN  plan-2  C21  0.020
 1VN  plan-2  C24  0.020
 1VN  plan-2  C20  0.020
 1VN  plan-2  C23  0.020
 1VN  plan-2  C19  0.020
 1VN  plan-2  C15  0.020
 1VN  plan-2  H9   0.020
 1VN  plan-2  H16  0.020
 1VN  plan-3  CL1  0.020
 1VN  plan-3  C8   0.020
 1VN  plan-3  C7   0.020
 1VN  plan-3  C6   0.020
 1VN  plan-3  C1   0.020
 1VN  plan-3  N11  0.020
 1VN  plan-3  C9   0.020
 1VN  plan-3  C10  0.020
 1VN  plan-3  C5   0.020
 1VN  plan-3  N4   0.020
 1VN  plan-3  C3   0.020
 1VN  plan-3  N12  0.020
 1VN  plan-3  N2   0.020
 1VN  plan-3  N14  0.020
 1VN  plan-3  H1   0.020
 1VN  plan-3  H4   0.020
 1VN  plan-4  C1   0.020
 1VN  plan-4  N11  0.020
 1VN  plan-4  H2   0.020
 1VN  plan-4  H3   0.020
 1VN  plan-5  C3   0.020
 1VN  plan-5  N12  0.020
 1VN  plan-5  H5   0.020
 1VN  plan-5  H6   0.020

