# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 12:02:06 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-(4-amino-6-methyl-1,3,5-triazin-2-yl)-N-(1H-pyrazol-3-yl)-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc(n1)n2c(Nc3cc[nH]n3)nc4ccccc24
#
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
 QAR  QAR  1-(4-amino-6-methyl-1,3,5-triazin-2-yl)-N-(1H-pyrazol-3-yl)-1H-benzimidazol-2-amine  ligand  36  23  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QAR
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
 QAR  N1    N  N     0  -0.467   3.1339  -2.4576  -0.0051
 QAR  N3    N  N     0  -0.552   0.9125  -1.7030  -0.0082
 QAR  C4    C  CR56  0   0.319   0.7557   1.9475  -0.0026
 QAR  C5    C  CR56  0   0.173  -0.5005   2.5690   0.0014
 QAR  C6    C  CR5   0   0.732  -0.9323   0.4792  -0.0066
 QAR  C7    C  CR16  0  -0.284   1.9309   2.6825  -0.0000
 QAR  C8    C  CR16  0  -0.281   1.8135   4.0693   0.0066
 QAR  C10   C  CR16  0  -0.343  -0.6028   3.9535   0.0079
 QAR  C13   C  CR15  0  -0.506  -3.9858   0.0097  -0.0049
 QAR  C14   C  CR15  0   0.032  -5.1065  -0.7908  -0.0005
 QAR  N8    N  NR15  0  -0.422  -4.6793  -2.0583  -0.0004
 QAR  N9    N  N     0  -0.329  -3.3518  -2.1618  -0.0045
 QAR  C12   C  CR5   0   0.464  -2.9197  -0.9127  -0.0072
 QAR  N6    N  NH1   0  -0.784  -1.5507  -0.7118  -0.0119
 QAR  N5    N  N     0  -0.528  -1.5143   1.6387  -0.0015
 QAR  C9    C  CR16  0  -0.264   0.5693   4.6966   0.0106
 QAR  N4    N  NR5   0  -0.711   0.4699   0.5723  -0.0083
 QAR  C2    C  CR6   0   0.698   1.3882  -0.4644  -0.0092
 QAR  N2    N  N     0  -0.492   2.6581  -0.1333  -0.0093
 QAR  C3    C  CR6   0   0.413   1.8355  -2.6674  -0.0082
 QAR  C11   C  CH3   0  -0.731   1.3376  -4.0715  -0.0312
 QAR  C1    C  CR6   0   0.593   3.5078  -1.1669  -0.0064
 QAR  N7    N  NH2   0  -0.804   4.8068  -0.8996  -0.0039
 QAR  H7    H  HCR6  0   0.280   2.8994   2.2108  -0.0035
 QAR  H8    H  HCR6  0   0.253   2.7136   4.6696   0.0090
 QAR  H10   H  HCR6  0   0.253  -1.5736   4.4318   0.0109
 QAR  H14   H  HCR5  0   0.290  -6.1546  -0.5417   0.0026
 QAR  HN6   H  HNH1  0   0.431  -0.9382  -1.5266  -0.0130
 QAR  H9    H  HCR6  0   0.253   0.5161   5.7775   0.0157
 QAR  H11   H  HCH3  0   0.271   0.8930  -4.2854  -1.0049
 QAR  H11A  H  HCH3  0   0.258   2.1444  -4.7774   0.1447
 QAR  H11B  H  HCH3  0   0.263   0.5581  -4.2138   0.7164
 QAR  HN7   H  HNH2  0   0.415   5.1355   0.0507  -0.0034
 QAR  HN7A  H  HNH2  0   0.413   5.4806  -1.6454  -0.0002
 QAR  HN8   H  HNR5  0   0.422  -5.2427  -2.8926   0.0026
 QAR  H13   H  HCR5  0   0.274  -3.9385   1.0821  -0.0067

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
 QAR  C1   N1    aromatic  1.344  0.020  1.344
 QAR  C3   N1    aromatic  1.315  0.020  1.315
 QAR  C2   N3    aromatic  1.327  0.020  1.327
 QAR  N3   C3    aromatic  1.335  0.020  1.335
 QAR  C5   C4    aromatic  1.402  0.020  1.402
 QAR  C4   C7    aromatic  1.386  0.020  1.386
 QAR  C4   N4    aromatic  1.405  0.020  1.405
 QAR  C10  C5    aromatic  1.388  0.020  1.388
 QAR  C5   N5    aromatic  1.376  0.020  1.376
 QAR  N5   C6    aromatic  1.297  0.020  1.297
 QAR  C6   N6    single    1.342  0.020  1.342
 QAR  C6   N4    aromatic  1.405  0.020  1.405
 QAR  C8   C7    aromatic  1.392  0.020  1.392
 QAR  C7   H7    single    0.930  0.020  1.080
 QAR  C9   C8    aromatic  1.393  0.020  1.393
 QAR  C8   H8    single    0.930  0.020  1.080
 QAR  C10  C9    aromatic  1.388  0.020  1.388
 QAR  C10  H10   single    0.930  0.020  1.080
 QAR  C12  C13   aromatic  1.410  0.020  1.410
 QAR  C14  C13   aromatic  1.377  0.020  1.377
 QAR  C13  H13   single    0.930  0.020  1.080
 QAR  N8   C14   aromatic  1.338  0.020  1.338
 QAR  C14  H14   single    0.930  0.020  1.080
 QAR  N9   N8    aromatic  1.332  0.020  1.332
 QAR  N9   C12   aromatic  1.322  0.020  1.322
 QAR  C12  N6    single    1.384  0.020  1.384
 QAR  N6   HN6   single    0.860  0.020  1.020
 QAR  C9   H9    single    0.930  0.020  1.080
 QAR  N4   C2    single    1.385  0.020  1.385
 QAR  C2   N2    aromatic  1.312  0.020  1.312
 QAR  N2   C1    aromatic  1.338  0.020  1.338
 QAR  C3   C11   single    1.490  0.020  1.490
 QAR  C11  H11   single    0.970  0.020  1.090
 QAR  C11  H11A  single    0.970  0.020  1.090
 QAR  C11  H11B  single    0.970  0.020  1.090
 QAR  C1   N7    single    1.326  0.020  1.326
 QAR  N7   HN7   single    0.860  0.020  1.020
 QAR  N7   HN7A  single    0.860  0.020  1.020
 QAR  N8   HN8   single    0.860  0.020  1.020

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
 QAR  C1    N1   C3    115.34  3.000
 QAR  C3    N3   C2    115.24  3.000
 QAR  N4    C4   C7    133.76  3.000
 QAR  N4    C4   C5    104.58  3.000
 QAR  C7    C4   C5    121.65  3.000
 QAR  N5    C5   C10   128.32  3.000
 QAR  N5    C5   C4    111.13  3.000
 QAR  C10   C5   C4    120.55  3.000
 QAR  N4    C6   N5    112.85  3.000
 QAR  N4    C6   N6    121.24  3.000
 QAR  N5    C6   N6    125.91  3.000
 QAR  H7    C7   C8    120.81  3.000
 QAR  H7    C7   C4    122.01  3.000
 QAR  C8    C7   C4    117.18  3.000
 QAR  H8    C8   C9    119.54  3.000
 QAR  H8    C8   C7    118.86  3.000
 QAR  C9    C8   C7    121.60  3.000
 QAR  H10   C10  C9    121.40  3.000
 QAR  H10   C10  C5    120.45  3.000
 QAR  C9    C10  C5    118.15  3.000
 QAR  H13   C13  C12   128.34  3.000
 QAR  H13   C13  C14   128.06  3.000
 QAR  C12   C13  C14   103.59  3.000
 QAR  H14   C14  N8    122.00  3.000
 QAR  H14   C14  C13   131.09  3.000
 QAR  N8    C14  C13   106.91  3.000
 QAR  HN8   N8   N9    119.58  3.000
 QAR  HN8   N8   C14   127.34  3.000
 QAR  N9    N8   C14   113.08  3.000
 QAR  C12   N9   N8    104.62  3.000
 QAR  N6    C12  N9    117.43  3.000
 QAR  N6    C12  C13   130.78  3.000
 QAR  N9    C12  C13   111.79  3.000
 QAR  HN6   N6   C12   118.58  3.000
 QAR  HN6   N6   C6    115.63  3.000
 QAR  C12   N6   C6    125.79  3.000
 QAR  C6    N5   C5    105.89  3.000
 QAR  H9    C9   C10   119.56  3.000
 QAR  H9    C9   C8    119.58  3.000
 QAR  C10   C9   C8    120.87  3.000
 QAR  C2    N4   C6    127.74  3.000
 QAR  C2    N4   C4    126.72  3.000
 QAR  C6    N4   C4    105.54  3.000
 QAR  N2    C2   N4    116.92  3.000
 QAR  N2    C2   N3    125.62  3.000
 QAR  N4    C2   N3    117.45  3.000
 QAR  C1    N2   C2    114.81  3.000
 QAR  C11   C3   N3    116.72  3.000
 QAR  C11   C3   N1    118.71  3.000
 QAR  N3    C3   N1    124.57  3.000
 QAR  H11B  C11  H11A  109.59  3.000
 QAR  H11B  C11  H11   107.17  3.000
 QAR  H11A  C11  H11   108.64  3.000
 QAR  H11B  C11  C3    110.59  3.000
 QAR  H11A  C11  C3    111.20  3.000
 QAR  H11   C11  C3    109.55  3.000
 QAR  N7    C1   N2    117.80  3.000
 QAR  N7    C1   N1    117.78  3.000
 QAR  N2    C1   N1    124.42  3.000
 QAR  HN7A  N7   HN7   118.82  3.000
 QAR  HN7A  N7   C1    120.47  3.000
 QAR  HN7   N7   C1    120.71  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
 QAR  CONST_01  C2    N2   C1   N1      0.00   0.0  0
 QAR  CONST_02  C2    N3   C3   N1      0.00   0.0  0
 QAR  CONST_03  C4    N4   C2   N3    180.00   0.0  0
 QAR  CONST_04  C6    N4   C2   N3      0.00   0.0  0
 QAR  CONST_05  C1    N2   C2   N3      0.00   0.0  0
 QAR  CONST_06  C1    N1   C3   N3      0.00   0.0  0
 QAR  CONST_07  C9    C10  C5   C4      0.00   0.0  0
 QAR  CONST_08  C6    N5   C5   C4      0.00   0.0  0
 QAR  CONST_09  C9    C8   C7   C4      0.00   0.0  0
 QAR  CONST_10  N5    C6   N4   C4      0.00   0.0  0
 QAR  CONST_11  N2    C2   N4   C4      0.00   0.0  0
 QAR  CONST_12  C8    C7   C4   C5      0.00   0.0  0
 QAR  CONST_13  C6    N4   C4   C5      0.00   0.0  0
 QAR  CONST_14  C2    N4   C4   C5    180.00   0.0  0
 QAR  CONST_15  C8    C9   C10  C5      0.00   0.0  0
 QAR  CONST_16  N4    C6   N5   C5      0.00   0.0  0
 QAR  CONST_17  C10   C5   N5   C6    180.00   0.0  0
 QAR  CONST_18  C7    C4   N4   C6    180.00   0.0  0
 QAR  CONST_19  N2    C2   N4   C6    180.00   0.0  0
 QAR  CONST_20  C10   C5   C4   C7      0.00   0.0  0
 QAR  CONST_21  N5    C5   C4   C7    180.00   0.0  0
 QAR  CONST_22  C2    N4   C4   C7      0.00   0.0  0
 QAR  CONST_23  C10   C9   C8   C7      0.00   0.0  0
 QAR  CONST_24  N4    C4   C7   C8    180.00   0.0  0
 QAR  CONST_25  N4    C4   C5   C10   180.00   0.0  0
 QAR  CONST_26  N8    N9   C12  C13     0.00   0.0  0
 QAR  CONST_27  N9    N8   C14  C13     0.00   0.0  0
 QAR  CONST_28  N9    C12  C13  C14     0.00   0.0  0
 QAR  CONST_29  C12   N9   N8   C14     0.00   0.0  0
 QAR  CONST_30  C12   C13  C14  N8      0.00   0.0  0
 QAR  CONST_31  N4    C4   C5   N5      0.00   0.0  0
 QAR  CONST_32  C9    C10  C5   N5    180.00   0.0  0
 QAR  CONST_33  C2    N4   C6   N5    180.00   0.0  0
 QAR  CONST_34  C3    N3   C2   N4    180.00   0.0  0
 QAR  CONST_35  C1    N2   C2   N4    180.00   0.0  0
 QAR  CONST_36  C3    N3   C2   N2      0.00   0.0  0
 QAR  CONST_37  C3    N1   C1   N2      0.00   0.0  0
 QAR  CONST_38  N6    C6   N4   C4    180.00   0.0  0
 QAR  CONST_39  N6    C6   N5   C5    180.00   0.0  0
 QAR  CONST_40  N6    C12  C13  C14   180.00   0.0  0
 QAR  CONST_41  N6    C12  N9   N8    180.00   0.0  0
 QAR  CONST_42  C2    N4   C6   N6      0.00   0.0  0
 QAR  CONST_43  C11   C3   N3   C2    180.00   0.0  0
 QAR  CONST_44  N7    C1   N2   C2    180.00   0.0  0
 QAR  CONST_45  N7    C1   N1   C3    180.00   0.0  0
 QAR  CONST_46  C1    N1   C3   C11   180.00   0.0  0
 QAR  CONST_47  H10   C10  C5   C4    180.00   0.0  0
 QAR  CONST_48  H8    C8   C7   C4    180.00   0.0  0
 QAR  CONST_49  H7    C7   C4   C5    180.00   0.0  0
 QAR  CONST_50  H9    C9   C10  C5    180.00   0.0  0
 QAR  CONST_51  HN8   N8   C14  C13   180.00   0.0  0
 QAR  CONST_52  H13   C13  C14  N8    180.00   0.0  0
 QAR  CONST_53  H14   C14  N8   N9    180.00   0.0  0
 QAR  CONST_54  HN7   N7   C1   N1    180.00   0.0  0
 QAR  CONST_55  HN7A  N7   C1   N1      0.00   0.0  0
 QAR  Var_01    C13   C12  N6   C6      0.47  30.0  2
 QAR  Var_02    N5    C6   N6   C12    -0.29  30.0  1
 QAR  Var_03    H11   C11  C3   N1   -109.41  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
 QAR  plan-1  C13   0.020
 QAR  plan-1  C14   0.020
 QAR  plan-1  N8    0.020
 QAR  plan-1  N9    0.020
 QAR  plan-1  C12   0.020
 QAR  plan-1  N6    0.020
 QAR  plan-1  H14   0.020
 QAR  plan-1  HN8   0.020
 QAR  plan-1  H13   0.020
 QAR  plan-2  N1    0.020
 QAR  plan-2  N3    0.020
 QAR  plan-2  N4    0.020
 QAR  plan-2  C2    0.020
 QAR  plan-2  N2    0.020
 QAR  plan-2  C3    0.020
 QAR  plan-2  C11   0.020
 QAR  plan-2  C1    0.020
 QAR  plan-2  N7    0.020
 QAR  plan-3  C4    0.020
 QAR  plan-3  C5    0.020
 QAR  plan-3  C6    0.020
 QAR  plan-3  C7    0.020
 QAR  plan-3  C8    0.020
 QAR  plan-3  C10   0.020
 QAR  plan-3  N6    0.020
 QAR  plan-3  N5    0.020
 QAR  plan-3  C9    0.020
 QAR  plan-3  N4    0.020
 QAR  plan-3  C2    0.020
 QAR  plan-3  H7    0.020
 QAR  plan-3  H8    0.020
 QAR  plan-3  H10   0.020
 QAR  plan-3  H9    0.020
 QAR  plan-4  C1    0.020
 QAR  plan-4  N7    0.020
 QAR  plan-4  HN7   0.020
 QAR  plan-4  HN7A  0.020

