# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:14:59 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: [(4-{2-[(3-hydroxyphenyl)amino]-1H-benzimidazol-1-yl}-1,3,5-triazin-2-yl)amino]acetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(Nc2nc3ccccc3n2c4ncnc(NCC#N)n4)c1
#
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
 QAQ  QAQ  '[(4-{2-[(3-hydroxyphenyl)amino]-1H-benzimidazol-1-yl}-1,3,5-triazin-2-yl)amino]acetonitrile'  ligand  41  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QAQ
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
 QAQ  N1    N  N     0  -0.565  -1.4011   0.5042  -0.0995
 QAQ  N3    N  N     0  -0.458  -3.2637   1.9506   0.0473
 QAQ  C4    C  CR56  0   0.317   1.7091   2.4056   0.0739
 QAQ  C5    C  CR56  0   0.186   2.9307   1.7245   0.0163
 QAQ  C6    C  CR5   0   0.733   1.4553   0.1841  -0.1024
 QAQ  C7    C  CR16  0  -0.281   1.6546   3.7868   0.1848
 QAQ  C8    C  CR16  0  -0.279   2.8662   4.4685   0.2354
 QAQ  C10   C  CR16  0  -0.339   4.1329   2.4164   0.0679
 QAQ  C13   C  CR6   0   0.392   1.3486  -2.2748  -0.2762
 QAQ  C15   C  CR16  0  -0.233   3.1105  -3.8954  -0.3809
 QAQ  C17   C  CR6   0   0.380   0.8399  -4.6364  -0.4347
 QAQ  N8    N  NS    0  -0.260  -5.8989   0.4245   2.1951
 QAQ  C12   C  CSP   0   0.131  -5.4838   0.1644   1.1554
 QAQ  N7    N  NH1   0  -0.650  -3.5348  -0.3112  -0.1826
 QAQ  C1    C  CR6   0   0.690  -2.7158   0.7383  -0.0757
 QAQ  C3    C  CR16  0   0.118  -2.3919   2.9321   0.1408
 QAQ  N2    N  N     0  -0.468  -1.0741   2.8173   0.1306
 QAQ  C2    C  CR6   0   0.718  -0.6333   1.5724   0.0088
 QAQ  N4    N  NR5   0  -0.715   0.7354   1.3931  -0.0057
 QAQ  C9    C  CR16  0  -0.263   4.0867   3.7982   0.1789
 QAQ  N5    N  N     0  -0.529   2.7375   0.3667  -0.0912
 QAQ  C18   C  CR16  0  -0.507   0.4183  -3.3176  -0.3484
 QAQ  C14   C  CR16  0  -0.345   2.7123  -2.5668  -0.2923
 QAQ  C16   C  CR16  0  -0.358   2.2021  -4.9357  -0.4526
 QAQ  O1    O  OH1   0  -0.634  -0.0286  -5.6640  -0.5024
 QAQ  H7    H  HCR6  0   0.282   0.7214   4.3218   0.2324
 QAQ  H8    H  HCR6  0   0.255   2.8527   5.5469   0.3209
 QAQ  H10   H  HCR6  0   0.256   5.0739   1.8839   0.0219
 QAQ  H15   H  HCR6  0   0.258   4.1696  -4.1189  -0.3944
 QAQ  H11   H  HCH2  0   0.344  -5.3999  -1.1326  -0.4737
 QAQ  H11A  H  HCH2  0   0.324  -5.3060   0.5735  -0.8805
 QAQ  HN7   H  HNH1  0   0.424  -3.1359  -1.2350  -0.2304
 QAQ  H3    H  HCR6  0   0.284  -2.7904   3.9356   0.2391
 QAQ  H9    H  HCR6  0   0.255   5.0084   4.3636   0.2234
 QAQ  HN6   H  HNH1  0   0.447  -0.2021  -0.9142  -0.1912
 QAQ  H18   H  HCR6  0   0.273  -0.6442  -3.0944  -0.3341
 QAQ  H14   H  HCR6  0   0.286   3.4460  -1.7807  -0.2388
 QAQ  H16   H  HCR6  0   0.261   2.5325  -5.9642  -0.5212
 QAQ  HO1   H  HOH1  0   0.475  -0.9367  -5.3426  -0.4784
 QAQ  N6    N  NH1   0  -0.827   0.8113  -0.9942  -0.1908
 QAQ  C11   C  CH2   0  -0.379  -4.9643  -0.1817  -0.1721

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
 QAQ  C2   N1    aromatic  1.320  0.020  1.320
 QAQ  N1   C1    aromatic  1.336  0.020  1.336
 QAQ  C1   N3    aromatic  1.336  0.020  1.336
 QAQ  C3   N3    aromatic  1.316  0.020  1.316
 QAQ  C5   C4    aromatic  1.400  0.020  1.400
 QAQ  C4   C7    aromatic  1.387  0.020  1.387
 QAQ  C4   N4    aromatic  1.407  0.020  1.407
 QAQ  C10  C5    aromatic  1.388  0.020  1.388
 QAQ  C5   N5    aromatic  1.376  0.020  1.376
 QAQ  N5   C6    aromatic  1.295  0.020  1.295
 QAQ  C6   N6    single    1.346  0.020  1.346
 QAQ  C6   N4    aromatic  1.410  0.020  1.410
 QAQ  C8   C7    aromatic  1.391  0.020  1.391
 QAQ  C7   H7    single    0.930  0.020  1.080
 QAQ  C9   C8    aromatic  1.394  0.020  1.394
 QAQ  C8   H8    single    0.930  0.020  1.080
 QAQ  C10  C9    aromatic  1.387  0.020  1.387
 QAQ  C10  H10   single    0.930  0.020  1.080
 QAQ  C14  C13   aromatic  1.395  0.020  1.395
 QAQ  C13  N6    single    1.391  0.020  1.391
 QAQ  C13  C18   aromatic  1.399  0.020  1.399
 QAQ  C15  C14   aromatic  1.390  0.020  1.390
 QAQ  C15  C16   aromatic  1.383  0.020  1.383
 QAQ  C15  H15   single    0.930  0.020  1.080
 QAQ  C16  C17   aromatic  1.395  0.020  1.395
 QAQ  C17  C18   aromatic  1.387  0.020  1.387
 QAQ  C17  O1    single    1.347  0.020  1.347
 QAQ  C12  N8    triple    1.149  0.020  1.149
 QAQ  C11  C12   single    1.467  0.020  1.467
 QAQ  C11  N7    single    1.435  0.020  1.435
 QAQ  C11  H11   single    0.970  0.020  1.090
 QAQ  C11  H11A  single    0.970  0.020  1.090
 QAQ  C1   N7    single    1.336  0.020  1.336
 QAQ  N7   HN7   single    0.860  0.020  1.020
 QAQ  N2   C3    aromatic  1.323  0.020  1.323
 QAQ  C3   H3    single    0.930  0.020  1.080
 QAQ  C2   N2    aromatic  1.326  0.020  1.326
 QAQ  N4   C2    single    1.381  0.020  1.381
 QAQ  C9   H9    single    0.930  0.020  1.080
 QAQ  N6   HN6   single    0.860  0.020  1.020
 QAQ  C18  H18   single    0.930  0.020  1.080
 QAQ  C14  H14   single    0.930  0.020  1.080
 QAQ  C16  H16   single    0.930  0.020  1.080
 QAQ  O1   HO1   single    0.850  0.020  0.980

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
 QAQ  C2    N1   C1   115.42  3.000
 QAQ  C3    N3   C1   114.31  3.000
 QAQ  N4    C4   C7   133.95  3.000
 QAQ  N4    C4   C5   104.56  3.000
 QAQ  C7    C4   C5   121.48  3.000
 QAQ  N5    C5   C10  128.06  3.000
 QAQ  N5    C5   C4   111.16  3.000
 QAQ  C10   C5   C4   120.78  3.000
 QAQ  N6    C6   N5   126.71  3.000
 QAQ  N6    C6   N4   120.72  3.000
 QAQ  N5    C6   N4   112.57  3.000
 QAQ  H7    C7   C8   120.64  3.000
 QAQ  H7    C7   C4   122.18  3.000
 QAQ  C8    C7   C4   117.18  3.000
 QAQ  H8    C8   C9   119.58  3.000
 QAQ  H8    C8   C7   118.71  3.000
 QAQ  C9    C8   C7   121.71  3.000
 QAQ  H10   C10  C9   121.51  3.000
 QAQ  H10   C10  C5   120.41  3.000
 QAQ  C9    C10  C5   118.08  3.000
 QAQ  C14   C13  C18  119.57  3.000
 QAQ  C18   C13  N6   115.62  3.000
 QAQ  C14   C13  N6   124.82  3.000
 QAQ  H15   C15  C16  119.13  3.000
 QAQ  H15   C15  C14  118.58  3.000
 QAQ  C16   C15  C14  122.29  3.000
 QAQ  O1    C17  C16  117.73  3.000
 QAQ  O1    C17  C18  122.16  3.000
 QAQ  C16   C17  C18  120.11  3.000
 QAQ  C11   C12  N8   180.00  3.000
 QAQ  HN7   N7   C1   118.79  3.000
 QAQ  HN7   N7   C11  118.51  3.000
 QAQ  C1    N7   C11  122.63  3.000
 QAQ  N7    C1   N3   117.97  3.000
 QAQ  N7    C1   N1   117.67  3.000
 QAQ  N3    C1   N1   124.36  3.000
 QAQ  H3    C3   N2   116.57  3.000
 QAQ  H3    C3   N3   116.95  3.000
 QAQ  N2    C3   N3   126.48  3.000
 QAQ  C2    N2   C3   114.42  3.000
 QAQ  N4    C2   N2   116.90  3.000
 QAQ  N4    C2   N1   118.08  3.000
 QAQ  N2    C2   N1   125.02  3.000
 QAQ  C2    N4   C6   128.18  3.000
 QAQ  C2    N4   C4   126.31  3.000
 QAQ  C6    N4   C4   105.52  3.000
 QAQ  H9    C9   C10  119.69  3.000
 QAQ  H9    C9   C8   119.54  3.000
 QAQ  C10   C9   C8   120.77  3.000
 QAQ  C6    N5   C5   106.19  3.000
 QAQ  H18   C18  C17  119.58  3.000
 QAQ  H18   C18  C13  119.78  3.000
 QAQ  C17   C18  C13  120.64  3.000
 QAQ  H14   C14  C15  120.39  3.000
 QAQ  H14   C14  C13  120.85  3.000
 QAQ  C15   C14  C13  118.75  3.000
 QAQ  H16   C16  C17  120.19  3.000
 QAQ  H16   C16  C15  121.16  3.000
 QAQ  C17   C16  C15  118.65  3.000
 QAQ  HO1   O1   C17  110.61  3.000
 QAQ  HN6   N6   C13  117.21  3.000
 QAQ  HN6   N6   C6   114.09  3.000
 QAQ  C13   N6   C6   128.69  3.000
 QAQ  H11A  C11  H11  107.44  3.000
 QAQ  H11A  C11  N7   111.70  3.000
 QAQ  H11   C11  N7   108.52  3.000
 QAQ  H11A  C11  C12  108.27  3.000
 QAQ  H11   C11  C12  108.37  3.000
 QAQ  N7    C11  C12  112.37  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
 QAQ  CONST_01  C3   N2   C2   N1      0.00   0.0  0
 QAQ  CONST_02  C4   N4   C2   N1    180.00   0.0  0
 QAQ  CONST_03  C6   N4   C2   N1      0.00   0.0  0
 QAQ  CONST_04  C3   N3   C1   N1      0.00   0.0  0
 QAQ  CONST_05  C2   N1   C1   N3      0.00   0.0  0
 QAQ  CONST_06  C2   N2   C3   N3      0.00   0.0  0
 QAQ  CONST_07  C9   C10  C5   C4      0.00   0.0  0
 QAQ  CONST_08  C6   N5   C5   C4      0.00   0.0  0
 QAQ  CONST_09  C9   C8   C7   C4      0.00   0.0  0
 QAQ  CONST_10  N5   C6   N4   C4      0.00   0.0  0
 QAQ  CONST_11  N2   C2   N4   C4      0.00   0.0  0
 QAQ  CONST_12  C8   C7   C4   C5      0.00   0.0  0
 QAQ  CONST_13  C6   N4   C4   C5      0.00   0.0  0
 QAQ  CONST_14  C2   N4   C4   C5    180.00   0.0  0
 QAQ  CONST_15  C8   C9   C10  C5      0.00   0.0  0
 QAQ  CONST_16  N4   C6   N5   C5      0.00   0.0  0
 QAQ  CONST_17  C10  C5   N5   C6    180.00   0.0  0
 QAQ  CONST_18  C7   C4   N4   C6    180.00   0.0  0
 QAQ  CONST_19  N2   C2   N4   C6    180.00   0.0  0
 QAQ  CONST_20  C10  C5   C4   C7      0.00   0.0  0
 QAQ  CONST_21  N5   C5   C4   C7    180.00   0.0  0
 QAQ  CONST_22  C2   N4   C4   C7      0.00   0.0  0
 QAQ  CONST_23  C10  C9   C8   C7      0.00   0.0  0
 QAQ  CONST_24  N4   C4   C7   C8    180.00   0.0  0
 QAQ  CONST_25  N4   C4   C5   C10   180.00   0.0  0
 QAQ  CONST_26  C16  C15  C14  C13     0.00   0.0  0
 QAQ  CONST_27  C16  C17  C18  C13     0.00   0.0  0
 QAQ  CONST_28  C18  C13  C14  C15     0.00   0.0  0
 QAQ  CONST_29  C18  C17  C16  C15     0.00   0.0  0
 QAQ  CONST_30  C14  C15  C16  C17     0.00   0.0  0
 QAQ  CONST_31  C14  C13  C18  C17     0.00   0.0  0
 QAQ  CONST_32  N2   C2   N1   C1      0.00   0.0  0
 QAQ  CONST_33  N4   C2   N1   C1    180.00   0.0  0
 QAQ  CONST_34  N2   C3   N3   C1      0.00   0.0  0
 QAQ  CONST_35  N4   C2   N2   C3    180.00   0.0  0
 QAQ  CONST_36  N5   C6   N4   C2    180.00   0.0  0
 QAQ  CONST_37  N5   C5   C4   N4      0.00   0.0  0
 QAQ  CONST_38  N5   C5   C10  C9    180.00   0.0  0
 QAQ  CONST_39  N6   C6   N4   C4    180.00   0.0  0
 QAQ  CONST_40  N6   C6   N5   C5    180.00   0.0  0
 QAQ  CONST_41  O1   C17  C18  C13   180.00   0.0  0
 QAQ  CONST_42  N6   C13  C14  C15   180.00   0.0  0
 QAQ  CONST_43  O1   C17  C16  C15   180.00   0.0  0
 QAQ  CONST_44  N6   C13  C18  C17   180.00   0.0  0
 QAQ  CONST_45  C2   N1   C1   N7    180.00   0.0  0
 QAQ  CONST_46  C3   N3   C1   N7    180.00   0.0  0
 QAQ  CONST_47  N6   C6   N4   C2      0.00   0.0  0
 QAQ  CONST_48  H10  C10  C5   C4    180.00   0.0  0
 QAQ  CONST_49  H8   C8   C7   C4    180.00   0.0  0
 QAQ  CONST_50  H7   C7   C4   C5    180.00   0.0  0
 QAQ  CONST_51  H9   C9   C10  C5    180.00   0.0  0
 QAQ  CONST_52  H15  C15  C14  C13   180.00   0.0  0
 QAQ  CONST_53  H3   C3   N3   C1    180.00   0.0  0
 QAQ  CONST_54  H14  C14  C13  C18   180.00   0.0  0
 QAQ  CONST_55  H16  C16  C17  C18   180.00   0.0  0
 QAQ  CONST_56  H18  C18  C13  C14   180.00   0.0  0
 QAQ  CONST_57  C11  N7   C1   N1    180.00   0.0  0
 QAQ  CONST_58  C11  N7   C1   N3      0.00   0.0  0
 QAQ  CONST_59  HN7  N7   C1   N1      0.00   0.0  0
 QAQ  Var_01    C14  C13  N6   C6     -0.37  30.0  2
 QAQ  Var_02    N5   C6   N6   C13     0.70  30.0  1
 QAQ  Var_03    C1   N7   C11  C12   -71.58  30.0  3
 QAQ  Var_04    N7   C11  C12  N8   -123.86  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
 QAQ  plan-1  N1   0.020
 QAQ  plan-1  N3   0.020
 QAQ  plan-1  N7   0.020
 QAQ  plan-1  C1   0.020
 QAQ  plan-1  C3   0.020
 QAQ  plan-1  N2   0.020
 QAQ  plan-1  C2   0.020
 QAQ  plan-1  N4   0.020
 QAQ  plan-1  H3   0.020
 QAQ  plan-2  C13  0.020
 QAQ  plan-2  C15  0.020
 QAQ  plan-2  C17  0.020
 QAQ  plan-2  C18  0.020
 QAQ  plan-2  C14  0.020
 QAQ  plan-2  C16  0.020
 QAQ  plan-2  O1   0.020
 QAQ  plan-2  H15  0.020
 QAQ  plan-2  H18  0.020
 QAQ  plan-2  H14  0.020
 QAQ  plan-2  H16  0.020
 QAQ  plan-2  N6   0.020
 QAQ  plan-3  C4   0.020
 QAQ  plan-3  C5   0.020
 QAQ  plan-3  C6   0.020
 QAQ  plan-3  C7   0.020
 QAQ  plan-3  C8   0.020
 QAQ  plan-3  C10  0.020
 QAQ  plan-3  C2   0.020
 QAQ  plan-3  N4   0.020
 QAQ  plan-3  C9   0.020
 QAQ  plan-3  N5   0.020
 QAQ  plan-3  H7   0.020
 QAQ  plan-3  H8   0.020
 QAQ  plan-3  H10  0.020
 QAQ  plan-3  H9   0.020
 QAQ  plan-3  N6   0.020
 QAQ  plan-4  N7   0.020
 QAQ  plan-4  C1   0.020
 QAQ  plan-4  HN7  0.020
 QAQ  plan-4  C11  0.020

