# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 07:58:58 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-chloranyl-4-[[1-methyl-3-(3-methyl-3-oxidanyl-butyl)-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(CCC(C)(C)O)c2cc(Nc3ccnc(Cl)c3C#N)ccc12
#
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
 NQQ  NQQ  2-chloranyl-4-[[1-methyl-3-(3-methyl-3-oxidanyl-butyl)-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile  ligand  47  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NQQ
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
 NQQ  CL   CL  CL    0  -0.066   5.0698  67.7809  177.2526
 NQQ  C6   C   CH3   0  -0.656  12.1980  72.5839  183.4129
 NQQ  C5   C   CH3   0  -0.692   9.7947  72.7807  184.0604
 NQQ  C8   C   CR56  0   0.339   9.6383  66.5717  184.9716
 NQQ  C4   C   CT    0   0.195  11.1512  72.1931  184.4486
 NQQ  N3   N   N     0  -0.413   7.4093  66.8825  177.9053
 NQQ  N1   N   NR5   0  -0.593  10.0874  68.6713  185.5737
 NQQ  N4   N   NS    0  -0.234   3.8572  68.6422  180.5781
 NQQ  C16  C   CR6   0  -0.087   6.0704  67.6451  179.7386
 NQQ  C15  C   CR6   0   0.145   6.3141  67.3919  178.3871
 NQQ  C14  C   CR16  0  -0.053   8.3694  66.5879  178.7943
 NQQ  C13  C   CR16  0  -0.384   8.2680  66.7833  180.1470
 NQQ  C12  C   CR6   0   0.515   7.0844  67.3320  180.6762
 NQQ  N2   N   NH1   0  -0.777   6.9088  67.5635  181.9867
 NQQ  C11  C   CR6   0   0.249   7.8463  67.2326  182.9960
 NQQ  C10  C   CR16  0  -0.292   8.1222  65.8977  183.2770
 NQQ  C9   C   CR16  0  -0.320   9.0364  65.5483  184.2672
 NQQ  N    N   NR5   0  -0.587  10.5594  66.5608  185.9920
 NQQ  C    C   CH3   0  -0.545  11.1277  65.3772  186.5843
 NQQ  C18  C   CR16  0  -0.361   8.4584  68.2674  183.7038
 NQQ  C7   C   CR56  0   0.348   9.3450  67.9126  184.6992
 NQQ  C1   C   CR5   0   0.673  10.8569  67.8507  186.3683
 NQQ  O    O   O     0  -0.499  11.6391  68.2021  187.2318
 NQQ  C3   C   CH2   0  -0.456  11.0935  70.6595  184.5299
 NQQ  O1   O   OH1   0  -0.676  11.5932  72.7396  185.6857
 NQQ  H1   H   HCH3  0   0.233  13.1795  72.1841  183.6745
 NQQ  H2   H   HCH3  0   0.228  11.9288  72.1921  182.4316
 NQQ  H3   H   HCH3  0   0.232  12.2810  73.6688  183.3302
 NQQ  H4   H   HCH3  0   0.228   9.0369  72.6167  184.8305
 NQQ  H5   H   HCH3  0   0.241   9.8733  73.8577  183.9048
 NQQ  H6   H   HCH3  0   0.234   9.4257  72.3350  183.1359
 NQQ  H7   H   HCH2  0   0.264  10.4663  70.4153  186.5923
 NQQ  H8   H   HCH2  0   0.259   9.1310  70.4886  185.4600
 NQQ  H9   H   HCR6  0   0.289   9.2804  66.1713  178.3836
 NQQ  H10  H   HCR6  0   0.299   9.0972  66.5245  180.7882
 NQQ  H11  H   HNH1  0   0.418   6.0813  68.0607  182.2831
 NQQ  H12  H   HCR6  0   0.275   7.6171  65.1200  182.7194
 NQQ  H13  H   HCR6  0   0.280   9.2501  64.5089  184.4778
 NQQ  H14  H   HCH3  0   0.268  11.8435  65.6682  187.3471
 NQQ  H15  H   HCH3  0   0.254  10.3525  64.7684  187.0484
 NQQ  H16  H   HCH3  0   0.272  11.6434  64.7812  185.8322
 NQQ  H17  H   HCR6  0   0.297   8.2405  69.3004  183.4648
 NQQ  H18  H   HCH2  0   0.256  10.8015  70.2681  183.5507
 NQQ  H19  H   HCH2  0   0.261  12.0994  70.2789  184.7318
 NQQ  H20  H   HOH1  0   0.437  10.8613  72.7368  186.3102
 NQQ  C2   C   CH2   0  -0.331  10.1477  70.1152  185.5948
 NQQ  C17  C   CSP   0   0.034   4.8416  68.1962  180.1751

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
 NQQ  CL   C15  single    1.728  0.020  1.728
 NQQ  N3   C15  aromatic  1.300  0.020  1.300
 NQQ  N3   C14  aromatic  1.341  0.020  1.341
 NQQ  C15  C16  aromatic  1.396  0.020  1.396
 NQQ  C14  C13  aromatic  1.371  0.020  1.371
 NQQ  C16  C17  single    1.416  0.020  1.416
 NQQ  C16  C12  aromatic  1.416  0.020  1.416
 NQQ  C17  N4   triple    1.153  0.020  1.153
 NQQ  C13  C12  aromatic  1.408  0.020  1.408
 NQQ  C12  N2   single    1.342  0.020  1.342
 NQQ  N2   C11  single    1.417  0.020  1.417
 NQQ  C11  C10  aromatic  1.392  0.020  1.392
 NQQ  C11  C18  aromatic  1.395  0.020  1.395
 NQQ  C10  C9   aromatic  1.392  0.020  1.392
 NQQ  C18  C7   aromatic  1.379  0.020  1.379
 NQQ  C6   C4   single    1.524  0.020  1.524
 NQQ  C5   C4   single    1.528  0.020  1.528
 NQQ  C9   C8   aromatic  1.380  0.020  1.380
 NQQ  C3   C4   single    1.537  0.020  1.537
 NQQ  C3   C2   single    1.525  0.020  1.525
 NQQ  C4   O1   single    1.423  0.020  1.423
 NQQ  C7   C8   aromatic  1.399  0.020  1.399
 NQQ  C7   N1   single    1.375  0.020  1.375
 NQQ  C8   N    single    1.375  0.020  1.375
 NQQ  N1   C2   single    1.445  0.020  1.445
 NQQ  N1   C1   single    1.377  0.020  1.377
 NQQ  N    C1   single    1.376  0.020  1.376
 NQQ  N    C    single    1.440  0.020  1.440
 NQQ  C1   O    double    1.217  0.020  1.217
 NQQ  C6   H1   single    0.970  0.020  1.090
 NQQ  C6   H2   single    0.970  0.020  1.090
 NQQ  C6   H3   single    0.970  0.020  1.090
 NQQ  C5   H4   single    0.970  0.020  1.090
 NQQ  C5   H5   single    0.970  0.020  1.090
 NQQ  C5   H6   single    0.970  0.020  1.090
 NQQ  C2   H7   single    0.970  0.020  1.090
 NQQ  C2   H8   single    0.970  0.020  1.090
 NQQ  C14  H9   single    0.930  0.020  1.080
 NQQ  C13  H10  single    0.930  0.020  1.080
 NQQ  N2   H11  single    0.860  0.020  1.020
 NQQ  C10  H12  single    0.930  0.020  1.080
 NQQ  C9   H13  single    0.930  0.020  1.080
 NQQ  C    H14  single    0.970  0.020  1.090
 NQQ  C    H15  single    0.970  0.020  1.090
 NQQ  C    H16  single    0.970  0.020  1.090
 NQQ  C18  H17  single    0.930  0.020  1.080
 NQQ  C3   H18  single    0.970  0.020  1.090
 NQQ  C3   H19  single    0.970  0.020  1.090
 NQQ  O1   H20  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
 NQQ  H3   C6   H2   107.93  3.000
 NQQ  H3   C6   H1   108.30  3.000
 NQQ  H2   C6   H1   107.82  3.000
 NQQ  H3   C6   C4   111.02  3.000
 NQQ  H2   C6   C4   110.49  3.000
 NQQ  H1   C6   C4   111.16  3.000
 NQQ  H6   C5   H5   107.88  3.000
 NQQ  H6   C5   H4   107.54  3.000
 NQQ  H5   C5   H4   107.38  3.000
 NQQ  H6   C5   C4   111.00  3.000
 NQQ  H5   C5   C4   110.60  3.000
 NQQ  H4   C5   C4   112.26  3.000
 NQQ  C7   C8   N    107.01  3.000
 NQQ  N    C8   C9   131.68  3.000
 NQQ  C7   C8   C9   121.31  3.000
 NQQ  O1   C4   C3   110.42  3.000
 NQQ  O1   C4   C5   110.42  3.000
 NQQ  C3   C4   C5   111.33  3.000
 NQQ  O1   C4   C6   106.21  3.000
 NQQ  C3   C4   C6   108.53  3.000
 NQQ  C5   C4   C6   109.79  3.000
 NQQ  C14  N3   C15  116.32  3.000
 NQQ  C1   N1   C7   109.86  3.000
 NQQ  C1   N1   C2   124.30  3.000
 NQQ  C7   N1   C2   125.65  3.000
 NQQ  C12  C16  C15  118.41  3.000
 NQQ  C12  C16  C17  120.23  3.000
 NQQ  C15  C16  C17  121.36  3.000
 NQQ  C16  C15  N3   125.21  3.000
 NQQ  C16  C15  CL   117.96  3.000
 NQQ  N3   C15  CL   116.83  3.000
 NQQ  H9   C14  C13  119.44  3.000
 NQQ  H9   C14  N3   115.81  3.000
 NQQ  C13  C14  N3   124.75  3.000
 NQQ  H10  C13  C12  121.06  3.000
 NQQ  H10  C13  C14  119.68  3.000
 NQQ  C12  C13  C14  119.26  3.000
 NQQ  N2   C12  C13  122.97  3.000
 NQQ  N2   C12  C16  120.97  3.000
 NQQ  C13  C12  C16  116.06  3.000
 NQQ  H11  N2   C11  116.63  3.000
 NQQ  H11  N2   C12  118.59  3.000
 NQQ  C11  N2   C12  124.66  3.000
 NQQ  C18  C11  C10  121.46  3.000
 NQQ  C18  C11  N2   118.59  3.000
 NQQ  C10  C11  N2   119.94  3.000
 NQQ  H12  C10  C9   119.52  3.000
 NQQ  H12  C10  C11  119.52  3.000
 NQQ  C9   C10  C11  120.96  3.000
 NQQ  H13  C9   C10  120.61  3.000
 NQQ  H13  C9   C8   121.79  3.000
 NQQ  C10  C9   C8   117.59  3.000
 NQQ  C1   N    C    124.92  3.000
 NQQ  C    N    C8   125.18  3.000
 NQQ  C1   N    C8   109.90  3.000
 NQQ  H16  C    H15  108.98  3.000
 NQQ  H16  C    H14  108.63  3.000
 NQQ  H15  C    H14  108.63  3.000
 NQQ  H16  C    N    110.64  3.000
 NQQ  H15  C    N    110.71  3.000
 NQQ  H14  C    N    109.20  3.000
 NQQ  H17  C18  C7   122.29  3.000
 NQQ  H17  C18  C11  120.49  3.000
 NQQ  C7   C18  C11  117.22  3.000
 NQQ  C18  C7   N1   131.60  3.000
 NQQ  N1   C7   C8   106.96  3.000
 NQQ  C18  C7   C8   121.44  3.000
 NQQ  O    C1   N    127.13  3.000
 NQQ  O    C1   N1   126.61  3.000
 NQQ  N    C1   N1   106.26  3.000
 NQQ  H19  C3   H18  106.61  3.000
 NQQ  H19  C3   C2   108.49  3.000
 NQQ  H18  C3   C2   109.38  3.000
 NQQ  H19  C3   C4   108.81  3.000
 NQQ  H18  C3   C4   108.64  3.000
 NQQ  C2   C3   C4   114.61  3.000
 NQQ  H20  O1   C4   109.08  3.000
 NQQ  H8   C2   H7   106.94  3.000
 NQQ  H8   C2   C3   111.68  3.000
 NQQ  H7   C2   C3   111.09  3.000
 NQQ  H8   C2   N1   107.52  3.000
 NQQ  H7   C2   N1   107.50  3.000
 NQQ  C3   C2   N1   111.86  3.000
 NQQ  C16  C17  N4   180.00  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
 NQQ  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 NQQ  CONST_02  C11  C18  C7   C8      0.00   0.0  0
 NQQ  CONST_03  C12  C16  C15  N3      0.00   0.0  0
 NQQ  CONST_04  C12  C13  C14  N3      0.00   0.0  0
 NQQ  CONST_05  C14  N3   C15  C16     0.00   0.0  0
 NQQ  CONST_06  C14  C13  C12  C16     0.00   0.0  0
 NQQ  CONST_07  C13  C14  N3   C15     0.00   0.0  0
 NQQ  CONST_08  C13  C12  C16  C15     0.00   0.0  0
 NQQ  CONST_09  C7   C18  C11  C10     0.00   0.0  0
 NQQ  CONST_10  C7   C8   C9   C10     0.00   0.0  0
 NQQ  CONST_11  C18  C11  C10  C9      0.00   0.0  0
 NQQ  CONST_12  C18  C7   C8   C9      0.00   0.0  0
 NQQ  CONST_13  C1   N1   C7   C8      0.00   0.0  0
 NQQ  CONST_14  N1   C1   N    C8      0.00   0.0  0
 NQQ  CONST_15  N    C8   C7   N1      0.00   0.0  0
 NQQ  CONST_16  C7   N1   C1   N       0.00   0.0  0
 NQQ  CONST_17  C1   N    C8   C7      0.00   0.0  0
 NQQ  CONST_18  C14  N3   C15  CL    180.00   0.0  0
 NQQ  CONST_19  C12  C16  C15  CL    180.00   0.0  0
 NQQ  CONST_20  C17  C16  C15  N3    180.00   0.0  0
 NQQ  CONST_21  C13  C12  C16  C17   180.00   0.0  0
 NQQ  CONST_22  N2   C12  C16  C15   180.00   0.0  0
 NQQ  CONST_23  N2   C12  C13  C14   180.00   0.0  0
 NQQ  CONST_24  C9   C10  C11  N2    180.00   0.0  0
 NQQ  CONST_25  C7   C18  C11  N2    180.00   0.0  0
 NQQ  CONST_26  C2   N1   C7   C8    180.00   0.0  0
 NQQ  CONST_27  O    C1   N    C8    180.00   0.0  0
 NQQ  CONST_28  N    C1   N1   C2    180.00   0.0  0
 NQQ  CONST_29  C    N    C1   N1    180.00   0.0  0
 NQQ  CONST_30  C7   C8   N    C     180.00   0.0  0
 NQQ  CONST_31  O    C1   N1   C7    180.00   0.0  0
 NQQ  CONST_32  H12  C10  C9   C8    180.00   0.0  0
 NQQ  CONST_33  H17  C18  C7   C8    180.00   0.0  0
 NQQ  CONST_34  H10  C13  C14  N3    180.00   0.0  0
 NQQ  CONST_35  H9   C14  N3   C15   180.00   0.0  0
 NQQ  CONST_36  H13  C9   C10  C11   180.00   0.0  0
 NQQ  CONST_37  O    C1   N1   C2      0.00   0.0  0
 NQQ  CONST_38  O    C1   N    C       0.00   0.0  0
 NQQ  Var_01    C11  N2   C12  C16   177.36  30.0  2
 NQQ  Var_02    C10  C11  N2   C12   -67.05  30.0  2
 NQQ  Var_03    C3   C2   N1   C7    -80.12  30.0  3
 NQQ  Var_04    H14  C    N    C8    178.52  30.0  3
 NQQ  Var_05    N1   C2   C3   C4    177.03  30.0  3
 NQQ  Var_06    C2   C3   C4   C6    176.28  30.0  2
 NQQ  Var_07    H4   C5   C4   C6   -173.82  30.0  3
 NQQ  Var_08    H1   C6   C4   C5    179.39  30.0  3

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
 NQQ  plan-1  CL   0.020
 NQQ  plan-1  N3   0.020
 NQQ  plan-1  N4   0.020
 NQQ  plan-1  C16  0.020
 NQQ  plan-1  C15  0.020
 NQQ  plan-1  C14  0.020
 NQQ  plan-1  C13  0.020
 NQQ  plan-1  C12  0.020
 NQQ  plan-1  N2   0.020
 NQQ  plan-1  H9   0.020
 NQQ  plan-1  H10  0.020
 NQQ  plan-1  C17  0.020
 NQQ  plan-2  C8   0.020
 NQQ  plan-2  N1   0.020
 NQQ  plan-2  N2   0.020
 NQQ  plan-2  C11  0.020
 NQQ  plan-2  C10  0.020
 NQQ  plan-2  C9   0.020
 NQQ  plan-2  N    0.020
 NQQ  plan-2  C    0.020
 NQQ  plan-2  C18  0.020
 NQQ  plan-2  C7   0.020
 NQQ  plan-2  C1   0.020
 NQQ  plan-2  O    0.020
 NQQ  plan-2  H12  0.020
 NQQ  plan-2  H13  0.020
 NQQ  plan-2  H17  0.020
 NQQ  plan-2  C2   0.020

