# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 21:40:40 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-chloranyl-4-[[1-methyl-3-[(2~{S})-2-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](O)CN1C(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12
#
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
 NR8  NR8  2-chloranyl-4-[[1-methyl-3-[(2~{S})-2-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile  ligand  44  26  .  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_NR8
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
 NR8  C1   C   CR16  0  -0.053  25.1637   -9.0879  11.9653
 NR8  C2   C   CR16  0  -0.384  25.2110   -9.3592  13.3079
 NR8  C3   C   CR6   0   0.516  26.3955   -9.8794  13.8629
 NR8  C4   C   CR6   0  -0.087  27.4679  -10.0840  12.9613
 NR8  C5   C   CSP   0   0.029  28.7032  -10.5947  13.4283
 NR8  C6   C   CR6   0   0.260  25.5315   -9.9441  16.1491
 NR8  C7   C   CR16  0  -0.350  24.9561  -11.0388  16.7936
 NR8  C8   C   CR56  0   0.330  24.0197  -10.7748  17.7717
 NR8  C9   C   CR5   0   0.677  22.4684  -10.8575  19.4059
 NR8  C10  C   CR56  0   0.341  23.6389   -9.4640  18.0805
 NR8  C11  C   CR16  0  -0.319  24.1991   -8.3813  17.4322
 NR8  C12  C   CR16  0  -0.294  25.1662   -8.6385  16.4656
 NR8  C15  C   CH1   0   0.033  22.3781  -13.7340  17.7317
 NR8  C16  C   CH2   0  -0.454  22.5032  -15.2509  17.8013
 NR8  C17  C   CH3   0  -0.676  23.8202  -15.8167  17.2816
 NR8  O    O   O     0  -0.498  21.7002  -11.2836  20.2478
 NR8  N3   N   NR5   0  -0.599  23.2957  -11.6067  18.5975
 NR8  O1   O   OH1   0  -0.667  22.5567  -13.3244  16.3927
 NR8  N4   N   NR5   0  -0.587  22.6907   -9.5419  19.0732
 NR8  N2   N   NH1   0  -0.777  26.5222  -10.1799  15.1652
 NR8  N    N   N     0  -0.413  26.1795   -9.2789  11.1106
 NR8  C    C   CR6   0   0.146  27.2759   -9.7619  11.6161
 NR8  CL   CL  CL    0  -0.067  28.5925  -10.0154  10.5263
 NR8  N1   N   NS    0  -0.232  29.7011  -10.9939  13.8474
 NR8  H1   H   HCR6  0   0.289  24.2521   -8.6945  11.5334
 NR8  H2   H   HCR6  0   0.301  24.3403   -9.1818  13.9215
 NR8  H3   H   HCR6  0   0.279  25.2338  -12.0480  16.5215
 NR8  H4   H   HCR6  0   0.281  23.9157   -7.3652  17.6716
 NR8  H5   H   HCR6  0   0.277  25.6440   -7.8122  15.9559
 NR8  H6   H   HCH3  0   0.270  21.3153   -8.7802  20.4159
 NR8  H7   H   HCH3  0   0.257  22.7598   -7.7836  20.2046
 NR8  H8   H   HCH3  0   0.257  21.5111   -7.8217  18.9452
 NR8  H9   H   HCH2  0   0.271  23.2077  -13.3607  19.6885
 NR8  H10  H   HCH2  0   0.265  24.4041  -13.3326  18.4047
 NR8  H11  H   HCH1  0   0.228  21.3718  -13.4654  18.0805
 NR8  H12  H   HCH2  0   0.238  21.6739  -15.6858  17.2381
 NR8  H13  H   HCH2  0   0.230  22.3531  -15.5548  18.8408
 NR8  H14  H   HCH3  0   0.234  23.8107  -16.9052  17.3404
 NR8  H15  H   HCH3  0   0.228  23.9916  -15.5468  16.2403
 NR8  H16  H   HCH3  0   0.221  24.6786  -15.4742  17.8613
 NR8  H17  H   HOH1  0   0.454  22.1918  -12.4413  16.2862
 NR8  H18  H   HNH1  0   0.417  27.3540  -10.6649  15.4688
 NR8  C13  C   CH3   0  -0.537  22.0371   -8.4168  19.6909
 NR8  C14  C   CH2   0  -0.335  23.3816  -13.0483  18.6582

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
 NR8  CL   C    single    1.728  0.020  1.728
 NR8  N    C    aromatic  1.300  0.020  1.300
 NR8  N    C1   aromatic  1.341  0.020  1.341
 NR8  C    C4   aromatic  1.396  0.020  1.396
 NR8  C1   C2   aromatic  1.371  0.020  1.371
 NR8  C4   C5   single    1.416  0.020  1.416
 NR8  C4   C3   aromatic  1.416  0.020  1.416
 NR8  C5   N1   triple    1.154  0.020  1.154
 NR8  C2   C3   aromatic  1.408  0.020  1.408
 NR8  C3   N2   single    1.342  0.020  1.342
 NR8  N2   C6   single    1.416  0.020  1.416
 NR8  C6   C12  aromatic  1.392  0.020  1.392
 NR8  C6   C7   aromatic  1.395  0.020  1.395
 NR8  O1   C15  single    1.412  0.020  1.412
 NR8  C12  C11  aromatic  1.391  0.020  1.391
 NR8  C7   C8   aromatic  1.380  0.020  1.380
 NR8  C17  C16  single    1.525  0.020  1.525
 NR8  C11  C10  aromatic  1.381  0.020  1.381
 NR8  C15  C16  single    1.524  0.020  1.524
 NR8  C15  C14  single    1.528  0.020  1.528
 NR8  C8   C10  aromatic  1.400  0.020  1.400
 NR8  C8   N3   single    1.378  0.020  1.378
 NR8  C10  N4   single    1.375  0.020  1.375
 NR8  N3   C14  single    1.445  0.020  1.445
 NR8  N3   C9   single    1.378  0.020  1.378
 NR8  N4   C9   single    1.375  0.020  1.375
 NR8  N4   C13  single    1.440  0.020  1.440
 NR8  C9   O    double    1.217  0.020  1.217
 NR8  C1   H1   single    0.930  0.020  1.080
 NR8  C2   H2   single    0.930  0.020  1.080
 NR8  C7   H3   single    0.930  0.020  1.080
 NR8  C11  H4   single    0.930  0.020  1.080
 NR8  C12  H5   single    0.930  0.020  1.080
 NR8  C13  H6   single    0.970  0.020  1.090
 NR8  C13  H7   single    0.970  0.020  1.090
 NR8  C13  H8   single    0.970  0.020  1.090
 NR8  C14  H9   single    0.970  0.020  1.090
 NR8  C14  H10  single    0.970  0.020  1.090
 NR8  C15  H11  single    0.970  0.020  1.090
 NR8  C16  H12  single    0.970  0.020  1.090
 NR8  C16  H13  single    0.970  0.020  1.090
 NR8  C17  H14  single    0.970  0.020  1.090
 NR8  C17  H15  single    0.970  0.020  1.090
 NR8  C17  H16  single    0.970  0.020  1.090
 NR8  O1   H17  single    0.850  0.020  0.980
 NR8  N2   H18  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
 NR8  H1   C1   N    115.80  3.000
 NR8  H1   C1   C2   119.46  3.000
 NR8  N    C1   C2   124.75  3.000
 NR8  H2   C2   C3   121.01  3.000
 NR8  H2   C2   C1   119.76  3.000
 NR8  C3   C2   C1   119.23  3.000
 NR8  N2   C3   C4   120.92  3.000
 NR8  N2   C3   C2   122.99  3.000
 NR8  C4   C3   C2   116.08  3.000
 NR8  C    C4   C5   121.39  3.000
 NR8  C5   C4   C3   120.19  3.000
 NR8  C    C4   C3   118.42  3.000
 NR8  N1   C5   C4   180.00  3.000
 NR8  N2   C6   C12  119.85  3.000
 NR8  C12  C6   C7   121.52  3.000
 NR8  N2   C6   C7   118.63  3.000
 NR8  H3   C7   C8   122.09  3.000
 NR8  H3   C7   C6   120.68  3.000
 NR8  C8   C7   C6   117.23  3.000
 NR8  N3   C8   C10  106.88  3.000
 NR8  N3   C8   C7   131.76  3.000
 NR8  C10  C8   C7   121.36  3.000
 NR8  N4   C9   N3   106.33  3.000
 NR8  N4   C9   O    127.19  3.000
 NR8  N3   C9   O    126.47  3.000
 NR8  N4   C10  C11  131.55  3.000
 NR8  N4   C10  C8   107.09  3.000
 NR8  C11  C10  C8   121.36  3.000
 NR8  H4   C11  C12  120.63  3.000
 NR8  H4   C11  C10  121.76  3.000
 NR8  C12  C11  C10  117.60  3.000
 NR8  H5   C12  C11  119.53  3.000
 NR8  H5   C12  C6   119.56  3.000
 NR8  C11  C12  C6   120.91  3.000
 NR8  H11  C15  O1   110.26  3.000
 NR8  H11  C15  C16  107.71  3.000
 NR8  O1   C15  C16  108.78  3.000
 NR8  H11  C15  C14  107.41  3.000
 NR8  C16  C15  C14  111.41  3.000
 NR8  O1   C15  C14  111.21  3.000
 NR8  H13  C16  H12  105.97  3.000
 NR8  H13  C16  C17  109.85  3.000
 NR8  H12  C16  C17  109.40  3.000
 NR8  H13  C16  C15  108.00  3.000
 NR8  H12  C16  C15  108.08  3.000
 NR8  C17  C16  C15  115.14  3.000
 NR8  H16  C17  H15  107.84  3.000
 NR8  H16  C17  H14  106.96  3.000
 NR8  H15  C17  H14  107.48  3.000
 NR8  H16  C17  C16  112.46  3.000
 NR8  H15  C17  C16  111.70  3.000
 NR8  H14  C17  C16  110.16  3.000
 NR8  C14  N3   C9   123.59  3.000
 NR8  C9   N3   C8   109.80  3.000
 NR8  C14  N3   C8   126.60  3.000
 NR8  H17  O1   C15  108.87  3.000
 NR8  C13  N4   C10  125.33  3.000
 NR8  C13  N4   C9   124.77  3.000
 NR8  C10  N4   C9   109.90  3.000
 NR8  H18  N2   C6   116.58  3.000
 NR8  H18  N2   C3   118.49  3.000
 NR8  C6   N2   C3   124.80  3.000
 NR8  C    N    C1   116.35  3.000
 NR8  CL   C    N    116.86  3.000
 NR8  N    C    C4   125.17  3.000
 NR8  CL   C    C4   117.97  3.000
 NR8  H8   C13  H7   109.00  3.000
 NR8  H8   C13  H6   108.60  3.000
 NR8  H7   C13  H6   108.70  3.000
 NR8  H8   C13  N4   110.62  3.000
 NR8  H7   C13  N4   110.80  3.000
 NR8  H6   C13  N4   109.06  3.000
 NR8  H10  C14  H9   107.11  3.000
 NR8  H10  C14  N3   107.80  3.000
 NR8  H9   C14  N3   108.41  3.000
 NR8  H10  C14  C15  110.95  3.000
 NR8  H9   C14  C15  109.85  3.000
 NR8  N3   C14  C15  112.52  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
 NR8  CONST_01  C4   C    N    C1      0.00   0.0  0
 NR8  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 NR8  CONST_03  C    N    C1   C2      0.00   0.0  0
 NR8  CONST_04  C    C4   C3   C2      0.00   0.0  0
 NR8  CONST_05  N    C    C4   C3      0.00   0.0  0
 NR8  CONST_06  N    C1   C2   C3      0.00   0.0  0
 NR8  CONST_07  C10  C11  C12  C6      0.00   0.0  0
 NR8  CONST_08  C10  C8   C7   C6      0.00   0.0  0
 NR8  CONST_09  C11  C12  C6   C7      0.00   0.0  0
 NR8  CONST_10  C11  C10  C8   C7      0.00   0.0  0
 NR8  CONST_11  C12  C6   C7   C8      0.00   0.0  0
 NR8  CONST_12  C12  C11  C10  C8      0.00   0.0  0
 NR8  CONST_13  C9   N4   C10  C8      0.00   0.0  0
 NR8  CONST_14  N4   C9   N3   C8      0.00   0.0  0
 NR8  CONST_15  C10  C8   N3   C9      0.00   0.0  0
 NR8  CONST_16  N3   C9   N4   C10     0.00   0.0  0
 NR8  CONST_17  N4   C10  C8   N3      0.00   0.0  0
 NR8  CONST_18  CL   C    N    C1    180.00   0.0  0
 NR8  CONST_19  N2   C3   C2   C1    180.00   0.0  0
 NR8  CONST_20  C5   C4   C3   C2    180.00   0.0  0
 NR8  CONST_21  CL   C    C4   C3    180.00   0.0  0
 NR8  CONST_22  N    C    C4   C5    180.00   0.0  0
 NR8  CONST_23  N2   C6   C7   C8    180.00   0.0  0
 NR8  CONST_24  N2   C6   C12  C11   180.00   0.0  0
 NR8  CONST_25  C    C4   C3   N2    180.00   0.0  0
 NR8  CONST_26  C13  N4   C10  C8    180.00   0.0  0
 NR8  CONST_27  O    C9   N3   C8    180.00   0.0  0
 NR8  CONST_28  C14  N3   C8   C10   180.00   0.0  0
 NR8  CONST_29  O    C9   N4   C10   180.00   0.0  0
 NR8  CONST_30  N3   C9   N4   C13   180.00   0.0  0
 NR8  CONST_31  N4   C9   N3   C14   180.00   0.0  0
 NR8  CONST_32  H1   C1   C2   C3    180.00   0.0  0
 NR8  CONST_33  H2   C2   C3   C4    180.00   0.0  0
 NR8  CONST_34  H4   C11  C12  C6    180.00   0.0  0
 NR8  CONST_35  H5   C12  C6   C7    180.00   0.0  0
 NR8  CONST_36  H3   C7   C8   C10   180.00   0.0  0
 NR8  CONST_37  O    C9   N4   C13     0.00   0.0  0
 NR8  CONST_38  O    C9   N3   C14     0.00   0.0  0
 NR8  Var_01    C6   N2   C3   C2     -3.95  30.0  2
 NR8  Var_02    C12  C6   N2   C3    -65.25  30.0  2
 NR8  Var_03    C15  C14  N3   C8    -91.87  30.0  3
 NR8  Var_04    H6   C13  N4   C9     -2.78  30.0  3
 NR8  Var_05    H14  C17  C16  C15  -178.26  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NR8  chir_01  C15  O1  C16  C14  negativ

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
 NR8  plan-1  C1   0.020
 NR8  plan-1  C2   0.020
 NR8  plan-1  C3   0.020
 NR8  plan-1  C4   0.020
 NR8  plan-1  C5   0.020
 NR8  plan-1  N2   0.020
 NR8  plan-1  N    0.020
 NR8  plan-1  C    0.020
 NR8  plan-1  CL   0.020
 NR8  plan-1  N1   0.020
 NR8  plan-1  H1   0.020
 NR8  plan-1  H2   0.020
 NR8  plan-2  C6   0.020
 NR8  plan-2  C7   0.020
 NR8  plan-2  C8   0.020
 NR8  plan-2  C9   0.020
 NR8  plan-2  C10  0.020
 NR8  plan-2  C11  0.020
 NR8  plan-2  C12  0.020
 NR8  plan-2  O    0.020
 NR8  plan-2  N3   0.020
 NR8  plan-2  N4   0.020
 NR8  plan-2  N2   0.020
 NR8  plan-2  H3   0.020
 NR8  plan-2  H4   0.020
 NR8  plan-2  H5   0.020
 NR8  plan-2  C13  0.020
 NR8  plan-2  C14  0.020

