# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:56:01 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 6-azanyl-4-(3-methylphenyl)-1~{H}-pyrrolo[2,3-b]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)c2cc(N)nc3[nH]cc(C#N)c23
#
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
 A3K  A3K  6-azanyl-4-(3-methylphenyl)-1~{H}-pyrrolo[2,3-b]pyridine-3-carbonitrile  ligand  31  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3K
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
 A3K  C01  C  CH3   0  -0.725   4.3149   1.7887  -1.2739
 A3K  C23  C  CR6   0   0.115   3.3931   0.9839  -0.4046
 A3K  C21  C  CR16  0  -0.349   2.0129   1.1161  -0.5200
 A3K  C24  C  CR16  0  -0.306   3.8942   0.0703   0.5207
 A3K  C26  C  CR16  0  -0.225   3.0372  -0.6903   1.3033
 A3K  C28  C  CR16  0  -0.308   1.6638  -0.5558   1.1725
 A3K  C30  C  CR6   0   0.050   1.1416   0.3519   0.2542
 A3K  C31  C  CR6   0   0.145  -0.3167   0.5362   0.1266
 A3K  C15  C  CR56  0   0.056  -1.2043  -0.5364  -0.0675
 A3K  C19  C  CR16  0  -0.463  -0.8704   1.7967   0.2039
 A3K  C18  C  CR6   0   0.463  -2.2727   1.9866   0.1164
 A3K  N05  N  NH2   0  -0.841  -2.7890   3.2454   0.1580
 A3K  N17  N  N     0  -0.483  -3.1219   0.9803  -0.0408
 A3K  C16  C  CR56  0   0.478  -2.5688  -0.2189  -0.1333
 A3K  N13  N  NR15  0  -0.660  -3.2624  -1.3786  -0.3333
 A3K  C10  C  CR15  0   0.037  -2.4063  -2.4205  -0.4177
 A3K  C12  C  CR5   0  -0.202  -1.1194  -1.9595  -0.2636
 A3K  C09  C  CSP   0  -0.056   0.0186  -2.7853  -0.3548
 A3K  N08  N  NS    0  -0.264   0.9348  -3.4826  -0.4418
 A3K  H1   H  HCH3  0   0.251   4.5384   1.2586  -2.2020
 A3K  H2   H  HCH3  0   0.245   3.8728   2.7463  -1.5472
 A3K  H3   H  HCH3  0   0.245   5.2646   1.9831  -0.7767
 A3K  H4   H  HCR6  0   0.248   1.6028   1.8223  -1.2335
 A3K  H5   H  HCR6  0   0.250   4.9660  -0.0436   0.6338
 A3K  H6   H  HCR6  0   0.256   3.4430  -1.3867   2.0258
 A3K  H7   H  HCR6  0   0.257   1.0011  -1.1341   1.8035
 A3K  H8   H  HCR6  0   0.268  -0.2319   2.6573   0.3596
 A3K  H9   H  HNH2  0   0.394  -2.2261   3.9714   0.5677
 A3K  H10  H  HNH2  0   0.385  -3.7744   3.3259   0.3468
 A3K  H11  H  HNR5  0   0.423  -4.2651  -1.4460  -0.4155
 A3K  H12  H  HCR5  0   0.316  -2.7544  -3.4256  -0.5884

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
 A3K  C01  C23  single    1.501  0.020  1.501
 A3K  C23  C24  aromatic  1.394  0.020  1.394
 A3K  C23  C21  aromatic  1.391  0.020  1.391
 A3K  C24  C26  aromatic  1.388  0.020  1.388
 A3K  C21  C30  aromatic  1.394  0.020  1.394
 A3K  N08  C09  triple    1.155  0.020  1.155
 A3K  C26  C28  aromatic  1.386  0.020  1.386
 A3K  C09  C12  single    1.409  0.020  1.409
 A3K  C30  C28  aromatic  1.393  0.020  1.393
 A3K  C30  C31  single    1.475  0.020  1.475
 A3K  C12  C15  aromatic  1.439  0.020  1.439
 A3K  C12  C10  aromatic  1.376  0.020  1.376
 A3K  C31  C15  aromatic  1.406  0.020  1.406
 A3K  C31  C19  aromatic  1.379  0.020  1.379
 A3K  C15  C16  aromatic  1.402  0.020  1.402
 A3K  C10  N13  aromatic  1.351  0.020  1.351
 A3K  C19  C18  aromatic  1.418  0.020  1.418
 A3K  N13  C16  aromatic  1.366  0.020  1.366
 A3K  C16  N17  aromatic  1.324  0.020  1.324
 A3K  C18  N17  aromatic  1.326  0.020  1.326
 A3K  C18  N05  single    1.361  0.020  1.361
 A3K  C01  H1   single    0.970  0.020  1.090
 A3K  C01  H2   single    0.970  0.020  1.090
 A3K  C01  H3   single    0.970  0.020  1.090
 A3K  C21  H4   single    0.930  0.020  1.080
 A3K  C24  H5   single    0.930  0.020  1.080
 A3K  C26  H6   single    0.930  0.020  1.080
 A3K  C28  H7   single    0.930  0.020  1.080
 A3K  C19  H8   single    0.930  0.020  1.080
 A3K  N05  H9   single    0.890  0.020  1.040
 A3K  N05  H10  single    0.890  0.020  1.040
 A3K  N13  H11  single    0.860  0.020  1.020
 A3K  C10  H12  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
 A3K  H3   C01  H2   108.14  3.000
 A3K  H3   C01  H1   107.22  3.000
 A3K  H2   C01  H1   107.25  3.000
 A3K  H3   C01  C23  111.52  3.000
 A3K  H2   C01  C23  111.55  3.000
 A3K  H1   C01  C23  110.96  3.000
 A3K  C24  C23  C21  118.30  3.000
 A3K  C21  C23  C01  120.68  3.000
 A3K  C24  C23  C01  121.01  3.000
 A3K  H4   C21  C30  119.09  3.000
 A3K  H4   C21  C23  119.44  3.000
 A3K  C30  C21  C23  121.46  3.000
 A3K  H5   C24  C26  119.62  3.000
 A3K  H5   C24  C23  119.59  3.000
 A3K  C26  C24  C23  120.78  3.000
 A3K  H6   C26  C28  119.79  3.000
 A3K  H6   C26  C24  119.84  3.000
 A3K  C28  C26  C24  120.36  3.000
 A3K  H7   C28  C30  120.20  3.000
 A3K  H7   C28  C26  119.98  3.000
 A3K  C30  C28  C26  119.80  3.000
 A3K  C31  C30  C28  120.60  3.000
 A3K  C31  C30  C21  120.09  3.000
 A3K  C28  C30  C21  119.29  3.000
 A3K  C19  C31  C15  116.85  3.000
 A3K  C19  C31  C30  120.41  3.000
 A3K  C15  C31  C30  122.74  3.000
 A3K  C12  C15  C16  105.96  3.000
 A3K  C16  C15  C31  116.62  3.000
 A3K  C12  C15  C31  137.40  3.000
 A3K  H8   C19  C18  119.06  3.000
 A3K  H8   C19  C31  119.85  3.000
 A3K  C18  C19  C31  121.07  3.000
 A3K  N17  C18  N05  117.55  3.000
 A3K  N05  C18  C19  119.80  3.000
 A3K  N17  C18  C19  122.62  3.000
 A3K  H10  N05  H9   114.44  3.000
 A3K  H10  N05  C18  116.80  3.000
 A3K  H9   N05  C18  117.88  3.000
 A3K  C16  N17  C18  115.35  3.000
 A3K  N13  C16  N17  124.55  3.000
 A3K  N17  C16  C15  127.47  3.000
 A3K  N13  C16  C15  107.98  3.000
 A3K  H11  N13  C10  124.99  3.000
 A3K  H11  N13  C16  125.00  3.000
 A3K  C10  N13  C16  110.00  3.000
 A3K  H12  C10  C12  129.25  3.000
 A3K  H12  C10  N13  121.64  3.000
 A3K  C12  C10  N13  109.11  3.000
 A3K  C09  C12  C10  123.49  3.000
 A3K  C10  C12  C15  106.94  3.000
 A3K  C09  C12  C15  129.50  3.000
 A3K  N08  C09  C12  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
 A3K  CONST_01  C28  C26  C24  C23    0.00   0.0  0
 A3K  CONST_02  C28  C30  C21  C23    0.00   0.0  0
 A3K  CONST_03  C31  C30  C21  C23  180.00   0.0  0
 A3K  CONST_04  C26  C24  C23  C21    0.00   0.0  0
 A3K  CONST_05  C26  C28  C30  C21    0.00   0.0  0
 A3K  CONST_08  C30  C21  C23  C24    0.00   0.0  0
 A3K  CONST_09  C30  C28  C26  C24    0.00   0.0  0
 A3K  CONST_10  C31  C30  C28  C26  180.00   0.0  0
 A3K  CONST_13  C12  C15  C31  C30    0.00   0.0  0
 A3K  CONST_14  C16  C15  C31  C30  180.00   0.0  0
 A3K  CONST_15  C18  C19  C31  C30  180.00   0.0  0
 A3K  CONST_16  C10  C12  C15  C31  180.00   0.0  0
 A3K  CONST_17  N13  C16  C15  C31  180.00   0.0  0
 A3K  CONST_18  N17  C16  C15  C31    0.00   0.0  0
 A3K  CONST_19  N17  C18  C19  C31    0.00   0.0  0
 A3K  CONST_20  N13  C10  C12  C15    0.00   0.0  0
 A3K  CONST_21  C18  C19  C31  C15    0.00   0.0  0
 A3K  CONST_22  C10  N13  C16  C15    0.00   0.0  0
 A3K  CONST_23  C18  N17  C16  C15    0.00   0.0  0
 A3K  CONST_24  C12  C15  C31  C19  180.00   0.0  0
 A3K  CONST_25  C16  C15  C31  C19    0.00   0.0  0
 A3K  CONST_26  C16  N17  C18  C19    0.00   0.0  0
 A3K  CONST_27  N13  C16  N17  C18  180.00   0.0  0
 A3K  CONST_28  C12  C15  C16  N17  180.00   0.0  0
 A3K  CONST_29  C10  N13  C16  N17  180.00   0.0  0
 A3K  CONST_30  C10  C12  C15  C16    0.00   0.0  0
 A3K  CONST_31  C12  C10  N13  C16    0.00   0.0  0
 A3K  CONST_32  C12  C15  C16  N13    0.00   0.0  0
 A3K  CONST_33  C26  C24  C23  C01  180.00   0.0  0
 A3K  CONST_34  C30  C21  C23  C01  180.00   0.0  0
 A3K  CONST_35  C09  C12  C15  C31    0.00   0.0  0
 A3K  CONST_36  N05  C18  C19  C31  180.00   0.0  0
 A3K  CONST_37  C16  N17  C18  N05  180.00   0.0  0
 A3K  CONST_38  C09  C12  C15  C16  180.00   0.0  0
 A3K  CONST_39  C09  C12  C10  N13  180.00   0.0  0
 A3K  CONST_40  H6   C26  C24  C23  180.00   0.0  0
 A3K  CONST_41  H5   C24  C23  C21  180.00   0.0  0
 A3K  CONST_42  H7   C28  C30  C21  180.00   0.0  0
 A3K  CONST_43  H4   C21  C23  C24  180.00   0.0  0
 A3K  CONST_44  H8   C19  C31  C30    0.00   0.0  0
 A3K  CONST_45  H12  C10  C12  C15  180.00   0.0  0
 A3K  CONST_46  H11  N13  C16  C15  180.00   0.0  0
 A3K  Var_01    H1   C01  C23  C21  -89.73  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
 A3K  plan-1  C01  0.020
 A3K  plan-1  C23  0.020
 A3K  plan-1  C21  0.020
 A3K  plan-1  C24  0.020
 A3K  plan-1  C26  0.020
 A3K  plan-1  C28  0.020
 A3K  plan-1  C30  0.020
 A3K  plan-1  C31  0.020
 A3K  plan-1  H4   0.020
 A3K  plan-1  H5   0.020
 A3K  plan-1  H6   0.020
 A3K  plan-1  H7   0.020
 A3K  plan-2  C30  0.020
 A3K  plan-2  C31  0.020
 A3K  plan-2  C15  0.020
 A3K  plan-2  C19  0.020
 A3K  plan-2  C18  0.020
 A3K  plan-2  N05  0.020
 A3K  plan-2  N17  0.020
 A3K  plan-2  C16  0.020
 A3K  plan-2  N13  0.020
 A3K  plan-2  C10  0.020
 A3K  plan-2  C12  0.020
 A3K  plan-2  C09  0.020
 A3K  plan-2  N08  0.020
 A3K  plan-2  H8   0.020
 A3K  plan-2  H11  0.020
 A3K  plan-2  H12  0.020
 A3K  plan-3  C18  0.020
 A3K  plan-3  N05  0.020
 A3K  plan-3  H9   0.020
 A3K  plan-3  H10  0.020

