# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 18:53:07 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-[3-(6-cyano-9H-pyrrolo[2,3-b:5,4-c']dipyridin-3-yl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cccc(c1)c2cnc3[nH]c4cnc(cc4c3c2)C#N
#
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
 3XK  3XK  N-[3-(6-cyano-9H-pyrrolo[2,3-b:5,4-c']dipyridin-3-yl)phenyl]acetamide  ligand  38  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XK
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
 3XK  C7   C  CR56  0   0.145  -3.1579  -0.1924  -0.1115
 3XK  C9   C  CR6   0   0.174  -5.2423   0.7228  -0.7275
 3XK  N1   N  N     0  -0.420  -0.6117  -2.4459   0.9280
 3XK  C2   C  CR16  0  -0.098   0.4918  -1.7153   0.9363
 3XK  N2   N  NR15  0  -0.756  -2.9549  -2.3652   0.4805
 3XK  C10  C  CR16  0  -0.385  -3.8834   0.9133  -0.5277
 3XK  C4   C  CR56  0   0.024  -1.7827  -0.4480   0.2064
 3XK  N3   N  N     0  -0.411  -5.8902  -0.4373  -0.5485
 3XK  N5   N  NS    0  -0.247  -6.7028   2.7117  -1.5002
 3XK  C6   C  CR56  0   0.287  -3.8392  -1.4122   0.0758
 3XK  C19  C  CSP   0   0.050  -6.0546   1.8233  -1.1576
 3XK  C8   C  CR16  0  -0.094  -5.2128  -1.4926  -0.1541
 3XK  C3   C  CR56  0   0.478  -1.7091  -1.8087   0.5657
 3XK  C5   C  CR16  0  -0.282  -0.6117   0.2917   0.2218
 3XK  C1   C  CR6   0  -0.020   0.5627  -0.3540   0.5929
 3XK  C11  C  CR6   0   0.105   1.8512   0.3618   0.6353
 3XK  C16  C  CR16  0  -0.422   3.0167  -0.2614   0.2033
 3XK  C15  C  CR6   0   0.404   4.2485   0.3952   0.2334
 3XK  N4   N  NH1   0  -0.739   5.3558  -0.3320  -0.2120
 3XK  C17  C  C     0   0.511   6.6032   0.1085  -0.5274
 3XK  O1   O  O     0  -0.470   6.9643   1.2654  -0.4082
 3XK  C18  C  CH3   0  -0.785   7.5101  -0.9611  -1.0814
 3XK  C14  C  CR16  0  -0.323   4.3082   1.7074   0.7037
 3XK  C13  C  CR16  0  -0.230   3.1413   2.3279   1.1286
 3XK  C12  C  CR16  0  -0.330   1.9211   1.6750   1.1016
 3XK  H1   H  HCR6  0   0.270   1.3934  -2.2286   1.2526
 3XK  H2   H  HNR5  0   0.424  -3.1741  -3.3287   0.6812
 3XK  H3   H  HCR6  0   0.291  -3.4258   1.8794  -0.6922
 3XK  H4   H  HCR6  0   0.292  -5.7577  -2.4191  -0.0153
 3XK  H5   H  HCR6  0   0.273  -0.6066   1.3365  -0.0632
 3XK  H6   H  HCR6  0   0.269   2.9707  -1.2715  -0.1888
 3XK  H7   H  HNH1  0   0.416   5.1792  -1.3102  -0.3817
 3XK  H8   H  HCH3  0   0.277   7.5155  -0.8918  -2.1707
 3XK  H9   H  HCH3  0   0.269   8.5282  -0.7947  -0.7357
 3XK  H10  H  HCH3  0   0.256   7.2074  -1.9713  -0.8118
 3XK  H11  H  HCR6  0   0.280   5.2412   2.2435   0.7492
 3XK  H12  H  HCR6  0   0.262   3.1963   3.3426   1.5011
 3XK  H13  H  HCR6  0   0.257   1.0319   2.1754   1.4632

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
 3XK  N5   C19  triple    1.152  0.020  1.152
 3XK  C19  C9   single    1.434  0.020  1.434
 3XK  C9   C10  aromatic  1.387  0.020  1.387
 3XK  C9   N3   aromatic  1.341  0.020  1.341
 3XK  C10  C7   aromatic  1.386  0.020  1.386
 3XK  N3   C8   aromatic  1.315  0.020  1.315
 3XK  C7   C6   aromatic  1.410  0.020  1.410
 3XK  C7   C4   aromatic  1.434  0.020  1.434
 3XK  C8   C6   aromatic  1.395  0.020  1.395
 3XK  C12  C13  aromatic  1.384  0.020  1.384
 3XK  C12  C11  aromatic  1.395  0.020  1.395
 3XK  C13  C14  aromatic  1.388  0.020  1.388
 3XK  C6   N2   aromatic  1.362  0.020  1.362
 3XK  C5   C4   aromatic  1.385  0.020  1.385
 3XK  C5   C1   aromatic  1.391  0.020  1.391
 3XK  C4   C3   aromatic  1.409  0.020  1.409
 3XK  C14  C15  aromatic  1.395  0.020  1.395
 3XK  C11  C1   single    1.475  0.020  1.475
 3XK  C11  C16  aromatic  1.390  0.020  1.390
 3XK  C1   C2   aromatic  1.406  0.020  1.406
 3XK  N2   C3   aromatic  1.367  0.020  1.367
 3XK  C3   N1   aromatic  1.320  0.020  1.320
 3XK  C2   N1   aromatic  1.323  0.020  1.323
 3XK  C16  C15  aromatic  1.396  0.020  1.396
 3XK  C15  N4   single    1.398  0.020  1.398
 3XK  N4   C17  single    1.360  0.020  1.360
 3XK  C17  O1   double    1.218  0.020  1.218
 3XK  C17  C18  single    1.508  0.020  1.508
 3XK  C2   H1   single    0.930  0.020  1.080
 3XK  N2   H2   single    0.860  0.020  1.020
 3XK  C10  H3   single    0.930  0.020  1.080
 3XK  C8   H4   single    0.930  0.020  1.080
 3XK  C5   H5   single    0.930  0.020  1.080
 3XK  C16  H6   single    0.930  0.020  1.080
 3XK  N4   H7   single    0.860  0.020  1.020
 3XK  C18  H8   single    0.970  0.020  1.090
 3XK  C18  H9   single    0.970  0.020  1.090
 3XK  C18  H10  single    0.970  0.020  1.090
 3XK  C14  H11  single    0.930  0.020  1.080
 3XK  C13  H12  single    0.930  0.020  1.080
 3XK  C12  H13  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
 3XK  C6   C7   C4   106.24  3.000
 3XK  C4   C7   C10  135.26  3.000
 3XK  C6   C7   C10  118.49  3.000
 3XK  C19  C9   N3   115.49  3.000
 3XK  N3   C9   C10  124.97  3.000
 3XK  C19  C9   C10  119.53  3.000
 3XK  C3   N1   C2   115.37  3.000
 3XK  H1   C2   C1   119.18  3.000
 3XK  H1   C2   N1   115.70  3.000
 3XK  C1   C2   N1   125.11  3.000
 3XK  H2   N2   C3   125.08  3.000
 3XK  H2   N2   C6   125.93  3.000
 3XK  C3   N2   C6   108.99  3.000
 3XK  H3   C10  C9   121.02  3.000
 3XK  H3   C10  C7   122.45  3.000
 3XK  C9   C10  C7   116.52  3.000
 3XK  C5   C4   C3   117.94  3.000
 3XK  C3   C4   C7   106.18  3.000
 3XK  C5   C4   C7   135.88  3.000
 3XK  C8   N3   C9   119.05  3.000
 3XK  C8   C6   N2   130.40  3.000
 3XK  N2   C6   C7   109.35  3.000
 3XK  C8   C6   C7   120.25  3.000
 3XK  N5   C19  C9   180.00  3.000
 3XK  H4   C8   C6   121.55  3.000
 3XK  H4   C8   N3   117.75  3.000
 3XK  C6   C8   N3   120.70  3.000
 3XK  C4   C3   N2   109.24  3.000
 3XK  N2   C3   N1   125.33  3.000
 3XK  C4   C3   N1   125.43  3.000
 3XK  H5   C5   C1   120.94  3.000
 3XK  H5   C5   C4   121.08  3.000
 3XK  C1   C5   C4   117.97  3.000
 3XK  C11  C1   C5   121.35  3.000
 3XK  C11  C1   C2   120.47  3.000
 3XK  C5   C1   C2   118.18  3.000
 3XK  C12  C11  C16  118.92  3.000
 3XK  C16  C11  C1   120.39  3.000
 3XK  C12  C11  C1   120.68  3.000
 3XK  H6   C16  C15  118.89  3.000
 3XK  H6   C16  C11  119.62  3.000
 3XK  C15  C16  C11  121.47  3.000
 3XK  C14  C15  N4   124.26  3.000
 3XK  N4   C15  C16  116.58  3.000
 3XK  C14  C15  C16  119.16  3.000
 3XK  H7   N4   C17  115.84  3.000
 3XK  H7   N4   C15  114.81  3.000
 3XK  C17  N4   C15  129.20  3.000
 3XK  C18  C17  O1   122.11  3.000
 3XK  C18  C17  N4   114.02  3.000
 3XK  O1   C17  N4   123.85  3.000
 3XK  H10  C18  H9   108.87  3.000
 3XK  H10  C18  H8   107.91  3.000
 3XK  H9   C18  H8   107.62  3.000
 3XK  H10  C18  C17  113.58  3.000
 3XK  H9   C18  C17  109.73  3.000
 3XK  H8   C18  C17  108.94  3.000
 3XK  H11  C14  C13  119.52  3.000
 3XK  H11  C14  C15  121.30  3.000
 3XK  C13  C14  C15  119.18  3.000
 3XK  H12  C13  C12  119.58  3.000
 3XK  H12  C13  C14  118.80  3.000
 3XK  C12  C13  C14  121.61  3.000
 3XK  H13  C12  C13  119.98  3.000
 3XK  H13  C12  C11  120.36  3.000
 3XK  C13  C12  C11  119.65  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
 3XK  CONST_01  N3   C9   C10  C7     0.00   0.0  0
 3XK  CONST_02  N3   C8   C6   C7     0.00   0.0  0
 3XK  CONST_03  C3   N2   C6   C7     0.00   0.0  0
 3XK  CONST_04  C1   C5   C4   C7   180.00   0.0  0
 3XK  CONST_05  N2   C3   C4   C7     0.00   0.0  0
 3XK  CONST_06  N1   C3   C4   C7   180.00   0.0  0
 3XK  CONST_07  C6   C7   C10  C9     0.00   0.0  0
 3XK  CONST_08  C4   C7   C10  C9   180.00   0.0  0
 3XK  CONST_09  C6   C8   N3   C9     0.00   0.0  0
 3XK  CONST_10  C5   C4   C3   N1     0.00   0.0  0
 3XK  CONST_11  C6   N2   C3   N1   180.00   0.0  0
 3XK  CONST_12  C5   C1   C2   N1     0.00   0.0  0
 3XK  CONST_13  C11  C1   C2   N1   180.00   0.0  0
 3XK  CONST_14  C4   C5   C1   C2     0.00   0.0  0
 3XK  CONST_17  C4   C3   N1   C2     0.00   0.0  0
 3XK  CONST_18  N2   C3   N1   C2   180.00   0.0  0
 3XK  CONST_19  C10  C7   C6   N2   180.00   0.0  0
 3XK  CONST_20  C4   C7   C6   N2     0.00   0.0  0
 3XK  CONST_21  N3   C8   C6   N2   180.00   0.0  0
 3XK  CONST_22  C5   C4   C3   N2   180.00   0.0  0
 3XK  CONST_23  C8   N3   C9   C10    0.00   0.0  0
 3XK  CONST_24  C8   C6   C7   C10    0.00   0.0  0
 3XK  CONST_25  C5   C4   C7   C10    0.00   0.0  0
 3XK  CONST_26  C3   C4   C7   C10  180.00   0.0  0
 3XK  CONST_27  C8   C6   C7   C4   180.00   0.0  0
 3XK  CONST_28  C11  C1   C5   C4   180.00   0.0  0
 3XK  CONST_29  C6   N2   C3   C4     0.00   0.0  0
 3XK  CONST_30  C5   C4   C7   C6   180.00   0.0  0
 3XK  CONST_31  C3   C4   C7   C6     0.00   0.0  0
 3XK  CONST_32  C3   N2   C6   C8   180.00   0.0  0
 3XK  CONST_33  C1   C5   C4   C3     0.00   0.0  0
 3XK  CONST_34  C1   C2   N1   C3     0.00   0.0  0
 3XK  CONST_37  C13  C12  C11  C1   180.00   0.0  0
 3XK  CONST_38  C15  C16  C11  C1   180.00   0.0  0
 3XK  CONST_39  C14  C13  C12  C11    0.00   0.0  0
 3XK  CONST_40  C14  C15  C16  C11    0.00   0.0  0
 3XK  CONST_41  C13  C12  C11  C16    0.00   0.0  0
 3XK  CONST_42  C13  C14  C15  C16    0.00   0.0  0
 3XK  CONST_43  C12  C13  C14  C15    0.00   0.0  0
 3XK  CONST_44  C12  C11  C16  C15    0.00   0.0  0
 3XK  CONST_45  C19  C9   C10  C7   180.00   0.0  0
 3XK  CONST_46  C8   N3   C9   C19  180.00   0.0  0
 3XK  CONST_47  N4   C15  C16  C11  180.00   0.0  0
 3XK  CONST_48  C13  C14  C15  N4   180.00   0.0  0
 3XK  CONST_49  H4   C8   C6   C7   180.00   0.0  0
 3XK  CONST_50  H2   N2   C6   C7   180.00   0.0  0
 3XK  CONST_51  H5   C5   C4   C7     0.00   0.0  0
 3XK  CONST_52  H3   C10  C7   C4     0.00   0.0  0
 3XK  CONST_53  H1   C2   N1   C3   180.00   0.0  0
 3XK  CONST_54  H13  C12  C11  C1     0.00   0.0  0
 3XK  CONST_55  H6   C16  C11  C1     0.00   0.0  0
 3XK  CONST_56  H12  C13  C12  C11  180.00   0.0  0
 3XK  CONST_57  H11  C14  C15  C16  180.00   0.0  0
 3XK  CONST_58  C17  N4   C15  C16  180.00   0.0  0
 3XK  CONST_59  C14  C15  N4   C17    0.00   0.0  0
 3XK  CONST_60  H7   N4   C15  C16    0.00   0.0  0
 3XK  CONST_61  O1   C17  N4   C15    0.00   0.0  0
 3XK  CONST_62  C18  C17  N4   C15  180.00   0.0  0
 3XK  Var_01    H8   C18  C17  N4    98.28  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
 3XK  plan-1  C1   0.020
 3XK  plan-1  C11  0.020
 3XK  plan-1  C16  0.020
 3XK  plan-1  C15  0.020
 3XK  plan-1  N4   0.020
 3XK  plan-1  C14  0.020
 3XK  plan-1  C13  0.020
 3XK  plan-1  C12  0.020
 3XK  plan-1  H6   0.020
 3XK  plan-1  H11  0.020
 3XK  plan-1  H12  0.020
 3XK  plan-1  H13  0.020
 3XK  plan-2  C7   0.020
 3XK  plan-2  C9   0.020
 3XK  plan-2  N1   0.020
 3XK  plan-2  C2   0.020
 3XK  plan-2  N2   0.020
 3XK  plan-2  C10  0.020
 3XK  plan-2  C4   0.020
 3XK  plan-2  N3   0.020
 3XK  plan-2  N5   0.020
 3XK  plan-2  C6   0.020
 3XK  plan-2  C19  0.020
 3XK  plan-2  C8   0.020
 3XK  plan-2  C3   0.020
 3XK  plan-2  C5   0.020
 3XK  plan-2  C1   0.020
 3XK  plan-2  C11  0.020
 3XK  plan-2  H1   0.020
 3XK  plan-2  H2   0.020
 3XK  plan-2  H3   0.020
 3XK  plan-2  H4   0.020
 3XK  plan-2  H5   0.020
 3XK  plan-3  C15  0.020
 3XK  plan-3  N4   0.020
 3XK  plan-3  C17  0.020
 3XK  plan-3  O1   0.020
 3XK  plan-3  C18  0.020
 3XK  plan-3  H7   0.020

