# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:42:18 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-[1-(2,5-difluorobenzyl)-1H-pyrazol-4-yl]-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cnc3[nH]cc(c4cnn(Cc5cc(F)ccc5F)c4)c3c2
#
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
 3DK  3DK  3-[1-(2,5-difluorobenzyl)-1H-pyrazol-4-yl]-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine  ligand  45  29  .  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_3DK
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
 3DK  F29  F  F     0  -0.313  -6.9628   1.6759  -0.8782
 3DK  C24  C  CR6   0   0.533  -6.3327   0.5289  -0.5807
 3DK  C23  C  CR16  0  -0.435  -5.3673   0.5356   0.4056
 3DK  C25  C  CR16  0  -0.400  -6.6740  -0.6216  -1.2647
 3DK  C26  C  CR16  0  -0.389  -6.0219  -1.8023  -0.9438
 3DK  C27  C  CR6   0   0.530  -5.0543  -1.7943   0.0425
 3DK  F28  F  F     0  -0.306  -4.4388  -2.9469   0.3433
 3DK  C22  C  CR6   0  -0.051  -4.7056  -0.6437   0.7330
 3DK  C21  C  CH2   0  -0.401  -3.6230  -0.6413   1.7790
 3DK  N17  N  NR5   0  -0.262  -2.3254  -0.3685   1.1986
 3DK  C16  C  CR15  0   0.006  -1.6848   0.8149   1.1743
 3DK  N18  N  N     0  -0.268  -1.6843  -1.3088   0.5164
 3DK  C19  C  CR15  0  -0.120  -0.5993  -0.7210   0.0499
 3DK  C10  C  CR5   0  -0.180  -0.5353   0.6360   0.4306
 3DK  C9   C  CR5   0  -0.024   0.4914   1.6138   0.1178
 3DK  C8   C  CR15  0  -0.068   0.3229   2.9653  -0.0383
 3DK  N7   N  NR15  0  -0.666   1.5177   3.5647  -0.3178
 3DK  C4   C  CR56  0   0.470   2.4922   2.6173  -0.3576
 3DK  N3   N  N     0  -0.416   3.7756   2.8237  -0.5997
 3DK  C2   C  CR16  0  -0.144   4.5395   1.7453  -0.5751
 3DK  C5   C  CR56  0   0.007   1.8891   1.3693  -0.0863
 3DK  C6   C  CR16  0  -0.353   2.7269   0.2604  -0.0426
 3DK  C1   C  CR6   0  -0.002   4.0821   0.4430  -0.2943
 3DK  C11  C  CR5   0  -0.147   5.0149  -0.6808  -0.2755
 3DK  C15  C  CR15  0   0.010   6.3779  -0.6635  -0.0436
 3DK  N14  N  NR5   0  -0.265   6.8086  -1.9327  -0.1260
 3DK  C20  C  CH3   0  -0.505   8.1610  -2.4112   0.0319
 3DK  N13  N  N     0  -0.280   5.8268  -2.7845  -0.3975
 3DK  C12  C  CR15  0  -0.099   4.7373  -2.0460  -0.4889
 3DK  H1   H  HCR6  0   0.289  -5.1312   1.4561   0.9258
 3DK  H2   H  HCR6  0   0.294  -7.4357  -0.6039  -2.0322
 3DK  H3   H  HCR6  0   0.293  -6.2659  -2.7222  -1.4582
 3DK  H4   H  HCH2  0   0.296  -3.8206   0.1350   2.5162
 3DK  H5   H  HCH2  0   0.298  -3.5715  -1.5888   2.3120
 3DK  H6   H  HCR5  0   0.289  -2.0691   1.6808   1.6900
 3DK  H7   H  HCR5  0   0.251   0.1023  -1.2786  -0.5527
 3DK  H8   H  HCR5  0   0.291  -0.5806   3.5513   0.0199
 3DK  H9   H  HNR5  0   0.413   1.6522   4.5502  -0.4746
 3DK  H10  H  HCR6  0   0.251   5.5899   1.9042  -0.7953
 3DK  H11  H  HCR6  0   0.247   2.3422  -0.7220   0.2028
 3DK  H12  H  HCR5  0   0.290   7.0525   0.1469   0.1815
 3DK  H13  H  HCH3  0   0.261   8.2058  -3.1618   0.8181
 3DK  H14  H  HCH3  0   0.260   8.5224  -2.8450  -0.8985
 3DK  H15  H  HCH3  0   0.259   8.8012  -1.5770   0.3035
 3DK  H16  H  HCR5  0   0.256   3.7871  -2.5064  -0.7178

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
 3DK  F28  C27  single    1.341  0.020  1.341
 3DK  N7   C8   aromatic  1.366  0.020  1.366
 3DK  N7   C4   aromatic  1.360  0.020  1.360
 3DK  C8   C9   aromatic  1.371  0.020  1.371
 3DK  C16  N17  aromatic  1.346  0.020  1.346
 3DK  C16  C10  aromatic  1.381  0.020  1.381
 3DK  C27  C26  aromatic  1.382  0.020  1.382
 3DK  C27  C22  aromatic  1.386  0.020  1.386
 3DK  C4   N3   aromatic  1.322  0.020  1.322
 3DK  C4   C5   aromatic  1.412  0.020  1.412
 3DK  C21  N17  single    1.447  0.020  1.447
 3DK  C21  C22  single    1.505  0.020  1.505
 3DK  C9   C10  single    1.452  0.020  1.452
 3DK  C9   C5   aromatic  1.434  0.020  1.434
 3DK  N3   C2   aromatic  1.322  0.020  1.322
 3DK  C26  C25  aromatic  1.386  0.020  1.386
 3DK  N17  N18  aromatic  1.327  0.020  1.327
 3DK  C22  C23  aromatic  1.391  0.020  1.391
 3DK  C10  C19  aromatic  1.411  0.020  1.411
 3DK  C5   C6   aromatic  1.390  0.020  1.390
 3DK  C2   C1   aromatic  1.409  0.020  1.409
 3DK  C25  C24  aromatic  1.381  0.020  1.381
 3DK  C23  C24  aromatic  1.380  0.020  1.380
 3DK  C6   C1   aromatic  1.390  0.020  1.390
 3DK  C1   C11  single    1.461  0.020  1.461
 3DK  N18  C19  aromatic  1.319  0.020  1.319
 3DK  C24  F29  single    1.342  0.020  1.342
 3DK  C11  C15  aromatic  1.383  0.020  1.383
 3DK  C11  C12  aromatic  1.409  0.020  1.409
 3DK  C15  N14  aromatic  1.343  0.020  1.343
 3DK  C12  N13  aromatic  1.319  0.020  1.319
 3DK  N14  N13  aromatic  1.328  0.020  1.328
 3DK  N14  C20  single    1.443  0.020  1.443
 3DK  C23  H1   single    0.930  0.020  1.080
 3DK  C25  H2   single    0.930  0.020  1.080
 3DK  C26  H3   single    0.930  0.020  1.080
 3DK  C21  H4   single    0.970  0.020  1.090
 3DK  C21  H5   single    0.970  0.020  1.090
 3DK  C16  H6   single    0.930  0.020  1.080
 3DK  C19  H7   single    0.930  0.020  1.080
 3DK  C8   H8   single    0.930  0.020  1.080
 3DK  N7   H9   single    0.860  0.020  1.020
 3DK  C2   H10  single    0.930  0.020  1.080
 3DK  C6   H11  single    0.930  0.020  1.080
 3DK  C15  H12  single    0.930  0.020  1.080
 3DK  C20  H13  single    0.970  0.020  1.090
 3DK  C20  H14  single    0.970  0.020  1.090
 3DK  C20  H15  single    0.970  0.020  1.090
 3DK  C12  H16  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
 3DK  C25  C24  C23  122.06  3.000
 3DK  C23  C24  F29  118.86  3.000
 3DK  C25  C24  F29  119.08  3.000
 3DK  H1   C23  C22  120.24  3.000
 3DK  H1   C23  C24  119.98  3.000
 3DK  C22  C23  C24  119.78  3.000
 3DK  H2   C25  C26  120.63  3.000
 3DK  H2   C25  C24  120.79  3.000
 3DK  C26  C25  C24  118.58  3.000
 3DK  H3   C26  C27  120.15  3.000
 3DK  H3   C26  C25  120.53  3.000
 3DK  C27  C26  C25  119.32  3.000
 3DK  C22  C27  F28  119.09  3.000
 3DK  C22  C27  C26  122.44  3.000
 3DK  F28  C27  C26  118.47  3.000
 3DK  C21  C22  C27  121.89  3.000
 3DK  C21  C22  C23  120.28  3.000
 3DK  C27  C22  C23  117.82  3.000
 3DK  H5   C21  H4   107.32  3.000
 3DK  H5   C21  N17  108.54  3.000
 3DK  H4   C21  N17  107.45  3.000
 3DK  H5   C21  C22  111.90  3.000
 3DK  H4   C21  C22  109.95  3.000
 3DK  N17  C21  C22  111.49  3.000
 3DK  N18  N17  C16  112.58  3.000
 3DK  N18  N17  C21  120.38  3.000
 3DK  C16  N17  C21  126.84  3.000
 3DK  H6   C16  C10  131.16  3.000
 3DK  H6   C16  N17  121.85  3.000
 3DK  C10  C16  N17  106.98  3.000
 3DK  C19  N18  N17  105.27  3.000
 3DK  H7   C19  C10  128.15  3.000
 3DK  H7   C19  N18  120.11  3.000
 3DK  C10  C19  N18  111.74  3.000
 3DK  C9   C10  C19  128.44  3.000
 3DK  C19  C10  C16  103.42  3.000
 3DK  C9   C10  C16  128.13  3.000
 3DK  C5   C9   C8   105.77  3.000
 3DK  C5   C9   C10  127.25  3.000
 3DK  C8   C9   C10  126.98  3.000
 3DK  H8   C8   N7   120.36  3.000
 3DK  H8   C8   C9   129.23  3.000
 3DK  N7   C8   C9   110.40  3.000
 3DK  H9   N7   C4   125.57  3.000
 3DK  H9   N7   C8   125.34  3.000
 3DK  C4   N7   C8   109.10  3.000
 3DK  C5   C4   N3   125.98  3.000
 3DK  C5   C4   N7   107.70  3.000
 3DK  N3   C4   N7   126.32  3.000
 3DK  C2   N3   C4   115.48  3.000
 3DK  H10  C2   C1   119.35  3.000
 3DK  H10  C2   N3   115.87  3.000
 3DK  C1   C2   N3   124.78  3.000
 3DK  C6   C5   C4   116.97  3.000
 3DK  C6   C5   C9   135.97  3.000
 3DK  C4   C5   C9   107.03  3.000
 3DK  H11  C6   C1   120.42  3.000
 3DK  H11  C6   C5   121.09  3.000
 3DK  C1   C6   C5   118.48  3.000
 3DK  C11  C1   C6   121.27  3.000
 3DK  C11  C1   C2   120.43  3.000
 3DK  C6   C1   C2   118.29  3.000
 3DK  C12  C11  C15  103.40  3.000
 3DK  C12  C11  C1   128.14  3.000
 3DK  C15  C11  C1   128.47  3.000
 3DK  H12  C15  N14  121.51  3.000
 3DK  H12  C15  C11  131.39  3.000
 3DK  N14  C15  C11  107.10  3.000
 3DK  N13  N14  C20  120.17  3.000
 3DK  C20  N14  C15  127.39  3.000
 3DK  N13  N14  C15  112.44  3.000
 3DK  H15  C20  H14  108.91  3.000
 3DK  H15  C20  H13  108.96  3.000
 3DK  H14  C20  H13  109.22  3.000
 3DK  H15  C20  N14  108.97  3.000
 3DK  H14  C20  N14  110.48  3.000
 3DK  H13  C20  N14  110.27  3.000
 3DK  C12  N13  N14  105.41  3.000
 3DK  H16  C12  N13  120.16  3.000
 3DK  H16  C12  C11  128.18  3.000
 3DK  N13  C12  C11  111.66  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
 3DK  CONST_01  C27  C26  C25  C24    0.00   0.0  0
 3DK  CONST_02  C27  C22  C23  C24    0.00   0.0  0
 3DK  CONST_03  C26  C27  C22  C23    0.00   0.0  0
 3DK  CONST_04  C26  C25  C24  C23    0.00   0.0  0
 3DK  CONST_05  C22  C27  C26  C25    0.00   0.0  0
 3DK  CONST_06  C22  C23  C24  C25    0.00   0.0  0
 3DK  CONST_07  C9   C10  C16  N17  180.00   0.0  0
 3DK  CONST_08  C19  C10  C16  N17    0.00   0.0  0
 3DK  CONST_09  C10  C19  N18  N17    0.00   0.0  0
 3DK  CONST_10  C19  N18  N17  C16    0.00   0.0  0
 3DK  CONST_13  N18  C19  C10  C16    0.00   0.0  0
 3DK  CONST_14  C10  C16  N17  N18    0.00   0.0  0
 3DK  CONST_15  C9   C10  C19  N18  180.00   0.0  0
 3DK  CONST_18  N7   C8   C9   C10  180.00   0.0  0
 3DK  CONST_19  C4   C5   C9   C10  180.00   0.0  0
 3DK  CONST_20  C6   C5   C9   C10    0.00   0.0  0
 3DK  CONST_21  C4   N7   C8   C9     0.00   0.0  0
 3DK  CONST_22  N7   C4   C5   C9     0.00   0.0  0
 3DK  CONST_23  N3   C4   C5   C9   180.00   0.0  0
 3DK  CONST_24  C1   C6   C5   C9   180.00   0.0  0
 3DK  CONST_25  N3   C4   N7   C8   180.00   0.0  0
 3DK  CONST_26  C5   C4   N7   C8     0.00   0.0  0
 3DK  CONST_27  C4   C5   C9   C8     0.00   0.0  0
 3DK  CONST_28  C6   C5   C9   C8   180.00   0.0  0
 3DK  CONST_29  C5   C9   C8   N7     0.00   0.0  0
 3DK  CONST_30  C2   N3   C4   N7   180.00   0.0  0
 3DK  CONST_31  C6   C5   C4   N7   180.00   0.0  0
 3DK  CONST_32  C1   C2   N3   C4     0.00   0.0  0
 3DK  CONST_33  C1   C6   C5   C4     0.00   0.0  0
 3DK  CONST_34  C6   C5   C4   N3     0.00   0.0  0
 3DK  CONST_35  C6   C1   C2   N3     0.00   0.0  0
 3DK  CONST_36  C11  C1   C2   N3   180.00   0.0  0
 3DK  CONST_37  C5   C4   N3   C2     0.00   0.0  0
 3DK  CONST_38  C5   C6   C1   C2     0.00   0.0  0
 3DK  CONST_41  C11  C1   C6   C5   180.00   0.0  0
 3DK  CONST_44  N14  C15  C11  C1   180.00   0.0  0
 3DK  CONST_45  N13  C12  C11  C1   180.00   0.0  0
 3DK  CONST_46  N13  N14  C15  C11    0.00   0.0  0
 3DK  CONST_47  N14  N13  C12  C11    0.00   0.0  0
 3DK  CONST_48  N13  C12  C11  C15    0.00   0.0  0
 3DK  CONST_49  C12  N13  N14  C15    0.00   0.0  0
 3DK  CONST_50  C12  C11  C15  N14    0.00   0.0  0
 3DK  CONST_51  C26  C25  C24  F29  180.00   0.0  0
 3DK  CONST_52  C22  C23  C24  F29  180.00   0.0  0
 3DK  CONST_53  C21  C22  C23  C24  180.00   0.0  0
 3DK  CONST_54  F28  C27  C22  C23  180.00   0.0  0
 3DK  CONST_55  F28  C27  C26  C25  180.00   0.0  0
 3DK  CONST_56  C21  C22  C27  C26  180.00   0.0  0
 3DK  CONST_57  C10  C16  N17  C21  180.00   0.0  0
 3DK  CONST_58  C19  N18  N17  C21  180.00   0.0  0
 3DK  CONST_59  C20  N14  C15  C11  180.00   0.0  0
 3DK  CONST_60  C12  N13  N14  C20  180.00   0.0  0
 3DK  CONST_61  H3   C26  C25  C24  180.00   0.0  0
 3DK  CONST_62  H2   C25  C24  C23  180.00   0.0  0
 3DK  CONST_63  H1   C23  C24  C25  180.00   0.0  0
 3DK  CONST_64  H7   C19  N18  N17  180.00   0.0  0
 3DK  CONST_65  H6   C16  N17  N18  180.00   0.0  0
 3DK  CONST_66  H8   C8   C9   C10    0.00   0.0  0
 3DK  CONST_67  H9   N7   C8   C9   180.00   0.0  0
 3DK  CONST_68  H11  C6   C5   C9     0.00   0.0  0
 3DK  CONST_69  H10  C2   N3   C4   180.00   0.0  0
 3DK  CONST_70  H12  C15  C11  C1     0.00   0.0  0
 3DK  CONST_71  H16  C12  C11  C1     0.00   0.0  0
 3DK  Var_01    N17  C21  C22  C23  -89.11  30.0  2
 3DK  Var_02    C16  N17  C21  C22   98.60  30.0  2
 3DK  Var_03    H13  C20  N14  C15  123.43  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
 3DK  plan-1  C21  0.020
 3DK  plan-1  N17  0.020
 3DK  plan-1  C16  0.020
 3DK  plan-1  N18  0.020
 3DK  plan-1  C19  0.020
 3DK  plan-1  C10  0.020
 3DK  plan-1  C9   0.020
 3DK  plan-1  H6   0.020
 3DK  plan-1  H7   0.020
 3DK  plan-2  C1   0.020
 3DK  plan-2  C11  0.020
 3DK  plan-2  C15  0.020
 3DK  plan-2  N14  0.020
 3DK  plan-2  C20  0.020
 3DK  plan-2  N13  0.020
 3DK  plan-2  C12  0.020
 3DK  plan-2  H12  0.020
 3DK  plan-2  H16  0.020
 3DK  plan-3  F29  0.020
 3DK  plan-3  C24  0.020
 3DK  plan-3  C23  0.020
 3DK  plan-3  C25  0.020
 3DK  plan-3  C26  0.020
 3DK  plan-3  C27  0.020
 3DK  plan-3  F28  0.020
 3DK  plan-3  C22  0.020
 3DK  plan-3  C21  0.020
 3DK  plan-3  H1   0.020
 3DK  plan-3  H2   0.020
 3DK  plan-3  H3   0.020
 3DK  plan-4  C10  0.020
 3DK  plan-4  C9   0.020
 3DK  plan-4  C8   0.020
 3DK  plan-4  N7   0.020
 3DK  plan-4  C4   0.020
 3DK  plan-4  N3   0.020
 3DK  plan-4  C2   0.020
 3DK  plan-4  C5   0.020
 3DK  plan-4  C6   0.020
 3DK  plan-4  C1   0.020
 3DK  plan-4  C11  0.020
 3DK  plan-4  H8   0.020
 3DK  plan-4  H9   0.020
 3DK  plan-4  H10  0.020
 3DK  plan-4  H11  0.020

