# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 06:31:55 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 5-(2-azanylpyridin-4-yl)-~{N}-[[2,6-bis(fluoranyl)phenyl]methyl]-2-methyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(NCc2c(F)cccc2F)c3c([nH]cc3c4ccnc(N)c4)n1
#
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
 R05  R05  5-(2-azanylpyridin-4-yl)-~{N}-[[2,6-bis(fluoranyl)phenyl]methyl]-2-methyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  43  27  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R05
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
 R05  C1   C  CH3   0  -0.728  -8.4958   1.4269  29.9673
 R05  C2   C  CR6   0   0.342  -7.9712   0.0996  30.4192
 R05  N1   N  N     0  -0.469  -8.8316  -0.7647  30.9236
 R05  C3   C  CR56  0   0.485  -8.2773  -1.9363  31.2449
 R05  C4   C  CR56  0  -0.119  -6.9360  -2.2922  31.0841
 R05  C5   C  CR5   0  -0.013  -6.7988  -3.6488  31.5353
 R05  C6   C  CR15  0  -0.049  -8.0444  -4.0263  31.9618
 R05  N2   N  NR15  0  -0.665  -8.9251  -2.9968  31.7852
 R05  C7   C  CR6   0   0.117  -5.6282  -4.5247  31.4900
 R05  C8   C  CR16  0  -0.451  -5.3172  -5.3548  32.5523
 R05  C9   C  CR6   0   0.467  -4.2015  -6.2045  32.4599
 R05  N3   N  NH2   0  -0.837  -3.9007  -7.0709  33.4673
 R05  N4   N  N     0  -0.461  -3.4109  -6.2273  31.3871
 R05  C10  C  CR16  0  -0.050  -3.7216  -5.4280  30.3722
 R05  C11  C  CR16  0  -0.464  -4.8028  -4.5709  30.3553
 R05  C12  C  CR6   0   0.464  -6.1048  -1.2448  30.6233
 R05  N5   N  NH1   0  -0.665  -4.7700  -1.3776  30.5540
 R05  C13  C  CH2   0  -0.341  -3.8633  -0.3911  30.0166
 R05  C14  C  CR6   0  -0.298  -2.9486  -1.0189  28.9995
 R05  C15  C  CR6   0   0.546  -1.6008  -1.2483  29.2305
 R05  F1   F  F     0  -0.305  -1.0852  -0.8681  30.4081
 R05  C16  C  CR16  0  -0.417  -0.7643  -1.8530  28.3102
 R05  C17  C  CR16  0  -0.234  -1.3007  -2.2594  27.0986
 R05  C18  C  CR16  0  -0.415  -2.6464  -2.0651  26.8160
 R05  C19  C  CR6   0   0.556  -3.4311  -1.4542  27.7715
 R05  F2   F  F     0  -0.304  -4.7330  -1.2677  27.5166
 R05  N6   N  N     0  -0.501  -6.6538  -0.0845  30.2756
 R05  H1   H  HCH3  0   0.249  -8.3228   1.5601  28.8982
 R05  H2   H  HCH3  0   0.242  -9.5622   1.5147  30.1597
 R05  H3   H  HCH3  0   0.248  -7.9780   2.2405  30.4767
 R05  H4   H  HCR5  0   0.294  -8.3752  -4.9778  32.3460
 R05  H5   H  HNR5  0   0.413  -9.9105  -3.0302  31.9936
 R05  H6   H  HCR6  0   0.259  -5.9126  -5.3410  33.4570
 R05  H7   H  HNH2  0   0.381  -2.9658  -7.4444  33.4739
 R05  H8   H  HNH2  0   0.390  -4.2828  -6.8865  34.3797
 R05  H9   H  HCR6  0   0.254  -3.0642  -5.4778  29.5101
 R05  H10  H  HCR6  0   0.270  -5.0174  -3.9808  29.4744
 R05  H11  H  HNH1  0   0.412  -4.3593  -2.2322  30.8941
 R05  H12  H  HCH2  0   0.269  -3.2822   0.0693  30.8162
 R05  H13  H  HCH2  0   0.282  -4.4527   0.4028  29.5631
 R05  H14  H  HCR6  0   0.283   0.2814  -2.0051  28.5410
 R05  H15  H  HCR6  0   0.280  -0.6648  -2.7363  26.3655
 R05  H16  H  HCR6  0   0.283  -3.0755  -2.3816  25.8749

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
 R05  C18  C19  aromatic  1.379  0.020  1.379
 R05  C18  C17  aromatic  1.389  0.020  1.389
 R05  F2   C19  single    1.340  0.020  1.340
 R05  C19  C14  aromatic  1.389  0.020  1.389
 R05  C17  C16  aromatic  1.386  0.020  1.386
 R05  C16  C15  aromatic  1.383  0.020  1.383
 R05  C14  C15  aromatic  1.387  0.020  1.387
 R05  C14  C13  single    1.505  0.020  1.505
 R05  C15  F1   single    1.341  0.020  1.341
 R05  C13  N5   single    1.444  0.020  1.444
 R05  N5   C12  single    1.343  0.020  1.343
 R05  N6   C12  aromatic  1.330  0.020  1.330
 R05  N6   C2   aromatic  1.338  0.020  1.338
 R05  C1   C2   single    1.497  0.020  1.497
 R05  C12  C4   aromatic  1.414  0.020  1.414
 R05  C10  C11  aromatic  1.380  0.020  1.380
 R05  C10  N4   aromatic  1.329  0.020  1.329
 R05  C2   N1   aromatic  1.320  0.020  1.320
 R05  C11  C7   aromatic  1.404  0.020  1.404
 R05  C4   C3   aromatic  1.397  0.020  1.397
 R05  C4   C5   aromatic  1.436  0.020  1.436
 R05  N1   C3   aromatic  1.335  0.020  1.335
 R05  N4   C9   aromatic  1.333  0.020  1.333
 R05  C7   C5   single    1.463  0.020  1.463
 R05  C7   C8   aromatic  1.384  0.020  1.384
 R05  C3   N2   aromatic  1.355  0.020  1.355
 R05  C5   C6   aromatic  1.370  0.020  1.370
 R05  N2   C6   aromatic  1.366  0.020  1.366
 R05  C9   C8   aromatic  1.405  0.020  1.405
 R05  C9   N3   single    1.362  0.020  1.362
 R05  C1   H1   single    0.970  0.020  1.090
 R05  C1   H2   single    0.970  0.020  1.090
 R05  C1   H3   single    0.970  0.020  1.090
 R05  C6   H4   single    0.930  0.020  1.080
 R05  N2   H5   single    0.860  0.020  1.020
 R05  C8   H6   single    0.930  0.020  1.080
 R05  N3   H7   single    0.890  0.020  1.040
 R05  N3   H8   single    0.890  0.020  1.040
 R05  C10  H9   single    0.930  0.020  1.080
 R05  C11  H10  single    0.930  0.020  1.080
 R05  N5   H11  single    0.860  0.020  1.020
 R05  C13  H12  single    0.970  0.020  1.090
 R05  C13  H13  single    0.970  0.020  1.090
 R05  C16  H14  single    0.930  0.020  1.080
 R05  C17  H15  single    0.930  0.020  1.080
 R05  C18  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
 R05  H3   C1   H2   108.83  3.000
 R05  H3   C1   H1   106.94  3.000
 R05  H2   C1   H1   108.61  3.000
 R05  H3   C1   C2   110.74  3.000
 R05  H2   C1   C2   111.22  3.000
 R05  H1   C1   C2   110.39  3.000
 R05  N6   C2   N1   126.36  3.000
 R05  N1   C2   C1   117.88  3.000
 R05  N6   C2   C1   115.76  3.000
 R05  C3   N1   C2   113.32  3.000
 R05  N2   C3   C4   107.79  3.000
 R05  N2   C3   N1   125.75  3.000
 R05  C4   C3   N1   126.46  3.000
 R05  C12  C4   C5   138.22  3.000
 R05  C5   C4   C3   107.23  3.000
 R05  C12  C4   C3   114.40  3.000
 R05  C7   C5   C6   124.92  3.000
 R05  C6   C5   C4   105.74  3.000
 R05  C7   C5   C4   129.22  3.000
 R05  H4   C6   N2   120.89  3.000
 R05  H4   C6   C5   129.28  3.000
 R05  N2   C6   C5   109.77  3.000
 R05  H5   N2   C6   125.35  3.000
 R05  H5   N2   C3   125.16  3.000
 R05  C6   N2   C3   109.46  3.000
 R05  C11  C7   C8   117.95  3.000
 R05  C8   C7   C5   121.02  3.000
 R05  C11  C7   C5   121.01  3.000
 R05  H6   C8   C9   119.94  3.000
 R05  H6   C8   C7   120.67  3.000
 R05  C9   C8   C7   119.38  3.000
 R05  N4   C9   N3   116.96  3.000
 R05  N3   C9   C8   120.74  3.000
 R05  N4   C9   C8   122.28  3.000
 R05  H8   N3   H7   114.49  3.000
 R05  H8   N3   C9   118.04  3.000
 R05  H7   N3   C9   116.48  3.000
 R05  C10  N4   C9   117.77  3.000
 R05  H9   C10  C11  119.57  3.000
 R05  H9   C10  N4   115.94  3.000
 R05  C11  C10  N4   124.49  3.000
 R05  H10  C11  C10  120.28  3.000
 R05  H10  C11  C7   121.58  3.000
 R05  C10  C11  C7   118.11  3.000
 R05  N6   C12  N5   118.88  3.000
 R05  N6   C12  C4   119.26  3.000
 R05  N5   C12  C4   121.85  3.000
 R05  H11  N5   C13  116.71  3.000
 R05  H11  N5   C12  118.14  3.000
 R05  C13  N5   C12  125.15  3.000
 R05  H13  C13  H12  106.64  3.000
 R05  H13  C13  C14  110.61  3.000
 R05  H12  C13  C14  110.35  3.000
 R05  H13  C13  N5   108.28  3.000
 R05  H12  C13  N5   110.50  3.000
 R05  C14  C13  N5   110.38  3.000
 R05  C19  C14  C15  115.66  3.000
 R05  C15  C14  C13  123.18  3.000
 R05  C19  C14  C13  121.12  3.000
 R05  C16  C15  F1   118.42  3.000
 R05  F1   C15  C14  118.25  3.000
 R05  C16  C15  C14  123.33  3.000
 R05  H14  C16  C17  121.30  3.000
 R05  H14  C16  C15  120.29  3.000
 R05  C17  C16  C15  118.42  3.000
 R05  H15  C17  C18  119.57  3.000
 R05  H15  C17  C16  119.64  3.000
 R05  C18  C17  C16  120.79  3.000
 R05  H16  C18  C19  120.44  3.000
 R05  H16  C18  C17  121.37  3.000
 R05  C19  C18  C17  118.19  3.000
 R05  F2   C19  C18  118.87  3.000
 R05  F2   C19  C14  117.52  3.000
 R05  C18  C19  C14  123.61  3.000
 R05  C12  N6   C2   119.90  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
 R05  CONST_01  C4   C12  N6   C2      0.00   0.0  0
 R05  CONST_02  C4   C3   N1   C2      0.00   0.0  0
 R05  CONST_03  N2   C3   N1   C2    180.00   0.0  0
 R05  CONST_04  C12  N6   C2   N1      0.00   0.0  0
 R05  CONST_05  C12  C4   C3   N1      0.00   0.0  0
 R05  CONST_06  C5   C4   C3   N1    180.00   0.0  0
 R05  CONST_07  C6   N2   C3   N1    180.00   0.0  0
 R05  CONST_08  N6   C12  C4   C3      0.00   0.0  0
 R05  CONST_09  C7   C5   C4   C3    180.00   0.0  0
 R05  CONST_10  C6   C5   C4   C3      0.00   0.0  0
 R05  CONST_11  N6   C2   N1   C3      0.00   0.0  0
 R05  CONST_12  C5   C6   N2   C3      0.00   0.0  0
 R05  CONST_13  C6   N2   C3   C4      0.00   0.0  0
 R05  CONST_16  N2   C6   C5   C4      0.00   0.0  0
 R05  CONST_17  N6   C12  C4   C5    180.00   0.0  0
 R05  CONST_18  N2   C3   C4   C5      0.00   0.0  0
 R05  CONST_19  C10  C11  C7   C5    180.00   0.0  0
 R05  CONST_20  C9   C8   C7   C5    180.00   0.0  0
 R05  CONST_21  C12  C4   C5   C6    180.00   0.0  0
 R05  CONST_24  C12  C4   C3   N2    180.00   0.0  0
 R05  CONST_25  C7   C5   C6   N2    180.00   0.0  0
 R05  CONST_26  N4   C10  C11  C7      0.00   0.0  0
 R05  CONST_27  C12  C4   C5   C7      0.00   0.0  0
 R05  CONST_28  N4   C9   C8   C7      0.00   0.0  0
 R05  CONST_29  C10  C11  C7   C8      0.00   0.0  0
 R05  CONST_30  C10  N4   C9   C8      0.00   0.0  0
 R05  CONST_31  C11  C10  N4   C9      0.00   0.0  0
 R05  CONST_32  C11  C7   C8   C9      0.00   0.0  0
 R05  CONST_33  C17  C18  C19  C14     0.00   0.0  0
 R05  CONST_34  C17  C16  C15  C14     0.00   0.0  0
 R05  CONST_35  C18  C17  C16  C15     0.00   0.0  0
 R05  CONST_36  C18  C19  C14  C15     0.00   0.0  0
 R05  CONST_37  C19  C18  C17  C16     0.00   0.0  0
 R05  CONST_38  C19  C14  C15  C16     0.00   0.0  0
 R05  CONST_39  C12  N6   C2   C1    180.00   0.0  0
 R05  CONST_40  C3   N1   C2   C1    180.00   0.0  0
 R05  CONST_41  N5   C12  N6   C2    180.00   0.0  0
 R05  CONST_42  N5   C12  C4   C3    180.00   0.0  0
 R05  CONST_43  N5   C12  C4   C5      0.00   0.0  0
 R05  CONST_44  N3   C9   C8   C7    180.00   0.0  0
 R05  CONST_45  C10  N4   C9   N3    180.00   0.0  0
 R05  CONST_46  C18  C19  C14  C13   180.00   0.0  0
 R05  CONST_47  C16  C15  C14  C13   180.00   0.0  0
 R05  CONST_48  F2   C19  C14  C15   180.00   0.0  0
 R05  CONST_49  C17  C16  C15  F1    180.00   0.0  0
 R05  CONST_50  C19  C14  C15  F1    180.00   0.0  0
 R05  CONST_51  F2   C19  C18  C17   180.00   0.0  0
 R05  CONST_52  H5   N2   C3   N1      0.00   0.0  0
 R05  CONST_53  H4   C6   N2   C3    180.00   0.0  0
 R05  CONST_54  H10  C11  C7   C5      0.00   0.0  0
 R05  CONST_55  H6   C8   C7   C5      0.00   0.0  0
 R05  CONST_56  H9   C10  C11  C7    180.00   0.0  0
 R05  CONST_57  H16  C18  C19  C14   180.00   0.0  0
 R05  CONST_58  H14  C16  C15  C14   180.00   0.0  0
 R05  CONST_59  H15  C17  C16  C15   180.00   0.0  0
 R05  CONST_60  C13  N5   C12  C4    180.00   0.0  0
 R05  CONST_61  N6   C12  N5   C13     0.00   0.0  0
 R05  CONST_62  H11  N5   C12  C4      0.00   0.0  0
 R05  Var_01    C14  C13  N5   C12  -128.74  30.0  2
 R05  Var_02    C19  C14  C13  N5     69.34  30.0  2
 R05  Var_03    H1   C1   C2   N1   -118.46  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
 R05  plan-1  C5   0.020
 R05  plan-1  C7   0.020
 R05  plan-1  C8   0.020
 R05  plan-1  C9   0.020
 R05  plan-1  N3   0.020
 R05  plan-1  N4   0.020
 R05  plan-1  C10  0.020
 R05  plan-1  C11  0.020
 R05  plan-1  H6   0.020
 R05  plan-1  H9   0.020
 R05  plan-1  H10  0.020
 R05  plan-2  C13  0.020
 R05  plan-2  C14  0.020
 R05  plan-2  C15  0.020
 R05  plan-2  F1   0.020
 R05  plan-2  C16  0.020
 R05  plan-2  C17  0.020
 R05  plan-2  C18  0.020
 R05  plan-2  C19  0.020
 R05  plan-2  F2   0.020
 R05  plan-2  H14  0.020
 R05  plan-2  H15  0.020
 R05  plan-2  H16  0.020
 R05  plan-3  C1   0.020
 R05  plan-3  C2   0.020
 R05  plan-3  N1   0.020
 R05  plan-3  C3   0.020
 R05  plan-3  C4   0.020
 R05  plan-3  C5   0.020
 R05  plan-3  C6   0.020
 R05  plan-3  N2   0.020
 R05  plan-3  C7   0.020
 R05  plan-3  C12  0.020
 R05  plan-3  N5   0.020
 R05  plan-3  N6   0.020
 R05  plan-3  H4   0.020
 R05  plan-3  H5   0.020
 R05  plan-4  C9   0.020
 R05  plan-4  N3   0.020
 R05  plan-4  H7   0.020
 R05  plan-4  H8   0.020
 R05  plan-5  C12  0.020
 R05  plan-5  N5   0.020
 R05  plan-5  C13  0.020
 R05  plan-5  H11  0.020

