# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 23:18:47 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 6-fluoro-N-[(5-fluoro-2-methoxypyridin-3-yl)methyl]-5-[(5-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(F)cc1CNc2ccc(Cc3c[nH]c4ncc(C)cc34)c(F)n2
#
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
 622  622  6-fluoro-N-[(5-fluoro-2-methoxypyridin-3-yl)methyl]-5-[(5-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)methyl]pyridin-2-amine  ligand  48  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_622
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
 622  C1   C  CR6   0  -0.001  -4.6044   1.9268  -0.7357
 622  C10  C  CR6   0   0.530  -1.0549  -1.6246  -1.3850
 622  C11  C  CR6   0   0.509   0.8862  -1.2644  -0.2697
 622  C12  C  CR16  0  -0.407   0.3033  -1.7327   0.9206
 622  C13  C  CR16  0  -0.162  -1.0138  -2.1390   0.8807
 622  C14  C  CH2   0  -0.325   3.1039  -0.9142   0.7482
 622  C15  C  CR6   0  -0.066   4.3611  -0.1692   0.4124
 622  C16  C  CR6   0   0.515   4.3955   1.2390   0.3676
 622  C17  C  CR16  0  -0.201   6.6020   1.2778  -0.2160
 622  C18  C  CR6   0   0.421   6.6619  -0.0930  -0.1979
 622  C19  C  CR16  0  -0.325   5.5326  -0.8337   0.1168
 622  C2   C  CR16  0  -0.122  -5.4304   2.2376   0.3573
 622  C20  C  CH3   0  -0.415   3.2743   3.2989   0.6474
 622  C21  C  CH3   0  -0.723  -4.3232   2.9618  -1.7865
 622  C3   C  CR56  0   0.458  -5.2504   0.1812   1.2148
 622  C4   C  CR56  0   0.009  -4.4034  -0.2719   0.1790
 622  C5   C  CR16  0  -0.289  -4.0820   0.6441  -0.8195
 622  C6   C  CR5   0  -0.019  -4.0912  -1.6398   0.4591
 622  C7   C  CR15  0  -0.058  -4.7440  -1.9431   1.6202
 622  C8   C  CH2   0  -0.624  -3.2027  -2.5400  -0.3379
 622  C9   C  CR6   0  -0.135  -1.7600  -2.1039  -0.2970
 622  F1   F  F     0  -0.308   7.8122  -0.7205  -0.4852
 622  N1   N  N     0  -0.423  -5.7618   1.3955   1.3251
 622  N2   N  NR15  0  -0.672  -5.4407  -0.8556   2.0759
 622  N3   N  N     0  -0.484   0.1845  -1.2241  -1.4060
 622  N4   N  NH1   0  -0.651   2.1623  -0.8210  -0.3415
 622  N5   N  N     0  -0.447   5.4730   1.9260   0.0673
 622  O1   O  O2    0  -0.463   3.2623   1.8786   0.6544
 622  H1   H  HCR6  0   0.276   0.8630  -1.7823   1.8435
 622  H2   H  HCR6  0   0.266  -1.4823  -2.4986   1.7894
 622  H3   H  HCH2  0   0.254   3.3532  -1.9562   0.9789
 622  H4   H  HCH2  0   0.260   2.6584  -0.4916   1.6524
 622  H5   H  HCR6  0   0.284   7.4737   1.8740  -0.4612
 622  H6   H  HCR6  0   0.296   5.5720  -1.9161   0.1324
 622  H7   H  HCR6  0   0.246  -5.8400   3.2402   0.4385
 622  H8   H  HCH3  0   0.248   2.2639   3.6046   0.9054
 622  H9   H  HCH3  0   0.230   3.9721   3.7014   1.3828
 622  H10  H  HCH3  0   0.231   3.5324   3.6972  -0.3345
 622  H11  H  HCH3  0   0.246  -5.0902   2.9592  -2.5636
 622  H12  H  HCH3  0   0.243  -4.2975   3.9657  -1.3624
 622  H13  H  HCH3  0   0.244  -3.3657   2.7817  -2.2741
 622  H14  H  HCR6  0   0.243  -3.4393   0.3704  -1.6488
 622  H15  H  HCR5  0   0.288  -4.7655  -2.8734   2.1663
 622  H16  H  HCH2  0   0.269  -3.2819  -3.5571   0.0538
 622  H17  H  HCH2  0   0.264  -3.5513  -2.5928  -1.3705
 622  H18  H  HNR5  0   0.408  -5.9988  -0.8279   2.9129
 622  H19  H  HNH1  0   0.390   2.5295  -0.6817  -1.2693
 622  F2   F  F     0  -0.308  -1.6800  -1.5382  -2.5709

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
 622  N2   C3   aromatic  1.361  0.020  1.361
 622  N2   C7   aromatic  1.370  0.020  1.370
 622  N1   C3   aromatic  1.322  0.020  1.322
 622  N1   C2   aromatic  1.325  0.020  1.325
 622  C3   C4   aromatic  1.413  0.020  1.413
 622  C2   C1   aromatic  1.405  0.020  1.405
 622  C7   C6   aromatic  1.366  0.020  1.366
 622  C13  C12  aromatic  1.379  0.020  1.379
 622  C13  C9   aromatic  1.395  0.020  1.395
 622  C4   C6   aromatic  1.431  0.020  1.431
 622  C4   C5   aromatic  1.393  0.020  1.393
 622  C12  C11  aromatic  1.406  0.020  1.406
 622  C6   C8   single    1.495  0.020  1.495
 622  C1   C5   aromatic  1.388  0.020  1.388
 622  C1   C21  single    1.502  0.020  1.502
 622  C8   C9   single    1.508  0.020  1.508
 622  C9   C10  aromatic  1.382  0.020  1.382
 622  C11  N4   single    1.353  0.020  1.353
 622  C11  N3   aromatic  1.336  0.020  1.336
 622  N4   C14  single    1.443  0.020  1.443
 622  C10  N3   aromatic  1.303  0.020  1.303
 622  C10  F2   single    1.343  0.020  1.343
 622  C14  C15  single    1.500  0.020  1.500
 622  C19  C15  aromatic  1.379  0.020  1.379
 622  C19  C18  aromatic  1.387  0.020  1.387
 622  F1   C18  single    1.341  0.020  1.341
 622  C15  C16  aromatic  1.409  0.020  1.409
 622  C18  C17  aromatic  1.372  0.020  1.372
 622  C16  O1   single    1.332  0.020  1.332
 622  C16  N5   aromatic  1.313  0.020  1.313
 622  C17  N5   aromatic  1.332  0.020  1.332
 622  O1   C20  single    1.420  0.020  1.420
 622  C12  H1   single    0.930  0.020  1.080
 622  C13  H2   single    0.930  0.020  1.080
 622  C14  H3   single    0.970  0.020  1.090
 622  C14  H4   single    0.970  0.020  1.090
 622  C17  H5   single    0.930  0.020  1.080
 622  C19  H6   single    0.930  0.020  1.080
 622  C2   H7   single    0.930  0.020  1.080
 622  C20  H8   single    0.970  0.020  1.090
 622  C20  H9   single    0.970  0.020  1.090
 622  C20  H10  single    0.970  0.020  1.090
 622  C21  H11  single    0.970  0.020  1.090
 622  C21  H12  single    0.970  0.020  1.090
 622  C21  H13  single    0.970  0.020  1.090
 622  C5   H14  single    0.930  0.020  1.080
 622  C7   H15  single    0.930  0.020  1.080
 622  C8   H16  single    0.970  0.020  1.090
 622  C8   H17  single    0.970  0.020  1.090
 622  N2   H18  single    0.860  0.020  1.020
 622  N4   H19  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
 622  C5   C1   C21  121.63  3.000
 622  C21  C1   C2   120.14  3.000
 622  C5   C1   C2   118.22  3.000
 622  N3   C10  F2   114.13  3.000
 622  F2   C10  C9   118.67  3.000
 622  N3   C10  C9   127.20  3.000
 622  N4   C11  N3   116.13  3.000
 622  N3   C11  C12  120.83  3.000
 622  N4   C11  C12  123.04  3.000
 622  H1   C12  C13  120.40  3.000
 622  H1   C12  C11  121.59  3.000
 622  C13  C12  C11  118.01  3.000
 622  H2   C13  C9   119.02  3.000
 622  H2   C13  C12  119.10  3.000
 622  C9   C13  C12  121.88  3.000
 622  H4   C14  H3   106.63  3.000
 622  H4   C14  N4   109.50  3.000
 622  H3   C14  N4   111.64  3.000
 622  H4   C14  C15  109.56  3.000
 622  H3   C14  C15  109.20  3.000
 622  N4   C14  C15  110.23  3.000
 622  C19  C15  C16  117.00  3.000
 622  C16  C15  C14  121.60  3.000
 622  C19  C15  C14  121.39  3.000
 622  O1   C16  N5   119.74  3.000
 622  N5   C16  C15  123.38  3.000
 622  O1   C16  C15  116.88  3.000
 622  H5   C17  N5   117.51  3.000
 622  H5   C17  C18  121.14  3.000
 622  N5   C17  C18  121.35  3.000
 622  F1   C18  C19  119.81  3.000
 622  F1   C18  C17  120.13  3.000
 622  C19  C18  C17  120.06  3.000
 622  H6   C19  C18  120.49  3.000
 622  H6   C19  C15  120.62  3.000
 622  C18  C19  C15  118.89  3.000
 622  H7   C2   N1   115.97  3.000
 622  H7   C2   C1   118.96  3.000
 622  N1   C2   C1   125.08  3.000
 622  H10  C20  H9   108.72  3.000
 622  H10  C20  H8   109.33  3.000
 622  H9   C20  H8   109.33  3.000
 622  H10  C20  O1   111.82  3.000
 622  H9   C20  O1   111.78  3.000
 622  H8   C20  O1   105.80  3.000
 622  H13  C21  H12  107.80  3.000
 622  H13  C21  H11  107.37  3.000
 622  H12  C21  H11  107.19  3.000
 622  H13  C21  C1   111.34  3.000
 622  H12  C21  C1   111.52  3.000
 622  H11  C21  C1   111.40  3.000
 622  N2   C3   N1   126.35  3.000
 622  N1   C3   C4   125.99  3.000
 622  N2   C3   C4   107.66  3.000
 622  C6   C4   C5   135.96  3.000
 622  C5   C4   C3   116.94  3.000
 622  C6   C4   C3   107.09  3.000
 622  H14  C5   C4   121.28  3.000
 622  H14  C5   C1   120.17  3.000
 622  C4   C5   C1   118.55  3.000
 622  C8   C6   C7   127.12  3.000
 622  C8   C6   C4   126.94  3.000
 622  C7   C6   C4   105.93  3.000
 622  H15  C7   N2   120.41  3.000
 622  H15  C7   C6   129.13  3.000
 622  N2   C7   C6   110.46  3.000
 622  H17  C8   H16  105.72  3.000
 622  H17  C8   C9   110.21  3.000
 622  H16  C8   C9   109.20  3.000
 622  H17  C8   C6   110.11  3.000
 622  H16  C8   C6   109.04  3.000
 622  C9   C8   C6   112.34  3.000
 622  C8   C9   C13  121.85  3.000
 622  C8   C9   C10  124.54  3.000
 622  C13  C9   C10  113.61  3.000
 622  C3   N1   C2   115.22  3.000
 622  H18  N2   C7   125.50  3.000
 622  H18  N2   C3   125.64  3.000
 622  C7   N2   C3   108.86  3.000
 622  C11  N3   C10  118.47  3.000
 622  H19  N4   C14  117.81  3.000
 622  H19  N4   C11  115.98  3.000
 622  C14  N4   C11  123.65  3.000
 622  C17  N5   C16  119.31  3.000
 622  C20  O1   C16  118.15  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
 622  CONST_01  C3   N1   C2   C1      0.00   0.0  0
 622  CONST_02  C3   C4   C5   C1      0.00   0.0  0
 622  CONST_03  C6   C4   C5   C1    180.00   0.0  0
 622  CONST_04  C12  C13  C9   C10     0.00   0.0  0
 622  CONST_05  C12  C11  N3   C10     0.00   0.0  0
 622  CONST_06  C9   C13  C12  C11     0.00   0.0  0
 622  CONST_07  C9   C10  N3   C11     0.00   0.0  0
 622  CONST_08  N3   C11  C12  C13     0.00   0.0  0
 622  CONST_09  N3   C10  C9   C13     0.00   0.0  0
 622  CONST_10  C17  C18  C19  C15     0.00   0.0  0
 622  CONST_11  C17  N5   C16  C15     0.00   0.0  0
 622  CONST_12  C18  C19  C15  C16     0.00   0.0  0
 622  CONST_13  C18  C17  N5   C16     0.00   0.0  0
 622  CONST_14  N5   C16  C15  C19     0.00   0.0  0
 622  CONST_15  N5   C17  C18  C19     0.00   0.0  0
 622  CONST_16  N2   C3   N1   C2    180.00   0.0  0
 622  CONST_17  C4   C3   N1   C2      0.00   0.0  0
 622  CONST_18  C4   C5   C1   C2      0.00   0.0  0
 622  CONST_19  C6   C7   N2   C3      0.00   0.0  0
 622  CONST_20  C7   C6   C4   C3      0.00   0.0  0
 622  CONST_21  C7   N2   C3   C4      0.00   0.0  0
 622  CONST_22  N2   C7   C6   C4      0.00   0.0  0
 622  CONST_23  N2   C3   C4   C5    180.00   0.0  0
 622  CONST_24  N1   C3   C4   C5      0.00   0.0  0
 622  CONST_25  C7   C6   C4   C5    180.00   0.0  0
 622  CONST_26  N1   C2   C1   C5      0.00   0.0  0
 622  CONST_27  N2   C3   C4   C6      0.00   0.0  0
 622  CONST_28  N1   C3   C4   C6    180.00   0.0  0
 622  CONST_29  N1   C3   N2   C7    180.00   0.0  0
 622  CONST_30  N4   C11  N3   C10   180.00   0.0  0
 622  CONST_31  F2   C10  N3   C11   180.00   0.0  0
 622  CONST_32  C8   C9   C13  C12   180.00   0.0  0
 622  CONST_33  N4   C11  C12  C13   180.00   0.0  0
 622  CONST_34  F2   C10  C9   C13   180.00   0.0  0
 622  CONST_35  C18  C19  C15  C14   180.00   0.0  0
 622  CONST_36  N5   C16  C15  C14   180.00   0.0  0
 622  CONST_37  F1   C18  C19  C15   180.00   0.0  0
 622  CONST_38  O1   C16  N5   C17   180.00   0.0  0
 622  CONST_39  O1   C16  C15  C19   180.00   0.0  0
 622  CONST_40  N1   C2   C1   C21   180.00   0.0  0
 622  CONST_41  C4   C5   C1   C21   180.00   0.0  0
 622  CONST_42  C8   C6   C4   C3    180.00   0.0  0
 622  CONST_43  C8   C6   C4   C5      0.00   0.0  0
 622  CONST_44  N2   C7   C6   C8    180.00   0.0  0
 622  CONST_45  N3   C10  C9   C8    180.00   0.0  0
 622  CONST_46  N5   C17  C18  F1    180.00   0.0  0
 622  CONST_47  H2   C13  C9   C10   180.00   0.0  0
 622  CONST_48  H6   C19  C15  C16   180.00   0.0  0
 622  CONST_49  H5   C17  N5   C16   180.00   0.0  0
 622  CONST_50  H14  C5   C1   C2    180.00   0.0  0
 622  CONST_51  H15  C7   N2   C3    180.00   0.0  0
 622  CONST_52  H7   C2   N1   C3    180.00   0.0  0
 622  CONST_53  H18  N2   C3   C4    180.00   0.0  0
 622  CONST_54  H1   C12  C13  C9    180.00   0.0  0
 622  CONST_55  C14  N4   C11  C12     0.00   0.0  0
 622  CONST_56  N3   C11  N4   C14   180.00   0.0  0
 622  CONST_57  H19  N4   C11  C12   180.00   0.0  0
 622  Var_01    C6   C8   C9   C10  -113.06  30.0  2
 622  Var_02    C9   C8   C6   C4     66.84  30.0  2
 622  Var_03    C15  C14  N4   C11  -172.28  30.0  3
 622  Var_04    N4   C14  C15  C16    71.47  30.0  2
 622  Var_05    N5   C16  O1   C20    -1.17  30.0  2
 622  Var_06    H11  C21  C1   C2    -87.01  30.0  2
 622  Var_07    H8   C20  O1   C16  -179.92  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
 622  plan-1  C10  0.020
 622  plan-1  C11  0.020
 622  plan-1  C12  0.020
 622  plan-1  C13  0.020
 622  plan-1  C8   0.020
 622  plan-1  C9   0.020
 622  plan-1  N3   0.020
 622  plan-1  N4   0.020
 622  plan-1  H1   0.020
 622  plan-1  H2   0.020
 622  plan-1  F2   0.020
 622  plan-2  C14  0.020
 622  plan-2  C15  0.020
 622  plan-2  C16  0.020
 622  plan-2  C17  0.020
 622  plan-2  C18  0.020
 622  plan-2  C19  0.020
 622  plan-2  F1   0.020
 622  plan-2  N5   0.020
 622  plan-2  O1   0.020
 622  plan-2  H5   0.020
 622  plan-2  H6   0.020
 622  plan-3  C1   0.020
 622  plan-3  C2   0.020
 622  plan-3  C21  0.020
 622  plan-3  C3   0.020
 622  plan-3  C4   0.020
 622  plan-3  C5   0.020
 622  plan-3  C6   0.020
 622  plan-3  C7   0.020
 622  plan-3  C8   0.020
 622  plan-3  N1   0.020
 622  plan-3  N2   0.020
 622  plan-3  H7   0.020
 622  plan-3  H14  0.020
 622  plan-3  H15  0.020
 622  plan-3  H18  0.020
 622  plan-4  C11  0.020
 622  plan-4  C14  0.020
 622  plan-4  N4   0.020
 622  plan-4  H19  0.020

