# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:43:33 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 5-fluoro-2-({[3-(pyrimidin-2-yl)pyridin-2-yl]amino}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(F)ccc1CNc2ncccc2c3ncccn3
#
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
 2J6  2J6  5-fluoro-2-({[3-(pyrimidin-2-yl)pyridin-2-yl]amino}methyl)phenol  ligand  35  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2J6
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
 2J6  C9   C  CR6   0  -0.046  -2.1677  -0.9828   0.4718
 2J6  C2   C  CR16  0  -0.160   3.8579  -0.8191  -0.3152
 2J6  C10  C  CR16  0  -0.294  -3.1001  -0.9026   1.4968
 2J6  C4   C  CR6   0   0.503   1.5196  -1.1701   0.0660
 2J6  N5   N  N     0  -0.462   1.7053  -2.4872   0.0640
 2J6  C6   C  CR16  0  -0.049   2.9186  -2.9790  -0.1323
 2J6  C1   C  CR16  0  -0.350   4.0372  -2.1912  -0.3349
 2J6  C3   C  CR6   0  -0.151   2.6007  -0.2611  -0.1081
 2J6  N7   N  NH1   0  -0.742   0.2285  -0.7365   0.2018
 2J6  C8   C  CH2   0  -0.331  -0.8209  -1.6143   0.6952
 2J6  C11  C  CR16  0  -0.426  -4.3759  -0.3923   1.2963
 2J6  C12  C  CR6   0   0.524  -4.6932   0.0493   0.0278
 2J6  C13  C  CR16  0  -0.492  -3.7980   0.0134  -1.0220
 2J6  C14  C  CR6   0   0.339  -2.5257  -0.5038  -0.7975
 2J6  O15  O  OH1   0  -0.635  -1.6710  -0.5376  -1.8351
 2J6  F16  F  F     0  -0.317  -5.9193   0.5479  -0.2011
 2J6  C17  C  CR6   0   0.454   2.4701   1.2075  -0.0718
 2J6  N18  N  N     0  -0.485   1.3113   1.7431   0.3083
 2J6  C19  C  CR16  0   0.011   1.2189   3.0659   0.3492
 2J6  C20  C  CR16  0  -0.366   2.2789   3.8841   0.0116
 2J6  C21  C  CR16  0  -0.006   3.4447   3.2372  -0.3704
 2J6  N22  N  N     0  -0.427   3.5433   1.9201  -0.4131
 2J6  H2   H  HCR6  0   0.267  -2.8235  -1.2564   2.4825
 2J6  H3   H  HCR6  0   0.266   3.0014  -4.0604  -0.1231
 2J6  H4   H  HCR6  0   0.266   5.0107  -2.6326  -0.4920
 2J6  H5   H  HNH1  0   0.417   0.1635   0.2415   0.4742
 2J6  H6   H  HCH2  0   0.259  -0.6890  -1.8426   1.7575
 2J6  H7   H  HCH2  0   0.269  -0.7593  -2.5646   0.1633
 2J6  H8   H  HCR6  0   0.275  -5.0947  -0.3394   2.1022
 2J6  H9   H  HCR6  0   0.284  -4.0762   0.3827  -2.0010
 2J6  H10  H  HOH1  0   0.479  -0.7646  -0.6316  -1.4877
 2J6  H11  H  HCR6  0   0.284   0.2667   3.4765   0.6624
 2J6  H12  H  HCR6  0   0.289   2.2047   4.9606   0.0414
 2J6  H13  H  HCR6  0   0.281   4.3264   3.8010  -0.6531
 2J6  H1   H  HCR6  0   0.271   4.7031  -0.1599  -0.4550

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
 2J6  C6   C1   aromatic  1.383  0.020  1.383
 2J6  C6   N5   aromatic  1.324  0.020  1.324
 2J6  C1   C2   aromatic  1.384  0.020  1.384
 2J6  O15  C14  single    1.345  0.020  1.345
 2J6  N5   C4   aromatic  1.330  0.020  1.330
 2J6  C14  C13  aromatic  1.392  0.020  1.392
 2J6  C14  C9   aromatic  1.403  0.020  1.403
 2J6  C13  C12  aromatic  1.380  0.020  1.380
 2J6  C2   C3   aromatic  1.391  0.020  1.391
 2J6  C4   C3   aromatic  1.423  0.020  1.423
 2J6  C4   N7   single    1.369  0.020  1.369
 2J6  C8   C9   single    1.504  0.020  1.504
 2J6  C8   N7   single    1.454  0.020  1.454
 2J6  C3   C17  single    1.475  0.020  1.475
 2J6  C9   C10  aromatic  1.388  0.020  1.388
 2J6  C12  F16  single    1.343  0.020  1.343
 2J6  C12  C11  aromatic  1.380  0.020  1.380
 2J6  C10  C11  aromatic  1.389  0.020  1.389
 2J6  C17  N22  aromatic  1.333  0.020  1.333
 2J6  C17  N18  aromatic  1.332  0.020  1.332
 2J6  N22  C21  aromatic  1.321  0.020  1.321
 2J6  N18  C19  aromatic  1.327  0.020  1.327
 2J6  C21  C20  aromatic  1.387  0.020  1.387
 2J6  C19  C20  aromatic  1.381  0.020  1.381
 2J6  C2   H1   single    0.930  0.020  1.080
 2J6  C10  H2   single    0.930  0.020  1.080
 2J6  C6   H3   single    0.930  0.020  1.080
 2J6  C1   H4   single    0.930  0.020  1.080
 2J6  N7   H5   single    0.890  0.020  1.040
 2J6  C8   H6   single    0.970  0.020  1.090
 2J6  C8   H7   single    0.970  0.020  1.090
 2J6  C11  H8   single    0.930  0.020  1.080
 2J6  C13  H9   single    0.930  0.020  1.080
 2J6  O15  H10  single    0.850  0.020  0.980
 2J6  C19  H11  single    0.930  0.020  1.080
 2J6  C20  H12  single    0.930  0.020  1.080
 2J6  C21  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
 2J6  C14  C9   C8   120.41  3.000
 2J6  C8   C9   C10  121.07  3.000
 2J6  C14  C9   C10  118.48  3.000
 2J6  H1   C2   C3   118.77  3.000
 2J6  H1   C2   C1   120.10  3.000
 2J6  C3   C2   C1   121.13  3.000
 2J6  H2   C10  C11  119.08  3.000
 2J6  H2   C10  C9   118.79  3.000
 2J6  C11  C10  C9   122.13  3.000
 2J6  N7   C4   C3   121.76  3.000
 2J6  N7   C4   N5   116.46  3.000
 2J6  C3   C4   N5   121.75  3.000
 2J6  C6   N5   C4   119.74  3.000
 2J6  H3   C6   C1   120.49  3.000
 2J6  H3   C6   N5   116.04  3.000
 2J6  C1   C6   N5   123.46  3.000
 2J6  H4   C1   C6   121.16  3.000
 2J6  H4   C1   C2   121.59  3.000
 2J6  C6   C1   C2   117.25  3.000
 2J6  C17  C3   C4   124.45  3.000
 2J6  C17  C3   C2   118.90  3.000
 2J6  C4   C3   C2   116.65  3.000
 2J6  H5   N7   C8   116.31  3.000
 2J6  H5   N7   C4   113.04  3.000
 2J6  C8   N7   C4   121.54  3.000
 2J6  H7   C8   H6   106.54  3.000
 2J6  H7   C8   N7   108.65  3.000
 2J6  H6   C8   N7   111.60  3.000
 2J6  H7   C8   C9   110.11  3.000
 2J6  H6   C8   C9   109.85  3.000
 2J6  N7   C8   C9   110.02  3.000
 2J6  H8   C11  C12  121.10  3.000
 2J6  H8   C11  C10  121.42  3.000
 2J6  C12  C11  C10  117.48  3.000
 2J6  F16  C12  C13  118.17  3.000
 2J6  F16  C12  C11  119.03  3.000
 2J6  C13  C12  C11  122.80  3.000
 2J6  H9   C13  C14  120.50  3.000
 2J6  H9   C13  C12  120.82  3.000
 2J6  C14  C13  C12  118.68  3.000
 2J6  O15  C14  C13  117.77  3.000
 2J6  C13  C14  C9   120.41  3.000
 2J6  O15  C14  C9   121.82  3.000
 2J6  H10  O15  C14  108.56  3.000
 2J6  N22  C17  N18  123.96  3.000
 2J6  N18  C17  C3   118.98  3.000
 2J6  N22  C17  C3   117.05  3.000
 2J6  C19  N18  C17  118.06  3.000
 2J6  H11  C19  C20  121.39  3.000
 2J6  H11  C19  N18  116.62  3.000
 2J6  C20  C19  N18  121.99  3.000
 2J6  H12  C20  C21  122.04  3.000
 2J6  H12  C20  C19  122.10  3.000
 2J6  C21  C20  C19  115.86  3.000
 2J6  H13  C21  N22  116.69  3.000
 2J6  H13  C21  C20  120.86  3.000
 2J6  N22  C21  C20  122.45  3.000
 2J6  C21  N22  C17  117.68  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
 2J6  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 2J6  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 2J6  CONST_03  N5   C6   C1   C2      0.00   0.0  0
 2J6  CONST_04  N5   C4   C3   C2      0.00   0.0  0
 2J6  CONST_05  N22  C17  C3   C2      0.00   0.0  0
 2J6  CONST_06  N18  C17  C3   C2    180.00   0.0  0
 2J6  CONST_07  C13  C14  C9   C10     0.00   0.0  0
 2J6  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 2J6  CONST_09  C1   C6   N5   C4      0.00   0.0  0
 2J6  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 2J6  CONST_11  N22  C17  C3   C4    180.00   0.0  0
 2J6  CONST_12  N18  C17  C3   C4      0.00   0.0  0
 2J6  CONST_13  C17  C3   C4   N5    180.00   0.0  0
 2J6  CONST_14  C3   C2   C1   C6      0.00   0.0  0
 2J6  CONST_15  C3   C4   N5   C6      0.00   0.0  0
 2J6  CONST_16  C17  C3   C2   C1    180.00   0.0  0
 2J6  CONST_17  C21  N22  C17  C3    180.00   0.0  0
 2J6  CONST_18  C19  N18  C17  C3    180.00   0.0  0
 2J6  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 2J6  CONST_20  C14  C9   C10  C11     0.00   0.0  0
 2J6  CONST_21  C20  C21  N22  C17     0.00   0.0  0
 2J6  CONST_22  C20  C19  N18  C17     0.00   0.0  0
 2J6  CONST_23  C21  N22  C17  N18     0.00   0.0  0
 2J6  CONST_24  C21  C20  C19  N18     0.00   0.0  0
 2J6  CONST_25  N22  C17  N18  C19     0.00   0.0  0
 2J6  CONST_26  N22  C21  C20  C19     0.00   0.0  0
 2J6  CONST_27  N7   C4   C3   C2    180.00   0.0  0
 2J6  CONST_28  O15  C14  C9   C10   180.00   0.0  0
 2J6  CONST_29  F16  C12  C11  C10   180.00   0.0  0
 2J6  CONST_30  N7   C4   N5   C6    180.00   0.0  0
 2J6  CONST_31  C17  C3   C4   N7      0.00   0.0  0
 2J6  CONST_32  C13  C14  C9   C8    180.00   0.0  0
 2J6  CONST_33  C11  C10  C9   C8    180.00   0.0  0
 2J6  CONST_34  O15  C14  C13  C12   180.00   0.0  0
 2J6  CONST_35  F16  C12  C13  C14   180.00   0.0  0
 2J6  CONST_36  H9   C13  C14  C9    180.00   0.0  0
 2J6  CONST_37  H8   C11  C10  C9    180.00   0.0  0
 2J6  CONST_38  H3   C6   C1   C2    180.00   0.0  0
 2J6  CONST_39  H1   C2   C3   C4    180.00   0.0  0
 2J6  CONST_40  H4   C1   C6   N5    180.00   0.0  0
 2J6  CONST_41  H2   C10  C11  C12   180.00   0.0  0
 2J6  CONST_42  H13  C21  N22  C17   180.00   0.0  0
 2J6  CONST_43  H11  C19  N18  C17   180.00   0.0  0
 2J6  CONST_44  H12  C20  C19  N18   180.00   0.0  0
 2J6  Var_01    C4   N7   C8   C9   -168.18  30.0  3
 2J6  Var_02    N7   C8   C9   C10  -130.60  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
 2J6  plan-1  C2   0.020
 2J6  plan-1  C4   0.020
 2J6  plan-1  N5   0.020
 2J6  plan-1  C6   0.020
 2J6  plan-1  C1   0.020
 2J6  plan-1  C3   0.020
 2J6  plan-1  N7   0.020
 2J6  plan-1  C17  0.020
 2J6  plan-1  H3   0.020
 2J6  plan-1  H4   0.020
 2J6  plan-1  H1   0.020
 2J6  plan-2  C9   0.020
 2J6  plan-2  C10  0.020
 2J6  plan-2  C8   0.020
 2J6  plan-2  C11  0.020
 2J6  plan-2  C12  0.020
 2J6  plan-2  C13  0.020
 2J6  plan-2  C14  0.020
 2J6  plan-2  O15  0.020
 2J6  plan-2  F16  0.020
 2J6  plan-2  H2   0.020
 2J6  plan-2  H8   0.020
 2J6  plan-2  H9   0.020
 2J6  plan-3  C3   0.020
 2J6  plan-3  C17  0.020
 2J6  plan-3  N18  0.020
 2J6  plan-3  C19  0.020
 2J6  plan-3  C20  0.020
 2J6  plan-3  C21  0.020
 2J6  plan-3  N22  0.020
 2J6  plan-3  H11  0.020
 2J6  plan-3  H12  0.020
 2J6  plan-3  H13  0.020
 2J6  plan-4  C4   0.020
 2J6  plan-4  N7   0.020
 2J6  plan-4  C8   0.020
 2J6  plan-4  H5   0.020

