# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:04:42 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-2-yl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(CCc3cc(C)nc(N)c3)n2)c1
#
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
 XFM  XFM  6-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-2-yl}ethyl)-4-methylpyridin-2-amine  ligand  51  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XFM
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
 XFM  N1    N  N     0  -0.486   3.8659  -1.3377  -0.1455
 XFM  C2    C  CR6   0   0.278   4.1297  -0.2352   0.5599
 XFM  C3    C  CR16  0  -0.434   5.4053   0.1010   0.9736
 XFM  C4    C  CR6   0   0.206   6.4718  -0.7455   0.6461
 XFM  C5    C  CR16  0  -0.448   6.1962  -1.8869  -0.0775
 XFM  C6    C  CR6   0   0.441   4.8685  -2.1495  -0.4598
 XFM  C7    C  CH2   0  -0.493   2.9525   0.6443   0.8711
 XFM  C8    C  CH2   0  -0.491   2.3426   1.2609  -0.3945
 XFM  C9    C  CR6   0   0.236   1.1179   2.0659  -0.0723
 XFM  N10   N  N     0  -0.434   0.0014   1.3833   0.1670
 XFM  C11   C  CR6   0   0.241  -1.1104   2.0345   0.4984
 XFM  C12   C  CR16  0  -0.355  -1.1480   3.4207   0.6100
 XFM  C13   C  CR16  0  -0.146   0.0110   4.1387   0.3617
 XFM  C14   C  CR16  0  -0.354   1.1640   3.4544   0.0131
 XFM  C15   C  CH2   0  -0.491  -2.3409   1.1989   0.7033
 XFM  C16   C  CH2   0  -0.514  -2.9060   0.7066  -0.6366
 XFM  C17   C  CR6   0   0.240  -4.0967  -0.1844  -0.4376
 XFM  C18   C  CR16  0  -0.436  -3.9281  -1.5273  -0.0859
 XFM  C19   C  CR6   0   0.255  -5.0483  -2.3152   0.1152
 XFM  N20   N  N     0  -0.487  -6.2912  -1.8419  -0.0047
 XFM  C21   C  CR6   0   0.446  -6.4619  -0.5646  -0.3287
 XFM  C22   C  CR16  0  -0.461  -5.3808   0.3036  -0.5594
 XFM  N23   N  NH2   0  -0.838  -7.7470  -0.1057  -0.3876
 XFM  C24   C  CH3   0  -0.718  -4.9216  -3.7682   0.4608
 XFM  C25   C  CH3   0  -0.726   7.8699  -0.4039   1.0614
 XFM  N26   N  NH2   0  -0.839   4.5540  -3.2913  -1.1394
 XFM  H3    H  HCR6  0   0.243   5.5749   1.0063   1.5431
 XFM  H5    H  HCR6  0   0.255   6.9864  -2.5752  -0.3540
 XFM  H7    H  HCH2  0   0.249   2.1864   0.0534   1.3804
 XFM  H7A   H  HCH2  0   0.247   3.2520   1.4394   1.5570
 XFM  H8    H  HCH2  0   0.248   3.0864   1.8891  -0.8890
 XFM  H8A   H  HCH2  0   0.250   2.0794   0.4599  -1.0879
 XFM  H12   H  HCR6  0   0.261  -2.0670   3.9218   0.8848
 XFM  H13   H  HCR6  0   0.268   0.0151   5.2184   0.4375
 XFM  H14   H  HCR6  0   0.260   2.0855   3.9839  -0.1911
 XFM  H15   H  HCH2  0   0.255  -2.0911   0.3383   1.3284
 XFM  H15A  H  HCH2  0   0.253  -3.1039   1.7739   1.2318
 XFM  H16   H  HCH2  0   0.254  -3.1823   1.5663  -1.2513
 XFM  H16A  H  HCH2  0   0.255  -2.1240   0.1639  -1.1721
 XFM  H18   H  HCR6  0   0.244  -2.9361  -1.9491   0.0212
 XFM  H22   H  HCR6  0   0.254  -5.5591   1.3382  -0.8285
 XFM  HN23  H  HNH2  0   0.378  -8.4635  -0.8067  -0.4826
 XFM  HN2A  H  HNH2  0   0.387  -7.9176   0.7292  -0.9224
 XFM  H24   H  HCH3  0   0.245  -5.5259  -4.0159   1.3341
 XFM  H24A  H  HCH3  0   0.248  -5.2775  -4.3912  -0.3622
 XFM  H24B  H  HCH3  0   0.240  -3.8890  -4.0434   0.6675
 XFM  H25   H  HCH3  0   0.250   7.9183  -0.1745   2.1264
 XFM  H25A  H  HCH3  0   0.247   8.5637  -1.2174   0.8562
 XFM  H25B  H  HCH3  0   0.253   8.2228   0.4803   0.5280
 XFM  HN26  H  HNH2  0   0.387   5.2957  -3.7568  -1.6348
 XFM  HN2B  H  HNH2  0   0.379   3.6728  -3.2893  -1.6267

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
 XFM  C6   N1    aromatic  1.328  0.020  1.328
 XFM  C2   N1    aromatic  1.335  0.020  1.335
 XFM  C3   C2    aromatic  1.383  0.020  1.383
 XFM  C2   C7    single    1.502  0.020  1.502
 XFM  C4   C3    aromatic  1.400  0.020  1.400
 XFM  C3   H3    single    0.930  0.020  1.080
 XFM  C25  C4    single    1.498  0.020  1.498
 XFM  C4   C5    aromatic  1.379  0.020  1.379
 XFM  C5   C6    aromatic  1.406  0.020  1.406
 XFM  C5   H5    single    0.930  0.020  1.080
 XFM  C6   N26   single    1.366  0.020  1.366
 XFM  C7   C8    single    1.534  0.020  1.534
 XFM  C7   H7    single    0.970  0.020  1.090
 XFM  C7   H7A   single    0.970  0.020  1.090
 XFM  C9   C8    single    1.501  0.020  1.501
 XFM  C8   H8    single    0.970  0.020  1.090
 XFM  C8   H8A   single    0.970  0.020  1.090
 XFM  C14  C9    aromatic  1.392  0.020  1.392
 XFM  C9   N10   aromatic  1.330  0.020  1.330
 XFM  C11  N10   aromatic  1.330  0.020  1.330
 XFM  C12  C11   aromatic  1.391  0.020  1.391
 XFM  C11  C15   single    1.501  0.020  1.501
 XFM  C13  C12   aromatic  1.386  0.020  1.386
 XFM  C12  H12   single    0.930  0.020  1.080
 XFM  C13  C14   aromatic  1.385  0.020  1.385
 XFM  C13  H13   single    0.930  0.020  1.080
 XFM  C14  H14   single    0.930  0.020  1.080
 XFM  C15  C16   single    1.535  0.020  1.535
 XFM  C15  H15   single    0.970  0.020  1.090
 XFM  C15  H15A  single    0.970  0.020  1.090
 XFM  C16  C17   single    1.500  0.020  1.500
 XFM  C16  H16   single    0.970  0.020  1.090
 XFM  C16  H16A  single    0.970  0.020  1.090
 XFM  C18  C17   aromatic  1.398  0.020  1.398
 XFM  C17  C22   aromatic  1.379  0.020  1.379
 XFM  C18  C19   aromatic  1.384  0.020  1.384
 XFM  C18  H18   single    0.930  0.020  1.080
 XFM  C24  C19   single    1.499  0.020  1.499
 XFM  C19  N20   aromatic  1.335  0.020  1.335
 XFM  N20  C21   aromatic  1.329  0.020  1.329
 XFM  C22  C21   aromatic  1.406  0.020  1.406
 XFM  C21  N23   single    1.366  0.020  1.366
 XFM  C22  H22   single    0.930  0.020  1.080
 XFM  N23  HN23  single    0.890  0.020  1.040
 XFM  N23  HN2A  single    0.890  0.020  1.040
 XFM  C24  H24   single    0.970  0.020  1.090
 XFM  C24  H24A  single    0.970  0.020  1.090
 XFM  C24  H24B  single    0.970  0.020  1.090
 XFM  C25  H25   single    0.970  0.020  1.090
 XFM  C25  H25A  single    0.970  0.020  1.090
 XFM  C25  H25B  single    0.970  0.020  1.090
 XFM  N26  HN26  single    0.890  0.020  1.040
 XFM  N26  HN2B  single    0.890  0.020  1.040

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
 XFM  C6    N1   C2    118.73  3.000
 XFM  C7    C2   C3    121.24  3.000
 XFM  C7    C2   N1    115.99  3.000
 XFM  C3    C2   N1    122.76  3.000
 XFM  H3    C3   C4    120.60  3.000
 XFM  H3    C3   C2    120.34  3.000
 XFM  C4    C3   C2    119.05  3.000
 XFM  C25   C4   C5    121.38  3.000
 XFM  C5    C4   C3    118.09  3.000
 XFM  C25   C4   C3    120.53  3.000
 XFM  H5    C5   C6    120.02  3.000
 XFM  H5    C5   C4    120.91  3.000
 XFM  C6    C5   C4    119.06  3.000
 XFM  N26   C6   C5    120.59  3.000
 XFM  N26   C6   N1    117.07  3.000
 XFM  C5    C6   N1    122.30  3.000
 XFM  H7A   C7   H7    107.04  3.000
 XFM  H7A   C7   C8    109.55  3.000
 XFM  H7    C7   C8    108.84  3.000
 XFM  H7A   C7   C2    109.97  3.000
 XFM  H7    C7   C2    109.21  3.000
 XFM  C8    C7   C2    112.09  3.000
 XFM  H8A   C8   H8    107.38  3.000
 XFM  H8A   C8   C9    109.47  3.000
 XFM  H8    C8   C9    110.15  3.000
 XFM  H8A   C8   C7    108.96  3.000
 XFM  H8    C8   C7    109.51  3.000
 XFM  C9    C8   C7    111.28  3.000
 XFM  C14   C9   N10   121.91  3.000
 XFM  N10   C9   C8    116.63  3.000
 XFM  C14   C9   C8    121.42  3.000
 XFM  C11   N10  C9    119.67  3.000
 XFM  C15   C11  C12   121.43  3.000
 XFM  C15   C11  N10   116.52  3.000
 XFM  C12   C11  N10   122.02  3.000
 XFM  H12   C12  C13   121.05  3.000
 XFM  H12   C12  C11   120.31  3.000
 XFM  C13   C12  C11   118.64  3.000
 XFM  H13   C13  C14   120.48  3.000
 XFM  H13   C13  C12   120.50  3.000
 XFM  C14   C13  C12   119.03  3.000
 XFM  H14   C14  C13   120.96  3.000
 XFM  H14   C14  C9    120.31  3.000
 XFM  C13   C14  C9    118.73  3.000
 XFM  H15A  C15  H15   107.32  3.000
 XFM  H15A  C15  C16   109.52  3.000
 XFM  H15   C15  C16   109.33  3.000
 XFM  H15A  C15  C11   110.22  3.000
 XFM  H15   C15  C11   109.21  3.000
 XFM  C16   C15  C11   111.16  3.000
 XFM  H16A  C16  H16   107.23  3.000
 XFM  H16A  C16  C17   109.76  3.000
 XFM  H16   C16  C17   109.95  3.000
 XFM  H16A  C16  C15   108.89  3.000
 XFM  H16   C16  C15   109.38  3.000
 XFM  C17   C16  C15   111.51  3.000
 XFM  C22   C17  C18   118.31  3.000
 XFM  C22   C17  C16   121.14  3.000
 XFM  C18   C17  C16   120.53  3.000
 XFM  H18   C18  C19   120.34  3.000
 XFM  H18   C18  C17   120.61  3.000
 XFM  C19   C18  C17   119.05  3.000
 XFM  C24   C19  N20   116.29  3.000
 XFM  N20   C19  C18   122.58  3.000
 XFM  C24   C19  C18   121.12  3.000
 XFM  C21   N20  C19   118.83  3.000
 XFM  N23   C21  C22   120.60  3.000
 XFM  N23   C21  N20   117.02  3.000
 XFM  C22   C21  N20   122.34  3.000
 XFM  H22   C22  C21   120.26  3.000
 XFM  H22   C22  C17   120.86  3.000
 XFM  C21   C22  C17   118.89  3.000
 XFM  HN2A  N23  HN23  114.01  3.000
 XFM  HN2A  N23  C21   117.47  3.000
 XFM  HN23  N23  C21   116.08  3.000
 XFM  H24B  C24  H24A  107.94  3.000
 XFM  H24B  C24  H24   108.43  3.000
 XFM  H24A  C24  H24   107.06  3.000
 XFM  H24B  C24  C19   111.66  3.000
 XFM  H24A  C24  C19   110.60  3.000
 XFM  H24   C24  C19   110.98  3.000
 XFM  H25B  C25  H25A  107.89  3.000
 XFM  H25B  C25  H25   107.02  3.000
 XFM  H25A  C25  H25   108.24  3.000
 XFM  H25B  C25  C4    110.55  3.000
 XFM  H25A  C25  C4    111.85  3.000
 XFM  H25   C25  C4    111.11  3.000
 XFM  HN2B  N26  HN26  114.07  3.000
 XFM  HN2B  N26  C6    116.15  3.000
 XFM  HN26  N26  C6    117.53  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
 XFM  CONST_01  C4   C5   C6   N1     0.00   0.0  0
 XFM  CONST_02  C4   C3   C2   N1     0.00   0.0  0
 XFM  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 XFM  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 XFM  CONST_05  C6   N1   C2   C3     0.00   0.0  0
 XFM  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 XFM  CONST_07  C12  C13  C14  C9     0.00   0.0  0
 XFM  CONST_08  C12  C11  N10  C9     0.00   0.0  0
 XFM  CONST_09  C13  C14  C9   N10    0.00   0.0  0
 XFM  CONST_10  C13  C12  C11  N10    0.00   0.0  0
 XFM  CONST_11  C14  C9   N10  C11    0.00   0.0  0
 XFM  CONST_12  C14  C13  C12  C11    0.00   0.0  0
 XFM  CONST_13  N20  C19  C18  C17    0.00   0.0  0
 XFM  CONST_14  N20  C21  C22  C17    0.00   0.0  0
 XFM  CONST_15  C21  C22  C17  C18    0.00   0.0  0
 XFM  CONST_16  C21  N20  C19  C18    0.00   0.0  0
 XFM  CONST_17  C22  C17  C18  C19    0.00   0.0  0
 XFM  CONST_18  C22  C21  N20  C19    0.00   0.0  0
 XFM  CONST_19  N26  C6   N1   C2   180.00   0.0  0
 XFM  CONST_20  C25  C4   C3   C2   180.00   0.0  0
 XFM  CONST_21  C7   C2   C3   C4   180.00   0.0  0
 XFM  CONST_22  N26  C6   C5   C4   180.00   0.0  0
 XFM  CONST_23  C7   C2   N1   C6   180.00   0.0  0
 XFM  CONST_24  C25  C4   C5   C6   180.00   0.0  0
 XFM  CONST_25  C13  C14  C9   C8   180.00   0.0  0
 XFM  CONST_26  C11  N10  C9   C8   180.00   0.0  0
 XFM  CONST_27  C15  C11  N10  C9   180.00   0.0  0
 XFM  CONST_28  C15  C11  C12  C13  180.00   0.0  0
 XFM  CONST_29  C19  C18  C17  C16  180.00   0.0  0
 XFM  CONST_30  C21  C22  C17  C16  180.00   0.0  0
 XFM  CONST_31  C24  C19  C18  C17  180.00   0.0  0
 XFM  CONST_32  N23  C21  C22  C17  180.00   0.0  0
 XFM  CONST_33  N23  C21  N20  C19  180.00   0.0  0
 XFM  CONST_34  C24  C19  N20  C21  180.00   0.0  0
 XFM  CONST_35  H5   C5   C6   N1   180.00   0.0  0
 XFM  CONST_36  H3   C3   C2   N1   180.00   0.0  0
 XFM  CONST_37  H13  C13  C14  C9   180.00   0.0  0
 XFM  CONST_38  H14  C14  C9   N10  180.00   0.0  0
 XFM  CONST_39  H12  C12  C11  N10  180.00   0.0  0
 XFM  CONST_40  H22  C22  C17  C18  180.00   0.0  0
 XFM  CONST_41  H18  C18  C19  N20  180.00   0.0  0
 XFM  Var_01    C8   C7   C2   N1   -65.36  30.0  2
 XFM  Var_02    C9   C8   C7   C2   176.45  30.0  3
 XFM  Var_03    C14  C9   C8   C7   100.72  30.0  3
 XFM  Var_04    C16  C15  C11  N10  -74.15  30.0  2
 XFM  Var_05    C17  C16  C15  C11  177.22  30.0  3
 XFM  Var_06    C18  C17  C16  C15  -79.78  30.0  2
 XFM  Var_07    H25  C25  C4   C3    51.08  30.0  2
 XFM  Var_08    H24  C24  C19  C18  129.56  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
 XFM  plan-1  N1    0.020
 XFM  plan-1  C2    0.020
 XFM  plan-1  C3    0.020
 XFM  plan-1  C4    0.020
 XFM  plan-1  C5    0.020
 XFM  plan-1  C6    0.020
 XFM  plan-1  C7    0.020
 XFM  plan-1  C25   0.020
 XFM  plan-1  N26   0.020
 XFM  plan-1  H3    0.020
 XFM  plan-1  H5    0.020
 XFM  plan-2  C8    0.020
 XFM  plan-2  C9    0.020
 XFM  plan-2  N10   0.020
 XFM  plan-2  C11   0.020
 XFM  plan-2  C12   0.020
 XFM  plan-2  C13   0.020
 XFM  plan-2  C14   0.020
 XFM  plan-2  C15   0.020
 XFM  plan-2  H12   0.020
 XFM  plan-2  H13   0.020
 XFM  plan-2  H14   0.020
 XFM  plan-3  C16   0.020
 XFM  plan-3  C17   0.020
 XFM  plan-3  C18   0.020
 XFM  plan-3  C19   0.020
 XFM  plan-3  N20   0.020
 XFM  plan-3  C21   0.020
 XFM  plan-3  C22   0.020
 XFM  plan-3  N23   0.020
 XFM  plan-3  C24   0.020
 XFM  plan-3  H18   0.020
 XFM  plan-3  H22   0.020
 XFM  plan-4  C21   0.020
 XFM  plan-4  N23   0.020
 XFM  plan-4  HN23  0.020
 XFM  plan-4  HN2A  0.020
 XFM  plan-5  C6    0.020
 XFM  plan-5  N26   0.020
 XFM  plan-5  HN26  0.020
 XFM  plan-5  HN2B  0.020

