# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:01:16 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-(2-{5-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-3-yl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cncc(CCc3cc(C)nc(N)c3)c2)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
 XFK  XFK  6-(2-{5-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin-3-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_XFK
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
 XFK  N01   N  N     0  -0.484   4.1089   1.3448   0.2099
 XFK  C02   C  CR6   0   0.443   5.1989   2.0903   0.3515
 XFK  N02   N  NH2   0  -0.839   5.0649   3.2612   1.0387
 XFK  C03   C  CR16  0  -0.448   6.4344   1.7295  -0.2164
 XFK  C04   C  CR6   0   0.204   6.5207   0.5637  -0.9480
 XFK  C05   C  CR16  0  -0.433   5.3620  -0.2090  -1.0974
 XFK  C06   C  CR6   0   0.273   4.1897   0.2190  -0.5030
 XFK  C07   C  CH3   0  -0.726   7.8153   0.1158  -1.5543
 XFK  C08   C  CH2   0  -0.487   2.9243  -0.5851  -0.6013
 XFK  C09   C  CH2   0  -0.513   2.5404  -1.2023   0.7505
 XFK  N11   N  N     0  -0.398  -0.0176  -3.9416   0.4194
 XFK  C12   C  CR16  0  -0.117   1.1292  -3.2790   0.5010
 XFK  C13   C  CR6   0   0.048   1.2164  -1.9038   0.6903
 XFK  C14   C  CR16  0  -0.240   0.0195  -1.2051   0.7923
 XFK  C15   C  CR6   0   0.048  -1.1949  -1.8747   0.7150
 XFK  C16   C  CR16  0  -0.113  -1.1459  -3.2522   0.5240
 XFK  C17   C  CH2   0  -0.514  -2.5003  -1.1409   0.7969
 XFK  C18   C  CH2   0  -0.510  -2.9373  -0.6050  -0.5744
 XFK  C21   C  CR16  0  -0.459  -5.4299  -0.3451  -0.7099
 XFK  C22   C  CR6   0   0.445  -6.5754   0.4554  -0.5567
 XFK  N22   N  NH2   0  -0.838  -7.8153  -0.0457  -0.8328
 XFK  N23   N  N     0  -0.487  -6.5081   1.7296  -0.1860
 XFK  C24   C  CR6   0   0.255  -5.3099   2.2698   0.0485
 XFK  C25   C  CR16  0  -0.436  -4.1324   1.5536  -0.0776
 XFK  C26   C  CR6   0   0.238  -4.1917   0.2119  -0.4682
 XFK  HN02  H  HNH2  0   0.380   4.2636   3.3367   1.6433
 XFK  HN0A  H  HNH2  0   0.388   5.8986   3.6954   1.3968
 XFK  H03   H  HCR6  0   0.255   7.3019   2.3635  -0.0767
 XFK  H05   H  HCR6  0   0.243   5.3818  -1.1286  -1.6691
 XFK  H07   H  HCH3  0   0.253   8.1852  -0.7758  -1.0451
 XFK  H07A  H  HCH3  0   0.250   7.6871  -0.1472  -2.6046
 XFK  H07B  H  HCH3  0   0.247   8.5838   0.8836  -1.4847
 XFK  H08   H  HCH2  0   0.249   2.1125   0.0629  -0.9430
 XFK  H08A  H  HCH2  0   0.249   3.0370  -1.3744  -1.3471
 XFK  H09   H  HCH2  0   0.252   3.3193  -1.9034   1.0596
 XFK  H09A  H  HCH2  0   0.255   2.5055  -0.4123   1.5037
 XFK  H12   H  HCR6  0   0.252   2.0367  -3.8704   0.4201
 XFK  H14   H  HCR6  0   0.255   0.0341  -0.1302   0.9452
 XFK  H16   H  HCR6  0   0.253  -2.0685  -3.8221   0.4610
 XFK  H17   H  HCH2  0   0.258  -3.2783  -1.7988   1.1908
 XFK  H17A  H  HCH2  0   0.259  -2.4092  -0.3081   1.4987
 XFK  H18   H  HCH2  0   0.257  -2.1340   0.0063  -0.9934
 XFK  H18A  H  HCH2  0   0.256  -3.0892  -1.4416  -1.2601
 XFK  H21   H  HCR6  0   0.254  -5.5255  -1.3806  -1.0154
 XFK  HN22  H  HNH2  0   0.388  -7.9323  -1.0444  -0.7963
 XFK  HN2A  H  HNH2  0   0.379  -8.5944   0.4736  -0.4630
 XFK  H25   H  HCR6  0   0.244  -3.1798   2.0277   0.1246
 XFK  H27   H  HCH3  0   0.245  -5.9531   3.8772   1.3136
 XFK  H27A  H  HCH3  0   0.240  -4.3015   4.0545   0.7118
 XFK  H27B  H  HCH3  0   0.247  -5.6766   4.3426  -0.3555
 XFK  C27   C  CH3   0  -0.718  -5.3024   3.7129   0.4539

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
 XFK  N01  C06   aromatic  1.335  0.020  1.335
 XFK  N01  C02   aromatic  1.328  0.020  1.328
 XFK  N02  C02   single    1.364  0.020  1.364
 XFK  C02  C03   aromatic  1.407  0.020  1.407
 XFK  N02  HN02  single    0.890  0.020  1.040
 XFK  N02  HN0A  single    0.890  0.020  1.040
 XFK  C03  C04   aromatic  1.379  0.020  1.379
 XFK  C03  H03   single    0.930  0.020  1.080
 XFK  C05  C04   aromatic  1.401  0.020  1.401
 XFK  C04  C07   single    1.498  0.020  1.498
 XFK  C06  C05   aromatic  1.382  0.020  1.382
 XFK  C05  H05   single    0.930  0.020  1.080
 XFK  C08  C06   single    1.502  0.020  1.502
 XFK  C07  H07   single    0.970  0.020  1.090
 XFK  C07  H07A  single    0.970  0.020  1.090
 XFK  C07  H07B  single    0.970  0.020  1.090
 XFK  C08  C09   single    1.535  0.020  1.535
 XFK  C08  H08   single    0.970  0.020  1.090
 XFK  C08  H08A  single    0.970  0.020  1.090
 XFK  C13  C09   single    1.500  0.020  1.500
 XFK  C09  H09   single    0.970  0.020  1.090
 XFK  C09  H09A  single    0.970  0.020  1.090
 XFK  C16  N11   aromatic  1.326  0.020  1.326
 XFK  N11  C12   aromatic  1.327  0.020  1.327
 XFK  C12  C13   aromatic  1.391  0.020  1.391
 XFK  C12  H12   single    0.930  0.020  1.080
 XFK  C14  C13   aromatic  1.390  0.020  1.390
 XFK  C15  C14   aromatic  1.389  0.020  1.389
 XFK  C14  H14   single    0.930  0.020  1.080
 XFK  C17  C15   single    1.500  0.020  1.500
 XFK  C16  C15   aromatic  1.392  0.020  1.392
 XFK  C16  H16   single    0.930  0.020  1.080
 XFK  C17  C18   single    1.536  0.020  1.536
 XFK  C17  H17   single    0.970  0.020  1.090
 XFK  C17  H17A  single    0.970  0.020  1.090
 XFK  C26  C18   single    1.501  0.020  1.501
 XFK  C18  H18   single    0.970  0.020  1.090
 XFK  C18  H18A  single    0.970  0.020  1.090
 XFK  C22  C21   aromatic  1.406  0.020  1.406
 XFK  C26  C21   aromatic  1.379  0.020  1.379
 XFK  C21  H21   single    0.930  0.020  1.080
 XFK  N23  C22   aromatic  1.329  0.020  1.329
 XFK  C22  N22   single    1.366  0.020  1.366
 XFK  N22  HN22  single    0.890  0.020  1.040
 XFK  N22  HN2A  single    0.890  0.020  1.040
 XFK  C24  N23   aromatic  1.335  0.020  1.335
 XFK  C27  C24   single    1.499  0.020  1.499
 XFK  C24  C25   aromatic  1.384  0.020  1.384
 XFK  C25  C26   aromatic  1.399  0.020  1.399
 XFK  C25  H25   single    0.930  0.020  1.080
 XFK  C27  H27   single    0.970  0.020  1.090
 XFK  C27  H27A  single    0.970  0.020  1.090
 XFK  C27  H27B  single    0.970  0.020  1.090

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
 XFK  C06   N01  C02   118.72  3.000
 XFK  C03   C02  N02   120.65  3.000
 XFK  C03   C02  N01   122.26  3.000
 XFK  N02   C02  N01   117.05  3.000
 XFK  HN0A  N02  HN02  114.43  3.000
 XFK  HN0A  N02  C02   117.93  3.000
 XFK  HN02  N02  C02   116.44  3.000
 XFK  H03   C03  C04   120.87  3.000
 XFK  H03   C03  C02   120.06  3.000
 XFK  C04   C03  C02   119.07  3.000
 XFK  C07   C04  C05   120.45  3.000
 XFK  C07   C04  C03   121.44  3.000
 XFK  C05   C04  C03   118.11  3.000
 XFK  H05   C05  C06   120.36  3.000
 XFK  H05   C05  C04   120.63  3.000
 XFK  C06   C05  C04   119.01  3.000
 XFK  C08   C06  C05   121.36  3.000
 XFK  C08   C06  N01   115.80  3.000
 XFK  C05   C06  N01   122.82  3.000
 XFK  H07B  C07  H07A  108.34  3.000
 XFK  H07B  C07  H07   107.89  3.000
 XFK  H07A  C07  H07   106.99  3.000
 XFK  H07B  C07  C04   111.92  3.000
 XFK  H07A  C07  C04   111.12  3.000
 XFK  H07   C07  C04   110.39  3.000
 XFK  H08A  C08  H08   106.95  3.000
 XFK  H08A  C08  C09   109.68  3.000
 XFK  H08   C08  C09   109.14  3.000
 XFK  H08A  C08  C06   110.17  3.000
 XFK  H08   C08  C06   109.18  3.000
 XFK  C09   C08  C06   111.61  3.000
 XFK  H09A  C09  H09   106.97  3.000
 XFK  H09A  C09  C13   109.75  3.000
 XFK  H09   C09  C13   109.92  3.000
 XFK  H09A  C09  C08   108.93  3.000
 XFK  H09   C09  C08   109.20  3.000
 XFK  C13   C09  C08   111.94  3.000
 XFK  C16   N11  C12   118.09  3.000
 XFK  H12   C12  C13   119.74  3.000
 XFK  H12   C12  N11   116.46  3.000
 XFK  C13   C12  N11   123.79  3.000
 XFK  C14   C13  C12   116.94  3.000
 XFK  C14   C13  C09   121.49  3.000
 XFK  C12   C13  C09   121.55  3.000
 XFK  H14   C14  C15   119.79  3.000
 XFK  H14   C14  C13   119.77  3.000
 XFK  C15   C14  C13   120.44  3.000
 XFK  C17   C15  C16   121.50  3.000
 XFK  C16   C15  C14   117.01  3.000
 XFK  C17   C15  C14   121.47  3.000
 XFK  H16   C16  C15   119.83  3.000
 XFK  H16   C16  N11   116.44  3.000
 XFK  C15   C16  N11   123.73  3.000
 XFK  H17A  C17  H17   106.66  3.000
 XFK  H17A  C17  C18   109.34  3.000
 XFK  H17   C17  C18   109.23  3.000
 XFK  H17A  C17  C15   109.59  3.000
 XFK  H17   C17  C15   110.18  3.000
 XFK  C18   C17  C15   111.70  3.000
 XFK  H18A  C18  H18   106.85  3.000
 XFK  H18A  C18  C26   110.19  3.000
 XFK  H18   C18  C26   109.70  3.000
 XFK  H18A  C18  C17   109.44  3.000
 XFK  H18   C18  C17   109.16  3.000
 XFK  C26   C18  C17   111.38  3.000
 XFK  H21   C21  C26   120.96  3.000
 XFK  H21   C21  C22   120.19  3.000
 XFK  C26   C21  C22   118.85  3.000
 XFK  N23   C22  N22   117.02  3.000
 XFK  N22   C22  C21   120.59  3.000
 XFK  N23   C22  C21   122.35  3.000
 XFK  HN2A  N22  HN22  114.12  3.000
 XFK  HN2A  N22  C22   116.05  3.000
 XFK  HN22  N22  C22   117.54  3.000
 XFK  C24   N23  C22   118.84  3.000
 XFK  C27   C24  C25   121.24  3.000
 XFK  C25   C24  N23   122.56  3.000
 XFK  C27   C24  N23   116.20  3.000
 XFK  H25   C25  C26   120.62  3.000
 XFK  H25   C25  C24   120.31  3.000
 XFK  C26   C25  C24   119.07  3.000
 XFK  C25   C26  C21   118.33  3.000
 XFK  C25   C26  C18   120.43  3.000
 XFK  C21   C26  C18   121.21  3.000
 XFK  H27B  C27  H27A  108.05  3.000
 XFK  H27B  C27  H27   107.04  3.000
 XFK  H27A  C27  H27   108.34  3.000
 XFK  H27B  C27  C24   110.67  3.000
 XFK  H27A  C27  C24   111.76  3.000
 XFK  H27   C27  C24   110.80  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
 XFK  CONST_01  C04  C05  C06  N01     0.00   0.0  0
 XFK  CONST_02  C04  C03  C02  N01     0.00   0.0  0
 XFK  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 XFK  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 XFK  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 XFK  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 XFK  CONST_07  C14  C15  C16  N11     0.00   0.0  0
 XFK  CONST_08  C14  C13  C12  N11     0.00   0.0  0
 XFK  CONST_09  C15  C16  N11  C12     0.00   0.0  0
 XFK  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 XFK  CONST_11  C16  N11  C12  C13     0.00   0.0  0
 XFK  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 XFK  CONST_13  C24  N23  C22  C21     0.00   0.0  0
 XFK  CONST_14  C24  C25  C26  C21     0.00   0.0  0
 XFK  CONST_15  C25  C26  C21  C22     0.00   0.0  0
 XFK  CONST_16  C25  C24  N23  C22     0.00   0.0  0
 XFK  CONST_17  C26  C21  C22  N23     0.00   0.0  0
 XFK  CONST_18  C26  C25  C24  N23     0.00   0.0  0
 XFK  CONST_19  C08  C06  N01  C02   180.00   0.0  0
 XFK  CONST_20  C07  C04  C03  C02   180.00   0.0  0
 XFK  CONST_21  C06  N01  C02  N02   180.00   0.0  0
 XFK  CONST_22  C04  C03  C02  N02   180.00   0.0  0
 XFK  CONST_23  C08  C06  C05  C04   180.00   0.0  0
 XFK  CONST_24  C07  C04  C05  C06   180.00   0.0  0
 XFK  CONST_25  N11  C12  C13  C09   180.00   0.0  0
 XFK  CONST_26  C15  C14  C13  C09   180.00   0.0  0
 XFK  CONST_27  C17  C15  C16  N11   180.00   0.0  0
 XFK  CONST_28  C17  C15  C14  C13   180.00   0.0  0
 XFK  CONST_29  C22  C21  C26  C18   180.00   0.0  0
 XFK  CONST_30  C24  C25  C26  C18   180.00   0.0  0
 XFK  CONST_31  C27  C24  N23  C22   180.00   0.0  0
 XFK  CONST_32  C26  C21  C22  N22   180.00   0.0  0
 XFK  CONST_33  C24  N23  C22  N22   180.00   0.0  0
 XFK  CONST_34  C27  C24  C25  C26   180.00   0.0  0
 XFK  CONST_35  H05  C05  C06  N01   180.00   0.0  0
 XFK  CONST_36  H03  C03  C02  N01   180.00   0.0  0
 XFK  CONST_37  H16  C16  N11  C12   180.00   0.0  0
 XFK  CONST_38  H14  C14  C13  C12   180.00   0.0  0
 XFK  CONST_39  H12  C12  C13  C14   180.00   0.0  0
 XFK  CONST_40  H25  C25  C26  C21   180.00   0.0  0
 XFK  CONST_41  H21  C21  C22  N23   180.00   0.0  0
 XFK  Var_01    C09  C08  C06  N01   -68.51  30.0  1
 XFK  Var_02    C13  C09  C08  C06   174.90  30.0  3
 XFK  Var_03    C12  C13  C09  C08    97.12  30.0  2
 XFK  Var_04    C18  C17  C15  C14    85.46  30.0  2
 XFK  Var_05    C26  C18  C17  C15  -175.89  30.0  3
 XFK  Var_06    C21  C26  C18  C17   -95.92  30.0  2
 XFK  Var_07    H07  C07  C04  C03   110.69  30.0  2
 XFK  Var_08    H27  C27  C24  N23    54.01  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
 XFK  plan-1  N01   0.020
 XFK  plan-1  C02   0.020
 XFK  plan-1  N02   0.020
 XFK  plan-1  C03   0.020
 XFK  plan-1  C04   0.020
 XFK  plan-1  C05   0.020
 XFK  plan-1  C06   0.020
 XFK  plan-1  C07   0.020
 XFK  plan-1  C08   0.020
 XFK  plan-1  H03   0.020
 XFK  plan-1  H05   0.020
 XFK  plan-2  C09   0.020
 XFK  plan-2  N11   0.020
 XFK  plan-2  C12   0.020
 XFK  plan-2  C13   0.020
 XFK  plan-2  C14   0.020
 XFK  plan-2  C15   0.020
 XFK  plan-2  C16   0.020
 XFK  plan-2  C17   0.020
 XFK  plan-2  H12   0.020
 XFK  plan-2  H14   0.020
 XFK  plan-2  H16   0.020
 XFK  plan-3  C18   0.020
 XFK  plan-3  C21   0.020
 XFK  plan-3  C22   0.020
 XFK  plan-3  N22   0.020
 XFK  plan-3  N23   0.020
 XFK  plan-3  C24   0.020
 XFK  plan-3  C25   0.020
 XFK  plan-3  C26   0.020
 XFK  plan-3  H21   0.020
 XFK  plan-3  H25   0.020
 XFK  plan-3  C27   0.020
 XFK  plan-4  C02   0.020
 XFK  plan-4  N02   0.020
 XFK  plan-4  HN02  0.020
 XFK  plan-4  HN0A  0.020
 XFK  plan-5  C22   0.020
 XFK  plan-5  N22   0.020
 XFK  plan-5  HN22  0.020
 XFK  plan-5  HN2A  0.020

