# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:30:39 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6,6'-(pyridine-2,6-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cccc(CCc3cc(C)cc(N)n3)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
 XFL  XFL  6,6'-(pyridine-2,6-diyldiethane-2,1-diyl)bis(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_XFL
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
 XFL  N1    N  N     0  -0.433   0.0044   1.3030   0.0061
 XFL  C2    C  CR6   0   0.236   1.1251   1.9742  -0.2463
 XFL  C3    C  CR16  0  -0.354   1.1697   3.3650  -0.2334
 XFL  C4    C  CR16  0  -0.146   0.0097   4.0649   0.0573
 XFL  C5    C  CR16  0  -0.354  -1.1531   3.3593   0.3210
 XFL  C6    C  CR6   0   0.236  -1.1141   1.9687   0.2822
 XFL  N11   N  N     0  -0.484   3.9055  -1.4318  -0.0321
 XFL  C12   C  CR6   0   0.440   4.9323  -2.2357  -0.2824
 XFL  N12   N  NH2   0  -0.838   4.6645  -3.3998  -0.9451
 XFL  C13   C  CR16  0  -0.447   6.2519  -1.9025   0.0723
 XFL  C14   C  CR6   0   0.205   6.4942  -0.6958   0.6947
 XFL  C15   C  CR16  0  -0.432   5.4040   0.1456   0.9476
 XFL  C16   C  CR6   0   0.275   4.1381  -0.2638   0.5717
 XFL  C18   C  CH2   0  -0.493   2.9378   0.6066   0.8105
 XFL  C19   C  CH2   0  -0.491   2.3577   1.1560  -0.4993
 XFL  N21   N  N     0  -0.485  -3.8847  -1.4261  -0.0457
 XFL  C22   C  CR6   0   0.441  -4.9076  -2.2467   0.1630
 XFL  N22   N  NH2   0  -0.839  -4.6241  -3.4652   0.7109
 XFL  C23   C  CR16  0  -0.448  -6.2245  -1.9153  -0.2033
 XFL  C24   C  CR6   0   0.205  -6.4671  -0.6954  -0.7995
 XFL  C25   C  CR16  0  -0.432  -5.3794   0.1589  -1.0184
 XFL  C26   C  CR6   0   0.275  -4.1168  -0.2478  -0.6287
 XFL  C28   C  CH2   0  -0.493  -2.9195   0.6370  -0.8278
 XFL  C29   C  CH2   0  -0.491  -2.3502   1.1464   0.5025
 XFL  H3    H  HCR6  0   0.260   2.0948   3.8841  -0.4477
 XFL  H4    H  HCR6  0   0.268   0.0118   5.1470   0.0766
 XFL  H5    H  HCR6  0   0.260  -2.0766   3.8734   0.5532
 XFL  HN12  H  HNH2  0   0.379   3.7060  -3.7076  -0.9276
 XFL  HN1A  H  HNH2  0   0.387   5.3346  -4.1462  -0.8634
 XFL  H13   H  HCR6  0   0.255   7.0611  -2.5900  -0.1425
 XFL  H15   H  HCR6  0   0.243   5.5466   1.1003   1.4386
 XFL  H17   H  HCH3  0   0.253   8.2071   0.5738   0.4951
 XFL  H17A  H  HCH3  0   0.250   7.9155   0.0210   2.1335
 XFL  H17B  H  HCH3  0   0.247   8.5996  -1.0859   0.9400
 XFL  H18   H  HCH2  0   0.249   2.1663   0.0259   1.3229
 XFL  H18A  H  HCH2  0   0.247   3.2050   1.4363   1.4683
 XFL  H19   H  HCH2  0   0.250   2.1113   0.3212  -1.1585
 XFL  H19A  H  HCH2  0   0.248   3.1122   1.7610  -1.0066
 XFL  HN22  H  HNH2  0   0.379  -3.7527  -3.5342   1.2108
 XFL  HN2A  H  HNH2  0   0.387  -5.3822  -3.9719   1.1359
 XFL  H23   H  HCR6  0   0.255  -7.0314  -2.6142  -0.0171
 XFL  H25   H  HCR6  0   0.242  -5.5224   1.1247  -1.4869
 XFL  H27   H  HCH3  0   0.253  -8.1931   0.5524  -0.5775
 XFL  H27A  H  HCH3  0   0.250  -7.8737   0.0637  -2.2307
 XFL  H27B  H  HCH3  0   0.247  -8.5657  -1.0925  -1.0892
 XFL  H28   H  HCH2  0   0.249  -2.1415   0.0769  -1.3533
 XFL  H28A  H  HCH2  0   0.247  -3.1875   1.4858  -1.4606
 XFL  H29   H  HCH2  0   0.250  -2.1093   0.2923   1.1386
 XFL  H29A  H  HCH2  0   0.248  -3.1075   1.7378   1.0216
 XFL  C17   C  CH3   0  -0.727   7.8796  -0.2827   1.0867
 XFL  C27   C  CH3   0  -0.727  -7.8503  -0.2790  -1.1959

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
 XFL  N1   C6    aromatic  1.330  0.020  1.330
 XFL  N1   C2    aromatic  1.331  0.020  1.331
 XFL  C19  C2    single    1.501  0.020  1.501
 XFL  C2   C3    aromatic  1.392  0.020  1.392
 XFL  C3   C4    aromatic  1.386  0.020  1.386
 XFL  C3   H3    single    0.930  0.020  1.080
 XFL  C5   C4    aromatic  1.385  0.020  1.385
 XFL  C4   H4    single    0.930  0.020  1.080
 XFL  C6   C5    aromatic  1.392  0.020  1.392
 XFL  C5   H5    single    0.930  0.020  1.080
 XFL  C29  C6    single    1.501  0.020  1.501
 XFL  N11  C12   aromatic  1.328  0.020  1.328
 XFL  N11  C16   aromatic  1.335  0.020  1.335
 XFL  N12  C12   single    1.366  0.020  1.366
 XFL  C12  C13   aromatic  1.406  0.020  1.406
 XFL  N12  HN12  single    0.890  0.020  1.040
 XFL  N12  HN1A  single    0.890  0.020  1.040
 XFL  C13  C14   aromatic  1.379  0.020  1.379
 XFL  C13  H13   single    0.930  0.020  1.080
 XFL  C15  C14   aromatic  1.400  0.020  1.400
 XFL  C14  C17   single    1.498  0.020  1.498
 XFL  C16  C15   aromatic  1.383  0.020  1.383
 XFL  C15  H15   single    0.930  0.020  1.080
 XFL  C18  C16   single    1.502  0.020  1.502
 XFL  C17  H17   single    0.970  0.020  1.090
 XFL  C17  H17A  single    0.970  0.020  1.090
 XFL  C17  H17B  single    0.970  0.020  1.090
 XFL  C19  C18   single    1.534  0.020  1.534
 XFL  C18  H18   single    0.970  0.020  1.090
 XFL  C18  H18A  single    0.970  0.020  1.090
 XFL  C19  H19   single    0.970  0.020  1.090
 XFL  C19  H19A  single    0.970  0.020  1.090
 XFL  C22  N21   aromatic  1.328  0.020  1.328
 XFL  N21  C26   aromatic  1.335  0.020  1.335
 XFL  N22  C22   single    1.366  0.020  1.366
 XFL  C22  C23   aromatic  1.407  0.020  1.407
 XFL  N22  HN22  single    0.890  0.020  1.040
 XFL  N22  HN2A  single    0.890  0.020  1.040
 XFL  C23  C24   aromatic  1.379  0.020  1.379
 XFL  C23  H23   single    0.930  0.020  1.080
 XFL  C24  C27   single    1.498  0.020  1.498
 XFL  C24  C25   aromatic  1.400  0.020  1.400
 XFL  C26  C25   aromatic  1.383  0.020  1.383
 XFL  C25  H25   single    0.930  0.020  1.080
 XFL  C26  C28   single    1.502  0.020  1.502
 XFL  C27  H27   single    0.970  0.020  1.090
 XFL  C27  H27A  single    0.970  0.020  1.090
 XFL  C27  H27B  single    0.970  0.020  1.090
 XFL  C28  C29   single    1.534  0.020  1.534
 XFL  C28  H28   single    0.970  0.020  1.090
 XFL  C28  H28A  single    0.970  0.020  1.090
 XFL  C29  H29   single    0.970  0.020  1.090
 XFL  C29  H29A  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
 XFL  C6    N1   C2    119.68  3.000
 XFL  C19   C2   C3    121.34  3.000
 XFL  C3    C2   N1    121.96  3.000
 XFL  C19   C2   N1    116.67  3.000
 XFL  H3    C3   C4    120.99  3.000
 XFL  H3    C3   C2    120.33  3.000
 XFL  C4    C3   C2    118.68  3.000
 XFL  H4    C4   C5    120.49  3.000
 XFL  H4    C4   C3    120.48  3.000
 XFL  C5    C4   C3    119.03  3.000
 XFL  H5    C5   C6    120.31  3.000
 XFL  H5    C5   C4    121.00  3.000
 XFL  C6    C5   C4    118.69  3.000
 XFL  C29   C6   C5    121.35  3.000
 XFL  C29   C6   N1    116.66  3.000
 XFL  C5    C6   N1    121.96  3.000
 XFL  C16   N11  C12   118.69  3.000
 XFL  C13   C12  N12   120.54  3.000
 XFL  C13   C12  N11   122.31  3.000
 XFL  N12   C12  N11   117.12  3.000
 XFL  HN1A  N12  HN12  113.94  3.000
 XFL  HN1A  N12  C12   117.52  3.000
 XFL  HN12  N12  C12   116.02  3.000
 XFL  H13   C13  C14   120.90  3.000
 XFL  H13   C13  C12   120.03  3.000
 XFL  C14   C13  C12   119.07  3.000
 XFL  C17   C14  C15   120.47  3.000
 XFL  C17   C14  C13   121.46  3.000
 XFL  C15   C14  C13   118.07  3.000
 XFL  H15   C15  C16   120.32  3.000
 XFL  H15   C15  C14   120.61  3.000
 XFL  C16   C15  C14   119.07  3.000
 XFL  C18   C16  C15   121.13  3.000
 XFL  C18   C16  N11   116.08  3.000
 XFL  C15   C16  N11   122.78  3.000
 XFL  H18A  C18  H18   107.10  3.000
 XFL  H18A  C18  C19   109.55  3.000
 XFL  H18   C18  C19   108.87  3.000
 XFL  H18A  C18  C16   109.91  3.000
 XFL  H18   C18  C16   109.32  3.000
 XFL  C19   C18  C16   111.96  3.000
 XFL  H19A  C19  H19   107.40  3.000
 XFL  H19A  C19  C18   109.49  3.000
 XFL  H19   C19  C18   109.09  3.000
 XFL  H19A  C19  C2    110.10  3.000
 XFL  H19   C19  C2    109.46  3.000
 XFL  C18   C19  C2    111.21  3.000
 XFL  C26   N21  C22   118.70  3.000
 XFL  C23   C22  N22   120.60  3.000
 XFL  C23   C22  N21   122.32  3.000
 XFL  N22   C22  N21   117.03  3.000
 XFL  HN2A  N22  HN22  114.07  3.000
 XFL  HN2A  N22  C22   117.54  3.000
 XFL  HN22  N22  C22   116.10  3.000
 XFL  H23   C23  C24   120.92  3.000
 XFL  H23   C23  C22   120.03  3.000
 XFL  C24   C23  C22   119.05  3.000
 XFL  C27   C24  C25   120.42  3.000
 XFL  C25   C24  C23   118.07  3.000
 XFL  C27   C24  C23   121.51  3.000
 XFL  H25   C25  C26   120.32  3.000
 XFL  H25   C25  C24   120.61  3.000
 XFL  C26   C25  C24   119.07  3.000
 XFL  C28   C26  C25   121.15  3.000
 XFL  C28   C26  N21   116.06  3.000
 XFL  C25   C26  N21   122.78  3.000
 XFL  H28A  C28  H28   107.12  3.000
 XFL  H28A  C28  C29   109.60  3.000
 XFL  H28   C28  C29   108.84  3.000
 XFL  H28A  C28  C26   109.82  3.000
 XFL  H28   C28  C26   109.22  3.000
 XFL  C29   C28  C26   112.11  3.000
 XFL  H29A  C29  H29   107.44  3.000
 XFL  H29A  C29  C28   109.55  3.000
 XFL  H29   C29  C28   109.10  3.000
 XFL  H29A  C29  C6    110.13  3.000
 XFL  H29   C29  C6    109.41  3.000
 XFL  C28   C29  C6    111.11  3.000
 XFL  H17B  C17  H17A  108.25  3.000
 XFL  H17B  C17  H17   107.92  3.000
 XFL  H17A  C17  H17   106.98  3.000
 XFL  H17B  C17  C14   111.89  3.000
 XFL  H17A  C17  C14   111.01  3.000
 XFL  H17   C17  C14   110.61  3.000
 XFL  H27B  C27  H27A  108.29  3.000
 XFL  H27B  C27  H27   107.90  3.000
 XFL  H27A  C27  H27   106.95  3.000
 XFL  H27B  C27  C24   111.91  3.000
 XFL  H27A  C27  C24   111.00  3.000
 XFL  H27   C27  C24   110.60  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
 XFL  CONST_01  C4   C5   C6   N1     0.00   0.0  0
 XFL  CONST_02  C4   C3   C2   N1     0.00   0.0  0
 XFL  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 XFL  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 XFL  CONST_05  C6   N1   C2   C3     0.00   0.0  0
 XFL  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 XFL  CONST_07  C14  C13  C12  N11    0.00   0.0  0
 XFL  CONST_08  C14  C15  C16  N11    0.00   0.0  0
 XFL  CONST_09  C15  C16  N11  C12    0.00   0.0  0
 XFL  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 XFL  CONST_11  C16  N11  C12  C13    0.00   0.0  0
 XFL  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 XFL  CONST_13  C24  C23  C22  N21    0.00   0.0  0
 XFL  CONST_14  C24  C25  C26  N21    0.00   0.0  0
 XFL  CONST_15  C25  C26  N21  C22    0.00   0.0  0
 XFL  CONST_16  C25  C24  C23  C22    0.00   0.0  0
 XFL  CONST_17  C26  N21  C22  C23    0.00   0.0  0
 XFL  CONST_18  C26  C25  C24  C23    0.00   0.0  0
 XFL  CONST_19  C29  C6   N1   C2   180.00   0.0  0
 XFL  CONST_20  C19  C2   C3   C4   180.00   0.0  0
 XFL  CONST_21  C29  C6   C5   C4   180.00   0.0  0
 XFL  CONST_22  C19  C2   N1   C6   180.00   0.0  0
 XFL  CONST_23  C18  C16  N11  C12  180.00   0.0  0
 XFL  CONST_24  C17  C14  C13  C12  180.00   0.0  0
 XFL  CONST_25  C16  N11  C12  N12  180.00   0.0  0
 XFL  CONST_26  C14  C13  C12  N12  180.00   0.0  0
 XFL  CONST_27  C18  C16  C15  C14  180.00   0.0  0
 XFL  CONST_28  C17  C14  C15  C16  180.00   0.0  0
 XFL  CONST_29  C28  C26  N21  C22  180.00   0.0  0
 XFL  CONST_30  C27  C24  C23  C22  180.00   0.0  0
 XFL  CONST_31  C26  N21  C22  N22  180.00   0.0  0
 XFL  CONST_32  C24  C23  C22  N22  180.00   0.0  0
 XFL  CONST_33  C28  C26  C25  C24  180.00   0.0  0
 XFL  CONST_34  C27  C24  C25  C26  180.00   0.0  0
 XFL  CONST_35  H5   C5   C6   N1   180.00   0.0  0
 XFL  CONST_36  H3   C3   C2   N1   180.00   0.0  0
 XFL  CONST_37  H4   C4   C3   C2   180.00   0.0  0
 XFL  CONST_38  H13  C13  C12  N11  180.00   0.0  0
 XFL  CONST_39  H15  C15  C16  N11  180.00   0.0  0
 XFL  CONST_40  H23  C23  C22  N21  180.00   0.0  0
 XFL  CONST_41  H25  C25  C26  N21  180.00   0.0  0
 XFL  Var_01    C28  C29  C6   N1   -76.42  30.0  2
 XFL  Var_02    C18  C19  C2   N1   -77.06  30.0  1
 XFL  Var_03    C16  C18  C19  C2   177.55  30.0  3
 XFL  Var_04    C26  C28  C29  C6   177.04  30.0  2
 XFL  Var_05    C19  C18  C16  N11  -68.67  30.0  1
 XFL  Var_06    C29  C28  C26  N21  -67.72  30.0  2
 XFL  Var_07    H17  C17  C14  C13  112.93  30.0  2
 XFL  Var_08    H27  C27  C24  C23  112.09  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
 XFL  plan-1  N1    0.020
 XFL  plan-1  C2    0.020
 XFL  plan-1  C3    0.020
 XFL  plan-1  C4    0.020
 XFL  plan-1  C5    0.020
 XFL  plan-1  C6    0.020
 XFL  plan-1  C19   0.020
 XFL  plan-1  C29   0.020
 XFL  plan-1  H3    0.020
 XFL  plan-1  H4    0.020
 XFL  plan-1  H5    0.020
 XFL  plan-2  N11   0.020
 XFL  plan-2  C12   0.020
 XFL  plan-2  N12   0.020
 XFL  plan-2  C13   0.020
 XFL  plan-2  C14   0.020
 XFL  plan-2  C15   0.020
 XFL  plan-2  C16   0.020
 XFL  plan-2  C18   0.020
 XFL  plan-2  H13   0.020
 XFL  plan-2  H15   0.020
 XFL  plan-2  C17   0.020
 XFL  plan-3  N21   0.020
 XFL  plan-3  C22   0.020
 XFL  plan-3  N22   0.020
 XFL  plan-3  C23   0.020
 XFL  plan-3  C24   0.020
 XFL  plan-3  C25   0.020
 XFL  plan-3  C26   0.020
 XFL  plan-3  C28   0.020
 XFL  plan-3  H23   0.020
 XFL  plan-3  H25   0.020
 XFL  plan-3  C27   0.020
 XFL  plan-4  C12   0.020
 XFL  plan-4  N12   0.020
 XFL  plan-4  HN12  0.020
 XFL  plan-4  HN1A  0.020
 XFL  plan-5  C22   0.020
 XFL  plan-5  N22   0.020
 XFL  plan-5  HN22  0.020
 XFL  plan-5  HN2A  0.020

