# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:34:46 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 6,6'-[(5-aminobenzene-1,3-diyl)diethane-2,1-diyl]bis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cc(N)cc(CCc3cc(C)cc(N)n3)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
 XFN  XFN  6,6'-[(5-aminobenzene-1,3-diyl)diethane-2,1-diyl]bis(4-methylpyridin-2-amine)  ligand  54  27  .  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_XFN
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
 XFN  C01   C  CR16  0  -0.399   1.1620   2.7427  -0.2043
 XFN  C02   C  CR6   0   0.334  -0.0031   3.4543   0.0986
 XFN  N02   N  NH2   0  -0.864   0.0147   4.8329   0.1869
 XFN  C03   C  CR16  0  -0.399  -1.1742   2.7366   0.3634
 XFN  C04   C  CR6   0   0.161  -1.1855   1.3479   0.3304
 XFN  C05   C  CR16  0  -0.419  -0.0119   0.6606   0.0309
 XFN  C06   C  CR6   0   0.161   1.1650   1.3539  -0.2383
 XFN  C07   C  CH2   0  -0.512  -2.4691   0.6003   0.5624
 XFN  C08   C  CH2   0  -0.512   2.4429   0.6117  -0.5150
 XFN  C09   C  CH2   0  -0.486   3.2891   0.4434   0.7547
 XFN  C11   C  CR6   0   0.440   5.4970  -2.3381  -0.0508
 XFN  N12   N  N     0  -0.484   4.4138  -1.6224   0.2289
 XFN  C13   C  CR6   0   0.274   4.5544  -0.3192   0.4838
 XFN  C14   C  CR16  0  -0.433   5.7821   0.3174   0.4723
 XFN  C15   C  CR6   0   0.205   6.9322  -0.4278   0.1862
 XFN  C16   C  CR16  0  -0.448   6.7846  -1.7729  -0.0800
 XFN  C18   C  CH3   0  -0.725   8.2807   0.2249   0.1810
 XFN  C34   C  CH2   0  -0.486  -3.3050   0.4945  -0.7211
 XFN  C35   C  CR6   0   0.275  -4.5697  -0.2864  -0.5051
 XFN  C36   C  CR16  0  -0.435  -5.8020   0.3412  -0.4913
 XFN  C37   C  CR6   0   0.205  -6.9515  -0.4223  -0.2555
 XFN  C38   C  CR16  0  -0.448  -6.7997  -1.7773  -0.0472
 XFN  C39   C  CR6   0   0.441  -5.5081  -2.3331  -0.0792
 XFN  N40   N  N     0  -0.485  -4.4242  -1.5976  -0.3008
 XFN  N41   N  NH2   0  -0.839  -5.3260  -3.6772   0.0732
 XFN  C42   C  CH3   0  -0.725  -8.3048   0.2202  -0.2467
 XFN  H01   H  HCR6  0   0.241   2.0774   3.2860  -0.4173
 XFN  HN02  H  HNH2  0   0.375   0.7582   5.2877  -0.3188
 XFN  HN0A  H  HNH2  0   0.376  -0.8697   5.2880   0.0260
 XFN  H03   H  HCR6  0   0.242  -2.0875   3.2745   0.5979
 XFN  H05   H  HCR6  0   0.227  -0.0153  -0.4238   0.0034
 XFN  H07   H  HCH2  0   0.245  -2.2554  -0.4058   0.9293
 XFN  H07A  H  HCH2  0   0.244  -3.0616   1.1013   1.3325
 XFN  H08   H  HCH2  0   0.245   2.2214  -0.3756  -0.9257
 XFN  H08A  H  HCH2  0   0.245   3.0317   1.1445  -1.2664
 XFN  H09   H  HCH2  0   0.245   3.5292   1.4263   1.1660
 XFN  H09A  H  HCH2  0   0.245   2.6988  -0.0859   1.5075
 XFN  H14   H  HCR6  0   0.243   5.8493   1.3775   0.6832
 XFN  H16   H  HCR6  0   0.255   7.6452  -2.3915  -0.3060
 XFN  HN17  H  HNH2  0   0.387   6.1025  -4.2695  -0.2571
 XFN  HN1A  H  HNH2  0   0.379   4.4408  -4.0622  -0.0503
 XFN  H18   H  HCH3  0   0.252   8.5349   0.5933   1.1761
 XFN  H18A  H  HCH3  0   0.246   9.0627  -0.4652  -0.1315
 XFN  H18B  H  HCH3  0   0.250   8.2962   1.0839  -0.4909
 XFN  H34   H  HCH2  0   0.244  -3.5454   1.4967  -1.0823
 XFN  H34A  H  HCH2  0   0.246  -2.7061   0.0079  -1.4958
 XFN  H36   H  HCR6  0   0.242  -5.8724   1.4095  -0.6541
 XFN  H38   H  HCR6  0   0.254  -7.6599  -2.4095   0.1377
 XFN  HN41  H  HNH2  0   0.388  -6.0565  -4.2018   0.5242
 XFN  HN4A  H  HNH2  0   0.379  -4.3947  -3.9774   0.3093
 XFN  H42   H  HCH3  0   0.253  -8.5881   0.5318  -1.2535
 XFN  H42A  H  HCH3  0   0.246  -9.0724  -0.4593   0.1203
 XFN  H42B  H  HCH3  0   0.249  -8.3110   1.1138   0.3782
 XFN  N17   N  NH2   0  -0.838   5.3107  -3.6567  -0.3553

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
 XFN  C06  C01   aromatic  1.389  0.020  1.389
 XFN  C01  C02   aromatic  1.398  0.020  1.398
 XFN  C01  H01   single    0.930  0.020  1.080
 XFN  C02  C03   aromatic  1.399  0.020  1.399
 XFN  C02  N02   single    1.382  0.020  1.382
 XFN  N02  HN02  single    0.890  0.020  1.040
 XFN  N02  HN0A  single    0.890  0.020  1.040
 XFN  C04  C03   aromatic  1.389  0.020  1.389
 XFN  C03  H03   single    0.930  0.020  1.080
 XFN  C05  C04   aromatic  1.393  0.020  1.393
 XFN  C04  C07   single    1.503  0.020  1.503
 XFN  C06  C05   aromatic  1.392  0.020  1.392
 XFN  C05  H05   single    0.930  0.020  1.080
 XFN  C08  C06   single    1.503  0.020  1.503
 XFN  C34  C07   single    1.535  0.020  1.535
 XFN  C07  H07   single    0.970  0.020  1.090
 XFN  C07  H07A  single    0.970  0.020  1.090
 XFN  C09  C08   single    1.535  0.020  1.535
 XFN  C08  H08   single    0.970  0.020  1.090
 XFN  C08  H08A  single    0.970  0.020  1.090
 XFN  C09  C13   single    1.502  0.020  1.502
 XFN  C09  H09   single    0.970  0.020  1.090
 XFN  C09  H09A  single    0.970  0.020  1.090
 XFN  N12  C11   aromatic  1.328  0.020  1.328
 XFN  N17  C11   single    1.366  0.020  1.366
 XFN  C11  C16   aromatic  1.406  0.020  1.406
 XFN  N12  C13   aromatic  1.335  0.020  1.335
 XFN  C13  C14   aromatic  1.383  0.020  1.383
 XFN  C14  C15   aromatic  1.400  0.020  1.400
 XFN  C14  H14   single    0.930  0.020  1.080
 XFN  C16  C15   aromatic  1.379  0.020  1.379
 XFN  C15  C18   single    1.498  0.020  1.498
 XFN  C16  H16   single    0.930  0.020  1.080
 XFN  N17  HN17  single    0.890  0.020  1.040
 XFN  N17  HN1A  single    0.890  0.020  1.040
 XFN  C18  H18   single    0.970  0.020  1.090
 XFN  C18  H18A  single    0.970  0.020  1.090
 XFN  C18  H18B  single    0.970  0.020  1.090
 XFN  C34  C35   single    1.502  0.020  1.502
 XFN  C34  H34   single    0.970  0.020  1.090
 XFN  C34  H34A  single    0.970  0.020  1.090
 XFN  N40  C35   aromatic  1.335  0.020  1.335
 XFN  C35  C36   aromatic  1.383  0.020  1.383
 XFN  C36  C37   aromatic  1.400  0.020  1.400
 XFN  C36  H36   single    0.930  0.020  1.080
 XFN  C38  C37   aromatic  1.379  0.020  1.379
 XFN  C37  C42   single    1.498  0.020  1.498
 XFN  C39  C38   aromatic  1.406  0.020  1.406
 XFN  C38  H38   single    0.930  0.020  1.080
 XFN  N40  C39   aromatic  1.328  0.020  1.328
 XFN  N41  C39   single    1.365  0.020  1.365
 XFN  N41  HN41  single    0.890  0.020  1.040
 XFN  N41  HN4A  single    0.890  0.020  1.040
 XFN  C42  H42   single    0.970  0.020  1.090
 XFN  C42  H42A  single    0.970  0.020  1.090
 XFN  C42  H42B  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
 XFN  H01   C01  C06   119.59  3.000
 XFN  H01   C01  C02   119.37  3.000
 XFN  C06   C01  C02   121.05  3.000
 XFN  C03   C02  N02   120.70  3.000
 XFN  N02   C02  C01   120.72  3.000
 XFN  C03   C02  C01   118.52  3.000
 XFN  HN0A  N02  HN02  111.33  3.000
 XFN  HN0A  N02  C02   115.42  3.000
 XFN  HN02  N02  C02   115.33  3.000
 XFN  H03   C03  C04   119.58  3.000
 XFN  H03   C03  C02   119.41  3.000
 XFN  C04   C03  C02   121.01  3.000
 XFN  C07   C04  C05   120.48  3.000
 XFN  C07   C04  C03   120.02  3.000
 XFN  C05   C04  C03   119.45  3.000
 XFN  H05   C05  C06   119.70  3.000
 XFN  H05   C05  C04   119.75  3.000
 XFN  C06   C05  C04   120.54  3.000
 XFN  C08   C06  C05   120.55  3.000
 XFN  C08   C06  C01   119.99  3.000
 XFN  C05   C06  C01   119.43  3.000
 XFN  H07A  C07  H07   106.95  3.000
 XFN  H07A  C07  C34   108.99  3.000
 XFN  H07   C07  C34   108.90  3.000
 XFN  H07A  C07  C04   110.10  3.000
 XFN  H07   C07  C04   110.05  3.000
 XFN  C34   C07  C04   111.72  3.000
 XFN  H08A  C08  H08   106.94  3.000
 XFN  H08A  C08  C09   108.96  3.000
 XFN  H08   C08  C09   108.89  3.000
 XFN  H08A  C08  C06   110.10  3.000
 XFN  H08   C08  C06   110.07  3.000
 XFN  C09   C08  C06   111.74  3.000
 XFN  H09A  C09  H09   107.16  3.000
 XFN  H09A  C09  C13   109.46  3.000
 XFN  H09   C09  C13   109.86  3.000
 XFN  H09A  C09  C08   108.96  3.000
 XFN  H09   C09  C08   109.51  3.000
 XFN  C13   C09  C08   111.77  3.000
 XFN  N17   C11  C16   120.54  3.000
 XFN  C16   C11  N12   122.31  3.000
 XFN  N17   C11  N12   117.12  3.000
 XFN  C13   N12  C11   118.70  3.000
 XFN  C14   C13  N12   122.76  3.000
 XFN  C14   C13  C09   121.04  3.000
 XFN  N12   C13  C09   116.18  3.000
 XFN  H14   C14  C15   120.65  3.000
 XFN  H14   C14  C13   120.27  3.000
 XFN  C15   C14  C13   119.08  3.000
 XFN  C18   C15  C16   121.37  3.000
 XFN  C18   C15  C14   120.55  3.000
 XFN  C16   C15  C14   118.08  3.000
 XFN  H16   C16  C15   120.80  3.000
 XFN  H16   C16  C11   120.13  3.000
 XFN  C15   C16  C11   119.07  3.000
 XFN  H18B  C18  H18A  108.19  3.000
 XFN  H18B  C18  H18   107.01  3.000
 XFN  H18A  C18  H18   107.97  3.000
 XFN  H18B  C18  C15   110.98  3.000
 XFN  H18A  C18  C15   111.80  3.000
 XFN  H18   C18  C15   110.71  3.000
 XFN  H34A  C34  H34   107.14  3.000
 XFN  H34A  C34  C35   109.37  3.000
 XFN  H34   C34  C35   109.83  3.000
 XFN  H34A  C34  C07   108.95  3.000
 XFN  H34   C34  C07   109.46  3.000
 XFN  C35   C34  C07   111.96  3.000
 XFN  N40   C35  C36   122.77  3.000
 XFN  C36   C35  C34   121.05  3.000
 XFN  N40   C35  C34   116.16  3.000
 XFN  H36   C36  C37   120.66  3.000
 XFN  H36   C36  C35   120.27  3.000
 XFN  C37   C36  C35   119.07  3.000
 XFN  C42   C37  C38   121.32  3.000
 XFN  C42   C37  C36   120.58  3.000
 XFN  C38   C37  C36   118.09  3.000
 XFN  H38   C38  C39   120.16  3.000
 XFN  H38   C38  C37   120.77  3.000
 XFN  C39   C38  C37   119.07  3.000
 XFN  N41   C39  N40   117.07  3.000
 XFN  N41   C39  C38   120.61  3.000
 XFN  N40   C39  C38   122.29  3.000
 XFN  C39   N40  C35   118.71  3.000
 XFN  HN4A  N41  HN41  114.27  3.000
 XFN  HN4A  N41  C39   116.32  3.000
 XFN  HN41  N41  C39   117.82  3.000
 XFN  H42B  C42  H42A  108.32  3.000
 XFN  H42B  C42  H42   107.06  3.000
 XFN  H42A  C42  H42   107.82  3.000
 XFN  H42B  C42  C37   111.10  3.000
 XFN  H42A  C42  C37   111.79  3.000
 XFN  H42   C42  C37   110.58  3.000
 XFN  HN1A  N17  HN17  113.89  3.000
 XFN  HN1A  N17  C11   116.04  3.000
 XFN  HN17  N17  C11   117.31  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
 XFN  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 XFN  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 XFN  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 XFN  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 XFN  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 XFN  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 XFN  CONST_07  C14  C13  N12  C11    0.00   0.0  0
 XFN  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 XFN  CONST_09  C15  C16  C11  N12    0.00   0.0  0
 XFN  CONST_10  C15  C14  C13  N12    0.00   0.0  0
 XFN  CONST_11  C16  C11  N12  C13    0.00   0.0  0
 XFN  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 XFN  CONST_13  C38  C39  N40  C35    0.00   0.0  0
 XFN  CONST_14  C38  C37  C36  C35    0.00   0.0  0
 XFN  CONST_15  C39  N40  C35  C36    0.00   0.0  0
 XFN  CONST_16  C39  C38  C37  C36    0.00   0.0  0
 XFN  CONST_17  N40  C35  C36  C37    0.00   0.0  0
 XFN  CONST_18  N40  C39  C38  C37    0.00   0.0  0
 XFN  CONST_19  C08  C06  C01  C02  180.00   0.0  0
 XFN  CONST_20  C07  C04  C03  C02  180.00   0.0  0
 XFN  CONST_21  C06  C01  C02  N02  180.00   0.0  0
 XFN  CONST_22  C04  C03  C02  N02  180.00   0.0  0
 XFN  CONST_23  C08  C06  C05  C04  180.00   0.0  0
 XFN  CONST_24  C07  C04  C05  C06  180.00   0.0  0
 XFN  CONST_25  C11  N12  C13  C09  180.00   0.0  0
 XFN  CONST_26  C15  C14  C13  C09  180.00   0.0  0
 XFN  CONST_27  C18  C15  C16  C11  180.00   0.0  0
 XFN  CONST_28  N17  C11  N12  C13  180.00   0.0  0
 XFN  CONST_29  C18  C15  C14  C13  180.00   0.0  0
 XFN  CONST_30  N17  C11  C16  C15  180.00   0.0  0
 XFN  CONST_31  C39  N40  C35  C34  180.00   0.0  0
 XFN  CONST_32  C37  C36  C35  C34  180.00   0.0  0
 XFN  CONST_33  N41  C39  N40  C35  180.00   0.0  0
 XFN  CONST_34  C42  C37  C36  C35  180.00   0.0  0
 XFN  CONST_35  N41  C39  C38  C37  180.00   0.0  0
 XFN  CONST_36  C42  C37  C38  C39  180.00   0.0  0
 XFN  CONST_37  H05  C05  C06  C01  180.00   0.0  0
 XFN  CONST_38  H03  C03  C02  C01  180.00   0.0  0
 XFN  CONST_39  H01  C01  C02  C03  180.00   0.0  0
 XFN  CONST_40  H16  C16  C11  N12  180.00   0.0  0
 XFN  CONST_41  H14  C14  C13  N12  180.00   0.0  0
 XFN  CONST_42  H38  C38  C37  C36  180.00   0.0  0
 XFN  CONST_43  H36  C36  C37  C38  180.00   0.0  0
 XFN  Var_01    C09  C08  C06  C01   83.25  30.0  2
 XFN  Var_02    C34  C07  C04  C03   83.43  30.0  2
 XFN  Var_03    C35  C34  C07  C04  178.32  30.0  1
 XFN  Var_04    C13  C09  C08  C06  178.99  30.0  2
 XFN  Var_05    N40  C35  C34  C07  -70.02  30.0  2
 XFN  Var_06    N12  C13  C09  C08  -70.91  30.0  2
 XFN  Var_07    H18  C18  C15  C14   63.90  30.0  2
 XFN  Var_08    H42  C42  C37  C36   69.92  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
 XFN  plan-1  C01   0.020
 XFN  plan-1  C02   0.020
 XFN  plan-1  N02   0.020
 XFN  plan-1  C03   0.020
 XFN  plan-1  C04   0.020
 XFN  plan-1  C05   0.020
 XFN  plan-1  C06   0.020
 XFN  plan-1  C07   0.020
 XFN  plan-1  C08   0.020
 XFN  plan-1  H01   0.020
 XFN  plan-1  H03   0.020
 XFN  plan-1  H05   0.020
 XFN  plan-2  C09   0.020
 XFN  plan-2  C11   0.020
 XFN  plan-2  N12   0.020
 XFN  plan-2  C13   0.020
 XFN  plan-2  C14   0.020
 XFN  plan-2  C15   0.020
 XFN  plan-2  C16   0.020
 XFN  plan-2  C18   0.020
 XFN  plan-2  H14   0.020
 XFN  plan-2  H16   0.020
 XFN  plan-2  N17   0.020
 XFN  plan-3  C34   0.020
 XFN  plan-3  C35   0.020
 XFN  plan-3  C36   0.020
 XFN  plan-3  C37   0.020
 XFN  plan-3  C38   0.020
 XFN  plan-3  C39   0.020
 XFN  plan-3  N40   0.020
 XFN  plan-3  N41   0.020
 XFN  plan-3  C42   0.020
 XFN  plan-3  H36   0.020
 XFN  plan-3  H38   0.020
 XFN  plan-4  C02   0.020
 XFN  plan-4  N02   0.020
 XFN  plan-4  HN02  0.020
 XFN  plan-4  HN0A  0.020
 XFN  plan-5  C39   0.020
 XFN  plan-5  N41   0.020
 XFN  plan-5  HN41  0.020
 XFN  plan-5  HN4A  0.020
 XFN  plan-6  C11   0.020
 XFN  plan-6  HN17  0.020
 XFN  plan-6  HN1A  0.020
 XFN  plan-6  N17   0.020

