# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:11:08 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cncc(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
 XFJ  XFJ  6,6'-(pyridine-3,5-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_XFJ
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
 XFJ  N01   N  N     0  -0.484   4.2515  -1.3891  -0.2573
 XFJ  C02   C  CR6   0   0.440   5.3804  -2.0533  -0.4789
 XFJ  N02   N  NH2   0  -0.838   5.2993  -3.1790  -1.2475
 XFJ  C03   C  CR16  0  -0.447   6.6220  -1.6092   0.0101
 XFJ  C04   C  CR6   0   0.204   6.6745  -0.4444   0.7469
 XFJ  C05   C  CR16  0  -0.433   5.4790   0.2496   0.9688
 XFJ  C06   C  CR6   0   0.275   4.3020  -0.2586   0.4507
 XFJ  C07   C  CH3   0  -0.726   7.9656   0.0630   1.3122
 XFJ  C08   C  CH2   0  -0.488   2.9983   0.4658   0.6304
 XFJ  C09   C  CH2   0  -0.514   2.4979   1.0644  -0.6909
 XFJ  N11   N  N     0  -0.398   0.0206   3.7931   0.0451
 XFJ  C12   C  CR16  0  -0.111   1.1446   3.1193  -0.1544
 XFJ  C13   C  CR6   0   0.047   1.1889   1.7757  -0.5174
 XFJ  C14   C  CR16  0  -0.242  -0.0276   1.1242  -0.6720
 XFJ  C15   C  CR6   0   0.051  -1.2216   1.8081  -0.4713
 XFJ  C16   C  CR16  0  -0.121  -1.1287   3.1477  -0.1098
 XFJ  C17   C  CH2   0  -0.513  -2.5523   1.1302  -0.6102
 XFJ  C18   C  CH2   0  -0.489  -2.8870   0.2603   0.6091
 XFJ  N21   N  N     0  -0.484  -5.2881   0.4056   0.4917
 XFJ  C22   C  CR6   0   0.440  -6.4959  -0.1203   0.3235
 XFJ  N22   N  NH2   0  -0.838  -7.5616   0.7290   0.4126
 XFJ  C23   C  CR16  0  -0.447  -6.6930  -1.4962   0.1083
 XFJ  C24   C  CR6   0   0.205  -5.5974  -2.3333   0.0755
 XFJ  C25   C  CR16  0  -0.433  -4.3298  -1.7671   0.2576
 XFJ  C26   C  CR6   0   0.276  -4.2265  -0.4033   0.4585
 XFJ  HN02  H  HNH2  0   0.379   4.3874  -3.5985  -1.3275
 XFJ  HN0A  H  HNH2  0   0.387   6.0513  -3.8437  -1.1776
 XFJ  H03   H  HCR6  0   0.255   7.5211  -2.1800  -0.1900
 XFJ  H05   H  HCR6  0   0.243   5.4728   1.1697   1.5400
 XFJ  H07   H  HCH3  0   0.249   8.0841   1.1303   1.1241
 XFJ  H07A  H  HCH3  0   0.254   7.9902  -0.0746   2.3948
 XFJ  H07B  H  HCH3  0   0.247   8.8240  -0.4572   0.8907
 XFJ  H08   H  HCH2  0   0.249   2.2462  -0.2270   1.0175
 XFJ  H08A  H  HCH2  0   0.249   3.1114   1.2593   1.3721
 XFJ  H09   H  HCH2  0   0.253   3.2485   1.7575  -1.0791
 XFJ  H09A  H  HCH2  0   0.254   2.3927   0.2664  -1.4288
 XFJ  H12   H  HCR6  0   0.252   2.0703   3.6735  -0.0271
 XFJ  H14   H  HCR6  0   0.254  -0.0463   0.0781  -0.9621
 XFJ  H16   H  HCR6  0   0.252  -2.0347   3.7242   0.0536
 XFJ  H17   H  HCH2  0   0.252  -3.3372   1.8780  -0.7401
 XFJ  H17A  H  HCH2  0   0.254  -2.5562   0.5056  -1.5074
 XFJ  H18   H  HCH2  0   0.248  -2.1109  -0.4963   0.7441
 XFJ  H18A  H  HCH2  0   0.249  -2.8873   0.8853   1.5062
 XFJ  HN22  H  HNH2  0   0.379  -7.3577   1.7073   0.2889
 XFJ  HN2A  H  HNH2  0   0.387  -8.4260   0.4356  -0.0109
 XFJ  H23   H  HCR6  0   0.255  -7.6944  -1.8851  -0.0327
 XFJ  H25   H  HCR6  0   0.244  -3.4413  -2.3856   0.2338
 XFJ  H27   H  HCH3  0   0.250  -5.1018  -4.1523  -0.9494
 XFJ  H27A  H  HCH3  0   0.253  -5.4584  -4.3596   0.7548
 XFJ  H27B  H  HCH3  0   0.247  -6.7735  -4.0779  -0.3860
 XFJ  C27   C  CH3   0  -0.727  -5.7478  -3.8077  -0.1411

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
 XFJ  N01  C06   aromatic  1.335  0.020  1.335
 XFJ  N01  C02   aromatic  1.328  0.020  1.328
 XFJ  N02  C02   single    1.366  0.020  1.366
 XFJ  C02  C03   aromatic  1.406  0.020  1.406
 XFJ  N02  HN02  single    0.890  0.020  1.040
 XFJ  N02  HN0A  single    0.890  0.020  1.040
 XFJ  C03  C04   aromatic  1.379  0.020  1.379
 XFJ  C03  H03   single    0.930  0.020  1.080
 XFJ  C05  C04   aromatic  1.400  0.020  1.400
 XFJ  C04  C07   single    1.498  0.020  1.498
 XFJ  C06  C05   aromatic  1.383  0.020  1.383
 XFJ  C05  H05   single    0.930  0.020  1.080
 XFJ  C08  C06   single    1.502  0.020  1.502
 XFJ  C07  H07   single    0.970  0.020  1.090
 XFJ  C07  H07A  single    0.970  0.020  1.090
 XFJ  C07  H07B  single    0.970  0.020  1.090
 XFJ  C08  C09   single    1.535  0.020  1.535
 XFJ  C08  H08   single    0.970  0.020  1.090
 XFJ  C08  H08A  single    0.970  0.020  1.090
 XFJ  C13  C09   single    1.500  0.020  1.500
 XFJ  C09  H09   single    0.970  0.020  1.090
 XFJ  C09  H09A  single    0.970  0.020  1.090
 XFJ  C16  N11   aromatic  1.327  0.020  1.327
 XFJ  N11  C12   aromatic  1.326  0.020  1.326
 XFJ  C12  C13   aromatic  1.393  0.020  1.393
 XFJ  C12  H12   single    0.930  0.020  1.080
 XFJ  C14  C13   aromatic  1.389  0.020  1.389
 XFJ  C15  C14   aromatic  1.391  0.020  1.391
 XFJ  C14  H14   single    0.930  0.020  1.080
 XFJ  C17  C15   single    1.500  0.020  1.500
 XFJ  C16  C15   aromatic  1.391  0.020  1.391
 XFJ  C16  H16   single    0.930  0.020  1.080
 XFJ  C17  C18   single    1.535  0.020  1.535
 XFJ  C17  H17   single    0.970  0.020  1.090
 XFJ  C17  H17A  single    0.970  0.020  1.090
 XFJ  C26  C18   single    1.502  0.020  1.502
 XFJ  C18  H18   single    0.970  0.020  1.090
 XFJ  C18  H18A  single    0.970  0.020  1.090
 XFJ  C22  N21   aromatic  1.328  0.020  1.328
 XFJ  C26  N21   aromatic  1.335  0.020  1.335
 XFJ  C23  C22   aromatic  1.406  0.020  1.406
 XFJ  C22  N22   single    1.366  0.020  1.366
 XFJ  N22  HN22  single    0.890  0.020  1.040
 XFJ  N22  HN2A  single    0.890  0.020  1.040
 XFJ  C24  C23   aromatic  1.379  0.020  1.379
 XFJ  C23  H23   single    0.930  0.020  1.080
 XFJ  C27  C24   single    1.498  0.020  1.498
 XFJ  C24  C25   aromatic  1.400  0.020  1.400
 XFJ  C25  C26   aromatic  1.382  0.020  1.382
 XFJ  C25  H25   single    0.930  0.020  1.080
 XFJ  C27  H27   single    0.970  0.020  1.090
 XFJ  C27  H27A  single    0.970  0.020  1.090
 XFJ  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
 XFJ  C06   N01  C02   118.67  3.000
 XFJ  C03   C02  N02   120.56  3.000
 XFJ  C03   C02  N01   122.30  3.000
 XFJ  N02   C02  N01   117.11  3.000
 XFJ  HN0A  N02  HN02  114.03  3.000
 XFJ  HN0A  N02  C02   117.46  3.000
 XFJ  HN02  N02  C02   116.22  3.000
 XFJ  H03   C03  C04   120.79  3.000
 XFJ  H03   C03  C02   120.13  3.000
 XFJ  C04   C03  C02   119.08  3.000
 XFJ  C07   C04  C05   120.55  3.000
 XFJ  C07   C04  C03   121.37  3.000
 XFJ  C05   C04  C03   118.08  3.000
 XFJ  H05   C05  C06   120.33  3.000
 XFJ  H05   C05  C04   120.64  3.000
 XFJ  C06   C05  C04   119.03  3.000
 XFJ  C08   C06  C05   121.11  3.000
 XFJ  C08   C06  N01   116.04  3.000
 XFJ  C05   C06  N01   122.83  3.000
 XFJ  H07B  C07  H07A  107.81  3.000
 XFJ  H07B  C07  H07   108.37  3.000
 XFJ  H07A  C07  H07   106.99  3.000
 XFJ  H07B  C07  C04   111.82  3.000
 XFJ  H07A  C07  C04   110.55  3.000
 XFJ  H07   C07  C04   111.12  3.000
 XFJ  H08A  C08  H08   106.93  3.000
 XFJ  H08A  C08  C09   109.59  3.000
 XFJ  H08   C08  C09   109.13  3.000
 XFJ  H08A  C08  C06   109.98  3.000
 XFJ  H08   C08  C06   109.49  3.000
 XFJ  C09   C08  C06   111.60  3.000
 XFJ  H09A  C09  H09   106.83  3.000
 XFJ  H09A  C09  C13   109.92  3.000
 XFJ  H09   C09  C13   109.87  3.000
 XFJ  H09A  C09  C08   109.16  3.000
 XFJ  H09   C09  C08   109.22  3.000
 XFJ  C13   C09  C08   111.72  3.000
 XFJ  C16   N11  C12   118.00  3.000
 XFJ  H12   C12  C13   119.71  3.000
 XFJ  H12   C12  N11   116.46  3.000
 XFJ  C13   C12  N11   123.83  3.000
 XFJ  C14   C13  C12   116.99  3.000
 XFJ  C14   C13  C09   121.95  3.000
 XFJ  C12   C13  C09   121.03  3.000
 XFJ  H14   C14  C15   119.84  3.000
 XFJ  H14   C14  C13   119.80  3.000
 XFJ  C15   C14  C13   120.36  3.000
 XFJ  C17   C15  C16   121.24  3.000
 XFJ  C16   C15  C14   117.00  3.000
 XFJ  C17   C15  C14   121.75  3.000
 XFJ  H16   C16  C15   119.65  3.000
 XFJ  H16   C16  N11   116.52  3.000
 XFJ  C15   C16  N11   123.83  3.000
 XFJ  H17A  C17  H17   106.92  3.000
 XFJ  H17A  C17  C18   109.11  3.000
 XFJ  H17   C17  C18   109.02  3.000
 XFJ  H17A  C17  C15   109.72  3.000
 XFJ  H17   C17  C15   109.84  3.000
 XFJ  C18   C17  C15   112.09  3.000
 XFJ  H18A  C18  H18   107.14  3.000
 XFJ  H18A  C18  C26   109.54  3.000
 XFJ  H18   C18  C26   109.88  3.000
 XFJ  H18A  C18  C17   109.14  3.000
 XFJ  H18   C18  C17   109.62  3.000
 XFJ  C26   C18  C17   111.42  3.000
 XFJ  C26   N21  C22   118.69  3.000
 XFJ  C23   C22  N22   120.60  3.000
 XFJ  N22   C22  N21   117.07  3.000
 XFJ  C23   C22  N21   122.29  3.000
 XFJ  HN2A  N22  HN22  113.93  3.000
 XFJ  HN2A  N22  C22   117.48  3.000
 XFJ  HN22  N22  C22   115.99  3.000
 XFJ  H23   C23  C24   120.88  3.000
 XFJ  H23   C23  C22   120.04  3.000
 XFJ  C24   C23  C22   119.08  3.000
 XFJ  C27   C24  C25   120.51  3.000
 XFJ  C25   C24  C23   118.07  3.000
 XFJ  C27   C24  C23   121.41  3.000
 XFJ  H25   C25  C26   120.36  3.000
 XFJ  H25   C25  C24   120.60  3.000
 XFJ  C26   C25  C24   119.04  3.000
 XFJ  C25   C26  N21   122.82  3.000
 XFJ  C25   C26  C18   121.13  3.000
 XFJ  N21   C26  C18   116.03  3.000
 XFJ  H27B  C27  H27A  108.00  3.000
 XFJ  H27B  C27  H27   108.24  3.000
 XFJ  H27A  C27  H27   106.96  3.000
 XFJ  H27B  C27  C24   111.80  3.000
 XFJ  H27A  C27  C24   110.64  3.000
 XFJ  H27   C27  C24   111.03  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
 XFJ  CONST_01  C04  C05  C06  N01    0.00   0.0  0
 XFJ  CONST_02  C04  C03  C02  N01    0.00   0.0  0
 XFJ  CONST_03  C05  C06  N01  C02    0.00   0.0  0
 XFJ  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 XFJ  CONST_05  C06  N01  C02  C03    0.00   0.0  0
 XFJ  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 XFJ  CONST_07  C14  C15  C16  N11    0.00   0.0  0
 XFJ  CONST_08  C14  C13  C12  N11    0.00   0.0  0
 XFJ  CONST_09  C15  C16  N11  C12    0.00   0.0  0
 XFJ  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 XFJ  CONST_11  C16  N11  C12  C13    0.00   0.0  0
 XFJ  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 XFJ  CONST_13  C24  C23  C22  N21    0.00   0.0  0
 XFJ  CONST_14  C24  C25  C26  N21    0.00   0.0  0
 XFJ  CONST_15  C25  C26  N21  C22    0.00   0.0  0
 XFJ  CONST_16  C25  C24  C23  C22    0.00   0.0  0
 XFJ  CONST_17  C26  N21  C22  C23    0.00   0.0  0
 XFJ  CONST_18  C26  C25  C24  C23    0.00   0.0  0
 XFJ  CONST_19  C08  C06  N01  C02  180.00   0.0  0
 XFJ  CONST_20  C07  C04  C03  C02  180.00   0.0  0
 XFJ  CONST_21  C06  N01  C02  N02  180.00   0.0  0
 XFJ  CONST_22  C04  C03  C02  N02  180.00   0.0  0
 XFJ  CONST_23  C08  C06  C05  C04  180.00   0.0  0
 XFJ  CONST_24  C07  C04  C05  C06  180.00   0.0  0
 XFJ  CONST_25  N11  C12  C13  C09  180.00   0.0  0
 XFJ  CONST_26  C15  C14  C13  C09  180.00   0.0  0
 XFJ  CONST_27  C17  C15  C16  N11  180.00   0.0  0
 XFJ  CONST_28  C17  C15  C14  C13  180.00   0.0  0
 XFJ  CONST_29  C22  N21  C26  C18  180.00   0.0  0
 XFJ  CONST_30  C24  C25  C26  C18  180.00   0.0  0
 XFJ  CONST_31  C27  C24  C23  C22  180.00   0.0  0
 XFJ  CONST_32  C26  N21  C22  N22  180.00   0.0  0
 XFJ  CONST_33  C24  C23  C22  N22  180.00   0.0  0
 XFJ  CONST_34  C27  C24  C25  C26  180.00   0.0  0
 XFJ  CONST_35  H05  C05  C06  N01  180.00   0.0  0
 XFJ  CONST_36  H03  C03  C02  N01  180.00   0.0  0
 XFJ  CONST_37  H16  C16  N11  C12  180.00   0.0  0
 XFJ  CONST_38  H14  C14  C13  C12  180.00   0.0  0
 XFJ  CONST_39  H12  C12  C13  C14  180.00   0.0  0
 XFJ  CONST_40  H23  C23  C22  N21  180.00   0.0  0
 XFJ  CONST_41  H25  C25  C26  N21  180.00   0.0  0
 XFJ  Var_01    C09  C08  C06  N01  -68.93  30.0  1
 XFJ  Var_02    C13  C09  C08  C06  179.39  30.0  3
 XFJ  Var_03    C12  C13  C09  C08   87.95  30.0  2
 XFJ  Var_04    C18  C17  C15  C14   77.19  30.0  3
 XFJ  Var_05    C26  C18  C17  C15  179.59  30.0  3
 XFJ  Var_06    N21  C26  C18  C17  -68.21  30.0  2
 XFJ  Var_07    H07  C07  C04  C03  133.79  30.0  2
 XFJ  Var_08    H27  C27  C24  C23  128.23  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
 XFJ  plan-1  N01   0.020
 XFJ  plan-1  C02   0.020
 XFJ  plan-1  N02   0.020
 XFJ  plan-1  C03   0.020
 XFJ  plan-1  C04   0.020
 XFJ  plan-1  C05   0.020
 XFJ  plan-1  C06   0.020
 XFJ  plan-1  C07   0.020
 XFJ  plan-1  C08   0.020
 XFJ  plan-1  H03   0.020
 XFJ  plan-1  H05   0.020
 XFJ  plan-2  C09   0.020
 XFJ  plan-2  N11   0.020
 XFJ  plan-2  C12   0.020
 XFJ  plan-2  C13   0.020
 XFJ  plan-2  C14   0.020
 XFJ  plan-2  C15   0.020
 XFJ  plan-2  C16   0.020
 XFJ  plan-2  C17   0.020
 XFJ  plan-2  H12   0.020
 XFJ  plan-2  H14   0.020
 XFJ  plan-2  H16   0.020
 XFJ  plan-3  C18   0.020
 XFJ  plan-3  N21   0.020
 XFJ  plan-3  C22   0.020
 XFJ  plan-3  N22   0.020
 XFJ  plan-3  C23   0.020
 XFJ  plan-3  C24   0.020
 XFJ  plan-3  C25   0.020
 XFJ  plan-3  C26   0.020
 XFJ  plan-3  H23   0.020
 XFJ  plan-3  H25   0.020
 XFJ  plan-3  C27   0.020
 XFJ  plan-4  C02   0.020
 XFJ  plan-4  N02   0.020
 XFJ  plan-4  HN02  0.020
 XFJ  plan-4  HN0A  0.020
 XFJ  plan-5  C22   0.020
 XFJ  plan-5  N22   0.020
 XFJ  plan-5  HN22  0.020
 XFJ  plan-5  HN2A  0.020

