# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:59:33 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 6,6'-pentane-1,5-diylbis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCCCCc2cc(C)cc(N)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
 QJ2  QJ2  6,6'-pentane-1,5-diylbis(4-methylpyridin-2-amine)  ligand  45  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QJ2
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
 QJ2  N22  N  NH2   0  -0.839  -5.5157   2.7339  -0.9540
 QJ2  C22  C  CR6   0   0.439  -5.1837   1.4806  -0.5227
 QJ2  C23  C  CR16  0  -0.448  -5.9740   0.3715  -0.8710
 QJ2  C24  C  CR6   0   0.205  -5.6420  -0.8711  -0.3714
 QJ2  C27  C  CH3   0  -0.727  -6.4466  -2.0884  -0.7108
 QJ2  C25  C  CR16  0  -0.431  -4.5251  -0.9673   0.4660
 QJ2  N21  N  N     0  -0.484  -4.1205   1.3758   0.2671
 QJ2  C26  C  CR6   0   0.271  -3.7972   0.1743   0.7520
 QJ2  C12  C  CH2   0  -0.490  -2.5531   0.1089   1.5902
 QJ2  C11  C  CH2   0  -0.417  -1.2892   0.1113   0.7280
 QJ2  C10  C  CH2   0  -0.422  -0.0125   0.0658   1.5571
 QJ2  C09  C  CH2   0  -0.416   1.2451   0.0287   0.6987
 QJ2  C08  C  CH2   0  -0.489   2.5259  -0.0144   1.5330
 QJ2  C06  C  CR6   0   0.277   3.7562  -0.1189   0.6780
 QJ2  N01  N  N     0  -0.485   3.9389  -1.2856   0.0538
 QJ2  C02  C  CR6   0   0.440   4.9945  -1.4276  -0.7394
 QJ2  N02  N  NH2   0  -0.840   5.1223  -2.6173  -1.3974
 QJ2  C03  C  CR16  0  -0.448   5.9290  -0.3961  -0.9398
 QJ2  C04  C  CR6   0   0.205   5.7436   0.8094  -0.2957
 QJ2  C05  C  CR16  0  -0.435   4.6252   0.9480   0.5352
 QJ2  C07  C  CH3   0  -0.726   6.6996   1.9479  -0.4816
 QJ2  H1   H  HNH2  0   0.378  -4.7885   3.4277  -0.8950
 QJ2  H2   H  HNH2  0   0.387  -6.0845   2.8060  -1.7813
 QJ2  H3   H  HCR6  0   0.254  -6.8308   0.4987  -1.5216
 QJ2  H4   H  HCH3  0   0.251  -5.8310  -2.8298  -1.2222
 QJ2  H5   H  HCH3  0   0.251  -6.8324  -2.5634   0.1922
 QJ2  H6   H  HCH3  0   0.246  -7.2910  -1.8487  -1.3549
 QJ2  H7   H  HCR6  0   0.241  -4.2261  -1.9228   0.8792
 QJ2  H8   H  HCH2  0   0.235  -2.5284   0.9656   2.2693
 QJ2  H9   H  HCH2  0   0.234  -2.5685  -0.7918   2.2091
 QJ2  H10  H  HCH2  0   0.220  -1.3155  -0.7474   0.0490
 QJ2  H11  H  HCH2  0   0.221  -1.2865   1.0045   0.0956
 QJ2  H12  H  HCH2  0   0.214   0.0219   0.9361   2.2217
 QJ2  H13  H  HCH2  0   0.214  -0.0324  -0.8148   2.2088
 QJ2  H14  H  HCH2  0   0.220   1.2149  -0.8461   0.0427
 QJ2  H15  H  HCH2  0   0.220   1.2689   0.9057   0.0434
 QJ2  H16  H  HCH2  0   0.234   2.5845   0.8780   2.1610
 QJ2  H17  H  HCH2  0   0.234   2.4845  -0.8752   2.2073
 QJ2  H18  H  HNH2  0   0.379   4.5920  -3.3899  -1.0298
 QJ2  H19  H  HNH2  0   0.387   6.0343  -2.8670  -1.7408
 QJ2  H20  H  HCR6  0   0.254   6.7788  -0.5540  -1.5931
 QJ2  H21  H  HCR6  0   0.240   4.4437   1.8757   1.0640
 QJ2  H22  H  HCH3  0   0.253   6.2176   2.7717  -1.0106
 QJ2  H23  H  HCH3  0   0.249   7.0351   2.3389   0.4795
 QJ2  H24  H  HCH3  0   0.246   7.5764   1.6504  -1.0546

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
 QJ2  C07  C04  single    1.498  0.020  1.498
 QJ2  C04  C03  aromatic  1.379  0.020  1.379
 QJ2  C04  C05  aromatic  1.400  0.020  1.400
 QJ2  C03  C02  aromatic  1.406  0.020  1.406
 QJ2  C05  C06  aromatic  1.383  0.020  1.383
 QJ2  C27  C24  single    1.498  0.020  1.498
 QJ2  C23  C24  aromatic  1.380  0.020  1.380
 QJ2  C23  C22  aromatic  1.406  0.020  1.406
 QJ2  N22  C22  single    1.366  0.020  1.366
 QJ2  C24  C25  aromatic  1.399  0.020  1.399
 QJ2  C02  N02  single    1.366  0.020  1.366
 QJ2  C02  N01  aromatic  1.328  0.020  1.328
 QJ2  C06  N01  aromatic  1.336  0.020  1.336
 QJ2  C06  C08  single    1.502  0.020  1.502
 QJ2  C22  N21  aromatic  1.329  0.020  1.329
 QJ2  C08  C09  single    1.529  0.020  1.529
 QJ2  C25  C26  aromatic  1.384  0.020  1.384
 QJ2  C09  C10  single    1.523  0.020  1.523
 QJ2  N21  C26  aromatic  1.335  0.020  1.335
 QJ2  C10  C11  single    1.523  0.020  1.523
 QJ2  C26  C12  single    1.502  0.020  1.502
 QJ2  C11  C12  single    1.530  0.020  1.530
 QJ2  N22  H1   single    0.890  0.020  1.040
 QJ2  N22  H2   single    0.890  0.020  1.040
 QJ2  C23  H3   single    0.930  0.020  1.080
 QJ2  C27  H4   single    0.970  0.020  1.090
 QJ2  C27  H5   single    0.970  0.020  1.090
 QJ2  C27  H6   single    0.970  0.020  1.090
 QJ2  C25  H7   single    0.930  0.020  1.080
 QJ2  C12  H8   single    0.970  0.020  1.090
 QJ2  C12  H9   single    0.970  0.020  1.090
 QJ2  C11  H10  single    0.970  0.020  1.090
 QJ2  C11  H11  single    0.970  0.020  1.090
 QJ2  C10  H12  single    0.970  0.020  1.090
 QJ2  C10  H13  single    0.970  0.020  1.090
 QJ2  C09  H14  single    0.970  0.020  1.090
 QJ2  C09  H15  single    0.970  0.020  1.090
 QJ2  C08  H16  single    0.970  0.020  1.090
 QJ2  C08  H17  single    0.970  0.020  1.090
 QJ2  N02  H18  single    0.890  0.020  1.040
 QJ2  N02  H19  single    0.890  0.020  1.040
 QJ2  C03  H20  single    0.930  0.020  1.080
 QJ2  C05  H21  single    0.930  0.020  1.080
 QJ2  C07  H22  single    0.970  0.020  1.090
 QJ2  C07  H23  single    0.970  0.020  1.090
 QJ2  C07  H24  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
 QJ2  H2   N22  H1   114.01  3.000
 QJ2  H2   N22  C22  117.55  3.000
 QJ2  H1   N22  C22  115.98  3.000
 QJ2  N21  C22  C23  122.34  3.000
 QJ2  N21  C22  N22  117.03  3.000
 QJ2  C23  C22  N22  120.59  3.000
 QJ2  H3   C23  C24  120.89  3.000
 QJ2  H3   C23  C22  120.05  3.000
 QJ2  C24  C23  C22  119.05  3.000
 QJ2  C25  C24  C27  120.56  3.000
 QJ2  C25  C24  C23  118.07  3.000
 QJ2  C27  C24  C23  121.37  3.000
 QJ2  H6   C27  H5   108.14  3.000
 QJ2  H6   C27  H4   108.06  3.000
 QJ2  H5   C27  H4   106.96  3.000
 QJ2  H6   C27  C24  111.81  3.000
 QJ2  H5   C27  C24  110.87  3.000
 QJ2  H4   C27  C24  110.82  3.000
 QJ2  H7   C25  C26  120.25  3.000
 QJ2  H7   C25  C24  120.61  3.000
 QJ2  C26  C25  C24  119.13  3.000
 QJ2  C26  N21  C22  118.72  3.000
 QJ2  C12  C26  N21  116.27  3.000
 QJ2  C12  C26  C25  121.01  3.000
 QJ2  N21  C26  C25  122.67  3.000
 QJ2  H9   C12  H8   107.12  3.000
 QJ2  H9   C12  C11  109.39  3.000
 QJ2  H8   C12  C11  109.27  3.000
 QJ2  H9   C12  C26  109.90  3.000
 QJ2  H8   C12  C26  109.35  3.000
 QJ2  C11  C12  C26  111.70  3.000
 QJ2  H11  C11  H10  106.37  3.000
 QJ2  H11  C11  C10  109.69  3.000
 QJ2  H10  C11  C10  109.53  3.000
 QJ2  H11  C11  C12  109.21  3.000
 QJ2  H10  C11  C12  109.17  3.000
 QJ2  C10  C11  C12  112.68  3.000
 QJ2  H13  C10  H12  106.16  3.000
 QJ2  H13  C10  C09  109.31  3.000
 QJ2  H12  C10  C09  109.59  3.000
 QJ2  H13  C10  C11  109.43  3.000
 QJ2  H12  C10  C11  109.44  3.000
 QJ2  C09  C10  C11  112.71  3.000
 QJ2  H15  C09  H14  106.39  3.000
 QJ2  H15  C09  C08  109.33  3.000
 QJ2  H14  C09  C08  109.13  3.000
 QJ2  H15  C09  C10  109.61  3.000
 QJ2  H14  C09  C10  109.55  3.000
 QJ2  C08  C09  C10  112.63  3.000
 QJ2  H17  C08  H16  106.88  3.000
 QJ2  H17  C08  C06  109.09  3.000
 QJ2  H16  C08  C06  109.88  3.000
 QJ2  H17  C08  C09  109.07  3.000
 QJ2  H16  C08  C09  109.60  3.000
 QJ2  C06  C08  C09  112.18  3.000
 QJ2  C05  C06  N01  122.65  3.000
 QJ2  N01  C06  C08  116.03  3.000
 QJ2  C05  C06  C08  121.31  3.000
 QJ2  C02  N01  C06  118.76  3.000
 QJ2  C03  C02  N02  120.55  3.000
 QJ2  N02  C02  N01  117.09  3.000
 QJ2  C03  C02  N01  122.34  3.000
 QJ2  H19  N02  H18  114.31  3.000
 QJ2  H19  N02  C02  117.75  3.000
 QJ2  H18  N02  C02  116.32  3.000
 QJ2  H20  C03  C04  120.96  3.000
 QJ2  H20  C03  C02  120.01  3.000
 QJ2  C04  C03  C02  119.03  3.000
 QJ2  C07  C04  C05  120.54  3.000
 QJ2  C05  C04  C03  118.10  3.000
 QJ2  C07  C04  C03  121.36  3.000
 QJ2  H21  C05  C04  120.55  3.000
 QJ2  H21  C05  C06  120.33  3.000
 QJ2  C04  C05  C06  119.12  3.000
 QJ2  H24  C07  H23  108.31  3.000
 QJ2  H24  C07  H22  107.87  3.000
 QJ2  H23  C07  H22  107.00  3.000
 QJ2  H24  C07  C04  111.81  3.000
 QJ2  H23  C07  C04  111.07  3.000
 QJ2  H22  C07  C04  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
 QJ2  CONST_01  C25  C24  C23  C22    0.00   0.0  0
 QJ2  CONST_02  C25  C26  N21  C22    0.00   0.0  0
 QJ2  CONST_03  C26  C25  C24  C23    0.00   0.0  0
 QJ2  CONST_04  C26  N21  C22  C23    0.00   0.0  0
 QJ2  CONST_05  N21  C22  C23  C24    0.00   0.0  0
 QJ2  CONST_06  N21  C26  C25  C24    0.00   0.0  0
 QJ2  CONST_07  C03  C04  C05  C06    0.00   0.0  0
 QJ2  CONST_08  C03  C02  N01  C06    0.00   0.0  0
 QJ2  CONST_09  C04  C03  C02  N01    0.00   0.0  0
 QJ2  CONST_10  C04  C05  C06  N01    0.00   0.0  0
 QJ2  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 QJ2  CONST_12  C05  C06  N01  C02    0.00   0.0  0
 QJ2  CONST_13  C24  C23  C22  N22  180.00   0.0  0
 QJ2  CONST_14  C26  N21  C22  N22  180.00   0.0  0
 QJ2  CONST_15  C27  C24  C23  C22  180.00   0.0  0
 QJ2  CONST_16  C12  C26  N21  C22  180.00   0.0  0
 QJ2  CONST_17  C12  C26  C25  C24  180.00   0.0  0
 QJ2  CONST_18  C26  C25  C24  C27  180.00   0.0  0
 QJ2  CONST_19  C04  C05  C06  C08  180.00   0.0  0
 QJ2  CONST_20  C02  N01  C06  C08  180.00   0.0  0
 QJ2  CONST_21  C07  C04  C05  C06  180.00   0.0  0
 QJ2  CONST_22  N02  C02  N01  C06  180.00   0.0  0
 QJ2  CONST_23  C07  C04  C03  C02  180.00   0.0  0
 QJ2  CONST_24  C04  C03  C02  N02  180.00   0.0  0
 QJ2  CONST_25  H7   C25  C24  C23  180.00   0.0  0
 QJ2  CONST_26  H3   C23  C24  C25  180.00   0.0  0
 QJ2  CONST_27  H20  C03  C02  N01  180.00   0.0  0
 QJ2  CONST_28  H21  C05  C06  N01  180.00   0.0  0
 QJ2  Var_01    C11  C12  C26  C25   99.31  30.0  2
 QJ2  Var_02    C05  C06  C08  C09  108.56  30.0  2
 QJ2  Var_03    H4   C27  C24  C23  119.50  30.0  2
 QJ2  Var_04    H22  C07  C04  C03  112.80  30.0  2
 QJ2  Var_05    C10  C11  C12  C26  179.17  30.0  1
 QJ2  Var_06    C06  C08  C09  C10  177.19  30.0  1
 QJ2  Var_07    C09  C10  C11  C12  178.39  30.0  2
 QJ2  Var_08    C08  C09  C10  C11  179.90  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
 QJ2  plan-1  N22  0.020
 QJ2  plan-1  C22  0.020
 QJ2  plan-1  C23  0.020
 QJ2  plan-1  C24  0.020
 QJ2  plan-1  C27  0.020
 QJ2  plan-1  C25  0.020
 QJ2  plan-1  N21  0.020
 QJ2  plan-1  C26  0.020
 QJ2  plan-1  C12  0.020
 QJ2  plan-1  H3   0.020
 QJ2  plan-1  H7   0.020
 QJ2  plan-2  C08  0.020
 QJ2  plan-2  C06  0.020
 QJ2  plan-2  N01  0.020
 QJ2  plan-2  C02  0.020
 QJ2  plan-2  N02  0.020
 QJ2  plan-2  C03  0.020
 QJ2  plan-2  C04  0.020
 QJ2  plan-2  C05  0.020
 QJ2  plan-2  C07  0.020
 QJ2  plan-2  H20  0.020
 QJ2  plan-2  H21  0.020
 QJ2  plan-3  N22  0.020
 QJ2  plan-3  C22  0.020
 QJ2  plan-3  H1   0.020
 QJ2  plan-3  H2   0.020
 QJ2  plan-4  C02  0.020
 QJ2  plan-4  N02  0.020
 QJ2  plan-4  H18  0.020
 QJ2  plan-4  H19  0.020

