# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:02:50 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 6,6'-heptane-1,7-diylbis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCCCCCCc2cc(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
 QJ4  QJ4  6,6'-heptane-1,7-diylbis(4-methylpyridin-2-amine)  ligand  51  23  .  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_QJ4
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
 QJ4  N22  N  NH2   0  -0.839   6.9180   0.4301  -2.7722
 QJ4  C22  C  CR6   0   0.439   6.5580   0.2550  -1.4657
 QJ4  C23  C  CR16  0  -0.447   7.2812   0.8770  -0.4343
 QJ4  C24  C  CR6   0   0.204   6.8612   0.7157   0.8710
 QJ4  C27  C  CH3   0  -0.726   7.5805   1.3787   2.0059
 QJ4  C25  C  CR16  0  -0.432   5.7294  -0.0716   1.1056
 QJ4  N21  N  N     0  -0.483   5.4829  -0.4912  -1.2305
 QJ4  C26  C  CR6   0   0.271   5.0767  -0.6513   0.0308
 QJ4  C14  C  CH2   0  -0.491   3.8331  -1.4684   0.2315
 QJ4  C13  C  CH2   0  -0.416   2.5647  -0.6412   0.0160
 QJ4  C12  C  CH2   0  -0.416   1.2930  -1.4626   0.1814
 QJ4  C11  C  CH2   0  -0.413   0.0247  -0.6349   0.0191
 QJ4  C10  C  CH2   0  -0.417  -1.2511  -1.4529   0.1742
 QJ4  C09  C  CH2   0  -0.415  -2.5128  -0.6079   0.0588
 QJ4  C08  C  CH2   0  -0.488  -3.7939  -1.4296   0.2066
 QJ4  C06  C  CR6   0   0.277  -5.0242  -0.5689   0.1701
 QJ4  N01  N  N     0  -0.485  -5.2126   0.2268   1.2263
 QJ4  C02  C  CR6   0   0.439  -6.2624   1.0406   1.2354
 QJ4  N02  N  NH2   0  -0.839  -6.3920   1.8755   2.3088
 QJ4  C03  C  CR16  0  -0.449  -7.1851   1.0882   0.1758
 QJ4  C04  C  CR6   0   0.205  -6.9984   0.2614  -0.9130
 QJ4  C05  C  CR16  0  -0.437  -5.8843  -0.5862  -0.9139
 QJ4  C07  C  CH3   0  -0.726  -7.9670   0.2504  -2.0561
 QJ4  H1   H  HNH2  0   0.386   7.8659   0.7142  -2.9554
 QJ4  H2   H  HNH2  0   0.378   6.5650  -0.2529  -3.4225
 QJ4  H3   H  HCR6  0   0.253   8.1597   1.4677  -0.6663
 QJ4  H4   H  HCH3  0   0.254   7.0240   2.2537   2.3470
 QJ4  H5   H  HCH3  0   0.248   7.6788   0.7082   2.8595
 QJ4  H6   H  HCH3  0   0.246   8.5748   1.7133   1.7139
 QJ4  H7   H  HCR6  0   0.241   5.3684  -0.2325   2.1139
 QJ4  H8   H  HCH2  0   0.234   3.8396  -2.3090  -0.4677
 QJ4  H9   H  HCH2  0   0.233   3.8224  -1.8891   1.2403
 QJ4  H10  H  HCH2  0   0.219   2.5563   0.1937   0.7244
 QJ4  H11  H  HCH2  0   0.220   2.5880  -0.1962  -0.9836
 QJ4  H12  H  HCH2  0   0.211   1.2918  -2.2806  -0.5475
 QJ4  H13  H  HCH2  0   0.210   1.2922  -1.9366   1.1692
 QJ4  H14  H  HCH2  0   0.209   0.0262   0.1762   0.7558
 QJ4  H15  H  HCH2  0   0.209   0.0282  -0.1507  -0.9638
 QJ4  H16  H  HCH2  0   0.211  -1.2699  -2.2460  -0.5815
 QJ4  H17  H  HCH2  0   0.210  -1.2434  -1.9594   1.1459
 QJ4  H18  H  HCH2  0   0.219  -2.4991   0.1745   0.8234
 QJ4  H19  H  HCH2  0   0.218  -2.5234  -0.0936  -0.9080
 QJ4  H20  H  HCH2  0   0.233  -3.8422  -2.1798  -0.5863
 QJ4  H21  H  HCH2  0   0.234  -3.7654  -1.9725   1.1565
 QJ4  H22  H  HNH2  0   0.379  -5.8871   1.6111   3.1388
 QJ4  H23  H  HNH2  0   0.387  -7.3028   2.2638   2.4888
 QJ4  H24  H  HCR6  0   0.254  -8.0292   1.7660   0.2200
 QJ4  H25  H  HCR6  0   0.241  -5.6963  -1.2502  -1.7485
 QJ4  H26  H  HCH3  0   0.248  -7.4471   0.2648  -3.0142
 QJ4  H27  H  HCH3  0   0.254  -8.5723  -0.6577  -2.0348
 QJ4  H28  H  HCH3  0   0.246  -8.6433   1.1027  -2.0204

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
 QJ4  C07  C04  single    1.498  0.020  1.498
 QJ4  C04  C03  aromatic  1.380  0.020  1.380
 QJ4  C04  C05  aromatic  1.400  0.020  1.400
 QJ4  C03  C02  aromatic  1.406  0.020  1.406
 QJ4  C05  C06  aromatic  1.384  0.020  1.384
 QJ4  C02  N02  single    1.366  0.020  1.366
 QJ4  C02  N01  aromatic  1.328  0.020  1.328
 QJ4  C06  N01  aromatic  1.336  0.020  1.336
 QJ4  C06  C08  single    1.502  0.020  1.502
 QJ4  C10  C09  single    1.523  0.020  1.523
 QJ4  C10  C11  single    1.523  0.020  1.523
 QJ4  C09  C08  single    1.529  0.020  1.529
 QJ4  C11  C12  single    1.523  0.020  1.523
 QJ4  C12  C13  single    1.523  0.020  1.523
 QJ4  C13  C14  single    1.530  0.020  1.530
 QJ4  C14  C26  single    1.501  0.020  1.501
 QJ4  N21  C22  aromatic  1.330  0.020  1.330
 QJ4  N21  C26  aromatic  1.335  0.020  1.335
 QJ4  N22  C22  single    1.367  0.020  1.367
 QJ4  C22  C23  aromatic  1.405  0.020  1.405
 QJ4  C26  C25  aromatic  1.385  0.020  1.385
 QJ4  C25  C24  aromatic  1.399  0.020  1.399
 QJ4  C23  C24  aromatic  1.381  0.020  1.381
 QJ4  C24  C27  single    1.498  0.020  1.498
 QJ4  N22  H1   single    0.890  0.020  1.040
 QJ4  N22  H2   single    0.890  0.020  1.040
 QJ4  C23  H3   single    0.930  0.020  1.080
 QJ4  C27  H4   single    0.970  0.020  1.090
 QJ4  C27  H5   single    0.970  0.020  1.090
 QJ4  C27  H6   single    0.970  0.020  1.090
 QJ4  C25  H7   single    0.930  0.020  1.080
 QJ4  C14  H8   single    0.970  0.020  1.090
 QJ4  C14  H9   single    0.970  0.020  1.090
 QJ4  C13  H10  single    0.970  0.020  1.090
 QJ4  C13  H11  single    0.970  0.020  1.090
 QJ4  C12  H12  single    0.970  0.020  1.090
 QJ4  C12  H13  single    0.970  0.020  1.090
 QJ4  C11  H14  single    0.970  0.020  1.090
 QJ4  C11  H15  single    0.970  0.020  1.090
 QJ4  C10  H16  single    0.970  0.020  1.090
 QJ4  C10  H17  single    0.970  0.020  1.090
 QJ4  C09  H18  single    0.970  0.020  1.090
 QJ4  C09  H19  single    0.970  0.020  1.090
 QJ4  C08  H20  single    0.970  0.020  1.090
 QJ4  C08  H21  single    0.970  0.020  1.090
 QJ4  N02  H22  single    0.890  0.020  1.040
 QJ4  N02  H23  single    0.890  0.020  1.040
 QJ4  C03  H24  single    0.930  0.020  1.080
 QJ4  C05  H25  single    0.930  0.020  1.080
 QJ4  C07  H26  single    0.970  0.020  1.090
 QJ4  C07  H27  single    0.970  0.020  1.090
 QJ4  C07  H28  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
 QJ4  H2   N22  H1   113.84  3.000
 QJ4  H2   N22  C22  115.98  3.000
 QJ4  H1   N22  C22  117.29  3.000
 QJ4  N21  C22  C23  122.34  3.000
 QJ4  C23  C22  N22  120.63  3.000
 QJ4  N21  C22  N22  117.00  3.000
 QJ4  H3   C23  C24  120.84  3.000
 QJ4  H3   C23  C22  120.10  3.000
 QJ4  C24  C23  C22  119.05  3.000
 QJ4  C25  C24  C27  120.70  3.000
 QJ4  C27  C24  C23  121.22  3.000
 QJ4  C25  C24  C23  118.07  3.000
 QJ4  H6   C27  H5   108.46  3.000
 QJ4  H6   C27  H4   107.63  3.000
 QJ4  H5   C27  H4   107.12  3.000
 QJ4  H6   C27  C24  111.79  3.000
 QJ4  H5   C27  C24  111.37  3.000
 QJ4  H4   C27  C24  110.28  3.000
 QJ4  H7   C25  C26  120.23  3.000
 QJ4  H7   C25  C24  120.63  3.000
 QJ4  C26  C25  C24  119.14  3.000
 QJ4  C26  N21  C22  118.72  3.000
 QJ4  C14  C26  N21  116.34  3.000
 QJ4  N21  C26  C25  122.67  3.000
 QJ4  C14  C26  C25  120.96  3.000
 QJ4  H9   C14  H8   107.12  3.000
 QJ4  H9   C14  C13  109.27  3.000
 QJ4  H8   C14  C13  109.31  3.000
 QJ4  H9   C14  C26  109.93  3.000
 QJ4  H8   C14  C26  109.15  3.000
 QJ4  C13  C14  C26  111.94  3.000
 QJ4  H11  C13  H10  106.32  3.000
 QJ4  H11  C13  C12  109.65  3.000
 QJ4  H10  C13  C12  109.55  3.000
 QJ4  H11  C13  C14  109.32  3.000
 QJ4  H10  C13  C14  109.12  3.000
 QJ4  C12  C13  C14  112.67  3.000
 QJ4  H13  C12  H12  106.07  3.000
 QJ4  H13  C12  C11  109.30  3.000
 QJ4  H12  C12  C11  109.51  3.000
 QJ4  H13  C12  C13  109.38  3.000
 QJ4  H12  C12  C13  109.35  3.000
 QJ4  C11  C12  C13  113.00  3.000
 QJ4  H15  C11  H14  106.03  3.000
 QJ4  H15  C11  C10  109.35  3.000
 QJ4  H14  C11  C10  109.28  3.000
 QJ4  H15  C11  C12  109.45  3.000
 QJ4  H14  C11  C12  109.23  3.000
 QJ4  C10  C11  C12  113.25  3.000
 QJ4  H17  C10  H16  106.09  3.000
 QJ4  H17  C10  C09  109.24  3.000
 QJ4  H16  C10  C09  109.59  3.000
 QJ4  H17  C10  C11  109.42  3.000
 QJ4  H16  C10  C11  109.44  3.000
 QJ4  C09  C10  C11  112.84  3.000
 QJ4  H19  C09  H18  106.33  3.000
 QJ4  H19  C09  C08  109.24  3.000
 QJ4  H18  C09  C08  109.10  3.000
 QJ4  H19  C09  C10  109.60  3.000
 QJ4  H18  C09  C10  109.48  3.000
 QJ4  C08  C09  C10  112.87  3.000
 QJ4  H21  C08  H20  106.88  3.000
 QJ4  H21  C08  C06  109.07  3.000
 QJ4  H20  C08  C06  109.86  3.000
 QJ4  H21  C08  C09  109.18  3.000
 QJ4  H20  C08  C09  109.62  3.000
 QJ4  C06  C08  C09  112.08  3.000
 QJ4  C05  C06  N01  122.63  3.000
 QJ4  N01  C06  C08  115.96  3.000
 QJ4  C05  C06  C08  121.39  3.000
 QJ4  C02  N01  C06  118.80  3.000
 QJ4  C03  C02  N02  120.61  3.000
 QJ4  N02  C02  N01  117.05  3.000
 QJ4  C03  C02  N01  122.30  3.000
 QJ4  H23  N02  H22  114.06  3.000
 QJ4  H23  N02  C02  117.54  3.000
 QJ4  H22  N02  C02  116.08  3.000
 QJ4  H24  C03  C04  120.83  3.000
 QJ4  H24  C03  C02  120.12  3.000
 QJ4  C04  C03  C02  119.05  3.000
 QJ4  C07  C04  C05  120.63  3.000
 QJ4  C05  C04  C03  118.10  3.000
 QJ4  C07  C04  C03  121.26  3.000
 QJ4  H25  C05  C04  120.66  3.000
 QJ4  H25  C05  C06  120.23  3.000
 QJ4  C04  C05  C06  119.11  3.000
 QJ4  H28  C07  H27  107.83  3.000
 QJ4  H28  C07  H26  108.35  3.000
 QJ4  H27  C07  H26  107.02  3.000
 QJ4  H28  C07  C04  111.76  3.000
 QJ4  H27  C07  C04  110.47  3.000
 QJ4  H26  C07  C04  111.23  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
 QJ4  CONST_01  C25  C26  N21  C22    0.00   0.0  0
 QJ4  CONST_02  C25  C24  C23  C22    0.00   0.0  0
 QJ4  CONST_03  C26  N21  C22  C23    0.00   0.0  0
 QJ4  CONST_04  C26  C25  C24  C23    0.00   0.0  0
 QJ4  CONST_05  N21  C26  C25  C24    0.00   0.0  0
 QJ4  CONST_06  N21  C22  C23  C24    0.00   0.0  0
 QJ4  CONST_07  C03  C04  C05  C06    0.00   0.0  0
 QJ4  CONST_08  C03  C02  N01  C06    0.00   0.0  0
 QJ4  CONST_09  C04  C03  C02  N01    0.00   0.0  0
 QJ4  CONST_10  C04  C05  C06  N01    0.00   0.0  0
 QJ4  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 QJ4  CONST_12  C05  C06  N01  C02    0.00   0.0  0
 QJ4  CONST_13  C26  N21  C22  N22  180.00   0.0  0
 QJ4  CONST_14  C24  C23  C22  N22  180.00   0.0  0
 QJ4  CONST_15  C14  C26  N21  C22  180.00   0.0  0
 QJ4  CONST_16  C27  C24  C23  C22  180.00   0.0  0
 QJ4  CONST_17  C14  C26  C25  C24  180.00   0.0  0
 QJ4  CONST_18  C26  C25  C24  C27  180.00   0.0  0
 QJ4  CONST_19  C04  C05  C06  C08  180.00   0.0  0
 QJ4  CONST_20  C02  N01  C06  C08  180.00   0.0  0
 QJ4  CONST_21  C07  C04  C05  C06  180.00   0.0  0
 QJ4  CONST_22  N02  C02  N01  C06  180.00   0.0  0
 QJ4  CONST_23  C07  C04  C03  C02  180.00   0.0  0
 QJ4  CONST_24  C04  C03  C02  N02  180.00   0.0  0
 QJ4  CONST_25  H7   C25  C24  C23  180.00   0.0  0
 QJ4  CONST_26  H3   C23  C24  C25  180.00   0.0  0
 QJ4  CONST_27  H24  C03  C02  N01  180.00   0.0  0
 QJ4  CONST_28  H25  C05  C06  N01  180.00   0.0  0
 QJ4  Var_01    C13  C14  C26  C25   95.89  30.0  1
 QJ4  Var_02    C05  C06  C08  C09  108.87  30.0  2
 QJ4  Var_03    H4   C27  C24  C23  102.76  30.0  2
 QJ4  Var_04    H26  C07  C04  C03  134.88  30.0  2
 QJ4  Var_05    C12  C13  C14  C26  178.57  30.0  1
 QJ4  Var_06    C06  C08  C09  C10  176.67  30.0  3
 QJ4  Var_07    C11  C12  C13  C14  177.88  30.0  1
 QJ4  Var_08    C10  C11  C12  C13  179.62  30.0  1
 QJ4  Var_09    C09  C10  C11  C12  177.98  30.0  1
 QJ4  Var_10    C08  C09  C10  C11  179.68  30.0  3

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
 QJ4  plan-1  N22  0.020
 QJ4  plan-1  C22  0.020
 QJ4  plan-1  C23  0.020
 QJ4  plan-1  C24  0.020
 QJ4  plan-1  C27  0.020
 QJ4  plan-1  C25  0.020
 QJ4  plan-1  N21  0.020
 QJ4  plan-1  C26  0.020
 QJ4  plan-1  C14  0.020
 QJ4  plan-1  H3   0.020
 QJ4  plan-1  H7   0.020
 QJ4  plan-2  C08  0.020
 QJ4  plan-2  C06  0.020
 QJ4  plan-2  N01  0.020
 QJ4  plan-2  C02  0.020
 QJ4  plan-2  N02  0.020
 QJ4  plan-2  C03  0.020
 QJ4  plan-2  C04  0.020
 QJ4  plan-2  C05  0.020
 QJ4  plan-2  C07  0.020
 QJ4  plan-2  H24  0.020
 QJ4  plan-2  H25  0.020
 QJ4  plan-3  N22  0.020
 QJ4  plan-3  C22  0.020
 QJ4  plan-3  H1   0.020
 QJ4  plan-3  H2   0.020
 QJ4  plan-4  C02  0.020
 QJ4  plan-4  N02  0.020
 QJ4  plan-4  H22  0.020
 QJ4  plan-4  H23  0.020

