# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 12:32:01 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 6,6'-{[5-(3-aminopropyl)benzene-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(CCCN)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
 12S  12S  6,6'-{[5-(3-aminopropyl)benzene-1,3-diyl]diethane-2,1-diyl}bis(4-methylpyridin-2-amine)  ligand  63  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_12S
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
 12S  N26  N  NH2   0  -0.838  -7.5244  -0.2160  -0.1179
 12S  C26  C  CR6   0   0.439  -6.4398  -0.9970   0.1668
 12S  C25  C  CR16  0  -0.447  -6.6037  -2.3449   0.5313
 12S  C24  C  CR6   0   0.205  -5.4897  -3.0929   0.8524
 12S  C27  C  CH3   0  -0.726  -5.6052  -4.5405   1.2193
 12S  C23  C  CR16  0  -0.435  -4.2394  -2.4647   0.8085
 12S  N21  N  N     0  -0.485  -5.2481  -0.4123   0.1276
 12S  C22  C  CR6   0   0.278  -4.1696  -1.1317   0.4461
 12S  C28  C  CH2   0  -0.487  -2.8530  -0.4128   0.3702
 12S  C29  C  CH2   0  -0.512  -2.4744  -0.0431  -1.0707
 12S  C5   C  CR6   0   0.177  -1.1789   0.7166  -1.1198
 12S  C4   C  CR16  0  -0.398   0.0393   0.0440  -1.1564
 12S  C6   C  CR16  0  -0.400  -1.1728   2.1074  -1.0778
 12S  C1   C  CR6   0   0.183   0.0188   2.8270  -1.0730
 12S  C7   C  CH2   0  -0.512   0.0045   4.3271  -0.9768
 12S  C8   C  CH2   0  -0.422  -0.0785   4.8039   0.4734
 12S  C9   C  CH2   0  -0.274  -0.0951   6.3204   0.5881
 12S  N10  N  NH2   0  -0.801  -0.1872   6.7331   1.9812
 12S  C2   C  CR16  0  -0.403   1.2203   2.1264  -1.1106
 12S  C3   C  CR6   0   0.177   1.2470   0.7354  -1.1534
 12S  C19  C  CH2   0  -0.511   2.5549  -0.0046  -1.1417
 12S  C18  C  CH2   0  -0.488   2.9813  -0.3678   0.2877
 12S  C12  C  CR6   0   0.278   4.2907  -1.1019   0.3171
 12S  C13  C  CR16  0  -0.433   5.4281  -0.5140   0.8396
 12S  N11  N  N     0  -0.485   4.2866  -2.3315  -0.2039
 12S  C16  C  CR6   0   0.439   5.4220  -3.0193  -0.2240
 12S  N16  N  NH2   0  -0.838   5.3923  -4.2543  -0.8075
 12S  C15  C  CR16  0  -0.448   6.6244  -2.5002   0.2885
 12S  C14  C  CR6   0   0.205   6.6304  -1.2314   0.8289
 12S  C17  C  CH3   0  -0.727   7.8836  -0.6267   1.3837
 12S  H1   H  HNH2  0   0.387  -8.3718  -0.6851  -0.3906
 12S  H2   H  HNH2  0   0.379  -7.3371   0.6237  -0.6414
 12S  H3   H  HCR6  0   0.254  -7.5941  -2.7837   0.5598
 12S  H4   H  HCH3  0   0.254  -5.2309  -5.1715   0.4108
 12S  H5   H  HCH3  0   0.249  -5.0132  -4.7729   2.1049
 12S  H6   H  HCH3  0   0.246  -6.6379  -4.8258   1.4129
 12S  H7   H  HCR6  0   0.243  -3.3367  -3.0106   1.0533
 12S  H8   H  HCH2  0   0.246  -2.9076   0.5010   0.9686
 12S  H9   H  HCH2  0   0.245  -2.0651  -1.0302   0.8066
 12S  H10  H  HCH2  0   0.246  -2.4007  -0.9563  -1.6670
 12S  H11  H  HCH2  0   0.246  -3.2770   0.5559  -1.5054
 12S  H12  H  HCR6  0   0.233   0.0472  -1.0410  -1.1932
 12S  H13  H  HCR6  0   0.232  -2.1160   2.6449  -1.0553
 12S  H14  H  HCH2  0   0.236   0.9057   4.7368  -1.4419
 12S  H15  H  HCH2  0   0.236  -0.8468   4.7254  -1.5364
 12S  H16  H  HCH2  0   0.221  -0.9829   4.3929   0.9351
 12S  H17  H  HCH2  0   0.223   0.7689   4.4070   1.0398
 12S  H18  H  HCH2  0   0.214   0.8350   6.7204   0.1744
 12S  H19  H  HCH2  0   0.189  -0.9062   6.7157  -0.0418
 12S  H20  H  HNH2  0   0.346  -0.1484   7.7428   2.0387
 12S  H21  H  HNH2  0   0.337  -1.0976   6.4772   2.3444
 12S  H23  H  HCR6  0   0.232   2.1552   2.6785  -1.1150
 12S  H24  H  HCH2  0   0.246   2.4804  -0.9199  -1.7327
 12S  H25  H  HCH2  0   0.246   3.3332   0.6086  -1.6028
 12S  H26  H  HCH2  0   0.246   3.0504   0.5419   0.8879
 12S  H27  H  HCH2  0   0.246   2.2064  -0.9912   0.7427
 12S  H28  H  HCR6  0   0.242   5.3852   0.4847   1.2562
 12S  H29  H  HNH2  0   0.379   4.4818  -4.6728  -0.9083
 12S  H30  H  HNH2  0   0.387   6.1126  -4.9063  -0.5452
 12S  H31  H  HCR6  0   0.255   7.5300  -3.0944   0.2553
 12S  H32  H  HCH3  0   0.252   8.1715   0.2566   0.8115
 12S  H33  H  HCH3  0   0.251   7.7386  -0.3036   2.4154
 12S  H34  H  HCH3  0   0.247   8.7159  -1.3283   1.3608

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
 12S  C17  C14  single    1.498  0.020  1.498
 12S  C14  C15  aromatic  1.379  0.020  1.379
 12S  C14  C13  aromatic  1.400  0.020  1.400
 12S  C15  C16  aromatic  1.406  0.020  1.406
 12S  C13  C12  aromatic  1.383  0.020  1.383
 12S  C16  N16  single    1.366  0.020  1.366
 12S  C16  N11  aromatic  1.328  0.020  1.328
 12S  C12  N11  aromatic  1.335  0.020  1.335
 12S  C12  C18  single    1.501  0.020  1.501
 12S  C19  C18  single    1.535  0.020  1.535
 12S  C19  C3   single    1.503  0.020  1.503
 12S  C2   C3   aromatic  1.392  0.020  1.392
 12S  C2   C1   aromatic  1.391  0.020  1.391
 12S  C7   C1   single    1.503  0.020  1.503
 12S  C7   C8   single    1.529  0.020  1.529
 12S  C3   C4   aromatic  1.392  0.020  1.392
 12S  C1   C6   aromatic  1.392  0.020  1.392
 12S  N10  C9   single    1.456  0.020  1.456
 12S  C8   C9   single    1.521  0.020  1.521
 12S  C4   C5   aromatic  1.392  0.020  1.392
 12S  C6   C5   aromatic  1.391  0.020  1.391
 12S  C5   C29  single    1.503  0.020  1.503
 12S  C29  C28  single    1.535  0.020  1.535
 12S  C28  C22  single    1.502  0.020  1.502
 12S  C22  N21  aromatic  1.335  0.020  1.335
 12S  C22  C23  aromatic  1.383  0.020  1.383
 12S  N21  C26  aromatic  1.328  0.020  1.328
 12S  C23  C24  aromatic  1.400  0.020  1.400
 12S  C26  N26  single    1.366  0.020  1.366
 12S  C26  C25  aromatic  1.406  0.020  1.406
 12S  C24  C25  aromatic  1.380  0.020  1.380
 12S  C24  C27  single    1.498  0.020  1.498
 12S  N26  H1   single    0.890  0.020  1.040
 12S  N26  H2   single    0.890  0.020  1.040
 12S  C25  H3   single    0.930  0.020  1.080
 12S  C27  H4   single    0.970  0.020  1.090
 12S  C27  H5   single    0.970  0.020  1.090
 12S  C27  H6   single    0.970  0.020  1.090
 12S  C23  H7   single    0.930  0.020  1.080
 12S  C28  H8   single    0.970  0.020  1.090
 12S  C28  H9   single    0.970  0.020  1.090
 12S  C29  H10  single    0.970  0.020  1.090
 12S  C29  H11  single    0.970  0.020  1.090
 12S  C4   H12  single    0.930  0.020  1.080
 12S  C6   H13  single    0.930  0.020  1.080
 12S  C7   H14  single    0.970  0.020  1.090
 12S  C7   H15  single    0.970  0.020  1.090
 12S  C8   H16  single    0.970  0.020  1.090
 12S  C8   H17  single    0.970  0.020  1.090
 12S  C9   H18  single    0.970  0.020  1.090
 12S  C9   H19  single    0.970  0.020  1.090
 12S  N10  H20  single    0.890  0.020  1.040
 12S  N10  H21  single    0.890  0.020  1.040
 12S  C2   H23  single    0.930  0.020  1.080
 12S  C19  H24  single    0.970  0.020  1.090
 12S  C19  H25  single    0.970  0.020  1.090
 12S  C18  H26  single    0.970  0.020  1.090
 12S  C18  H27  single    0.970  0.020  1.090
 12S  C13  H28  single    0.930  0.020  1.080
 12S  N16  H29  single    0.890  0.020  1.040
 12S  N16  H30  single    0.890  0.020  1.040
 12S  C15  H31  single    0.930  0.020  1.080
 12S  C17  H32  single    0.970  0.020  1.090
 12S  C17  H33  single    0.970  0.020  1.090
 12S  C17  H34  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
 12S  H2   N26  H1   113.85  3.000
 12S  H2   N26  C26  115.93  3.000
 12S  H1   N26  C26  117.28  3.000
 12S  N21  C26  C25  122.30  3.000
 12S  C25  C26  N26  120.63  3.000
 12S  N21  C26  N26  117.03  3.000
 12S  H3   C25  C24  120.81  3.000
 12S  H3   C25  C26  120.11  3.000
 12S  C24  C25  C26  119.08  3.000
 12S  C23  C24  C27  120.68  3.000
 12S  C27  C24  C25  121.25  3.000
 12S  C23  C24  C25  118.07  3.000
 12S  H6   C27  H5   108.34  3.000
 12S  H6   C27  H4   107.79  3.000
 12S  H5   C27  H4   106.99  3.000
 12S  H6   C27  C24  111.71  3.000
 12S  H5   C27  C24  111.29  3.000
 12S  H4   C27  C24  110.53  3.000
 12S  H7   C23  C22  120.19  3.000
 12S  H7   C23  C24  120.75  3.000
 12S  C22  C23  C24  119.06  3.000
 12S  C22  N21  C26  118.73  3.000
 12S  C28  C22  N21  115.99  3.000
 12S  N21  C22  C23  122.76  3.000
 12S  C28  C22  C23  121.25  3.000
 12S  H9   C28  H8   106.84  3.000
 12S  H9   C28  C29  109.47  3.000
 12S  H8   C28  C29  108.95  3.000
 12S  H9   C28  C22  109.97  3.000
 12S  H8   C28  C22  109.18  3.000
 12S  C29  C28  C22  112.27  3.000
 12S  H11  C29  H10  106.90  3.000
 12S  H11  C29  C5   110.08  3.000
 12S  H10  C29  C5   110.27  3.000
 12S  H11  C29  C28  108.94  3.000
 12S  H10  C29  C28  109.12  3.000
 12S  C5   C29  C28  111.42  3.000
 12S  C6   C5   C4   118.68  3.000
 12S  C6   C5   C29  120.54  3.000
 12S  C4   C5   C29  120.74  3.000
 12S  H12  C4   C3   119.36  3.000
 12S  H12  C4   C5   119.35  3.000
 12S  C3   C4   C5   121.29  3.000
 12S  H13  C6   C1   119.18  3.000
 12S  H13  C6   C5   119.45  3.000
 12S  C1   C6   C5   121.37  3.000
 12S  C2   C1   C7   120.83  3.000
 12S  C7   C1   C6   120.52  3.000
 12S  C2   C1   C6   118.61  3.000
 12S  H15  C7   H14  106.70  3.000
 12S  H15  C7   C8   109.24  3.000
 12S  H14  C7   C8   109.34  3.000
 12S  H15  C7   C1   109.76  3.000
 12S  H14  C7   C1   109.80  3.000
 12S  C8   C7   C1   111.87  3.000
 12S  H17  C8   H16  106.58  3.000
 12S  H17  C8   C9   109.34  3.000
 12S  H16  C8   C9   109.47  3.000
 12S  H17  C8   C7   109.63  3.000
 12S  H16  C8   C7   109.12  3.000
 12S  C9   C8   C7   112.52  3.000
 12S  H19  C9   H18  106.20  3.000
 12S  H19  C9   N10  113.53  3.000
 12S  H18  C9   N10  108.19  3.000
 12S  H19  C9   C8   108.85  3.000
 12S  H18  C9   C8   109.07  3.000
 12S  N10  C9   C8   110.82  3.000
 12S  H21  N10  H20  105.44  3.000
 12S  H21  N10  C9   109.17  3.000
 12S  H20  N10  C9   109.55  3.000
 12S  H23  C2   C3   119.44  3.000
 12S  H23  C2   C1   119.18  3.000
 12S  C3   C2   C1   121.37  3.000
 12S  C19  C3   C2   120.57  3.000
 12S  C2   C3   C4   118.68  3.000
 12S  C19  C3   C4   120.71  3.000
 12S  H25  C19  H24  106.89  3.000
 12S  H25  C19  C18  109.13  3.000
 12S  H24  C19  C18  108.94  3.000
 12S  H25  C19  C3   109.90  3.000
 12S  H24  C19  C3   110.43  3.000
 12S  C18  C19  C3   111.44  3.000
 12S  H27  C18  H26  106.92  3.000
 12S  H27  C18  C12  109.33  3.000
 12S  H26  C18  C12  109.96  3.000
 12S  H27  C18  C19  108.99  3.000
 12S  H26  C18  C19  109.40  3.000
 12S  C12  C18  C19  112.10  3.000
 12S  N11  C12  C13  122.78  3.000
 12S  N11  C12  C18  116.10  3.000
 12S  C13  C12  C18  121.12  3.000
 12S  H28  C13  C14  120.63  3.000
 12S  H28  C13  C12  120.32  3.000
 12S  C14  C13  C12  119.05  3.000
 12S  C16  N11  C12  118.70  3.000
 12S  C15  C16  N16  120.52  3.000
 12S  N16  C16  N11  117.14  3.000
 12S  C15  C16  N11  122.31  3.000
 12S  H30  N16  H29  113.83  3.000
 12S  H30  N16  C16  117.31  3.000
 12S  H29  N16  C16  115.97  3.000
 12S  H31  C15  C14  120.85  3.000
 12S  H31  C15  C16  120.07  3.000
 12S  C14  C15  C16  119.08  3.000
 12S  C17  C14  C15  121.35  3.000
 12S  C15  C14  C13  118.07  3.000
 12S  C17  C14  C13  120.58  3.000
 12S  H34  C17  H33  108.20  3.000
 12S  H34  C17  H32  107.99  3.000
 12S  H33  C17  H32  106.94  3.000
 12S  H34  C17  C14  111.81  3.000
 12S  H33  C17  C14  111.02  3.000
 12S  H32  C17  C14  110.69  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
 12S  CONST_01  C23  C22  N21  C26     0.00   0.0  0
 12S  CONST_02  C23  C24  C25  C26     0.00   0.0  0
 12S  CONST_03  C22  N21  C26  C25     0.00   0.0  0
 12S  CONST_04  C22  C23  C24  C25     0.00   0.0  0
 12S  CONST_05  N21  C22  C23  C24     0.00   0.0  0
 12S  CONST_06  N21  C26  C25  C24     0.00   0.0  0
 12S  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 12S  CONST_08  C2   C1   C6   C5      0.00   0.0  0
 12S  CONST_09  C1   C2   C3   C4      0.00   0.0  0
 12S  CONST_10  C1   C6   C5   C4      0.00   0.0  0
 12S  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 12S  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 12S  CONST_13  C15  C14  C13  C12     0.00   0.0  0
 12S  CONST_14  C15  C16  N11  C12     0.00   0.0  0
 12S  CONST_15  C16  C15  C14  C13     0.00   0.0  0
 12S  CONST_16  C16  N11  C12  C13     0.00   0.0  0
 12S  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 12S  CONST_18  C14  C13  C12  N11     0.00   0.0  0
 12S  CONST_19  C22  N21  C26  N26   180.00   0.0  0
 12S  CONST_20  C24  C25  C26  N26   180.00   0.0  0
 12S  CONST_21  C28  C22  N21  C26   180.00   0.0  0
 12S  CONST_22  C27  C24  C25  C26   180.00   0.0  0
 12S  CONST_23  C28  C22  C23  C24   180.00   0.0  0
 12S  CONST_24  C22  C23  C24  C27   180.00   0.0  0
 12S  CONST_25  C3   C4   C5   C29   180.00   0.0  0
 12S  CONST_26  C1   C6   C5   C29   180.00   0.0  0
 12S  CONST_27  C19  C3   C4   C5    180.00   0.0  0
 12S  CONST_28  C7   C1   C6   C5    180.00   0.0  0
 12S  CONST_29  C19  C3   C2   C1    180.00   0.0  0
 12S  CONST_30  C3   C2   C1   C7    180.00   0.0  0
 12S  CONST_31  C14  C13  C12  C18   180.00   0.0  0
 12S  CONST_32  C16  N11  C12  C18   180.00   0.0  0
 12S  CONST_33  C17  C14  C13  C12   180.00   0.0  0
 12S  CONST_34  N16  C16  N11  C12   180.00   0.0  0
 12S  CONST_35  C17  C14  C15  C16   180.00   0.0  0
 12S  CONST_36  C14  C15  C16  N16   180.00   0.0  0
 12S  CONST_37  H7   C23  C24  C25   180.00   0.0  0
 12S  CONST_38  H3   C25  C24  C23   180.00   0.0  0
 12S  CONST_39  H23  C2   C3   C4    180.00   0.0  0
 12S  CONST_40  H13  C6   C5   C4    180.00   0.0  0
 12S  CONST_41  H12  C4   C5   C6    180.00   0.0  0
 12S  CONST_42  H31  C15  C14  C13   180.00   0.0  0
 12S  CONST_43  H28  C13  C12  N11   180.00   0.0  0
 12S  Var_01    C29  C28  C22  C23   111.81  30.0  1
 12S  Var_02    C5   C29  C28  C22   178.02  30.0  1
 12S  Var_03    C4   C5   C29  C28    85.53  30.0  1
 12S  Var_04    C18  C19  C3   C4    -85.62  30.0  2
 12S  Var_05    C8   C7   C1   C6     84.89  30.0  3
 12S  Var_06    C12  C18  C19  C3   -179.71  30.0  3
 12S  Var_07    C13  C12  C18  C19   111.08  30.0  3
 12S  Var_08    H4   C27  C24  C25   107.13  30.0  2
 12S  Var_09    H32  C17  C14  C13   -63.14  30.0  2
 12S  Var_10    C9   C8   C7   C1   -179.95  30.0  3
 12S  Var_11    N10  C9   C8   C7    179.46  30.0  3
 12S  Var_12    H20  N10  C9   C8    177.08  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
 12S  plan-1  N26  0.020
 12S  plan-1  C26  0.020
 12S  plan-1  C25  0.020
 12S  plan-1  C24  0.020
 12S  plan-1  C27  0.020
 12S  plan-1  C23  0.020
 12S  plan-1  N21  0.020
 12S  plan-1  C22  0.020
 12S  plan-1  C28  0.020
 12S  plan-1  H3   0.020
 12S  plan-1  H7   0.020
 12S  plan-2  C29  0.020
 12S  plan-2  C5   0.020
 12S  plan-2  C4   0.020
 12S  plan-2  C6   0.020
 12S  plan-2  C1   0.020
 12S  plan-2  C7   0.020
 12S  plan-2  C2   0.020
 12S  plan-2  C3   0.020
 12S  plan-2  C19  0.020
 12S  plan-2  H12  0.020
 12S  plan-2  H13  0.020
 12S  plan-2  H23  0.020
 12S  plan-3  C18  0.020
 12S  plan-3  C12  0.020
 12S  plan-3  C13  0.020
 12S  plan-3  N11  0.020
 12S  plan-3  C16  0.020
 12S  plan-3  N16  0.020
 12S  plan-3  C15  0.020
 12S  plan-3  C14  0.020
 12S  plan-3  C17  0.020
 12S  plan-3  H28  0.020
 12S  plan-3  H31  0.020
 12S  plan-4  N26  0.020
 12S  plan-4  C26  0.020
 12S  plan-4  H1   0.020
 12S  plan-4  H2   0.020
 12S  plan-5  C16  0.020
 12S  plan-5  N16  0.020
 12S  plan-5  H29  0.020
 12S  plan-5  H30  0.020

