# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:23:42 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]icosane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNCN2CNCCNCN(CN1)CNCCNC2
#
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
 5KK  5KK  1,3,6,8,10,13,16,19-octaazabicyclo[6.6.6]icosane  ligand  50  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5KK
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
 5KK  C1   C  CH2   0  -0.140   2.4754  -0.0651   1.4073
 5KK  N1   N  NH1   0  -0.597   1.1038   0.2887   1.7397
 5KK  C4   C  CH2   0  -0.315   0.6050  -0.1198   3.0341
 5KK  C7   C  CH2   0  -0.266  -0.9124   0.0453   3.0758
 5KK  N4   N  NH1   0  -0.624  -1.5795  -0.8722   2.1639
 5KK  C11  C  CH2   0  -0.125  -2.6003  -0.3365   1.2654
 5KK  N8   N  NT    0  -0.455  -2.1814  -0.3712  -0.1221
 5KK  C10  C  CH2   0  -0.102  -1.9979   0.8872  -0.8021
 5KK  N6   N  NH1   0  -0.639  -1.1276   1.7640  -0.0473
 5KK  C8   C  CH2   0  -0.294  -0.5073   2.7889  -0.8772
 5KK  C6   C  CH2   0  -0.319   0.8546   2.3644  -1.4193
 5KK  N3   N  NH1   0  -0.602   1.8208   2.3002  -0.3337
 5KK  C3   C  CH2   0  -0.155   2.9569   1.4059  -0.4890
 5KK  N7   N  NT    0  -0.429   2.7889   0.0665   0.0132
 5KK  C2   C  CH2   0  -0.133   2.3512  -0.9787  -0.8598
 5KK  N2   N  NH1   0  -0.594   0.9281  -1.0254  -1.1669
 5KK  C5   C  CH2   0  -0.240   0.5633  -2.2568  -1.8418
 5KK  C9   C  CH2   0  -0.318  -0.8553  -2.7207  -1.5448
 5KK  N5   N  NH1   0  -0.587  -1.9024  -1.8173  -1.9940
 5KK  C12  C  CH2   0  -0.156  -2.8055  -1.3673  -0.9625
 5KK  H1   H  HCH2  0   0.202   3.2049   0.5339   1.9736
 5KK  H2   H  HCH2  0   0.219   2.6309  -1.1084   1.7008
 5KK  H3   H  HNH1  0   0.351   1.0141   1.2917   1.6332
 5KK  H5   H  HCH2  0   0.218   0.8583  -1.1738   3.1926
 5KK  H6   H  HCH2  0   0.207   1.0472   0.4321   3.8760
 5KK  H7   H  HCH2  0   0.205  -1.2478  -0.1158   4.1070
 5KK  H8   H  HCH2  0   0.199  -1.1545   1.0898   2.8365
 5KK  H9   H  HNH1  0   0.344  -0.8828  -1.3091   1.5757
 5KK  H11  H  HCH2  0   0.207  -3.5233  -0.9175   1.3759
 5KK  H12  H  HCH2  0   0.217  -2.8448   0.6865   1.5648
 5KK  H14  H  HCH2  0   0.205  -1.5939   0.6398  -1.7921
 5KK  H15  H  HCH2  0   0.177  -2.9581   1.4083  -0.9726
 5KK  H16  H  HNH1  0   0.373  -0.3922   1.1894   0.3514
 5KK  H18  H  HCH2  0   0.215  -1.1752   3.0365  -1.7083
 5KK  H19  H  HCH2  0   0.208  -0.3898   3.7178  -0.3066
 5KK  H20  H  HCH2  0   0.244   0.7612   1.3674  -1.8559
 5KK  H21  H  HCH2  0   0.197   1.1727   3.0451  -2.2221
 5KK  H22  H  HNH1  0   0.345   2.1493   3.2295  -0.1111
 5KK  H24  H  HCH2  0   0.207   3.2855   1.3204  -1.5334
 5KK  H25  H  HCH2  0   0.223   3.7812   1.8676   0.0642
 5KK  H27  H  HCH2  0   0.212   2.8992  -0.8867  -1.8047
 5KK  H28  H  HCH2  0   0.186   2.6837  -1.9316  -0.4113
 5KK  H29  H  HNH1  0   0.359   0.3904  -0.9150  -0.3164
 5KK  H31  H  HCH2  0   0.199   0.6923  -2.1458  -2.9251
 5KK  H32  H  HCH2  0   0.174   1.2248  -3.0888  -1.5450
 5KK  H33  H  HCH2  0   0.226  -0.9825  -3.7062  -2.0037
 5KK  H34  H  HCH2  0   0.211  -0.9447  -2.8823  -0.4635
 5KK  H35  H  HNH1  0   0.349  -2.4330  -2.2307  -2.7464
 5KK  H37  H  HCH2  0   0.207  -3.1386  -2.1850  -0.3074
 5KK  H38  H  HCH2  0   0.201  -3.7070  -0.9855  -1.4675

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
 5KK  C8   C6   single  1.526  0.020  1.526
 5KK  C8   N6   single  1.457  0.020  1.457
 5KK  C6   N3   single  1.455  0.020  1.455
 5KK  N3   C3   single  1.454  0.020  1.454
 5KK  N6   C10  single  1.448  0.020  1.448
 5KK  C10  N8   single  1.442  0.020  1.442
 5KK  C3   N7   single  1.440  0.020  1.440
 5KK  N1   C1   single  1.455  0.020  1.455
 5KK  N1   C4   single  1.446  0.020  1.446
 5KK  C1   N7   single  1.435  0.020  1.435
 5KK  N7   C2   single  1.430  0.020  1.430
 5KK  N8   C11  single  1.450  0.020  1.450
 5KK  N8   C12  single  1.445  0.020  1.445
 5KK  C4   C7   single  1.527  0.020  1.527
 5KK  C7   N4   single  1.456  0.020  1.456
 5KK  C11  N4   single  1.462  0.020  1.462
 5KK  N5   C12  single  1.443  0.020  1.443
 5KK  N5   C9   single  1.454  0.020  1.454
 5KK  C2   N2   single  1.457  0.020  1.457
 5KK  N2   C5   single  1.451  0.020  1.451
 5KK  C5   C9   single  1.522  0.020  1.522
 5KK  C1   H1   single  0.970  0.020  1.090
 5KK  C1   H2   single  0.970  0.020  1.090
 5KK  N1   H3   single  0.890  0.020  1.040
 5KK  C4   H5   single  0.970  0.020  1.090
 5KK  C4   H6   single  0.970  0.020  1.090
 5KK  C7   H7   single  0.970  0.020  1.090
 5KK  C7   H8   single  0.970  0.020  1.090
 5KK  N4   H9   single  0.890  0.020  1.040
 5KK  C11  H11  single  0.970  0.020  1.090
 5KK  C11  H12  single  0.970  0.020  1.090
 5KK  C10  H14  single  0.970  0.020  1.090
 5KK  C10  H15  single  0.970  0.020  1.090
 5KK  N6   H16  single  0.890  0.020  1.040
 5KK  C8   H18  single  0.970  0.020  1.090
 5KK  C8   H19  single  0.970  0.020  1.090
 5KK  C6   H20  single  0.970  0.020  1.090
 5KK  C6   H21  single  0.970  0.020  1.090
 5KK  N3   H22  single  0.890  0.020  1.040
 5KK  C3   H24  single  0.970  0.020  1.090
 5KK  C3   H25  single  0.970  0.020  1.090
 5KK  C2   H27  single  0.970  0.020  1.090
 5KK  C2   H28  single  0.970  0.020  1.090
 5KK  N2   H29  single  0.890  0.020  1.040
 5KK  C5   H31  single  0.970  0.020  1.090
 5KK  C5   H32  single  0.970  0.020  1.090
 5KK  C9   H33  single  0.970  0.020  1.090
 5KK  C9   H34  single  0.970  0.020  1.090
 5KK  N5   H35  single  0.890  0.020  1.040
 5KK  C12  H37  single  0.970  0.020  1.090
 5KK  C12  H38  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
 5KK  H2   C1   H1   106.65  3.000
 5KK  H2   C1   N7   108.47  3.000
 5KK  H1   C1   N7   107.77  3.000
 5KK  H2   C1   N1   107.72  3.000
 5KK  H1   C1   N1   112.02  3.000
 5KK  N7   C1   N1   113.93  3.000
 5KK  H3   N1   C4   110.08  3.000
 5KK  H3   N1   C1   107.48  3.000
 5KK  C4   N1   C1   117.45  3.000
 5KK  H6   C4   H5   106.21  3.000
 5KK  H6   C4   C7   108.94  3.000
 5KK  H5   C4   C7   109.26  3.000
 5KK  H6   C4   N1   113.88  3.000
 5KK  H5   C4   N1   108.75  3.000
 5KK  C7   C4   N1   109.68  3.000
 5KK  H8   C7   H7   106.10  3.000
 5KK  H8   C7   N4   111.21  3.000
 5KK  H7   C7   N4   110.89  3.000
 5KK  H8   C7   C4   108.41  3.000
 5KK  H7   C7   C4   108.29  3.000
 5KK  N4   C7   C4   111.73  3.000
 5KK  H9   N4   C11  106.38  3.000
 5KK  H9   N4   C7   108.73  3.000
 5KK  C11  N4   C7   118.31  3.000
 5KK  H12  C11  H11  106.26  3.000
 5KK  H12  C11  N8   110.43  3.000
 5KK  H11  C11  N8   109.09  3.000
 5KK  H12  C11  N4   109.31  3.000
 5KK  H11  C11  N4   109.38  3.000
 5KK  N8   C11  N4   112.19  3.000
 5KK  C12  N8   C10  112.47  3.000
 5KK  C12  N8   C11  116.64  3.000
 5KK  C10  N8   C11  117.85  3.000
 5KK  H15  C10  H14  106.67  3.000
 5KK  H15  C10  N6   108.48  3.000
 5KK  H14  C10  N6   112.68  3.000
 5KK  H15  C10  N8   111.93  3.000
 5KK  H14  C10  N8   105.99  3.000
 5KK  N6   C10  N8   111.05  3.000
 5KK  H16  N6   C8   108.26  3.000
 5KK  H16  N6   C10  107.31  3.000
 5KK  C8   N6   C10  112.64  3.000
 5KK  H19  C8   H18  105.60  3.000
 5KK  H19  C8   C6   108.96  3.000
 5KK  H18  C8   C6   109.74  3.000
 5KK  H19  C8   N6   110.18  3.000
 5KK  H18  C8   N6   109.37  3.000
 5KK  C6   C8   N6   112.74  3.000
 5KK  H21  C6   H20  107.33  3.000
 5KK  H21  C6   N3   112.34  3.000
 5KK  H20  C6   N3   108.35  3.000
 5KK  H21  C6   C8   110.20  3.000
 5KK  H20  C6   C8   108.64  3.000
 5KK  N3   C6   C8   109.87  3.000
 5KK  H22  N3   C3   109.58  3.000
 5KK  H22  N3   C6   109.86  3.000
 5KK  C3   N3   C6   117.80  3.000
 5KK  H25  C3   H24  106.74  3.000
 5KK  H25  C3   N7   107.69  3.000
 5KK  H24  C3   N7   107.10  3.000
 5KK  H25  C3   N3   105.96  3.000
 5KK  H24  C3   N3   112.53  3.000
 5KK  N7   C3   N3   116.33  3.000
 5KK  C2   N7   C3   120.16  3.000
 5KK  C2   N7   C1   117.33  3.000
 5KK  C3   N7   C1   116.71  3.000
 5KK  H28  C2   H27  105.78  3.000
 5KK  H28  C2   N2   110.61  3.000
 5KK  H27  C2   N2   108.02  3.000
 5KK  H28  C2   N7   106.89  3.000
 5KK  H27  C2   N7   108.17  3.000
 5KK  N2   C2   N7   116.81  3.000
 5KK  H29  N2   C5   110.48  3.000
 5KK  H29  N2   C2   109.78  3.000
 5KK  C5   N2   C2   111.77  3.000
 5KK  H32  C5   H31  105.75  3.000
 5KK  H32  C5   C9   106.05  3.000
 5KK  H31  C5   C9   109.46  3.000
 5KK  H32  C5   N2   111.35  3.000
 5KK  H31  C5   N2   110.13  3.000
 5KK  C9   C5   N2   113.72  3.000
 5KK  H34  C9   H33  105.73  3.000
 5KK  H34  C9   N5   109.72  3.000
 5KK  H33  C9   N5   110.26  3.000
 5KK  H34  C9   C5   108.25  3.000
 5KK  H33  C9   C5   107.51  3.000
 5KK  N5   C9   C5   114.94  3.000
 5KK  H35  N5   C12  109.37  3.000
 5KK  H35  N5   C9   110.75  3.000
 5KK  C12  N5   C9   115.06  3.000
 5KK  H38  C12  H37  106.44  3.000
 5KK  H38  C12  N5   107.01  3.000
 5KK  H37  C12  N5   112.56  3.000
 5KK  H38  C12  N8   112.41  3.000
 5KK  H37  C12  N8   107.28  3.000
 5KK  N5   C12  N8   111.13  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
 5KK  Var_01  C7   C4   N1   C1   -166.99  30.0  1
 5KK  Var_02  N3   C3   N7   C1    -58.58  30.0  1
 5KK  Var_03  N2   C2   N7   C1     73.99  30.0  1
 5KK  Var_04  C3   N7   C1   N1     74.45  30.0  1
 5KK  Var_05  N4   C7   C4   N1     66.46  30.0  1
 5KK  Var_06  N7   C1   N1   C4    165.11  30.0  1
 5KK  Var_07  C11  N4   C7   C4   -131.44  30.0  1
 5KK  Var_08  N8   C11  N4   C7    111.84  30.0  1
 5KK  Var_09  C10  N8   C11  N4   -114.88  30.0  1
 5KK  Var_10  N6   C10  N8   C11    52.04  30.0  1
 5KK  Var_11  N5   C12  N8   C11  -148.49  30.0  1
 5KK  Var_12  C8   N6   C10  N8    157.90  30.0  1
 5KK  Var_13  C9   N5   C12  N8     75.25  30.0  1
 5KK  Var_14  C6   C8   N6   C10   -92.29  30.0  1
 5KK  Var_15  N3   C6   C8   N6    -69.44  30.0  1
 5KK  Var_16  N7   C3   N3   C6    -91.22  30.0  1
 5KK  Var_17  C5   N2   C2   N7   -169.04  30.0  1
 5KK  Var_18  C9   C5   N2   C2    149.19  30.0  1
 5KK  Var_19  N5   C9   C5   N2     63.36  30.0  1
 5KK  Var_20  C12  N5   C9   C5   -123.16  30.0  1

