# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:15:22 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 6-(piperazin-1-yl)-9H-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1)c2ncnc3[nH]cnc23
#
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
 69P  69P  6-(piperazin-1-yl)-9H-purine  ligand  27  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_69P
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
 69P  N1    N  N     0  -0.497  -0.4279  -1.8139  -0.2128
 69P  C2    C  CR16  0   0.042  -1.6761  -2.1854  -0.4591
 69P  N3    N  N     0  -0.450  -2.7642  -1.4384  -0.4756
 69P  C4    C  CR56  0   0.456  -2.4774  -0.1656  -0.2076
 69P  C5    C  CR56  0  -0.015  -1.2232   0.3784   0.0689
 69P  C6    C  CR6   0   0.531  -0.1349  -0.5336   0.0631
 69P  N6    N  NT    0  -0.481   1.1481  -0.2180   0.3028
 69P  N7    N  N     0  -0.460  -1.3399   1.7327   0.2838
 69P  C8    C  CR15  0   0.116  -2.6076   1.9868   0.1454
 69P  N9    N  NR15  0  -0.646  -3.3406   0.8821  -0.1491
 69P  CBV   C  CH2   0  -0.320   3.3907  -0.7194  -0.5265
 69P  CBW   C  CH2   0  -0.314   2.7967   1.5487  -0.0674
 69P  CBX   C  CH2   0  -0.317   2.2036  -1.2198   0.2904
 69P  CBY   C  CH2   0  -0.335   1.5990   1.0879   0.7575
 69P  NDM   N  NH1   0  -0.579   3.8808   0.5842  -0.1142
 69P  H2    H  HCR6  0   0.248  -1.8152  -3.2411  -0.6699
 69P  H8    H  HCR5  0   0.290  -3.0643   2.9593   0.2459
 69P  HN9   H  HNR5  0   0.425  -4.3371   0.8491  -0.3007
 69P  HBV   H  HCH2  0   0.244   4.2010  -1.4471  -0.4584
 69P  HBVA  H  HCH2  0   0.227   3.0966  -0.6622  -1.5792
 69P  HBW   H  HCH2  0   0.226   2.4667   1.7522  -1.0909
 69P  HBWA  H  HCH2  0   0.244   3.1673   2.4897   0.3428
 69P  HBX   H  HCH2  0   0.232   2.5200  -1.4189   1.3218
 69P  HBXA  H  HCH2  0   0.271   1.8210  -2.1486  -0.1216
 69P  HBY   H  HCH2  0   0.287   0.7945   1.8130   0.6902
 69P  HBYA  H  HCH2  0   0.232   1.8918   1.0114   1.8124
 69P  HNDM  H  HNH1  0   0.343   4.2932   0.5053   0.8092

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
 69P  N1   C2    aromatic  1.325  0.020  1.325
 69P  N1   C6    aromatic  1.342  0.020  1.342
 69P  C2   N3    aromatic  1.320  0.020  1.320
 69P  N3   C4    aromatic  1.332  0.020  1.332
 69P  C4   C5    aromatic  1.395  0.020  1.395
 69P  C4   N9    aromatic  1.359  0.020  1.359
 69P  C5   C6    aromatic  1.420  0.020  1.420
 69P  C5   N7    aromatic  1.376  0.020  1.376
 69P  C6   N6    single    1.343  0.020  1.343
 69P  N6   CBX   single    1.455  0.020  1.455
 69P  N6   CBY   single    1.454  0.020  1.454
 69P  N7   C8    aromatic  1.300  0.020  1.300
 69P  C8   N9    aromatic  1.358  0.020  1.358
 69P  CBV  CBX   single    1.525  0.020  1.525
 69P  CBV  NDM   single    1.452  0.020  1.452
 69P  CBW  CBY   single    1.526  0.020  1.526
 69P  CBW  NDM   single    1.452  0.020  1.452
 69P  C2   H2    single    0.930  0.020  1.080
 69P  C8   H8    single    0.930  0.020  1.080
 69P  N9   HN9   single    0.860  0.020  1.020
 69P  CBV  HBV   single    0.970  0.020  1.090
 69P  CBV  HBVA  single    0.970  0.020  1.090
 69P  CBW  HBW   single    0.970  0.020  1.090
 69P  CBW  HBWA  single    0.970  0.020  1.090
 69P  CBX  HBX   single    0.970  0.020  1.090
 69P  CBX  HBXA  single    0.970  0.020  1.090
 69P  CBY  HBY   single    0.970  0.020  1.090
 69P  CBY  HBYA  single    0.970  0.020  1.090
 69P  NDM  HNDM  single    0.890  0.020  1.040

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
 69P  C6    N1   C2   120.74  3.000
 69P  H2    C2   N3   116.26  3.000
 69P  H2    C2   N1   115.42  3.000
 69P  N3    C2   N1   128.32  3.000
 69P  C4    N3   C2   111.15  3.000
 69P  N9    C4   C5   105.19  3.000
 69P  N9    C4   N3   127.49  3.000
 69P  C5    C4   N3   127.32  3.000
 69P  N7    C5   C6   134.24  3.000
 69P  N7    C5   C4   109.79  3.000
 69P  C6    C5   C4   115.97  3.000
 69P  N6    C6   C5   125.49  3.000
 69P  N6    C6   N1   118.00  3.000
 69P  C5    C6   N1   116.50  3.000
 69P  CBY   N6   CBX  113.32  3.000
 69P  CBY   N6   C6   124.27  3.000
 69P  CBX   N6   C6   121.98  3.000
 69P  C8    N7   C5   104.97  3.000
 69P  H8    C8   N9   121.66  3.000
 69P  H8    C8   N7   125.37  3.000
 69P  N9    C8   N7   112.98  3.000
 69P  HN9   N9   C8   126.34  3.000
 69P  HN9   N9   C4   126.59  3.000
 69P  C8    N9   C4   107.07  3.000
 69P  HBVA  CBV  HBV  107.12  3.000
 69P  HBVA  CBV  NDM  108.47  3.000
 69P  HBV   CBV  NDM  109.28  3.000
 69P  HBVA  CBV  CBX  108.85  3.000
 69P  HBV   CBV  CBX  109.00  3.000
 69P  NDM   CBV  CBX  113.89  3.000
 69P  HBWA  CBW  HBW  107.07  3.000
 69P  HBWA  CBW  NDM  109.35  3.000
 69P  HBW   CBW  NDM  108.58  3.000
 69P  HBWA  CBW  CBY  108.89  3.000
 69P  HBW   CBW  CBY  108.97  3.000
 69P  NDM   CBW  CBY  113.76  3.000
 69P  HBXA  CBX  HBX  107.65  3.000
 69P  HBXA  CBX  CBV  110.59  3.000
 69P  HBX   CBX  CBV  109.79  3.000
 69P  HBXA  CBX  N6   109.67  3.000
 69P  HBX   CBX  N6   109.03  3.000
 69P  CBV   CBX  N6   110.07  3.000
 69P  HBYA  CBY  HBY  107.69  3.000
 69P  HBYA  CBY  CBW  109.35  3.000
 69P  HBY   CBY  CBW  110.28  3.000
 69P  HBYA  CBY  N6   108.71  3.000
 69P  HBY   CBY  N6   110.53  3.000
 69P  CBW   CBY  N6   110.21  3.000
 69P  HNDM  NDM  CBW  109.02  3.000
 69P  HNDM  NDM  CBV  109.02  3.000
 69P  CBW   NDM  CBV  110.70  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
 69P  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 69P  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 69P  CONST_03  N7   C5   C6   N1    180.00   0.0  0
 69P  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 69P  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 69P  CONST_06  N9   C4   N3   C2    180.00   0.0  0
 69P  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 69P  CONST_08  C6   C5   C4   N3      0.00   0.0  0
 69P  CONST_09  N7   C5   C4   N3    180.00   0.0  0
 69P  CONST_10  C8   N9   C4   N3    180.00   0.0  0
 69P  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 69P  CONST_12  N7   C8   N9   C4      0.00   0.0  0
 69P  CONST_13  C8   N9   C4   C5      0.00   0.0  0
 69P  CONST_14  N9   C8   N7   C5      0.00   0.0  0
 69P  CONST_15  N9   C4   C5   C6    180.00   0.0  0
 69P  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 69P  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 69P  CONST_18  N6   C6   N1   C2    180.00   0.0  0
 69P  CONST_19  N6   C6   C5   C4    180.00   0.0  0
 69P  CONST_20  N7   C5   C6   N6      0.00   0.0  0
 69P  CONST_21  HN9  N9   C4   N3      0.00   0.0  0
 69P  CONST_22  H2   C2   N3   C4    180.00   0.0  0
 69P  CONST_23  H8   C8   N9   C4    180.00   0.0  0
 69P  Var_01    CBX  N6   C6   N1     -0.97  30.0  2
 69P  Var_02    CBV  CBX  N6   C6    133.00  30.0  1
 69P  Var_03    CBW  CBY  N6   C6   -133.12  30.0  1
 69P  Var_04    NDM  CBV  CBX  N6     53.19  30.0  1
 69P  Var_05    NDM  CBW  CBY  N6    -53.21  30.0  1
 69P  Var_06    CBY  CBW  NDM  CBV    52.18  30.0  1
 69P  Var_07    CBX  CBV  NDM  CBW   -52.26  30.0  1

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
 69P  plan-1  N1   0.020
 69P  plan-1  C2   0.020
 69P  plan-1  N3   0.020
 69P  plan-1  C4   0.020
 69P  plan-1  C5   0.020
 69P  plan-1  C6   0.020
 69P  plan-1  N6   0.020
 69P  plan-1  N7   0.020
 69P  plan-1  C8   0.020
 69P  plan-1  N9   0.020
 69P  plan-1  H2   0.020
 69P  plan-1  H8   0.020
 69P  plan-1  HN9  0.020

