# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:43:28 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 9-(4-azidobutyl)-8-bromanyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCCN=[N+]=[N-])c(Br)nc12
#
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
 JXB  JXB  9-(4-azidobutyl)-8-bromanyl-purin-6-amine  ligand  29  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JXB
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
 JXB  N    N   N     -1  -0.228   6.6907   0.0737  -0.3246
 JXB  C    C   CH2    0  -0.302   3.9322  -1.4403   0.7047
 JXB  C1   C   CH2    0  -0.444   2.9878  -1.0299  -0.4154
 JXB  C2   C   CH2    0  -0.441   1.5794  -0.7897   0.1121
 JXB  C3   C   CH2    0  -0.318   0.6276  -0.4160  -1.0149
 JXB  C4   C   CR5    0   0.280  -1.2443   1.0220  -0.0622
 JXB  C5   C   CR56   0   0.003  -2.7782  -0.3886   0.1655
 JXB  C6   C   CR6    0   0.458  -3.9417  -1.1401   0.4145
 JXB  C7   C   CR16   0   0.043  -2.8115  -2.9681  -0.4113
 JXB  C8   C   CR56   0   0.499  -1.7059  -1.0741  -0.3805
 JXB  N1   N   N      1   0.354   5.9770  -0.7518  -0.0499
 JXB  N2   N   N      0  -0.362   5.2920  -1.7185   0.2238
 JXB  N3   N   NR5    0  -0.512  -0.7148  -0.1459  -0.5343
 JXB  N4   N   N      0  -0.426  -2.4649   0.9321   0.3576
 JXB  N6   N   N      0  -0.472  -3.9172  -2.4425   0.1094
 JXB  N7   N   N      0  -0.457  -1.6670  -2.3671  -0.6887
 JXB  BR   BR  BR     0   0.037  -0.2679   2.5980  -0.0452
 JXB  H2   H   HCH2   0   0.251   3.9527  -0.6782   1.4898
 JXB  H3   H   HCH2   0   0.258   3.5929  -2.3680   1.1623
 JXB  H4   H   HCH2   0   0.238   3.3570  -0.1180  -0.8944
 JXB  H5   H   HCH2   0   0.243   2.9751  -1.8097  -1.1814
 JXB  H6   H   HCH2   0   0.246   1.2076  -1.6891   0.6101
 JXB  H7   H   HCH2   0   0.241   1.5954   0.0053   0.8631
 JXB  H8   H   HCH2   0   0.276   0.9846   0.4572  -1.5606
 JXB  H9   H   HCH2   0   0.280   0.5488  -1.2294  -1.7359
 JXB  H10  H   HCR6   0   0.254  -2.8607  -4.0286  -0.6337
 JXB  H11  H   HNH2   0   0.405  -5.8485  -1.1886   1.1213
 JXB  H12  H   HNH2   0   0.413  -5.0877   0.3589   1.1980
 JXB  N5   N   NH2    0  -0.815  -5.0491  -0.6091   0.9311

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
 JXB  N   N1   double    1.125  0.020  1.125
 JXB  N1  N2   double    1.216  0.020  1.216
 JXB  N2  C    single    1.469  0.020  1.469
 JXB  C   C1   single    1.522  0.020  1.522
 JXB  N5  C6   single    1.332  0.020  1.332
 JXB  C1  C2   single    1.523  0.020  1.523
 JXB  C6  N6   aromatic  1.338  0.020  1.338
 JXB  C6  C5   aromatic  1.407  0.020  1.407
 JXB  N6  C7   aromatic  1.330  0.020  1.330
 JXB  N4  C5   aromatic  1.371  0.020  1.371
 JXB  N4  C4   aromatic  1.294  0.020  1.294
 JXB  C5  C8   aromatic  1.385  0.020  1.385
 JXB  C7  N7   aromatic  1.322  0.020  1.322
 JXB  C2  C3   single    1.522  0.020  1.522
 JXB  C4  BR   single    1.854  0.020  1.854
 JXB  C4  N3   aromatic  1.366  0.020  1.366
 JXB  C8  N7   aromatic  1.330  0.020  1.330
 JXB  C8  N3   aromatic  1.367  0.020  1.367
 JXB  N3  C3   single    1.451  0.020  1.451
 JXB  C   H2   single    0.970  0.020  1.090
 JXB  C   H3   single    0.970  0.020  1.090
 JXB  C1  H4   single    0.970  0.020  1.090
 JXB  C1  H5   single    0.970  0.020  1.090
 JXB  C2  H6   single    0.970  0.020  1.090
 JXB  C2  H7   single    0.970  0.020  1.090
 JXB  C3  H8   single    0.970  0.020  1.090
 JXB  C3  H9   single    0.970  0.020  1.090
 JXB  C7  H10  single    0.930  0.020  1.080
 JXB  N5  H11  single    0.860  0.020  1.020
 JXB  N5  H12  single    0.860  0.020  1.020

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
 JXB  H3   C   H2   107.32  3.000
 JXB  H3   C   N2   105.35  3.000
 JXB  H2   C   N2   110.45  3.000
 JXB  H3   C   C1   110.23  3.000
 JXB  H2   C   C1   110.60  3.000
 JXB  N2   C   C1   112.62  3.000
 JXB  H5   C1  H4   106.96  3.000
 JXB  H5   C1  C2   110.15  3.000
 JXB  H4   C1  C2   109.40  3.000
 JXB  H5   C1  C    109.31  3.000
 JXB  H4   C1  C    109.73  3.000
 JXB  C2   C1  C    111.19  3.000
 JXB  H7   C2  H6   106.87  3.000
 JXB  H7   C2  C3   109.83  3.000
 JXB  H6   C2  C3   109.07  3.000
 JXB  H7   C2  C1   109.81  3.000
 JXB  H6   C2  C1   110.03  3.000
 JXB  C3   C2  C1   111.13  3.000
 JXB  H9   C3  H8   106.89  3.000
 JXB  H9   C3  N3   106.93  3.000
 JXB  H8   C3  N3   108.64  3.000
 JXB  H9   C3  C2   110.61  3.000
 JXB  H8   C3  C2   111.26  3.000
 JXB  N3   C3  C2   112.27  3.000
 JXB  BR   C4  N4   123.57  3.000
 JXB  BR   C4  N3   121.71  3.000
 JXB  N4   C4  N3   114.72  3.000
 JXB  N4   C5  C8   110.80  3.000
 JXB  C8   C5  C6   116.46  3.000
 JXB  N4   C5  C6   132.74  3.000
 JXB  N6   C6  N5   119.45  3.000
 JXB  N6   C6  C5   117.67  3.000
 JXB  N5   C6  C5   122.88  3.000
 JXB  H10  C7  N7   116.14  3.000
 JXB  H10  C7  N6   115.39  3.000
 JXB  N7   C7  N6   128.46  3.000
 JXB  N7   C8  N3   127.81  3.000
 JXB  N3   C8  C5   105.65  3.000
 JXB  N7   C8  C5   126.54  3.000
 JXB  N2   N1  N    174.52  3.000
 JXB  N1   N2  C    116.40  3.000
 JXB  C8   N3  C4   105.10  3.000
 JXB  C8   N3  C3   125.57  3.000
 JXB  C4   N3  C3   129.20  3.000
 JXB  C5   N4  C4   103.72  3.000
 JXB  C7   N6  C6   119.28  3.000
 JXB  C8   N7  C7   111.59  3.000
 JXB  H12  N5  H11  118.32  3.000
 JXB  H12  N5  C6   121.25  3.000
 JXB  H11  N5  C6   120.30  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
 JXB  CONST_01  C6   C5  N4  C4   180.00   0.0  0
 JXB  CONST_02  C8   C5  N4  C4     0.00   0.0  0
 JXB  CONST_03  C5   C8  N3  C4     0.00   0.0  0
 JXB  CONST_04  N7   C8  N3  C4   180.00   0.0  0
 JXB  CONST_05  C7   N6  C6  C5     0.00   0.0  0
 JXB  CONST_06  N3   C4  N4  C5     0.00   0.0  0
 JXB  CONST_07  C7   N7  C8  C5     0.00   0.0  0
 JXB  CONST_08  N7   C7  N6  C6     0.00   0.0  0
 JXB  CONST_09  N7   C8  C5  C6     0.00   0.0  0
 JXB  CONST_10  N3   C8  C5  C6   180.00   0.0  0
 JXB  CONST_11  N3   C8  N7  C7   180.00   0.0  0
 JXB  CONST_12  N6   C6  C5  C8     0.00   0.0  0
 JXB  CONST_13  N6   C7  N7  C8     0.00   0.0  0
 JXB  CONST_14  N4   C4  N3  C8     0.00   0.0  0
 JXB  CONST_15  N4   C5  C8  N3     0.00   0.0  0
 JXB  CONST_16  N6   C6  C5  N4   180.00   0.0  0
 JXB  CONST_17  N7   C8  C5  N4   180.00   0.0  0
 JXB  CONST_18  N4   C4  N3  C3   180.00   0.0  0
 JXB  CONST_19  C5   C8  N3  C3   180.00   0.0  0
 JXB  CONST_20  N7   C8  N3  C3     0.00   0.0  0
 JXB  CONST_21  BR   C4  N4  C5   180.00   0.0  0
 JXB  CONST_22  N5   C6  N6  C7   180.00   0.0  0
 JXB  CONST_23  N5   C6  C5  C8   180.00   0.0  0
 JXB  CONST_24  BR   C4  N3  C8   180.00   0.0  0
 JXB  CONST_25  N5   C6  C5  N4     0.00   0.0  0
 JXB  CONST_26  H10  C7  N6  C6   180.00   0.0  0
 JXB  CONST_27  H11  N5  C6  C5   180.00   0.0  0
 JXB  CONST_28  H12  N5  C6  C5     0.00   0.0  0
 JXB  Var_01    C4   N3  C3  C2    86.55  30.0  2
 JXB  Var_02    N3   C3  C2  C1  -178.43  30.0  3
 JXB  Var_03    C3   C2  C1  C   -178.46  30.0  3
 JXB  Var_04    N2   C   C1  C2   178.31  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
 JXB  plan-1  C3   0.020
 JXB  plan-1  C4   0.020
 JXB  plan-1  C5   0.020
 JXB  plan-1  C6   0.020
 JXB  plan-1  C7   0.020
 JXB  plan-1  C8   0.020
 JXB  plan-1  N3   0.020
 JXB  plan-1  N4   0.020
 JXB  plan-1  N6   0.020
 JXB  plan-1  N7   0.020
 JXB  plan-1  BR   0.020
 JXB  plan-1  H10  0.020
 JXB  plan-1  N5   0.020
 JXB  plan-2  C6   0.020
 JXB  plan-2  H11  0.020
 JXB  plan-2  H12  0.020
 JXB  plan-2  N5   0.020
 JXB  plan-3  N    0.020
 JXB  plan-3  C    0.020
 JXB  plan-3  N1   0.020
 JXB  plan-3  N2   0.020

