# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:54:34 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 9-(3-azanylpropyl)-8-bromanyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCn1c(Br)nc2c(N)ncnc12
#
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
 JXK  JXK  9-(3-azanylpropyl)-8-bromanyl-purin-6-amine  ligand  26  15  .  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_JXK
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
 JXK  C7   C   CR6   0   0.455  -3.3140   0.0591  -0.3181
 JXK  C6   C   CR16  0   0.043  -2.9580  -2.0965   0.4073
 JXK  C5   C   CR56  0   0.497  -1.1979  -0.7895   0.3413
 JXK  C1   C   CH2   0  -0.441   1.9466  -1.7509  -0.3421
 JXK  N3   N   N     0  -0.456  -1.6570  -2.0048   0.6238
 JXK  N    N   NH2   0  -0.798   3.7803  -3.2077  -1.0429
 JXK  C    C   CH2   0  -0.278   3.1010  -2.6341   0.1078
 JXK  C3   C   CR5   0   0.280   0.0368   0.9675   0.0384
 JXK  C4   C   CR56  0   0.004  -1.9380   0.2833  -0.1271
 JXK  N1   N   NR5   0  -0.509   0.0850  -0.3326   0.4540
 JXK  N2   N   N     0  -0.427  -1.1385   1.3817  -0.3110
 JXK  N4   N   N     0  -0.471  -3.7904  -1.1581  -0.0358
 JXK  N5   N   NH2   0  -0.815  -4.1435   0.9965  -0.7792
 JXK  BR   BR  BR    0   0.036   1.5520   2.0356   0.0048
 JXK  H8   H   HCR6  0   0.254  -3.4097  -3.0603   0.6165
 JXK  H4   H   HCH2  0   0.233   2.3299  -0.9687  -1.0017
 JXK  H5   H   HCH2  0   0.238   1.2324  -2.3409  -0.9246
 JXK  H11  H   HNH2  0   0.349   4.5910  -3.7265  -0.7306
 JXK  H1   H   HNH2  0   0.340   3.1748  -3.8906  -1.4817
 JXK  H2   H   HCH2  0   0.222   3.8204  -2.0266   0.6634
 JXK  H3   H   HCH2  0   0.197   2.7217  -3.3849   0.8161
 JXK  H6   H   HCH2  0   0.276   0.8499  -1.9126   1.5097
 JXK  H7   H   HCH2  0   0.274   1.9039  -0.5148   1.4405
 JXK  H9   H   HNH2  0   0.405  -5.1326   0.8173  -0.8112
 JXK  H10  H   HNH2  0   0.412  -3.8335   1.9449  -0.8993
 JXK  C2   C   CH2   0  -0.322   1.2289  -1.1333   0.8488

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
 JXK  N5  C7   single    1.334  0.020  1.334
 JXK  C7  N4   aromatic  1.337  0.020  1.337
 JXK  C7  C4   aromatic  1.407  0.020  1.407
 JXK  N4  C6   aromatic  1.330  0.020  1.330
 JXK  N2  C4   aromatic  1.371  0.020  1.371
 JXK  N2  C3   aromatic  1.294  0.020  1.294
 JXK  C4  C5   aromatic  1.385  0.020  1.385
 JXK  C6  N3   aromatic  1.322  0.020  1.322
 JXK  C3  BR   single    1.854  0.020  1.854
 JXK  C3  N1   aromatic  1.366  0.020  1.366
 JXK  C5  N3   aromatic  1.330  0.020  1.330
 JXK  C5  N1   aromatic  1.367  0.020  1.367
 JXK  N1  C2   single    1.451  0.020  1.451
 JXK  C1  C    single    1.522  0.020  1.522
 JXK  C1  C2   single    1.521  0.020  1.521
 JXK  C   N    single    1.454  0.020  1.454
 JXK  C6  H8   single    0.930  0.020  1.080
 JXK  C1  H4   single    0.970  0.020  1.090
 JXK  C1  H5   single    0.970  0.020  1.090
 JXK  N   H11  single    0.890  0.020  1.040
 JXK  N   H1   single    0.890  0.020  1.040
 JXK  C   H2   single    0.970  0.020  1.090
 JXK  C   H3   single    0.970  0.020  1.090
 JXK  C2  H6   single    0.970  0.020  1.090
 JXK  C2  H7   single    0.970  0.020  1.090
 JXK  N5  H9   single    0.860  0.020  1.020
 JXK  N5  H10  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
 JXK  N5   C7  N4   119.41  3.000
 JXK  N4   C7  C4   117.70  3.000
 JXK  N5   C7  C4   122.89  3.000
 JXK  H8   C6  N4   115.49  3.000
 JXK  H8   C6  N3   116.10  3.000
 JXK  N4   C6  N3   128.42  3.000
 JXK  N1   C5  C4   105.70  3.000
 JXK  N1   C5  N3   127.75  3.000
 JXK  C4   C5  N3   126.55  3.000
 JXK  H5   C1  H4   107.07  3.000
 JXK  H5   C1  C2   109.13  3.000
 JXK  H4   C1  C2   110.33  3.000
 JXK  H5   C1  C    109.85  3.000
 JXK  H4   C1  C    109.14  3.000
 JXK  C2   C1  C    111.23  3.000
 JXK  C5   N3  C6   111.62  3.000
 JXK  H1   N   H11  105.49  3.000
 JXK  H1   N   C    109.24  3.000
 JXK  H11  N   C    109.41  3.000
 JXK  H3   C   H2   106.20  3.000
 JXK  H3   C   N    113.67  3.000
 JXK  H2   C   N    108.30  3.000
 JXK  H3   C   C1   108.97  3.000
 JXK  H2   C   C1   109.08  3.000
 JXK  N    C   C1   110.46  3.000
 JXK  BR   C3  N2   123.57  3.000
 JXK  BR   C3  N1   121.67  3.000
 JXK  N2   C3  N1   114.76  3.000
 JXK  N2   C4  C5   110.75  3.000
 JXK  C5   C4  C7   116.42  3.000
 JXK  N2   C4  C7   132.82  3.000
 JXK  C3   N1  C2   129.49  3.000
 JXK  C2   N1  C5   125.31  3.000
 JXK  C3   N1  C5   105.07  3.000
 JXK  C4   N2  C3   103.71  3.000
 JXK  C6   N4  C7   119.30  3.000
 JXK  H10  N5  H9   117.89  3.000
 JXK  H10  N5  C7   120.84  3.000
 JXK  H9   N5  C7   119.83  3.000
 JXK  H7   C2  H6   106.97  3.000
 JXK  H7   C2  N1   108.83  3.000
 JXK  H6   C2  N1   106.58  3.000
 JXK  H7   C2  C1   111.29  3.000
 JXK  H6   C2  C1   110.39  3.000
 JXK  N1   C2  C1   112.52  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
 JXK  CONST_01  N3   C6  N4  C7     0.00   0.0  0
 JXK  CONST_02  C3   N2  C4  C7   180.00   0.0  0
 JXK  CONST_03  N3   C5  C4  C7     0.00   0.0  0
 JXK  CONST_04  N1   C5  C4  C7   180.00   0.0  0
 JXK  CONST_05  C4   C7  N4  C6     0.00   0.0  0
 JXK  CONST_06  C4   C5  N3  C6     0.00   0.0  0
 JXK  CONST_07  N1   C5  N3  C6   180.00   0.0  0
 JXK  CONST_08  N4   C7  C4  C5     0.00   0.0  0
 JXK  CONST_09  C3   N2  C4  C5     0.00   0.0  0
 JXK  CONST_10  N4   C6  N3  C5     0.00   0.0  0
 JXK  CONST_11  N2   C3  N1  C5     0.00   0.0  0
 JXK  CONST_12  N2   C4  C5  N3   180.00   0.0  0
 JXK  CONST_13  C3   N1  C5  N3   180.00   0.0  0
 JXK  CONST_14  C4   C5  N1  C3     0.00   0.0  0
 JXK  CONST_15  N1   C3  N2  C4     0.00   0.0  0
 JXK  CONST_16  N2   C4  C5  N1     0.00   0.0  0
 JXK  CONST_17  N4   C7  C4  N2   180.00   0.0  0
 JXK  CONST_18  N5   C7  N4  C6   180.00   0.0  0
 JXK  CONST_19  N5   C7  C4  C5   180.00   0.0  0
 JXK  CONST_20  BR   C3  N1  C5   180.00   0.0  0
 JXK  CONST_21  C2   N1  C5  N3     0.00   0.0  0
 JXK  CONST_22  N2   C3  N1  C2   180.00   0.0  0
 JXK  CONST_23  C4   C5  N1  C2   180.00   0.0  0
 JXK  CONST_24  BR   C3  N2  C4   180.00   0.0  0
 JXK  CONST_25  N5   C7  C4  N2     0.00   0.0  0
 JXK  CONST_26  H8   C6  N4  C7   180.00   0.0  0
 JXK  CONST_27  H9   N5  C7  C4   180.00   0.0  0
 JXK  CONST_28  H10  N5  C7  C4     0.00   0.0  0
 JXK  Var_01    C1   C2  N1  C5    91.61  30.0  2
 JXK  Var_02    N1   C2  C1  C   -177.41  30.0  3
 JXK  Var_03    C2   C1  C   N   -179.60  30.0  1
 JXK  Var_04    H11  N   C   C1   175.19  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
 JXK  plan-1  C7   0.020
 JXK  plan-1  C6   0.020
 JXK  plan-1  C5   0.020
 JXK  plan-1  N3   0.020
 JXK  plan-1  C3   0.020
 JXK  plan-1  C4   0.020
 JXK  plan-1  N1   0.020
 JXK  plan-1  N2   0.020
 JXK  plan-1  N4   0.020
 JXK  plan-1  N5   0.020
 JXK  plan-1  BR   0.020
 JXK  plan-1  H8   0.020
 JXK  plan-1  C2   0.020
 JXK  plan-2  C7   0.020
 JXK  plan-2  N5   0.020
 JXK  plan-2  H9   0.020
 JXK  plan-2  H10  0.020

