# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:56:36 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 9-(2-azidoethyl)-8-bromanyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCN=[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
 JYK  JYK  9-(2-azidoethyl)-8-bromanyl-purin-6-amine  ligand  23  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JYK
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
 JYK  N   N   N     -1  -0.208   4.9822  -1.4808  -0.0898
 JYK  C   C   CH2    0  -0.319   1.7518  -1.6696   0.6025
 JYK  C1  C   CH2    0  -0.342   1.0959  -1.1196  -0.6634
 JYK  C2  C   CR5    0   0.282  -0.2221   0.9551  -0.0009
 JYK  C3  C   CR56   0   0.005  -2.1659   0.1767   0.1333
 JYK  C4  C   CR6    0   0.461  -3.5349  -0.1093   0.2955
 JYK  C5  C   CR16   0   0.045  -3.0433  -2.2817  -0.2897
 JYK  C6  C   CR56   0   0.503  -1.3585  -0.8805  -0.2483
 JYK  N1  N   N      1   0.359   3.9615  -1.9156   0.0860
 JYK  N2  N   N      0  -0.355   2.9054  -2.4986   0.2619
 JYK  N3  N   NR5    0  -0.514  -0.0954  -0.3639  -0.3432
 JYK  N4  N   N      0  -0.423  -1.4282   1.3234   0.2830
 JYK  N6  N   N      0  -0.471  -3.9367  -1.3660   0.0730
 JYK  N7  N   N      0  -0.457  -1.7418  -2.1327  -0.4726
 JYK  BR  BR  BR     0   0.043   1.2395   2.0938   0.0363
 JYK  H2  H   HCH2   0   0.265   2.0242  -0.8588   1.2832
 JYK  H3  H   HCH2   0   0.279   1.0515  -2.3181   1.1256
 JYK  H4  H   HCH2   0   0.289   1.7826  -0.4876  -1.2258
 JYK  H5  H   HCH2   0   0.297   0.8004  -1.9402  -1.3151
 JYK  H6  H   HCR6   0   0.256  -3.4376  -3.2787  -0.4538
 JYK  H7  H   HNH2   0   0.406  -5.4011   0.5686   0.7326
 JYK  H8  H   HNH2   0   0.414  -4.1636   1.7691   0.7949
 JYK  N5  N   NH2    0  -0.814  -4.4267   0.8079   0.6653

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
 JYK  N5  C4  single    1.332  0.020  1.332
 JYK  C4  N6  aromatic  1.338  0.020  1.338
 JYK  C4  C3  aromatic  1.408  0.020  1.408
 JYK  N   N1  double    1.123  0.020  1.123
 JYK  N6  C5  aromatic  1.330  0.020  1.330
 JYK  N4  C3  aromatic  1.372  0.020  1.372
 JYK  N4  C2  aromatic  1.293  0.020  1.293
 JYK  C3  C6  aromatic  1.384  0.020  1.384
 JYK  C5  N7  aromatic  1.323  0.020  1.323
 JYK  N1  N2  double    1.219  0.020  1.219
 JYK  C2  BR  single    1.853  0.020  1.853
 JYK  C2  N3  aromatic  1.369  0.020  1.369
 JYK  C6  N7  aromatic  1.329  0.020  1.329
 JYK  C6  N3  aromatic  1.368  0.020  1.368
 JYK  N3  C1  single    1.447  0.020  1.447
 JYK  N2  C   single    1.461  0.020  1.461
 JYK  C   C1  single    1.528  0.020  1.528
 JYK  C   H2  single    0.970  0.020  1.090
 JYK  C   H3  single    0.970  0.020  1.090
 JYK  C1  H4  single    0.970  0.020  1.090
 JYK  C1  H5  single    0.970  0.020  1.090
 JYK  C5  H6  single    0.930  0.020  1.080
 JYK  N5  H7  single    0.860  0.020  1.020
 JYK  N5  H8  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
 JYK  H3  C   H2  107.64  3.000
 JYK  H3  C   N2  106.38  3.000
 JYK  H2  C   N2  111.67  3.000
 JYK  H3  C   C1  109.66  3.000
 JYK  H2  C   C1  110.84  3.000
 JYK  N2  C   C1  110.49  3.000
 JYK  H5  C1  H4  107.41  3.000
 JYK  H5  C1  N3  107.62  3.000
 JYK  H4  C1  N3  109.28  3.000
 JYK  H5  C1  C   109.94  3.000
 JYK  H4  C1  C   111.46  3.000
 JYK  N3  C1  C   110.99  3.000
 JYK  BR  C2  N4  123.81  3.000
 JYK  BR  C2  N3  121.61  3.000
 JYK  N4  C2  N3  114.58  3.000
 JYK  N4  C3  C6  110.79  3.000
 JYK  C6  C3  C4  116.35  3.000
 JYK  N4  C3  C4  132.86  3.000
 JYK  N6  C4  N5  119.47  3.000
 JYK  N6  C4  C3  117.62  3.000
 JYK  N5  C4  C3  122.90  3.000
 JYK  H6  C5  N7  116.13  3.000
 JYK  H6  C5  N6  115.46  3.000
 JYK  N7  C5  N6  128.41  3.000
 JYK  N7  C6  N3  127.63  3.000
 JYK  N3  C6  C3  105.63  3.000
 JYK  N7  C6  C3  126.75  3.000
 JYK  N2  N1  N   174.20  3.000
 JYK  N1  N2  C   116.51  3.000
 JYK  C6  N3  C2  105.14  3.000
 JYK  C6  N3  C1  125.34  3.000
 JYK  C2  N3  C1  129.42  3.000
 JYK  C3  N4  C2  103.87  3.000
 JYK  C5  N6  C4  119.36  3.000
 JYK  C6  N7  C5  111.51  3.000
 JYK  H8  N5  H7  118.21  3.000
 JYK  H8  N5  C4  121.29  3.000
 JYK  H7  N5  C4  120.23  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
 JYK  CONST_01  C4  C3  N4  C2  180.00   0.0  0
 JYK  CONST_02  C6  C3  N4  C2    0.00   0.0  0
 JYK  CONST_03  C3  C6  N3  C2    0.00   0.0  0
 JYK  CONST_04  N7  C6  N3  C2  180.00   0.0  0
 JYK  CONST_05  C5  N6  C4  C3    0.00   0.0  0
 JYK  CONST_06  N3  C2  N4  C3    0.00   0.0  0
 JYK  CONST_07  C5  N7  C6  C3    0.00   0.0  0
 JYK  CONST_08  N7  C5  N6  C4    0.00   0.0  0
 JYK  CONST_09  N7  C6  C3  C4    0.00   0.0  0
 JYK  CONST_10  N3  C6  C3  C4  180.00   0.0  0
 JYK  CONST_11  N3  C6  N7  C5  180.00   0.0  0
 JYK  CONST_12  N6  C4  C3  C6    0.00   0.0  0
 JYK  CONST_13  N6  C5  N7  C6    0.00   0.0  0
 JYK  CONST_14  N4  C2  N3  C6    0.00   0.0  0
 JYK  CONST_15  N4  C3  C6  N3    0.00   0.0  0
 JYK  CONST_16  N6  C4  C3  N4  180.00   0.0  0
 JYK  CONST_17  N7  C6  C3  N4  180.00   0.0  0
 JYK  CONST_18  N4  C2  N3  C1  180.00   0.0  0
 JYK  CONST_19  C3  C6  N3  C1  180.00   0.0  0
 JYK  CONST_20  N7  C6  N3  C1    0.00   0.0  0
 JYK  CONST_21  BR  C2  N4  C3  180.00   0.0  0
 JYK  CONST_22  N5  C4  N6  C5  180.00   0.0  0
 JYK  CONST_23  N5  C4  C3  C6  180.00   0.0  0
 JYK  CONST_24  BR  C2  N3  C6  180.00   0.0  0
 JYK  CONST_25  N5  C4  C3  N4    0.00   0.0  0
 JYK  CONST_26  H6  C5  N6  C4  180.00   0.0  0
 JYK  CONST_27  H7  N5  C4  C3  180.00   0.0  0
 JYK  CONST_28  H8  N5  C4  C3    0.00   0.0  0
 JYK  Var_01    C2  N3  C1  C    86.18  30.0  2
 JYK  Var_02    N3  C1  C   N2  176.51  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
 JYK  plan-1  C1  0.020
 JYK  plan-1  C2  0.020
 JYK  plan-1  C3  0.020
 JYK  plan-1  C4  0.020
 JYK  plan-1  C5  0.020
 JYK  plan-1  C6  0.020
 JYK  plan-1  N3  0.020
 JYK  plan-1  N4  0.020
 JYK  plan-1  N6  0.020
 JYK  plan-1  N7  0.020
 JYK  plan-1  BR  0.020
 JYK  plan-1  H6  0.020
 JYK  plan-1  N5  0.020
 JYK  plan-2  C4  0.020
 JYK  plan-2  H7  0.020
 JYK  plan-2  H8  0.020
 JYK  plan-2  N5  0.020
 JYK  plan-3  N   0.020
 JYK  plan-3  C   0.020
 JYK  plan-3  N1  0.020
 JYK  plan-3  N2  0.020

