# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:43:58 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 9-(3-azidopropyl)-8-bromanyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCN=[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
 JYE  JYE  9-(3-azidopropyl)-8-bromanyl-purin-6-amine  ligand  26  17  .  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_JYE
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
 JYE  C2   C   CR16   0   0.043   2.8204   2.7076   0.3668
 JYE  C4   C   CR56   0   0.500   1.4624   0.9867   0.4176
 JYE  C5   C   CR56   0   0.004   2.3805   0.1678  -0.2176
 JYE  C6   C   CR6    0   0.459   3.6130   0.7549  -0.5598
 JYE  C8   C   CR5    0   0.280   0.6861  -1.0190   0.1223
 JYE  CAE  C   CH2    0  -0.452  -1.8599   1.1391   0.1539
 JYE  CAF  C   CH2    0  -0.308  -3.1649   1.5970   0.7896
 JYE  N1   N   N      0  -0.471   3.7958   2.0425  -0.2463
 JYE  N3   N   N      0  -0.457   1.6292   2.2671   0.7344
 JYE  N6   N   NH2    0  -0.815   4.5875   0.0849  -1.1732
 JYE  N7   N   N      0  -0.425   1.8703  -1.0922  -0.3931
 JYE  N9   N   NR5    0  -0.511   0.3652   0.2032   0.6440
 JYE  NAA  N   N     -1  -0.223  -5.2895   0.6598  -1.5672
 JYE  NAH  N   N      0  -0.360  -4.1020   2.1395  -0.1997
 JYE  NAL  N   N      1   0.356  -4.6915   1.3272  -0.8878
 JYE  BR8  BR  BR     0   0.039  -0.5011  -2.4417   0.1698
 JYE  H1   H   HCR6   0   0.254   3.0352   3.7468   0.5907
 JYE  H2   H   HCH2   0   0.248  -2.0530   0.3355  -0.5617
 JYE  H3   H   HCH2   0   0.258  -1.4123   1.9664  -0.4006
 JYE  H4   H   HCH2   0   0.257  -3.6282   0.7810   1.3520
 JYE  H5   H   HCH2   0   0.265  -2.9786   2.4088   1.4904
 JYE  H6   H   HCH2   0   0.285  -0.6470   1.4587   1.9152
 JYE  H7   H   HCH2   0   0.280  -1.3144  -0.1562   1.8103
 JYE  H8   H   HNH2   0   0.406   5.4433   0.5499  -1.4226
 JYE  H9   H   HNH2   0   0.413   4.4671  -0.8733  -1.4511
 JYE  CAG  C   CH2    0  -0.327  -0.8863   0.6543   1.2201

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
 JYE  N6   C6   single    1.332  0.020  1.332
 JYE  C6   N1   aromatic  1.338  0.020  1.338
 JYE  C6   C5   aromatic  1.407  0.020  1.407
 JYE  N1   C2   aromatic  1.330  0.020  1.330
 JYE  N7   C5   aromatic  1.371  0.020  1.371
 JYE  N7   C8   aromatic  1.294  0.020  1.294
 JYE  C5   C4   aromatic  1.385  0.020  1.385
 JYE  C2   N3   aromatic  1.322  0.020  1.322
 JYE  C8   BR8  single    1.854  0.020  1.854
 JYE  C8   N9   aromatic  1.367  0.020  1.367
 JYE  C4   N3   aromatic  1.330  0.020  1.330
 JYE  C4   N9   aromatic  1.367  0.020  1.367
 JYE  N9   CAG  single    1.450  0.020  1.450
 JYE  CAE  CAG  single    1.523  0.020  1.523
 JYE  CAE  CAF  single    1.522  0.020  1.522
 JYE  CAF  NAH  single    1.467  0.020  1.467
 JYE  NAH  NAL  double    1.217  0.020  1.217
 JYE  NAL  NAA  double    1.125  0.020  1.125
 JYE  C2   H1   single    0.930  0.020  1.080
 JYE  CAE  H2   single    0.970  0.020  1.090
 JYE  CAE  H3   single    0.970  0.020  1.090
 JYE  CAF  H4   single    0.970  0.020  1.090
 JYE  CAF  H5   single    0.970  0.020  1.090
 JYE  CAG  H6   single    0.970  0.020  1.090
 JYE  CAG  H7   single    0.970  0.020  1.090
 JYE  N6   H8   single    0.860  0.020  1.020
 JYE  N6   H9   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
 JYE  H1   C2   N3   116.12  3.000
 JYE  H1   C2   N1   115.41  3.000
 JYE  N3   C2   N1   128.47  3.000
 JYE  N9   C4   N3   127.82  3.000
 JYE  N9   C4   C5   105.62  3.000
 JYE  N3   C4   C5   126.56  3.000
 JYE  N7   C5   C6   132.71  3.000
 JYE  N7   C5   C4   110.83  3.000
 JYE  C6   C5   C4   116.46  3.000
 JYE  N6   C6   N1   119.47  3.000
 JYE  N1   C6   C5   117.66  3.000
 JYE  N6   C6   C5   122.87  3.000
 JYE  BR8  C8   N9   121.74  3.000
 JYE  N9   C8   N7   114.68  3.000
 JYE  BR8  C8   N7   123.58  3.000
 JYE  H3   CAE  H2   107.28  3.000
 JYE  H3   CAE  CAG  109.55  3.000
 JYE  H2   CAE  CAG  109.70  3.000
 JYE  H3   CAE  CAF  109.61  3.000
 JYE  H2   CAE  CAF  110.06  3.000
 JYE  CAG  CAE  CAF  110.57  3.000
 JYE  H5   CAF  H4   107.33  3.000
 JYE  H5   CAF  NAH  105.53  3.000
 JYE  H4   CAF  NAH  110.61  3.000
 JYE  H5   CAF  CAE  110.27  3.000
 JYE  H4   CAF  CAE  110.70  3.000
 JYE  NAH  CAF  CAE  112.17  3.000
 JYE  C6   N1   C2   119.28  3.000
 JYE  C4   N3   C2   111.57  3.000
 JYE  H9   N6   H8   118.32  3.000
 JYE  H9   N6   C6   121.28  3.000
 JYE  H8   N6   C6   120.28  3.000
 JYE  C8   N7   C5   103.75  3.000
 JYE  CAG  N9   C8   129.24  3.000
 JYE  CAG  N9   C4   125.47  3.000
 JYE  C8   N9   C4   105.11  3.000
 JYE  NAL  NAH  CAF  116.36  3.000
 JYE  NAH  NAL  NAA  174.49  3.000
 JYE  H7   CAG  H6   106.84  3.000
 JYE  H7   CAG  N9   108.83  3.000
 JYE  H6   CAG  N9   107.07  3.000
 JYE  H7   CAG  CAE  111.39  3.000
 JYE  H6   CAG  CAE  110.61  3.000
 JYE  N9   CAG  CAE  111.88  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
 JYE  CONST_01  C5   C6   N1   C2     0.00   0.0  0
 JYE  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 JYE  CONST_03  N9   C4   N3   C2   180.00   0.0  0
 JYE  CONST_04  N1   C6   C5   C4     0.00   0.0  0
 JYE  CONST_05  C8   N7   C5   C4     0.00   0.0  0
 JYE  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 JYE  CONST_07  N7   C8   N9   C4     0.00   0.0  0
 JYE  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 JYE  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 JYE  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 JYE  CONST_11  C8   N7   C5   C6   180.00   0.0  0
 JYE  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 JYE  CONST_13  N9   C4   C5   C6   180.00   0.0  0
 JYE  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 JYE  CONST_15  N7   C5   C6   N1   180.00   0.0  0
 JYE  CONST_16  N7   C5   C4   N3   180.00   0.0  0
 JYE  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 JYE  CONST_18  N6   C6   N1   C2   180.00   0.0  0
 JYE  CONST_19  N6   C6   C5   C4   180.00   0.0  0
 JYE  CONST_20  BR8  C8   N9   C4   180.00   0.0  0
 JYE  CONST_21  BR8  C8   N7   C5   180.00   0.0  0
 JYE  CONST_22  CAG  N9   C4   C5   180.00   0.0  0
 JYE  CONST_23  N7   C8   N9   CAG  180.00   0.0  0
 JYE  CONST_24  N3   C4   N9   CAG    0.00   0.0  0
 JYE  CONST_25  N7   C5   C6   N6     0.00   0.0  0
 JYE  CONST_26  H1   C2   N3   C4   180.00   0.0  0
 JYE  CONST_27  H8   N6   C6   C5   180.00   0.0  0
 JYE  CONST_28  H9   N6   C6   C5     0.00   0.0  0
 JYE  Var_01    CAE  CAG  N9   C4    89.88  30.0  2
 JYE  Var_02    N9   CAG  CAE  CAF  179.65  30.0  3
 JYE  Var_03    NAH  CAF  CAE  CAG  176.90  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
 JYE  plan-1  C2   0.020
 JYE  plan-1  C4   0.020
 JYE  plan-1  C5   0.020
 JYE  plan-1  C6   0.020
 JYE  plan-1  C8   0.020
 JYE  plan-1  N1   0.020
 JYE  plan-1  N3   0.020
 JYE  plan-1  N6   0.020
 JYE  plan-1  N7   0.020
 JYE  plan-1  N9   0.020
 JYE  plan-1  BR8  0.020
 JYE  plan-1  H1   0.020
 JYE  plan-1  CAG  0.020
 JYE  plan-2  C6   0.020
 JYE  plan-2  N6   0.020
 JYE  plan-2  H8   0.020
 JYE  plan-2  H9   0.020
 JYE  plan-3  CAF  0.020
 JYE  plan-3  NAA  0.020
 JYE  plan-3  NAH  0.020
 JYE  plan-3  NAL  0.020

