# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:15:50 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-(6-azanyl-8-bromanyl-purin-9-yl)propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCO)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
 JYT  JYT  3-(6-azanyl-8-bromanyl-purin-9-yl)propan-1-ol  ligand  25  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_JYT
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
 JYT  C2   C   CR16  0   0.043   2.9244   2.1361   0.3889
 JYT  C4   C   CR56  0   0.498   1.1879   0.7976   0.3500
 JYT  C5   C   CR56  0   0.004   1.9429  -0.2669  -0.1126
 JYT  C6   C   CR6   0   0.459   3.3136  -0.0204  -0.3168
 JYT  C8   C   CR5   0   0.280  -0.0188  -0.9839   0.0721
 JYT  CAE  C   CH2   0  -0.141  -3.1481   2.5396   0.1283
 JYT  CAF  C   CH2   0  -0.468  -1.9636   1.7084  -0.3255
 JYT  N1   N   N     0  -0.472   3.7702   1.2085  -0.0512
 JYT  N3   N   N     0  -0.457   1.6269   2.0239   0.6169
 JYT  N6   N   NH2   0  -0.816   4.1577  -0.9504  -0.7618
 JYT  N7   N   N     0  -0.426   1.1612  -1.3807  -0.2804
 JYT  N9   N   NR5   0  -0.509  -0.0863   0.3196   0.4755
 JYT  OAB  O   OH1   0  -0.671  -3.7826   3.0757  -1.0104
 JYT  BR8  BR  BR    0   0.037  -1.5162  -2.0767   0.0551
 JYT  H1   H   HCR6  0   0.254   3.3607   3.1099   0.5839
 JYT  H2   H   HCH2  0   0.199  -3.8323   1.9082   0.7104
 JYT  H3   H   HCH2  0   0.196  -2.7982   3.3317   0.8039
 JYT  H4   H   HCH2  0   0.239  -2.3092   0.9123  -0.9899
 JYT  H5   H   HCH2  0   0.246  -1.2670   2.3304  -0.8936
 JYT  H6   H   HCH2  0   0.279  -0.8734   1.8887   1.5322
 JYT  H7   H   HCH2  0   0.276  -1.9074   0.4759   1.4610
 JYT  H8   H   HNH2  0   0.406   5.1342  -0.7373  -0.8720
 JYT  H9   H   HNH2  0   0.413   3.8507  -1.8889  -0.9469
 JYT  H10  H   HOH1  0   0.455  -4.5619   3.5571  -0.7191
 JYT  CAG  C   CH2   0  -0.325  -1.2407   1.1045   0.8707

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
 JYT  N6   C6   single    1.332  0.020  1.332
 JYT  C6   N1   aromatic  1.338  0.020  1.338
 JYT  C6   C5   aromatic  1.408  0.020  1.408
 JYT  N1   C2   aromatic  1.330  0.020  1.330
 JYT  N7   C5   aromatic  1.371  0.020  1.371
 JYT  N7   C8   aromatic  1.294  0.020  1.294
 JYT  C5   C4   aromatic  1.385  0.020  1.385
 JYT  C2   N3   aromatic  1.322  0.020  1.322
 JYT  C8   BR8  single    1.854  0.020  1.854
 JYT  C8   N9   aromatic  1.366  0.020  1.366
 JYT  C4   N3   aromatic  1.330  0.020  1.330
 JYT  C4   N9   aromatic  1.367  0.020  1.367
 JYT  CAF  CAE  single    1.517  0.020  1.517
 JYT  CAF  CAG  single    1.523  0.020  1.523
 JYT  N9   CAG  single    1.451  0.020  1.451
 JYT  CAE  OAB  single    1.409  0.020  1.409
 JYT  C2   H1   single    0.930  0.020  1.080
 JYT  CAE  H2   single    0.970  0.020  1.090
 JYT  CAE  H3   single    0.970  0.020  1.090
 JYT  CAF  H4   single    0.970  0.020  1.090
 JYT  CAF  H5   single    0.970  0.020  1.090
 JYT  CAG  H6   single    0.970  0.020  1.090
 JYT  CAG  H7   single    0.970  0.020  1.090
 JYT  N6   H8   single    0.860  0.020  1.020
 JYT  N6   H9   single    0.860  0.020  1.020
 JYT  OAB  H10  single    0.850  0.020  0.980

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
 JYT  H1   C2   N3   116.10  3.000
 JYT  H1   C2   N1   115.45  3.000
 JYT  N3   C2   N1   128.45  3.000
 JYT  N9   C4   N3   127.73  3.000
 JYT  N9   C4   C5   105.67  3.000
 JYT  N3   C4   C5   126.60  3.000
 JYT  N7   C5   C6   132.82  3.000
 JYT  N7   C5   C4   110.77  3.000
 JYT  C6   C5   C4   116.41  3.000
 JYT  N6   C6   N1   119.43  3.000
 JYT  N1   C6   C5   117.68  3.000
 JYT  N6   C6   C5   122.90  3.000
 JYT  BR8  C8   N9   121.68  3.000
 JYT  N9   C8   N7   114.72  3.000
 JYT  BR8  C8   N7   123.60  3.000
 JYT  H3   CAE  H2   106.69  3.000
 JYT  H3   CAE  OAB  111.48  3.000
 JYT  H2   CAE  OAB  111.50  3.000
 JYT  H3   CAE  CAF  109.30  3.000
 JYT  H2   CAE  CAF  109.28  3.000
 JYT  OAB  CAE  CAF  108.56  3.000
 JYT  H5   CAF  H4   107.46  3.000
 JYT  H5   CAF  CAG  109.36  3.000
 JYT  H4   CAF  CAG  109.81  3.000
 JYT  H5   CAF  CAE  109.96  3.000
 JYT  H4   CAF  CAE  109.52  3.000
 JYT  CAG  CAF  CAE  110.68  3.000
 JYT  C6   N1   C2   119.29  3.000
 JYT  C4   N3   C2   111.57  3.000
 JYT  H9   N6   H8   118.33  3.000
 JYT  H9   N6   C6   121.33  3.000
 JYT  H8   N6   C6   120.26  3.000
 JYT  C8   N7   C5   103.74  3.000
 JYT  CAG  N9   C8   129.49  3.000
 JYT  CAG  N9   C4   125.29  3.000
 JYT  C8   N9   C4   105.10  3.000
 JYT  H10  OAB  CAE  108.10  3.000
 JYT  H7   CAG  H6   107.00  3.000
 JYT  H7   CAG  N9   108.80  3.000
 JYT  H6   CAG  N9   106.65  3.000
 JYT  H7   CAG  CAF  111.33  3.000
 JYT  H6   CAG  CAF  110.58  3.000
 JYT  N9   CAG  CAF  112.24  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
 JYT  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 JYT  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 JYT  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 JYT  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 JYT  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 JYT  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 JYT  CONST_07  N7   C8   N9   C4      0.00   0.0  0
 JYT  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 JYT  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 JYT  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 JYT  CONST_11  C8   N7   C5   C6    180.00   0.0  0
 JYT  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 JYT  CONST_13  N9   C4   C5   C6    180.00   0.0  0
 JYT  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 JYT  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 JYT  CONST_16  N7   C5   C4   N3    180.00   0.0  0
 JYT  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 JYT  CONST_18  N6   C6   N1   C2    180.00   0.0  0
 JYT  CONST_19  N6   C6   C5   C4    180.00   0.0  0
 JYT  CONST_20  BR8  C8   N9   C4    180.00   0.0  0
 JYT  CONST_21  BR8  C8   N7   C5    180.00   0.0  0
 JYT  CONST_22  CAG  N9   C4   C5    180.00   0.0  0
 JYT  CONST_23  N7   C8   N9   CAG   180.00   0.0  0
 JYT  CONST_24  N3   C4   N9   CAG     0.00   0.0  0
 JYT  CONST_25  N7   C5   C6   N6      0.00   0.0  0
 JYT  CONST_26  H1   C2   N3   C4    180.00   0.0  0
 JYT  CONST_27  H8   N6   C6   C5    180.00   0.0  0
 JYT  CONST_28  H9   N6   C6   C5      0.00   0.0  0
 JYT  Var_01    CAF  CAG  N9   C4     91.00  30.0  2
 JYT  Var_02    N9   CAG  CAF  CAE  -179.02  30.0  3
 JYT  Var_03    OAB  CAE  CAF  CAG   179.99  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
 JYT  plan-1  C2   0.020
 JYT  plan-1  C4   0.020
 JYT  plan-1  C5   0.020
 JYT  plan-1  C6   0.020
 JYT  plan-1  C8   0.020
 JYT  plan-1  N1   0.020
 JYT  plan-1  N3   0.020
 JYT  plan-1  N6   0.020
 JYT  plan-1  N7   0.020
 JYT  plan-1  N9   0.020
 JYT  plan-1  BR8  0.020
 JYT  plan-1  H1   0.020
 JYT  plan-1  CAG  0.020
 JYT  plan-2  C6   0.020
 JYT  plan-2  N6   0.020
 JYT  plan-2  H8   0.020
 JYT  plan-2  H9   0.020

