# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:31:53 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 8-bromanyl-9-pent-4-ynyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCC#C)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
 JXT  JXT  8-bromanyl-9-pent-4-ynyl-purin-6-amine  ligand  26  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 PERFECT
;

data_comp_JXT
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
 JXT  C5   C   CR56  0   0.003   2.1178  -0.0474   0.1382
 JXT  C4   C   CR56  0   0.499   1.2052  -0.9219  -0.4270
 JXT  C2   C   CR16  0   0.043   2.6614  -2.5610  -0.4702
 JXT  C6   C   CR6   0   0.459   3.4043  -0.5591   0.3897
 JXT  C8   C   CR5   0   0.280   0.3382   1.0382  -0.0832
 JXT  CAA  C   CSP1  0  -0.557  -5.0007  -2.6872   1.4310
 JXT  CAD  C   CSP   0   0.286  -4.2910  -2.2745   0.5525
 JXT  CAF  C   CH2   0  -0.583  -3.4205  -1.7589  -0.4953
 JXT  CAG  C   CH2   0  -0.438  -2.0901  -1.2459   0.0575
 JXT  N1   N   N     0  -0.472   3.6386  -1.8363   0.0677
 JXT  N3   N   N     0  -0.457   1.4231  -2.1927  -0.7518
 JXT  N7   N   N     0  -0.425   1.5500   1.1827   0.3460
 JXT  N9   N   NR5   0  -0.514   0.0512  -0.2040  -0.5763
 JXT  BR8  BR  BR    0   0.038  -0.9281   2.3917  -0.0524
 JXT  H1   H   HCR6  0   0.254   2.9188  -3.5882  -0.7043
 JXT  H2   H   HNH2  0   0.406   5.2843  -0.2346   1.0957
 JXT  H3   H   HNH2  0   0.413   4.2305   1.1293   1.1907
 JXT  H4   H   H     0   0.278  -5.6307  -3.0553   2.2076
 JXT  H5   H   HCH2  0   0.277  -3.2407  -2.5458  -1.2328
 JXT  H6   H   HCH2  0   0.276  -3.9397  -0.9547  -1.0239
 JXT  H7   H   HCH2  0   0.251  -2.2767  -0.4538   0.7854
 JXT  H8   H   HCH2  0   0.257  -1.5730  -2.0511   0.5832
 JXT  H9   H   HCH2  0   0.284  -0.9723  -1.5234  -1.7720
 JXT  H10  H   HCH2  0   0.278  -1.7140   0.0572  -1.6379
 JXT  N6   N   NH2   0  -0.815   4.3795   0.1707   0.9290
 JXT  CAH  C   CH2   0  -0.322  -1.2089  -0.7247  -1.0693

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
 JXT  N6   C6   single    1.332  0.020  1.332
 JXT  C6   N1   aromatic  1.338  0.020  1.338
 JXT  C6   C5   aromatic  1.407  0.020  1.407
 JXT  N1   C2   aromatic  1.330  0.020  1.330
 JXT  N7   C5   aromatic  1.371  0.020  1.371
 JXT  N7   C8   aromatic  1.294  0.020  1.294
 JXT  C5   C4   aromatic  1.385  0.020  1.385
 JXT  C2   N3   aromatic  1.322  0.020  1.322
 JXT  C8   BR8  single    1.854  0.020  1.854
 JXT  C8   N9   aromatic  1.367  0.020  1.367
 JXT  C4   N3   aromatic  1.330  0.020  1.330
 JXT  C4   N9   aromatic  1.367  0.020  1.367
 JXT  CAG  CAF  single    1.529  0.020  1.529
 JXT  CAG  CAH  single    1.522  0.020  1.522
 JXT  N9   CAH  single    1.450  0.020  1.450
 JXT  CAF  CAD  single    1.456  0.020  1.456
 JXT  CAD  CAA  triple    1.202  0.020  1.202
 JXT  C2   H1   single    0.929  0.020  1.085
 JXT  N6   H2   single    0.868  0.020  1.013
 JXT  N6   H3   single    0.868  0.020  1.013
 JXT  CAA  H4   single    0.913  0.020  1.066
 JXT  CAF  H5   single    0.939  0.020  1.096
 JXT  CAF  H6   single    0.939  0.020  1.096
 JXT  CAG  H7   single    0.939  0.020  1.096
 JXT  CAG  H8   single    0.939  0.020  1.096
 JXT  CAH  H9   single    0.939  0.020  1.096
 JXT  CAH  H10  single    0.939  0.020  1.096

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
 JXT  N7   C5   C6   132.69  3.000
 JXT  N7   C5   C4   110.84  3.000
 JXT  C6   C5   C4   116.48  3.000
 JXT  N9   C4   N3   127.85  3.000
 JXT  N9   C4   C5   105.62  3.000
 JXT  N3   C4   C5   126.54  3.000
 JXT  H1   C2   N3   116.11  3.000
 JXT  H1   C2   N1   115.40  3.000
 JXT  N3   C2   N1   128.49  3.000
 JXT  N1   C6   N6   119.49  3.000
 JXT  N1   C6   C5   117.67  3.000
 JXT  N6   C6   C5   122.85  3.000
 JXT  BR8  C8   N9   121.74  3.000
 JXT  N9   C8   N7   114.70  3.000
 JXT  BR8  C8   N7   123.56  3.000
 JXT  H4   CAA  CAD  180.00  3.000
 JXT  CAF  CAD  CAA  180.00  3.000
 JXT  H6   CAF  H5   106.33  3.000
 JXT  H6   CAF  CAG  109.94  3.000
 JXT  H5   CAF  CAG  110.01  3.000
 JXT  H6   CAF  CAD  108.93  3.000
 JXT  H5   CAF  CAD  109.20  3.000
 JXT  CAG  CAF  CAD  112.25  3.000
 JXT  H8   CAG  H7   107.15  3.000
 JXT  H8   CAG  CAH  109.56  3.000
 JXT  H7   CAG  CAH  110.12  3.000
 JXT  H8   CAG  CAF  109.79  3.000
 JXT  H7   CAG  CAF  109.61  3.000
 JXT  CAH  CAG  CAF  110.54  3.000
 JXT  C6   N1   C2   119.26  3.000
 JXT  C2   N3   C4   111.57  3.000
 JXT  C8   N7   C5   103.74  3.000
 JXT  CAH  N9   C8   129.16  3.000
 JXT  CAH  N9   C4   125.60  3.000
 JXT  C8   N9   C4   105.10  3.000
 JXT  H3   N6   H2   118.35  3.000
 JXT  H3   N6   C6   121.31  3.000
 JXT  H2   N6   C6   120.34  3.000
 JXT  H10  CAH  H9   106.84  3.000
 JXT  H10  CAH  N9   108.80  3.000
 JXT  H9   CAH  N9   107.08  3.000
 JXT  H10  CAH  CAG  111.30  3.000
 JXT  H9   CAH  CAG  110.61  3.000
 JXT  N9   CAH  CAG  111.99  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
 JXT  CONST_01  C2   N1   C6   C5     0.00   0.0  0
 JXT  CONST_02  N9   C8   N7   C5     0.00   0.0  0
 JXT  CONST_03  C2   N3   C4   C5     0.00   0.0  0
 JXT  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 JXT  CONST_05  N1   C6   C5   C4     0.00   0.0  0
 JXT  CONST_06  C8   N7   C5   C4     0.00   0.0  0
 JXT  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 JXT  CONST_08  N7   C8   N9   C4     0.00   0.0  0
 JXT  CONST_09  N9   C4   N3   C2   180.00   0.0  0
 JXT  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 JXT  CONST_11  C8   N7   C5   C6   180.00   0.0  0
 JXT  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 JXT  CONST_13  N9   C4   C5   C6   180.00   0.0  0
 JXT  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 JXT  CONST_15  N7   C5   C6   N1   180.00   0.0  0
 JXT  CONST_16  N7   C5   C4   N3   180.00   0.0  0
 JXT  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 JXT  CONST_18  BR8  C8   N7   C5   180.00   0.0  0
 JXT  CONST_19  CAH  N9   C4   C5   180.00   0.0  0
 JXT  CONST_20  N6   C6   C5   C4   180.00   0.0  0
 JXT  CONST_21  BR8  C8   N9   C4   180.00   0.0  0
 JXT  CONST_22  N6   C6   N1   C2   180.00   0.0  0
 JXT  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 JXT  CONST_24  N7   C8   N9   CAH  180.00   0.0  0
 JXT  CONST_25  N3   C4   N9   CAH    0.00   0.0  0
 JXT  CONST_26  H1   C2   N3   C4   180.00   0.0  0
 JXT  CONST_27  H2   N6   C6   C5   180.00   0.0  0
 JXT  CONST_28  H3   N6   C6   C5     0.00   0.0  0
 JXT  Var_01    CAG  CAH  N9   C4    90.77  30.0  2
 JXT  Var_02    N9   CAH  CAG  CAF  178.79  30.0  3
 JXT  Var_03    CAG  CAF  CAD  CAA   28.05  30.0  2
 JXT  Var_04    CAH  CAG  CAF  CAD  179.67  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
 JXT  plan-1  C5   0.020
 JXT  plan-1  C4   0.020
 JXT  plan-1  C2   0.020
 JXT  plan-1  C6   0.020
 JXT  plan-1  C8   0.020
 JXT  plan-1  N1   0.020
 JXT  plan-1  N3   0.020
 JXT  plan-1  N7   0.020
 JXT  plan-1  N9   0.020
 JXT  plan-1  BR8  0.020
 JXT  plan-1  H1   0.020
 JXT  plan-1  N6   0.020
 JXT  plan-1  CAH  0.020
 JXT  plan-2  C6   0.020
 JXT  plan-2  H2   0.020
 JXT  plan-2  H3   0.020
 JXT  plan-2  N6   0.020

