# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:05:21 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 8-bromanyl-9-[(2~{R})-oxan-2-yl]purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@H]3CCCCO3)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
 JXH  JXH  8-bromanyl-9-[(2~{R})-oxan-2-yl]purin-6-amine  ligand  29  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_JXH
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
 JXH  C2   C   CR5   0   0.290   0.2291  -0.9919  -0.1634
 JXH  C3   C   CR56  0   0.002   2.2186  -0.3249  -0.0414
 JXH  C4   C   CR6   0   0.460   3.6110  -0.1325   0.0235
 JXH  C5   C   CR16  0   0.050   3.1856   2.1221   0.1959
 JXH  C6   C   CH1   0   0.215  -1.0233   1.2384  -0.0063
 JXH  C7   C   CH2   0  -0.471  -1.7657   1.3286  -1.3330
 JXH  C10  C   CH2   0  -0.190  -2.9597   1.6038   1.2623
 JXH  C1   C   CR56  0   0.501   1.4339   0.8118   0.0255
 JXH  C8   C   CH2   0  -0.458  -2.9941   2.2170  -1.1525
 JXH  C9   C   CH2   0  -0.458  -3.8273   1.7175   0.0225
 JXH  N1   N   NR5   0  -0.563   0.1387   0.3725  -0.0579
 JXH  N2   N   N     0  -0.459   1.8655   2.0633   0.1436
 JXH  N3   N   N     0  -0.424   1.4398  -1.4463  -0.1565
 JXH  N4   N   N     0  -0.471   4.0599   1.1217   0.1439
 JXH  N5   N   NH2   0  -0.814   4.4839  -1.1378  -0.0442
 JXH  O1   O   O2    0  -0.481  -1.8260   0.7778   1.0393
 JXH  BR1  BR  BR    0   0.040  -1.2458  -2.1063  -0.2836
 JXH  H1   H   HCR6  0   0.256   3.6150   3.1129   0.2967
 JXH  H2   H   HCH1  0   0.249  -0.6216   2.2347   0.2278
 JXH  H3   H   HCH2  0   0.255  -1.0908   1.7415  -2.0852
 JXH  H4   H   HCH2  0   0.242  -2.0764   0.3396  -1.6755
 JXH  H5   H   HCH2  0   0.209  -2.6331   2.6038   1.5808
 JXH  H6   H   HCH2  0   0.247  -3.5040   1.1522   2.0915
 JXH  H7   H   HCH2  0   0.228  -2.6765   3.2484  -0.9680
 JXH  H8   H   HCH2  0   0.250  -3.5835   2.2308  -2.0701
 JXH  H9   H   HCH2  0   0.231  -4.2600   0.7414  -0.2162
 JXH  H10  H   HCH2  0   0.244  -4.6570   2.3965   0.2288
 JXH  H11  H   HNH2  0   0.406   5.4667  -0.9602   0.0730
 JXH  H12  H   HNH2  0   0.413   4.1738  -2.0938  -0.0493

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
 JXH  N5   C4   single    1.333  0.020  1.333
 JXH  C4   N4   aromatic  1.337  0.020  1.337
 JXH  C4   C3   aromatic  1.407  0.020  1.407
 JXH  N4   C5   aromatic  1.330  0.020  1.330
 JXH  N3   C3   aromatic  1.370  0.020  1.370
 JXH  N3   C2   aromatic  1.293  0.020  1.293
 JXH  C3   C1   aromatic  1.383  0.020  1.383
 JXH  C5   N2   aromatic  1.322  0.020  1.322
 JXH  C7   C8   single    1.527  0.020  1.527
 JXH  C7   C6   single    1.523  0.020  1.523
 JXH  C2   BR1  single    1.852  0.020  1.852
 JXH  C2   N1   aromatic  1.371  0.020  1.371
 JXH  C1   N2   aromatic  1.329  0.020  1.329
 JXH  C1   N1   aromatic  1.370  0.020  1.370
 JXH  C8   C9   single    1.525  0.020  1.525
 JXH  N1   C6   single    1.450  0.020  1.450
 JXH  C6   O1   single    1.396  0.020  1.396
 JXH  C9   C10  single    1.517  0.020  1.517
 JXH  O1   C10  single    1.420  0.020  1.420
 JXH  C5   H1   single    0.930  0.020  1.080
 JXH  C6   H2   single    0.970  0.020  1.090
 JXH  C7   H3   single    0.970  0.020  1.090
 JXH  C7   H4   single    0.970  0.020  1.090
 JXH  C10  H5   single    0.970  0.020  1.090
 JXH  C10  H6   single    0.970  0.020  1.090
 JXH  C8   H7   single    0.970  0.020  1.090
 JXH  C8   H8   single    0.970  0.020  1.090
 JXH  C9   H9   single    0.970  0.020  1.090
 JXH  C9   H10  single    0.970  0.020  1.090
 JXH  N5   H11  single    0.860  0.020  1.020
 JXH  N5   H12  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
 JXH  BR1  C2   N3   122.30  3.000
 JXH  BR1  C2   N1   123.44  3.000
 JXH  N3   C2   N1   114.26  3.000
 JXH  N3   C3   C1   110.75  3.000
 JXH  C1   C3   C4   116.54  3.000
 JXH  N3   C3   C4   132.71  3.000
 JXH  N5   C4   N4   119.47  3.000
 JXH  N4   C4   C3   117.68  3.000
 JXH  N5   C4   C3   122.85  3.000
 JXH  H1   C5   N4   115.51  3.000
 JXH  H1   C5   N2   116.08  3.000
 JXH  N4   C5   N2   128.42  3.000
 JXH  H2   C6   O1   110.46  3.000
 JXH  H2   C6   N1   104.83  3.000
 JXH  O1   C6   N1   106.88  3.000
 JXH  H2   C6   C7   108.05  3.000
 JXH  O1   C6   C7   113.06  3.000
 JXH  N1   C6   C7   113.27  3.000
 JXH  H4   C7   H3   107.60  3.000
 JXH  H4   C7   C8   109.59  3.000
 JXH  H3   C7   C8   111.03  3.000
 JXH  H4   C7   C6   111.00  3.000
 JXH  H3   C7   C6   108.74  3.000
 JXH  C8   C7   C6   108.89  3.000
 JXH  H6   C10  H5   107.75  3.000
 JXH  H6   C10  O1   106.09  3.000
 JXH  H5   C10  O1   109.72  3.000
 JXH  H6   C10  C9   111.54  3.000
 JXH  H5   C10  C9   109.78  3.000
 JXH  O1   C10  C9   111.82  3.000
 JXH  N2   C1   N1   127.90  3.000
 JXH  N1   C1   C3   105.65  3.000
 JXH  N2   C1   C3   126.44  3.000
 JXH  H8   C8   H7   106.66  3.000
 JXH  H8   C8   C9   110.93  3.000
 JXH  H7   C8   C9   109.72  3.000
 JXH  H8   C8   C7   110.04  3.000
 JXH  H7   C8   C7   109.55  3.000
 JXH  C9   C8   C7   109.89  3.000
 JXH  H10  C9   H9   107.19  3.000
 JXH  H10  C9   C8   110.93  3.000
 JXH  H9   C9   C8   109.90  3.000
 JXH  H10  C9   C10  109.07  3.000
 JXH  H9   C9   C10  109.72  3.000
 JXH  C8   C9   C10  109.98  3.000
 JXH  C1   N1   C6   124.32  3.000
 JXH  C6   N1   C2   130.51  3.000
 JXH  C1   N1   C2   105.16  3.000
 JXH  C1   N2   C5   111.69  3.000
 JXH  C3   N3   C2   104.18  3.000
 JXH  C5   N4   C4   119.23  3.000
 JXH  H12  N5   H11  118.04  3.000
 JXH  H12  N5   C4   121.04  3.000
 JXH  H11  N5   C4   120.06  3.000
 JXH  C10  O1   C6   112.62  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
 JXH  CONST_01  C4   C3   N3  C2  180.00   0.0  0
 JXH  CONST_02  C1   C3   N3  C2    0.00   0.0  0
 JXH  CONST_03  C3   C1   N1  C2    0.00   0.0  0
 JXH  CONST_04  N2   C1   N1  C2  180.00   0.0  0
 JXH  CONST_05  C5   N4   C4  C3    0.00   0.0  0
 JXH  CONST_06  N1   C2   N3  C3    0.00   0.0  0
 JXH  CONST_07  C5   N2   C1  C3    0.00   0.0  0
 JXH  CONST_08  N2   C5   N4  C4    0.00   0.0  0
 JXH  CONST_09  N2   C1   C3  C4    0.00   0.0  0
 JXH  CONST_10  N1   C1   C3  C4  180.00   0.0  0
 JXH  CONST_11  N1   C1   N2  C5  180.00   0.0  0
 JXH  CONST_12  N4   C4   C3  C1    0.00   0.0  0
 JXH  CONST_13  N4   C5   N2  C1    0.00   0.0  0
 JXH  CONST_14  N3   C2   N1  C1    0.00   0.0  0
 JXH  CONST_15  N3   C3   C1  N1    0.00   0.0  0
 JXH  CONST_16  N3   C3   C1  N2  180.00   0.0  0
 JXH  CONST_17  N4   C4   C3  N3  180.00   0.0  0
 JXH  CONST_18  C6   N1   C1  C3  180.00   0.0  0
 JXH  CONST_19  N3   C2   N1  C6  180.00   0.0  0
 JXH  CONST_20  N2   C1   N1  C6    0.00   0.0  0
 JXH  CONST_21  BR1  C2   N3  C3  180.00   0.0  0
 JXH  CONST_22  N5   C4   N4  C5  180.00   0.0  0
 JXH  CONST_23  BR1  C2   N1  C6    0.00   0.0  0
 JXH  CONST_24  N5   C4   C3  C1  180.00   0.0  0
 JXH  CONST_25  BR1  C2   N1  C1  180.00   0.0  0
 JXH  CONST_26  N5   C4   C3  N3    0.00   0.0  0
 JXH  CONST_27  H1   C5   N4  C4  180.00   0.0  0
 JXH  CONST_28  H11  N5   C4  C3  180.00   0.0  0
 JXH  CONST_29  H12  N5   C4  C3    0.00   0.0  0
 JXH  Var_01    C9   C8   C7  C6  -53.08  30.0  1
 JXH  Var_02    C9   C10  O1  C6   58.26  30.0  1
 JXH  Var_03    C10  C9   C8  C7   53.69  30.0  1
 JXH  Var_04    O1   C10  C9  C8  -55.53  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JXH  chir_01  C6  C7  N1  O1  positiv

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
 JXH  plan-1  C2   0.020
 JXH  plan-1  C3   0.020
 JXH  plan-1  C4   0.020
 JXH  plan-1  C5   0.020
 JXH  plan-1  C6   0.020
 JXH  plan-1  C1   0.020
 JXH  plan-1  N1   0.020
 JXH  plan-1  N2   0.020
 JXH  plan-1  N3   0.020
 JXH  plan-1  N4   0.020
 JXH  plan-1  N5   0.020
 JXH  plan-1  BR1  0.020
 JXH  plan-1  H1   0.020
 JXH  plan-2  C4   0.020
 JXH  plan-2  N5   0.020
 JXH  plan-2  H11  0.020
 JXH  plan-2  H12  0.020

