# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:07:37 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-[6-azanyl-9-[(2~{R})-oxan-2-yl]purin-8-yl]prop-2-yn-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@H]3CCCCO3)c(nc12)C#CCO
#
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
 JY5  JY5  3-[6-azanyl-9-[(2~{R})-oxan-2-yl]purin-8-yl]prop-2-yn-1-ol  ligand  35  20  .  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_JY5
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
 JY5  CAQ  C  CSP   0   0.182   1.0439   1.6385   0.0594
 JY5  CAR  C  CSP   0  -0.007   2.1433   2.1251   0.0782
 JY5  CAS  C  CH2   0  -0.338   3.4883   2.6824   0.1056
 JY5  C2   C  CR16  0   0.047  -3.7046  -1.5460   0.0122
 JY5  C4   C  CR56  0   0.488  -1.7464  -0.5521   0.0095
 JY5  C5   C  CR56  0  -0.009  -2.3226   0.7091   0.0492
 JY5  C6   C  CR6   0   0.448  -3.7310   0.7537   0.0699
 JY5  C8   C  CR5   0   0.291  -0.2335   1.0307   0.0367
 JY5  CAK  C  CH1   0   0.211   0.6254  -1.3563  -0.0082
 JY5  CAL  C  CH2   0  -0.476   1.4534  -1.3391  -1.2877
 JY5  CAM  C  CH2   0  -0.459   2.6117  -2.3240  -1.1664
 JY5  CAN  C  CH2   0  -0.459   3.3967  -2.0346   0.1069
 JY5  CAO  C  CH2   0  -0.188   2.4564  -2.0593   1.2975
 JY5  N1   N  N     0  -0.472  -4.3929  -0.4081   0.0500
 JY5  N3   N  N     0  -0.462  -2.3936  -1.7142  -0.0123
 JY5  N7   N  N     0  -0.445  -1.3675   1.6820   0.0665
 JY5  N9   N  NR5   0  -0.578  -0.4014  -0.3361  -0.0041
 JY5  OAP  O  O2    0  -0.480   1.3857  -1.1414   1.1454
 JY5  OAT  O  OH1   0  -0.654   4.3328   1.8488  -0.6503
 JY5  H1   H  HCH2  0   0.244   3.4508   3.7065  -0.2864
 JY5  H2   H  HCH2  0   0.245   3.8083   2.7607   1.1522
 JY5  H3   H  HCR6  0   0.253  -4.3022  -2.4513  -0.0004
 JY5  H4   H  HCH1  0   0.247   0.0914  -2.3152   0.0519
 JY5  H5   H  HCH2  0   0.253   0.8024  -1.5957  -2.1258
 JY5  H6   H  HCH2  0   0.249   1.8451  -0.3367  -1.4719
 JY5  H7   H  HCH2  0   0.226   2.2270  -3.3486  -1.1362
 JY5  H8   H  HCH2  0   0.248   3.2516  -2.2554  -2.0472
 JY5  H9   H  HCH2  0   0.241   4.1835  -2.7761   0.2597
 JY5  H10  H  HCH2  0   0.232   3.8781  -1.0547   0.0357
 JY5  H11  H  HCH2  0   0.206   2.0613  -3.0759   1.4357
 JY5  H12  H  HCH2  0   0.245   2.9668  -1.7771   2.2185
 JY5  H13  H  HNH2  0   0.406  -5.4196   1.8855   0.1092
 JY5  H14  H  HNH2  0   0.414  -3.9461   2.7853   0.1074
 JY5  H15  H  HOH1  0   0.466   5.2229   2.2114  -0.5944
 JY5  N6   N  NH2   0  -0.813  -4.4142   1.8960   0.1122

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
 JY5  N6   C6   single    1.332  0.020  1.332
 JY5  C6   N1   aromatic  1.337  0.020  1.337
 JY5  C6   C5   aromatic  1.409  0.020  1.409
 JY5  OAT  CAS  single    1.407  0.020  1.407
 JY5  N1   C2   aromatic  1.330  0.020  1.330
 JY5  C5   N7   aromatic  1.364  0.020  1.364
 JY5  C5   C4   aromatic  1.387  0.020  1.387
 JY5  N7   C8   aromatic  1.308  0.020  1.308
 JY5  C2   N3   aromatic  1.322  0.020  1.322
 JY5  C4   N3   aromatic  1.330  0.020  1.330
 JY5  C4   N9   aromatic  1.362  0.020  1.362
 JY5  C8   CAQ  single    1.415  0.020  1.415
 JY5  C8   N9   aromatic  1.378  0.020  1.378
 JY5  OAP  CAO  single    1.418  0.020  1.418
 JY5  OAP  CAK  single    1.398  0.020  1.398
 JY5  CAQ  CAR  triple    1.202  0.020  1.202
 JY5  N9   CAK  single    1.447  0.020  1.447
 JY5  CAR  CAS  single    1.456  0.020  1.456
 JY5  CAO  CAN  single    1.517  0.020  1.517
 JY5  CAK  CAL  single    1.524  0.020  1.524
 JY5  CAN  CAM  single    1.524  0.020  1.524
 JY5  CAL  CAM  single    1.525  0.020  1.525
 JY5  CAS  H1   single    0.970  0.020  1.090
 JY5  CAS  H2   single    0.970  0.020  1.090
 JY5  C2   H3   single    0.930  0.020  1.080
 JY5  CAK  H4   single    0.970  0.020  1.090
 JY5  CAL  H5   single    0.970  0.020  1.090
 JY5  CAL  H6   single    0.970  0.020  1.090
 JY5  CAM  H7   single    0.970  0.020  1.090
 JY5  CAM  H8   single    0.970  0.020  1.090
 JY5  CAN  H9   single    0.970  0.020  1.090
 JY5  CAN  H10  single    0.970  0.020  1.090
 JY5  CAO  H11  single    0.970  0.020  1.090
 JY5  CAO  H12  single    0.970  0.020  1.090
 JY5  N6   H13  single    0.860  0.020  1.020
 JY5  N6   H14  single    0.860  0.020  1.020
 JY5  OAT  H15  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
 JY5  C8   CAQ  CAR  180.00  3.000
 JY5  CAS  CAR  CAQ  180.00  3.000
 JY5  H2   CAS  H1   106.51  3.000
 JY5  H2   CAS  OAT  112.31  3.000
 JY5  H1   CAS  OAT  112.43  3.000
 JY5  H2   CAS  CAR  108.34  3.000
 JY5  H1   CAS  CAR  108.60  3.000
 JY5  OAT  CAS  CAR  108.52  3.000
 JY5  H3   C2   N3   116.09  3.000
 JY5  H3   C2   N1   115.41  3.000
 JY5  N3   C2   N1   128.49  3.000
 JY5  N9   C4   N3   128.22  3.000
 JY5  N9   C4   C5   105.44  3.000
 JY5  N3   C4   C5   126.34  3.000
 JY5  N7   C5   C6   132.63  3.000
 JY5  N7   C5   C4   110.98  3.000
 JY5  C6   C5   C4   116.38  3.000
 JY5  N6   C6   N1   119.45  3.000
 JY5  N1   C6   C5   117.84  3.000
 JY5  N6   C6   C5   122.71  3.000
 JY5  N9   C8   N7   112.89  3.000
 JY5  N9   C8   CAQ  122.46  3.000
 JY5  N7   C8   CAQ  124.64  3.000
 JY5  H4   CAK  OAP  110.68  3.000
 JY5  H4   CAK  N9   105.67  3.000
 JY5  OAP  CAK  N9   105.96  3.000
 JY5  H4   CAK  CAL  108.64  3.000
 JY5  N9   CAK  CAL  112.33  3.000
 JY5  OAP  CAK  CAL  113.29  3.000
 JY5  H6   CAL  H5   107.46  3.000
 JY5  H6   CAL  CAM  109.50  3.000
 JY5  H5   CAL  CAM  111.23  3.000
 JY5  H6   CAL  CAK  110.29  3.000
 JY5  H5   CAL  CAK  108.53  3.000
 JY5  CAM  CAL  CAK  109.79  3.000
 JY5  H8   CAM  H7   106.69  3.000
 JY5  H8   CAM  CAN  111.14  3.000
 JY5  H7   CAM  CAN  109.61  3.000
 JY5  H8   CAM  CAL  109.92  3.000
 JY5  H7   CAM  CAL  109.86  3.000
 JY5  CAN  CAM  CAL  109.58  3.000
 JY5  H10  CAN  H9   107.47  3.000
 JY5  H10  CAN  CAO  109.77  3.000
 JY5  H9   CAN  CAO  109.01  3.000
 JY5  H10  CAN  CAM  110.03  3.000
 JY5  H9   CAN  CAM  111.06  3.000
 JY5  CAO  CAN  CAM  109.47  3.000
 JY5  H12  CAO  H11  107.54  3.000
 JY5  H12  CAO  OAP  106.05  3.000
 JY5  H11  CAO  OAP  109.91  3.000
 JY5  H12  CAO  CAN  111.63  3.000
 JY5  H11  CAO  CAN  109.66  3.000
 JY5  OAP  CAO  CAN  111.91  3.000
 JY5  C6   N1   C2   119.17  3.000
 JY5  C4   N3   C2   111.78  3.000
 JY5  C8   N7   C5   104.58  3.000
 JY5  CAK  N9   C8   127.80  3.000
 JY5  CAK  N9   C4   126.06  3.000
 JY5  C8   N9   C4   106.10  3.000
 JY5  CAO  OAP  CAK  113.54  3.000
 JY5  H15  OAT  CAS  107.49  3.000
 JY5  H14  N6   H13  118.36  3.000
 JY5  H14  N6   C6   121.32  3.000
 JY5  H13  N6   C6   120.26  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
 JY5  CONST_01  C5   C6   N1   C2     0.00   0.0  0
 JY5  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 JY5  CONST_03  N9   C4   N3   C2   180.00   0.0  0
 JY5  CONST_04  N1   C6   C5   C4     0.00   0.0  0
 JY5  CONST_05  C8   N7   C5   C4     0.00   0.0  0
 JY5  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 JY5  CONST_07  N7   C8   N9   C4     0.00   0.0  0
 JY5  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 JY5  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 JY5  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 JY5  CONST_11  C8   N7   C5   C6   180.00   0.0  0
 JY5  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 JY5  CONST_13  N9   C4   C5   C6   180.00   0.0  0
 JY5  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 JY5  CONST_15  N7   C5   C6   N1   180.00   0.0  0
 JY5  CONST_16  N7   C5   C4   N3   180.00   0.0  0
 JY5  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 JY5  CONST_18  CAK  N9   C4   C5   180.00   0.0  0
 JY5  CONST_19  N3   C4   N9   CAK    0.00   0.0  0
 JY5  CONST_20  N7   C8   N9   CAK  180.00   0.0  0
 JY5  CONST_21  C5   N7   C8   CAQ  180.00   0.0  0
 JY5  CONST_22  C4   N9   C8   CAQ  180.00   0.0  0
 JY5  CONST_23  CAK  N9   C8   CAQ    0.00   0.0  0
 JY5  CONST_24  N6   C6   N1   C2   180.00   0.0  0
 JY5  CONST_25  N6   C6   C5   C4   180.00   0.0  0
 JY5  CONST_26  N7   C5   C6   N6     0.00   0.0  0
 JY5  CONST_27  H3   C2   N3   C4   180.00   0.0  0
 JY5  CONST_28  H13  N6   C6   C5   180.00   0.0  0
 JY5  CONST_29  H14  N6   C6   C5     0.00   0.0  0
 JY5  Var_01    CAN  CAO  OAP  CAK   57.51  30.0  1
 JY5  Var_02    CAN  CAM  CAL  CAK  -53.05  30.0  1
 JY5  Var_03    CAO  CAN  CAM  CAL   55.00  30.0  1
 JY5  Var_04    OAP  CAO  CAN  CAM  -56.72  30.0  1
 JY5  Var_05    OAT  CAS  CAR  CAQ   42.47  30.0  3

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
 JY5  chir_01  CAK  OAP  N9  CAL  negativ

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
 JY5  plan-1  CAQ  0.020
 JY5  plan-1  CAR  0.020
 JY5  plan-1  C2   0.020
 JY5  plan-1  C4   0.020
 JY5  plan-1  C5   0.020
 JY5  plan-1  C6   0.020
 JY5  plan-1  C8   0.020
 JY5  plan-1  CAK  0.020
 JY5  plan-1  N1   0.020
 JY5  plan-1  N3   0.020
 JY5  plan-1  N7   0.020
 JY5  plan-1  N9   0.020
 JY5  plan-1  H3   0.020
 JY5  plan-1  N6   0.020
 JY5  plan-2  C6   0.020
 JY5  plan-2  H13  0.020
 JY5  plan-2  H14  0.020
 JY5  plan-2  N6   0.020

