# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 06:46:12 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)[C@@H]4CCCN4)[C@@H](O)[C@H]3O
#
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
 PR8  PR8  5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine  ligand  51  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PR8
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
 PR8  C     C  C     0   0.595  52.9785  84.5778  15.5448
 PR8  N     N  NH1   0  -0.600  53.2137  85.8781  17.5911
 PR8  O     O  O     0  -0.384  53.9336  83.8964  15.7543
 PR8  P     P  P     0   1.515  52.3703  83.2503  13.3140
 PR8  N1    N  N     0  -0.474  57.0186  77.7248   8.3679
 PR8  C2    C  CR16  0   0.042  56.8121  78.7643   7.5637
 PR8  N3    N  N     0  -0.459  56.3840  79.9745   7.8794
 PR8  C4    C  CR56  0   0.487  56.1557  80.0864   9.1865
 PR8  C5    C  CR56  0  -0.003  56.3188  79.0988  10.1443
 PR8  C6    C  CR6   0   0.458  56.7812  77.8538   9.6784
 PR8  N6    N  NH2   0  -0.816  56.9829  76.8105  10.4838
 PR8  N7    N  N     0  -0.451  55.9874  79.5696  11.3876
 PR8  C8    C  CR15  0   0.099  55.6338  80.8054  11.1841
 PR8  N9    N  NR5   0  -0.533  55.7151  81.1808   9.8701
 PR8  CA    C  CH1   0  -0.231  52.5281  85.7967  16.3196
 PR8  CB    C  CH2   0  -0.483  52.9241  87.0702  15.5419
 PR8  CD    C  CH2   0  -0.269  54.1211  87.0282  17.5963
 PR8  CG    C  CH2   0  -0.472  54.2946  87.3883  16.1256
 PR8  C1'   C  CH1   0   0.175  55.3993  82.4640   9.2640
 PR8  O10   O  O2    0  -0.584  52.1390  84.3582  14.4861
 PR8  O1P   O  OH1   0  -0.709  52.6265  81.8570  14.0072
 PR8  C2'   C  CH1   0  -0.048  53.9760  82.4975   8.6936
 PR8  O2'   O  OH1   0  -0.660  53.9852  83.3775   7.6032
 PR8  O2P   O  O     0  -0.684  51.2441  83.3709  12.3660
 PR8  C3'   C  CH1   0  -0.022  53.2104  83.0600   9.8861
 PR8  O3'   O  OH1   0  -0.674  51.9651  83.5732   9.5361
 PR8  C4'   C  CH1   0   0.023  54.2118  84.1003  10.3947
 PR8  O4'   O  O2    0  -0.495  55.4738  83.4558  10.2487
 PR8  C5'   C  CH2   0  -0.251  54.0282  84.6022  11.8045
 PR8  O5'   O  O2    0  -0.585  53.8242  83.5304  12.7418
 PR8  HN    H  HNH1  0   0.363  52.5583  85.9129  18.3561
 PR8  HN6   H  HNH2  0   0.404  57.3580  75.9527  10.1175
 PR8  HN6A  H  HNH2  0   0.411  56.8574  76.8895  11.4775
 PR8  H8    H  HCR5  0   0.293  55.3165  81.4882  11.9564
 PR8  HA    H  HCH1  0   0.295  51.4433  85.7324  16.4386
 PR8  HB    H  HCH2  0   0.254  52.9224  86.9527  14.4579
 PR8  HBA   H  HCH2  0   0.259  52.2114  87.8609  15.7819
 PR8  HD    H  HCH2  0   0.214  53.6969  87.8777  18.1423
 PR8  HDA   H  HCH2  0   0.225  55.0728  86.7794  18.0715
 PR8  HG    H  HCH2  0   0.236  55.0656  86.7677  15.6630
 PR8  HGA   H  HCH2  0   0.253  54.5831  88.4292  15.9844
 PR8  H1'   H  HCH1  0   0.284  56.1400  82.6329   8.4770
 PR8  HO1P  H  HOH1  0   0.515  51.8286  81.3321  14.1663
 PR8  H2'   H  HCH1  0   0.268  53.6311  81.4962   8.4109
 PR8  HO2'  H  HOH1  0   0.461  53.0750  83.5429   7.3341
 PR8  H3'   H  HCH1  0   0.230  53.1172  82.2473  10.6186
 PR8  HO3'  H  HOH1  0   0.464  51.4385  83.6235  10.3466
 PR8  H4'   H  HCH1  0   0.256  54.1698  84.9876   9.7498
 PR8  H5'   H  HCH2  0   0.289  54.9134  85.1450  12.1355
 PR8  H5'A  H  HCH2  0   0.263  53.1936  85.3070  11.8108
 PR8  H2    H  HCR6  0   0.253  57.0232  78.5903   6.5139

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
 PR8  O10  C     single    1.369  0.020  1.369
 PR8  C    O     double    1.192  0.020  1.192
 PR8  C    CA    single    1.513  0.020  1.513
 PR8  CA   N     single    1.447  0.020  1.447
 PR8  CD   N     single    1.465  0.020  1.465
 PR8  N    HN    single    0.890  0.020  1.040
 PR8  O2P  P     double    1.477  0.020  1.477
 PR8  O5'  P     single    1.587  0.020  1.587
 PR8  P    O1P   single    1.577  0.020  1.577
 PR8  P    O10   single    1.629  0.020  1.629
 PR8  C2   N1    aromatic  1.330  0.020  1.330
 PR8  N1   C6    aromatic  1.338  0.020  1.338
 PR8  C2   N3    aromatic  1.322  0.020  1.322
 PR8  C2   H2    single    0.930  0.020  1.080
 PR8  N3   C4    aromatic  1.332  0.020  1.332
 PR8  C4   N9    aromatic  1.364  0.020  1.364
 PR8  C4   C5    aromatic  1.385  0.020  1.385
 PR8  C6   C5    aromatic  1.407  0.020  1.407
 PR8  C5   N7    aromatic  1.370  0.020  1.370
 PR8  C6   N6    single    1.333  0.020  1.333
 PR8  N6   HN6   single    0.860  0.020  1.020
 PR8  N6   HN6A  single    0.860  0.020  1.020
 PR8  C8   N7    aromatic  1.301  0.020  1.301
 PR8  N9   C8    aromatic  1.369  0.020  1.369
 PR8  C8   H8    single    0.930  0.020  1.080
 PR8  C1'  N9    single    1.454  0.020  1.454
 PR8  CB   CA    single    1.544  0.020  1.544
 PR8  CA   HA    single    0.970  0.020  1.090
 PR8  CB   CG    single    1.523  0.020  1.523
 PR8  CB   HB    single    0.970  0.020  1.090
 PR8  CB   HBA   single    0.970  0.020  1.090
 PR8  CG   CD    single    1.524  0.020  1.524
 PR8  CD   HD    single    0.970  0.020  1.090
 PR8  CD   HDA   single    0.970  0.020  1.090
 PR8  CG   HG    single    0.970  0.020  1.090
 PR8  CG   HGA   single    0.970  0.020  1.090
 PR8  C2'  C1'   single    1.534  0.020  1.534
 PR8  C1'  O4'   single    1.400  0.020  1.400
 PR8  C1'  H1'   single    0.970  0.020  1.090
 PR8  O1P  HO1P  single    0.850  0.020  0.980
 PR8  O2'  C2'   single    1.401  0.020  1.401
 PR8  C2'  C3'   single    1.525  0.020  1.525
 PR8  C2'  H2'   single    0.970  0.020  1.090
 PR8  O2'  HO2'  single    0.850  0.020  0.980
 PR8  O3'  C3'   single    1.392  0.020  1.392
 PR8  C3'  C4'   single    1.531  0.020  1.531
 PR8  C3'  H3'   single    0.970  0.020  1.090
 PR8  O3'  HO3'  single    0.850  0.020  0.980
 PR8  C4'  O4'   single    1.425  0.020  1.425
 PR8  C4'  C5'   single    1.508  0.020  1.508
 PR8  C4'  H4'   single    0.970  0.020  1.090
 PR8  C5'  O5'   single    1.438  0.020  1.438
 PR8  C5'  H5'   single    0.970  0.020  1.090
 PR8  C5'  H5'A  single    0.970  0.020  1.090

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
 PR8  O10   C    CA   110.04  3.000
 PR8  CA    C    O    127.53  3.000
 PR8  O10   C    O    122.39  3.000
 PR8  HN    N    CD   111.90  3.000
 PR8  HN    N    CA   111.14  3.000
 PR8  CD    N    CA   109.93  3.000
 PR8  O5'   P    O2P  116.91  3.000
 PR8  O5'   P    O1P   99.53  3.000
 PR8  O2P   P    O1P  118.56  3.000
 PR8  O1P   P    O10  107.91  3.000
 PR8  O5'   P    O10  105.62  3.000
 PR8  O2P   P    O10  107.34  3.000
 PR8  C6    N1   C2   119.28  3.000
 PR8  H2    C2   N3   116.17  3.000
 PR8  H2    C2   N1   115.43  3.000
 PR8  N3    C2   N1   128.40  3.000
 PR8  C4    N3   C2   111.53  3.000
 PR8  N9    C4   C5   105.28  3.000
 PR8  C5    C4   N3   126.76  3.000
 PR8  N9    C4   N3   127.96  3.000
 PR8  N7    C5   C6   133.14  3.000
 PR8  N7    C5   C4   110.73  3.000
 PR8  C6    C5   C4   116.13  3.000
 PR8  N6    C6   C5   122.81  3.000
 PR8  N6    C6   N1   119.30  3.000
 PR8  C5    C6   N1   117.89  3.000
 PR8  HN6A  N6   HN6  118.30  3.000
 PR8  HN6A  N6   C6   121.13  3.000
 PR8  HN6   N6   C6   120.26  3.000
 PR8  C8    N7   C5   104.48  3.000
 PR8  H8    C8   N9   122.08  3.000
 PR8  H8    C8   N7   124.69  3.000
 PR8  N9    C8   N7   113.23  3.000
 PR8  C1'   N9   C8   129.00  3.000
 PR8  C1'   N9   C4   124.72  3.000
 PR8  C8    N9   C4   106.28  3.000
 PR8  HA    CA   CB   110.97  3.000
 PR8  HA    CA   N    112.20  3.000
 PR8  CB    CA   N    105.95  3.000
 PR8  HA    CA   C    107.69  3.000
 PR8  CB    CA   C    109.28  3.000
 PR8  N     CA   C    110.75  3.000
 PR8  HBA   CB   HB   107.21  3.000
 PR8  HBA   CB   CG   110.61  3.000
 PR8  HB    CB   CG   113.89  3.000
 PR8  HBA   CB   CA   108.62  3.000
 PR8  HB    CB   CA   114.30  3.000
 PR8  CG    CB   CA   102.12  3.000
 PR8  HDA   CD   HD   107.29  3.000
 PR8  HDA   CD   CG   111.99  3.000
 PR8  HD    CD   CG   109.99  3.000
 PR8  HDA   CD   N    111.24  3.000
 PR8  HD    CD   N    111.76  3.000
 PR8  CG    CD   N    104.63  3.000
 PR8  HGA   CG   HG   107.52  3.000
 PR8  HGA   CG   CD   112.39  3.000
 PR8  HG    CG   CD   110.78  3.000
 PR8  HGA   CG   CB   112.84  3.000
 PR8  HG    CG   CB   110.73  3.000
 PR8  CD    CG   CB   102.60  3.000
 PR8  H1'   C1'  O4'  111.15  3.000
 PR8  H1'   C1'  C2'  110.95  3.000
 PR8  O4'   C1'  C2'  107.19  3.000
 PR8  H1'   C1'  N9   106.81  3.000
 PR8  O4'   C1'  N9   108.70  3.000
 PR8  C2'   C1'  N9   112.08  3.000
 PR8  P     O10  C    125.34  3.000
 PR8  HO1P  O1P  P    114.66  3.000
 PR8  H2'   C2'  C3'  112.38  3.000
 PR8  H2'   C2'  O2'  112.03  3.000
 PR8  C3'   C2'  O2'  112.35  3.000
 PR8  H2'   C2'  C1'  111.59  3.000
 PR8  C3'   C2'  C1'  100.55  3.000
 PR8  O2'   C2'  C1'  107.27  3.000
 PR8  HO2'  O2'  C2'  108.60  3.000
 PR8  H3'   C3'  C4'  109.68  3.000
 PR8  H3'   C3'  O3'  111.39  3.000
 PR8  C4'   C3'  O3'  114.73  3.000
 PR8  H3'   C3'  C2'  106.94  3.000
 PR8  C4'   C3'  C2'  100.49  3.000
 PR8  O3'   C3'  C2'  112.87  3.000
 PR8  HO3'  O3'  C3'  107.18  3.000
 PR8  H4'   C4'  C5'  105.99  3.000
 PR8  H4'   C4'  O4'  109.84  3.000
 PR8  C5'   C4'  O4'  110.75  3.000
 PR8  H4'   C4'  C3'  109.21  3.000
 PR8  C5'   C4'  C3'  117.21  3.000
 PR8  O4'   C4'  C3'  103.77  3.000
 PR8  C4'   O4'  C1'  110.21  3.000
 PR8  H5'A  C5'  H5'  107.31  3.000
 PR8  H5'A  C5'  O5'  111.63  3.000
 PR8  H5'   C5'  O5'  106.76  3.000
 PR8  H5'A  C5'  C4'  108.26  3.000
 PR8  H5'   C5'  C4'  110.54  3.000
 PR8  O5'   C5'  C4'  112.24  3.000
 PR8  C5'   O5'  P    119.75  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
 PR8  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 PR8  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PR8  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 PR8  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 PR8  CONST_05  N9    C4   N3   C2   180.00   0.0  0
 PR8  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 PR8  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 PR8  CONST_08  C8    N9   C4   N3   180.00   0.0  0
 PR8  CONST_09  C6    C5   C4   N3     0.00   0.0  0
 PR8  CONST_10  N7    C5   C4   N3   180.00   0.0  0
 PR8  CONST_11  N7    C8   N9   C4     0.00   0.0  0
 PR8  CONST_12  C8    N7   C5   C4     0.00   0.0  0
 PR8  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 PR8  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 PR8  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 PR8  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 PR8  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 PR8  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 PR8  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 PR8  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 PR8  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 PR8  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 PR8  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 PR8  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 PR8  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 PR8  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 PR8  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 PR8  Var_01    CB    CG   CD   N     34.56  30.0  1
 PR8  Var_02    CG    CD   N    CA   -17.64  30.0  1
 PR8  Var_03    CD    CG   CB   CA   -37.60  30.0  1
 PR8  Var_04    C4'   C5'  O5'  P   -104.56  30.0  1
 PR8  Var_05    CA    C    O10  P    172.77  30.0  3
 PR8  Var_06    O2P   P    O10  C   -178.95  30.0  2

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
 PR8  chir_02  CA   C    N    CB   negativ
 PR8  chir_03  C1'  N9   C2'  O4'  negativ
 PR8  chir_04  C2'  O2'  C3'  C1'  positiv
 PR8  chir_05  C3'  O3'  C4'  C2'  positiv
 PR8  chir_06  C4'  O4'  C3'  C5'  negativ
 PR8  chir_07  P    O5'  O1P  O10  both

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
 PR8  plan-1  C6    0.020
 PR8  plan-1  N6    0.020
 PR8  plan-1  HN6   0.020
 PR8  plan-1  HN6A  0.020
 PR8  plan-2  N1    0.020
 PR8  plan-2  C2    0.020
 PR8  plan-2  N3    0.020
 PR8  plan-2  C4    0.020
 PR8  plan-2  C5    0.020
 PR8  plan-2  C6    0.020
 PR8  plan-2  N6    0.020
 PR8  plan-2  N7    0.020
 PR8  plan-2  C8    0.020
 PR8  plan-2  N9    0.020
 PR8  plan-2  C1'   0.020
 PR8  plan-2  H8    0.020
 PR8  plan-2  H2    0.020
 PR8  plan-3  C     0.020
 PR8  plan-3  O     0.020
 PR8  plan-3  CA    0.020
 PR8  plan-3  O10   0.020

