# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 15:47:44 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: (2S)-1-[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]pyrrolidine-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N4CCC[C@H]4C(O)=O)[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
 V2P  V2P  '(2S)-1-[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]pyrrolidine-2-carboxylic acid (non-preferred name)'  ligand  49  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V2P
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
 V2P  C    C  C      0   0.397  38.8562   2.3635  12.3079
 V2P  N    N  NT     0  -0.634  36.3124   2.2876  12.5071
 V2P  O    O  O      0  -0.600  38.7757   2.2561  11.0705
 V2P  C2   C  CR16   0   0.059  39.1292   2.2704  17.4165
 V2P  C4   C  CR56   0   0.509  37.5781   3.5781  16.5548
 V2P  C5   C  CR56   0   0.010  36.5841   2.6354  16.7597
 V2P  C6   C  CR6    0   0.460  36.9906   1.4214  17.3418
 V2P  C8   C  CR15   0   0.123  35.6518   4.2732  15.8041
 V2P  N9   N  NR5    0  -0.545  36.9639   4.6258  15.9414
 V2P  CA   C  CH1    0  -0.125  37.5977   2.0769  13.1525
 V2P  CB   C  CH2    0  -0.484  37.5623   0.5863  13.5372
 V2P  CG   C  CH2    0  -0.460  36.0779   0.2648  13.6459
 V2P  OXT  O  OC    -1  -0.622  39.8860   2.6199  12.9722
 V2P  CD   C  CH2    0  -0.248  35.4883   1.0941  12.5135
 V2P  O1A  O  O      0  -0.801  35.5789   3.8831  10.5137
 V2P  O2A  O  OP    -1  -0.803  34.3815   4.0570  12.7797
 V2P  O5'  O  O2     0  -0.625  36.8641   4.7330  12.5781
 V2P  C5'  C  CH2    0  -0.161  36.7263   6.1141  12.3608
 V2P  C4'  C  CH1    0  -0.029  37.3723   6.9121  13.4761
 V2P  O4'  O  O2     0  -0.495  36.7753   6.6106  14.7417
 V2P  C3'  C  CH1    0  -0.018  38.8670   6.6980  13.6817
 V2P  O3'  O  OH1    0  -0.670  39.4021   7.8785  14.2291
 V2P  C2'  C  CH1    0  -0.093  38.8967   5.5589  14.6934
 V2P  O2'  O  OH1    0  -0.686  40.0826   5.5677  15.4316
 V2P  C1'  C  CH1    0   0.237  37.6339   5.8562  15.5292
 V2P  N7   N  N      0  -0.462  35.3836   3.0910  16.2840
 V2P  N3   N  N      0  -0.511  38.8700   3.4467  16.8696
 V2P  N1   N  N      0  -0.475  38.2833   1.2773  17.6630
 V2P  N6   N  NH2    0  -0.817  36.1462   0.4177  17.5830
 V2P  H2   H  HCR5   0   0.286  34.9380   4.9174  15.3199
 V2P  H3   H  HCH1   0   0.217  37.6675   2.6646  14.0732
 V2P  H4   H  HCH2   0   0.234  38.1198   0.3890  14.4533
 V2P  H5   H  HCH2   0   0.221  38.0068  -0.0214  12.7433
 V2P  H6   H  HCH2   0   0.219  35.6790   0.6045  14.6050
 V2P  H7   H  HCH2   0   0.228  35.8608  -0.8000  13.5506
 V2P  H9   H  HCH2   0   0.191  35.5448   0.5368  11.5673
 V2P  H10  H  HCH2   0   0.214  34.4344   1.3310  12.6792
 V2P  H12  H  HCH2   0   0.213  37.1910   6.4185  11.4151
 V2P  H13  H  HCH2   0   0.215  35.6734   6.4145  12.3056
 V2P  H14  H  HCH1   0   0.259  37.1809   7.9678  13.2576
 V2P  H15  H  HCH1   0   0.241  39.3716   6.4222  12.7468
 V2P  H16  H  HOH1   0   0.449  40.2084   7.6460  14.7035
 V2P  H17  H  HCH1   0   0.282  38.7648   4.6142  14.1587
 V2P  H18  H  HOH1   0   0.460  40.0082   4.8288  16.0637
 V2P  H19  H  HCH1   0   0.253  37.8977   6.4076  16.4395
 V2P  H20  H  HNH2   0   0.403  36.4855  -0.4535  17.9534
 V2P  H21  H  HNH2   0   0.412  35.1800   0.4778  17.3131
 V2P  PA   P  P      0   1.317  35.6463   3.7564  12.0126
 V2P  H1   H  HCR6   0   0.256  40.1614   2.0912  17.6962

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
 V2P  CD   CG   single    1.522  0.020  1.522
 V2P  CD   N    single    1.450  0.020  1.450
 V2P  O1A  PA   deloc     1.506  0.020  1.506
 V2P  CG   CB   single    1.523  0.020  1.523
 V2P  O    C    deloc     1.245  0.020  1.245
 V2P  N    PA   single    1.687  0.020  1.687
 V2P  N    CA   single    1.454  0.020  1.454
 V2P  PA   O2A  deloc     1.509  0.020  1.509
 V2P  PA   O5'  single    1.660  0.020  1.660
 V2P  CB   CA   single    1.540  0.020  1.540
 V2P  C    CA   single    1.543  0.020  1.543
 V2P  C    OXT  deloc     1.252  0.020  1.252
 V2P  C5'  O5'  single    1.405  0.020  1.405
 V2P  C5'  C4'  single    1.516  0.020  1.516
 V2P  C4'  C3'  single    1.524  0.020  1.524
 V2P  C4'  O4'  single    1.431  0.020  1.431
 V2P  C3'  O3'  single    1.407  0.020  1.407
 V2P  C3'  C2'  single    1.524  0.020  1.524
 V2P  O4'  C1'  single    1.388  0.020  1.388
 V2P  C2'  O2'  single    1.397  0.020  1.397
 V2P  C2'  C1'  single    1.543  0.020  1.543
 V2P  C1'  N9   single    1.460  0.020  1.460
 V2P  N3   C2   aromatic  1.323  0.020  1.323
 V2P  N3   C4   aromatic  1.336  0.020  1.336
 V2P  N9   C4   aromatic  1.361  0.020  1.361
 V2P  N9   C8   aromatic  1.366  0.020  1.366
 V2P  C2   N1   aromatic  1.328  0.020  1.328
 V2P  C4   C5   aromatic  1.385  0.020  1.385
 V2P  C8   N7   aromatic  1.304  0.020  1.304
 V2P  N1   C6   aromatic  1.340  0.020  1.340
 V2P  C5   N7   aromatic  1.369  0.020  1.369
 V2P  C5   C6   aromatic  1.406  0.020  1.406
 V2P  C6   N6   single    1.334  0.020  1.334
 V2P  C2   H1   single    0.930  0.020  1.080
 V2P  C8   H2   single    0.930  0.020  1.080
 V2P  CA   H3   single    0.970  0.020  1.090
 V2P  CB   H4   single    0.970  0.020  1.090
 V2P  CB   H5   single    0.970  0.020  1.090
 V2P  CG   H6   single    0.970  0.020  1.090
 V2P  CG   H7   single    0.970  0.020  1.090
 V2P  CD   H9   single    0.970  0.020  1.090
 V2P  CD   H10  single    0.970  0.020  1.090
 V2P  C5'  H12  single    0.970  0.020  1.090
 V2P  C5'  H13  single    0.970  0.020  1.090
 V2P  C4'  H14  single    0.970  0.020  1.090
 V2P  C3'  H15  single    0.970  0.020  1.090
 V2P  O3'  H16  single    0.850  0.020  0.980
 V2P  C2'  H17  single    0.970  0.020  1.090
 V2P  O2'  H18  single    0.850  0.020  0.980
 V2P  C1'  H19  single    0.970  0.020  1.090
 V2P  N6   H20  single    0.860  0.020  1.020
 V2P  N6   H21  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
 V2P  OXT  C    CA   114.75  3.000
 V2P  OXT  C    O    126.76  3.000
 V2P  CA   C    O    118.39  3.000
 V2P  PA   N    CD   119.57  3.000
 V2P  PA   N    CA   127.27  3.000
 V2P  CD   N    CA   112.41  3.000
 V2P  H1   C2   N1   115.79  3.000
 V2P  H1   C2   N3   116.11  3.000
 V2P  N1   C2   N3   128.10  3.000
 V2P  N3   C4   N9   128.20  3.000
 V2P  N9   C4   C5   105.48  3.000
 V2P  N3   C4   C5   126.30  3.000
 V2P  N7   C5   C6   133.19  3.000
 V2P  C6   C5   C4   116.19  3.000
 V2P  N7   C5   C4   110.56  3.000
 V2P  N6   C6   N1   119.11  3.000
 V2P  N6   C6   C5   122.79  3.000
 V2P  N1   C6   C5   118.10  3.000
 V2P  H2   C8   N7   124.87  3.000
 V2P  H2   C8   N9   121.86  3.000
 V2P  N7   C8   N9   113.25  3.000
 V2P  C1'  N9   C8   129.05  3.000
 V2P  C8   N9   C4   106.27  3.000
 V2P  C1'  N9   C4   124.67  3.000
 V2P  H3   CA   CB   108.12  3.000
 V2P  H3   CA   N    110.61  3.000
 V2P  CB   CA   N    103.35  3.000
 V2P  H3   CA   C    107.99  3.000
 V2P  CB   CA   C    109.60  3.000
 V2P  N    CA   C    116.83  3.000
 V2P  H5   CB   H4   107.54  3.000
 V2P  H5   CB   CG   109.31  3.000
 V2P  H4   CB   CG   113.59  3.000
 V2P  H5   CB   CA   110.31  3.000
 V2P  H4   CB   CA   111.92  3.000
 V2P  CG   CB   CA   104.16  3.000
 V2P  H7   CG   H6   107.90  3.000
 V2P  H7   CG   CD   112.93  3.000
 V2P  H6   CG   CD   110.01  3.000
 V2P  H7   CG   CB   113.19  3.000
 V2P  H6   CG   CB   110.66  3.000
 V2P  CD   CG   CB   102.09  3.000
 V2P  H10  CD   H9   106.85  3.000
 V2P  H10  CD   CG   112.26  3.000
 V2P  H9   CD   CG   110.13  3.000
 V2P  H10  CD   N    111.73  3.000
 V2P  H9   CD   N    112.59  3.000
 V2P  CG   CD   N    103.38  3.000
 V2P  C5'  O5'  PA   116.98  3.000
 V2P  H13  C5'  H12  106.71  3.000
 V2P  H13  C5'  C4'  107.58  3.000
 V2P  H12  C5'  C4'  107.92  3.000
 V2P  H13  C5'  O5'  111.80  3.000
 V2P  H12  C5'  O5'  111.39  3.000
 V2P  C4'  C5'  O5'  111.22  3.000
 V2P  H14  C4'  C3'  109.50  3.000
 V2P  H14  C4'  O4'  107.85  3.000
 V2P  C3'  C4'  O4'  105.08  3.000
 V2P  H14  C4'  C5'  106.64  3.000
 V2P  O4'  C4'  C5'  111.22  3.000
 V2P  C3'  C4'  C5'  116.31  3.000
 V2P  C1'  O4'  C4'  110.99  3.000
 V2P  H15  C3'  C2'  111.64  3.000
 V2P  H15  C3'  O3'  111.56  3.000
 V2P  C2'  C3'  O3'  111.19  3.000
 V2P  H15  C3'  C4'  111.80  3.000
 V2P  C2'  C3'  C4'  102.34  3.000
 V2P  O3'  C3'  C4'  107.92  3.000
 V2P  H16  O3'  C3'  107.89  3.000
 V2P  H17  C2'  C1'  109.43  3.000
 V2P  H17  C2'  O2'  111.49  3.000
 V2P  C1'  C2'  O2'  114.03  3.000
 V2P  H17  C2'  C3'  108.59  3.000
 V2P  C1'  C2'  C3'  101.52  3.000
 V2P  O2'  C2'  C3'  111.26  3.000
 V2P  H18  O2'  C2'  105.84  3.000
 V2P  H19  C1'  C2'  110.47  3.000
 V2P  H19  C1'  O4'  110.27  3.000
 V2P  C2'  C1'  O4'  107.67  3.000
 V2P  H19  C1'  N9   107.45  3.000
 V2P  C2'  C1'  N9   111.47  3.000
 V2P  O4'  C1'  N9   109.53  3.000
 V2P  C8   N7   C5   104.43  3.000
 V2P  C4   N3   C2   111.98  3.000
 V2P  C6   N1   C2   119.33  3.000
 V2P  H21  N6   H20  118.37  3.000
 V2P  H21  N6   C6   121.00  3.000
 V2P  H20  N6   C6   120.33  3.000
 V2P  O5'  PA   O2A  108.93  3.000
 V2P  O5'  PA   O1A  108.80  3.000
 V2P  O2A  PA   O1A  116.85  3.000
 V2P  O5'  PA   N     97.05  3.000
 V2P  O2A  PA   N    110.81  3.000
 V2P  O1A  PA   N    112.50  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
 V2P  CONST_01  N9   C4   N3   C2   180.00   0.0  0
 V2P  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 V2P  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 V2P  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 V2P  CONST_05  N7   C8   N9   C4     0.00   0.0  0
 V2P  CONST_06  C8   N7   C5   C4     0.00   0.0  0
 V2P  CONST_07  N1   C6   C5   C4     0.00   0.0  0
 V2P  CONST_08  C8   N9   C4   C5     0.00   0.0  0
 V2P  CONST_09  N9   C8   N7   C5     0.00   0.0  0
 V2P  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 V2P  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 V2P  CONST_12  N9   C4   C5   C6   180.00   0.0  0
 V2P  CONST_13  C8   N7   C5   C6   180.00   0.0  0
 V2P  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 V2P  CONST_15  N7   C5   C4   N9     0.00   0.0  0
 V2P  CONST_16  N3   C4   C5   N7   180.00   0.0  0
 V2P  CONST_17  N1   C6   C5   N7   180.00   0.0  0
 V2P  CONST_18  C1'  N9   C4   C5   180.00   0.0  0
 V2P  CONST_19  N3   C4   N9   C1'    0.00   0.0  0
 V2P  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 V2P  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 V2P  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 V2P  CONST_23  N6   C6   C5   N7     0.00   0.0  0
 V2P  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 V2P  CONST_25  H2   C8   N9   C4   180.00   0.0  0
 V2P  CONST_26  H20  N6   C6   C5   180.00   0.0  0
 V2P  CONST_27  H21  N6   C6   C5     0.00   0.0  0
 V2P  Var_01    CB   CG   CD   N    -35.29  30.0  1
 V2P  Var_02    CG   CD   N    CA    20.96  30.0  1
 V2P  Var_03    CD   CG   CB   CA    37.17  30.0  1
 V2P  Var_04    O1A  PA   N    CA   110.87  30.0  3
 V2P  Var_05    C4'  C5'  O5'  PA   148.53  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
 V2P  chir_01  CA   N    CB   C    negativ
 V2P  chir_03  C4'  C5'  C3'  O4'  positiv
 V2P  chir_04  C3'  O3'  C2'  C4'  negativ
 V2P  chir_05  C2'  O2'  C1'  C3'  negativ
 V2P  chir_06  C1'  O4'  N9   C2'  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
 V2P  plan-1  C6   0.020
 V2P  plan-1  N6   0.020
 V2P  plan-1  H20  0.020
 V2P  plan-1  H21  0.020
 V2P  plan-2  C2   0.020
 V2P  plan-2  C4   0.020
 V2P  plan-2  C5   0.020
 V2P  plan-2  C6   0.020
 V2P  plan-2  C8   0.020
 V2P  plan-2  N9   0.020
 V2P  plan-2  C1'  0.020
 V2P  plan-2  N7   0.020
 V2P  plan-2  N3   0.020
 V2P  plan-2  N1   0.020
 V2P  plan-2  N6   0.020
 V2P  plan-2  H2   0.020
 V2P  plan-2  H1   0.020
 V2P  plan-3  C    0.020
 V2P  plan-3  O    0.020
 V2P  plan-3  CA   0.020
 V2P  plan-3  OXT  0.020

