# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:40:37 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: {2-[(3S,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxypyrrolidin-1-yl]-2-oxoethyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3CN(C[C@H]3O)C(=O)C[P](O)(O)=O
#
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
 3ZE  3ZE  '{2-[(3S,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-hydroxypyrrolidin-1-yl]-2-oxoethyl}phosphonic acid'  ligand  39  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3ZE
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
 3ZE  C4   C  CR56  0   0.504   3.0889   0.0342  -0.0453
 3ZE  C5   C  CR56  0  -0.096   3.9139  -0.9589  -0.5379
 3ZE  C6   C  CR6   0   0.503   5.3239  -0.7793  -0.4548
 3ZE  C8   C  CR15  0   0.099   1.9392  -1.6357  -0.8692
 3ZE  N1   N  NR16  0  -0.730   5.6296   0.4470   0.1502
 3ZE  N3   N  N     0  -0.519   3.4317   1.1937   0.5304
 3ZE  OAF  O  OH1   0  -0.741  -6.2727   0.2365   1.1379
 3ZE  PAX  P  P     0   1.375  -5.1603  -0.2745   0.1033
 3ZE  OAG  O  OH1   0  -0.746  -4.3863  -1.4926   0.8143
 3ZE  OAD  O  O     0  -0.699  -5.6264  -0.6979  -1.2345
 3ZE  CAI  C  CH2   0  -0.878  -4.0254   1.1360   0.1182
 3ZE  CAO  C  C     0   0.535  -2.8260   0.8587  -0.7662
 3ZE  OAB  O  O     0  -0.488  -2.9277   0.9084  -1.9834
 3ZE  NAV  N  NT    0  -0.463  -1.6697   0.5519  -0.1613
 3ZE  CAK  C  CH2   0  -0.237  -0.4694   0.3172  -0.9474
 3ZE  CAJ  C  CH2   0  -0.307  -1.4239   0.4472   1.2737
 3ZE  CAT  C  CH1   0   0.015  -0.0846  -0.2763   1.3518
 3ZE  OAE  O  OH1   0  -0.655  -0.2082  -1.6596   1.1673
 3ZE  CAU  C  CH1   0  -0.172   0.6226   0.2925   0.1225
 3ZE  N9   N  NR5   0  -0.516   1.8199  -0.4055  -0.2670
 3ZE  C2   C  CR6   0   0.702   4.7290   1.3667   0.6085
 3ZE  O6   O  O     0  -0.476   6.2145  -1.5255  -0.8268
 3ZE  N7   N  N     0  -0.447   3.1727  -1.9925  -1.0509
 3ZE  H1   H  HCR5  0   0.289   1.0782  -2.2161  -1.1590
 3ZE  H2   H  HNR6  0   0.423   6.6159   0.6539   0.2428
 3ZE  H3   H  HNH2  0   0.416   4.5872   3.1683   1.5212
 3ZE  H4   H  HNH2  0   0.417   6.2075   2.6490   1.2543
 3ZE  H5   H  HOH1  0   0.499  -7.0694  -0.3119   1.1709
 3ZE  H6   H  HOH1  0   0.493  -4.2897  -1.4324   1.7734
 3ZE  H7   H  HCH2  0   0.334  -4.5632   1.9848  -0.3092
 3ZE  H8   H  HCH2  0   0.319  -3.7712   1.3976   1.1454
 3ZE  H9   H  HCH2  0   0.259  -0.5386  -0.6254  -1.4956
 3ZE  H10  H  HCH2  0   0.271  -0.3036   1.1130  -1.6728
 3ZE  H11  H  HCH2  0   0.264  -1.3505   1.4344   1.7385
 3ZE  H12  H  HCH2  0   0.258  -2.2035  -0.1121   1.7888
 3ZE  H13  H  HCH1  0   0.260   0.4421  -0.0261   2.2783
 3ZE  H14  H  HOH1  0   0.464  -0.5951  -2.0472   1.9586
 3ZE  H15  H  HCH1  0   0.309   0.9191   1.3174   0.3515
 3ZE  N2   N  NH2   0  -0.837   5.2221   2.4836   1.1502

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
 3ZE  OAD  PAX  double    1.479  0.020  1.479
 3ZE  OAF  PAX  single    1.603  0.020  1.603
 3ZE  PAX  OAG  single    1.609  0.020  1.609
 3ZE  PAX  CAI  single    1.810  0.020  1.810
 3ZE  OAB  CAO  double    1.222  0.020  1.222
 3ZE  CAI  CAO  single    1.516  0.020  1.516
 3ZE  CAO  NAV  single    1.341  0.020  1.341
 3ZE  NAV  CAJ  single    1.460  0.020  1.460
 3ZE  NAV  CAK  single    1.454  0.020  1.454
 3ZE  CAJ  CAT  single    1.524  0.020  1.524
 3ZE  CAK  CAU  single    1.529  0.020  1.529
 3ZE  OAE  CAT  single    1.401  0.020  1.401
 3ZE  CAT  CAU  single    1.528  0.020  1.528
 3ZE  CAU  N9   single    1.440  0.020  1.440
 3ZE  C8   N9   aromatic  1.375  0.020  1.375
 3ZE  C8   N7   aromatic  1.297  0.020  1.297
 3ZE  N9   C4   aromatic  1.361  0.020  1.361
 3ZE  N7   C5   aromatic  1.371  0.020  1.371
 3ZE  C4   C5   aromatic  1.382  0.020  1.382
 3ZE  C4   N3   single    1.339  0.020  1.339
 3ZE  C5   C6   single    1.424  0.020  1.424
 3ZE  N3   C2   double    1.311  0.020  1.311
 3ZE  C6   O6   double    1.220  0.020  1.220
 3ZE  C6   N1   single    1.401  0.020  1.401
 3ZE  C2   N1   single    1.366  0.020  1.366
 3ZE  C2   N2   single    1.336  0.020  1.336
 3ZE  C8   H1   single    0.930  0.020  1.080
 3ZE  N1   H2   single    0.860  0.020  1.020
 3ZE  N2   H3   single    0.860  0.020  1.020
 3ZE  N2   H4   single    0.860  0.020  1.020
 3ZE  OAF  H5   single    0.850  0.020  0.980
 3ZE  OAG  H6   single    0.850  0.020  0.980
 3ZE  CAI  H7   single    0.970  0.020  1.090
 3ZE  CAI  H8   single    0.970  0.020  1.090
 3ZE  CAK  H9   single    0.970  0.020  1.090
 3ZE  CAK  H10  single    0.970  0.020  1.090
 3ZE  CAJ  H11  single    0.970  0.020  1.090
 3ZE  CAJ  H12  single    0.970  0.020  1.090
 3ZE  CAT  H13  single    0.970  0.020  1.090
 3ZE  OAE  H14  single    0.850  0.020  0.980
 3ZE  CAU  H15  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
 3ZE  N9   C4   N3   126.04  3.000
 3ZE  N3   C4   C5   128.51  3.000
 3ZE  N9   C4   C5   105.45  3.000
 3ZE  N7   C5   C6   130.70  3.000
 3ZE  C6   C5   C4   118.67  3.000
 3ZE  N7   C5   C4   110.63  3.000
 3ZE  O6   C6   N1   120.51  3.000
 3ZE  N1   C6   C5   110.59  3.000
 3ZE  O6   C6   C5   128.90  3.000
 3ZE  H1   C8   N7   125.02  3.000
 3ZE  H1   C8   N9   122.02  3.000
 3ZE  N7   C8   N9   112.95  3.000
 3ZE  H2   N1   C2   118.30  3.000
 3ZE  H2   N1   C6   115.53  3.000
 3ZE  C2   N1   C6   126.17  3.000
 3ZE  C2   N3   C4   113.15  3.000
 3ZE  H5   OAF  PAX  114.37  3.000
 3ZE  CAI  PAX  OAD  115.35  3.000
 3ZE  CAI  PAX  OAG  106.54  3.000
 3ZE  OAD  PAX  OAG  109.56  3.000
 3ZE  CAI  PAX  OAF  100.45  3.000
 3ZE  OAG  PAX  OAF  106.86  3.000
 3ZE  OAD  PAX  OAF  117.17  3.000
 3ZE  H6   OAG  PAX  116.08  3.000
 3ZE  H8   CAI  H7   107.29  3.000
 3ZE  H8   CAI  CAO  114.15  3.000
 3ZE  H7   CAI  CAO  107.67  3.000
 3ZE  H8   CAI  PAX  109.94  3.000
 3ZE  H7   CAI  PAX  107.07  3.000
 3ZE  CAO  CAI  PAX  110.41  3.000
 3ZE  NAV  CAO  OAB  122.03  3.000
 3ZE  NAV  CAO  CAI  117.46  3.000
 3ZE  OAB  CAO  CAI  120.51  3.000
 3ZE  CAJ  NAV  CAK  112.39  3.000
 3ZE  CAK  NAV  CAO  120.34  3.000
 3ZE  CAJ  NAV  CAO  127.25  3.000
 3ZE  H10  CAK  H9   107.80  3.000
 3ZE  H10  CAK  CAU  111.65  3.000
 3ZE  H9   CAK  CAU  112.48  3.000
 3ZE  H10  CAK  NAV  111.57  3.000
 3ZE  H9   CAK  NAV  110.99  3.000
 3ZE  CAU  CAK  NAV  102.35  3.000
 3ZE  H12  CAJ  H11  108.10  3.000
 3ZE  H12  CAJ  CAT  111.16  3.000
 3ZE  H11  CAJ  CAT  110.35  3.000
 3ZE  H12  CAJ  NAV  112.42  3.000
 3ZE  H11  CAJ  NAV  111.37  3.000
 3ZE  CAT  CAJ  NAV  103.44  3.000
 3ZE  H13  CAT  CAU  111.91  3.000
 3ZE  H13  CAT  OAE  112.31  3.000
 3ZE  CAU  CAT  OAE  107.60  3.000
 3ZE  H13  CAT  CAJ  110.96  3.000
 3ZE  CAU  CAT  CAJ  100.88  3.000
 3ZE  OAE  CAT  CAJ  112.61  3.000
 3ZE  H14  OAE  CAT  108.96  3.000
 3ZE  H15  CAU  N9   106.63  3.000
 3ZE  H15  CAU  CAT  107.85  3.000
 3ZE  N9   CAU  CAT  114.97  3.000
 3ZE  H15  CAU  CAK  109.01  3.000
 3ZE  N9   CAU  CAK  114.36  3.000
 3ZE  CAT  CAU  CAK  103.79  3.000
 3ZE  CAU  N9   C8   128.65  3.000
 3ZE  C8   N9   C4   106.23  3.000
 3ZE  CAU  N9   C4   125.07  3.000
 3ZE  N3   C2   N2   119.99  3.000
 3ZE  N2   C2   N1   117.10  3.000
 3ZE  N3   C2   N1   122.91  3.000
 3ZE  C8   N7   C5   104.74  3.000
 3ZE  H4   N2   H3   117.99  3.000
 3ZE  H4   N2   C2   122.81  3.000
 3ZE  H3   N2   C2   119.10  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
 3ZE  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 3ZE  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 3ZE  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 3ZE  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 3ZE  CONST_05  N7   C5   C4   N9      0.00   0.0  0
 3ZE  CONST_06  CAU  N9   C4   C5    180.00   0.0  0
 3ZE  CONST_07  CAU  N9   C4   N3      0.00   0.0  0
 3ZE  CONST_08  N7   C8   N9   CAU   180.00   0.0  0
 3ZE  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 3ZE  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 3ZE  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 3ZE  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 3ZE  CONST_13  N2   C2   N1   C6    180.00   0.0  0
 3ZE  CONST_14  O6   C6   N1   C2    180.00   0.0  0
 3ZE  CONST_15  H1   C8   N9   C4    180.00   0.0  0
 3ZE  CONST_16  H2   N1   C6   C5    180.00   0.0  0
 3ZE  CONST_17  CAJ  NAV  CAO  CAI     0.00   0.0  0
 3ZE  CONST_18  CAK  NAV  CAO  CAI   180.00   0.0  0
 3ZE  CONST_19  CAJ  NAV  CAO  OAB   180.00   0.0  0
 3ZE  CONST_20  CAK  NAV  CAO  OAB     0.00   0.0  0
 3ZE  CONST_21  H3   N2   C2   N1    180.00   0.0  0
 3ZE  CONST_22  H4   N2   C2   N1      0.00   0.0  0
 3ZE  Var_01    CAT  CAJ  NAV  CAK   -16.36  30.0  1
 3ZE  Var_02    CAU  CAK  NAV  CAJ    -9.49  30.0  1
 3ZE  Var_03    NAV  CAO  CAI  PAX  -104.30  30.0  3
 3ZE  Var_04    CAO  CAI  PAX  OAF   177.59  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
 3ZE  chir_01  CAT  CAJ  OAE  CAU  negativ
 3ZE  chir_02  CAU  N9   CAT  CAK  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
 3ZE  plan-1  C4   0.020
 3ZE  plan-1  C5   0.020
 3ZE  plan-1  C6   0.020
 3ZE  plan-1  C8   0.020
 3ZE  plan-1  N1   0.020
 3ZE  plan-1  N3   0.020
 3ZE  plan-1  CAU  0.020
 3ZE  plan-1  N9   0.020
 3ZE  plan-1  C2   0.020
 3ZE  plan-1  O6   0.020
 3ZE  plan-1  N7   0.020
 3ZE  plan-1  H1   0.020
 3ZE  plan-1  H2   0.020
 3ZE  plan-1  H3   0.020
 3ZE  plan-1  H4   0.020
 3ZE  plan-1  N2   0.020
 3ZE  plan-2  CAI  0.020
 3ZE  plan-2  CAO  0.020
 3ZE  plan-2  OAB  0.020
 3ZE  plan-2  NAV  0.020
 3ZE  plan-2  CAK  0.020
 3ZE  plan-2  CAJ  0.020

