# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:09:33 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  37  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 PERFECT
;

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   0.478   2.9777   0.0759   0.0018
 3ZE  C5   C  CR56   0  -0.093   3.6388  -1.0388  -0.4796
 3ZE  C6   C  CR6    0   0.508   5.0574  -1.0921  -0.3716
 3ZE  C8   C  CR15   0   0.042   1.5843  -1.3836  -0.8346
 3ZE  N1   N  NR16   0  -0.601   5.5502   0.0700   0.2375
 3ZE  N3   N  N      0  -0.593   3.5007   1.1692   0.5763
 3ZE  OAF  O  OP    -1  -0.960  -5.5880  -1.0930   1.4736
 3ZE  PAX  P  P      0   1.140  -4.3152  -1.1042   0.6349
 3ZE  OAG  O  OP    -1  -0.926  -3.0606  -1.4432   1.4874
 3ZE  OAD  O  O      0  -0.818  -4.3832  -1.8890  -0.6662
 3ZE  CAI  C  CH2    0  -0.891  -4.1004   0.7022   0.1174
 3ZE  CAO  C  C      0   0.588  -2.9064   0.8844  -0.7565
 3ZE  OAB  O  O      0  -0.614  -2.9701   0.7826  -1.9801
 3ZE  NAV  N  NR5    0  -0.432  -1.7126   1.1207  -0.1632
 3ZE  CAK  C  CH2    0  -0.256  -0.4807   0.9467  -0.9189
 3ZE  CAJ  C  CH2    0  -0.282  -1.4319   1.1314   1.2657
 3ZE  CAT  C  CR15   0   0.003  -0.2353   0.1961   1.3677
 3ZE  OAE  O  OH1    0  -0.684  -0.5778  -1.1373   1.1811
 3ZE  CAU  C  CR15   0  -0.185   0.5769   0.7123   0.1709
 3ZE  N9   N  NR5    0  -0.446   1.6586  -0.1519  -0.2347
 3ZE  C2   C  CR6    0   0.590   4.8046   1.1263   0.6767
 3ZE  O6   O  O      0  -0.472   5.8212  -1.9757  -0.7259
 3ZE  N7   N  N      0  -0.452   2.7463  -1.9393  -1.0024
 3ZE  H1   H  HCR5   0   0.302   0.6412  -1.8132  -1.1294
 3ZE  H2   H  HNR6   0   0.438   6.5537   0.1041   0.3667
 3ZE  H3   H  HNH2   0   0.423   4.9491   2.9791   1.4488
 3ZE  H4   H  HNH2   0   0.398   6.4576   2.2438   1.1404
 3ZE  H7   H  HCH2   0   0.287  -4.9863   0.9818  -0.4552
 3ZE  H8   H  HCH2   0   0.259  -4.0764   1.3345   1.0062
 3ZE  H9   H  HCH2   0   0.265  -0.5699   0.0960  -1.5965
 3ZE  H10  H  HCH2   0   0.262  -0.2365   1.8204  -1.5264
 3ZE  H11  H  HCH2   0   0.191  -1.1606   2.1377   1.6007
 3ZE  H12  H  HCH2   0   0.261  -2.2731   0.7881   1.8584
 3ZE  H13  H  HCR5   0   0.259   0.3139   0.3531   2.3060
 3ZE  H14  H  HOH1   0   0.458  -1.5903  -1.2544   1.2417
 3ZE  H15  H  HCR5   0   0.325   1.0349   1.6632   0.4485
 3ZE  N2   N  NH2    0  -0.771   5.4657   2.1355   1.2662

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  deloc     1.521  0.020  1.521
 3ZE  OAF  PAX  deloc     1.524  0.020  1.524
 3ZE  PAX  OAG  deloc     1.554  0.020  1.554
 3ZE  PAX  CAI  single    1.891  0.020  1.891
 3ZE  OAB  CAO  double    1.230  0.020  1.230
 3ZE  CAI  CAO  single    1.491  0.020  1.491
 3ZE  CAO  NAV  single    1.354  0.020  1.354
 3ZE  NAV  CAJ  single    1.456  0.020  1.456
 3ZE  NAV  CAK  single    1.456  0.020  1.456
 3ZE  CAJ  CAT  single    1.522  0.020  1.522
 3ZE  CAK  CAU  single    1.537  0.020  1.537
 3ZE  OAE  CAT  single    1.389  0.020  1.389
 3ZE  CAT  CAU  single    1.536  0.020  1.536
 3ZE  CAU  N9   single    1.443  0.020  1.443
 3ZE  C8   N9   aromatic  1.372  0.020  1.372
 3ZE  C8   N7   aromatic  1.299  0.020  1.299
 3ZE  N9   C4   aromatic  1.359  0.020  1.359
 3ZE  N7   C5   aromatic  1.371  0.020  1.371
 3ZE  C4   C5   aromatic  1.383  0.020  1.383
 3ZE  C4   N3   single    1.341  0.020  1.341
 3ZE  C5   C6   single    1.424  0.020  1.424
 3ZE  N3   C2   double    1.308  0.020  1.308
 3ZE  C6   O6   double    1.221  0.020  1.221
 3ZE  C6   N1   single    1.402  0.020  1.402
 3ZE  C2   N1   single    1.366  0.020  1.366
 3ZE  C2   N2   single    1.343  0.020  1.343
 3ZE  C8   H1   single    0.930  0.020  1.080
 3ZE  N1   H2   single    0.860  0.020  1.020
 3ZE  N2   H3   single    0.890  0.020  1.040
 3ZE  N2   H4   single    0.890  0.020  1.040
 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   126.12  3.000
 3ZE  N3   C4   C5   128.31  3.000
 3ZE  N9   C4   C5   105.57  3.000
 3ZE  N7   C5   C6   130.75  3.000
 3ZE  C6   C5   C4   118.70  3.000
 3ZE  N7   C5   C4   110.54  3.000
 3ZE  O6   C6   N1   120.42  3.000
 3ZE  N1   C6   C5   110.63  3.000
 3ZE  O6   C6   C5   128.95  3.000
 3ZE  H1   C8   N7   125.25  3.000
 3ZE  H1   C8   N9   121.67  3.000
 3ZE  N7   C8   N9   113.08  3.000
 3ZE  H2   N1   C2   118.30  3.000
 3ZE  H2   N1   C6   115.59  3.000
 3ZE  C2   N1   C6   126.10  3.000
 3ZE  C2   N3   C4   113.25  3.000
 3ZE  CAI  PAX  OAD  105.30  3.000
 3ZE  CAI  PAX  OAG  105.47  3.000
 3ZE  OAD  PAX  OAG  113.13  3.000
 3ZE  CAI  PAX  OAF  103.79  3.000
 3ZE  OAG  PAX  OAF  111.95  3.000
 3ZE  OAD  PAX  OAF  115.92  3.000
 3ZE  H8   CAI  H7   107.27  3.000
 3ZE  H8   CAI  CAO  112.90  3.000
 3ZE  H7   CAI  CAO  108.13  3.000
 3ZE  H8   CAI  PAX  109.46  3.000
 3ZE  H7   CAI  PAX  107.22  3.000
 3ZE  CAO  CAI  PAX  111.60  3.000
 3ZE  NAV  CAO  OAB  119.75  3.000
 3ZE  NAV  CAO  CAI  118.08  3.000
 3ZE  OAB  CAO  CAI  122.13  3.000
 3ZE  CAJ  NAV  CAK  110.32  3.000
 3ZE  CAK  NAV  CAO  119.85  3.000
 3ZE  CAJ  NAV  CAO  126.96  3.000
 3ZE  H10  CAK  H9   107.26  3.000
 3ZE  H10  CAK  CAU  111.27  3.000
 3ZE  H9   CAK  CAU  112.19  3.000
 3ZE  H10  CAK  NAV  112.49  3.000
 3ZE  H9   CAK  NAV  110.26  3.000
 3ZE  CAU  CAK  NAV  103.44  3.000
 3ZE  H12  CAJ  H11  108.41  3.000
 3ZE  H12  CAJ  CAT  112.24  3.000
 3ZE  H11  CAJ  CAT  110.45  3.000
 3ZE  H12  CAJ  NAV  112.61  3.000
 3ZE  H11  CAJ  NAV  110.78  3.000
 3ZE  CAT  CAJ  NAV  102.28  3.000
 3ZE  H13  CAT  CAU  110.68  3.000
 3ZE  H13  CAT  OAE  112.03  3.000
 3ZE  CAU  CAT  OAE  110.39  3.000
 3ZE  H13  CAT  CAJ  111.25  3.000
 3ZE  CAU  CAT  CAJ   99.04  3.000
 3ZE  OAE  CAT  CAJ  112.76  3.000
 3ZE  H14  OAE  CAT  110.28  3.000
 3ZE  H15  CAU  N9   106.19  3.000
 3ZE  H15  CAU  CAT  108.46  3.000
 3ZE  N9   CAU  CAT  114.48  3.000
 3ZE  H15  CAU  CAK  109.65  3.000
 3ZE  N9   CAU  CAK  114.08  3.000
 3ZE  CAT  CAU  CAK  103.88  3.000
 3ZE  CAU  N9   C8   128.32  3.000
 3ZE  C8   N9   C4   106.20  3.000
 3ZE  CAU  N9   C4   125.33  3.000
 3ZE  N3   C2   N2   119.98  3.000
 3ZE  N2   C2   N1   116.98  3.000
 3ZE  N3   C2   N1   123.01  3.000
 3ZE  C8   N7   C5   104.60  3.000
 3ZE  H4   N2   H3   116.04  3.000
 3ZE  H4   N2   C2   120.77  3.000
 3ZE  H3   N2   C2   117.20  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_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  Var_01    CAT  CAJ  NAV  CAK   -31.92  30.0  1
 3ZE  Var_02    CAU  CAK  NAV  CAJ     5.32  30.0  1
 3ZE  Var_03    NAV  CAO  CAI  PAX   -88.17  30.0  3
 3ZE  Var_04    CAO  CAI  PAX  OAF  -178.40  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

