# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 04:03:03 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-phenyl-propanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)c4ccccc4
#
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
 8PZ  8PZ  '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-phenyl-propanoyl]sulfamate'  ligand  57  34  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8PZ
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
 8PZ  C1   C  CR56  0   0.491  -3.3110  -1.3134  -0.8880
 8PZ  C2   C  CR56  0  -0.014  -2.5195  -2.2896  -1.4715
 8PZ  C3   C  CR6   0   0.458  -3.1975  -3.3142  -2.1568
 8PZ  C4   C  CR15  0   0.108  -1.1795  -0.9413  -0.5518
 8PZ  N1   N  N     0  -0.474  -4.5343  -3.2645  -2.1938
 8PZ  N2   N  N     0  -0.458  -4.6392  -1.2495  -0.9163
 8PZ  C5   C  CR16  0  -0.318   4.2210  -1.8538   1.8886
 8PZ  C6   C  CR16  0  -0.237   5.0577  -2.8214   2.4254
 8PZ  C7   C  CR16  0  -0.269   5.0503  -4.1136   1.9135
 8PZ  C8   C  CR16  0  -0.238   4.2008  -4.4299   0.8628
 8PZ  C9   C  CR16  0  -0.321   3.3644  -3.4575   0.3286
 8PZ  C10  C  CR6   0   0.175   3.3646  -2.1616   0.8338
 8PZ  C11  C  CH1   0  -0.196   2.4562  -1.1108   0.2291
 8PZ  N3   N  NH2   0  -0.793   1.6494  -0.3574   1.1794
 8PZ  C12  C  CH2   0  -0.575   3.2780  -0.1242  -0.6088
 8PZ  C13  C  C     0   0.592   2.3661   0.8812  -1.2648
 8PZ  O1   O  O     0  -0.418   1.5283   0.5961  -2.0854
 8PZ  N4   N  NC1   0  -0.829   2.5468   2.1778  -0.8264
 8PZ  S1   S  S     0   1.622   1.6339   3.4731  -1.3307
 8PZ  O2   O  OS    0  -0.632   2.1048   4.5825  -0.5400
 8PZ  O3   O  OS    0  -0.609   1.5921   3.5503  -2.7635
 8PZ  C14  C  CH2   0  -0.211  -0.1278   2.8113   0.4776
 8PZ  C15  C  CH1   0  -0.041  -1.6366   2.7946   0.6097
 8PZ  O5   O  O2    0  -0.483  -2.2094   1.8528  -0.2918
 8PZ  C16  C  CH1   0  -0.030  -2.0653   2.3591   2.0072
 8PZ  O6   O  OH1   0  -0.664  -3.3162   2.9264   2.2854
 8PZ  C17  C  CH1   0  -0.057  -2.1797   0.8430   1.8186
 8PZ  O7   O  OH1   0  -0.651  -3.0374   0.2049   2.7142
 8PZ  C18  C  CH1   0   0.210  -2.7540   0.7622   0.4042
 8PZ  N5   N  NR5   0  -0.544  -2.4327  -0.4545  -0.2893
 8PZ  N6   N  N     0  -0.454  -1.1886  -2.0362  -1.2499
 8PZ  C19  C  CR16  0   0.047  -5.1625  -2.2604  -1.5888
 8PZ  N7   N  NH2   0  -0.817  -2.5638  -4.3154  -2.7683
 8PZ  H1   H  HCR5  0   0.304  -0.2920  -0.4433  -0.1866
 8PZ  H2   H  HCR6  0   0.245   4.2417  -0.8512   2.3008
 8PZ  H3   H  HCR6  0   0.257   5.7165  -2.5677   3.2460
 8PZ  H4   H  HCR6  0   0.257   5.7032  -4.8677   2.3332
 8PZ  H5   H  HCR6  0   0.257   4.1852  -5.4343   0.4596
 8PZ  H6   H  HCR6  0   0.250   2.7019  -3.7109  -0.4917
 8PZ  H7   H  HCH1  0   0.269   1.7660  -1.6252  -0.4463
 8PZ  H8   H  HNH2  0   0.369   1.1384  -0.9929   1.7803
 8PZ  H9   H  HNH2  0   0.363   2.2334   0.2003   1.7924
 8PZ  H11  H  HCH2  0   0.278   4.0287   0.3641   0.0168
 8PZ  H12  H  HCH2  0   0.305   3.8131  -0.6634  -1.3922
 8PZ  H13  H  HNC1  0   0.456   3.2569   2.3866  -0.1346
 8PZ  H14  H  HCH2  0   0.262   0.3279   1.8581   0.7622
 8PZ  H15  H  HCH2  0   0.275   0.2785   3.6034   1.1100
 8PZ  H16  H  HCH1  0   0.281  -2.0258   3.7894   0.3744
 8PZ  H17  H  HCH1  0   0.261  -1.3187   2.6205   2.7690
 8PZ  H18  H  HOH1  0   0.451  -3.7489   2.3793   2.9519
 8PZ  H19  H  HCH1  0   0.248  -1.1730   0.4059   1.8431
 8PZ  H20  H  HOH1  0   0.472  -2.5484  -0.0121   3.5143
 8PZ  H21  H  HCH1  0   0.267  -3.8470   0.8166   0.4358
 8PZ  H22  H  HCR6  0   0.252  -6.2449  -2.2785  -1.6582
 8PZ  H23  H  HNH2  0   0.404  -3.0863  -5.0482  -3.2161
 8PZ  H24  H  HNH2  0   0.411  -1.5638  -4.4022  -2.7235
 8PZ  O4   O  OC2   0  -0.565   0.1629   3.0705  -0.9110

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
 8PZ  C8   C7   aromatic  1.388  0.020  1.388
 8PZ  C8   C9   aromatic  1.389  0.020  1.389
 8PZ  C7   C6   aromatic  1.390  0.020  1.390
 8PZ  N7   C3   single    1.333  0.020  1.333
 8PZ  C9   C10  aromatic  1.391  0.020  1.391
 8PZ  C6   C5   aromatic  1.387  0.020  1.387
 8PZ  C3   N1   aromatic  1.338  0.020  1.338
 8PZ  C3   C2   aromatic  1.407  0.020  1.407
 8PZ  N1   C19  aromatic  1.330  0.020  1.330
 8PZ  C2   N6   aromatic  1.373  0.020  1.373
 8PZ  C2   C1   aromatic  1.386  0.020  1.386
 8PZ  C10  C5   aromatic  1.393  0.020  1.393
 8PZ  C10  C11  single    1.515  0.020  1.515
 8PZ  N6   C4   aromatic  1.299  0.020  1.299
 8PZ  C19  N2   aromatic  1.322  0.020  1.322
 8PZ  C1   N2   aromatic  1.330  0.020  1.330
 8PZ  C1   N5   aromatic  1.367  0.020  1.367
 8PZ  C4   N5   aromatic  1.370  0.020  1.370
 8PZ  C11  N3   single    1.457  0.020  1.457
 8PZ  C11  C12  single    1.533  0.020  1.533
 8PZ  N5   C18  single    1.437  0.020  1.437
 8PZ  O6   C16  single    1.401  0.020  1.401
 8PZ  C16  C17  single    1.532  0.020  1.532
 8PZ  C16  C15  single    1.525  0.020  1.525
 8PZ  C17  C18  single    1.529  0.020  1.529
 8PZ  C17  O7   single    1.395  0.020  1.395
 8PZ  C12  C13  single    1.508  0.020  1.508
 8PZ  C18  O5   single    1.404  0.020  1.404
 8PZ  C15  C14  single    1.515  0.020  1.515
 8PZ  C15  O5   single    1.424  0.020  1.424
 8PZ  C14  O4   single    1.442  0.020  1.442
 8PZ  C13  N4   single    1.381  0.020  1.381
 8PZ  C13  O1   double    1.207  0.020  1.207
 8PZ  N4   S1   single    1.663  0.020  1.663
 8PZ  O4   S1   single    1.582  0.020  1.582
 8PZ  O2   S1   deloc     1.441  0.020  1.441
 8PZ  S1   O3   deloc     1.435  0.020  1.435
 8PZ  C4   H1   single    0.930  0.020  1.080
 8PZ  C5   H2   single    0.930  0.020  1.080
 8PZ  C6   H3   single    0.930  0.020  1.080
 8PZ  C7   H4   single    0.930  0.020  1.080
 8PZ  C8   H5   single    0.930  0.020  1.080
 8PZ  C9   H6   single    0.930  0.020  1.080
 8PZ  C11  H7   single    0.970  0.020  1.090
 8PZ  N3   H8   single    0.890  0.020  1.040
 8PZ  N3   H9   single    0.890  0.020  1.040
 8PZ  C12  H11  single    0.970  0.020  1.090
 8PZ  C12  H12  single    0.970  0.020  1.090
 8PZ  N4   H13  single    0.860  0.020  1.020
 8PZ  C14  H14  single    0.970  0.020  1.090
 8PZ  C14  H15  single    0.970  0.020  1.090
 8PZ  C15  H16  single    0.970  0.020  1.090
 8PZ  C16  H17  single    0.970  0.020  1.090
 8PZ  O6   H18  single    0.850  0.020  0.980
 8PZ  C17  H19  single    0.970  0.020  1.090
 8PZ  O7   H20  single    0.850  0.020  0.980
 8PZ  C18  H21  single    0.970  0.020  1.090
 8PZ  C19  H22  single    0.930  0.020  1.080
 8PZ  N7   H23  single    0.860  0.020  1.020
 8PZ  N7   H24  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
 8PZ  N5   C1   N2   128.38  3.000
 8PZ  N5   C1   C2   105.08  3.000
 8PZ  N2   C1   C2   126.54  3.000
 8PZ  N6   C2   C3   132.86  3.000
 8PZ  N6   C2   C1   110.84  3.000
 8PZ  C3   C2   C1   116.29  3.000
 8PZ  N7   C3   N1   119.34  3.000
 8PZ  N1   C3   C2   117.89  3.000
 8PZ  N7   C3   C2   122.77  3.000
 8PZ  H1   C4   N6   125.15  3.000
 8PZ  H1   C4   N5   121.51  3.000
 8PZ  N6   C4   N5   113.35  3.000
 8PZ  C19  N1   C3   119.16  3.000
 8PZ  C19  N2   C1   111.67  3.000
 8PZ  H2   C5   C10  120.26  3.000
 8PZ  H2   C5   C6   119.10  3.000
 8PZ  C10  C5   C6   120.64  3.000
 8PZ  H3   C6   C7   120.02  3.000
 8PZ  H3   C6   C5   119.80  3.000
 8PZ  C7   C6   C5   120.18  3.000
 8PZ  H4   C7   C8   120.27  3.000
 8PZ  H4   C7   C6   120.12  3.000
 8PZ  C8   C7   C6   119.61  3.000
 8PZ  H5   C8   C9   119.84  3.000
 8PZ  H5   C8   C7   120.16  3.000
 8PZ  C9   C8   C7   120.00  3.000
 8PZ  H6   C9   C10  119.51  3.000
 8PZ  H6   C9   C8   119.68  3.000
 8PZ  C10  C9   C8   120.82  3.000
 8PZ  C11  C10  C9   120.08  3.000
 8PZ  C11  C10  C5   121.17  3.000
 8PZ  C9   C10  C5   118.75  3.000
 8PZ  H7   C11  C12  107.66  3.000
 8PZ  H7   C11  N3   107.25  3.000
 8PZ  C12  C11  N3   108.70  3.000
 8PZ  H7   C11  C10  107.36  3.000
 8PZ  C12  C11  C10  110.06  3.000
 8PZ  N3   C11  C10  115.50  3.000
 8PZ  H9   N3   H8   106.09  3.000
 8PZ  H9   N3   C11  111.10  3.000
 8PZ  H8   N3   C11  110.00  3.000
 8PZ  H12  C12  H11  107.16  3.000
 8PZ  H12  C12  C13  108.29  3.000
 8PZ  H11  C12  C13  111.52  3.000
 8PZ  H12  C12  C11  109.70  3.000
 8PZ  H11  C12  C11  110.06  3.000
 8PZ  C13  C12  C11  110.04  3.000
 8PZ  N4   C13  O1   121.91  3.000
 8PZ  O1   C13  C12  123.94  3.000
 8PZ  N4   C13  C12  114.14  3.000
 8PZ  H13  N4   S1   115.55  3.000
 8PZ  H13  N4   C13  120.15  3.000
 8PZ  S1   N4   C13  124.29  3.000
 8PZ  O4   S1   O3   104.56  3.000
 8PZ  O3   S1   O2   121.04  3.000
 8PZ  O4   S1   O2   110.74  3.000
 8PZ  O3   S1   N4   111.14  3.000
 8PZ  O2   S1   N4   104.70  3.000
 8PZ  O4   S1   N4   103.40  3.000
 8PZ  H15  C14  H14  109.05  3.000
 8PZ  H15  C14  C15  109.15  3.000
 8PZ  H14  C14  C15  112.50  3.000
 8PZ  H15  C14  O4   110.62  3.000
 8PZ  H14  C14  O4   108.84  3.000
 8PZ  C15  C14  O4   106.66  3.000
 8PZ  H16  C15  C16  110.90  3.000
 8PZ  H16  C15  O5   108.80  3.000
 8PZ  C16  C15  O5   106.15  3.000
 8PZ  H16  C15  C14  109.00  3.000
 8PZ  O5   C15  C14  110.65  3.000
 8PZ  C16  C15  C14  111.28  3.000
 8PZ  C18  O5   C15  110.86  3.000
 8PZ  H17  C16  C17  111.82  3.000
 8PZ  H17  C16  O6   111.89  3.000
 8PZ  C17  C16  O6   111.00  3.000
 8PZ  H17  C16  C15  112.12  3.000
 8PZ  C17  C16  C15  101.00  3.000
 8PZ  O6   C16  C15  108.49  3.000
 8PZ  H18  O6   C16  107.94  3.000
 8PZ  H19  C17  C18  110.13  3.000
 8PZ  H19  C17  O7   111.56  3.000
 8PZ  C18  C17  O7   109.81  3.000
 8PZ  H19  C17  C16  108.83  3.000
 8PZ  O7   C17  C16  114.81  3.000
 8PZ  C18  C17  C16  101.20  3.000
 8PZ  H20  O7   C17  108.94  3.000
 8PZ  H21  C18  N5   106.22  3.000
 8PZ  H21  C18  C17  110.22  3.000
 8PZ  N5   C18  C17  114.04  3.000
 8PZ  H21  C18  O5   111.29  3.000
 8PZ  C17  C18  O5   105.78  3.000
 8PZ  N5   C18  O5   109.38  3.000
 8PZ  C18  N5   C4   126.73  3.000
 8PZ  C18  N5   C1   126.86  3.000
 8PZ  C4   N5   C1   106.30  3.000
 8PZ  C4   N6   C2   104.43  3.000
 8PZ  H22  C19  N2   116.11  3.000
 8PZ  H22  C19  N1   115.45  3.000
 8PZ  N2   C19  N1   128.44  3.000
 8PZ  H24  N7   H23  118.30  3.000
 8PZ  H24  N7   C3   121.16  3.000
 8PZ  H23  N7   C3   120.31  3.000
 8PZ  C14  O4   S1   119.25  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
 8PZ  CONST_01  N1   C3   C2   C1     0.00   0.0  0
 8PZ  CONST_02  C4   N6   C2   C1     0.00   0.0  0
 8PZ  CONST_03  N1   C19  N2   C1     0.00   0.0  0
 8PZ  CONST_04  N6   C4   N5   C1     0.00   0.0  0
 8PZ  CONST_05  C19  N1   C3   C2     0.00   0.0  0
 8PZ  CONST_06  N5   C4   N6   C2     0.00   0.0  0
 8PZ  CONST_07  C19  N2   C1   C2     0.00   0.0  0
 8PZ  CONST_08  C4   N5   C1   C2     0.00   0.0  0
 8PZ  CONST_09  N2   C19  N1   C3     0.00   0.0  0
 8PZ  CONST_10  C4   N6   C2   C3   180.00   0.0  0
 8PZ  CONST_11  N2   C1   C2   C3     0.00   0.0  0
 8PZ  CONST_12  N5   C1   C2   C3   180.00   0.0  0
 8PZ  CONST_13  N2   C1   N5   C4   180.00   0.0  0
 8PZ  CONST_14  N6   C2   C3   N1   180.00   0.0  0
 8PZ  CONST_15  N6   C2   C1   N2   180.00   0.0  0
 8PZ  CONST_16  C8   C7   C6   C5     0.00   0.0  0
 8PZ  CONST_17  C8   C9   C10  C5     0.00   0.0  0
 8PZ  CONST_18  C9   C8   C7   C6     0.00   0.0  0
 8PZ  CONST_19  C9   C10  C5   C6     0.00   0.0  0
 8PZ  CONST_20  C10  C9   C8   C7     0.00   0.0  0
 8PZ  CONST_21  C10  C5   C6   C7     0.00   0.0  0
 8PZ  CONST_22  N6   C2   C1   N5     0.00   0.0  0
 8PZ  CONST_23  C19  N2   C1   N5   180.00   0.0  0
 8PZ  CONST_24  C18  N5   C1   C2   180.00   0.0  0
 8PZ  CONST_25  C18  N5   C1   N2     0.00   0.0  0
 8PZ  CONST_26  N6   C4   N5   C18  180.00   0.0  0
 8PZ  CONST_27  N7   C3   C2   C1   180.00   0.0  0
 8PZ  CONST_28  C11  C10  C5   C6   180.00   0.0  0
 8PZ  CONST_29  C11  C10  C9   C8   180.00   0.0  0
 8PZ  CONST_30  N7   C3   C2   N6     0.00   0.0  0
 8PZ  CONST_31  N7   C3   N1   C19  180.00   0.0  0
 8PZ  CONST_32  H22  C19  N2   C1   180.00   0.0  0
 8PZ  CONST_33  H1   C4   N5   C1   180.00   0.0  0
 8PZ  CONST_34  H4   C7   C6   C5   180.00   0.0  0
 8PZ  CONST_35  H6   C9   C10  C5   180.00   0.0  0
 8PZ  CONST_36  H5   C8   C7   C6   180.00   0.0  0
 8PZ  CONST_37  H2   C5   C6   C7   180.00   0.0  0
 8PZ  CONST_38  H3   C6   C7   C8   180.00   0.0  0
 8PZ  CONST_39  H23  N7   C3   C2   180.00   0.0  0
 8PZ  CONST_40  H24  N7   C3   C2     0.00   0.0  0
 8PZ  CONST_41  S1   N4   C13  C12  180.00   0.0  0
 8PZ  CONST_42  S1   N4   C13  O1     0.00   0.0  0
 8PZ  CONST_43  H13  N4   C13  C12    0.00   0.0  0
 8PZ  Var_01    C15  C14  O4   S1   166.33  30.0  2
 8PZ  Var_02    N4   C13  C12  C11  114.89  30.0  3
 8PZ  Var_03    O4   S1   N4   C13   59.57  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
 8PZ  chir_01  C11  C10  N3   C12  negativ
 8PZ  chir_02  C15  C16  C14  O5   negativ
 8PZ  chir_03  C16  O6   C17  C15  negativ
 8PZ  chir_04  C17  O7   C18  C16  negativ
 8PZ  chir_05  C18  O5   N5   C17  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
 8PZ  plan-1  C5   0.020
 8PZ  plan-1  C6   0.020
 8PZ  plan-1  C7   0.020
 8PZ  plan-1  C8   0.020
 8PZ  plan-1  C9   0.020
 8PZ  plan-1  C10  0.020
 8PZ  plan-1  C11  0.020
 8PZ  plan-1  H2   0.020
 8PZ  plan-1  H3   0.020
 8PZ  plan-1  H4   0.020
 8PZ  plan-1  H5   0.020
 8PZ  plan-1  H6   0.020
 8PZ  plan-2  C1   0.020
 8PZ  plan-2  C2   0.020
 8PZ  plan-2  C3   0.020
 8PZ  plan-2  C4   0.020
 8PZ  plan-2  N1   0.020
 8PZ  plan-2  N2   0.020
 8PZ  plan-2  C18  0.020
 8PZ  plan-2  N5   0.020
 8PZ  plan-2  N6   0.020
 8PZ  plan-2  C19  0.020
 8PZ  plan-2  N7   0.020
 8PZ  plan-2  H1   0.020
 8PZ  plan-2  H22  0.020
 8PZ  plan-3  C3   0.020
 8PZ  plan-3  N7   0.020
 8PZ  plan-3  H23  0.020
 8PZ  plan-3  H24  0.020
 8PZ  plan-4  C12  0.020
 8PZ  plan-4  C13  0.020
 8PZ  plan-4  O1   0.020
 8PZ  plan-4  N4   0.020
 8PZ  plan-4  S1   0.020
 8PZ  plan-4  H13  0.020

