# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:22:18 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)nc(nc23)c4cccnc4
#
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
 JPE  JPE  '[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate'  ligand  57  35  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JPE
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
 JPE  N    N  NH2   0  -0.775  -2.9733   2.5291   1.2251
 JPE  C    C  CH1   0  -0.263  -4.1753   2.0617   0.5681
 JPE  O    O  OH1   0  -0.665  -5.3960   4.0835   0.7245
 JPE  O3   O  OS    0  -0.629  -5.3538  -2.4437  -0.8639
 JPE  S    S  S     0   1.629  -4.3958  -1.4801  -1.3424
 JPE  O2   O  OS    0  -0.607  -4.3842  -1.0541  -2.7128
 JPE  N1   N  NC1   0  -0.835  -4.5591  -0.1728  -0.3236
 JPE  C2   C  C     0   0.594  -3.7844   0.9638  -0.4041
 JPE  O1   O  O     0  -0.409  -2.8770   1.0679  -1.1918
 JPE  C1   C  CH2   0  -0.133  -4.9623   3.1233  -0.2054
 JPE  O4   O  OC2   0  -0.565  -2.9181  -1.9746  -1.0657
 JPE  C3   C  CH2   0  -0.195  -2.5619  -2.4314   0.2516
 JPE  C4   C  CH1   0  -0.034  -1.1073  -2.8463   0.1921
 JPE  O5   O  O2    0  -0.483  -0.3012  -1.7629  -0.2622
 JPE  C7   C  CH1   0   0.212   0.6180  -1.3907   0.7331
 JPE  C6   C  CH1   0  -0.046   0.0147  -1.8927   2.0400
 JPE  O6   O  OH1   0  -0.650   1.0050  -1.9972   3.0143
 JPE  C5   C  CH1   0  -0.044  -0.5882  -3.2241   1.5785
 JPE  O7   O  OH1   0  -0.663   0.4039  -4.2031   1.4292
 JPE  N2   N  NR5   0  -0.561   0.8459   0.0240   0.6760
 JPE  C10  C  CR15  0   0.121  -0.0507   1.0374   0.8981
 JPE  N3   N  N     0  -0.451   0.4548   2.2192   0.7111
 JPE  C9   C  CR56  0  -0.027   1.7538   1.9841   0.3410
 JPE  C11  C  CR6   0   0.471   2.8273   2.8283   0.0008
 JPE  N4   N  NH2   0  -0.822   2.7267   4.1570  -0.0062
 JPE  N5   N  N     0  -0.506   3.9894   2.2594  -0.3271
 JPE  C12  C  CR6   0   0.406   4.1083   0.9312  -0.3225
 JPE  N6   N  N     0  -0.482   3.1668   0.0496  -0.0161
 JPE  C8   C  CR56  0   0.519   2.0175   0.6259   0.3065
 JPE  C13  C  CR6   0  -0.106   5.4324   0.3903  -0.6978
 JPE  C17  C  CR16  0  -0.075   5.6685  -0.9849  -0.7123
 JPE  N7   N  N     0  -0.402   6.8315  -1.5296  -1.0402
 JPE  C16  C  CR16  0  -0.066   7.8293  -0.7179  -1.3744
 JPE  C15  C  CR16  0  -0.313   7.7070   0.6631  -1.3929
 JPE  C14  C  CR16  0  -0.165   6.4897   1.2251  -1.0490
 JPE  H1   H  HNH2  0   0.355  -2.3668   3.0035   0.5663
 JPE  H2   H  HNH2  0   0.366  -3.2196   3.2097   1.9319
 JPE  H4   H  HCH1  0   0.277  -4.8347   1.6478   1.3364
 JPE  H5   H  HOH1  0   0.461  -5.8201   4.8004   0.2442
 JPE  H6   H  HNC1  0   0.459  -5.2873  -0.2513   0.3768
 JPE  H7   H  HCH2  0   0.208  -4.3087   3.5596  -0.9715
 JPE  H8   H  HCH2  0   0.207  -5.8061   2.6511  -0.7270
 JPE  H9   H  HCH2  0   0.251  -2.7202  -1.6293   0.9778
 JPE  H10  H  HCH2  0   0.281  -3.1744  -3.2888   0.5357
 JPE  H11  H  HCH1  0   0.282  -1.0050  -3.6874  -0.5001
 JPE  H12  H  HCH1  0   0.263   1.5946  -1.8584   0.5678
 JPE  H13  H  HCH1  0   0.250  -0.8009  -1.2292   2.3576
 JPE  H14  H  HOH1  0   0.472   0.5887  -2.0303   3.8817
 JPE  H15  H  HCH1  0   0.263  -1.3954  -3.5609   2.2422
 JPE  H16  H  HOH1  0   0.453   0.9320  -4.2187   2.2362
 JPE  H17  H  HCR5  0   0.285  -1.0728   0.8598   1.1981
 JPE  H18  H  HNH2  0   0.413   1.8671   4.6155   0.2401
 JPE  H19  H  HNH2  0   0.405   3.5173   4.7256  -0.2565
 JPE  H20  H  HCR6  0   0.265   4.8722  -1.6694  -0.4449
 JPE  H21  H  HCR6  0   0.268   8.7695  -1.1878  -1.6406
 JPE  H22  H  HCR6  0   0.273   8.5488   1.2815  -1.6725
 JPE  H23  H  HCR6  0   0.268   6.3560   2.2981  -1.0512

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
 JPE  N7   C16  aromatic  1.329  0.020  1.329
 JPE  N7   C17  aromatic  1.325  0.020  1.325
 JPE  C16  C15  aromatic  1.387  0.020  1.387
 JPE  C15  C14  aromatic  1.384  0.020  1.384
 JPE  C17  C13  aromatic  1.395  0.020  1.395
 JPE  C14  C13  aromatic  1.392  0.020  1.392
 JPE  O6   C6   single    1.393  0.020  1.393
 JPE  C13  C12  single    1.479  0.020  1.479
 JPE  C12  N5   aromatic  1.333  0.020  1.333
 JPE  C12  N6   aromatic  1.326  0.020  1.326
 JPE  N5   C11  aromatic  1.335  0.020  1.335
 JPE  C6   C5   single    1.533  0.020  1.533
 JPE  C6   C7   single    1.524  0.020  1.524
 JPE  O7   C5   single    1.402  0.020  1.402
 JPE  N6   C8   aromatic  1.326  0.020  1.326
 JPE  C11  N4   single    1.333  0.020  1.333
 JPE  C11  C9   aromatic  1.407  0.020  1.407
 JPE  C8   C9   aromatic  1.384  0.020  1.384
 JPE  C8   N2   aromatic  1.368  0.020  1.368
 JPE  C5   C4   single    1.528  0.020  1.528
 JPE  C9   N3   aromatic  1.371  0.020  1.371
 JPE  N2   C7   single    1.434  0.020  1.434
 JPE  N2   C10  aromatic  1.371  0.020  1.371
 JPE  C7   O5   single    1.405  0.020  1.405
 JPE  N3   C10  aromatic  1.299  0.020  1.299
 JPE  O3   S    deloc     1.441  0.020  1.441
 JPE  C4   O5   single    1.425  0.020  1.425
 JPE  C4   C3   single    1.514  0.020  1.514
 JPE  C3   O4   single    1.439  0.020  1.439
 JPE  S    O4   single    1.583  0.020  1.583
 JPE  S    O2   deloc     1.435  0.020  1.435
 JPE  S    N1   single    1.665  0.020  1.665
 JPE  N1   C2   single    1.378  0.020  1.378
 JPE  C2   O1   double    1.206  0.020  1.206
 JPE  C2   C    single    1.518  0.020  1.518
 JPE  O    C1   single    1.405  0.020  1.405
 JPE  C1   C    single    1.531  0.020  1.531
 JPE  C    N    single    1.447  0.020  1.447
 JPE  N    H1   single    0.890  0.020  1.040
 JPE  N    H2   single    0.890  0.020  1.040
 JPE  C    H4   single    0.970  0.020  1.090
 JPE  O    H5   single    0.850  0.020  0.980
 JPE  N1   H6   single    0.860  0.020  1.020
 JPE  C1   H7   single    0.970  0.020  1.090
 JPE  C1   H8   single    0.970  0.020  1.090
 JPE  C3   H9   single    0.970  0.020  1.090
 JPE  C3   H10  single    0.970  0.020  1.090
 JPE  C4   H11  single    0.970  0.020  1.090
 JPE  C7   H12  single    0.970  0.020  1.090
 JPE  C6   H13  single    0.970  0.020  1.090
 JPE  O6   H14  single    0.850  0.020  0.980
 JPE  C5   H15  single    0.970  0.020  1.090
 JPE  O7   H16  single    0.850  0.020  0.980
 JPE  C10  H17  single    0.930  0.020  1.080
 JPE  N4   H18  single    0.860  0.020  1.020
 JPE  N4   H19  single    0.860  0.020  1.020
 JPE  C17  H20  single    0.930  0.020  1.080
 JPE  C16  H21  single    0.930  0.020  1.080
 JPE  C15  H22  single    0.930  0.020  1.080
 JPE  C14  H23  single    0.930  0.020  1.080

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
 JPE  H2   N    H1   106.56  3.000
 JPE  H2   N    C    109.40  3.000
 JPE  H1   N    C    110.68  3.000
 JPE  H4   C    C1   107.90  3.000
 JPE  H4   C    C2   109.36  3.000
 JPE  C1   C    C2   108.08  3.000
 JPE  H4   C    N    107.69  3.000
 JPE  C1   C    N    115.61  3.000
 JPE  C2   C    N    108.09  3.000
 JPE  H5   O    C1   108.36  3.000
 JPE  O4   S    N1   103.29  3.000
 JPE  N1   S    O2   110.60  3.000
 JPE  O4   S    O2   104.61  3.000
 JPE  N1   S    O3   104.87  3.000
 JPE  O2   S    O3   121.40  3.000
 JPE  O4   S    O3   110.73  3.000
 JPE  H6   N1   C2   120.55  3.000
 JPE  H6   N1   S    115.62  3.000
 JPE  C2   N1   S    123.82  3.000
 JPE  O1   C2   N1   122.17  3.000
 JPE  O1   C2   C    123.35  3.000
 JPE  N1   C2   C    114.49  3.000
 JPE  H8   C1   H7   107.27  3.000
 JPE  H8   C1   O    111.77  3.000
 JPE  H7   C1   O    111.97  3.000
 JPE  H8   C1   C    109.66  3.000
 JPE  H7   C1   C    108.79  3.000
 JPE  O    C1   C    107.34  3.000
 JPE  C3   O4   S    119.36  3.000
 JPE  H10  C3   H9   108.79  3.000
 JPE  H10  C3   C4   109.52  3.000
 JPE  H9   C3   C4   111.48  3.000
 JPE  H10  C3   O4   110.41  3.000
 JPE  H9   C3   O4   109.83  3.000
 JPE  C4   C3   O4   106.79  3.000
 JPE  H11  C4   C5   110.62  3.000
 JPE  H11  C4   O5   109.27  3.000
 JPE  C5   C4   O5   106.56  3.000
 JPE  H11  C4   C3   109.00  3.000
 JPE  O5   C4   C3   110.35  3.000
 JPE  C5   C4   C3   111.01  3.000
 JPE  C7   O5   C4   110.23  3.000
 JPE  H12  C7   N2   105.87  3.000
 JPE  H12  C7   C6   109.97  3.000
 JPE  N2   C7   C6   114.95  3.000
 JPE  H12  C7   O5   111.31  3.000
 JPE  N2   C7   O5   109.70  3.000
 JPE  C6   C7   O5   105.14  3.000
 JPE  H13  C6   C5   108.65  3.000
 JPE  H13  C6   O6   111.77  3.000
 JPE  C5   C6   O6   115.15  3.000
 JPE  H13  C6   C7   110.05  3.000
 JPE  C5   C6   C7   100.58  3.000
 JPE  O6   C6   C7   110.06  3.000
 JPE  H14  O6   C6   108.98  3.000
 JPE  H15  C5   O7   111.75  3.000
 JPE  H15  C5   C6   111.94  3.000
 JPE  O7   C5   C6   111.12  3.000
 JPE  H15  C5   C4   112.00  3.000
 JPE  O7   C5   C4   108.45  3.000
 JPE  C6   C5   C4   101.07  3.000
 JPE  H16  O7   C5   108.04  3.000
 JPE  C8   N2   C10  106.18  3.000
 JPE  C10  N2   C7   128.22  3.000
 JPE  C8   N2   C7   125.51  3.000
 JPE  H17  C10  N3   123.92  3.000
 JPE  H17  C10  N2   122.84  3.000
 JPE  N3   C10  N2   113.24  3.000
 JPE  C9   N3   C10  104.57  3.000
 JPE  C8   C9   C11  115.93  3.000
 JPE  C8   C9   N3   110.83  3.000
 JPE  C11  C9   N3   133.25  3.000
 JPE  N5   C11  N4   119.30  3.000
 JPE  N4   C11  C9   122.80  3.000
 JPE  N5   C11  C9   117.90  3.000
 JPE  H19  N4   H18  118.40  3.000
 JPE  H19  N4   C11  120.38  3.000
 JPE  H18  N4   C11  121.22  3.000
 JPE  C12  N5   C11  120.08  3.000
 JPE  C13  C12  N6   116.82  3.000
 JPE  N6   C12  N5   126.86  3.000
 JPE  C13  C12  N5   116.31  3.000
 JPE  C8   N6   C12  112.51  3.000
 JPE  N6   C8   C9   126.72  3.000
 JPE  C9   C8   N2   105.18  3.000
 JPE  N6   C8   N2   128.10  3.000
 JPE  C14  C13  C17  117.38  3.000
 JPE  C14  C13  C12  121.65  3.000
 JPE  C17  C13  C12  120.98  3.000
 JPE  H20  C17  N7   116.50  3.000
 JPE  H20  C17  C13  119.71  3.000
 JPE  N7   C17  C13  123.79  3.000
 JPE  C16  N7   C17  118.03  3.000
 JPE  H21  C16  C15  120.32  3.000
 JPE  H21  C16  N7   116.62  3.000
 JPE  C15  C16  N7   123.06  3.000
 JPE  H22  C15  C14  121.11  3.000
 JPE  H22  C15  C16  120.29  3.000
 JPE  C14  C15  C16  118.60  3.000
 JPE  H23  C14  C15  120.74  3.000
 JPE  H23  C14  C13  120.11  3.000
 JPE  C15  C14  C13  119.15  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
 JPE  CONST_01  C12  N6   C8   N2   180.00   0.0  0
 JPE  CONST_02  C11  C9   C8   N2   180.00   0.0  0
 JPE  CONST_03  N3   C9   C8   N2     0.00   0.0  0
 JPE  CONST_04  C9   N3   C10  N2     0.00   0.0  0
 JPE  CONST_05  N6   C8   N2   C10  180.00   0.0  0
 JPE  CONST_06  C9   C8   N2   C10    0.00   0.0  0
 JPE  CONST_07  C11  C9   N3   C10  180.00   0.0  0
 JPE  CONST_08  C8   C9   N3   C10    0.00   0.0  0
 JPE  CONST_09  N5   C11  C9   N3   180.00   0.0  0
 JPE  CONST_10  N6   C8   C9   N3   180.00   0.0  0
 JPE  CONST_11  C8   N2   C10  N3     0.00   0.0  0
 JPE  CONST_12  C12  N5   C11  C9     0.00   0.0  0
 JPE  CONST_13  C12  N6   C8   C9     0.00   0.0  0
 JPE  CONST_14  C13  C12  N5   C11  180.00   0.0  0
 JPE  CONST_15  N6   C12  N5   C11    0.00   0.0  0
 JPE  CONST_16  N6   C8   C9   C11    0.00   0.0  0
 JPE  CONST_17  C17  C13  C12  N5   180.00   0.0  0
 JPE  CONST_18  C14  C13  C12  N5     0.00   0.0  0
 JPE  CONST_19  C8   N6   C12  N5     0.00   0.0  0
 JPE  CONST_20  C8   C9   C11  N5     0.00   0.0  0
 JPE  CONST_21  N7   C17  C13  C12  180.00   0.0  0
 JPE  CONST_22  C15  C14  C13  C12  180.00   0.0  0
 JPE  CONST_23  C17  C13  C12  N6     0.00   0.0  0
 JPE  CONST_24  C14  C13  C12  N6   180.00   0.0  0
 JPE  CONST_25  C13  C12  N6   C8   180.00   0.0  0
 JPE  CONST_26  C16  N7   C17  C13    0.00   0.0  0
 JPE  CONST_27  C16  C15  C14  C13    0.00   0.0  0
 JPE  CONST_28  C15  C16  N7   C17    0.00   0.0  0
 JPE  CONST_29  C15  C14  C13  C17    0.00   0.0  0
 JPE  CONST_30  C14  C15  C16  N7     0.00   0.0  0
 JPE  CONST_31  C14  C13  C17  N7     0.00   0.0  0
 JPE  CONST_32  N6   C8   N2   C7     0.00   0.0  0
 JPE  CONST_33  C9   C8   N2   C7   180.00   0.0  0
 JPE  CONST_34  N3   C10  N2   C7   180.00   0.0  0
 JPE  CONST_35  N4   C11  C9   N3     0.00   0.0  0
 JPE  CONST_36  C12  N5   C11  N4   180.00   0.0  0
 JPE  CONST_37  C8   C9   C11  N4   180.00   0.0  0
 JPE  CONST_38  H17  C10  N2   C7     0.00   0.0  0
 JPE  CONST_39  H20  C17  C13  C12    0.00   0.0  0
 JPE  CONST_40  H23  C14  C13  C12    0.00   0.0  0
 JPE  CONST_41  H22  C15  C14  C13  180.00   0.0  0
 JPE  CONST_42  H21  C16  N7   C17  180.00   0.0  0
 JPE  CONST_43  H18  N4   C11  C9     0.00   0.0  0
 JPE  CONST_44  H19  N4   C11  C9   180.00   0.0  0
 JPE  CONST_45  S    N1   C2   C    180.00   0.0  0
 JPE  CONST_46  O1   C2   N1   S      0.00   0.0  0
 JPE  CONST_47  H6   N1   C2   C      0.00   0.0  0
 JPE  Var_01    C4   C3   O4   S    179.35  30.0  2
 JPE  Var_02    C2   N1   S    O3   177.60  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
 JPE  chir_01  C   C2  C1  N   positiv
 JPE  chir_02  C4  O5  C5  C3  negativ
 JPE  chir_03  C7  O5  N2  C6  negativ
 JPE  chir_04  C6  O6  C7  C5  negativ
 JPE  chir_05  C5  O7  C4  C6  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
 JPE  plan-1  C12  0.020
 JPE  plan-1  C13  0.020
 JPE  plan-1  C17  0.020
 JPE  plan-1  N7   0.020
 JPE  plan-1  C16  0.020
 JPE  plan-1  C15  0.020
 JPE  plan-1  C14  0.020
 JPE  plan-1  H20  0.020
 JPE  plan-1  H21  0.020
 JPE  plan-1  H22  0.020
 JPE  plan-1  H23  0.020
 JPE  plan-2  C7   0.020
 JPE  plan-2  N2   0.020
 JPE  plan-2  C10  0.020
 JPE  plan-2  N3   0.020
 JPE  plan-2  C9   0.020
 JPE  plan-2  C11  0.020
 JPE  plan-2  N4   0.020
 JPE  plan-2  N5   0.020
 JPE  plan-2  C12  0.020
 JPE  plan-2  N6   0.020
 JPE  plan-2  C8   0.020
 JPE  plan-2  C13  0.020
 JPE  plan-2  H17  0.020
 JPE  plan-3  C11  0.020
 JPE  plan-3  N4   0.020
 JPE  plan-3  H18  0.020
 JPE  plan-3  H19  0.020
 JPE  plan-4  C    0.020
 JPE  plan-4  S    0.020
 JPE  plan-4  N1   0.020
 JPE  plan-4  C2   0.020
 JPE  plan-4  O1   0.020
 JPE  plan-4  H6   0.020

