# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:10:41 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(Nc4cccc(c4)C#C)ncnc23
#
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
 6O2  6O2  '[(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate'  ligand  49  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6O2
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
 6O2  C8   C  CR6   0  -0.029  -7.1492  -0.8140  -0.2868
 6O2  C5   C  CR6   0   0.530  -2.7628   0.0067  -0.0271
 6O2  C6   C  CR6   0   0.389  -4.8479  -1.3547   0.2012
 6O2  N1   N  N     0  -0.445  -1.2398   2.2592  -0.6972
 6O2  C2   C  CR15  0   0.211   1.7208   1.8129  -0.0807
 6O2  N3   N  NH1   0  -0.773  -3.4855  -1.0886   0.2992
 6O2  C4   C  CR16  0   0.064  -2.5451   2.1403  -0.8490
 6O2  C13  C  CSP1  0  -0.556  -8.9383   0.9350  -1.1036
 6O2  C12  C  CSP   0   0.302  -8.1181   0.1350  -0.7347
 6O2  C7   C  CR16  0  -0.351  -5.8038  -0.4404  -0.2369
 6O2  C9   C  CR16  0  -0.303  -7.5513  -2.0929   0.0957
 6O2  C10  C  CR16  0  -0.235  -6.5926  -2.9961   0.5284
 6O2  C11  C  CR16  0  -0.356  -5.2584  -2.6377   0.5817
 6O2  N2   N  N     0  -0.490  -3.3181   1.0962  -0.5477
 6O2  C3   C  CR56  0   0.503  -0.6983   1.1630  -0.1760
 6O2  C14  C  CR56  0  -0.029  -1.3737   0.0073   0.1838
 6O2  N4   N  N     0  -0.452  -0.5087  -0.9287   0.6835
 6O2  C15  C  CR15  0   0.116   0.6556  -0.3527   0.6307
 6O2  N    N  NR5   0  -0.541   0.6113   0.9168   0.1212
 6O2  O1   O  O     0  -0.486   2.7074   1.1611  -0.8322
 6O2  C16  C  CR15  0  -0.047   2.4063   2.2506   1.2121
 6O2  O2   O  OH1   0  -0.650   1.7199   3.3250   1.7748
 6O2  C17  C  CR15  0  -0.036   3.8149   2.5732   0.7031
 6O2  O3   O  OH1   0  -0.664   3.8435   3.8107   0.0457
 6O2  C1   C  CR15  0  -0.046   4.0081   1.4709  -0.3326
 6O2  C    C  CH2   0  -0.183   4.6487   0.2442   0.2826
 6O2  O    O  OC2   0  -0.577   4.7092  -0.7611  -0.7395
 6O2  S    S  S     0   1.583   4.9107  -2.2782  -0.2915
 6O2  O4   O  OS    0  -0.632   5.1018  -2.9711  -1.5422
 6O2  O5   O  OS    0  -0.652   5.9109  -2.3514   0.7494
 6O2  N5   N  NC2   0  -0.903   3.4653  -2.6110   0.4071
 6O2  H1   H  HCR5  0   0.269   1.3186   2.6837  -0.6099
 6O2  H2   H  HNH1  0   0.422  -2.9358  -1.8485   0.6746
 6O2  H3   H  HCR6  0   0.259  -3.0611   2.9950  -1.2710
 6O2  H4   H  H     0   0.284  -9.6651   1.6417  -1.4331
 6O2  H5   H  HCR6  0   0.295  -5.5136   0.5518  -0.5406
 6O2  H6   H  HCR6  0   0.262  -8.5953  -2.3715   0.0557
 6O2  H7   H  HCR6  0   0.269  -6.8865  -3.9928   0.8286
 6O2  H8   H  HCR6  0   0.277  -4.5225  -3.3578   0.9201
 6O2  H9   H  HCR5  0   0.299   1.5835  -0.8122   0.9385
 6O2  H10  H  HCR5  0   0.252   2.4649   1.4009   1.9047
 6O2  H11  H  HOH1  0   0.472   1.9643   3.4004   2.7028
 6O2  H12  H  HCR5  0   0.262   4.5610   2.5199   1.5066
 6O2  H13  H  HOH1  0   0.452   3.4105   4.4598   0.6125
 6O2  H14  H  HCR5  0   0.282   4.6273   1.8228  -1.1629
 6O2  H15  H  HCH2  0   0.274   5.6575   0.4889   0.6184
 6O2  H16  H  HCH2  0   0.246   4.0749  -0.1147   1.1422
 6O2  H17  H  HNC2  0   0.427   2.7501  -2.8864  -0.2572
 6O2  H18  H  HNC2  0   0.432   3.5410  -3.2758   1.1683

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
 6O2  N5   S    single    1.639  0.020  1.639
 6O2  O4   S    deloc     1.442  0.020  1.442
 6O2  S    O5   deloc     1.445  0.020  1.445
 6O2  S    O    single    1.595  0.020  1.595
 6O2  O    C    single    1.435  0.020  1.435
 6O2  C    C1   single    1.515  0.020  1.515
 6O2  C1   C17  single    1.525  0.020  1.525
 6O2  C1   O1   single    1.427  0.020  1.427
 6O2  O3   C17  single    1.402  0.020  1.402
 6O2  C17  C16  single    1.532  0.020  1.532
 6O2  O1   C2   single    1.401  0.020  1.401
 6O2  C16  C2   single    1.527  0.020  1.527
 6O2  C16  O2   single    1.394  0.020  1.394
 6O2  C2   N    single    1.440  0.020  1.440
 6O2  C15  N    aromatic  1.369  0.020  1.369
 6O2  C15  N4   aromatic  1.300  0.020  1.300
 6O2  N    C3   aromatic  1.365  0.020  1.365
 6O2  N4   C14  aromatic  1.369  0.020  1.369
 6O2  C3   N1   aromatic  1.329  0.020  1.329
 6O2  C3   C14  aromatic  1.386  0.020  1.386
 6O2  N1   C4   aromatic  1.319  0.020  1.319
 6O2  C14  C5   aromatic  1.405  0.020  1.405
 6O2  C4   N2   aromatic  1.334  0.020  1.334
 6O2  C5   N2   aromatic  1.329  0.020  1.329
 6O2  C5   N3   single    1.352  0.020  1.352
 6O2  N3   C6   single    1.392  0.020  1.392
 6O2  C11  C6   aromatic  1.400  0.020  1.400
 6O2  C11  C10  aromatic  1.382  0.020  1.382
 6O2  C6   C7   aromatic  1.393  0.020  1.393
 6O2  C10  C9   aromatic  1.386  0.020  1.386
 6O2  C7   C8   aromatic  1.397  0.020  1.397
 6O2  C9   C8   aromatic  1.394  0.020  1.394
 6O2  C8   C12  single    1.428  0.020  1.428
 6O2  C12  C13  triple    1.204  0.020  1.204
 6O2  C2   H1   single    0.939  0.020  1.096
 6O2  N3   H2   single    0.868  0.020  1.013
 6O2  C4   H3   single    0.929  0.020  1.085
 6O2  C13  H4   single    0.913  0.020  1.066
 6O2  C7   H5   single    0.929  0.020  1.085
 6O2  C9   H6   single    0.929  0.020  1.085
 6O2  C10  H7   single    0.929  0.020  1.085
 6O2  C11  H8   single    0.929  0.020  1.085
 6O2  C15  H9   single    0.929  0.020  1.085
 6O2  C16  H10  single    0.939  0.020  1.096
 6O2  O2   H11  single    0.832  0.020  0.971
 6O2  C17  H12  single    0.939  0.020  1.096
 6O2  O3   H13  single    0.832  0.020  0.971
 6O2  C1   H14  single    0.939  0.020  1.096
 6O2  C    H15  single    0.939  0.020  1.096
 6O2  C    H16  single    0.939  0.020  1.096
 6O2  N5   H17  single    0.868  0.020  1.013
 6O2  N5   H18  single    0.868  0.020  1.013

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
 6O2  C9   C8   C7   120.88  3.000
 6O2  C9   C8   C12  120.00  3.000
 6O2  C7   C8   C12  119.12  3.000
 6O2  C14  C5   N2   118.13  3.000
 6O2  N2   C5   N3   122.36  3.000
 6O2  C14  C5   N3   119.51  3.000
 6O2  C11  C6   C7   119.06  3.000
 6O2  C7   C6   N3   124.64  3.000
 6O2  C11  C6   N3   116.31  3.000
 6O2  C3   N1   C4   111.95  3.000
 6O2  H1   C2   C16  110.23  3.000
 6O2  H1   C2   O1   111.67  3.000
 6O2  C16  C2   O1   105.74  3.000
 6O2  H1   C2   N    106.23  3.000
 6O2  C16  C2   N    113.92  3.000
 6O2  O1   C2   N    109.16  3.000
 6O2  H2   N3   C6   114.53  3.000
 6O2  H2   N3   C5   114.09  3.000
 6O2  C6   N3   C5   131.38  3.000
 6O2  H3   C4   N2   115.42  3.000
 6O2  H3   C4   N1   116.40  3.000
 6O2  N2   C4   N1   128.17  3.000
 6O2  H4   C13  C12  180.00  3.000
 6O2  C13  C12  C8   180.00  3.000
 6O2  H5   C7   C6   120.53  3.000
 6O2  H5   C7   C8   119.71  3.000
 6O2  C6   C7   C8   119.76  3.000
 6O2  H6   C9   C10  120.76  3.000
 6O2  H6   C9   C8   120.31  3.000
 6O2  C10  C9   C8   118.93  3.000
 6O2  H7   C10  C11  119.37  3.000
 6O2  H7   C10  C9   119.93  3.000
 6O2  C11  C10  C9   120.70  3.000
 6O2  H8   C11  C10  119.68  3.000
 6O2  H8   C11  C6   119.65  3.000
 6O2  C10  C11  C6   120.67  3.000
 6O2  C4   N2   C5   119.21  3.000
 6O2  N    C3   C14  105.10  3.000
 6O2  C14  C3   N1   126.22  3.000
 6O2  N    C3   N1   128.67  3.000
 6O2  N4   C14  C3   110.91  3.000
 6O2  C3   C14  C5   116.31  3.000
 6O2  N4   C14  C5   132.78  3.000
 6O2  C15  N4   C14  104.37  3.000
 6O2  H9   C15  N    121.90  3.000
 6O2  H9   C15  N4   124.70  3.000
 6O2  N    C15  N4   113.40  3.000
 6O2  C15  N    C3   106.22  3.000
 6O2  C3   N    C2   126.60  3.000
 6O2  C15  N    C2   127.18  3.000
 6O2  C1   O1   C2   110.67  3.000
 6O2  H10  C16  C17  108.87  3.000
 6O2  H10  C16  O2   111.61  3.000
 6O2  C17  C16  O2   115.13  3.000
 6O2  H10  C16  C2   109.64  3.000
 6O2  O2   C16  C2   109.98  3.000
 6O2  C17  C16  C2   101.06  3.000
 6O2  H11  O2   C16  108.94  3.000
 6O2  H12  C17  C1   112.08  3.000
 6O2  H12  C17  O3   111.86  3.000
 6O2  C1   C17  O3   108.48  3.000
 6O2  H12  C17  C16  111.81  3.000
 6O2  O3   C17  C16  111.13  3.000
 6O2  C1   C17  C16  100.95  3.000
 6O2  H13  O3   C17  108.02  3.000
 6O2  H14  C1   C    109.23  3.000
 6O2  H14  C1   C17  110.78  3.000
 6O2  C    C1   C17  111.30  3.000
 6O2  H14  C1   O1   108.66  3.000
 6O2  C17  C1   O1   106.21  3.000
 6O2  C    C1   O1   110.60  3.000
 6O2  H16  C    H15  108.46  3.000
 6O2  H16  C    O    110.61  3.000
 6O2  H15  C    O    109.72  3.000
 6O2  H16  C    C1   111.28  3.000
 6O2  H15  C    C1   109.54  3.000
 6O2  O    C    C1   107.22  3.000
 6O2  S    O    C    118.15  3.000
 6O2  N5   S    O5   107.03  3.000
 6O2  O5   S    O4   120.56  3.000
 6O2  N5   S    O4   112.88  3.000
 6O2  O5   S    O    109.75  3.000
 6O2  O4   S    O    103.31  3.000
 6O2  N5   S    O    101.62  3.000
 6O2  H18  N5   H17  111.50  3.000
 6O2  H18  N5   S    112.79  3.000
 6O2  H17  N5   S    113.44  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
 6O2  CONST_01  C11  C6   C7   C8     0.00   0.0  0
 6O2  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 6O2  CONST_03  C15  N4   C14  C5   180.00   0.0  0
 6O2  CONST_04  N    C3   C14  C5   180.00   0.0  0
 6O2  CONST_05  N1   C3   C14  C5     0.00   0.0  0
 6O2  CONST_06  N1   C4   N2   C5     0.00   0.0  0
 6O2  CONST_07  C9   C10  C11  C6     0.00   0.0  0
 6O2  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 6O2  CONST_09  C15  N    C3   N1   180.00   0.0  0
 6O2  CONST_10  N4   C14  C3   N1   180.00   0.0  0
 6O2  CONST_11  N    C3   N1   C4   180.00   0.0  0
 6O2  CONST_12  C14  C3   N1   C4     0.00   0.0  0
 6O2  CONST_13  C14  C5   N2   C4     0.00   0.0  0
 6O2  CONST_14  C10  C11  C6   C7     0.00   0.0  0
 6O2  CONST_15  C10  C9   C8   C7     0.00   0.0  0
 6O2  CONST_16  C3   N1   C4   N2     0.00   0.0  0
 6O2  CONST_17  N4   C14  C5   N2   180.00   0.0  0
 6O2  CONST_18  C3   C14  C5   N2     0.00   0.0  0
 6O2  CONST_19  N4   C15  N    C3     0.00   0.0  0
 6O2  CONST_20  C15  N4   C14  C3     0.00   0.0  0
 6O2  CONST_21  N    C15  N4   C14    0.00   0.0  0
 6O2  CONST_22  C15  N    C3   C14    0.00   0.0  0
 6O2  CONST_23  N    C3   C14  N4     0.00   0.0  0
 6O2  CONST_24  C2   N    C3   N1     0.00   0.0  0
 6O2  CONST_25  N4   C15  N    C2   180.00   0.0  0
 6O2  CONST_26  C14  C3   N    C2   180.00   0.0  0
 6O2  CONST_27  N3   C6   C7   C8   180.00   0.0  0
 6O2  CONST_28  C12  C8   C7   C6   180.00   0.0  0
 6O2  CONST_29  N4   C14  C5   N3     0.00   0.0  0
 6O2  CONST_30  C3   C14  C5   N3   180.00   0.0  0
 6O2  CONST_31  C4   N2   C5   N3   180.00   0.0  0
 6O2  CONST_32  C10  C11  C6   N3   180.00   0.0  0
 6O2  CONST_33  C10  C9   C8   C12  180.00   0.0  0
 6O2  CONST_34  H7   C10  C9   C8   180.00   0.0  0
 6O2  CONST_35  H3   C4   N2   C5   180.00   0.0  0
 6O2  CONST_36  H9   C15  N    C2     0.00   0.0  0
 6O2  CONST_37  H8   C11  C6   C7   180.00   0.0  0
 6O2  CONST_38  H6   C9   C8   C7   180.00   0.0  0
 6O2  CONST_39  H5   C7   C8   C9   180.00   0.0  0
 6O2  Var_01    C11  C6   N3   C5   177.19  30.0  2
 6O2  Var_02    C14  C5   N3   C6   179.84  30.0  2
 6O2  Var_03    N5   S    O    C     70.13  30.0  2
 6O2  Var_04    H17  N5   S    O     83.94  30.0  3
 6O2  Var_05    H15  C    O    S     79.66  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
 6O2  chir_01  C2   O1  C16  N    positiv
 6O2  chir_02  C16  O2  C2   C17  negativ
 6O2  chir_03  C17  O3  C1   C16  positiv
 6O2  chir_04  C1   O1  C17  C    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
 6O2  plan-1  C8   0.020
 6O2  plan-1  C6   0.020
 6O2  plan-1  N3   0.020
 6O2  plan-1  C13  0.020
 6O2  plan-1  C12  0.020
 6O2  plan-1  C7   0.020
 6O2  plan-1  C9   0.020
 6O2  plan-1  C10  0.020
 6O2  plan-1  C11  0.020
 6O2  plan-1  H5   0.020
 6O2  plan-1  H6   0.020
 6O2  plan-1  H7   0.020
 6O2  plan-1  H8   0.020
 6O2  plan-2  C5   0.020
 6O2  plan-2  N1   0.020
 6O2  plan-2  C2   0.020
 6O2  plan-2  N3   0.020
 6O2  plan-2  C4   0.020
 6O2  plan-2  N2   0.020
 6O2  plan-2  C3   0.020
 6O2  plan-2  C14  0.020
 6O2  plan-2  N4   0.020
 6O2  plan-2  C15  0.020
 6O2  plan-2  N    0.020
 6O2  plan-2  H3   0.020
 6O2  plan-2  H9   0.020

