# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:32:56 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{S})-2-[2,6-bis(azanyl)purin-9-yl]-5-(methylsulfanylmethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)nc(N)nc23
#
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
 5S7  5S7  (2~{R},3~{R},4~{S},5~{S})-2-[2,6-bis(azanyl)purin-9-yl]-5-(methylsulfanylmethyl)oxolane-3,4-diol  ligand  37  21  .  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_5S7
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
 5S7  C2   C  CR6   0   0.524  -3.7821   0.6287  -0.6608
 5S7  C4   C  CR56  0   0.507  -1.7328  -0.0654  -0.2374
 5S7  C5   C  CR56  0  -0.049  -2.1549  -1.3474   0.0749
 5S7  C6   C  CR6   0   0.458  -3.5425  -1.5715  -0.0079
 5S7  C8   C  CR15  0   0.093  -0.0530  -1.3739   0.2956
 5S7  O3'  O  OH1   0  -0.668   2.2779   3.3562  -0.0896
 5S7  C3'  C  CH1   0  -0.012   2.3977   2.1587   0.6308
 5S7  C4'  C  CH1   0  -0.003   2.8538   1.0573  -0.3174
 5S7  C5'  C  CH2   0  -0.584   3.5696  -0.0668   0.4150
 5S7  S5'  S  S2    0  -0.020   3.7311  -1.5138  -0.6651
 5S7  CS   C  CH3   0  -0.767   4.8799  -2.4837   0.3354
 5S7  C2'  C  CH1   0  -0.056   1.0222   1.6279   1.0447
 5S7  O2'  O  OH1   0  -0.652   0.1243   2.6013   1.4871
 5S7  C1'  C  CH1   0   0.221   0.5225   1.0189  -0.2687
 5S7  O4'  O  O2    0  -0.492   1.6631   0.5867  -0.9540
 5S7  N9   N  NR5   0  -0.546  -0.3763  -0.0941  -0.0891
 5S7  N7   N  N     0  -0.450  -1.0880  -2.1495   0.4017
 5S7  N3   N  N     0  -0.512  -2.4920   0.9586  -0.6068
 5S7  N1   N  N     0  -0.522  -4.3296  -0.5637  -0.3768
 5S7  N6   N  NH2   0  -0.821  -4.0908  -2.7598   0.2607
 5S7  N2   N  NH2   0  -0.825  -4.6437   1.5890  -1.0810
 5S7  H1   H  HCR5  0   0.285   0.9719  -1.6799   0.4495
 5S7  H2   H  HOH1  0   0.450   1.6482   3.9209   0.3741
 5S7  H3   H  HCH1  0   0.252   3.0759   2.2600   1.4879
 5S7  H4   H  HCH1  0   0.270   3.5136   1.4513  -1.0947
 5S7  H5   H  HCH2  0   0.289   4.5652   0.2834   0.6956
 5S7  H6   H  HCH2  0   0.266   3.0522  -0.3552   1.3339
 5S7  H7   H  HCH3  0   0.264   4.4439  -2.7346   1.3011
 5S7  H8   H  HCH3  0   0.276   5.0873  -3.4065  -0.2028
 5S7  H9   H  HCH3  0   0.263   5.8161  -1.9492   0.4892
 5S7  H10  H  HCH1  0   0.251   1.1525   0.8342   1.7907
 5S7  H11  H  HOH1  0   0.469   0.2898   2.7758   2.4193
 5S7  H12  H  HCH1  0   0.261  -0.0315   1.7675  -0.8451
 5S7  H13  H  HNH2  0   0.408  -3.5331  -3.5157   0.6162
 5S7  H14  H  HNH2  0   0.399  -5.0900  -2.8697   0.2524
 5S7  H15  H  HNH2  0   0.387  -5.6215   1.4489  -0.8938
 5S7  H16  H  HNH2  0   0.388  -4.3259   2.5427  -1.0488

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
 5S7  CS   S5'  single    1.806  0.020  1.806
 5S7  C5'  S5'  single    1.813  0.020  1.813
 5S7  C5'  C4'  single    1.521  0.020  1.521
 5S7  O3'  C3'  single    1.403  0.020  1.403
 5S7  C3'  C4'  single    1.523  0.020  1.523
 5S7  C3'  C2'  single    1.531  0.020  1.531
 5S7  C4'  O4'  single    1.430  0.020  1.430
 5S7  C2'  O2'  single    1.396  0.020  1.396
 5S7  C2'  C1'  single    1.532  0.020  1.532
 5S7  O4'  C1'  single    1.399  0.020  1.399
 5S7  C1'  N9   single    1.442  0.020  1.442
 5S7  N3   C4   aromatic  1.327  0.020  1.327
 5S7  N3   C2   aromatic  1.333  0.020  1.333
 5S7  N9   C4   aromatic  1.365  0.020  1.365
 5S7  N9   C8   aromatic  1.375  0.020  1.375
 5S7  N2   C2   single    1.357  0.020  1.357
 5S7  C4   C5   aromatic  1.385  0.020  1.385
 5S7  C2   N1   aromatic  1.342  0.020  1.342
 5S7  C8   N7   aromatic  1.298  0.020  1.298
 5S7  C5   N7   aromatic  1.374  0.020  1.374
 5S7  C5   C6   aromatic  1.408  0.020  1.408
 5S7  N1   C6   aromatic  1.331  0.020  1.331
 5S7  C6   N6   single    1.336  0.020  1.336
 5S7  C8   H1   single    0.930  0.020  1.080
 5S7  O3'  H2   single    0.850  0.020  0.980
 5S7  C3'  H3   single    0.970  0.020  1.090
 5S7  C4'  H4   single    0.970  0.020  1.090
 5S7  C5'  H5   single    0.970  0.020  1.090
 5S7  C5'  H6   single    0.970  0.020  1.090
 5S7  CS   H7   single    0.970  0.020  1.090
 5S7  CS   H8   single    0.970  0.020  1.090
 5S7  CS   H9   single    0.970  0.020  1.090
 5S7  C2'  H10  single    0.970  0.020  1.090
 5S7  O2'  H11  single    0.850  0.020  0.980
 5S7  C1'  H12  single    0.970  0.020  1.090
 5S7  N6   H13  single    0.860  0.020  1.020
 5S7  N6   H14  single    0.860  0.020  1.020
 5S7  N2   H15  single    0.890  0.020  1.040
 5S7  N2   H16  single    0.890  0.020  1.040

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
 5S7  N2   C2   N1   115.80  3.000
 5S7  N1   C2   N3   127.31  3.000
 5S7  N2   C2   N3   116.87  3.000
 5S7  N3   C4   N9   127.95  3.000
 5S7  N9   C4   C5   105.00  3.000
 5S7  N3   C4   C5   127.05  3.000
 5S7  N7   C5   C6   133.33  3.000
 5S7  C6   C5   C4   115.74  3.000
 5S7  N7   C5   C4   110.93  3.000
 5S7  N6   C6   N1   119.11  3.000
 5S7  N6   C6   C5   122.29  3.000
 5S7  N1   C6   C5   118.60  3.000
 5S7  H1   C8   N7   125.14  3.000
 5S7  H1   C8   N9   121.76  3.000
 5S7  N7   C8   N9   113.06  3.000
 5S7  H2   O3'  C3'  107.98  3.000
 5S7  H3   C3'  C2'  112.08  3.000
 5S7  H3   C3'  C4'  111.58  3.000
 5S7  C2'  C3'  C4'  100.76  3.000
 5S7  H3   C3'  O3'  112.03  3.000
 5S7  C2'  C3'  O3'  110.98  3.000
 5S7  C4'  C3'  O3'  108.86  3.000
 5S7  H4   C4'  O4'  107.74  3.000
 5S7  H4   C4'  C5'  108.95  3.000
 5S7  O4'  C4'  C5'  111.29  3.000
 5S7  H4   C4'  C3'  111.28  3.000
 5S7  O4'  C4'  C3'  105.41  3.000
 5S7  C5'  C4'  C3'  112.06  3.000
 5S7  H6   C5'  H5   107.46  3.000
 5S7  H6   C5'  S5'  109.42  3.000
 5S7  H5   C5'  S5'  109.14  3.000
 5S7  H6   C5'  C4'  112.15  3.000
 5S7  H5   C5'  C4'  108.41  3.000
 5S7  S5'  C5'  C4'  110.18  3.000
 5S7  CS   S5'  C5'   98.93  3.000
 5S7  H9   CS   H8   108.80  3.000
 5S7  H9   CS   H7   109.39  3.000
 5S7  H8   CS   H7   108.63  3.000
 5S7  H9   CS   S5'  111.20  3.000
 5S7  H8   CS   S5'  107.62  3.000
 5S7  H7   CS   S5'  111.12  3.000
 5S7  H10  C2'  C1'  109.52  3.000
 5S7  H10  C2'  O2'  111.43  3.000
 5S7  C1'  C2'  O2'  109.82  3.000
 5S7  H10  C2'  C3'  109.14  3.000
 5S7  C1'  C2'  C3'  101.48  3.000
 5S7  O2'  C2'  C3'  114.94  3.000
 5S7  H11  O2'  C2'  108.82  3.000
 5S7  H12  C1'  N9   106.13  3.000
 5S7  H12  C1'  O4'  111.45  3.000
 5S7  N9   C1'  O4'  109.32  3.000
 5S7  H12  C1'  C2'  110.15  3.000
 5S7  N9   C1'  C2'  113.80  3.000
 5S7  O4'  C1'  C2'  106.08  3.000
 5S7  C1'  O4'  C4'  111.05  3.000
 5S7  C1'  N9   C8   127.36  3.000
 5S7  C8   N9   C4   106.48  3.000
 5S7  C1'  N9   C4   126.14  3.000
 5S7  C8   N7   C5   104.53  3.000
 5S7  C4   N3   C2   111.96  3.000
 5S7  C6   N1   C2   119.34  3.000
 5S7  H14  N6   H13  118.20  3.000
 5S7  H14  N6   C6   120.24  3.000
 5S7  H13  N6   C6   120.84  3.000
 5S7  H16  N2   H15  115.69  3.000
 5S7  H16  N2   C2   117.42  3.000
 5S7  H15  N2   C2   117.46  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
 5S7  CONST_01  N9   C4   N3   C2   180.00   0.0  0
 5S7  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 5S7  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 5S7  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 5S7  CONST_05  N7   C8   N9   C4     0.00   0.0  0
 5S7  CONST_06  C8   N7   C5   C4     0.00   0.0  0
 5S7  CONST_07  N1   C6   C5   C4     0.00   0.0  0
 5S7  CONST_08  C8   N9   C4   C5     0.00   0.0  0
 5S7  CONST_09  N9   C8   N7   C5     0.00   0.0  0
 5S7  CONST_10  N3   C4   C5   C6     0.00   0.0  0
 5S7  CONST_11  N9   C4   C5   C6   180.00   0.0  0
 5S7  CONST_12  C8   N7   C5   C6   180.00   0.0  0
 5S7  CONST_13  N3   C2   N1   C6     0.00   0.0  0
 5S7  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 5S7  CONST_15  N7   C5   C4   N9     0.00   0.0  0
 5S7  CONST_16  N3   C4   C5   N7   180.00   0.0  0
 5S7  CONST_17  N1   C6   C5   N7   180.00   0.0  0
 5S7  CONST_18  C1'  N9   C4   C5   180.00   0.0  0
 5S7  CONST_19  N3   C4   N9   C1'    0.00   0.0  0
 5S7  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 5S7  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 5S7  CONST_22  N2   C2   N3   C4   180.00   0.0  0
 5S7  CONST_23  N6   C6   C5   C4   180.00   0.0  0
 5S7  CONST_24  N2   C2   N1   C6   180.00   0.0  0
 5S7  CONST_25  N6   C6   C5   N7     0.00   0.0  0
 5S7  CONST_26  H1   C8   N9   C4   180.00   0.0  0
 5S7  CONST_27  H13  N6   C6   C5     0.00   0.0  0
 5S7  CONST_28  H14  N6   C6   C5   180.00   0.0  0
 5S7  Var_01    H7   CS   S5'  C5'   61.75  30.0  3
 5S7  Var_02    H5   C5'  S5'  CS    49.92  30.0  2

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
 5S7  chir_01  C3'  O3'  C4'  C2'  positiv
 5S7  chir_02  C4'  O4'  C3'  C5'  negativ
 5S7  chir_03  C2'  O2'  C3'  C1'  positiv
 5S7  chir_04  C1'  O4'  N9   C2'  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
 5S7  plan-1  C2   0.020
 5S7  plan-1  C4   0.020
 5S7  plan-1  C5   0.020
 5S7  plan-1  C6   0.020
 5S7  plan-1  C8   0.020
 5S7  plan-1  C1'  0.020
 5S7  plan-1  N9   0.020
 5S7  plan-1  N7   0.020
 5S7  plan-1  N3   0.020
 5S7  plan-1  N1   0.020
 5S7  plan-1  N6   0.020
 5S7  plan-1  N2   0.020
 5S7  plan-1  H1   0.020
 5S7  plan-2  C6   0.020
 5S7  plan-2  N6   0.020
 5S7  plan-2  H13  0.020
 5S7  plan-2  H14  0.020
 5S7  plan-3  C2   0.020
 5S7  plan-3  N2   0.020
 5S7  plan-3  H15  0.020
 5S7  plan-3  H16  0.020

