# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 12:43:29 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@@H]4CO[P@@](S)(=O)O[C@H]4[C@H]3O)c(SCc5ccccc5)nc12
#
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
 HR6  HR6  '(2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide'  ligand  48  30  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HR6
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
 HR6  S1P  S  S2    0  -0.355  -3.5353   0.4375  -1.3023
 HR6  P    P  P     0   1.244  -3.2225   2.3190  -0.4585
 HR6  O2P  O  O     0  -0.643  -4.1835   3.3669  -0.8313
 HR6  O5'  O  O2    0  -0.568  -3.1469   2.0999   1.1267
 HR6  C5'  C  CH2   0  -0.218  -2.0756   1.3678   1.7508
 HR6  O3'  O  O2    0  -0.569  -1.7149   2.6242  -0.9353
 HR6  C3'  C  CH1   0  -0.022  -0.7090   1.8660  -0.2816
 HR6  C2'  C  CH1   0  -0.068   0.7216   2.3004  -0.5351
 HR6  O2'  O  OH1   0  -0.650   0.7750   3.6929  -0.5381
 HR6  C4'  C  CH1   0   0.009  -0.8005   1.9964   1.2300
 HR6  O4'  O  O2    0  -0.490   0.3873   1.3723   1.6617
 HR6  C1'  C  CH1   0   0.165   1.4019   1.6962   0.7370
 HR6  N9   N  NR5   0  -0.577   2.1819   0.5095   0.4809
 HR6  C4   C  CR56  0   0.491   3.5023   0.5504   0.1181
 HR6  N3   N  N     0  -0.460   4.2810   1.6212   0.0120
 HR6  C2   C  CR16  0   0.042   5.5065   1.2947  -0.3686
 HR6  N1   N  N     0  -0.470   5.9902   0.0865  -0.6354
 HR6  C6   C  CR6   0   0.450   5.1876  -0.9799  -0.5277
 HR6  N6   N  NH2   0  -0.817   5.6683  -2.1921  -0.8114
 HR6  C5   C  CR56  0   0.016   3.8571  -0.7614  -0.1311
 HR6  N7   N  N     0  -0.455   2.7925  -1.6000   0.0741
 HR6  C8   C  CR5   0   0.316   1.8137  -0.8177   0.4257
 HR6  S2   S  S2    0   0.079   0.2029  -1.3662   0.8049
 HR6  C9   C  CH2   0  -0.622   0.2472  -3.0224   0.0392
 HR6  C10  C  CR6   0   0.093  -1.1582  -3.5446   0.0732
 HR6  C15  C  CR16  0  -0.290  -1.5528  -4.4581   1.0454
 HR6  C14  C  CR16  0  -0.240  -2.8600  -4.9263   1.0836
 HR6  C11  C  CR16  0  -0.265  -2.0955  -3.0950  -0.8546
 HR6  C12  C  CR16  0  -0.242  -3.4011  -3.5608  -0.8179
 HR6  C13  C  CR16  0  -0.264  -3.7866  -4.4788   0.1519
 HR6  H1   H  HSH1  0   0.277  -4.6900   0.2112  -0.6609
 HR6  H2   H  HCH2  0   0.289  -2.2001   1.4903   2.8246
 HR6  H3   H  HCH2  0   0.254  -2.1492   0.3059   1.5037
 HR6  H4   H  HCH1  0   0.280  -0.7978   0.8094  -0.5631
 HR6  H5   H  HCH1  0   0.286   1.1448   1.8631  -1.4450
 HR6  H6   H  HOH1  0   0.469   1.6603   3.9732  -0.7925
 HR6  H7   H  HCH1  0   0.277  -0.8029   3.0574   1.5151
 HR6  H8   H  HCH1  0   0.291   2.0901   2.4348   1.1590
 HR6  H9   H  HCR6  0   0.254   6.2071   2.1149  -0.4793
 HR6  H10  H  HNH2  0   0.404   6.6458  -2.3112  -1.0141
 HR6  H11  H  HNH2  0   0.411   5.1159  -3.0163  -0.6514
 HR6  H12  H  HCH2  0   0.303   0.6175  -2.9196  -0.9800
 HR6  H13  H  HCH2  0   0.300   0.9290  -3.6612   0.5974
 HR6  H14  H  HCR6  0   0.257  -0.8328  -4.8122   1.7734
 HR6  H15  H  HCR6  0   0.259  -3.1527  -5.6404   1.8425
 HR6  H16  H  HCR6  0   0.252  -1.8016  -2.3773  -1.6115
 HR6  H17  H  HCR6  0   0.257  -4.1185  -3.2090  -1.5479
 HR6  H18  H  HCR6  0   0.259  -4.8051  -4.8436   0.1796

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
 HR6  O2P  P    double    1.470  0.020  1.470
 HR6  O5'  C5'  single    1.440  0.020  1.440
 HR6  O5'  P    single    1.602  0.020  1.602
 HR6  C5'  C4'  single    1.514  0.020  1.514
 HR6  P    O3'  single    1.610  0.020  1.610
 HR6  P    S1P  single    2.086  0.020  2.086
 HR6  C4'  O4'  single    1.410  0.020  1.410
 HR6  C4'  C3'  single    1.520  0.020  1.520
 HR6  O3'  C3'  single    1.419  0.020  1.419
 HR6  O4'  C1'  single    1.410  0.020  1.410
 HR6  C3'  C2'  single    1.516  0.020  1.516
 HR6  O2'  C2'  single    1.394  0.020  1.394
 HR6  C2'  C1'  single    1.564  0.020  1.564
 HR6  C1'  N9   single    1.443  0.020  1.443
 HR6  N3   C4   aromatic  1.328  0.020  1.328
 HR6  N3   C2   aromatic  1.324  0.020  1.324
 HR6  N9   C4   aromatic  1.370  0.020  1.370
 HR6  N9   C8   aromatic  1.378  0.020  1.378
 HR6  C4   C5   aromatic  1.382  0.020  1.382
 HR6  C2   N1   aromatic  1.329  0.020  1.329
 HR6  S2   C8   single    1.743  0.020  1.743
 HR6  S2   C9   single    1.825  0.020  1.825
 HR6  C8   N7   aromatic  1.301  0.020  1.301
 HR6  N1   C6   aromatic  1.339  0.020  1.339
 HR6  C5   N7   aromatic  1.371  0.020  1.371
 HR6  C5   C6   aromatic  1.406  0.020  1.406
 HR6  C6   N6   single    1.335  0.020  1.335
 HR6  C15  C14  aromatic  1.389  0.020  1.389
 HR6  C15  C10  aromatic  1.391  0.020  1.391
 HR6  C14  C13  aromatic  1.388  0.020  1.388
 HR6  C9   C10  single    1.500  0.020  1.500
 HR6  C10  C11  aromatic  1.393  0.020  1.393
 HR6  C13  C12  aromatic  1.390  0.020  1.390
 HR6  C11  C12  aromatic  1.387  0.020  1.387
 HR6  S1P  H1   single    1.200  0.020  1.300
 HR6  C5'  H2   single    0.970  0.020  1.090
 HR6  C5'  H3   single    0.970  0.020  1.090
 HR6  C3'  H4   single    0.970  0.020  1.090
 HR6  C2'  H5   single    0.970  0.020  1.090
 HR6  O2'  H6   single    0.850  0.020  0.980
 HR6  C4'  H7   single    0.970  0.020  1.090
 HR6  C1'  H8   single    0.970  0.020  1.090
 HR6  C2   H9   single    0.930  0.020  1.080
 HR6  N6   H10  single    0.860  0.020  1.020
 HR6  N6   H11  single    0.860  0.020  1.020
 HR6  C9   H12  single    0.970  0.020  1.090
 HR6  C9   H13  single    0.970  0.020  1.090
 HR6  C15  H14  single    0.930  0.020  1.080
 HR6  C14  H15  single    0.930  0.020  1.080
 HR6  C11  H16  single    0.930  0.020  1.080
 HR6  C12  H17  single    0.930  0.020  1.080
 HR6  C13  H18  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
 HR6  H1   S1P  P     95.04  3.000
 HR6  O3'  P    O5'  105.94  3.000
 HR6  O3'  P    O2P  113.70  3.000
 HR6  O5'  P    O2P  112.29  3.000
 HR6  O3'  P    S1P  101.04  3.000
 HR6  O5'  P    S1P  106.50  3.000
 HR6  O2P  P    S1P  116.26  3.000
 HR6  C5'  O5'  P    122.25  3.000
 HR6  H3   C5'  H2   108.96  3.000
 HR6  H3   C5'  C4'  112.48  3.000
 HR6  H2   C5'  C4'  112.90  3.000
 HR6  H3   C5'  O5'  110.24  3.000
 HR6  H2   C5'  O5'  106.59  3.000
 HR6  C4'  C5'  O5'  105.45  3.000
 HR6  C3'  O3'  P    115.21  3.000
 HR6  H4   C3'  C4'  109.45  3.000
 HR6  H4   C3'  C2'  108.02  3.000
 HR6  C4'  C3'  C2'  101.45  3.000
 HR6  H4   C3'  O3'  109.81  3.000
 HR6  C2'  C3'  O3'  116.02  3.000
 HR6  C4'  C3'  O3'  111.69  3.000
 HR6  H5   C2'  C1'  110.70  3.000
 HR6  H5   C2'  O2'  112.49  3.000
 HR6  C1'  C2'  O2'  111.78  3.000
 HR6  H5   C2'  C3'  112.91  3.000
 HR6  C1'  C2'  C3'   99.42  3.000
 HR6  O2'  C2'  C3'  108.83  3.000
 HR6  H6   O2'  C2'  109.07  3.000
 HR6  H7   C4'  O4'  110.49  3.000
 HR6  H7   C4'  C3'  109.94  3.000
 HR6  O4'  C4'  C3'  102.47  3.000
 HR6  H7   C4'  C5'  108.05  3.000
 HR6  C3'  C4'  C5'  110.93  3.000
 HR6  O4'  C4'  C5'  114.86  3.000
 HR6  C1'  O4'  C4'  107.68  3.000
 HR6  H8   C1'  N9   106.47  3.000
 HR6  H8   C1'  O4'  110.77  3.000
 HR6  N9   C1'  O4'  108.44  3.000
 HR6  H8   C1'  C2'  109.06  3.000
 HR6  N9   C1'  C2'  114.11  3.000
 HR6  O4'  C1'  C2'  108.00  3.000
 HR6  C8   N9   C4   106.00  3.000
 HR6  C8   N9   C1'  130.88  3.000
 HR6  C4   N9   C1'  122.92  3.000
 HR6  C5   C4   N3   126.90  3.000
 HR6  C5   C4   N9   105.48  3.000
 HR6  N3   C4   N9   127.61  3.000
 HR6  C2   N3   C4   111.52  3.000
 HR6  H9   C2   N1   115.60  3.000
 HR6  H9   C2   N3   116.16  3.000
 HR6  N1   C2   N3   128.24  3.000
 HR6  C6   N1   C2   119.33  3.000
 HR6  C5   C6   N6   122.83  3.000
 HR6  N6   C6   N1   119.37  3.000
 HR6  C5   C6   N1   117.80  3.000
 HR6  H11  N6   H10  118.00  3.000
 HR6  H11  N6   C6   120.87  3.000
 HR6  H10  N6   C6   120.04  3.000
 HR6  N7   C5   C6   133.03  3.000
 HR6  C6   C5   C4   116.20  3.000
 HR6  N7   C5   C4   110.76  3.000
 HR6  C8   N7   C5   104.88  3.000
 HR6  S2   C8   N7   124.37  3.000
 HR6  N7   C8   N9   112.87  3.000
 HR6  S2   C8   N9   122.76  3.000
 HR6  C9   S2   C8    99.89  3.000
 HR6  H13  C9   H12  108.80  3.000
 HR6  H13  C9   C10  111.78  3.000
 HR6  H12  C9   C10  111.88  3.000
 HR6  H13  C9   S2   109.43  3.000
 HR6  H12  C9   S2   108.37  3.000
 HR6  C10  C9   S2   106.48  3.000
 HR6  C11  C10  C15  119.10  3.000
 HR6  C11  C10  C9   120.20  3.000
 HR6  C15  C10  C9   120.68  3.000
 HR6  H14  C15  C14  119.79  3.000
 HR6  H14  C15  C10  119.71  3.000
 HR6  C14  C15  C10  120.50  3.000
 HR6  H15  C14  C13  120.18  3.000
 HR6  H15  C14  C15  119.75  3.000
 HR6  C13  C14  C15  120.07  3.000
 HR6  H16  C11  C12  119.76  3.000
 HR6  H16  C11  C10  119.75  3.000
 HR6  C12  C11  C10  120.49  3.000
 HR6  H17  C12  C13  120.10  3.000
 HR6  H17  C12  C11  119.80  3.000
 HR6  C13  C12  C11  120.10  3.000
 HR6  H18  C13  C12  120.10  3.000
 HR6  H18  C13  C14  120.16  3.000
 HR6  C12  C13  C14  119.74  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
 HR6  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 HR6  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 HR6  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 HR6  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 HR6  CONST_05  N1   C2   N3   C4      0.00   0.0  0
 HR6  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 HR6  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 HR6  CONST_08  N1   C6   C5   C4      0.00   0.0  0
 HR6  CONST_09  C8   N9   C4   N3    180.00   0.0  0
 HR6  CONST_10  N7   C5   C4   N3    180.00   0.0  0
 HR6  CONST_11  C6   C5   C4   N3      0.00   0.0  0
 HR6  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 HR6  CONST_13  C5   C4   N3   C2      0.00   0.0  0
 HR6  CONST_14  C5   C6   N1   C2      0.00   0.0  0
 HR6  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 HR6  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 HR6  CONST_17  C8   N9   C4   C5      0.00   0.0  0
 HR6  CONST_18  C13  C14  C15  C10     0.00   0.0  0
 HR6  CONST_19  C13  C12  C11  C10     0.00   0.0  0
 HR6  CONST_20  C12  C13  C14  C15     0.00   0.0  0
 HR6  CONST_21  C12  C11  C10  C15     0.00   0.0  0
 HR6  CONST_22  C11  C10  C15  C14     0.00   0.0  0
 HR6  CONST_23  C11  C12  C13  C14     0.00   0.0  0
 HR6  CONST_24  N3   C4   N9   C1'     0.00   0.0  0
 HR6  CONST_25  C5   C4   N9   C1'   180.00   0.0  0
 HR6  CONST_26  N7   C8   N9   C1'   180.00   0.0  0
 HR6  CONST_27  S2   C8   N9   C1'     0.00   0.0  0
 HR6  CONST_28  S2   C8   N9   C4    180.00   0.0  0
 HR6  CONST_29  N6   C6   C5   C4    180.00   0.0  0
 HR6  CONST_30  N6   C6   N1   C2    180.00   0.0  0
 HR6  CONST_31  N7   C5   C6   N6      0.00   0.0  0
 HR6  CONST_32  S2   C8   N7   C5    180.00   0.0  0
 HR6  CONST_33  C14  C15  C10  C9    180.00   0.0  0
 HR6  CONST_34  C12  C11  C10  C9    180.00   0.0  0
 HR6  CONST_35  H9   C2   N3   C4    180.00   0.0  0
 HR6  CONST_36  H15  C14  C15  C10   180.00   0.0  0
 HR6  CONST_37  H17  C12  C11  C10   180.00   0.0  0
 HR6  CONST_38  H18  C13  C14  C15   180.00   0.0  0
 HR6  CONST_39  H16  C11  C10  C15   180.00   0.0  0
 HR6  CONST_40  H14  C15  C10  C11   180.00   0.0  0
 HR6  CONST_41  H10  N6   C6   N1      0.00   0.0  0
 HR6  CONST_42  H11  N6   C6   N1    180.00   0.0  0
 HR6  Var_01    C4'  C5'  O5'  P      52.21  30.0  1
 HR6  Var_02    O3'  P    O5'  C5'   -40.49  30.0  1
 HR6  Var_03    C10  C9   S2   C8   -170.47  30.0  3
 HR6  Var_04    C15  C10  C9   S2   -100.55  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
 HR6  chir_02  C3'  C4'  O3'  C2'  negativ
 HR6  chir_03  C2'  O2'  C3'  C1'  positiv
 HR6  chir_04  C4'  O4'  C5'  C3'  positiv
 HR6  chir_05  C1'  O4'  N9   C2'  negativ
 HR6  chir_06  P    O5'  O3'  S1P  both

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
 HR6  plan-1  C9   0.020
 HR6  plan-1  C10  0.020
 HR6  plan-1  C15  0.020
 HR6  plan-1  C14  0.020
 HR6  plan-1  C11  0.020
 HR6  plan-1  C12  0.020
 HR6  plan-1  C13  0.020
 HR6  plan-1  H14  0.020
 HR6  plan-1  H15  0.020
 HR6  plan-1  H16  0.020
 HR6  plan-1  H17  0.020
 HR6  plan-1  H18  0.020
 HR6  plan-2  C1'  0.020
 HR6  plan-2  N9   0.020
 HR6  plan-2  C4   0.020
 HR6  plan-2  N3   0.020
 HR6  plan-2  C2   0.020
 HR6  plan-2  N1   0.020
 HR6  plan-2  C6   0.020
 HR6  plan-2  N6   0.020
 HR6  plan-2  C5   0.020
 HR6  plan-2  N7   0.020
 HR6  plan-2  C8   0.020
 HR6  plan-2  S2   0.020
 HR6  plan-2  H9   0.020
 HR6  plan-3  C6   0.020
 HR6  plan-3  N6   0.020
 HR6  plan-3  H10  0.020
 HR6  plan-3  H11  0.020

