# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:24:44 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-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(SCc5ccc(F)cc5)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
 HR4  HR4  '(2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-9H-purin-9-yl}-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide'  ligand  48  31  .  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_HR4
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
 HR4  F1   F  F     0  -0.339   5.1325   4.3576   0.1098
 HR4  C13  C  CR6   0   0.488   3.8296   4.0346   0.1248
 HR4  C14  C  CR16  0  -0.385   3.3384   3.1985  -0.8611
 HR4  C15  C  CR16  0  -0.221   1.9935   2.8675  -0.8355
 HR4  C12  C  CR16  0  -0.369   3.0243   4.5502   1.1204
 HR4  C11  C  CR16  0  -0.237   1.6783   4.2079   1.1271
 HR4  C10  C  CR6   0   0.028   1.1485   3.3697   0.1524
 HR4  C9   C  CH2   0  -0.603  -0.2964   2.9700   0.1766
 HR4  S1   S  S2    0   0.113  -0.3441   1.2846   0.8764
 HR4  C8   C  CR5   0   0.319  -1.9737   0.8241   0.4670
 HR4  N7   N  N     0  -0.486  -2.9059   1.6607   0.1129
 HR4  C5   C  CR56  0   0.011  -4.0068   0.8801  -0.1268
 HR4  C6   C  CR6   0   0.448  -5.3169   1.1708  -0.5451
 HR4  N6   N  NH2   0  -0.764  -5.7319   2.4092  -0.8172
 HR4  N1   N  N     0  -0.533  -6.1683   0.1462  -0.6859
 HR4  C2   C  CR16  0   0.047  -5.7496  -1.0887  -0.4308
 HR4  N3   N  N     0  -0.435  -4.5486  -1.4815  -0.0350
 HR4  C4   C  CR56  0   0.466  -3.7210  -0.4517   0.1043
 HR4  N9   N  NR5   0  -0.491  -2.4066  -0.4841   0.4876
 HR4  C1'  C  CR15  0   0.149  -1.7001  -1.7185   0.7471
 HR4  C2'  C  CR15  0  -0.047  -1.1047  -2.3847  -0.5351
 HR4  O2'  O  OH1   0  -0.699  -1.2124  -3.7733  -0.4922
 HR4  O4'  O  O     0  -0.478  -0.6362  -1.4507   1.6325
 HR4  C4'  C  CR15  0  -0.007   0.5126  -2.1108   1.1484
 HR4  C3'  C  CR15  0  -0.018   0.3509  -1.9999  -0.3582
 HR4  O3'  O  O2    0  -0.503   1.2960  -2.8088  -1.0424
 HR4  C5'  C  CH2   0  -0.219   1.8294  -1.5099   1.5961
 HR4  O5'  O  O2    0  -0.508   2.8511  -2.2783   0.9309
 HR4  P    P  P     0   1.247   2.8346  -2.5384  -0.6480
 HR4  S2   S  S2    0  -0.346   3.1486  -0.6915  -1.5646
 HR4  O2P  O  O     0  -0.632   3.7391  -3.6274  -1.0454
 HR4  H1   H  HCR6  0   0.275   3.9924   2.8136  -1.6327
 HR4  H2   H  HCR6  0   0.280   1.5958   2.2096  -1.5983
 HR4  H3   H  HCR6  0   0.255   3.4356   5.2043   1.8782
 HR4  H4   H  HCR6  0   0.275   1.0377   4.6078   1.9030
 HR4  H5   H  HCH2  0   0.292  -0.8926   3.6395   0.7937
 HR4  H6   H  HCH2  0   0.275  -0.7241   2.9399  -0.8244
 HR4  H7   H  HNH2  0   0.394  -5.1438   3.2028  -0.6314
 HR4  H8   H  HNH2  0   0.380  -6.6982   2.5797  -1.0373
 HR4  H9   H  HCR6  0   0.275  -6.4863  -1.8720  -0.5715
 HR4  H10  H  HCR5  0   0.317  -2.4223  -2.4001   1.2060
 HR4  H11  H  HCR5  0   0.290  -1.5515  -1.9578  -1.4384
 HR4  H12  H  HOH1  0   0.454  -2.1188  -4.0237  -0.6998
 HR4  H13  H  HCR5  0   0.207   0.5021  -3.1672   1.4485
 HR4  H14  H  HCR5  0   0.252   0.4658  -0.9522  -0.6649
 HR4  H15  H  HCH2  0   0.208   1.9210  -0.4553   1.3280
 HR4  H16  H  HCH2  0   0.283   2.0037  -1.6211   2.6641
 HR4  H17  H  HSH1  0   0.294   4.2110  -0.3319  -0.8303

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
 HR4  O2P  P    double    1.470  0.020  1.470
 HR4  O5'  C5'  single    1.441  0.020  1.441
 HR4  O5'  P    single    1.600  0.020  1.600
 HR4  C5'  C4'  single    1.515  0.020  1.515
 HR4  P    O3'  single    1.611  0.020  1.611
 HR4  P    S2   single    2.086  0.020  2.086
 HR4  C4'  O4'  single    1.411  0.020  1.411
 HR4  C4'  C3'  single    1.519  0.020  1.519
 HR4  O3'  C3'  single    1.420  0.020  1.420
 HR4  O4'  C1'  single    1.410  0.020  1.410
 HR4  C3'  C2'  single    1.516  0.020  1.516
 HR4  O2'  C2'  single    1.393  0.020  1.393
 HR4  C1'  C2'  single    1.563  0.020  1.563
 HR4  C1'  N9   single    1.446  0.020  1.446
 HR4  N3   C4   aromatic  1.328  0.020  1.328
 HR4  N3   C2   aromatic  1.324  0.020  1.324
 HR4  N9   C4   aromatic  1.370  0.020  1.370
 HR4  N9   C8   aromatic  1.378  0.020  1.378
 HR4  C4   C5   aromatic  1.382  0.020  1.382
 HR4  C2   N1   aromatic  1.329  0.020  1.329
 HR4  S1   C8   single    1.742  0.020  1.742
 HR4  S1   C9   single    1.826  0.020  1.826
 HR4  C8   N7   aromatic  1.302  0.020  1.302
 HR4  N1   C6   aromatic  1.340  0.020  1.340
 HR4  C5   N7   aromatic  1.371  0.020  1.371
 HR4  C5   C6   aromatic  1.406  0.020  1.406
 HR4  C6   N6   single    1.334  0.020  1.334
 HR4  C9   C10  single    1.499  0.020  1.499
 HR4  C15  C10  aromatic  1.394  0.020  1.394
 HR4  C15  C14  aromatic  1.385  0.020  1.385
 HR4  C10  C11  aromatic  1.390  0.020  1.390
 HR4  C14  C13  aromatic  1.383  0.020  1.383
 HR4  C11  C12  aromatic  1.389  0.020  1.389
 HR4  C13  C12  aromatic  1.380  0.020  1.380
 HR4  C13  F1   single    1.342  0.020  1.342
 HR4  C14  H1   single    0.930  0.020  1.080
 HR4  C15  H2   single    0.930  0.020  1.080
 HR4  C12  H3   single    0.930  0.020  1.080
 HR4  C11  H4   single    0.930  0.020  1.080
 HR4  C9   H5   single    0.970  0.020  1.090
 HR4  C9   H6   single    0.970  0.020  1.090
 HR4  N6   H7   single    0.860  0.020  1.020
 HR4  N6   H8   single    0.860  0.020  1.020
 HR4  C2   H9   single    0.930  0.020  1.080
 HR4  C1'  H10  single    0.970  0.020  1.090
 HR4  C2'  H11  single    0.970  0.020  1.090
 HR4  O2'  H12  single    0.850  0.020  0.980
 HR4  C4'  H13  single    0.970  0.020  1.090
 HR4  C3'  H14  single    0.970  0.020  1.090
 HR4  C5'  H15  single    0.970  0.020  1.090
 HR4  C5'  H16  single    0.970  0.020  1.090
 HR4  S2   H17  single    1.200  0.020  1.300

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
 HR4  C12  C13  C14  122.19  3.000
 HR4  C12  C13  F1   118.97  3.000
 HR4  C14  C13  F1   118.83  3.000
 HR4  H1   C14  C15  120.99  3.000
 HR4  H1   C14  C13  120.58  3.000
 HR4  C15  C14  C13  118.43  3.000
 HR4  H2   C15  C10  119.71  3.000
 HR4  H2   C15  C14  119.25  3.000
 HR4  C10  C15  C14  121.04  3.000
 HR4  H3   C12  C11  120.93  3.000
 HR4  H3   C12  C13  120.60  3.000
 HR4  C11  C12  C13  118.47  3.000
 HR4  H4   C11  C10  119.97  3.000
 HR4  H4   C11  C12  119.07  3.000
 HR4  C10  C11  C12  120.97  3.000
 HR4  C9   C10  C11  121.10  3.000
 HR4  C11  C10  C15  118.89  3.000
 HR4  C9   C10  C15  119.98  3.000
 HR4  H6   C9   H5   108.85  3.000
 HR4  H6   C9   S1   108.46  3.000
 HR4  H5   C9   S1   109.65  3.000
 HR4  H6   C9   C10  111.77  3.000
 HR4  H5   C9   C10  111.91  3.000
 HR4  S1   C9   C10  106.11  3.000
 HR4  C8   S1   C9   100.28  3.000
 HR4  N9   C8   N7   112.90  3.000
 HR4  N7   C8   S1   124.33  3.000
 HR4  N9   C8   S1   122.77  3.000
 HR4  C5   N7   C8   104.88  3.000
 HR4  C4   C5   C6   116.23  3.000
 HR4  C6   C5   N7   133.06  3.000
 HR4  C4   C5   N7   110.71  3.000
 HR4  N1   C6   N6   119.40  3.000
 HR4  N6   C6   C5   122.86  3.000
 HR4  N1   C6   C5   117.74  3.000
 HR4  H8   N6   H7   117.96  3.000
 HR4  H8   N6   C6   120.06  3.000
 HR4  H7   N6   C6   120.88  3.000
 HR4  C2   N1   C6   119.37  3.000
 HR4  H9   C2   N3   116.15  3.000
 HR4  H9   C2   N1   115.62  3.000
 HR4  N3   C2   N1   128.23  3.000
 HR4  C4   N3   C2   111.50  3.000
 HR4  N9   C4   N3   127.51  3.000
 HR4  N9   C4   C5   105.55  3.000
 HR4  N3   C4   C5   126.93  3.000
 HR4  C1'  N9   C4   122.64  3.000
 HR4  C4   N9   C8   105.95  3.000
 HR4  C1'  N9   C8   131.28  3.000
 HR4  H10  C1'  O4'  110.68  3.000
 HR4  H10  C1'  C2'  109.28  3.000
 HR4  O4'  C1'  C2'  107.98  3.000
 HR4  H10  C1'  N9   106.54  3.000
 HR4  C2'  C1'  N9   113.76  3.000
 HR4  O4'  C1'  N9   108.62  3.000
 HR4  H11  C2'  C3'  112.91  3.000
 HR4  H11  C2'  O2'  112.49  3.000
 HR4  C3'  C2'  O2'  108.87  3.000
 HR4  H11  C2'  C1'  110.82  3.000
 HR4  O2'  C2'  C1'  111.72  3.000
 HR4  C3'  C2'  C1'   99.32  3.000
 HR4  H12  O2'  C2'  108.98  3.000
 HR4  C4'  O4'  C1'  108.07  3.000
 HR4  H13  C4'  C5'  108.00  3.000
 HR4  H13  C4'  C3'  109.89  3.000
 HR4  C5'  C4'  C3'  110.90  3.000
 HR4  H13  C4'  O4'  110.40  3.000
 HR4  C3'  C4'  O4'  102.68  3.000
 HR4  C5'  C4'  O4'  114.88  3.000
 HR4  H14  C3'  O3'  109.84  3.000
 HR4  H14  C3'  C4'  109.61  3.000
 HR4  O3'  C3'  C4'  111.43  3.000
 HR4  H14  C3'  C2'  108.07  3.000
 HR4  O3'  C3'  C2'  116.00  3.000
 HR4  C4'  C3'  C2'  101.50  3.000
 HR4  P    O3'  C3'  114.97  3.000
 HR4  H16  C5'  H15  109.05  3.000
 HR4  H16  C5'  O5'  106.56  3.000
 HR4  H15  C5'  O5'  110.00  3.000
 HR4  H16  C5'  C4'  112.89  3.000
 HR4  H15  C5'  C4'  112.54  3.000
 HR4  O5'  C5'  C4'  105.56  3.000
 HR4  P    O5'  C5'  122.33  3.000
 HR4  O2P  P    S2   116.39  3.000
 HR4  S2   P    O5'  106.75  3.000
 HR4  O2P  P    O5'  112.38  3.000
 HR4  S2   P    O3'  100.65  3.000
 HR4  O5'  P    O3'  106.18  3.000
 HR4  O2P  P    O3'  113.38  3.000
 HR4  H17  S2   P     96.66  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
 HR4  CONST_01  C10  C15  C14  C13    0.00   0.0  0
 HR4  CONST_02  C10  C11  C12  C13    0.00   0.0  0
 HR4  CONST_03  C11  C10  C15  C14    0.00   0.0  0
 HR4  CONST_04  C11  C12  C13  C14    0.00   0.0  0
 HR4  CONST_05  C12  C11  C10  C15    0.00   0.0  0
 HR4  CONST_06  C12  C13  C14  C15    0.00   0.0  0
 HR4  CONST_07  N3   C4   N9   C8   180.00   0.0  0
 HR4  CONST_08  C5   C4   N9   C8     0.00   0.0  0
 HR4  CONST_09  C4   C5   N7   C8     0.00   0.0  0
 HR4  CONST_10  C6   C5   N7   C8   180.00   0.0  0
 HR4  CONST_11  C4   N9   C8   N7     0.00   0.0  0
 HR4  CONST_12  N3   C4   C5   N7   180.00   0.0  0
 HR4  CONST_13  N9   C4   C5   N7     0.00   0.0  0
 HR4  CONST_14  N1   C6   C5   N7   180.00   0.0  0
 HR4  CONST_15  C2   N3   C4   C5     0.00   0.0  0
 HR4  CONST_16  N9   C8   N7   C5     0.00   0.0  0
 HR4  CONST_17  C2   N1   C6   C5     0.00   0.0  0
 HR4  CONST_18  N3   C2   N1   C6     0.00   0.0  0
 HR4  CONST_19  N3   C4   C5   C6     0.00   0.0  0
 HR4  CONST_20  N9   C4   C5   C6   180.00   0.0  0
 HR4  CONST_21  C4   N3   C2   N1     0.00   0.0  0
 HR4  CONST_22  C4   C5   C6   N1     0.00   0.0  0
 HR4  CONST_23  N9   C4   N3   C2   180.00   0.0  0
 HR4  CONST_24  C1'  N9   C8   N7   180.00   0.0  0
 HR4  CONST_25  C1'  N9   C4   C5   180.00   0.0  0
 HR4  CONST_26  C1'  N9   C4   N3     0.00   0.0  0
 HR4  CONST_27  C15  C14  C13  F1   180.00   0.0  0
 HR4  CONST_28  C11  C12  C13  F1   180.00   0.0  0
 HR4  CONST_29  C9   C10  C15  C14  180.00   0.0  0
 HR4  CONST_30  C9   C10  C11  C12  180.00   0.0  0
 HR4  CONST_31  C1'  N9   C8   S1     0.00   0.0  0
 HR4  CONST_32  C4   N9   C8   S1   180.00   0.0  0
 HR4  CONST_33  C5   N7   C8   S1   180.00   0.0  0
 HR4  CONST_34  N6   C6   C5   N7     0.00   0.0  0
 HR4  CONST_35  C2   N1   C6   N6   180.00   0.0  0
 HR4  CONST_36  C4   C5   C6   N6   180.00   0.0  0
 HR4  CONST_37  H2   C15  C14  C13  180.00   0.0  0
 HR4  CONST_38  H4   C11  C12  C13  180.00   0.0  0
 HR4  CONST_39  H3   C12  C13  C14  180.00   0.0  0
 HR4  CONST_40  H1   C14  C13  C12  180.00   0.0  0
 HR4  CONST_41  H9   C2   N1   C6   180.00   0.0  0
 HR4  CONST_42  H7   N6   C6   C5     0.00   0.0  0
 HR4  CONST_43  H8   N6   C6   C5   180.00   0.0  0
 HR4  Var_01    O5'  P    O3'  C3'   38.77  30.0  1
 HR4  Var_02    H15  C5'  O5'  P    -70.32  30.0  1
 HR4  Var_03    S1   C9   C10  C15   77.24  30.0  2
 HR4  Var_04    N9   C8   S1   C9   163.62  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
 HR4  chir_01  C1'  O4'  C2'  N9   positiv
 HR4  chir_02  C2'  O2'  C1'  C3'  negativ
 HR4  chir_03  C4'  O4'  C3'  C5'  negativ
 HR4  chir_04  C3'  O3'  C4'  C2'  positiv
 HR4  chir_05  P    O5'  O3'  S2   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
 HR4  plan-1  F1   0.020
 HR4  plan-1  C13  0.020
 HR4  plan-1  C14  0.020
 HR4  plan-1  C15  0.020
 HR4  plan-1  C12  0.020
 HR4  plan-1  C11  0.020
 HR4  plan-1  C10  0.020
 HR4  plan-1  C9   0.020
 HR4  plan-1  H1   0.020
 HR4  plan-1  H2   0.020
 HR4  plan-1  H3   0.020
 HR4  plan-1  H4   0.020
 HR4  plan-2  S1   0.020
 HR4  plan-2  C8   0.020
 HR4  plan-2  N7   0.020
 HR4  plan-2  C5   0.020
 HR4  plan-2  C6   0.020
 HR4  plan-2  N6   0.020
 HR4  plan-2  N1   0.020
 HR4  plan-2  C2   0.020
 HR4  plan-2  N3   0.020
 HR4  plan-2  C4   0.020
 HR4  plan-2  N9   0.020
 HR4  plan-2  C1'  0.020
 HR4  plan-2  H9   0.020
 HR4  plan-3  C6   0.020
 HR4  plan-3  N6   0.020
 HR4  plan-3  H7   0.020
 HR4  plan-3  H8   0.020

