# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:00:58 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCCC(O)=O)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
 DU8  DU8  '3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanylpropanoic acid'  ligand  42  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DU8
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
 DU8  C1   C  CR16   0   0.043   1.8101   4.4839   0.7108
 DU8  O1   O  O2     0  -0.488  -1.8591   0.5885   0.5756
 DU8  C2   C  CR6    0   0.445   3.3549   2.7926   0.9238
 DU8  C3   C  CR56   0   0.005   2.3205   1.8890   0.6283
 DU8  C4   C  CR56   0   0.490   1.0738   2.4407   0.3953
 DU8  C5   C  CR5    0   0.319   1.0406   0.2517   0.2287
 DU8  C6   C  CH1    0  -0.037  -1.4477   1.1012  -1.7145
 DU8  C7   C  CH1    0  -0.027  -2.4991  -0.0259  -1.5757
 DU8  O2   O  OH1    0  -0.670  -1.9747   2.2159  -2.3742
 DU8  C10  C  CH2    0  -0.342  -3.5104  -1.1411   0.4701
 DU8  C11  C  CH2    0  -0.533   1.8940  -2.2970  -0.3012
 DU8  C12  C  CH2    0  -0.596   1.4883  -3.7368  -0.5551
 DU8  C13  C  C      0   0.428   2.6856  -4.6721  -0.8262
 DU8  C8   C  CH1    0   0.029  -2.9927   0.1438  -0.1399
 DU8  C9   C  CH1    0   0.182  -1.1329   1.4672  -0.2424
 DU8  N1   N  N      0  -0.471   3.0571   4.0974   0.9581
 DU8  N2   N  N      0  -0.459   0.7604   3.7311   0.4221
 DU8  N3   N  NR5    0  -0.579   0.2517   1.3769   0.1333
 DU8  N4   N  N      0  -0.455   2.2785   0.5217   0.5264
 DU8  N5   N  NH2    0  -0.818   4.6120   2.4035   1.1539
 DU8  N6   N  N      0  -0.355  -3.9555  -0.9738   1.8548
 DU8  N7   N  N      1   0.355  -5.0610  -0.4891   2.0142
 DU8  N8   N  N     -1  -0.218  -6.0652  -0.0532   2.2699
 DU8  O3   O  OH1    0  -0.657  -3.5670   0.1110  -2.4725
 DU8  O4   O  OC    -1  -0.621   2.3960  -5.8573  -1.0810
 DU8  O5   O  O      0  -0.601   3.8258  -4.1761  -0.7672
 DU8  S1   S  S2     0   0.040   0.3724  -1.3378  -0.0031
 DU8  H1   H  HCR6   0   0.252   1.6327   5.5529   0.7566
 DU8  H2   H  HCH1   0   0.252  -0.5471   0.7430  -2.2268
 DU8  H3   H  HCH1   0   0.255  -2.0040  -0.9955  -1.6852
 DU8  H4   H  HOH1   0   0.450  -2.7975   1.9322  -2.7976
 DU8  H5   H  HCH2   0   0.273  -4.3120  -1.5324  -0.1621
 DU8  H6   H  HCH2   0   0.267  -2.7152  -1.8850   0.4969
 DU8  H7   H  HCH2   0   0.274   2.5378  -2.2102   0.5708
 DU8  H8   H  HCH2   0   0.272   2.4097  -1.8666  -1.1577
 DU8  H9   H  HCH2   0   0.244   0.9341  -4.1302   0.3033
 DU8  H10  H  HCH2   0   0.242   0.8018  -3.7960  -1.4050
 DU8  H11  H  HCH1   0   0.251  -3.7819   0.9118  -0.1248
 DU8  H12  H  HCH1   0   0.272  -1.4280   2.5091  -0.0766
 DU8  H13  H  HNH2   0   0.410   4.8442   1.4287   1.2279
 DU8  H14  H  HNH2   0   0.402   5.2983   3.0756   1.4505
 DU8  H16  H  HOH1   0   0.474  -3.3832  -0.4087  -3.2616

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
 DU8  O5   C13  deloc     1.245  0.020  1.245
 DU8  N5   C2   single    1.336  0.020  1.336
 DU8  C13  O4   deloc     1.246  0.020  1.246
 DU8  C13  C12  single    1.543  0.020  1.543
 DU8  N4   C3   aromatic  1.372  0.020  1.372
 DU8  N4   C5   aromatic  1.301  0.020  1.301
 DU8  C2   C3   aromatic  1.405  0.020  1.405
 DU8  C2   N1   aromatic  1.339  0.020  1.339
 DU8  C11  S1   single    1.823  0.020  1.823
 DU8  C11  C12  single    1.517  0.020  1.517
 DU8  N6   N7   double    1.218  0.020  1.218
 DU8  N6   C10  single    1.464  0.020  1.464
 DU8  C3   C4   aromatic  1.383  0.020  1.383
 DU8  S1   C5   single    1.740  0.020  1.740
 DU8  C5   N3   aromatic  1.378  0.020  1.378
 DU8  N1   C1   aromatic  1.329  0.020  1.329
 DU8  N7   N8   double    1.124  0.020  1.124
 DU8  O1   C8   single    1.412  0.020  1.412
 DU8  O1   C9   single    1.403  0.020  1.403
 DU8  C4   N3   aromatic  1.370  0.020  1.370
 DU8  C4   N2   aromatic  1.328  0.020  1.328
 DU8  N3   C9   single    1.437  0.020  1.437
 DU8  C1   N2   aromatic  1.324  0.020  1.324
 DU8  C10  C8   single    1.514  0.020  1.514
 DU8  C8   C7   single    1.528  0.020  1.528
 DU8  C9   C6   single    1.549  0.020  1.549
 DU8  C7   C6   single    1.548  0.020  1.548
 DU8  C7   O3   single    1.401  0.020  1.401
 DU8  C6   O2   single    1.398  0.020  1.398
 DU8  C1   H1   single    0.930  0.020  1.080
 DU8  C6   H2   single    0.970  0.020  1.090
 DU8  C7   H3   single    0.970  0.020  1.090
 DU8  O2   H4   single    0.850  0.020  0.980
 DU8  C10  H5   single    0.970  0.020  1.090
 DU8  C10  H6   single    0.970  0.020  1.090
 DU8  C11  H7   single    0.970  0.020  1.090
 DU8  C11  H8   single    0.970  0.020  1.090
 DU8  C12  H9   single    0.970  0.020  1.090
 DU8  C12  H10  single    0.970  0.020  1.090
 DU8  C8   H11  single    0.970  0.020  1.090
 DU8  C9   H12  single    0.970  0.020  1.090
 DU8  N5   H13  single    0.860  0.020  1.020
 DU8  N5   H14  single    0.860  0.020  1.020
 DU8  O3   H16  single    0.850  0.020  0.980

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
 DU8  H1   C1   N2   116.11  3.000
 DU8  H1   C1   N1   115.62  3.000
 DU8  N2   C1   N1   128.27  3.000
 DU8  C9   O1   C8   108.50  3.000
 DU8  N5   C2   N1   119.26  3.000
 DU8  N1   C2   C3   117.93  3.000
 DU8  N5   C2   C3   122.80  3.000
 DU8  N4   C3   C4   110.94  3.000
 DU8  C4   C3   C2   116.27  3.000
 DU8  N4   C3   C2   132.79  3.000
 DU8  N3   C4   N2   128.09  3.000
 DU8  N2   C4   C3   126.64  3.000
 DU8  N3   C4   C3   105.27  3.000
 DU8  S1   C5   N4   125.83  3.000
 DU8  S1   C5   N3   121.14  3.000
 DU8  N4   C5   N3   113.02  3.000
 DU8  H2   C6   C9   110.74  3.000
 DU8  H2   C6   O2   110.47  3.000
 DU8  C9   C6   O2   109.67  3.000
 DU8  H2   C6   C7   111.22  3.000
 DU8  O2   C6   C7   111.52  3.000
 DU8  C9   C6   C7   103.00  3.000
 DU8  H3   C7   O3   111.55  3.000
 DU8  H3   C7   C8   109.79  3.000
 DU8  O3   C7   C8   110.15  3.000
 DU8  H3   C7   C6   109.21  3.000
 DU8  O3   C7   C6   112.91  3.000
 DU8  C8   C7   C6   102.88  3.000
 DU8  H4   O2   C6   107.04  3.000
 DU8  H6   C10  H5   107.76  3.000
 DU8  H6   C10  N6   106.07  3.000
 DU8  H5   C10  N6   111.40  3.000
 DU8  H6   C10  C8   109.88  3.000
 DU8  H5   C10  C8   108.75  3.000
 DU8  N6   C10  C8   112.84  3.000
 DU8  H8   C11  H7   108.60  3.000
 DU8  H8   C11  S1   108.42  3.000
 DU8  H7   C11  S1   108.73  3.000
 DU8  H8   C11  C12  111.73  3.000
 DU8  H7   C11  C12  111.61  3.000
 DU8  S1   C11  C12  107.67  3.000
 DU8  H10  C12  H9   105.78  3.000
 DU8  H10  C12  C13  108.51  3.000
 DU8  H9   C12  C13  108.22  3.000
 DU8  H10  C12  C11  110.43  3.000
 DU8  H9   C12  C11  110.19  3.000
 DU8  C13  C12  C11  113.39  3.000
 DU8  O5   C13  O4   126.97  3.000
 DU8  O4   C13  C12  115.59  3.000
 DU8  O5   C13  C12  117.44  3.000
 DU8  H11  C8   C10  109.97  3.000
 DU8  H11  C8   C7   108.78  3.000
 DU8  C10  C8   C7   113.27  3.000
 DU8  H11  C8   O1   110.40  3.000
 DU8  C7   C8   O1   104.58  3.000
 DU8  C10  C8   O1   109.73  3.000
 DU8  H12  C9   N3   106.24  3.000
 DU8  H12  C9   C6   108.28  3.000
 DU8  N3   C9   C6   115.42  3.000
 DU8  H12  C9   O1   111.59  3.000
 DU8  C6   C9   O1   107.51  3.000
 DU8  N3   C9   O1   107.87  3.000
 DU8  C2   N1   C1   119.18  3.000
 DU8  C4   N2   C1   111.71  3.000
 DU8  C9   N3   C5   128.39  3.000
 DU8  C9   N3   C4   125.40  3.000
 DU8  C5   N3   C4   106.11  3.000
 DU8  C5   N4   C3   104.65  3.000
 DU8  H14  N5   H13  117.97  3.000
 DU8  H14  N5   C2   119.90  3.000
 DU8  H13  N5   C2   120.84  3.000
 DU8  N7   N6   C10  116.45  3.000
 DU8  N8   N7   N6   174.37  3.000
 DU8  H16  O3   C7   109.06  3.000
 DU8  C11  S1   C5   100.48  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
 DU8  CONST_01  C3   C2   N1   C1      0.00   0.0  0
 DU8  CONST_02  C3   C4   N2   C1      0.00   0.0  0
 DU8  CONST_03  N3   C4   N2   C1    180.00   0.0  0
 DU8  CONST_04  C5   N4   C3   C2    180.00   0.0  0
 DU8  CONST_05  N3   C4   C3   C2    180.00   0.0  0
 DU8  CONST_06  N2   C4   C3   C2      0.00   0.0  0
 DU8  CONST_07  N2   C1   N1   C2      0.00   0.0  0
 DU8  CONST_08  N3   C5   N4   C3      0.00   0.0  0
 DU8  CONST_09  C5   N3   C4   C3      0.00   0.0  0
 DU8  CONST_10  C5   N4   C3   C4      0.00   0.0  0
 DU8  CONST_11  N1   C2   C3   C4      0.00   0.0  0
 DU8  CONST_12  N4   C5   N3   C4      0.00   0.0  0
 DU8  CONST_13  N1   C1   N2   C4      0.00   0.0  0
 DU8  CONST_14  N2   C4   N3   C5    180.00   0.0  0
 DU8  CONST_15  N4   C3   C2   N1    180.00   0.0  0
 DU8  CONST_16  N4   C3   C4   N2    180.00   0.0  0
 DU8  CONST_17  N4   C3   C4   N3      0.00   0.0  0
 DU8  CONST_18  C9   N3   C4   C3    180.00   0.0  0
 DU8  CONST_19  N4   C5   N3   C9    180.00   0.0  0
 DU8  CONST_20  N2   C4   N3   C9      0.00   0.0  0
 DU8  CONST_21  N5   C2   N1   C1    180.00   0.0  0
 DU8  CONST_22  S1   C5   N4   C3    180.00   0.0  0
 DU8  CONST_23  N5   C2   C3   C4    180.00   0.0  0
 DU8  CONST_24  S1   C5   N3   C4    180.00   0.0  0
 DU8  CONST_25  S1   C5   N3   C9      0.00   0.0  0
 DU8  CONST_26  N5   C2   C3   N4      0.00   0.0  0
 DU8  CONST_27  H1   C1   N1   C2    180.00   0.0  0
 DU8  CONST_28  H13  N5   C2   C3      0.00   0.0  0
 DU8  CONST_29  H14  N5   C2   C3    180.00   0.0  0
 DU8  Var_01    N4   C5   S1   C11   -19.02  30.0  2
 DU8  Var_02    C12  C11  S1   C5   -178.93  30.0  1
 DU8  Var_03    O5   C13  C12  C11     2.24  30.0  1
 DU8  Var_04    S1   C11  C12  C13   179.96  30.0  1
 DU8  Var_05    H5   C10  N6   N7    -42.97  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
 DU8  chir_01  C6  C9  C7  O2   negativ
 DU8  chir_02  C7  O3  C8  C6   positiv
 DU8  chir_03  C8  O1  C7  C10  negativ
 DU8  chir_04  C9  O1  N3  C6   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
 DU8  plan-1  C1   0.020
 DU8  plan-1  C2   0.020
 DU8  plan-1  C3   0.020
 DU8  plan-1  C4   0.020
 DU8  plan-1  C5   0.020
 DU8  plan-1  C9   0.020
 DU8  plan-1  N1   0.020
 DU8  plan-1  N2   0.020
 DU8  plan-1  N3   0.020
 DU8  plan-1  N4   0.020
 DU8  plan-1  N5   0.020
 DU8  plan-1  S1   0.020
 DU8  plan-1  H1   0.020
 DU8  plan-2  C2   0.020
 DU8  plan-2  N5   0.020
 DU8  plan-2  H13  0.020
 DU8  plan-2  H14  0.020
 DU8  plan-3  C12  0.020
 DU8  plan-3  C13  0.020
 DU8  plan-3  O4   0.020
 DU8  plan-3  O5   0.020
 DU8  plan-4  C10  0.020
 DU8  plan-4  N6   0.020
 DU8  plan-4  N7   0.020
 DU8  plan-4  N8   0.020

