# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:33:05 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: azanylidene-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[2-oxidanylidene-2-(2-sulfanylethylamino)ethyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino]azanium
#   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(SCC(=O)NCCS)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
 E3K  E3K  azanylidene-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[2-oxidanylidene-2-(2-sulfanylethylamino)ethyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino]azanium  ligand  49  29  .  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_E3K
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
 E3K  C2   C  CR16  0   0.044   4.6841   3.1724  -0.6163
 E3K  C3   C  CR56  0   0.497   2.9706   1.8408  -0.2960
 E3K  C4   C  CR56  0   0.004   2.0648   2.8798  -0.4018
 E3K  C5   C  CR5   0   0.346   0.9018   1.1462  -0.0713
 E3K  C6   C  CH2   0  -0.673  -1.7859   1.1384   0.3091
 E3K  C7   C  C     0   0.586  -2.9997   0.2520   0.5107
 E3K  N8   N  N     1   0.528  -1.1054  -2.7686  -1.4232
 E3K  N9   N  N     0  -0.322  -2.0591  -2.2245  -1.8205
 E3K  C10  C  CR15  0   0.197   2.7393  -0.6000   0.1359
 E3K  C11  C  CR15  0  -0.012   2.0140  -2.7902  -0.0467
 E3K  C12  C  CH2   0  -0.370   0.5792  -3.2521   0.1496
 E3K  C14  C  CR15  0   0.004   2.6022  -1.1437   1.5568
 E3K  C1   C  CR6   0   0.451   2.6046   4.1566  -0.6336
 E3K  C13  C  CR15  0  -0.058   2.7487  -2.6484   1.3002
 E3K  C8   C  CH2   0  -0.285  -5.4312   0.2180   0.7374
 E3K  C9   C  CH2   0  -0.550  -5.9722  -0.3154  -0.5835
 E3K  N1   N  NH2   0  -0.818   1.8493   5.2491  -0.7555
 E3K  N2   N  N     0  -0.470   3.9354   4.2633  -0.7350
 E3K  N3   N  N     0  -0.457   4.2913   1.9277  -0.3958
 E3K  N4   N  N     0  -0.455   0.7771   2.4247  -0.2636
 E3K  N5   N  NH1   0  -0.624  -4.1675   0.8980   0.5641
 E3K  N6   N  NR5   0  -0.588   2.2120   0.7195  -0.0749
 E3K  N7   N  N     0  -0.117  -0.0840  -3.2402  -1.1663
 E3K  O1   O  O     0  -0.489  -2.8846  -0.9610   0.6214
 E3K  O2   O  O     0  -0.494   2.0375  -1.5124  -0.6704
 E3K  O3   O  OH1   0  -0.657   4.1108  -2.9365   1.1823
 E3K  O4   O  OH1   0  -0.647   3.5606  -0.5616   2.3738
 E3K  S1   S  S2    0   0.044  -0.3914   0.0057   0.1417
 E3K  S2   S  S2    0  -0.254  -7.5544  -1.1604  -0.2550
 E3K  H1   H  HCR6  0   0.253   5.7536   3.3259  -0.7114
 E3K  H2   H  HCH2  0   0.323  -1.8868   1.7545  -0.5849
 E3K  H3   H  HCH2  0   0.328  -1.6427   1.8031   1.1624
 E3K  H4   H  H     0   0.493  -2.9252  -2.7744  -1.7942
 E3K  H5   H  HCR5  0   0.279   3.7985  -0.5460  -0.1389
 E3K  H6   H  HCR5  0   0.301   2.5226  -3.5141  -0.6902
 E3K  H7   H  HCH2  0   0.361   0.5713  -4.2985   0.4549
 E3K  H8   H  HCH2  0   0.314   0.0058  -2.6595   0.8611
 E3K  H9   H  HCR5  0   0.249   1.5832  -0.9546   1.9213
 E3K  H10  H  HCR5  0   0.271   2.2703  -3.2491   2.0836
 E3K  H11  H  HCH2  0   0.271  -6.1328   0.9292   1.1720
 E3K  H12  H  HCH2  0   0.259  -5.3066  -0.5948   1.4536
 E3K  H13  H  HCH2  0   0.275  -6.1333   0.5041  -1.2830
 E3K  H14  H  HCH2  0   0.269  -5.2676  -1.0192  -1.0256
 E3K  H15  H  HNH2  0   0.411   0.8480   5.1995  -0.6929
 E3K  H16  H  HNH2  0   0.404   2.2743   6.1450  -0.9203
 E3K  H17  H  HNH1  0   0.416  -4.1841   1.8958   0.4246
 E3K  H18  H  HOH1  0   0.464   4.2163  -3.8858   1.0628
 E3K  H19  H  HOH1  0   0.467   3.3420  -0.7476   3.2922
 E3K  H20  H  HSH1  0   0.230  -7.8658  -1.4373  -1.5250

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
 E3K  C9   C8   single    1.524  0.020  1.524
 E3K  C9   S2   single    1.824  0.020  1.824
 E3K  C8   N5   single    1.445  0.020  1.445
 E3K  O1   C7   double    1.224  0.020  1.224
 E3K  N5   C7   single    1.336  0.020  1.336
 E3K  C7   C6   single    1.516  0.020  1.516
 E3K  N9   N8   double    1.168  0.020  1.168
 E3K  N8   N7   double    1.154  0.020  1.154
 E3K  N1   C1   single    1.334  0.020  1.334
 E3K  C6   S1   single    1.804  0.020  1.804
 E3K  N7   C12  single    1.474  0.020  1.474
 E3K  N4   C4   aromatic  1.373  0.020  1.373
 E3K  N4   C5   aromatic  1.299  0.020  1.299
 E3K  C1   C4   aromatic  1.405  0.020  1.405
 E3K  C1   N2   aromatic  1.339  0.020  1.339
 E3K  C4   C3   aromatic  1.382  0.020  1.382
 E3K  S1   C5   single    1.737  0.020  1.737
 E3K  C5   N6   aromatic  1.378  0.020  1.378
 E3K  N2   C2   aromatic  1.328  0.020  1.328
 E3K  O2   C11  single    1.422  0.020  1.422
 E3K  O2   C10  single    1.405  0.020  1.405
 E3K  C3   N6   aromatic  1.372  0.020  1.372
 E3K  C3   N3   aromatic  1.327  0.020  1.327
 E3K  N6   C10  single    1.436  0.020  1.436
 E3K  C2   N3   aromatic  1.324  0.020  1.324
 E3K  C12  C11  single    1.520  0.020  1.520
 E3K  C11  C13  single    1.541  0.020  1.541
 E3K  C10  C14  single    1.528  0.020  1.528
 E3K  C14  C13  single    1.533  0.020  1.533
 E3K  C14  O4   single    1.387  0.020  1.387
 E3K  C13  O3   single    1.397  0.020  1.397
 E3K  C2   H1   single    0.930  0.020  1.080
 E3K  C6   H2   single    0.970  0.020  1.090
 E3K  C6   H3   single    0.970  0.020  1.090
 E3K  N9   H4   single    0.890  0.020  1.040
 E3K  C10  H5   single    0.970  0.020  1.090
 E3K  C11  H6   single    0.970  0.020  1.090
 E3K  C12  H7   single    0.970  0.020  1.090
 E3K  C12  H8   single    0.970  0.020  1.090
 E3K  C14  H9   single    0.970  0.020  1.090
 E3K  C13  H10  single    0.970  0.020  1.090
 E3K  C8   H11  single    0.970  0.020  1.090
 E3K  C8   H12  single    0.970  0.020  1.090
 E3K  C9   H13  single    0.970  0.020  1.090
 E3K  C9   H14  single    0.970  0.020  1.090
 E3K  N1   H15  single    0.860  0.020  1.020
 E3K  N1   H16  single    0.860  0.020  1.020
 E3K  N5   H17  single    0.860  0.020  1.020
 E3K  O3   H18  single    0.850  0.020  0.980
 E3K  O4   H19  single    0.850  0.020  0.980
 E3K  S2   H20  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
 E3K  H1   C2   N3   116.12  3.000
 E3K  H1   C2   N2   115.58  3.000
 E3K  N3   C2   N2   128.30  3.000
 E3K  N6   C3   N3   128.02  3.000
 E3K  N3   C3   C4   126.65  3.000
 E3K  N6   C3   C4   105.33  3.000
 E3K  N4   C4   C1   132.69  3.000
 E3K  C1   C4   C3   116.35  3.000
 E3K  N4   C4   C3   110.96  3.000
 E3K  S1   C5   N6   120.31  3.000
 E3K  N6   C5   N4   113.31  3.000
 E3K  S1   C5   N4   126.36  3.000
 E3K  H3   C6   H2   108.01  3.000
 E3K  H3   C6   S1   110.70  3.000
 E3K  H2   C6   S1   110.50  3.000
 E3K  H3   C6   C7   110.92  3.000
 E3K  H2   C6   C7   111.43  3.000
 E3K  S1   C6   C7   105.31  3.000
 E3K  O1   C7   N5   123.93  3.000
 E3K  N5   C7   C6   114.99  3.000
 E3K  O1   C7   C6   121.08  3.000
 E3K  N7   N8   N9   171.53  3.000
 E3K  H4   N9   N8   115.53  3.000
 E3K  H5   C10  O2   111.77  3.000
 E3K  H5   C10  N6   105.83  3.000
 E3K  O2   C10  N6   109.20  3.000
 E3K  H5   C10  C14  109.73  3.000
 E3K  N6   C10  C14  115.50  3.000
 E3K  O2   C10  C14  104.94  3.000
 E3K  H6   C11  O2   109.20  3.000
 E3K  H6   C11  C13  110.70  3.000
 E3K  O2   C11  C13  107.03  3.000
 E3K  H6   C11  C12  108.29  3.000
 E3K  C13  C11  C12  111.42  3.000
 E3K  O2   C11  C12  110.20  3.000
 E3K  H8   C12  H7   109.61  3.000
 E3K  H8   C12  N7   109.99  3.000
 E3K  H7   C12  N7   104.75  3.000
 E3K  H8   C12  C11  114.58  3.000
 E3K  H7   C12  C11  109.56  3.000
 E3K  N7   C12  C11  107.88  3.000
 E3K  H9   C14  O4   111.91  3.000
 E3K  H9   C14  C13  108.24  3.000
 E3K  O4   C14  C13  116.38  3.000
 E3K  H9   C14  C10  109.30  3.000
 E3K  O4   C14  C10  109.66  3.000
 E3K  C13  C14  C10  100.66  3.000
 E3K  N2   C1   N1   119.39  3.000
 E3K  N2   C1   C4   117.82  3.000
 E3K  N1   C1   C4   122.80  3.000
 E3K  H10  C13  O3   111.87  3.000
 E3K  H10  C13  C14  112.10  3.000
 E3K  O3   C13  C14  108.03  3.000
 E3K  H10  C13  C11  111.47  3.000
 E3K  O3   C13  C11  111.84  3.000
 E3K  C14  C13  C11  101.02  3.000
 E3K  H12  C8   H11  107.35  3.000
 E3K  H12  C8   N5   109.24  3.000
 E3K  H11  C8   N5   107.68  3.000
 E3K  H12  C8   C9   110.43  3.000
 E3K  H11  C8   C9   110.22  3.000
 E3K  N5   C8   C9   111.78  3.000
 E3K  H14  C9   H13  108.72  3.000
 E3K  H14  C9   S2   109.56  3.000
 E3K  H13  C9   S2   109.63  3.000
 E3K  H14  C9   C8   110.38  3.000
 E3K  H13  C9   C8   110.23  3.000
 E3K  S2   C9   C8   108.31  3.000
 E3K  H16  N1   H15  118.41  3.000
 E3K  H16  N1   C1   120.37  3.000
 E3K  H15  N1   C1   121.22  3.000
 E3K  C1   N2   C2   119.21  3.000
 E3K  C3   N3   C2   111.68  3.000
 E3K  C5   N4   C4   104.54  3.000
 E3K  H17  N5   C8   117.91  3.000
 E3K  H17  N5   C7   119.20  3.000
 E3K  C8   N5   C7   122.79  3.000
 E3K  C10  N6   C5   129.28  3.000
 E3K  C10  N6   C3   124.85  3.000
 E3K  C5   N6   C3   105.85  3.000
 E3K  C12  N7   N8   126.90  3.000
 E3K  C11  O2   C10  109.87  3.000
 E3K  H18  O3   C13  108.70  3.000
 E3K  H19  O4   C14  108.91  3.000
 E3K  C6   S1   C5   100.05  3.000
 E3K  H20  S2   C9    97.29  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
 E3K  CONST_01  C4   C1   N2  C2      0.00   0.0  0
 E3K  CONST_02  C4   C3   N3  C2      0.00   0.0  0
 E3K  CONST_03  N6   C3   N3  C2    180.00   0.0  0
 E3K  CONST_04  C5   N4   C4  C3      0.00   0.0  0
 E3K  CONST_05  N2   C1   C4  C3      0.00   0.0  0
 E3K  CONST_06  N4   C5   N6  C3      0.00   0.0  0
 E3K  CONST_07  N2   C2   N3  C3      0.00   0.0  0
 E3K  CONST_08  N6   C5   N4  C4      0.00   0.0  0
 E3K  CONST_09  C5   N6   C3  C4      0.00   0.0  0
 E3K  CONST_10  C1   C4   N4  C5    180.00   0.0  0
 E3K  CONST_11  N3   C3   N6  C5    180.00   0.0  0
 E3K  CONST_12  N6   C3   C4  C1    180.00   0.0  0
 E3K  CONST_13  N3   C3   C4  C1      0.00   0.0  0
 E3K  CONST_14  N3   C2   N2  C1      0.00   0.0  0
 E3K  CONST_15  N4   C4   C1  N2    180.00   0.0  0
 E3K  CONST_16  N4   C4   C3  N3    180.00   0.0  0
 E3K  CONST_17  N6   C3   C4  N4      0.00   0.0  0
 E3K  CONST_18  C10  N6   C3  C4    180.00   0.0  0
 E3K  CONST_19  N4   C5   N6  C10   180.00   0.0  0
 E3K  CONST_20  N3   C3   N6  C10     0.00   0.0  0
 E3K  CONST_21  N1   C1   N2  C2    180.00   0.0  0
 E3K  CONST_22  N1   C1   C4  C3    180.00   0.0  0
 E3K  CONST_23  S1   C5   N6  C3    180.00   0.0  0
 E3K  CONST_24  S1   C5   N4  C4    180.00   0.0  0
 E3K  CONST_25  S1   C5   N6  C10     0.00   0.0  0
 E3K  CONST_26  N4   C4   C1  N1      0.00   0.0  0
 E3K  CONST_27  H1   C2   N3  C3    180.00   0.0  0
 E3K  CONST_28  H15  N1   C1  C4      0.00   0.0  0
 E3K  CONST_29  H16  N1   C1  C4    180.00   0.0  0
 E3K  CONST_30  C8   N5   C7  C6    180.00   0.0  0
 E3K  CONST_31  O1   C7   N5  C8      0.00   0.0  0
 E3K  CONST_32  H17  N5   C7  C6      0.00   0.0  0
 E3K  Var_01    N4   C5   S1  C6     -9.59  30.0  2
 E3K  Var_02    C7   C6   S1  C5   -179.74  30.0  1
 E3K  Var_03    C11  C12  N7  N8   -130.89  30.0  3
 E3K  Var_04    C9   C8   N5  C7    -83.05  30.0  1
 E3K  Var_05    S2   C9   C8  N5    179.63  30.0  1
 E3K  Var_06    S1   C6   C7  N5   -175.51  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
 E3K  chir_01  C10  O2  N6   C14  negativ
 E3K  chir_02  C11  O2  C12  C13  positiv
 E3K  chir_03  C14  O4  C13  C10  positiv
 E3K  chir_04  C13  O3  C11  C14  positiv

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
 E3K  plan-1  C2   0.020
 E3K  plan-1  C3   0.020
 E3K  plan-1  C4   0.020
 E3K  plan-1  C5   0.020
 E3K  plan-1  C10  0.020
 E3K  plan-1  C1   0.020
 E3K  plan-1  N1   0.020
 E3K  plan-1  N2   0.020
 E3K  plan-1  N3   0.020
 E3K  plan-1  N4   0.020
 E3K  plan-1  N6   0.020
 E3K  plan-1  S1   0.020
 E3K  plan-1  H1   0.020
 E3K  plan-2  C1   0.020
 E3K  plan-2  N1   0.020
 E3K  plan-2  H15  0.020
 E3K  plan-2  H16  0.020
 E3K  plan-3  C6   0.020
 E3K  plan-3  C7   0.020
 E3K  plan-3  C8   0.020
 E3K  plan-3  N5   0.020
 E3K  plan-3  O1   0.020
 E3K  plan-3  H17  0.020
 E3K  plan-4  N8   0.020
 E3K  plan-4  N9   0.020
 E3K  plan-4  C12  0.020
 E3K  plan-4  N7   0.020
 E3K  plan-4  H4   0.020

