# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 22:51:37 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: [(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{R})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC[S@@+](C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)Cc4ccccc4[N](=O)=O)C(O)=O
#
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
 EU9  EU9  '[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{R})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium'  ligand  61  36  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EU9
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
 EU9  O17  O  O      0  -0.606  -16.1781  32.8652  -27.3635
 EU9  C15  C  C      0   0.394  -16.3082  31.8112  -28.0157
 EU9  O16  O  OC    -1  -0.591  -15.4151  31.1637  -28.5940
 EU9  C14  C  CH1    0  -0.199  -17.7605  31.2832  -28.1431
 EU9  N18  N  NH2    0  -0.811  -17.8904  29.9516  -28.7171
 EU9  C13  C  CH2    0  -0.437  -18.5900  32.2669  -28.9657
 EU9  C12  C  CH2    0  -0.547  -20.0006  31.7672  -29.2032
 EU9  S11  S  S3     1   0.402  -20.0328  30.4194  -30.4518
 EU9  C7   C  CH2   -1  -0.695  -21.2987  31.1217  -31.5872
 EU9  C3   C  CR6    0   0.199  -21.3647  30.4665  -32.9315
 EU9  C21  C  CR16   0  -0.278  -22.4671  29.6578  -33.1898
 EU9  C1   C  CR16   0  -0.219  -22.6762  29.0765  -34.4289
 EU9  C61  C  CR16   0  -0.248  -21.7812  29.3063  -35.4615
 EU9  C51  C  CR16   0  -0.280  -20.6801  30.1129  -35.2433
 EU9  C41  C  CR6    0   0.196  -20.4714  30.6755  -33.9901
 EU9  N8   N  N      1   0.344  -19.2893  31.5125  -33.8402
 EU9  O10  O  O      0  -0.386  -18.9301  31.8078  -32.7219
 EU9  O9   O  O     -1  -0.361  -18.7152  31.8704  -34.8388
 EU9  C19  C  CH2    0  -0.595  -20.9554  29.1032  -29.5936
 EU9  C20  C  CH1    0   0.043  -20.6453  27.7398  -30.1777
 EU9  O24  O  O2     0  -0.484  -20.6783  27.8181  -31.5892
 EU9  C23  C  CH1    0   0.171  -19.8022  26.8725  -32.1643
 EU9  C22  C  CH1    0  -0.050  -19.1082  26.1491  -31.0031
 EU9  O26  O  OH1    0  -0.657  -19.8379  24.9760  -30.7681
 EU9  C27  C  CH1    0  -0.015  -19.2694  27.1512  -29.8605
 EU9  O25  O  OH1    0  -0.658  -19.1912  26.5126  -28.6239
 EU9  N9   N  NR5    0  -0.533  -18.9056  27.5483  -33.0683
 EU9  C8   C  CR15   0   0.101  -17.9734  28.5119  -32.7807
 EU9  N7   N  N      0  -0.441  -17.3848  28.9919  -33.8339
 EU9  C5   C  CR5    0  -0.011  -17.9581  28.3209  -34.8827
 EU9  C6   C  C      0   0.461  -17.7929  28.4092  -36.2773
 EU9  N6   N  NH2    0  -0.817  -16.9375  29.2574  -36.8480
 EU9  N1   N  N      0  -0.467  -18.5418  27.6107  -37.0464
 EU9  C2   C  C1     0   0.041  -19.4054  26.7797  -36.4691
 EU9  N3   N  N      0  -0.453  -19.6562  26.6178  -35.1812
 EU9  C4   C  CR5    0   0.505  -18.9073  27.4196  -34.4310
 EU9  H2   H  HCH1   0   0.232  -18.2044  31.2497  -27.1429
 EU9  H3   H  HNH2   0   0.350  -17.1729  29.8445  -29.4275
 EU9  H4   H  HNH2   0   0.359  -17.6580  29.2636  -28.0112
 EU9  H6   H  HCH2   0   0.248  -18.1074  32.4904  -29.9220
 EU9  H7   H  HCH2   0   0.269  -18.6679  33.2157  -28.4330
 EU9  H8   H  HCH2   0   0.325  -20.6461  32.5550  -29.5883
 EU9  H9   H  HCH2   0   0.315  -20.4554  31.3761  -28.2937
 EU9  H10  H  HCH2   0   0.347  -21.0445  32.1769  -31.6645
 EU9  H11  H  HCH2   0   0.344  -22.2629  31.0535  -31.0842
 EU9  H12  H  HCR6   0   0.280  -23.1830  29.4865  -32.3965
 EU9  H13  H  HCR6   0   0.279  -23.5442  28.4512  -34.5881
 EU9  H14  H  HCR6   0   0.281  -21.9378  28.8669  -36.4366
 EU9  H15  H  HCR6   0   0.312  -19.9903  30.3097  -36.0501
 EU9  H16  H  HCH2   0   0.333  -22.0171  29.3416  -29.6527
 EU9  H17  H  HCH2   0   0.333  -20.6519  29.1430  -28.5480
 EU9  H18  H  HCH1   0   0.272  -21.4162  27.0540  -29.8025
 EU9  H19  H  HCH1   0   0.284  -20.3587  26.1570  -32.7744
 EU9  H20  H  HCH1   0   0.268  -18.0562  25.9390  -31.2292
 EU9  H21  H  HOH1   0   0.458  -19.5452  24.5938  -29.9329
 EU9  H22  H  HCH1   0   0.254  -18.5051  27.9284  -29.9618
 EU9  H23  H  HOH1   0   0.467  -19.0101  27.1614  -27.9372
 EU9  H24  H  HCR5   0   0.301  -17.7518  28.8180  -31.7696
 EU9  H25  H  HNH2   0   0.404  -16.8656  29.3108  -37.8495
 EU9  H26  H  HNH2   0   0.411  -16.3890  29.8916  -36.2939
 EU9  H27  H  H      0   0.253  -19.9781  26.1577  -37.1489

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
 EU9  N6   C6   single    1.333  0.020  1.333
 EU9  N1   C6   aromatic  1.338  0.020  1.338
 EU9  N1   C2   aromatic  1.330  0.020  1.330
 EU9  C6   C5   aromatic  1.407  0.020  1.407
 EU9  C2   N3   aromatic  1.322  0.020  1.322
 EU9  C61  C1   aromatic  1.386  0.020  1.386
 EU9  C61  C51  aromatic  1.382  0.020  1.382
 EU9  C5   C4   aromatic  1.385  0.020  1.385
 EU9  C5   N7   aromatic  1.371  0.020  1.371
 EU9  N3   C4   aromatic  1.329  0.020  1.329
 EU9  C1   C21  aromatic  1.385  0.020  1.385
 EU9  C51  C41  aromatic  1.389  0.020  1.389
 EU9  C4   N9   aromatic  1.369  0.020  1.369
 EU9  N7   C8   aromatic  1.298  0.020  1.298
 EU9  O9   N8   single    1.206  0.020  1.206
 EU9  C21  C3   aromatic  1.391  0.020  1.391
 EU9  C41  N8   single    1.456  0.020  1.456
 EU9  C41  C3   aromatic  1.401  0.020  1.401
 EU9  N9   C8   aromatic  1.371  0.020  1.371
 EU9  N9   C23  single    1.441  0.020  1.441
 EU9  N8   O10  double    1.211  0.020  1.211
 EU9  C3   C7   single    1.497  0.020  1.497
 EU9  C23  O24  single    1.412  0.020  1.412
 EU9  C23  C22  single    1.534  0.020  1.534
 EU9  O24  C20  single    1.414  0.020  1.414
 EU9  C22  O26  single    1.401  0.020  1.401
 EU9  C22  C27  single    1.528  0.020  1.528
 EU9  C7   S11  single    1.840  0.020  1.840
 EU9  C20  C27  single    1.530  0.020  1.530
 EU9  C20  C19  single    1.515  0.020  1.515
 EU9  C27  O25  single    1.394  0.020  1.394
 EU9  S11  C19  single    1.822  0.020  1.822
 EU9  S11  C12  single    1.838  0.020  1.838
 EU9  O17  C15  deloc     1.246  0.020  1.246
 EU9  C13  C12  single    1.515  0.020  1.515
 EU9  C13  C14  single    1.527  0.020  1.527
 EU9  C15  O16  deloc     1.245  0.020  1.245
 EU9  C15  C14  single    1.551  0.020  1.551
 EU9  C14  N18  single    1.456  0.020  1.456
 EU9  C14  H2   single    0.970  0.020  1.090
 EU9  N18  H3   single    0.890  0.020  1.040
 EU9  N18  H4   single    0.890  0.020  1.040
 EU9  C13  H6   single    0.970  0.020  1.090
 EU9  C13  H7   single    0.970  0.020  1.090
 EU9  C12  H8   single    0.970  0.020  1.090
 EU9  C12  H9   single    0.970  0.020  1.090
 EU9  C7   H10  single    0.970  0.020  1.090
 EU9  C7   H11  single    0.970  0.020  1.090
 EU9  C21  H12  single    0.930  0.020  1.080
 EU9  C1   H13  single    0.930  0.020  1.080
 EU9  C61  H14  single    0.930  0.020  1.080
 EU9  C51  H15  single    0.930  0.020  1.080
 EU9  C19  H16  single    0.970  0.020  1.090
 EU9  C19  H17  single    0.970  0.020  1.090
 EU9  C20  H18  single    0.970  0.020  1.090
 EU9  C23  H19  single    0.970  0.020  1.090
 EU9  C22  H20  single    0.970  0.020  1.090
 EU9  O26  H21  single    0.850  0.020  0.980
 EU9  C27  H22  single    0.970  0.020  1.090
 EU9  O25  H23  single    0.850  0.020  0.980
 EU9  C8   H24  single    0.930  0.020  1.080
 EU9  N6   H25  single    0.860  0.020  1.020
 EU9  N6   H26  single    0.860  0.020  1.020
 EU9  C2   H27  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
 EU9  C14  C15  O16  117.16  3.000
 EU9  C14  C15  O17  115.38  3.000
 EU9  O16  C15  O17  127.43  3.000
 EU9  H2   C14  C13  106.95  3.000
 EU9  H2   C14  N18  107.22  3.000
 EU9  C13  C14  N18  109.17  3.000
 EU9  H2   C14  C15  108.37  3.000
 EU9  N18  C14  C15  115.30  3.000
 EU9  C13  C14  C15  109.49  3.000
 EU9  H4   N18  H3   104.71  3.000
 EU9  H4   N18  C14  109.03  3.000
 EU9  H3   N18  C14  108.02  3.000
 EU9  H7   C13  H6   106.30  3.000
 EU9  H7   C13  C12  107.27  3.000
 EU9  H6   C13  C12  109.94  3.000
 EU9  H7   C13  C14  109.63  3.000
 EU9  H6   C13  C14  111.26  3.000
 EU9  C12  C13  C14  112.19  3.000
 EU9  H9   C12  H8   107.91  3.000
 EU9  H9   C12  S11  107.25  3.000
 EU9  H8   C12  S11  106.25  3.000
 EU9  H9   C12  C13  112.10  3.000
 EU9  H8   C12  C13  111.64  3.000
 EU9  S11  C12  C13  111.39  3.000
 EU9  C19  S11  C7   102.59  3.000
 EU9  C19  S11  C12  102.63  3.000
 EU9  C7   S11  C12   98.71  3.000
 EU9  H11  C7   H10  107.47  3.000
 EU9  H11  C7   C3   110.38  3.000
 EU9  H10  C7   C3   111.78  3.000
 EU9  H11  C7   S11  107.46  3.000
 EU9  H10  C7   S11  104.67  3.000
 EU9  C3   C7   S11  114.68  3.000
 EU9  C41  C3   C21  116.85  3.000
 EU9  C41  C3   C7   125.82  3.000
 EU9  C21  C3   C7   117.13  3.000
 EU9  H12  C21  C1   119.32  3.000
 EU9  H12  C21  C3   118.69  3.000
 EU9  C1   C21  C3   121.99  3.000
 EU9  H13  C1   C61  120.30  3.000
 EU9  H13  C1   C21  119.71  3.000
 EU9  C61  C1   C21  119.99  3.000
 EU9  H14  C61  C51  119.67  3.000
 EU9  H14  C61  C1   120.75  3.000
 EU9  C51  C61  C1   119.58  3.000
 EU9  H15  C51  C41  120.29  3.000
 EU9  H15  C51  C61  119.82  3.000
 EU9  C41  C51  C61  119.89  3.000
 EU9  N8   C41  C51  116.58  3.000
 EU9  N8   C41  C3   121.71  3.000
 EU9  C51  C41  C3   121.69  3.000
 EU9  O9   N8   O10  123.43  3.000
 EU9  O10  N8   C41  118.42  3.000
 EU9  O9   N8   C41  118.15  3.000
 EU9  H17  C19  H16  108.39  3.000
 EU9  H17  C19  C20  110.24  3.000
 EU9  H16  C19  C20  112.04  3.000
 EU9  H17  C19  S11  106.53  3.000
 EU9  H16  C19  S11  108.04  3.000
 EU9  C20  C19  S11  111.40  3.000
 EU9  H18  C20  C27  108.68  3.000
 EU9  H18  C20  O24  111.06  3.000
 EU9  C27  C20  O24  104.44  3.000
 EU9  H18  C20  C19  106.65  3.000
 EU9  C27  C20  C19  116.76  3.000
 EU9  O24  C20  C19  109.28  3.000
 EU9  C23  O24  C20  110.80  3.000
 EU9  H19  C23  N9   105.88  3.000
 EU9  H19  C23  C22  110.14  3.000
 EU9  N9   C23  C22  114.48  3.000
 EU9  H19  C23  O24  110.49  3.000
 EU9  C22  C23  O24  106.76  3.000
 EU9  N9   C23  O24  109.12  3.000
 EU9  H20  C22  C27  112.40  3.000
 EU9  H20  C22  O26  111.95  3.000
 EU9  C27  C22  O26  111.63  3.000
 EU9  H20  C22  C23  111.61  3.000
 EU9  C27  C22  C23  102.06  3.000
 EU9  O26  C22  C23  106.62  3.000
 EU9  H21  O26  C22  108.60  3.000
 EU9  H22  C27  O25  111.60  3.000
 EU9  H22  C27  C22  108.83  3.000
 EU9  O25  C27  C22  110.91  3.000
 EU9  H22  C27  C20  109.61  3.000
 EU9  O25  C27  C20  114.25  3.000
 EU9  C22  C27  C20  101.08  3.000
 EU9  H23  O25  C27  109.56  3.000
 EU9  C4   N9   C8   106.01  3.000
 EU9  C8   N9   C23  128.37  3.000
 EU9  C4   N9   C23  125.41  3.000
 EU9  H24  C8   N7   124.19  3.000
 EU9  H24  C8   N9   122.37  3.000
 EU9  N7   C8   N9   113.44  3.000
 EU9  C5   N7   C8   104.49  3.000
 EU9  C4   C5   C6   116.39  3.000
 EU9  C4   C5   N7   110.84  3.000
 EU9  C6   C5   N7   132.73  3.000
 EU9  N1   C6   N6   119.53  3.000
 EU9  N1   C6   C5   117.82  3.000
 EU9  N6   C6   C5   122.65  3.000
 EU9  H26  N6   H25  118.46  3.000
 EU9  H26  N6   C6   121.05  3.000
 EU9  H25  N6   C6   120.40  3.000
 EU9  C2   N1   C6   119.13  3.000
 EU9  H27  C2   N3   116.11  3.000
 EU9  H27  C2   N1   115.40  3.000
 EU9  N3   C2   N1   128.49  3.000
 EU9  C4   N3   C2   111.66  3.000
 EU9  N3   C4   C5   126.50  3.000
 EU9  N3   C4   N9   128.27  3.000
 EU9  C5   C4   N9   105.23  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
 EU9  CONST_01  C61  C1   C21  C3     0.00   0.0  0
 EU9  CONST_02  C61  C51  C41  C3     0.00   0.0  0
 EU9  CONST_03  C51  C61  C1   C21    0.00   0.0  0
 EU9  CONST_04  C51  C41  C3   C21    0.00   0.0  0
 EU9  CONST_05  C41  C51  C61  C1     0.00   0.0  0
 EU9  CONST_06  C41  C3   C21  C1     0.00   0.0  0
 EU9  CONST_07  C6   C5   C4   N9   180.00   0.0  0
 EU9  CONST_08  N7   C5   C4   N9     0.00   0.0  0
 EU9  CONST_09  C2   N3   C4   N9   180.00   0.0  0
 EU9  CONST_10  C5   N7   C8   N9     0.00   0.0  0
 EU9  CONST_11  C6   C5   N7   C8   180.00   0.0  0
 EU9  CONST_12  C4   C5   N7   C8     0.00   0.0  0
 EU9  CONST_13  C5   C4   N9   C8     0.00   0.0  0
 EU9  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 EU9  CONST_15  N1   C6   C5   N7   180.00   0.0  0
 EU9  CONST_16  N3   C4   C5   N7   180.00   0.0  0
 EU9  CONST_17  C4   N9   C8   N7     0.00   0.0  0
 EU9  CONST_18  C2   N1   C6   C5     0.00   0.0  0
 EU9  CONST_19  C2   N3   C4   C5     0.00   0.0  0
 EU9  CONST_20  N3   C2   N1   C6     0.00   0.0  0
 EU9  CONST_21  N3   C4   C5   C6     0.00   0.0  0
 EU9  CONST_22  C4   C5   C6   N1     0.00   0.0  0
 EU9  CONST_23  C4   N3   C2   N1     0.00   0.0  0
 EU9  CONST_24  C5   C4   N9   C23  180.00   0.0  0
 EU9  CONST_25  N3   C4   N9   C23    0.00   0.0  0
 EU9  CONST_26  N7   C8   N9   C23  180.00   0.0  0
 EU9  CONST_27  C1   C21  C3   C7   180.00   0.0  0
 EU9  CONST_28  C51  C41  C3   C7   180.00   0.0  0
 EU9  CONST_29  N8   C41  C3   C21  180.00   0.0  0
 EU9  CONST_30  N8   C41  C51  C61  180.00   0.0  0
 EU9  CONST_31  N6   C6   C5   N7     0.00   0.0  0
 EU9  CONST_32  C2   N1   C6   N6   180.00   0.0  0
 EU9  CONST_33  C4   C5   C6   N6   180.00   0.0  0
 EU9  CONST_34  H13  C1   C21  C3   180.00   0.0  0
 EU9  CONST_35  H15  C51  C41  C3   180.00   0.0  0
 EU9  CONST_36  H14  C61  C1   C21  180.00   0.0  0
 EU9  CONST_37  H12  C21  C1   C61  180.00   0.0  0
 EU9  CONST_38  H24  C8   N9   C23    0.00   0.0  0
 EU9  CONST_39  H27  C2   N1   C6   180.00   0.0  0
 EU9  CONST_40  O9   N8   C41  C3   180.00   0.0  0
 EU9  CONST_42  O9   N8   C41  C51    0.00   0.0  0
 EU9  CONST_43  O10  N8   C41  C51  180.00   0.0  0
 EU9  CONST_44  H25  N6   C6   C5   180.00   0.0  0
 EU9  CONST_45  H26  N6   C6   C5     0.00   0.0  0
 EU9  Var_01    C21  C3   C7   S11  107.82  30.0  2
 EU9  Var_02    S11  C12  C13  C14  -74.21  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
 EU9  chir_01  C14  C13  C15  N18  positiv
 EU9  chir_02  S11  C7   C19  C12  positiv
 EU9  chir_03  C20  O24  C27  C19  negativ
 EU9  chir_04  C23  O24  N9   C22  negativ
 EU9  chir_05  C22  O26  C23  C27  negativ
 EU9  chir_06  C27  O25  C20  C22  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
 EU9  plan-1  C7   0.020
 EU9  plan-1  C3   0.020
 EU9  plan-1  C21  0.020
 EU9  plan-1  C1   0.020
 EU9  plan-1  C61  0.020
 EU9  plan-1  C51  0.020
 EU9  plan-1  C41  0.020
 EU9  plan-1  N8   0.020
 EU9  plan-1  H12  0.020
 EU9  plan-1  H13  0.020
 EU9  plan-1  H14  0.020
 EU9  plan-1  H15  0.020
 EU9  plan-2  C23  0.020
 EU9  plan-2  N9   0.020
 EU9  plan-2  C8   0.020
 EU9  plan-2  N7   0.020
 EU9  plan-2  C5   0.020
 EU9  plan-2  C6   0.020
 EU9  plan-2  N6   0.020
 EU9  plan-2  N1   0.020
 EU9  plan-2  C2   0.020
 EU9  plan-2  N3   0.020
 EU9  plan-2  C4   0.020
 EU9  plan-2  H24  0.020
 EU9  plan-2  H27  0.020
 EU9  plan-3  C41  0.020
 EU9  plan-3  N8   0.020
 EU9  plan-3  O10  0.020
 EU9  plan-3  O9   0.020
 EU9  plan-4  C6   0.020
 EU9  plan-4  N6   0.020
 EU9  plan-4  H25  0.020
 EU9  plan-4  H26  0.020
 EU9  plan-5  O17  0.020
 EU9  plan-5  C15  0.020
 EU9  plan-5  O16  0.020
 EU9  plan-5  C14  0.020

