# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 04:53:08 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(3-oxidanylpropyl)azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[C@H](CC[C@@H]([NH3+])C(O)=O)[NH2+]CCCO)[C@@H](O)[C@H]3O
#
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
 76K  76K  '[(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(3-oxidanylpropyl)azanium'  ligand  61  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_76K
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
 76K  C2   C  CR6    0   0.459  -4.9981  -2.3361  -0.9877
 76K  C6   C  CR56   0   0.489  -3.8113  -0.3973  -0.3084
 76K  C8   C  CR15   0   0.115  -1.7552  -1.0555  -0.6413
 76K  C10  C  CR56   0  -0.002  -3.7601  -1.6944  -0.7933
 76K  C11  C  CH1    0   0.182  -2.0626   1.3222   0.2254
 76K  C13  C  CH1    0   0.024  -0.0249   1.3941   1.3529
 76K  C14  C  CH2    0  -0.492   1.1637   0.4516   1.3305
 76K  C15  C  CH1    0  -0.105   2.2103   0.7479   0.2627
 76K  C16  C  CH2    0  -0.451   3.2701  -0.3425   0.1606
 76K  C25  C  CH2    0  -0.500   4.0832   4.0804  -0.2086
 76K  C26  C  CH2    0  -0.138   4.7205   4.7549  -1.4107
 76K  C28  C  CH1    0  -0.024  -1.1042   0.9869   2.3548
 76K  N1   N  NH2    0  -0.816  -5.0978  -3.5845  -1.4436
 76K  N3   N  N      0  -0.473  -6.1100  -1.6507  -0.6988
 76K  C4   C  CR16   0   0.040  -6.0051  -0.4048  -0.2439
 76K  N5   N  N      0  -0.460  -4.9093   0.2986  -0.0173
 76K  N7   N  NR5    0  -0.542  -2.5094  -0.0011  -0.2034
 76K  N9   N  N      0  -0.447  -2.4642  -2.0868  -0.9957
 76K  O12  O  O2     0  -0.496  -0.6760   1.4003   0.0844
 76K  C17  C  CH2    0  -0.473   2.6885  -1.6545  -0.3607
 76K  C18  C  CH1    0  -0.268   3.7455  -2.6339  -0.8301
 76K  N19  N  NT3    1  -0.792   4.6331  -3.0630   0.2867
 76K  C20  C  C      0   0.474   3.1755  -3.9231  -1.4905
 76K  O21  O  OC    -1  -0.564   2.1940  -3.7673  -2.2229
 76K  O22  O  O      0  -0.592   3.8049  -4.9681  -1.2348
 76K  N23  N  NT2    1  -0.688   2.8779   2.0629   0.5625
 76K  O27  O  OH1    0  -0.668   5.1869   6.0208  -1.0084
 76K  O29  O  OH1    0  -0.655  -0.8148   1.5238   3.6121
 76K  C30  C  CH1    0  -0.049  -2.3657   1.5630   1.7029
 76K  O31  O  OH1    0  -0.663  -2.4453   2.9483   1.8925
 76K  H46  H  HCR5   0   0.275  -0.6802  -1.0060  -0.6964
 76K  H32  H  HCH1   0   0.292  -2.5497   2.0617  -0.4154
 76K  H33  H  HCH1   0   0.250   0.2924   2.4187   1.5907
 76K  H47  H  HCH2   0   0.289   1.6327   0.4575   2.3192
 76K  H48  H  HCH2   0   0.273   0.8025  -0.5672   1.1764
 76K  H34  H  HCH1   0   0.306   1.7313   0.8808  -0.7095
 76K  H49  H  HCH2   0   0.274   4.0617  -0.0187  -0.5203
 76K  H50  H  HCH2   0   0.260   3.7332  -0.4815   1.1425
 76K  H54  H  HCH2   0   0.296   2.7898   2.7996  -1.3820
 76K  H53  H  HCH2   0   0.298   4.3353   2.0622  -0.9461
 76K  H55  H  HCH2   0   0.257   3.2711   4.7063   0.1719
 76K  H56  H  HCH2   0   0.260   4.8233   3.9725   0.5883
 76K  H57  H  HCH2   0   0.202   5.5352   4.1250  -1.7903
 76K  H58  H  HCH2   0   0.203   3.9789   4.8353  -2.2157
 76K  H41  H  HCH1   0   0.252  -1.1849  -0.1072   2.3906
 76K  H43  H  HNH2   0   0.412  -4.2796  -4.1217  -1.6708
 76K  H44  H  HNH2   0   0.404  -5.9999  -4.0073  -1.5778
 76K  H45  H  HCR6   0   0.253  -6.9449   0.0942  -0.0328
 76K  H52  H  HCH2   0   0.263   2.0654  -2.1356   0.3983
 76K  H51  H  HCH2   0   0.275   2.0416  -1.4574  -1.2169
 76K  H35  H  HCH1   0   0.311   4.3996  -2.1501  -1.5603
 76K  H36  H  HNT3   0   0.466   5.4283  -2.4489   0.4471
 76K  H37  H  HNT3   0   0.460   4.1313  -3.1602   1.1693
 76K  H38  H  HNT3   0   0.457   4.9700  -4.0035   0.0365
 76K  H39  H  HNT2   0   0.472   2.1893   2.7175   0.9385
 76K  H40  H  HNT2   0   0.468   3.5544   1.9353   1.3194
 76K  H59  H  HOH1   0   0.457   5.5530   6.4631  -1.7796
 76K  H60  H  HOH1   0   0.471  -1.3063   1.0363   4.2808
 76K  H42  H  HCH1   0   0.267  -3.2792   1.0512   2.0259
 76K  H61  H  HOH1   0   0.454  -2.1880   3.1374   2.8032
 76K  C24  C  CH2    0  -0.302   3.5414   2.7195  -0.5983

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
 76K  O22  C20  deloc     1.246  0.020  1.246
 76K  C20  O21  deloc     1.234  0.020  1.234
 76K  C20  C18  single    1.557  0.020  1.557
 76K  C17  C18  single    1.516  0.020  1.516
 76K  C17  C16  single    1.527  0.020  1.527
 76K  O27  C26  single    1.408  0.020  1.408
 76K  C18  N19  single    1.490  0.020  1.490
 76K  C15  C16  single    1.524  0.020  1.524
 76K  C15  N23  single    1.505  0.020  1.505
 76K  C15  C14  single    1.524  0.020  1.524
 76K  C25  C26  single    1.519  0.020  1.519
 76K  C25  C24  single    1.516  0.020  1.516
 76K  N23  C24  single    1.490  0.020  1.490
 76K  O29  C28  single    1.397  0.020  1.397
 76K  O31  C30  single    1.400  0.020  1.400
 76K  C13  C14  single    1.517  0.020  1.517
 76K  C13  O12  single    1.426  0.020  1.426
 76K  C13  C28  single    1.528  0.020  1.528
 76K  O12  C11  single    1.396  0.020  1.396
 76K  C28  C30  single    1.532  0.020  1.532
 76K  C30  C11  single    1.527  0.020  1.527
 76K  C11  N7   single    1.461  0.020  1.461
 76K  N7   C8   aromatic  1.368  0.020  1.368
 76K  N7   C6   aromatic  1.365  0.020  1.365
 76K  C8   N9   aromatic  1.301  0.020  1.301
 76K  N5   C6   aromatic  1.332  0.020  1.332
 76K  N5   C4   aromatic  1.322  0.020  1.322
 76K  C6   C10  aromatic  1.386  0.020  1.386
 76K  N9   C10  aromatic  1.369  0.020  1.369
 76K  C10  C2   aromatic  1.408  0.020  1.408
 76K  C4   N3   aromatic  1.331  0.020  1.331
 76K  N3   C2   aromatic  1.338  0.020  1.338
 76K  C2   N1   single    1.333  0.020  1.333
 76K  C8   H46  single    0.930  0.020  1.080
 76K  C11  H32  single    0.970  0.020  1.090
 76K  C13  H33  single    0.970  0.020  1.090
 76K  C14  H47  single    0.970  0.020  1.090
 76K  C14  H48  single    0.970  0.020  1.090
 76K  C15  H34  single    0.970  0.020  1.090
 76K  C16  H49  single    0.970  0.020  1.090
 76K  C16  H50  single    0.970  0.020  1.090
 76K  C24  H54  single    0.970  0.020  1.090
 76K  C24  H53  single    0.970  0.020  1.090
 76K  C25  H55  single    0.970  0.020  1.090
 76K  C25  H56  single    0.970  0.020  1.090
 76K  C26  H57  single    0.970  0.020  1.090
 76K  C26  H58  single    0.970  0.020  1.090
 76K  C28  H41  single    0.970  0.020  1.090
 76K  N1   H43  single    0.860  0.020  1.020
 76K  N1   H44  single    0.860  0.020  1.020
 76K  C4   H45  single    0.930  0.020  1.080
 76K  C17  H52  single    0.970  0.020  1.090
 76K  C17  H51  single    0.970  0.020  1.090
 76K  C18  H35  single    0.970  0.020  1.090
 76K  N19  H36  single    0.890  0.020  1.040
 76K  N19  H37  single    0.890  0.020  1.040
 76K  N19  H38  single    0.890  0.020  1.040
 76K  N23  H39  single    0.890  0.020  1.040
 76K  N23  H40  single    0.890  0.020  1.040
 76K  O27  H59  single    0.850  0.020  0.980
 76K  O29  H60  single    0.850  0.020  0.980
 76K  C30  H42  single    0.970  0.020  1.090
 76K  O31  H61  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
 76K  N3   C2   N1   119.45  3.000
 76K  N1   C2   C10  122.68  3.000
 76K  N3   C2   C10  117.88  3.000
 76K  N7   C6   N5   128.15  3.000
 76K  N5   C6   C10  126.58  3.000
 76K  N7   C6   C10  105.27  3.000
 76K  H46  C8   N9   124.50  3.000
 76K  H46  C8   N7   122.06  3.000
 76K  N9   C8   N7   113.43  3.000
 76K  N9   C10  C6   110.79  3.000
 76K  N9   C10  C2   132.94  3.000
 76K  C6   C10  C2   116.26  3.000
 76K  H32  C11  C30  111.84  3.000
 76K  H32  C11  O12  110.22  3.000
 76K  C30  C11  O12  106.62  3.000
 76K  H32  C11  N7   107.72  3.000
 76K  C30  C11  N7   111.47  3.000
 76K  O12  C11  N7   108.95  3.000
 76K  H33  C13  O12  108.69  3.000
 76K  H33  C13  C28  108.09  3.000
 76K  O12  C13  C28  105.19  3.000
 76K  H33  C13  C14  110.87  3.000
 76K  C28  C13  C14  113.43  3.000
 76K  O12  C13  C14  110.33  3.000
 76K  H48  C14  H47  105.92  3.000
 76K  H48  C14  C15  108.04  3.000
 76K  H47  C14  C15  109.73  3.000
 76K  H48  C14  C13  108.81  3.000
 76K  H47  C14  C13  108.61  3.000
 76K  C15  C14  C13  115.31  3.000
 76K  H34  C15  N23  105.41  3.000
 76K  H34  C15  C16  109.42  3.000
 76K  N23  C15  C16  109.27  3.000
 76K  H34  C15  C14  110.25  3.000
 76K  N23  C15  C14  109.57  3.000
 76K  C16  C15  C14  112.66  3.000
 76K  H50  C16  H49  106.86  3.000
 76K  H50  C16  C17  110.99  3.000
 76K  H49  C16  C17  108.52  3.000
 76K  H50  C16  C15  108.97  3.000
 76K  H49  C16  C15  109.48  3.000
 76K  C17  C16  C15  111.89  3.000
 76K  H56  C25  H55  107.80  3.000
 76K  H56  C25  C26  109.68  3.000
 76K  H55  C25  C26  109.44  3.000
 76K  H56  C25  C24  109.93  3.000
 76K  H55  C25  C24  109.75  3.000
 76K  C26  C25  C24  110.20  3.000
 76K  H58  C26  H57  106.86  3.000
 76K  H58  C26  O27  111.57  3.000
 76K  H57  C26  O27  111.65  3.000
 76K  H58  C26  C25  109.24  3.000
 76K  H57  C26  C25  109.29  3.000
 76K  O27  C26  C25  108.19  3.000
 76K  H41  C28  C30  109.15  3.000
 76K  H41  C28  O29  111.64  3.000
 76K  C30  C28  O29  114.13  3.000
 76K  H41  C28  C13  109.81  3.000
 76K  C30  C28  C13  101.67  3.000
 76K  O29  C28  C13  109.96  3.000
 76K  H44  N1   H43  118.40  3.000
 76K  H44  N1   C2   120.45  3.000
 76K  H43  N1   C2   121.15  3.000
 76K  C4   N3   C2   119.21  3.000
 76K  H45  C4   N5   116.11  3.000
 76K  H45  C4   N3   115.40  3.000
 76K  N5   C4   N3   128.48  3.000
 76K  C4   N5   C6   111.59  3.000
 76K  C11  N7   C8   128.56  3.000
 76K  C8   N7   C6   106.11  3.000
 76K  C11  N7   C6   125.26  3.000
 76K  C10  N9   C8   104.39  3.000
 76K  C13  O12  C11  111.31  3.000
 76K  H51  C17  H52  106.64  3.000
 76K  H51  C17  C18  106.69  3.000
 76K  H52  C17  C18  109.15  3.000
 76K  H51  C17  C16  109.78  3.000
 76K  H52  C17  C16  110.98  3.000
 76K  C18  C17  C16  113.29  3.000
 76K  H35  C18  C20  107.60  3.000
 76K  H35  C18  N19  105.76  3.000
 76K  C20  C18  N19  107.32  3.000
 76K  H35  C18  C17  109.77  3.000
 76K  N19  C18  C17  111.68  3.000
 76K  C20  C18  C17  114.29  3.000
 76K  H38  N19  H37  106.51  3.000
 76K  H38  N19  H36  109.50  3.000
 76K  H37  N19  H36  107.80  3.000
 76K  H38  N19  C18  106.01  3.000
 76K  H37  N19  C18  112.52  3.000
 76K  H36  N19  C18  114.20  3.000
 76K  O22  C20  O21  128.97  3.000
 76K  O21  C20  C18  116.00  3.000
 76K  O22  C20  C18  114.99  3.000
 76K  H40  N23  H39  104.68  3.000
 76K  H40  N23  C24  109.70  3.000
 76K  H39  N23  C24  107.73  3.000
 76K  H40  N23  C15  109.37  3.000
 76K  H39  N23  C15  109.52  3.000
 76K  C24  N23  C15  115.31  3.000
 76K  H59  O27  C26  108.10  3.000
 76K  H60  O29  C28  108.95  3.000
 76K  H42  C30  O31  112.00  3.000
 76K  H42  C30  C28  112.66  3.000
 76K  O31  C30  C28  111.17  3.000
 76K  H42  C30  C11  112.14  3.000
 76K  C28  C30  C11  100.89  3.000
 76K  O31  C30  C11  107.35  3.000
 76K  H61  O31  C30  107.85  3.000
 76K  H53  C24  H54  108.55  3.000
 76K  H53  C24  N23  107.93  3.000
 76K  H54  C24  N23  106.61  3.000
 76K  H53  C24  C25  111.34  3.000
 76K  H54  C24  C25  111.45  3.000
 76K  N23  C24  C25  110.77  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
 76K  CONST_01  N7   C6   C10  C2    180.00   0.0  0
 76K  CONST_02  N5   C6   C10  C2      0.00   0.0  0
 76K  CONST_03  C8   N9   C10  C2    180.00   0.0  0
 76K  CONST_04  N5   C4   N3   C2      0.00   0.0  0
 76K  CONST_05  N9   C8   N7   C6      0.00   0.0  0
 76K  CONST_06  N3   C4   N5   C6      0.00   0.0  0
 76K  CONST_07  C8   N9   C10  C6      0.00   0.0  0
 76K  CONST_08  N3   C2   C10  C6      0.00   0.0  0
 76K  CONST_09  N5   C6   N7   C8    180.00   0.0  0
 76K  CONST_10  C10  C6   N7   C8      0.00   0.0  0
 76K  CONST_11  C4   N5   C6   C10     0.00   0.0  0
 76K  CONST_12  N7   C8   N9   C10     0.00   0.0  0
 76K  CONST_13  C4   N3   C2   C10     0.00   0.0  0
 76K  CONST_14  N9   C10  C2   N3    180.00   0.0  0
 76K  CONST_15  N7   C6   N5   C4    180.00   0.0  0
 76K  CONST_16  N9   C10  C6   N5    180.00   0.0  0
 76K  CONST_17  N9   C10  C6   N7      0.00   0.0  0
 76K  CONST_18  C11  N7   C6   C10   180.00   0.0  0
 76K  CONST_19  N9   C8   N7   C11   180.00   0.0  0
 76K  CONST_20  N5   C6   N7   C11     0.00   0.0  0
 76K  CONST_21  N1   C2   C10  C6    180.00   0.0  0
 76K  CONST_22  N9   C10  C2   N1      0.00   0.0  0
 76K  CONST_23  C4   N3   C2   N1    180.00   0.0  0
 76K  CONST_24  H45  C4   N3   C2    180.00   0.0  0
 76K  CONST_25  H46  C8   N7   C6    180.00   0.0  0
 76K  CONST_26  H43  N1   C2   C10     0.00   0.0  0
 76K  CONST_27  H44  N1   C2   C10   180.00   0.0  0
 76K  Var_01    C18  C17  C16  C15   164.36  30.0  1
 76K  Var_02    C25  C24  N23  C15   175.56  30.0  3
 76K  Var_03    O27  C26  C25  C24   178.98  30.0  3
 76K  Var_04    N23  C24  C25  C26  -178.35  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
 76K  chir_01  C11  O12  C30  N7   positiv
 76K  chir_02  C13  O12  C14  C28  positiv
 76K  chir_03  C15  N23  C14  C16  positiv
 76K  chir_04  C28  O29  C13  C30  positiv
 76K  chir_05  C18  C20  C17  N19  negativ
 76K  chir_06  C30  O31  C28  C11  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
 76K  plan-1  C2   0.020
 76K  plan-1  C6   0.020
 76K  plan-1  C8   0.020
 76K  plan-1  C10  0.020
 76K  plan-1  C11  0.020
 76K  plan-1  N1   0.020
 76K  plan-1  N3   0.020
 76K  plan-1  C4   0.020
 76K  plan-1  N5   0.020
 76K  plan-1  N7   0.020
 76K  plan-1  N9   0.020
 76K  plan-1  H46  0.020
 76K  plan-1  H45  0.020
 76K  plan-2  C2   0.020
 76K  plan-2  N1   0.020
 76K  plan-2  H43  0.020
 76K  plan-2  H44  0.020
 76K  plan-3  C18  0.020
 76K  plan-3  C20  0.020
 76K  plan-3  O21  0.020
 76K  plan-3  O22  0.020

