# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 14:20:01 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: [(2~{R},5~{S})-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]-(phenylmethyl)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+]Cc4ccccc4)[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
 76O  76O  '[(2~{R},5~{S})-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]-(phenylmethyl)azanium'  ligand  65  34  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_76O
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
 76O  C2   C  CR6   0   0.459  -1.5766  31.9856  -17.9111
 76O  C6   C  CR56  0   0.488   0.4731  30.8337  -18.2117
 76O  C8   C  CR15  0   0.107   0.1157  29.0574  -16.9892
 76O  C10  C  CR56  0  -0.002  -0.7799  30.8617  -17.6217
 76O  C11  C  CH1   0   0.181   2.3733  29.2147  -18.1613
 76O  C13  C  CH1   0   0.016   3.4313  27.6039  -16.8548
 76O  C14  C  CH2   0  -0.493   2.9681  26.4721  -15.9645
 76O  C15  C  CH1   0  -0.083   2.8699  25.1206  -16.6699
 76O  C16  C  CH2   0  -0.500   4.1507  24.7220  -17.4103
 76O  C25  C  CR6   0   0.086   1.0602  22.9960  -14.0412
 76O  C26  C  CR16  0  -0.283   1.6069  22.8636  -12.7681
 76O  C27  C  CR16  0  -0.238   1.3914  21.7066  -12.0334
 76O  C28  C  CR16  0  -0.253   0.6270  20.6768  -12.5666
 76O  C31  C  CH1   0   0.004   3.5797  28.9541  -16.1505
 76O  N1   N  NH2   0  -0.815  -2.7997  32.1518  -17.4073
 76O  N3   N  N     0  -0.473  -1.0673  32.9216  -18.7201
 76O  C4   C  CR16  0   0.042   0.1579  32.7600  -19.2125
 76O  N5   N  N     0  -0.459   0.9973  31.7578  -19.0139
 76O  N7   N  NR5   0  -0.536   1.0404  29.6654  -17.7944
 76O  N9   N  N     0  -0.449  -0.9839  29.7404  -16.8619
 76O  O12  O  O2    0  -0.502   2.4789  27.8446  -17.8891
 76O  C17  C  CH2   0  -0.501   4.1376  25.1845  -18.8727
 76O  C18  C  CH1   0  -0.250   5.5223  25.5716  -19.3986
 76O  N19  N  NT3   1  -0.777   5.3819  26.4410  -20.5927
 76O  C20  C  C     0   0.589   6.3706  24.3761  -19.7911
 76O  O21  O  OH1   0  -0.568   6.6335  23.6261  -18.7449
 76O  O22  O  O     0  -0.416   6.7304  24.1637  -20.9176
 76O  N23  N  NT2   1  -0.678   2.5777  24.0581  -15.6486
 76O  C29  C  CR16  0  -0.239   0.0771  20.8053  -13.8354
 76O  C30  C  CR16  0  -0.283   0.2942  21.9616  -14.5709
 76O  O32  O  OH1   0  -0.660   4.8019  29.1034  -15.4938
 76O  C33  C  CH1   0  -0.055   3.4586  29.9079  -17.3396
 76O  O34  O  OH1   0  -0.660   4.6211  29.9014  -18.1240
 76O  H49  H  HCR5  0   0.290   0.2979  28.1001  -16.5282
 76O  H35  H  HCH1  0   0.290   2.4985  29.4077  -19.2299
 76O  H36  H  HCH1  0   0.244   4.4035  27.3524  -17.2975
 76O  H51  H  HCH2  0   0.274   2.0105  26.7460  -15.5159
 76O  H50  H  HCH2  0   0.280   3.6924  26.3885  -15.1479
 76O  H37  H  HCH1  0   0.323   2.0137  25.0917  -17.3467
 76O  H52  H  HCH2  0   0.293   4.2696  23.6382  -17.3831
 76O  H53  H  HCH2  0   0.276   5.0103  25.1294  -16.8712
 76O  H56  H  HCH2  0   0.321   1.4455  25.1030  -14.2174
 76O  H57  H  HCH2  0   0.321   0.5223  24.4198  -15.5672
 76O  H58  H  HCR6  0   0.265   2.1953  23.6689  -12.3444
 76O  H59  H  HCR6  0   0.266   1.8158  21.6103  -11.0429
 76O  H60  H  HCR6  0   0.266   0.4558  19.7765  -11.9911
 76O  H44  H  HCH1  0   0.251   2.7314  29.1150  -15.4723
 76O  H47  H  HNH2  0   0.404  -3.3636  32.9331  -17.6943
 76O  H46  H  HNH2  0   0.412  -3.2258  31.4422  -16.8377
 76O  H48  H  HCR6  0   0.253   0.5087  33.5568  -19.8597
 76O  H54  H  HCH2  0   0.292   3.4874  26.0523  -18.9884
 76O  H55  H  HCH2  0   0.308   3.7007  24.4099  -19.5061
 76O  H38  H  HCH1  0   0.355   6.0628  26.1664  -18.6581
 76O  H39  H  HNT3  0   0.472   4.9038  27.3109  -20.3553
 76O  H41  H  HNT3  0   0.487   6.2855  26.7086  -20.9868
 76O  H40  H  HNT3  0   0.480   4.8465  26.0011  -21.3431
 76O  H1   H  HOH1  0   0.502   7.1522  22.8460  -18.9986
 76O  H43  H  HNT2  0   0.475   2.5236  23.1611  -16.1362
 76O  H42  H  HNT2  0   0.470   3.3725  23.9649  -15.0103
 76O  H61  H  HCR6  0   0.266  -0.5242  20.0078  -14.2514
 76O  H62  H  HCR6  0   0.265  -0.1408  22.0644  -15.5580
 76O  H63  H  HOH1  0   0.472   4.6793  28.9677  -14.5505
 76O  H45  H  HCH1  0   0.272   3.1659  30.9207  -17.0405
 76O  H64  H  HOH1  0   0.461   5.3730  30.1152  -17.5601
 76O  C24  C  CH2   0  -0.404   1.3206  24.2292  -14.8516

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
 76O  O22  C20  double    1.201  0.020  1.201
 76O  N19  C18  single    1.484  0.020  1.484
 76O  C20  C18  single    1.518  0.020  1.518
 76O  C20  O21  single    1.314  0.020  1.314
 76O  C18  C17  single    1.531  0.020  1.531
 76O  N3   C4   aromatic  1.330  0.020  1.330
 76O  N3   C2   aromatic  1.338  0.020  1.338
 76O  N1   C2   single    1.333  0.020  1.333
 76O  C17  C16  single    1.534  0.020  1.534
 76O  C4   N5   aromatic  1.322  0.020  1.322
 76O  C2   C10  aromatic  1.408  0.020  1.408
 76O  N5   C6   aromatic  1.331  0.020  1.331
 76O  C10  C6   aromatic  1.385  0.020  1.385
 76O  C10  N9   aromatic  1.370  0.020  1.370
 76O  C6   N7   aromatic  1.364  0.020  1.364
 76O  N9   C8   aromatic  1.301  0.020  1.301
 76O  N7   C8   aromatic  1.369  0.020  1.369
 76O  N7   C11  single    1.454  0.020  1.454
 76O  C11  O12  single    1.401  0.020  1.401
 76O  C11  C33  single    1.528  0.020  1.528
 76O  O12  C13  single    1.426  0.020  1.426
 76O  C16  C15  single    1.532  0.020  1.532
 76O  O34  C33  single    1.402  0.020  1.402
 76O  C33  C31  single    1.529  0.020  1.529
 76O  C15  N23  single    1.502  0.020  1.502
 76O  C15  C14  single    1.528  0.020  1.528
 76O  C13  C31  single    1.530  0.020  1.530
 76O  C13  C14  single    1.513  0.020  1.513
 76O  C31  O32  single    1.395  0.020  1.395
 76O  N23  C24  single    1.498  0.020  1.498
 76O  C24  C25  single    1.498  0.020  1.498
 76O  C30  C25  aromatic  1.392  0.020  1.392
 76O  C30  C29  aromatic  1.387  0.020  1.387
 76O  C25  C26  aromatic  1.392  0.020  1.392
 76O  C29  C28  aromatic  1.389  0.020  1.389
 76O  C26  C27  aromatic  1.387  0.020  1.387
 76O  C28  C27  aromatic  1.389  0.020  1.389
 76O  C8   H49  single    0.930  0.020  1.080
 76O  C11  H35  single    0.970  0.020  1.090
 76O  C13  H36  single    0.970  0.020  1.090
 76O  C14  H51  single    0.970  0.020  1.090
 76O  C14  H50  single    0.970  0.020  1.090
 76O  C15  H37  single    0.970  0.020  1.090
 76O  C16  H52  single    0.970  0.020  1.090
 76O  C16  H53  single    0.970  0.020  1.090
 76O  C24  H56  single    0.970  0.020  1.090
 76O  C24  H57  single    0.970  0.020  1.090
 76O  C26  H58  single    0.930  0.020  1.080
 76O  C27  H59  single    0.930  0.020  1.080
 76O  C28  H60  single    0.930  0.020  1.080
 76O  C31  H44  single    0.970  0.020  1.090
 76O  N1   H47  single    0.860  0.020  1.020
 76O  N1   H46  single    0.860  0.020  1.020
 76O  C4   H48  single    0.930  0.020  1.080
 76O  C17  H54  single    0.970  0.020  1.090
 76O  C17  H55  single    0.970  0.020  1.090
 76O  C18  H38  single    0.970  0.020  1.090
 76O  N19  H39  single    0.890  0.020  1.040
 76O  N19  H41  single    0.890  0.020  1.040
 76O  N19  H40  single    0.890  0.020  1.040
 76O  O21  H1   single    0.850  0.020  0.980
 76O  N23  H43  single    0.890  0.020  1.040
 76O  N23  H42  single    0.890  0.020  1.040
 76O  C29  H61  single    0.930  0.020  1.080
 76O  C30  H62  single    0.930  0.020  1.080
 76O  O32  H63  single    0.850  0.020  0.980
 76O  C33  H45  single    0.970  0.020  1.090
 76O  O34  H64  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
 76O  N3   C2   N1   119.37  3.000
 76O  N1   C2   C10  122.75  3.000
 76O  N3   C2   C10  117.87  3.000
 76O  N7   C6   N5   127.95  3.000
 76O  N7   C6   C10  105.26  3.000
 76O  N5   C6   C10  126.78  3.000
 76O  H49  C8   N9   124.57  3.000
 76O  H49  C8   N7   122.13  3.000
 76O  N9   C8   N7   113.30  3.000
 76O  N9   C10  C6   110.75  3.000
 76O  N9   C10  C2   133.11  3.000
 76O  C6   C10  C2   116.14  3.000
 76O  H35  C11  C33  111.37  3.000
 76O  H35  C11  O12  110.73  3.000
 76O  C33  C11  O12  106.60  3.000
 76O  H35  C11  N7   107.27  3.000
 76O  C33  C11  N7   112.02  3.000
 76O  O12  C11  N7   108.86  3.000
 76O  H36  C13  O12  109.74  3.000
 76O  H36  C13  C31  107.58  3.000
 76O  O12  C13  C31  104.45  3.000
 76O  H36  C13  C14  109.71  3.000
 76O  C31  C13  C14  114.77  3.000
 76O  O12  C13  C14  110.40  3.000
 76O  H50  C14  H51  107.03  3.000
 76O  H50  C14  C15  108.63  3.000
 76O  H51  C14  C15  110.80  3.000
 76O  H50  C14  C13  107.07  3.000
 76O  H51  C14  C13  108.82  3.000
 76O  C15  C14  C13  114.20  3.000
 76O  H37  C15  N23  104.49  3.000
 76O  H37  C15  C16  110.43  3.000
 76O  N23  C15  C16  107.88  3.000
 76O  H37  C15  C14  111.10  3.000
 76O  N23  C15  C14  108.92  3.000
 76O  C16  C15  C14  113.55  3.000
 76O  H53  C16  H52  105.80  3.000
 76O  H53  C16  C17  111.37  3.000
 76O  H52  C16  C17  108.92  3.000
 76O  H53  C16  C15  108.79  3.000
 76O  H52  C16  C15  109.73  3.000
 76O  C17  C16  C15  112.03  3.000
 76O  C30  C25  C26  119.58  3.000
 76O  C26  C25  C24  120.31  3.000
 76O  C30  C25  C24  120.10  3.000
 76O  H58  C26  C27  119.80  3.000
 76O  H58  C26  C25  120.02  3.000
 76O  C27  C26  C25  120.18  3.000
 76O  H59  C27  C28  120.09  3.000
 76O  H59  C27  C26  119.88  3.000
 76O  C28  C27  C26  120.03  3.000
 76O  H60  C28  C29  120.01  3.000
 76O  H60  C28  C27  119.98  3.000
 76O  C29  C28  C27  120.01  3.000
 76O  H44  C31  C33  109.13  3.000
 76O  H44  C31  O32  111.73  3.000
 76O  C33  C31  O32  111.63  3.000
 76O  H44  C31  C13  109.80  3.000
 76O  O32  C31  C13  113.33  3.000
 76O  C33  C31  C13  100.65  3.000
 76O  H46  N1   H47  118.21  3.000
 76O  H46  N1   C2   121.02  3.000
 76O  H47  N1   C2   120.24  3.000
 76O  C4   N3   C2   119.30  3.000
 76O  H48  C4   N5   116.17  3.000
 76O  H48  C4   N3   115.43  3.000
 76O  N5   C4   N3   128.40  3.000
 76O  C4   N5   C6   111.51  3.000
 76O  C11  N7   C8   129.06  3.000
 76O  C11  N7   C6   124.72  3.000
 76O  C8   N7   C6   106.22  3.000
 76O  C10  N9   C8   104.46  3.000
 76O  C13  O12  C11  110.87  3.000
 76O  H55  C17  H54  105.33  3.000
 76O  H55  C17  C18  110.00  3.000
 76O  H54  C17  C18  107.55  3.000
 76O  H55  C17  C16  110.04  3.000
 76O  H54  C17  C16  110.26  3.000
 76O  C18  C17  C16  113.33  3.000
 76O  H38  C18  C20  109.12  3.000
 76O  H38  C18  N19  105.86  3.000
 76O  C20  C18  N19  107.84  3.000
 76O  H38  C18  C17  110.62  3.000
 76O  C20  C18  C17  113.28  3.000
 76O  N19  C18  C17  109.82  3.000
 76O  H40  N19  H41  107.04  3.000
 76O  H40  N19  H39  107.00  3.000
 76O  H41  N19  H39  106.31  3.000
 76O  H40  N19  C18  112.86  3.000
 76O  H41  N19  C18  112.35  3.000
 76O  H39  N19  C18  110.89  3.000
 76O  O22  C20  O21  125.86  3.000
 76O  O21  C20  C18  110.83  3.000
 76O  O22  C20  C18  123.31  3.000
 76O  H1   O21  C20  110.95  3.000
 76O  H42  N23  H43  104.99  3.000
 76O  H42  N23  C24  109.28  3.000
 76O  H43  N23  C24  108.03  3.000
 76O  H42  N23  C15  109.71  3.000
 76O  H43  N23  C15  107.85  3.000
 76O  C24  N23  C15  116.36  3.000
 76O  H61  C29  C30  119.83  3.000
 76O  H61  C29  C28  120.21  3.000
 76O  C30  C29  C28  119.96  3.000
 76O  H62  C30  C29  119.94  3.000
 76O  H62  C30  C25  119.81  3.000
 76O  C29  C30  C25  120.25  3.000
 76O  H63  O32  C31  109.59  3.000
 76O  H45  C33  O34  112.23  3.000
 76O  H45  C33  C31  112.67  3.000
 76O  O34  C33  C31  111.49  3.000
 76O  H45  C33  C11  112.11  3.000
 76O  C31  C33  C11  101.04  3.000
 76O  O34  C33  C11  106.62  3.000
 76O  H64  O34  C33  108.57  3.000
 76O  H57  C24  H56  109.09  3.000
 76O  H57  C24  N23  106.59  3.000
 76O  H56  C24  N23  107.81  3.000
 76O  H57  C24  C25  111.85  3.000
 76O  H56  C24  C25  111.47  3.000
 76O  N23  C24  C25  109.84  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
 76O  CONST_01  N5   C4   N3   C2     0.00   0.0  0
 76O  CONST_02  N5   C6   C10  C2     0.00   0.0  0
 76O  CONST_03  N7   C6   C10  C2   180.00   0.0  0
 76O  CONST_04  C8   N9   C10  C2   180.00   0.0  0
 76O  CONST_05  N3   C4   N5   C6     0.00   0.0  0
 76O  CONST_06  N3   C2   C10  C6     0.00   0.0  0
 76O  CONST_07  C8   N9   C10  C6     0.00   0.0  0
 76O  CONST_08  N9   C8   N7   C6     0.00   0.0  0
 76O  CONST_09  N5   C6   N7   C8   180.00   0.0  0
 76O  CONST_10  C10  C6   N7   C8     0.00   0.0  0
 76O  CONST_11  C4   N3   C2   C10    0.00   0.0  0
 76O  CONST_12  C4   N5   C6   C10    0.00   0.0  0
 76O  CONST_13  N7   C8   N9   C10    0.00   0.0  0
 76O  CONST_14  C28  C29  C30  C25    0.00   0.0  0
 76O  CONST_15  C28  C27  C26  C25    0.00   0.0  0
 76O  CONST_16  C29  C30  C25  C26    0.00   0.0  0
 76O  CONST_17  C29  C28  C27  C26    0.00   0.0  0
 76O  CONST_18  C30  C25  C26  C27    0.00   0.0  0
 76O  CONST_19  C30  C29  C28  C27    0.00   0.0  0
 76O  CONST_20  N9   C10  C2   N3   180.00   0.0  0
 76O  CONST_21  N7   C6   N5   C4   180.00   0.0  0
 76O  CONST_22  N9   C10  C6   N5   180.00   0.0  0
 76O  CONST_23  N9   C10  C6   N7     0.00   0.0  0
 76O  CONST_24  C11  N7   C6   C10  180.00   0.0  0
 76O  CONST_25  N5   C6   N7   C11    0.00   0.0  0
 76O  CONST_26  N9   C8   N7   C11  180.00   0.0  0
 76O  CONST_27  N1   C2   C10  C6   180.00   0.0  0
 76O  CONST_28  C29  C30  C25  C24  180.00   0.0  0
 76O  CONST_29  C27  C26  C25  C24  180.00   0.0  0
 76O  CONST_30  C4   N3   C2   N1   180.00   0.0  0
 76O  CONST_31  N9   C10  C2   N1     0.00   0.0  0
 76O  CONST_32  H48  C4   N3   C2   180.00   0.0  0
 76O  CONST_33  H49  C8   N7   C6   180.00   0.0  0
 76O  CONST_34  H61  C29  C30  C25  180.00   0.0  0
 76O  CONST_35  H59  C27  C26  C25  180.00   0.0  0
 76O  CONST_36  H62  C30  C25  C26  180.00   0.0  0
 76O  CONST_37  H60  C28  C27  C26  180.00   0.0  0
 76O  CONST_38  H58  C26  C27  C28  180.00   0.0  0
 76O  CONST_39  H47  N1   C2   C10  180.00   0.0  0
 76O  CONST_40  H46  N1   C2   C10    0.00   0.0  0
 76O  CONST_41  H1   O21  C20  C18  180.00   0.0  0
 76O  Var_01    N23  C24  C25  C26   88.22  30.0  2
 76O  Var_02    C25  C24  N23  C15  171.11  30.0  3
 76O  Var_03    C18  C17  C16  C15  146.25  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
 76O  chir_01  C11  N7   O12  C33  positiv
 76O  chir_02  C13  O12  C31  C14  negativ
 76O  chir_03  C15  N23  C14  C16  negativ
 76O  chir_04  C31  O32  C33  C13  negativ
 76O  chir_05  C18  N19  C20  C17  positiv
 76O  chir_06  C33  C11  O34  C31  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
 76O  plan-1  C25  0.020
 76O  plan-1  C26  0.020
 76O  plan-1  C27  0.020
 76O  plan-1  C28  0.020
 76O  plan-1  C29  0.020
 76O  plan-1  C30  0.020
 76O  plan-1  H58  0.020
 76O  plan-1  H59  0.020
 76O  plan-1  H60  0.020
 76O  plan-1  H61  0.020
 76O  plan-1  H62  0.020
 76O  plan-1  C24  0.020
 76O  plan-2  C2   0.020
 76O  plan-2  C6   0.020
 76O  plan-2  C8   0.020
 76O  plan-2  C10  0.020
 76O  plan-2  C11  0.020
 76O  plan-2  N1   0.020
 76O  plan-2  N3   0.020
 76O  plan-2  C4   0.020
 76O  plan-2  N5   0.020
 76O  plan-2  N7   0.020
 76O  plan-2  N9   0.020
 76O  plan-2  H49  0.020
 76O  plan-2  H48  0.020
 76O  plan-3  C2   0.020
 76O  plan-3  N1   0.020
 76O  plan-3  H47  0.020
 76O  plan-3  H46  0.020
 76O  plan-4  C18  0.020
 76O  plan-4  C20  0.020
 76O  plan-4  O21  0.020
 76O  plan-4  O22  0.020
 76O  plan-4  H1   0.020

