# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 15:41:04 2021
#   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]-[(2~{R})-2-oxidanylpropyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)C[NH2+][C@@H](CC[C@@H]([NH3+])C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 76L  76L  '[(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]-[(2~{R})-2-oxidanylpropyl]azanium'  ligand  62  31  .  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_76L
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
 76L  C1   C  CH3   0  -0.711  10.0875  18.6536  30.9370
 76L  C2   C  CH1   0   0.007  10.4001  17.7929  29.7232
 76L  C6   C  CH1   0  -0.081  13.8492  16.2254  30.2748
 76L  C7   C  CH2   0  -0.496  15.1478  17.0039  30.5046
 76L  C8   C  CH2   0  -0.467  16.2541  16.5622  29.5472
 76L  C11  C  C     0   0.595  18.6001  17.0854  28.7685
 76L  C14  C  CH2   0  -0.490  13.6197  15.0634  31.2352
 76L  C15  C  CR15  0   0.035  14.6576  13.9624  31.1517
 76L  C23  C  CR15  0   0.101  15.8046  14.4722  34.5894
 76L  C25  C  CR56  0  -0.001  17.1149  13.5491  35.9656
 76L  C26  C  CR6   0   0.460  17.8799  13.0831  37.0519
 76L  C31  C  CR56  0   0.487  17.3990  12.9831  34.7338
 76L  O3   O  OH1   0  -0.667  11.0013  18.5286  28.6779
 76L  C4   C  CH2   0  -0.328  11.3568  16.6519  30.0297
 76L  N5   N  NT2   1  -0.694  12.7024  17.1878  30.3818
 76L  C9   C  CH1   0  -0.261  17.6143  17.1323  29.9270
 76L  N10  N  NT3   1  -0.789  18.1543  16.4360  31.1280
 76L  O13  O  OH1   0  -0.583  19.7829  16.6305  29.1260
 76L  O16  O  O     0  -0.522  15.8884  14.3527  31.7657
 76L  C17  C  CR15  0   0.160  16.4797  13.2760  32.4386
 76L  C18  C  CR15  0  -0.067  15.6145  12.0388  32.1505
 76L  O19  O  OH1   0  -0.655  16.0152  11.4107  30.9680
 76L  C20  C  CR15  0   0.020  14.2545  12.6962  31.9055
 76L  O21  O  OH1   0  -0.654  13.3494  11.9590  31.1497
 76L  N22  N  NR5   0  -0.535  16.5488  13.5881  33.8554
 76L  N24  N  N     0  -0.448  16.1154  14.4796  35.8525
 76L  N28  N  N     0  -0.473  18.8032  12.1455  36.8092
 76L  C29  C  CR16  0   0.043  18.9624  11.6927  35.5686
 76L  N30  N  N     0  -0.458  18.3097  12.0475  34.4748
 76L  H45  H  HCH3  0   0.249   9.6408  18.0519  31.7280
 76L  H46  H  HCH3  0   0.234  10.9721  19.1504  31.3402
 76L  H44  H  HCH3  0   0.260   9.3691  19.4318  30.6756
 76L  H32  H  HCH1  0   0.253   9.4697  17.3183  29.3870
 76L  H35  H  HCH1  0   0.318  13.8072  15.8651  29.2440
 76L  H50  H  HCH2  0   0.263  15.4278  16.9237  31.5567
 76L  H51  H  HCH2  0   0.290  14.9802  18.0693  30.3268
 76L  H52  H  HCH2  0   0.303  16.0050  16.9276  28.5517
 76L  H53  H  HCH2  0   0.283  16.3326  15.4764  29.4641
 76L  H54  H  HCH2  0   0.270  13.5496  15.4369  32.2620
 76L  H55  H  HCH2  0   0.293  12.6631  14.5919  30.9997
 76L  H40  H  HCR5  0   0.259  14.8385  13.7058  30.1001
 76L  H58  H  HCR5  0   0.297  15.0500  15.0994  34.1405
 76L  H47  H  HOH1  0   0.467  10.5410  19.3680  28.5780
 76L  H49  H  HCH2  0   0.306  10.9861  16.0526  30.8565
 76L  H48  H  HCH2  0   0.312  11.4873  16.0120  29.1578
 76L  H33  H  HNT2  0   0.468  12.6819  17.5912  31.3210
 76L  H36  H  HCH1  0   0.366  17.5154  18.1834  30.2120
 76L  H37  H  HNT3  0   0.475  17.4703  16.4401  31.8849
 76L  H39  H  HNT3  0   0.475  18.3913  15.4605  30.9426
 76L  H1   H  HOH1  0   0.504  20.4011  16.6346  28.3776
 76L  H41  H  HCR5  0   0.285  17.5090  13.1256  32.0987
 76L  H42  H  HCR5  0   0.273  15.6085  11.3520  33.0044
 76L  H56  H  HOH1  0   0.463  16.8532  10.9633  31.1239
 76L  H43  H  HCR5  0   0.241  13.8296  12.9816  32.8787
 76L  H57  H  HOH1  0   0.466  12.9276  11.3063  31.7169
 76L  H60  H  HNH2  0   0.405  18.3240  13.2138  39.0320
 76L  H59  H  HNH2  0   0.412  17.0671  14.2701  38.5018
 76L  H61  H  HCR6  0   0.254  19.7277  10.9342  35.4445
 76L  H34  H  HNT2  0   0.465  12.8872  17.9711  29.7477
 76L  H38  H  HNT3  0   0.490  18.9914  16.8884  31.4990
 76L  O12  O  O     0  -0.411  18.3001  17.4616  27.6698
 76L  N27  N  NH2   0  -0.815  17.7143  13.5290  38.2971

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
 76L  O12  C11  double    1.199  0.020  1.199
 76L  C11  O13  single    1.317  0.020  1.317
 76L  C11  C9   single    1.522  0.020  1.522
 76L  O3   C2   single    1.413  0.020  1.413
 76L  C8   C9   single    1.523  0.020  1.523
 76L  C8   C7   single    1.528  0.020  1.528
 76L  C9   N10  single    1.490  0.020  1.490
 76L  C2   C4   single    1.520  0.020  1.520
 76L  C2   C1   single    1.521  0.020  1.521
 76L  C6   C7   single    1.531  0.020  1.531
 76L  C6   N5   single    1.501  0.020  1.501
 76L  C6   C14  single    1.525  0.020  1.525
 76L  N5   C4   single    1.491  0.020  1.491
 76L  O21  C20  single    1.391  0.020  1.391
 76L  O19  C18  single    1.398  0.020  1.398
 76L  C15  C14  single    1.515  0.020  1.515
 76L  C15  O16  single    1.430  0.020  1.430
 76L  C15  C20  single    1.528  0.020  1.528
 76L  O16  C17  single    1.401  0.020  1.401
 76L  C20  C18  single    1.530  0.020  1.530
 76L  C18  C17  single    1.537  0.020  1.537
 76L  C17  N22  single    1.452  0.020  1.452
 76L  N22  C23  aromatic  1.369  0.020  1.369
 76L  N22  C31  aromatic  1.364  0.020  1.364
 76L  C23  N24  aromatic  1.301  0.020  1.301
 76L  N30  C31  aromatic  1.331  0.020  1.331
 76L  N30  C29  aromatic  1.322  0.020  1.322
 76L  C31  C25  aromatic  1.385  0.020  1.385
 76L  N24  C25  aromatic  1.370  0.020  1.370
 76L  C29  N28  aromatic  1.330  0.020  1.330
 76L  C25  C26  aromatic  1.408  0.020  1.408
 76L  N28  C26  aromatic  1.338  0.020  1.338
 76L  C26  N27  single    1.333  0.020  1.333
 76L  C1   H45  single    0.970  0.020  1.090
 76L  C1   H46  single    0.970  0.020  1.090
 76L  C1   H44  single    0.970  0.020  1.090
 76L  C2   H32  single    0.970  0.020  1.090
 76L  C6   H35  single    0.970  0.020  1.090
 76L  C7   H50  single    0.970  0.020  1.090
 76L  C7   H51  single    0.970  0.020  1.090
 76L  C8   H52  single    0.970  0.020  1.090
 76L  C8   H53  single    0.970  0.020  1.090
 76L  C14  H54  single    0.970  0.020  1.090
 76L  C14  H55  single    0.970  0.020  1.090
 76L  C15  H40  single    0.970  0.020  1.090
 76L  C23  H58  single    0.930  0.020  1.080
 76L  O3   H47  single    0.850  0.020  0.980
 76L  C4   H49  single    0.970  0.020  1.090
 76L  C4   H48  single    0.970  0.020  1.090
 76L  N5   H33  single    0.890  0.020  1.040
 76L  C9   H36  single    0.970  0.020  1.090
 76L  N10  H37  single    0.890  0.020  1.040
 76L  N10  H39  single    0.890  0.020  1.040
 76L  O13  H1   single    0.850  0.020  0.980
 76L  C17  H41  single    0.970  0.020  1.090
 76L  C18  H42  single    0.970  0.020  1.090
 76L  O19  H56  single    0.850  0.020  0.980
 76L  C20  H43  single    0.970  0.020  1.090
 76L  O21  H57  single    0.850  0.020  0.980
 76L  N27  H60  single    0.860  0.020  1.020
 76L  N27  H59  single    0.860  0.020  1.020
 76L  C29  H61  single    0.930  0.020  1.080
 76L  N5   H34  single    0.890  0.020  1.040
 76L  N10  H38  single    0.890  0.020  1.040

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
 76L  H44  C1   H46  107.31  3.000
 76L  H44  C1   H45  107.33  3.000
 76L  H46  C1   H45  108.38  3.000
 76L  H44  C1   C2   110.36  3.000
 76L  H46  C1   C2   112.70  3.000
 76L  H45  C1   C2   110.56  3.000
 76L  H32  C2   C4   105.71  3.000
 76L  H32  C2   O3   111.07  3.000
 76L  C4   C2   O3   105.80  3.000
 76L  H32  C2   C1   108.37  3.000
 76L  C4   C2   C1   113.16  3.000
 76L  O3   C2   C1   112.54  3.000
 76L  H35  C6   N5   104.44  3.000
 76L  H35  C6   C14  109.70  3.000
 76L  N5   C6   C14  109.19  3.000
 76L  H35  C6   C7   109.98  3.000
 76L  C14  C6   C7   114.86  3.000
 76L  N5   C6   C7   108.13  3.000
 76L  H51  C7   H50  105.52  3.000
 76L  H51  C7   C8   106.91  3.000
 76L  H50  C7   C8   113.38  3.000
 76L  H51  C7   C6   109.94  3.000
 76L  H50  C7   C6   108.95  3.000
 76L  C8   C7   C6   111.89  3.000
 76L  H53  C8   H52  106.29  3.000
 76L  H53  C8   C9   109.09  3.000
 76L  H52  C8   C9   107.85  3.000
 76L  H53  C8   C7   112.78  3.000
 76L  H52  C8   C7   108.06  3.000
 76L  C9   C8   C7   112.46  3.000
 76L  O13  C11  O12  125.57  3.000
 76L  O13  C11  C9   112.70  3.000
 76L  O12  C11  C9   121.71  3.000
 76L  H55  C14  H54  107.06  3.000
 76L  H55  C14  C15  105.92  3.000
 76L  H54  C14  C15  110.08  3.000
 76L  H55  C14  C6   108.97  3.000
 76L  H54  C14  C6   109.90  3.000
 76L  C15  C14  C6   114.57  3.000
 76L  H40  C15  C20  108.81  3.000
 76L  H40  C15  O16  109.47  3.000
 76L  C20  C15  O16  103.97  3.000
 76L  H40  C15  C14  109.61  3.000
 76L  C20  C15  C14  113.22  3.000
 76L  O16  C15  C14  111.57  3.000
 76L  H58  C23  N24  124.60  3.000
 76L  H58  C23  N22  122.17  3.000
 76L  N24  C23  N22  113.23  3.000
 76L  N24  C25  C31  110.71  3.000
 76L  N24  C25  C26  133.22  3.000
 76L  C31  C25  C26  116.07  3.000
 76L  N28  C26  N27  119.31  3.000
 76L  N27  C26  C25  122.85  3.000
 76L  N28  C26  C25  117.83  3.000
 76L  N30  C31  N22  127.80  3.000
 76L  N30  C31  C25  126.92  3.000
 76L  N22  C31  C25  105.28  3.000
 76L  H47  O3   C2   109.11  3.000
 76L  H48  C4   H49  109.03  3.000
 76L  H48  C4   N5   106.99  3.000
 76L  H49  C4   N5   109.06  3.000
 76L  H48  C4   C2   110.79  3.000
 76L  H49  C4   C2   110.65  3.000
 76L  N5   C4   C2   110.24  3.000
 76L  H34  N5   H33  105.70  3.000
 76L  H34  N5   C4   106.94  3.000
 76L  H33  N5   C4   109.93  3.000
 76L  H34  N5   C6   107.96  3.000
 76L  H33  N5   C6   109.50  3.000
 76L  C4   N5   C6   116.25  3.000
 76L  H36  C9   N10  105.79  3.000
 76L  H36  C9   C11  106.65  3.000
 76L  N10  C9   C11  111.38  3.000
 76L  H36  C9   C8   110.12  3.000
 76L  N10  C9   C8   110.48  3.000
 76L  C11  C9   C8   112.16  3.000
 76L  H38  N10  H39  107.39  3.000
 76L  H38  N10  H37  106.15  3.000
 76L  H39  N10  H37  107.11  3.000
 76L  H38  N10  C9   112.52  3.000
 76L  H39  N10  C9   112.61  3.000
 76L  H37  N10  C9   110.69  3.000
 76L  H1   O13  C11  111.18  3.000
 76L  C17  O16  C15  111.10  3.000
 76L  H41  C17  N22  106.72  3.000
 76L  H41  C17  C18  111.14  3.000
 76L  N22  C17  C18  112.50  3.000
 76L  H41  C17  O16  110.70  3.000
 76L  N22  C17  O16  108.88  3.000
 76L  C18  C17  O16  106.92  3.000
 76L  H42  C18  C20  112.89  3.000
 76L  H42  C18  O19  112.28  3.000
 76L  C20  C18  O19  108.21  3.000
 76L  H42  C18  C17  111.19  3.000
 76L  C20  C18  C17  100.63  3.000
 76L  O19  C18  C17  111.04  3.000
 76L  H56  O19  C18  108.75  3.000
 76L  H43  C20  O21  111.54  3.000
 76L  H43  C20  C18  108.25  3.000
 76L  O21  C20  C18  115.95  3.000
 76L  H43  C20  C15  108.88  3.000
 76L  C18  C20  C15  101.57  3.000
 76L  O21  C20  C15  110.06  3.000
 76L  H57  O21  C20  108.94  3.000
 76L  C17  N22  C31  124.23  3.000
 76L  C31  N22  C23  106.26  3.000
 76L  C17  N22  C23  129.49  3.000
 76L  C25  N24  C23  104.52  3.000
 76L  C29  N28  C26  119.36  3.000
 76L  H61  C29  N30  116.19  3.000
 76L  H61  C29  N28  115.41  3.000
 76L  N30  C29  N28  128.40  3.000
 76L  C29  N30  C31  111.43  3.000
 76L  H59  N27  H60  118.22  3.000
 76L  H59  N27  C26  121.12  3.000
 76L  H60  N27  C26  120.17  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
 76L  CONST_01  N30  C31  N22  C23   180.00   0.0  0
 76L  CONST_02  C25  C31  N22  C23     0.00   0.0  0
 76L  CONST_03  C31  C25  N24  C23     0.00   0.0  0
 76L  CONST_04  C26  C25  N24  C23   180.00   0.0  0
 76L  CONST_05  C29  N30  C31  C25     0.00   0.0  0
 76L  CONST_06  N22  C23  N24  C25     0.00   0.0  0
 76L  CONST_07  C29  N28  C26  C25     0.00   0.0  0
 76L  CONST_08  N22  C31  C25  C26   180.00   0.0  0
 76L  CONST_09  N30  C31  C25  C26     0.00   0.0  0
 76L  CONST_10  N30  C29  N28  C26     0.00   0.0  0
 76L  CONST_11  N24  C23  N22  C31     0.00   0.0  0
 76L  CONST_12  N28  C29  N30  C31     0.00   0.0  0
 76L  CONST_13  N28  C26  C25  C31     0.00   0.0  0
 76L  CONST_14  C29  N30  C31  N22   180.00   0.0  0
 76L  CONST_15  N24  C25  C31  N22     0.00   0.0  0
 76L  CONST_16  N30  C31  C25  N24   180.00   0.0  0
 76L  CONST_17  N28  C26  C25  N24   180.00   0.0  0
 76L  CONST_18  C17  N22  C31  C25   180.00   0.0  0
 76L  CONST_19  N24  C23  N22  C17   180.00   0.0  0
 76L  CONST_20  N30  C31  N22  C17     0.00   0.0  0
 76L  CONST_21  N27  C26  C25  C31   180.00   0.0  0
 76L  CONST_22  N27  C26  C25  N24     0.00   0.0  0
 76L  CONST_23  C29  N28  C26  N27   180.00   0.0  0
 76L  CONST_24  H58  C23  N24  C25   180.00   0.0  0
 76L  CONST_25  H61  C29  N28  C26   180.00   0.0  0
 76L  CONST_26  H60  N27  C26  C25   180.00   0.0  0
 76L  CONST_27  H59  N27  C26  C25     0.00   0.0  0
 76L  CONST_28  H1   O13  C11  C9    180.00   0.0  0
 76L  Var_01    C6   N5   C4   C2   -160.81  30.0  2
 76L  Var_02    C9   C8   C7   C6   -169.31  30.0  1

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
 76L  chir_01  C2   O3   C4   C1   negativ
 76L  chir_02  C6   N5   C7   C14  negativ
 76L  chir_03  C15  O16  C14  C20  positiv
 76L  chir_04  C9   N10  C8   C11  positiv
 76L  chir_05  C17  O16  C18  N22  positiv
 76L  chir_06  C18  O19  C17  C20  negativ
 76L  chir_07  C20  O21  C18  C15  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
 76L  plan-1  C23  0.020
 76L  plan-1  C25  0.020
 76L  plan-1  C26  0.020
 76L  plan-1  C31  0.020
 76L  plan-1  C17  0.020
 76L  plan-1  N22  0.020
 76L  plan-1  N24  0.020
 76L  plan-1  N28  0.020
 76L  plan-1  C29  0.020
 76L  plan-1  N30  0.020
 76L  plan-1  H58  0.020
 76L  plan-1  H61  0.020
 76L  plan-1  N27  0.020
 76L  plan-2  C26  0.020
 76L  plan-2  H60  0.020
 76L  plan-2  H59  0.020
 76L  plan-2  N27  0.020
 76L  plan-3  C11  0.020
 76L  plan-3  C9   0.020
 76L  plan-3  O13  0.020
 76L  plan-3  H1   0.020
 76L  plan-3  O12  0.020

