# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 22:00:59 2021
#   Inital geometry file: a 142 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-methylpropyl)azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 76M  76M  '[(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-methylpropyl)azanium'  ligand  64  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_76M
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
 76M  C1   C  CH3   0  -0.654   8.9811  17.2881  29.3530
 76M  C2   C  CH1   0  -0.289  10.2838  17.8205  29.9409
 76M  C3   C  CH3   0  -0.670  10.0654  18.3385  31.3595
 76M  C6   C  CH1   0  -0.075  13.7988  16.2027  30.1596
 76M  C7   C  CH2   0  -0.496  15.1165  16.9550  30.3746
 76M  C8   C  CH2   0  -0.467  16.1897  16.5127  29.3801
 76M  C11  C  C     0   0.595  18.5203  17.0107  28.5425
 76M  C14  C  CH2   0  -0.493  13.5746  15.0309  31.1101
 76M  C15  C  CR15  0   0.035  14.6005  13.9207  31.0024
 76M  C23  C  CR15  0   0.101  15.7970  14.4249  34.4171
 76M  C25  C  CR56  0  -0.001  17.1044  13.4855  35.7845
 76M  C26  C  CR6   0   0.459  17.8728  13.0123  36.8652
 76M  C31  C  CR56  0   0.487  17.3660  12.9086  34.5526
 76M  C4   C  CH2   0  -0.283  11.3169  16.7029  29.8938
 76M  N5   N  NT2   1  -0.695  12.6672  17.1814  30.3079
 76M  C9   C  CH1   0  -0.261  17.5690  17.0562  29.7293
 76M  N10  N  NT3   1  -0.789  18.1324  16.3351  30.9047
 76M  O13  O  OH1   0  -0.583  19.7010  16.5199  28.8563
 76M  O16  O  O     0  -0.522  15.8465  14.2943  31.5952
 76M  C17  C  CR15  0   0.159  16.4328  13.2119  32.2633
 76M  C18  C  CR15  0  -0.067  15.5521  11.9842  31.9825
 76M  O19  O  OH1   0  -0.655  15.9298  11.3586  30.7913
 76M  C20  C  CR15  0   0.020  14.1956  12.6562  31.7588
 76M  O21  O  OH1   0  -0.654  13.2721  11.9302  31.0144
 76M  N22  N  NR5   0  -0.535  16.5177  13.5243  33.6797
 76M  N24  N  N     0  -0.448  16.1202  14.4326  35.6769
 76M  N28  N  N     0  -0.473  18.7774  12.0578  36.6182
 76M  C29  C  CR16  0   0.043  18.9159  11.5959  35.3786
 76M  N30  N  N     0  -0.458  18.2582  11.9564  34.2896
 76M  H44  H  HCH3  0   0.245   8.2165  18.0643  29.3543
 76M  H43  H  HCH3  0   0.240   9.1103  16.9496  28.3245
 76M  H45  H  HCH3  0   0.228   8.6042  16.4484  29.9403
 76M  H46  H  HCH1  0   0.256  10.6377  18.6429  29.3091
 76M  H49  H  HCH3  0   0.232  10.9599  18.7846  31.7980
 76M  H48  H  HCH3  0   0.253   9.2988  19.1129  31.3663
 76M  H47  H  HCH3  0   0.232   9.7331  17.5334  32.0185
 76M  H34  H  HCH1  0   0.316  13.7303  15.8591  29.1246
 76M  H52  H  HCH2  0   0.263  15.4211  16.8478  31.4173
 76M  H53  H  HCH2  0   0.290  14.9652  18.0271  30.2236
 76M  H55  H  HCH2  0   0.304  15.9177  16.8988  28.3985
 76M  H54  H  HCH2  0   0.283  16.2490  15.4274  29.2761
 76M  H56  H  HCH2  0   0.269  13.5229  15.3946  32.1416
 76M  H57  H  HCH2  0   0.291  12.6118  14.5677  30.8867
 76M  H39  H  HCR5  0   0.259  14.7594  13.6669  29.9467
 76M  H60  H  HCR5  0   0.296  15.0492  15.0636  33.9728
 76M  H51  H  HCH2  0   0.289  11.0278  15.8886  30.5559
 76M  H50  H  HCH2  0   0.301  11.4287  16.3087  28.8847
 76M  H32  H  HNT2  0   0.464  12.6358  17.5192  31.2725
 76M  H33  H  HNT2  0   0.472  12.8922  18.0038  29.7442
 76M  H35  H  HCH1  0   0.366  17.4938  18.1044  30.0315
 76M  H36  H  HNT3  0   0.476  17.4694  16.3358  31.6799
 76M  H38  H  HNT3  0   0.474  18.3527  15.3596  30.7001
 76M  H37  H  HNT3  0   0.490  18.9846  16.7722  31.2594
 76M  H1   H  HOH1  0   0.504  20.2967  16.5218  28.0897
 76M  H40  H  HCR5  0   0.287  17.4573  13.0520  31.9139
 76M  H41  H  HCR5  0   0.273  15.5511  11.2940  32.8338
 76M  H58  H  HOH1  0   0.463  16.7659  10.9032  30.9328
 76M  H42  H  HCR5  0   0.242  13.7877  12.9431  32.7387
 76M  H59  H  HOH1  0   0.466  12.8430  11.2888  31.5889
 76M  H62  H  HNH2  0   0.405  18.3396  13.1462  38.8399
 76M  H61  H  HNH2  0   0.412  17.0954  14.2209  38.3165
 76M  H63  H  HCR6  0   0.254  19.6667  10.8236  35.2507
 76M  O12  O  O     0  -0.411  18.1980  17.4163  27.4607
 76M  N27  N  NH2   0  -0.815  17.7279  13.4679  38.1095

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
 76M  O12  C11  double    1.199  0.020  1.199
 76M  C11  O13  single    1.317  0.020  1.317
 76M  C11  C9   single    1.522  0.020  1.522
 76M  C8   C9   single    1.523  0.020  1.523
 76M  C8   C7   single    1.529  0.020  1.529
 76M  C9   N10  single    1.490  0.020  1.490
 76M  C2   C1   single    1.525  0.020  1.525
 76M  C2   C4   single    1.523  0.020  1.523
 76M  C2   C3   single    1.526  0.020  1.526
 76M  C6   C7   single    1.532  0.020  1.532
 76M  C6   N5   single    1.503  0.020  1.503
 76M  C6   C14  single    1.525  0.020  1.525
 76M  N5   C4   single    1.491  0.020  1.491
 76M  O19  C18  single    1.398  0.020  1.398
 76M  O21  C20  single    1.391  0.020  1.391
 76M  C15  C14  single    1.516  0.020  1.516
 76M  C15  O16  single    1.430  0.020  1.430
 76M  C15  C20  single    1.528  0.020  1.528
 76M  O16  C17  single    1.401  0.020  1.401
 76M  C20  C18  single    1.530  0.020  1.530
 76M  C18  C17  single    1.537  0.020  1.537
 76M  C17  N22  single    1.453  0.020  1.453
 76M  N22  C23  aromatic  1.369  0.020  1.369
 76M  N22  C31  aromatic  1.364  0.020  1.364
 76M  C23  N24  aromatic  1.301  0.020  1.301
 76M  N30  C31  aromatic  1.331  0.020  1.331
 76M  N30  C29  aromatic  1.322  0.020  1.322
 76M  C31  C25  aromatic  1.385  0.020  1.385
 76M  N24  C25  aromatic  1.370  0.020  1.370
 76M  C29  N28  aromatic  1.330  0.020  1.330
 76M  C25  C26  aromatic  1.408  0.020  1.408
 76M  N28  C26  aromatic  1.338  0.020  1.338
 76M  C26  N27  single    1.333  0.020  1.333
 76M  C1   H44  single    0.970  0.020  1.090
 76M  C1   H43  single    0.970  0.020  1.090
 76M  C1   H45  single    0.970  0.020  1.090
 76M  C2   H46  single    0.970  0.020  1.090
 76M  C3   H49  single    0.970  0.020  1.090
 76M  C3   H48  single    0.970  0.020  1.090
 76M  C3   H47  single    0.970  0.020  1.090
 76M  C6   H34  single    0.970  0.020  1.090
 76M  C7   H52  single    0.970  0.020  1.090
 76M  C7   H53  single    0.970  0.020  1.090
 76M  C8   H55  single    0.970  0.020  1.090
 76M  C8   H54  single    0.970  0.020  1.090
 76M  C14  H56  single    0.970  0.020  1.090
 76M  C14  H57  single    0.970  0.020  1.090
 76M  C15  H39  single    0.970  0.020  1.090
 76M  C23  H60  single    0.930  0.020  1.080
 76M  C4   H51  single    0.970  0.020  1.090
 76M  C4   H50  single    0.970  0.020  1.090
 76M  N5   H32  single    0.890  0.020  1.040
 76M  N5   H33  single    0.890  0.020  1.040
 76M  C9   H35  single    0.970  0.020  1.090
 76M  N10  H36  single    0.890  0.020  1.040
 76M  N10  H38  single    0.890  0.020  1.040
 76M  N10  H37  single    0.890  0.020  1.040
 76M  O13  H1   single    0.850  0.020  0.980
 76M  C17  H40  single    0.970  0.020  1.090
 76M  C18  H41  single    0.970  0.020  1.090
 76M  O19  H58  single    0.850  0.020  0.980
 76M  C20  H42  single    0.970  0.020  1.090
 76M  O21  H59  single    0.850  0.020  0.980
 76M  N27  H62  single    0.860  0.020  1.020
 76M  N27  H61  single    0.860  0.020  1.020
 76M  C29  H63  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
 76M  H45  C1   H43  108.04  3.000
 76M  H45  C1   H44  107.76  3.000
 76M  H43  C1   H44  107.78  3.000
 76M  H45  C1   C2   110.86  3.000
 76M  H43  C1   C2   111.76  3.000
 76M  H44  C1   C2   110.50  3.000
 76M  H46  C2   C4   108.29  3.000
 76M  H46  C2   C3   109.11  3.000
 76M  C4   C2   C3   112.03  3.000
 76M  H46  C2   C1   108.40  3.000
 76M  C3   C2   C1   110.77  3.000
 76M  C4   C2   C1   108.14  3.000
 76M  H47  C3   H48  107.82  3.000
 76M  H47  C3   H49  107.95  3.000
 76M  H48  C3   H49  106.48  3.000
 76M  H47  C3   C2   110.75  3.000
 76M  H48  C3   C2   110.35  3.000
 76M  H49  C3   C2   113.26  3.000
 76M  H34  C6   N5   104.54  3.000
 76M  H34  C6   C14  109.84  3.000
 76M  N5   C6   C14  109.14  3.000
 76M  H34  C6   C7   109.95  3.000
 76M  C14  C6   C7   114.58  3.000
 76M  N5   C6   C7   108.28  3.000
 76M  H53  C7   H52  105.48  3.000
 76M  H53  C7   C8   106.92  3.000
 76M  H52  C7   C8   113.40  3.000
 76M  H53  C7   C6   110.06  3.000
 76M  H52  C7   C6   109.02  3.000
 76M  C8   C7   C6   111.74  3.000
 76M  H54  C8   H55  106.26  3.000
 76M  H54  C8   C9   109.10  3.000
 76M  H55  C8   C9   107.83  3.000
 76M  H54  C8   C7   112.81  3.000
 76M  H55  C8   C7   107.97  3.000
 76M  C9   C8   C7   112.55  3.000
 76M  O13  C11  O12  125.60  3.000
 76M  O13  C11  C9   112.70  3.000
 76M  O12  C11  C9   121.69  3.000
 76M  H57  C14  H56  106.99  3.000
 76M  H57  C14  C15  105.76  3.000
 76M  H56  C14  C15  110.01  3.000
 76M  H57  C14  C6   109.15  3.000
 76M  H56  C14  C6   109.81  3.000
 76M  C15  C14  C6   114.77  3.000
 76M  H39  C15  C20  108.86  3.000
 76M  H39  C15  O16  109.46  3.000
 76M  C20  C15  O16  104.00  3.000
 76M  H39  C15  C14  109.62  3.000
 76M  C20  C15  C14  113.06  3.000
 76M  O16  C15  C14  111.66  3.000
 76M  H60  C23  N24  124.58  3.000
 76M  H60  C23  N22  122.17  3.000
 76M  N24  C23  N22  113.25  3.000
 76M  N24  C25  C31  110.71  3.000
 76M  N24  C25  C26  133.20  3.000
 76M  C31  C25  C26  116.08  3.000
 76M  N28  C26  N27  119.32  3.000
 76M  N27  C26  C25  122.84  3.000
 76M  N28  C26  C25  117.83  3.000
 76M  N30  C31  N22  127.82  3.000
 76M  N30  C31  C25  126.88  3.000
 76M  N22  C31  C25  105.29  3.000
 76M  H50  C4   H51  108.66  3.000
 76M  H50  C4   N5   106.29  3.000
 76M  H51  C4   N5   108.16  3.000
 76M  H50  C4   C2   111.34  3.000
 76M  H51  C4   C2   110.49  3.000
 76M  N5   C4   C2   111.73  3.000
 76M  H33  N5   H32  105.14  3.000
 76M  H33  N5   C4   107.72  3.000
 76M  H32  N5   C4   109.88  3.000
 76M  H33  N5   C6   107.68  3.000
 76M  H32  N5   C6   109.35  3.000
 76M  C4   N5   C6   116.44  3.000
 76M  H35  C9   N10  105.78  3.000
 76M  H35  C9   C11  106.69  3.000
 76M  N10  C9   C11  111.37  3.000
 76M  H35  C9   C8   110.07  3.000
 76M  N10  C9   C8   110.53  3.000
 76M  C11  C9   C8   112.13  3.000
 76M  H37  N10  H38  107.37  3.000
 76M  H37  N10  H36  106.15  3.000
 76M  H38  N10  H36  107.05  3.000
 76M  H37  N10  C9   112.49  3.000
 76M  H38  N10  C9   112.71  3.000
 76M  H36  N10  C9   110.70  3.000
 76M  H1   O13  C11  111.18  3.000
 76M  C17  O16  C15  111.14  3.000
 76M  H40  C17  N22  106.74  3.000
 76M  H40  C17  C18  111.19  3.000
 76M  N22  C17  C18  112.54  3.000
 76M  H40  C17  O16  110.64  3.000
 76M  N22  C17  O16  108.87  3.000
 76M  C18  C17  O16  106.88  3.000
 76M  H41  C18  C20  112.91  3.000
 76M  H41  C18  O19  112.36  3.000
 76M  C20  C18  O19  108.15  3.000
 76M  H41  C18  C17  111.21  3.000
 76M  C20  C18  C17  100.60  3.000
 76M  O19  C18  C17  111.01  3.000
 76M  H58  O19  C18  108.74  3.000
 76M  H42  C20  O21  111.52  3.000
 76M  H42  C20  C18  108.25  3.000
 76M  O21  C20  C18  115.96  3.000
 76M  H42  C20  C15  108.88  3.000
 76M  C18  C20  C15  101.59  3.000
 76M  O21  C20  C15  110.06  3.000
 76M  H59  O21  C20  108.94  3.000
 76M  C17  N22  C31  124.27  3.000
 76M  C31  N22  C23  106.24  3.000
 76M  C17  N22  C23  129.47  3.000
 76M  C25  N24  C23  104.51  3.000
 76M  C29  N28  C26  119.36  3.000
 76M  H63  C29  N30  116.19  3.000
 76M  H63  C29  N28  115.42  3.000
 76M  N30  C29  N28  128.39  3.000
 76M  C29  N30  C31  111.45  3.000
 76M  H61  N27  H62  118.23  3.000
 76M  H61  N27  C26  121.11  3.000
 76M  H62  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
 76M  CONST_01  N30  C31  N22  C23   180.00   0.0  0
 76M  CONST_02  C25  C31  N22  C23     0.00   0.0  0
 76M  CONST_03  C31  C25  N24  C23     0.00   0.0  0
 76M  CONST_04  C26  C25  N24  C23   180.00   0.0  0
 76M  CONST_05  C29  N30  C31  C25     0.00   0.0  0
 76M  CONST_06  N22  C23  N24  C25     0.00   0.0  0
 76M  CONST_07  C29  N28  C26  C25     0.00   0.0  0
 76M  CONST_08  N22  C31  C25  C26   180.00   0.0  0
 76M  CONST_09  N30  C31  C25  C26     0.00   0.0  0
 76M  CONST_10  N30  C29  N28  C26     0.00   0.0  0
 76M  CONST_11  N24  C23  N22  C31     0.00   0.0  0
 76M  CONST_12  N28  C29  N30  C31     0.00   0.0  0
 76M  CONST_13  N28  C26  C25  C31     0.00   0.0  0
 76M  CONST_14  C29  N30  C31  N22   180.00   0.0  0
 76M  CONST_15  N24  C25  C31  N22     0.00   0.0  0
 76M  CONST_16  N30  C31  C25  N24   180.00   0.0  0
 76M  CONST_17  N28  C26  C25  N24   180.00   0.0  0
 76M  CONST_18  C17  N22  C31  C25   180.00   0.0  0
 76M  CONST_19  N24  C23  N22  C17   180.00   0.0  0
 76M  CONST_20  N30  C31  N22  C17     0.00   0.0  0
 76M  CONST_21  N27  C26  C25  C31   180.00   0.0  0
 76M  CONST_22  N27  C26  C25  N24     0.00   0.0  0
 76M  CONST_23  C29  N28  C26  N27   180.00   0.0  0
 76M  CONST_24  H60  C23  N24  C25   180.00   0.0  0
 76M  CONST_25  H63  C29  N28  C26   180.00   0.0  0
 76M  CONST_26  H62  N27  C26  C25   180.00   0.0  0
 76M  CONST_27  H61  N27  C26  C25     0.00   0.0  0
 76M  CONST_28  H1   O13  C11  C9    180.00   0.0  0
 76M  Var_01    N5   C4   C2   C1    173.56  30.0  3
 76M  Var_02    C6   N5   C4   C2   -173.64  30.0  1
 76M  Var_03    C9   C8   C7   C6   -169.67  30.0  1
 76M  Var_04    H49  C3   C2   C1   -176.55  30.0  3
 76M  Var_05    H44  C1   C2   C3     57.73  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
 76M  chir_01  C6   C7   N5   C14  positiv
 76M  chir_02  C15  O16  C14  C20  positiv
 76M  chir_03  C9   N10  C11  C8   negativ
 76M  chir_04  C17  O16  C18  N22  positiv
 76M  chir_05  C18  O19  C17  C20  negativ
 76M  chir_06  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
 76M  plan-1  C23  0.020
 76M  plan-1  C25  0.020
 76M  plan-1  C26  0.020
 76M  plan-1  C31  0.020
 76M  plan-1  C17  0.020
 76M  plan-1  N22  0.020
 76M  plan-1  N24  0.020
 76M  plan-1  N28  0.020
 76M  plan-1  C29  0.020
 76M  plan-1  N30  0.020
 76M  plan-1  H60  0.020
 76M  plan-1  H63  0.020
 76M  plan-1  N27  0.020
 76M  plan-2  C26  0.020
 76M  plan-2  H62  0.020
 76M  plan-2  H61  0.020
 76M  plan-2  N27  0.020
 76M  plan-3  C11  0.020
 76M  plan-3  C9   0.020
 76M  plan-3  O13  0.020
 76M  plan-3  H1   0.020
 76M  plan-3  O12  0.020

