# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 16:12:19 2020
#   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  63  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_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  -0.655   4.6374   4.0472  -3.0446
 76M  C2   C  CH1    0  -0.285   3.9799   3.9501  -1.6716
 76M  C3   C  CH3    0  -0.674   2.9259   5.0398  -1.5011
 76M  C6   C  CH1    0  -0.107   2.1974   1.0076   0.1167
 76M  C7   C  CH2    0  -0.447   3.2078  -0.1317   0.0312
 76M  C8   C  CH2    0  -0.481   2.5111  -1.4876   0.1217
 76M  C11  C  C      0   0.474   2.6251  -4.0207  -0.2996
 76M  C14  C  CH2    0  -0.494   1.5041   1.0759   1.4733
 76M  C15  C  CH1    0  -0.019   0.2566   1.9493   1.5165
 76M  C23  C  CR15   0   0.122  -1.5319  -1.2929   0.0230
 76M  C25  C  CR56   0  -0.010  -3.4243  -1.5539  -0.8741
 76M  C26  C  CR6    0   0.458  -4.5883  -1.9539  -1.5558
 76M  C31  C  CR56   0   0.495  -3.4772  -0.3254  -0.2367
 76M  C4   C  CH2    0  -0.284   3.3995   2.5504  -1.5157
 76M  N5   N  NT2    1  -0.693   2.8780   2.3243  -0.1363
 76M  C9   C  CH1    0  -0.262   3.3747  -2.6556  -0.3046
 76M  N10  N  NT3    1  -0.794   4.5748  -2.8096   0.5629
 76M  O16  O  O2     0  -0.490  -0.6717   1.5278   0.5134
 76M  C17  C  CH1    0   0.218  -1.8179   0.9734   1.1031
 76M  C18  C  CH1    0  -0.054  -1.4290   0.6636   2.5484
 76M  O19  O  OH1    0  -0.651  -2.5733   0.6172   3.3439
 76M  C20  C  CH1    0  -0.014  -0.4815   1.8293   2.8462
 76M  O21  O  OH1    0  -0.667  -1.2026   3.0113   3.0676
 76M  N22  N  NR5    0  -0.544  -2.2490  -0.1688   0.3431
 76M  N24  N  N      0  -0.441  -2.1967  -2.1403  -0.7008
 76M  N28  N  N      0  -0.473  -5.6402  -1.1278  -1.5346
 76M  C29  C  CR16   0   0.048  -5.5457   0.0258  -0.8792
 76M  N30  N  N      0  -0.457  -4.5138   0.5070  -0.2076
 76M  H44  H  HCH3   0   0.228   3.9024   3.9164  -3.8414
 76M  H43  H  HCH3   0   0.245   5.0971   5.0268  -3.1749
 76M  H45  H  HCH3   0   0.239   5.4150   3.2936  -3.1741
 76M  H46  H  HCH1   0   0.257   4.7563   4.0822  -0.9102
 76M  H49  H  HCH3   0   0.235   2.1247   4.9238  -2.2334
 76M  H48  H  HCH3   0   0.229   2.4750   5.0588  -0.5062
 76M  H47  H  HCH3   0   0.255   3.3741   6.0220  -1.6499
 76M  H34  H  HCH1   0   0.311   1.4651   0.8981  -0.6858
 76M  H52  H  HCH2   0   0.277   3.7376  -0.0842  -0.9224
 76M  H53  H  HCH2   0   0.260   3.9562  -0.0150   0.8210
 76M  H55  H  HCH2   0   0.261   2.1382  -1.6754   1.1326
 76M  H54  H  HCH2   0   0.271   1.6476  -1.4944  -0.5444
 76M  H56  H  HCH2   0   0.271   1.2357   0.0604   1.7675
 76M  H57  H  HCH2   0   0.285   2.2142   1.4242   2.2293
 76M  H39  H  HCH1   0   0.263   0.5074   3.0004   1.3338
 76M  H51  H  HCH2   0   0.292   2.5675   2.3842  -2.2009
 76M  H50  H  HCH2   0   0.302   4.1610   1.7973  -1.7016
 76M  H32  H  HNT2   0   0.463   2.2216   3.0761   0.0809
 76M  H33  H  HNT2   0   0.464   3.6419   2.4412   0.5340
 76M  H35  H  HCH1   0   0.311   3.7568  -2.4874  -1.3147
 76M  H36  H  HNT3   0   0.460   4.3967  -2.5520   1.5334
 76M  H38  H  HNT3   0   0.456   4.7906  -3.8178   0.5585
 76M  H37  H  HNT3   0   0.467   5.3870  -2.2847   0.2458
 76M  H40  H  HCH1   0   0.267  -2.6555   1.6788   1.0851
 76M  H41  H  HCH1   0   0.251  -0.8687  -0.2790   2.5935
 76M  H58  H  HOH1   0   0.472  -2.3697   0.1447   4.1574
 76M  H42  H  HCH1   0   0.259   0.2051   1.6080   3.6732
 76M  H59  H  HOH1   0   0.452  -1.9336   2.8099   3.6644
 76M  H62  H  HNH2   0   0.411  -3.8725  -3.6970  -2.3331
 76M  H61  H  HNH2   0   0.404  -5.4963  -3.3157  -2.7584
 76M  H63  H  HCR6   0   0.254  -6.4329   0.6494  -0.9021
 76M  O12  O  O      0  -0.593   3.3097  -4.9933   0.0748
 76M  N27  N  NH2    0  -0.814  -4.6844  -3.1200  -2.1981
 76M  O13  O  OC    -1  -0.559   1.4552  -3.9990  -0.6934
 76M  H60  H  HCR5   0   0.275  -0.5128  -1.4384   0.3484

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  deloc     1.247  0.020  1.247
 76M  C11  O13  deloc     1.235  0.020  1.235
 76M  C11  C9   single    1.557  0.020  1.557
 76M  C8   C9   single    1.514  0.020  1.514
 76M  C8   C7   single    1.527  0.020  1.527
 76M  C9   N10  single    1.489  0.020  1.489
 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    1.525  0.020  1.525
 76M  C6   N5   single    1.504  0.020  1.504
 76M  C6   C14  single    1.525  0.020  1.525
 76M  N5   C4   single    1.492  0.020  1.492
 76M  O19  C18  single    1.394  0.020  1.394
 76M  O21  C20  single    1.402  0.020  1.402
 76M  C15  C14  single    1.523  0.020  1.523
 76M  C15  O16  single    1.430  0.020  1.430
 76M  C15  C20  single    1.526  0.020  1.526
 76M  O16  C17  single    1.403  0.020  1.403
 76M  C20  C18  single    1.532  0.020  1.532
 76M  C18  C17  single    1.528  0.020  1.528
 76M  C17  N22  single    1.438  0.020  1.438
 76M  N22  C23  aromatic  1.371  0.020  1.371
 76M  N22  C31  aromatic  1.367  0.020  1.367
 76M  C23  N24  aromatic  1.298  0.020  1.298
 76M  N30  C31  aromatic  1.330  0.020  1.330
 76M  N30  C29  aromatic  1.322  0.020  1.322
 76M  C31  C25  aromatic  1.385  0.020  1.385
 76M  N24  C25  aromatic  1.371  0.020  1.371
 76M  C29  N28  aromatic  1.330  0.020  1.330
 76M  C25  C26  aromatic  1.407  0.020  1.407
 76M  N28  C26  aromatic  1.338  0.020  1.338
 76M  C26  N27  single    1.335  0.020  1.335
 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  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  107.82  3.000
 76M  H45  C1   H44  108.09  3.000
 76M  H43  C1   H44  107.72  3.000
 76M  H45  C1   C2   111.73  3.000
 76M  H43  C1   C2   110.28  3.000
 76M  H44  C1   C2   111.04  3.000
 76M  H46  C2   C4   108.05  3.000
 76M  H46  C2   C3   109.02  3.000
 76M  C4   C2   C3   112.44  3.000
 76M  H46  C2   C1   108.20  3.000
 76M  C3   C2   C1   110.66  3.000
 76M  C4   C2   C1   108.35  3.000
 76M  H47  C3   H48  106.16  3.000
 76M  H47  C3   H49  107.82  3.000
 76M  H48  C3   H49  108.05  3.000
 76M  H47  C3   C2   110.14  3.000
 76M  H48  C3   C2   113.54  3.000
 76M  H49  C3   C2   110.87  3.000
 76M  H34  C6   N5   105.53  3.000
 76M  H34  C6   C14  110.70  3.000
 76M  N5   C6   C14  108.44  3.000
 76M  H34  C6   C7   109.16  3.000
 76M  C14  C6   C7   112.61  3.000
 76M  N5   C6   C7   110.17  3.000
 76M  H53  C7   H52  107.09  3.000
 76M  H53  C7   C8   111.34  3.000
 76M  H52  C7   C8   108.16  3.000
 76M  H53  C7   C6   109.45  3.000
 76M  H52  C7   C6   109.75  3.000
 76M  C8   C7   C6   110.96  3.000
 76M  H54  C8   H55  107.07  3.000
 76M  H54  C8   C9   105.95  3.000
 76M  H55  C8   C9   108.81  3.000
 76M  H54  C8   C7   109.30  3.000
 76M  H55  C8   C7   111.27  3.000
 76M  C9   C8   C7   114.08  3.000
 76M  O13  C11  O12  129.03  3.000
 76M  O13  C11  C9   116.09  3.000
 76M  O12  C11  C9   114.86  3.000
 76M  H57  C14  H56  105.64  3.000
 76M  H57  C14  C15  109.23  3.000
 76M  H56  C14  C15  108.94  3.000
 76M  H57  C14  C6   109.50  3.000
 76M  H56  C14  C6   108.06  3.000
 76M  C15  C14  C6   115.03  3.000
 76M  H39  C15  C20  109.36  3.000
 76M  H39  C15  O16  108.32  3.000
 76M  C20  C15  O16  105.91  3.000
 76M  H39  C15  C14  110.96  3.000
 76M  C20  C15  C14  112.07  3.000
 76M  O16  C15  C14  110.04  3.000
 76M  H60  C23  N24  124.31  3.000
 76M  H60  C23  N22  122.26  3.000
 76M  N24  C23  N22  113.43  3.000
 76M  N24  C25  C31  110.81  3.000
 76M  N24  C25  C26  132.86  3.000
 76M  C31  C25  C26  116.33  3.000
 76M  N28  C26  N27  119.38  3.000
 76M  N27  C26  C25  122.76  3.000
 76M  N28  C26  C25  117.86  3.000
 76M  N30  C31  N22  128.27  3.000
 76M  N30  C31  C25  126.52  3.000
 76M  N22  C31  C25  105.22  3.000
 76M  H50  C4   H51  108.75  3.000
 76M  H50  C4   N5   107.34  3.000
 76M  H51  C4   N5   106.93  3.000
 76M  H50  C4   C2   110.62  3.000
 76M  H51  C4   C2   111.50  3.000
 76M  N5   C4   C2   111.53  3.000
 76M  H33  N5   H32  104.86  3.000
 76M  H33  N5   C4   109.12  3.000
 76M  H32  N5   C4   108.04  3.000
 76M  H33  N5   C6   109.13  3.000
 76M  H32  N5   C6   108.53  3.000
 76M  C4   N5   C6   116.52  3.000
 76M  H35  C9   N10  105.83  3.000
 76M  H35  C9   C11  107.83  3.000
 76M  N10  C9   C11  107.19  3.000
 76M  H35  C9   C8   109.94  3.000
 76M  N10  C9   C8   112.06  3.000
 76M  C11  C9   C8   113.62  3.000
 76M  H37  N10  H38  109.63  3.000
 76M  H37  N10  H36  107.80  3.000
 76M  H38  N10  H36  106.72  3.000
 76M  H37  N10  C9   114.10  3.000
 76M  H38  N10  C9   105.51  3.000
 76M  H36  N10  C9   112.81  3.000
 76M  C17  O16  C15  110.60  3.000
 76M  H40  C17  N22  105.88  3.000
 76M  H40  C17  C18  109.92  3.000
 76M  N22  C17  C18  114.52  3.000
 76M  H40  C17  O16  111.31  3.000
 76M  N22  C17  O16  109.67  3.000
 76M  C18  C17  O16  105.64  3.000
 76M  H41  C18  C20  109.26  3.000
 76M  H41  C18  O19  111.53  3.000
 76M  C20  C18  O19  114.97  3.000
 76M  H41  C18  C17  110.05  3.000
 76M  C20  C18  C17  100.78  3.000
 76M  O19  C18  C17  109.72  3.000
 76M  H58  O19  C18  108.96  3.000
 76M  H42  C20  O21  111.88  3.000
 76M  H42  C20  C18  112.34  3.000
 76M  O21  C20  C18  110.74  3.000
 76M  H42  C20  C15  111.72  3.000
 76M  C18  C20  C15  100.93  3.000
 76M  O21  C20  C15  108.67  3.000
 76M  H59  O21  C20  108.14  3.000
 76M  C17  N22  C31  125.76  3.000
 76M  C31  N22  C23  106.08  3.000
 76M  C17  N22  C23  128.15  3.000
 76M  C25  N24  C23  104.46  3.000
 76M  C29  N28  C26  119.18  3.000
 76M  H63  C29  N30  116.10  3.000
 76M  H63  C29  N28  115.47  3.000
 76M  N30  C29  N28  128.43  3.000
 76M  C29  N30  C31  111.69  3.000
 76M  H61  N27  H62  117.74  3.000
 76M  H61  N27  C26  119.75  3.000
 76M  H62  N27  C26  120.53  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    0.00   0.0  0
 76M  CONST_27  H61  N27  C26  C25  180.00   0.0  0
 76M  Var_01    N5   C4   C2   C1   173.35  30.0  3
 76M  Var_02    C6   N5   C4   C2   176.14  30.0  1
 76M  Var_03    C9   C8   C7   C6   165.15  30.0  1
 76M  Var_04    H49  C3   C2   C1    62.30  30.0  3
 76M  Var_05    H44  C1   C2   C3   -60.90  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  H63  0.020
 76M  plan-1  N27  0.020
 76M  plan-1  H60  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  O12  0.020
 76M  plan-3  O13  0.020

