# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 17:12:28 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]-[(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  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_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  -0.694   4.2445   4.2124  -3.0599
 76L  C2   C  CH1    0  -0.007   3.8446   3.9232  -1.6262
 76L  C6   C  CH1    0  -0.107   2.2373   0.9311   0.1621
 76L  C7   C  CH2    0  -0.445   3.2220  -0.2275   0.0465
 76L  C8   C  CH2    0  -0.482   2.5033  -1.5721   0.1199
 76L  C11  C  C      0   0.474   2.5871  -4.1033  -0.3201
 76L  C14  C  CH2    0  -0.493   1.5594   1.0018   1.5256
 76L  C15  C  CH1    0  -0.021   0.3397   1.9141   1.5847
 76L  C23  C  CR15   0   0.121  -1.5030  -1.2667   0.0459
 76L  C25  C  CR56   0  -0.011  -3.3652  -1.4553  -0.9286
 76L  C26  C  CR6    0   0.459  -4.5133  -1.8090  -1.6616
 76L  C31  C  CR56   0   0.495  -3.4068  -0.2367  -0.2719
 76L  O3   O  OH1    0  -0.656   2.8188   4.7718  -1.1538
 76L  C4   C  CH2    0  -0.315   3.4263   2.4640  -1.4765
 76L  N5   N  NT2    1  -0.689   2.9494   2.2284  -0.0871
 76L  C9   C  CH1    0  -0.260   3.3581  -2.7503  -0.2979
 76L  N10  N  NT3    1  -0.795   4.5350  -2.9307   0.5961
 76L  O16  O  O2     0  -0.490  -0.5987   1.5441   0.5704
 76L  C17  C  CH1    0   0.217  -1.7564   0.9945   1.1424
 76L  C18  C  CH1    0  -0.057  -1.3829   0.6522   2.5847
 76L  O19  O  OH1    0  -0.651  -2.5327   0.6218   3.3734
 76L  C20  C  CH1    0  -0.012  -0.4082   1.7888   2.9079
 76L  O21  O  OH1    0  -0.667  -1.1020   2.9839   3.1460
 76L  N22  N  NR5    0  -0.544  -2.1986  -0.1274   0.3588
 76L  N24  N  N      0  -0.440  -2.1633  -2.0817  -0.7180
 76L  N28  N  N      0  -0.473  -5.5409  -0.9523  -1.6651
 76L  C29  C  CR16   0   0.048  -5.4377   0.1867  -0.9862
 76L  N30  N  N      0  -0.457  -4.4188   0.6260  -0.2676
 76L  H45  H  HCH3   0   0.237   3.4101   4.0471  -3.7447
 76L  H46  H  HCH3   0   0.257   4.5732   5.2459  -3.1611
 76L  H44  H  HCH3   0   0.246   5.0656   3.5676  -3.3726
 76L  H32  H  HCH1   0   0.261   4.7017   4.1056  -0.9720
 76L  H35  H  HCH1   0   0.309   1.4920   0.8477  -0.6315
 76L  H50  H  HCH2   0   0.278   3.7431  -0.1701  -0.9122
 76L  H51  H  HCH2   0   0.259   3.9813  -0.1378   0.8299
 76L  H52  H  HCH2   0   0.262   2.1136  -1.7599   1.1245
 76L  H53  H  HCH2   0   0.271   1.6495  -1.5629  -0.5585
 76L  H54  H  HCH2   0   0.272   1.2615  -0.0089   1.8082
 76L  H55  H  HCH2   0   0.285   2.2851   1.3176   2.2809
 76L  H40  H  HCH1   0   0.265   0.6258   2.9596   1.4242
 76L  H47  H  HOH1   0   0.458   2.1166   4.8133  -1.8141
 76L  H49  H  HCH2   0   0.295   2.6001   2.2184  -2.1456
 76L  H48  H  HCH2   0   0.306   4.2562   1.7926  -1.6798
 76L  H33  H  HNT2   0   0.455   2.3332   3.0144   0.1435
 76L  H36  H  HCH1   0   0.310   3.7650  -2.5796  -1.2977
 76L  H37  H  HNT3   0   0.460   4.3433  -2.6621   1.5609
 76L  H39  H  HNT3   0   0.456   4.7216  -3.9454   0.6011
 76L  H41  H  HCH1   0   0.267  -2.5833   1.7123   1.1314
 76L  H42  H  HCH1   0   0.252  -0.8468  -0.3046   2.6187
 76L  H56  H  HOH1   0   0.472  -2.3467   0.1278   4.1783
 76L  H43  H  HCH1   0   0.258   0.2674   1.5358   3.7349
 76L  H57  H  HOH1   0   0.452  -1.8399   2.7898   3.7367
 76L  H60  H  HNH2   0   0.411  -3.8258  -3.5705  -2.4277
 76L  H59  H  HNH2   0   0.404  -5.4239  -3.1349  -2.9043
 76L  H61  H  HCR6   0   0.254  -6.3050   0.8367  -1.0316
 76L  H34  H  HNT2   0   0.464   3.7346   2.3099   0.5634
 76L  H38  H  HNT3   0   0.467   5.3680  -2.4303   0.2934
 76L  O12  O  O      0  -0.593   3.2399  -5.0861   0.0841
 76L  N27  N  NH2    0  -0.815  -4.6165  -2.9577  -2.3317
 76L  O13  O  OC    -1  -0.559   1.4345  -4.0635  -0.7599
 76L  H58  H  HCR5   0   0.276  -0.5032  -1.4486   0.4098

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  deloc     1.247  0.020  1.247
 76L  C11  O13  deloc     1.234  0.020  1.234
 76L  C11  C9   single    1.557  0.020  1.557
 76L  O3   C2   single    1.413  0.020  1.413
 76L  C8   C9   single    1.514  0.020  1.514
 76L  C8   C7   single    1.526  0.020  1.526
 76L  C9   N10  single    1.489  0.020  1.489
 76L  C2   C4   single    1.525  0.020  1.525
 76L  C2   C1   single    1.516  0.020  1.516
 76L  C6   C7   single    1.525  0.020  1.525
 76L  C6   N5   single    1.501  0.020  1.501
 76L  C6   C14  single    1.524  0.020  1.524
 76L  N5   C4   single    1.488  0.020  1.488
 76L  O21  C20  single    1.402  0.020  1.402
 76L  O19  C18  single    1.395  0.020  1.395
 76L  C15  C14  single    1.524  0.020  1.524
 76L  C15  O16  single    1.430  0.020  1.430
 76L  C15  C20  single    1.525  0.020  1.525
 76L  O16  C17  single    1.403  0.020  1.403
 76L  C20  C18  single    1.532  0.020  1.532
 76L  C18  C17  single    1.529  0.020  1.529
 76L  C17  N22  single    1.438  0.020  1.438
 76L  N22  C23  aromatic  1.371  0.020  1.371
 76L  N22  C31  aromatic  1.367  0.020  1.367
 76L  C23  N24  aromatic  1.298  0.020  1.298
 76L  N30  C31  aromatic  1.330  0.020  1.330
 76L  N30  C29  aromatic  1.322  0.020  1.322
 76L  C31  C25  aromatic  1.385  0.020  1.385
 76L  N24  C25  aromatic  1.372  0.020  1.372
 76L  C29  N28  aromatic  1.330  0.020  1.330
 76L  C25  C26  aromatic  1.407  0.020  1.407
 76L  N28  C26  aromatic  1.338  0.020  1.338
 76L  C26  N27  single    1.334  0.020  1.334
 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  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  107.90  3.000
 76L  H44  C1   H45  107.83  3.000
 76L  H46  C1   H45  108.42  3.000
 76L  H44  C1   C2   110.92  3.000
 76L  H46  C1   C2   110.39  3.000
 76L  H45  C1   C2   111.26  3.000
 76L  H32  C2   C4   108.41  3.000
 76L  H32  C2   O3   105.60  3.000
 76L  C4   C2   O3   110.04  3.000
 76L  H32  C2   C1   109.09  3.000
 76L  C4   C2   C1   110.34  3.000
 76L  O3   C2   C1   113.15  3.000
 76L  H35  C6   N5   105.62  3.000
 76L  H35  C6   C14  110.49  3.000
 76L  N5   C6   C14  108.63  3.000
 76L  H35  C6   C7   109.13  3.000
 76L  C14  C6   C7   112.97  3.000
 76L  N5   C6   C7   109.74  3.000
 76L  H51  C7   H50  107.02  3.000
 76L  H51  C7   C8   111.37  3.000
 76L  H50  C7   C8   108.24  3.000
 76L  H51  C7   C6   109.36  3.000
 76L  H50  C7   C6   109.55  3.000
 76L  C8   C7   C6   111.20  3.000
 76L  H53  C8   H52  107.09  3.000
 76L  H53  C8   C9   106.07  3.000
 76L  H52  C8   C9   108.72  3.000
 76L  H53  C8   C7   109.35  3.000
 76L  H52  C8   C7   111.30  3.000
 76L  C9   C8   C7   113.97  3.000
 76L  O13  C11  O12  129.03  3.000
 76L  O13  C11  C9   116.06  3.000
 76L  O12  C11  C9   114.89  3.000
 76L  H55  C14  H54  105.64  3.000
 76L  H55  C14  C15  109.35  3.000
 76L  H54  C14  C15  109.02  3.000
 76L  H55  C14  C6   109.63  3.000
 76L  H54  C14  C6   108.07  3.000
 76L  C15  C14  C6   114.73  3.000
 76L  H40  C15  C20  109.49  3.000
 76L  H40  C15  O16  108.32  3.000
 76L  C20  C15  O16  105.80  3.000
 76L  H40  C15  C14  110.88  3.000
 76L  C20  C15  C14  112.14  3.000
 76L  O16  C15  C14  110.03  3.000
 76L  H58  C23  N24  124.33  3.000
 76L  H58  C23  N22  122.21  3.000
 76L  N24  C23  N22  113.46  3.000
 76L  N24  C25  C31  110.82  3.000
 76L  N24  C25  C26  132.85  3.000
 76L  C31  C25  C26  116.33  3.000
 76L  N28  C26  N27  119.39  3.000
 76L  N27  C26  C25  122.77  3.000
 76L  N28  C26  C25  117.84  3.000
 76L  N30  C31  N22  128.26  3.000
 76L  N30  C31  C25  126.53  3.000
 76L  N22  C31  C25  105.22  3.000
 76L  H47  O3   C2   109.00  3.000
 76L  H48  C4   H49  108.93  3.000
 76L  H48  C4   N5   108.76  3.000
 76L  H49  C4   N5   107.12  3.000
 76L  H48  C4   C2   111.30  3.000
 76L  H49  C4   C2   111.27  3.000
 76L  N5   C4   C2   109.33  3.000
 76L  H34  N5   H33  104.90  3.000
 76L  H34  N5   C4   109.59  3.000
 76L  H33  N5   C4   106.34  3.000
 76L  H34  N5   C6   109.12  3.000
 76L  H33  N5   C6   109.89  3.000
 76L  C4   N5   C6   116.37  3.000
 76L  H36  C9   N10  105.90  3.000
 76L  H36  C9   C11  107.87  3.000
 76L  N10  C9   C11  107.14  3.000
 76L  H36  C9   C8   109.94  3.000
 76L  N10  C9   C8   112.01  3.000
 76L  C11  C9   C8   113.60  3.000
 76L  H38  N10  H39  109.69  3.000
 76L  H38  N10  H37  107.81  3.000
 76L  H39  N10  H37  106.77  3.000
 76L  H38  N10  C9   114.13  3.000
 76L  H39  N10  C9   105.36  3.000
 76L  H37  N10  C9   112.80  3.000
 76L  C17  O16  C15  110.70  3.000
 76L  H41  C17  N22  105.89  3.000
 76L  H41  C17  C18  109.93  3.000
 76L  N22  C17  C18  114.49  3.000
 76L  H41  C17  O16  111.23  3.000
 76L  N22  C17  O16  109.70  3.000
 76L  C18  C17  O16  105.71  3.000
 76L  H42  C18  C20  109.24  3.000
 76L  H42  C18  O19  111.49  3.000
 76L  C20  C18  O19  114.93  3.000
 76L  H42  C18  C17  110.11  3.000
 76L  C20  C18  C17  100.85  3.000
 76L  O19  C18  C17  109.70  3.000
 76L  H56  O19  C18  108.95  3.000
 76L  H43  C20  O21  111.91  3.000
 76L  H43  C20  C18  112.31  3.000
 76L  O21  C20  C18  110.69  3.000
 76L  H43  C20  C15  111.77  3.000
 76L  C18  C20  C15  100.95  3.000
 76L  O21  C20  C15  108.66  3.000
 76L  H57  O21  C20  108.12  3.000
 76L  C17  N22  C31  125.83  3.000
 76L  C31  N22  C23  106.06  3.000
 76L  C17  N22  C23  128.07  3.000
 76L  C25  N24  C23  104.45  3.000
 76L  C29  N28  C26  119.17  3.000
 76L  H61  C29  N30  116.10  3.000
 76L  H61  C29  N28  115.45  3.000
 76L  N30  C29  N28  128.45  3.000
 76L  C29  N30  C31  111.67  3.000
 76L  H59  N27  H60  118.03  3.000
 76L  H59  N27  C26  120.00  3.000
 76L  H60  N27  C26  120.81  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    0.00   0.0  0
 76L  CONST_27  H59  N27  C26  C25  180.00   0.0  0
 76L  Var_01    C6   N5   C4   C2   167.80  30.0  1
 76L  Var_02    C9   C8   C7   C6   166.86  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  H61  0.020
 76L  plan-1  N27  0.020
 76L  plan-1  H58  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  O12  0.020
 76L  plan-3  O13  0.020

