# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 07:42:58 2021
#   Inital geometry file: a 136 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]-propyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[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
 76H  76H  '[(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]-propyl-azanium'  ligand  61  30  .  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_76H
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
 76H  C4   C  CR56  0   0.488  -2.1926   -4.2463  18.5638
 76H  C5   C  CR56  0  -0.000  -0.9664   -4.3598  17.9292
 76H  C6   C  CR6   0   0.459  -0.2522   -3.1613  17.7387
 76H  C8   C  CR15  0   0.102  -1.7461   -6.3191  18.0341
 76H  N1   N  N     0  -0.473  -0.8041   -2.0270  18.1848
 76H  N3   N  N     0  -0.459  -2.7543   -3.1266  19.0167
 76H  C    C  C     0   0.592  -4.6254   -9.9295  23.2411
 76H  CA   C  CH1   0  -0.260  -3.7709   -9.8404  21.9851
 76H  N    N  NT3   1  -0.788  -3.0166   -8.5578  21.9282
 76H  CB   C  CH2   0  -0.470  -4.6108  -10.0175  20.7271
 76H  CAM  C  CH2   0  -0.494  -3.7741  -10.2867  19.4771
 76H  CAY  C  CH1   0  -0.083  -4.6360  -10.2388  18.2119
 76H  NAR  N  NT2   1  -0.683  -4.1738  -11.3211  17.2795
 76H  CAK  C  CH2   0  -0.292  -5.0104  -11.5412  16.0642
 76H  CAJ  C  CH2   0  -0.464  -4.6216  -12.8293  15.3645
 76H  CAA  C  CH3   0  -0.666  -5.4975  -13.0584  14.1411
 76H  CBB  C  CH1   0   0.032  -5.0796   -7.7106  18.2920
 76H  OAS  O  O2    0  -0.522  -4.0810   -7.2797  19.2235
 76H  CAZ  C  CH1   0   0.018  -5.3505   -6.4809  17.4263
 76H  OAF  O  OH1   0  -0.654  -6.6141   -6.5767  16.8525
 76H  CBA  C  CH1   0  -0.069  -5.1527   -5.3422  18.4274
 76H  OAG  O  OH1   0  -0.657  -6.2923   -5.2587  19.2316
 76H  CBC  C  CH1   0   0.168  -3.9609   -5.8858  19.2275
 76H  N9   N  NR5   0  -0.539  -2.6882   -5.5162  18.6185
 76H  N7   N  N     0  -0.448  -0.7056   -5.6650  17.6072
 76H  C2   C  CR16  0   0.041  -1.9910   -2.0727  18.7841
 76H  N6   N  NH2   0  -0.815   0.9329   -3.1164  17.1305
 76H  H1   H  HCR5  0   0.291  -1.8718   -7.3869  17.9543
 76H  H3   H  HCH1  0   0.366  -3.0166  -10.6286  22.0537
 76H  H4   H  HNT3  0   0.489  -2.3893   -8.4335  22.7248
 76H  H5   H  HNT3  0   0.478  -2.4249   -8.5245  21.0982
 76H  H8   H  HCH2  0   0.285  -5.2641   -9.1497  20.6150
 76H  H7   H  HCH2  0   0.305  -5.2677  -10.8722  20.8850
 76H  H9   H  HCH2  0   0.292  -3.3288  -11.2787  19.5900
 76H  H10  H  HCH2  0   0.257  -2.9338   -9.5980  19.3669
 76H  H11  H  HCH1  0   0.319  -5.6651  -10.5129  18.4564
 76H  H32  H  HNT2  0   0.470  -4.1450  -12.1958  17.8079
 76H  H15  H  HCH2  0   0.294  -4.8755  -10.6846  15.4077
 76H  H14  H  HCH2  0   0.293  -6.0466  -11.5670  16.3993
 76H  H17  H  HCH2  0   0.249  -4.7251  -13.6691  16.0564
 76H  H16  H  HCH2  0   0.252  -3.5711  -12.7859  15.0674
 76H  H20  H  HCH3  0   0.246  -5.2148  -13.9807  13.6361
 76H  H18  H  HCH3  0   0.232  -6.5492  -13.1389  14.4180
 76H  H19  H  HCH3  0   0.232  -5.3998  -12.2422  13.4250
 76H  H23  H  HCH1  0   0.259  -5.9945   -7.9665  18.8407
 76H  H24  H  HCH1  0   0.244  -4.5651   -6.4017  16.6609
 76H  H25  H  HOH1  0   0.466  -6.6795   -5.9420  16.1325
 76H  H26  H  HCH1  0   0.275  -4.9148   -4.3888  17.9442
 76H  H27  H  HOH1  0   0.463  -6.2149   -4.4855  19.7997
 76H  H28  H  HCH1  0   0.290  -3.9559   -5.5129  20.2557
 76H  H29  H  HCR6  0   0.253  -2.3785   -1.1179  19.1228
 76H  H31  H  HNH2  0   0.405   1.4244   -2.2436  17.0425
 76H  H30  H  HNH2  0   0.412   1.3989   -3.9570  16.8374
 76H  H2   H  HOH1  0   0.504  -4.9983   -8.9861  24.8459
 76H  H6   H  HNT3  0   0.473  -3.6287   -7.7419  21.8915
 76H  H12  H  HNT2  0   0.466  -3.2064  -11.1472  16.9976
 76H  CAN  C  CH2   0  -0.490  -4.6229   -8.9050  17.4749
 76H  OXT  O  OH1   0  -0.583  -4.4609   -8.8978  24.0423
 76H  O    O  O     0  -0.411  -5.3465  -10.8659  23.4448
 76H  H21  H  HCH2  0   0.266  -3.6280   -8.7136  17.0604
 76H  H22  H  HCH2  0   0.294  -5.3132   -8.9597  16.6300

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
 76H  CAA  CAJ  single    1.522  0.020  1.522
 76H  CAJ  CAK  single    1.517  0.020  1.517
 76H  CAK  NAR  single    1.492  0.020  1.492
 76H  N6   C6   single    1.333  0.020  1.333
 76H  OAF  CAZ  single    1.391  0.020  1.391
 76H  NAR  CAY  single    1.501  0.020  1.501
 76H  CAZ  CBB  single    1.528  0.020  1.528
 76H  CAZ  CBA  single    1.529  0.020  1.529
 76H  N7   C5   aromatic  1.369  0.020  1.369
 76H  N7   C8   aromatic  1.301  0.020  1.301
 76H  CAN  CAY  single    1.524  0.020  1.524
 76H  CAN  CBB  single    1.517  0.020  1.517
 76H  C6   C5   aromatic  1.408  0.020  1.408
 76H  C6   N1   aromatic  1.338  0.020  1.338
 76H  C5   C4   aromatic  1.385  0.020  1.385
 76H  C8   N9   aromatic  1.369  0.020  1.369
 76H  N1   C2   aromatic  1.330  0.020  1.330
 76H  CAY  CAM  single    1.532  0.020  1.532
 76H  CBB  OAS  single    1.432  0.020  1.432
 76H  CBA  CBC  single    1.535  0.020  1.535
 76H  CBA  OAG  single    1.397  0.020  1.397
 76H  C4   N9   aromatic  1.364  0.020  1.364
 76H  C4   N3   aromatic  1.332  0.020  1.332
 76H  N9   CBC  single    1.458  0.020  1.458
 76H  C2   N3   aromatic  1.322  0.020  1.322
 76H  CBC  OAS  single    1.399  0.020  1.399
 76H  CAM  CB   single    1.528  0.020  1.528
 76H  CB   CA   single    1.523  0.020  1.523
 76H  CA   N    single    1.489  0.020  1.489
 76H  CA   C    single    1.522  0.020  1.522
 76H  C    O    double    1.199  0.020  1.199
 76H  C    OXT  single    1.317  0.020  1.317
 76H  C8   H1   single    0.930  0.020  1.080
 76H  CA   H3   single    0.970  0.020  1.090
 76H  N    H4   single    0.890  0.020  1.040
 76H  N    H5   single    0.890  0.020  1.040
 76H  CB   H8   single    0.970  0.020  1.090
 76H  CB   H7   single    0.970  0.020  1.090
 76H  CAM  H9   single    0.970  0.020  1.090
 76H  CAM  H10  single    0.970  0.020  1.090
 76H  CAY  H11  single    0.970  0.020  1.090
 76H  NAR  H32  single    0.890  0.020  1.040
 76H  CAK  H15  single    0.970  0.020  1.090
 76H  CAK  H14  single    0.970  0.020  1.090
 76H  CAJ  H17  single    0.970  0.020  1.090
 76H  CAJ  H16  single    0.970  0.020  1.090
 76H  CAA  H20  single    0.970  0.020  1.090
 76H  CAA  H18  single    0.970  0.020  1.090
 76H  CAA  H19  single    0.970  0.020  1.090
 76H  CAN  H21  single    0.970  0.020  1.090
 76H  CAN  H22  single    0.970  0.020  1.090
 76H  CBB  H23  single    0.970  0.020  1.090
 76H  CAZ  H24  single    0.970  0.020  1.090
 76H  OAF  H25  single    0.850  0.020  0.980
 76H  CBA  H26  single    0.970  0.020  1.090
 76H  OAG  H27  single    0.850  0.020  0.980
 76H  CBC  H28  single    0.970  0.020  1.090
 76H  C2   H29  single    0.930  0.020  1.080
 76H  N6   H31  single    0.860  0.020  1.020
 76H  N6   H30  single    0.860  0.020  1.020
 76H  OXT  H2   single    0.850  0.020  0.980
 76H  N    H6   single    0.890  0.020  1.040
 76H  NAR  H12  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
 76H  N9   C4   N3   128.00  3.000
 76H  N3   C4   C5   126.72  3.000
 76H  N9   C4   C5   105.28  3.000
 76H  N7   C5   C6   133.07  3.000
 76H  C6   C5   C4   116.18  3.000
 76H  N7   C5   C4   110.76  3.000
 76H  N6   C6   N1   119.36  3.000
 76H  N1   C6   C5   117.86  3.000
 76H  N6   C6   C5   122.78  3.000
 76H  H1   C8   N7   124.54  3.000
 76H  H1   C8   N9   122.15  3.000
 76H  N7   C8   N9   113.30  3.000
 76H  C2   N1   C6   119.28  3.000
 76H  C2   N3   C4   111.52  3.000
 76H  OXT  C    CA   112.72  3.000
 76H  OXT  C    O    125.70  3.000
 76H  CA   C    O    121.57  3.000
 76H  H3   CA   CB   110.40  3.000
 76H  H3   CA   N    105.90  3.000
 76H  CB   CA   N    110.36  3.000
 76H  H3   CA   C    107.06  3.000
 76H  N    CA   C    111.50  3.000
 76H  CB   CA   C    111.42  3.000
 76H  H6   N    H5   107.01  3.000
 76H  H6   N    H4   107.40  3.000
 76H  H5   N    H4   105.92  3.000
 76H  H6   N    CA   112.71  3.000
 76H  H5   N    CA   110.68  3.000
 76H  H4   N    CA   112.71  3.000
 76H  H7   CB   H8   106.12  3.000
 76H  H7   CB   CAM  108.09  3.000
 76H  H8   CB   CAM  112.55  3.000
 76H  H7   CB   CA   107.70  3.000
 76H  H8   CB   CA   108.80  3.000
 76H  CAM  CB   CA   113.22  3.000
 76H  H10  CAM  H9   105.62  3.000
 76H  H10  CAM  CAY  109.26  3.000
 76H  H9   CAM  CAY  110.05  3.000
 76H  H10  CAM  CB   113.13  3.000
 76H  H9   CAM  CB   107.36  3.000
 76H  CAY  CAM  CB   111.23  3.000
 76H  H11  CAY  CAN  109.62  3.000
 76H  H11  CAY  NAR  104.36  3.000
 76H  CAN  CAY  NAR  109.15  3.000
 76H  H11  CAY  CAM  109.71  3.000
 76H  CAN  CAY  CAM  114.96  3.000
 76H  NAR  CAY  CAM  108.49  3.000
 76H  H12  NAR  H32  105.15  3.000
 76H  H12  NAR  CAK  109.33  3.000
 76H  H32  NAR  CAK  108.10  3.000
 76H  H12  NAR  CAY  109.87  3.000
 76H  H32  NAR  CAY  107.73  3.000
 76H  CAK  NAR  CAY  116.08  3.000
 76H  H14  CAK  H15  108.80  3.000
 76H  H14  CAK  CAJ  111.45  3.000
 76H  H15  CAK  CAJ  111.02  3.000
 76H  H14  CAK  NAR  106.64  3.000
 76H  H15  CAK  NAR  107.82  3.000
 76H  CAJ  CAK  NAR  110.94  3.000
 76H  H16  CAJ  H17  107.08  3.000
 76H  H16  CAJ  CAA  109.92  3.000
 76H  H17  CAJ  CAA  109.80  3.000
 76H  H16  CAJ  CAK  109.77  3.000
 76H  H17  CAJ  CAK  109.65  3.000
 76H  CAA  CAJ  CAK  110.56  3.000
 76H  H19  CAA  H18  107.97  3.000
 76H  H19  CAA  H20  107.83  3.000
 76H  H18  CAA  H20  107.80  3.000
 76H  H19  CAA  CAJ  111.33  3.000
 76H  H18  CAA  CAJ  111.23  3.000
 76H  H20  CAA  CAJ  110.54  3.000
 76H  H23  CBB  CAZ  108.86  3.000
 76H  H23  CBB  OAS  109.05  3.000
 76H  CAZ  CBB  OAS  104.48  3.000
 76H  H23  CBB  CAN  109.68  3.000
 76H  OAS  CBB  CAN  112.16  3.000
 76H  CAZ  CBB  CAN  112.44  3.000
 76H  CBC  OAS  CBB  111.19  3.000
 76H  H24  CAZ  CBA  108.04  3.000
 76H  H24  CAZ  OAF  111.51  3.000
 76H  CBA  CAZ  OAF  116.03  3.000
 76H  H24  CAZ  CBB  109.01  3.000
 76H  CBA  CAZ  CBB  101.86  3.000
 76H  OAF  CAZ  CBB  109.83  3.000
 76H  H25  OAF  CAZ  108.97  3.000
 76H  H26  CBA  CBC  111.70  3.000
 76H  H26  CBA  OAG  112.28  3.000
 76H  CBC  CBA  OAG  110.76  3.000
 76H  H26  CBA  CAZ  112.80  3.000
 76H  OAG  CBA  CAZ  108.41  3.000
 76H  CBC  CBA  CAZ  100.25  3.000
 76H  H27  OAG  CBA  108.79  3.000
 76H  H28  CBC  N9   107.59  3.000
 76H  H28  CBC  CBA  111.89  3.000
 76H  N9   CBC  CBA  111.73  3.000
 76H  H28  CBC  OAS  110.04  3.000
 76H  N9   CBC  OAS  109.04  3.000
 76H  CBA  CBC  OAS  106.54  3.000
 76H  CBC  N9   C8   129.07  3.000
 76H  CBC  N9   C4   124.72  3.000
 76H  C8   N9   C4   106.19  3.000
 76H  C8   N7   C5   104.46  3.000
 76H  H29  C2   N3   116.14  3.000
 76H  H29  C2   N1   115.41  3.000
 76H  N3   C2   N1   128.44  3.000
 76H  H30  N6   H31  118.29  3.000
 76H  H30  N6   C6   121.15  3.000
 76H  H31  N6   C6   120.25  3.000
 76H  H22  CAN  H21  106.87  3.000
 76H  H22  CAN  CBB  105.41  3.000
 76H  H21  CAN  CBB  109.87  3.000
 76H  H22  CAN  CAY  108.95  3.000
 76H  H21  CAN  CAY  110.12  3.000
 76H  CBB  CAN  CAY  115.21  3.000
 76H  H2   OXT  C    111.30  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
 76H  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 76H  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 76H  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 76H  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 76H  CONST_05  N9   C8   N7   C5      0.00   0.0  0
 76H  CONST_06  C2   N1   C6   C5      0.00   0.0  0
 76H  CONST_07  C8   N9   C4   C5      0.00   0.0  0
 76H  CONST_08  C2   N3   C4   C5      0.00   0.0  0
 76H  CONST_09  C8   N7   C5   C6    180.00   0.0  0
 76H  CONST_10  N9   C4   C5   C6    180.00   0.0  0
 76H  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 76H  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 76H  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 76H  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 76H  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 76H  CONST_16  N7   C5   C4   N9      0.00   0.0  0
 76H  CONST_17  C2   N3   C4   N9    180.00   0.0  0
 76H  CONST_18  CBC  N9   C4   C5    180.00   0.0  0
 76H  CONST_19  CBC  N9   C4   N3      0.00   0.0  0
 76H  CONST_20  N7   C8   N9   CBC   180.00   0.0  0
 76H  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 76H  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 76H  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 76H  CONST_24  H1   C8   N9   C4    180.00   0.0  0
 76H  CONST_25  H29  C2   N3   C4    180.00   0.0  0
 76H  CONST_26  H31  N6   C6   C5    180.00   0.0  0
 76H  CONST_27  H30  N6   C6   C5      0.00   0.0  0
 76H  CONST_28  H2   OXT  C    O       0.00   0.0  0
 76H  Var_01    CAY  CAM  CB   CA   -171.08  30.0  3
 76H  Var_02    CAJ  CAK  NAR  CAY  -168.01  30.0  2
 76H  Var_03    CAA  CAJ  CAK  NAR   178.94  30.0  1
 76H  Var_04    H20  CAA  CAJ  CAK   179.71  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
 76H  chir_01  CA   CB   N    C    negativ
 76H  chir_02  CAY  NAR  CAN  CAM  positiv
 76H  chir_03  CBB  OAS  CAN  CAZ  positiv
 76H  chir_04  CAZ  OAF  CBB  CBA  positiv
 76H  chir_05  CBA  OAG  CAZ  CBC  positiv
 76H  chir_06  CBC  OAS  N9   CBA  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
 76H  plan-1  C4   0.020
 76H  plan-1  C5   0.020
 76H  plan-1  C6   0.020
 76H  plan-1  C8   0.020
 76H  plan-1  N1   0.020
 76H  plan-1  N3   0.020
 76H  plan-1  CBC  0.020
 76H  plan-1  N9   0.020
 76H  plan-1  N7   0.020
 76H  plan-1  C2   0.020
 76H  plan-1  N6   0.020
 76H  plan-1  H1   0.020
 76H  plan-1  H29  0.020
 76H  plan-2  C6   0.020
 76H  plan-2  N6   0.020
 76H  plan-2  H31  0.020
 76H  plan-2  H30  0.020
 76H  plan-3  C    0.020
 76H  plan-3  CA   0.020
 76H  plan-3  H2   0.020
 76H  plan-3  OXT  0.020
 76H  plan-3  O    0.020

