# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 15:42:53 2020
#   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  60  30  .  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_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   0.496   3.1358  -0.1897   0.3209
 76H  C5   C  CR56   0  -0.011   3.0301  -1.4820   0.8061
 76H  C6   C  CR6    0   0.461   4.0681  -1.9196   1.6492
 76H  C8   C  CR15   0   0.117   1.3233  -1.1834  -0.3973
 76H  N1   N  N      0  -0.474   5.0579  -1.0609   1.9193
 76H  N3   N  N      0  -0.458   4.1128   0.6750   0.5789
 76H  C    C  C      0   0.473  -2.8038  -3.7951   0.0139
 76H  CA   C  CH1    0  -0.266  -3.5100  -2.4159   0.1646
 76H  N    N  NT3    1  -0.793  -4.7376  -2.4557  -0.6778
 76H  CB   C  CH2    0  -0.472  -2.6254  -1.2363  -0.1787
 76H  CAM  C  CH2    0  -0.451  -3.2902   0.1229   0.0326
 76H  CAY  C  CH1    0  -0.103  -2.2538   1.2416   0.0045
 76H  NAR  N  NT2    1  -0.685  -2.8681   2.5346   0.4624
 76H  CAK  C  CH2    0  -0.290  -3.2386   2.6045   1.9064
 76H  CAJ  C  CH2    0  -0.465  -3.6690   4.0061   2.2896
 76H  CAA  C  CH3    0  -0.667  -4.0259   4.0725   3.7678
 76H  CBB  C  CH1    0  -0.022  -0.3828   2.2960  -1.4105
 76H  OAS  O  O2     0  -0.488   0.5738   1.8028  -0.4707
 76H  CAZ  C  CH1    0  -0.009   0.3086   2.2441  -2.7680
 76H  OAF  O  OH1    0  -0.667   1.0630   3.4141  -2.9337
 76H  CBA  C  CH1    0  -0.065   1.2228   1.0287  -2.5838
 76H  OAG  O  OH1    0  -0.651   2.3417   1.0052  -3.4162
 76H  CBC  C  CH1    0   0.215   1.6631   1.2105  -1.1309
 76H  N9   N  NR5    0  -0.546   2.0318  -0.0102  -0.4665
 76H  N7   N  N      0  -0.437   1.8875  -2.0848   0.3455
 76H  C2   C  CR16   0   0.048   5.0242   0.1563   1.3841
 76H  N6   N  NH2    0  -0.815   4.0928  -3.1377   2.1909
 76H  H1   H  HCR5   0   0.280   0.3934  -1.3239  -0.9276
 76H  H3   H  HCH1   0   0.310  -3.8612  -2.3301   1.1963
 76H  H5   H  HNT3   0   0.467  -5.5159  -1.9174  -0.3035
 76H  H8   H  HCH2   0   0.273  -1.7515  -1.3130   0.4692
 76H  H7   H  HCH2   0   0.258  -2.2724  -1.3467  -1.2079
 76H  H9   H  HCH2   0   0.261  -4.0552   0.3133  -0.7265
 76H  H10  H  HCH2   0   0.276  -3.7948   0.1104   1.0012
 76H  H11  H  HCH1   0   0.306  -1.4734   1.0229   0.7359
 76H  H32  H  HNT2   0   0.469  -2.2139   3.2967   0.2730
 76H  H15  H  HCH2   0   0.294  -4.0380   1.8881   2.0773
 76H  H14  H  HCH2   0   0.291  -2.3616   2.2873   2.4689
 76H  H17  H  HCH2   0   0.249  -2.8613   4.7098   2.0722
 76H  H16  H  HCH2   0   0.251  -4.5280   4.3069   1.6850
 76H  H20  H  HCH3   0   0.232  -4.8480   3.3981   4.0099
 76H  H18  H  HCH3   0   0.232  -3.1749   3.7999   4.3929
 76H  H19  H  HCH3   0   0.246  -4.3310   5.0810   4.0420
 76H  H23  H  HCH1   0   0.268  -0.6092   3.3365  -1.1534
 76H  H24  H  HCH1   0   0.258  -0.4096   2.1002  -3.5851
 76H  H25  H  HOH1   0   0.451   1.7685   3.2295  -3.5655
 76H  H26  H  HCH1   0   0.254   0.6250   0.1151  -2.6886
 76H  H27  H  HOH1   0   0.472   2.0964   0.6074  -4.2578
 76H  H28  H  HCH1   0   0.268   2.5445   1.8577  -1.0843
 76H  H29  H  HCR6   0   0.254   5.8550   0.8033   1.6451
 76H  H31  H  HNH2   0   0.412   3.4079  -3.8290   1.9400
 76H  H30  H  HNH2   0   0.404   4.8833  -3.4301   2.7390
 76H  H6   H  HNT3   0   0.460  -4.5695  -2.1380  -1.6320
 76H  H12  H  HNT2   0   0.464  -3.6886   2.7468  -0.1098
 76H  OXT  O  OC    -1  -0.558  -1.6200  -3.8393   0.3605
 76H  O    O  O      0  -0.594  -3.5322  -4.7132  -0.4123
 76H  CAN  C  CH2    0  -0.495  -1.6472   1.4441  -1.3791
 76H  H4   H  HNT3   0   0.456  -5.0026  -3.4494  -0.7399
 76H  H21  H  HCH2   0   0.270  -1.4266   0.4596  -1.7956
 76H  H22  H  HCH2   0   0.284  -2.3938   1.8847  -2.0465

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    1.515  0.020  1.515
 76H  CAK  NAR  single    1.492  0.020  1.492
 76H  N6   C6   single    1.333  0.020  1.333
 76H  OAF  CAZ  single    1.402  0.020  1.402
 76H  NAR  CAY  single    1.503  0.020  1.503
 76H  CAZ  CBB  single    1.524  0.020  1.524
 76H  CAZ  CBA  single    1.532  0.020  1.532
 76H  N7   C5   aromatic  1.371  0.020  1.371
 76H  N7   C8   aromatic  1.297  0.020  1.297
 76H  CAN  CAY  single    1.524  0.020  1.524
 76H  CAN  CBB  single    1.525  0.020  1.525
 76H  C6   C5   aromatic  1.407  0.020  1.407
 76H  C6   N1   aromatic  1.338  0.020  1.338
 76H  C5   C4   aromatic  1.384  0.020  1.384
 76H  C8   N9   aromatic  1.372  0.020  1.372
 76H  N1   C2   aromatic  1.330  0.020  1.330
 76H  CAY  CAM  single    1.525  0.020  1.525
 76H  CBB  OAS  single    1.429  0.020  1.429
 76H  CBA  CBC  single    1.529  0.020  1.529
 76H  CBA  OAG  single    1.395  0.020  1.395
 76H  C4   N9   aromatic  1.368  0.020  1.368
 76H  C4   N3   aromatic  1.330  0.020  1.330
 76H  N9   CBC  single    1.438  0.020  1.438
 76H  C2   N3   aromatic  1.322  0.020  1.322
 76H  CBC  OAS  single    1.405  0.020  1.405
 76H  CAM  CB   single    1.528  0.020  1.528
 76H  CB   CA   single    1.514  0.020  1.514
 76H  CA   N    single    1.489  0.020  1.489
 76H  CA   C    single    1.557  0.020  1.557
 76H  C    O    deloc     1.247  0.020  1.247
 76H  C    OXT  deloc     1.234  0.020  1.234
 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  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   128.26  3.000
 76H  N3   C4   C5   126.51  3.000
 76H  N9   C4   C5   105.22  3.000
 76H  N7   C5   C6   132.78  3.000
 76H  C6   C5   C4   116.36  3.000
 76H  N7   C5   C4   110.86  3.000
 76H  N6   C6   N1   119.39  3.000
 76H  N1   C6   C5   117.84  3.000
 76H  N6   C6   C5   122.77  3.000
 76H  H1   C8   N7   124.43  3.000
 76H  H1   C8   N9   122.09  3.000
 76H  N7   C8   N9   113.48  3.000
 76H  C2   N1   C6   119.17  3.000
 76H  C2   N3   C4   111.68  3.000
 76H  OXT  C    CA   116.07  3.000
 76H  OXT  C    O    129.04  3.000
 76H  CA   C    O    114.86  3.000
 76H  H3   CA   CB   109.91  3.000
 76H  H3   CA   N    105.73  3.000
 76H  CB   CA   N    111.97  3.000
 76H  H3   CA   C    107.85  3.000
 76H  N    CA   C    107.19  3.000
 76H  CB   CA   C    113.79  3.000
 76H  H6   N    H5   107.79  3.000
 76H  H6   N    H4   106.65  3.000
 76H  H5   N    H4   109.61  3.000
 76H  H6   N    CA   112.65  3.000
 76H  H5   N    CA   114.09  3.000
 76H  H4   N    CA   105.77  3.000
 76H  H7   CB   H8   107.06  3.000
 76H  H7   CB   CAM  111.13  3.000
 76H  H8   CB   CAM  109.22  3.000
 76H  H7   CB   CA   108.86  3.000
 76H  H8   CB   CA   106.18  3.000
 76H  CAM  CB   CA   114.06  3.000
 76H  H10  CAM  H9   107.11  3.000
 76H  H10  CAM  CAY  109.79  3.000
 76H  H9   CAM  CAY  109.55  3.000
 76H  H10  CAM  CB   108.27  3.000
 76H  H9   CAM  CB   111.29  3.000
 76H  CAY  CAM  CB   110.75  3.000
 76H  H11  CAY  CAN  110.51  3.000
 76H  H11  CAY  NAR  105.09  3.000
 76H  CAN  CAY  NAR  108.96  3.000
 76H  H11  CAY  CAM  109.06  3.000
 76H  CAN  CAY  CAM  112.61  3.000
 76H  NAR  CAY  CAM  110.35  3.000
 76H  H12  NAR  H32  104.78  3.000
 76H  H12  NAR  CAK  109.42  3.000
 76H  H32  NAR  CAK  107.65  3.000
 76H  H12  NAR  CAY  109.63  3.000
 76H  H32  NAR  CAY  108.87  3.000
 76H  CAK  NAR  CAY  115.89  3.000
 76H  H14  CAK  H15  108.60  3.000
 76H  H14  CAK  CAJ  111.56  3.000
 76H  H15  CAK  CAJ  111.16  3.000
 76H  H14  CAK  NAR  106.63  3.000
 76H  H15  CAK  NAR  107.69  3.000
 76H  CAJ  CAK  NAR  111.01  3.000
 76H  H16  CAJ  H17  107.07  3.000
 76H  H16  CAJ  CAA  109.94  3.000
 76H  H17  CAJ  CAA  109.78  3.000
 76H  H16  CAJ  CAK  109.75  3.000
 76H  H17  CAJ  CAK  109.59  3.000
 76H  CAA  CAJ  CAK  110.64  3.000
 76H  H19  CAA  H18  107.81  3.000
 76H  H19  CAA  H20  107.80  3.000
 76H  H18  CAA  H20  107.84  3.000
 76H  H19  CAA  CAJ  110.53  3.000
 76H  H18  CAA  CAJ  111.27  3.000
 76H  H20  CAA  CAJ  111.43  3.000
 76H  H23  CBB  CAZ  109.58  3.000
 76H  H23  CBB  OAS  108.17  3.000
 76H  CAZ  CBB  OAS  105.68  3.000
 76H  H23  CBB  CAN  110.76  3.000
 76H  OAS  CBB  CAN  110.42  3.000
 76H  CAZ  CBB  CAN  112.05  3.000
 76H  CBC  OAS  CBB  110.83  3.000
 76H  H24  CAZ  CBA  112.09  3.000
 76H  H24  CAZ  OAF  111.94  3.000
 76H  CBA  CAZ  OAF  110.81  3.000
 76H  H24  CAZ  CBB  111.76  3.000
 76H  CBA  CAZ  CBB  100.98  3.000
 76H  OAF  CAZ  CBB  108.72  3.000
 76H  H25  OAF  CAZ  108.13  3.000
 76H  H26  CBA  CBC  110.29  3.000
 76H  H26  CBA  OAG  111.48  3.000
 76H  CBC  CBA  OAG  109.76  3.000
 76H  H26  CBA  CAZ  108.91  3.000
 76H  OAG  CBA  CAZ  114.85  3.000
 76H  CBC  CBA  CAZ  101.06  3.000
 76H  H27  OAG  CBA  108.93  3.000
 76H  H28  CBC  N9   106.02  3.000
 76H  H28  CBC  CBA  110.04  3.000
 76H  N9   CBC  CBA  114.33  3.000
 76H  H28  CBC  OAS  110.80  3.000
 76H  N9   CBC  OAS  109.86  3.000
 76H  CBA  CBC  OAS  105.87  3.000
 76H  CBC  N9   C8   128.08  3.000
 76H  CBC  N9   C4   125.75  3.000
 76H  C8   N9   C4   106.00  3.000
 76H  C8   N7   C5   104.43  3.000
 76H  H29  C2   N3   116.13  3.000
 76H  H29  C2   N1   115.44  3.000
 76H  N3   C2   N1   128.43  3.000
 76H  H30  N6   H31  118.16  3.000
 76H  H30  N6   C6   120.11  3.000
 76H  H31  N6   C6   120.96  3.000
 76H  H22  CAN  H21  105.58  3.000
 76H  H22  CAN  CBB  109.16  3.000
 76H  H21  CAN  CBB  109.17  3.000
 76H  H22  CAN  CAY  109.61  3.000
 76H  H21  CAN  CAY  107.88  3.000
 76H  CBB  CAN  CAY  115.01  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      0.00   0.0  0
 76H  CONST_27  H30  N6   C6   C5    180.00   0.0  0
 76H  Var_01    CAY  CAM  CB   CA    165.93  30.0  1
 76H  Var_02    CAJ  CAK  NAR  CAY   172.30  30.0  1
 76H  Var_03    CAA  CAJ  CAK  NAR  -179.20  30.0  1
 76H  Var_04    H20  CAA  CAJ  CAK   -60.38  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  OXT  0.020
 76H  plan-3  O    0.020

