# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 23:15:34 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: [(2~{S},5~{S})-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]-pentyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[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
 76J  76J  '[(2~{S},5~{S})-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]-pentyl-azanium'  ligand  67  32  .  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_76J
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
 76J  C1   C  CH3   0  -0.670  20.9863  11.3182  62.6993
 76J  C2   C  CH2   0  -0.426  21.2149  12.5090  63.6210
 76J  C3   C  CH2   0  -0.443  19.9299  13.1913  64.0833
 76J  C5   C  CH2   0  -0.318  17.7666  12.9474  65.4231
 76J  C7   C  CH1   0  -0.076  16.8520  14.7675  66.9391
 76J  C8   C  CH2   0  -0.533  17.2709  15.4790  68.2287
 76J  C10  C  CH1   0  -0.262  15.7057  14.2370  69.8408
 76J  C12  C  C     0   0.598  15.6854  13.3957  71.1086
 76J  C15  C  CH2   0  -0.507  16.2720  15.7161  65.8956
 76J  C16  C  CH1   0   0.046  14.7934  15.9826  66.0935
 76J  O17  O  O2    0  -0.552  14.5330  16.6662  67.3307
 76J  C19  C  CH1   0  -0.065  12.9594  17.4483  65.7613
 76J  C21  C  CH1   0   0.016  14.1873  16.8987  65.0329
 76J  C24  C  CR15  0   0.107  15.4102  19.3620  67.2494
 76J  C26  C  CR56  0  -0.002  14.3184  21.0915  67.7757
 76J  C27  C  CR6   0   0.461  13.8131  22.3614  68.1142
 76J  C4   C  CH2   0  -0.476  19.0469  12.2924  64.9432
 76J  N6   N  NT2   1  -0.689  18.0523  14.0574  66.3812
 76J  C9   C  CH2   0  -0.468  17.1381  14.6422  69.4959
 76J  N11  N  NT3   1  -0.827  14.8226  15.4289  69.9483
 76J  O13  O  O     0  -0.413  16.3739  12.4202  71.2241
 76J  O14  O  OH1   0  -0.582  14.8438  13.8514  72.0124
 76J  C18  C  CH1   0   0.175  13.5278  17.6395  67.1753
 76J  O20  O  OH1   0  -0.654  11.9698  16.4633  65.7495
 76J  O22  O  OH1   0  -0.653  13.9370  16.1744  63.8734
 76J  N23  N  NR5   0  -0.536  14.1087  18.9535  67.3747
 76J  N25  N  N     0  -0.446  15.5750  20.6298  67.4841
 76J  N28  N  NH2   0  -0.814  14.5834  23.4447  68.2069
 76J  N29  N  N     0  -0.473  12.4988  22.4700  68.3414
 76J  C30  C  CR16  0   0.044  11.7283  21.3905  68.2416
 76J  N31  N  N     0  -0.459  12.0826  20.1543  67.9335
 76J  C32  C  CR56  0   0.491  13.3918  20.0643  67.7127
 76J  H44  H  HCH3  0   0.233  21.9342  10.9104  62.3472
 76J  H46  H  HCH3  0   0.223  20.4513  10.5089  63.1971
 76J  H45  H  HCH3  0   0.219  20.4047  11.6071  61.8217
 76J  H48  H  HCH2  0   0.219  21.7904  12.1928  64.4963
 76J  H47  H  HCH2  0   0.231  21.8308  13.2488  63.1045
 76J  H50  H  HCH2  0   0.226  20.2113  14.0956  64.6339
 76J  H49  H  HCH2  0   0.231  19.3616  13.5293  63.2106
 76J  H53  H  HCH2  0   0.294  17.1951  13.3596  64.5930
 76J  H54  H  HCH2  0   0.309  17.1363  12.2389  65.9564
 76J  H35  H  HCH1  0   0.303  16.1323  13.9683  67.1360
 76J  H55  H  HCH2  0   0.311  18.3116  15.8008  68.1377
 76J  H56  H  HCH2  0   0.276  16.7209  16.4138  68.3267
 76J  H36  H  HCH1  0   0.356  15.2688  13.6183  69.0540
 76J  H59  H  HCH2  0   0.294  16.3561  15.2856  64.8949
 76J  H60  H  HCH2  0   0.281  16.8463  16.6469  65.8799
 76J  H40  H  HCH1  0   0.274  14.2537  15.0288  66.1020
 76J  H42  H  HCH1  0   0.279  12.6097  18.3997  65.3448
 76J  H43  H  HCH1  0   0.245  14.8766  17.7338  64.8456
 76J  H63  H  HCR5  0   0.290  16.2056  18.6801  66.9927
 76J  H51  H  HCH2  0   0.273  18.7390  11.4128  64.3750
 76J  H52  H  HCH2  0   0.251  19.6095  11.9157  65.8033
 76J  H34  H  HNT2  0   0.472  18.5989  13.6679  67.1526
 76J  H33  H  HNT2  0   0.471  18.6713  14.7439  65.9437
 76J  H57  H  HCH2  0   0.290  17.7227  13.7243  69.4196
 76J  H58  H  HCH2  0   0.302  17.5629  15.2040  70.3305
 76J  H38  H  HNT3  0   0.485  13.8828  15.1845  70.2650
 76J  H39  H  HNT3  0   0.476  15.1823  16.1291  70.5992
 76J  H37  H  HNT3  0   0.485  14.7025  15.8845  69.0291
 76J  H1   H  HOH1  0   0.504  14.8432  13.2909  72.8050
 76J  H41  H  HCH1  0   0.298  12.7559  17.5125  67.9384
 76J  H61  H  HOH1  0   0.465  11.1719  16.8171  66.1559
 76J  H62  H  HOH1  0   0.467  13.7906  16.7886  63.1472
 76J  H64  H  HNH2  0   0.405  14.1870  24.3252  68.4867
 76J  H65  H  HNH2  0   0.412  15.5798  23.3854  68.0923
 76J  H66  H  HCR6  0   0.254  10.6738  21.5508  68.4386

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
 76J  C1   C2   single    1.523  0.020  1.523
 76J  C2   C3   single    1.527  0.020  1.527
 76J  C3   C4   single    1.525  0.020  1.525
 76J  C4   C5   single    1.516  0.020  1.516
 76J  O22  C21  single    1.390  0.020  1.390
 76J  C5   N6   single    1.494  0.020  1.494
 76J  C21  C16  single    1.527  0.020  1.527
 76J  C21  C19  single    1.530  0.020  1.530
 76J  C15  C16  single    1.515  0.020  1.515
 76J  C15  C7   single    1.525  0.020  1.525
 76J  N6   C7   single    1.502  0.020  1.502
 76J  C16  O17  single    1.437  0.020  1.437
 76J  C19  O20  single    1.396  0.020  1.396
 76J  C19  C18  single    1.536  0.020  1.536
 76J  C7   C8   single    1.531  0.020  1.531
 76J  N25  C24  aromatic  1.300  0.020  1.300
 76J  N25  C26  aromatic  1.370  0.020  1.370
 76J  N28  C27  single    1.332  0.020  1.332
 76J  C24  N23  aromatic  1.370  0.020  1.370
 76J  C26  C27  aromatic  1.408  0.020  1.408
 76J  C26  C32  aromatic  1.385  0.020  1.385
 76J  C27  N29  aromatic  1.338  0.020  1.338
 76J  N23  C32  aromatic  1.365  0.020  1.365
 76J  N23  C18  single    1.450  0.020  1.450
 76J  C32  N31  aromatic  1.331  0.020  1.331
 76J  N29  C30  aromatic  1.330  0.020  1.330
 76J  O17  C18  single    1.408  0.020  1.408
 76J  N31  C30  aromatic  1.322  0.020  1.322
 76J  C8   C9   single    1.524  0.020  1.524
 76J  C9   C10  single    1.528  0.020  1.528
 76J  C10  N11  single    1.487  0.020  1.487
 76J  C10  C12  single    1.522  0.020  1.522
 76J  O13  C12  double    1.200  0.020  1.200
 76J  C12  O14  single    1.316  0.020  1.316
 76J  C1   H44  single    0.970  0.020  1.090
 76J  C1   H46  single    0.970  0.020  1.090
 76J  C1   H45  single    0.970  0.020  1.090
 76J  C2   H48  single    0.970  0.020  1.090
 76J  C2   H47  single    0.970  0.020  1.090
 76J  C3   H50  single    0.970  0.020  1.090
 76J  C3   H49  single    0.970  0.020  1.090
 76J  C5   H53  single    0.970  0.020  1.090
 76J  C5   H54  single    0.970  0.020  1.090
 76J  C7   H35  single    0.970  0.020  1.090
 76J  C8   H55  single    0.970  0.020  1.090
 76J  C8   H56  single    0.970  0.020  1.090
 76J  C10  H36  single    0.970  0.020  1.090
 76J  C15  H59  single    0.970  0.020  1.090
 76J  C15  H60  single    0.970  0.020  1.090
 76J  C16  H40  single    0.970  0.020  1.090
 76J  C19  H42  single    0.970  0.020  1.090
 76J  C21  H43  single    0.970  0.020  1.090
 76J  C24  H63  single    0.930  0.020  1.080
 76J  C4   H51  single    0.970  0.020  1.090
 76J  C4   H52  single    0.970  0.020  1.090
 76J  N6   H34  single    0.890  0.020  1.040
 76J  N6   H33  single    0.890  0.020  1.040
 76J  C9   H57  single    0.970  0.020  1.090
 76J  C9   H58  single    0.970  0.020  1.090
 76J  N11  H38  single    0.890  0.020  1.040
 76J  N11  H39  single    0.890  0.020  1.040
 76J  N11  H37  single    0.890  0.020  1.040
 76J  O14  H1   single    0.850  0.020  0.980
 76J  C18  H41  single    0.970  0.020  1.090
 76J  O20  H61  single    0.850  0.020  0.980
 76J  O22  H62  single    0.850  0.020  0.980
 76J  N28  H64  single    0.860  0.020  1.020
 76J  N28  H65  single    0.860  0.020  1.020
 76J  C30  H66  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
 76J  H45  C1   H46  107.58  3.000
 76J  H45  C1   H44  107.62  3.000
 76J  H46  C1   H44  107.24  3.000
 76J  H45  C1   C2   111.07  3.000
 76J  H46  C1   C2   112.18  3.000
 76J  H44  C1   C2   110.94  3.000
 76J  H47  C2   H48  106.10  3.000
 76J  H47  C2   C3   108.37  3.000
 76J  H48  C2   C3   109.24  3.000
 76J  H47  C2   C1   109.15  3.000
 76J  H48  C2   C1   109.70  3.000
 76J  C3   C2   C1   113.98  3.000
 76J  H49  C3   H50  106.20  3.000
 76J  H49  C3   C4   109.32  3.000
 76J  H50  C3   C4   110.60  3.000
 76J  H49  C3   C2   109.48  3.000
 76J  H50  C3   C2   107.75  3.000
 76J  C4   C3   C2   113.24  3.000
 76J  H54  C5   H53  108.43  3.000
 76J  H54  C5   N6   106.28  3.000
 76J  H53  C5   N6   107.94  3.000
 76J  H54  C5   C4   111.29  3.000
 76J  H53  C5   C4   111.44  3.000
 76J  N6   C5   C4   111.25  3.000
 76J  H35  C7   N6   104.32  3.000
 76J  H35  C7   C15  109.12  3.000
 76J  N6   C7   C15  110.11  3.000
 76J  H35  C7   C8   111.60  3.000
 76J  N6   C7   C8   108.29  3.000
 76J  C15  C7   C8   113.04  3.000
 76J  H56  C8   H55  103.63  3.000
 76J  H56  C8   C9   110.64  3.000
 76J  H55  C8   C9   108.29  3.000
 76J  H56  C8   C7   109.65  3.000
 76J  H55  C8   C7   109.10  3.000
 76J  C9   C8   C7   114.91  3.000
 76J  H36  C10  N11  105.58  3.000
 76J  H36  C10  C9   111.26  3.000
 76J  N11  C10  C9   111.12  3.000
 76J  H36  C10  C12  106.36  3.000
 76J  N11  C10  C12  112.02  3.000
 76J  C9   C10  C12  110.32  3.000
 76J  O14  C12  O13  125.62  3.000
 76J  O14  C12  C10  112.91  3.000
 76J  O13  C12  C10  121.48  3.000
 76J  H60  C15  H59  106.36  3.000
 76J  H60  C15  C16  111.37  3.000
 76J  H59  C15  C16  105.31  3.000
 76J  H60  C15  C7   109.85  3.000
 76J  H59  C15  C7   110.64  3.000
 76J  C16  C15  C7   113.03  3.000
 76J  H40  C16  C21  109.39  3.000
 76J  H40  C16  O17  108.54  3.000
 76J  C21  C16  O17  103.93  3.000
 76J  H40  C16  C15  109.17  3.000
 76J  O17  C16  C15  111.89  3.000
 76J  C21  C16  C15  113.71  3.000
 76J  C18  O17  C16  111.29  3.000
 76J  H42  C19  O20  112.53  3.000
 76J  H42  C19  C18  111.10  3.000
 76J  O20  C19  C18  110.96  3.000
 76J  H42  C19  C21  112.78  3.000
 76J  C18  C19  C21  100.72  3.000
 76J  O20  C19  C21  108.14  3.000
 76J  H43  C21  O22  111.52  3.000
 76J  H43  C21  C19  108.15  3.000
 76J  O22  C21  C19  116.10  3.000
 76J  H43  C21  C16  108.99  3.000
 76J  C19  C21  C16  101.74  3.000
 76J  O22  C21  C16  109.78  3.000
 76J  H63  C24  N25  124.48  3.000
 76J  H63  C24  N23  122.27  3.000
 76J  N25  C24  N23  113.25  3.000
 76J  C32  C26  N25  110.73  3.000
 76J  C32  C26  C27  116.09  3.000
 76J  N25  C26  C27  133.18  3.000
 76J  N29  C27  N28  119.34  3.000
 76J  N29  C27  C26  117.81  3.000
 76J  N28  C27  C26  122.85  3.000
 76J  H52  C4   H51  106.06  3.000
 76J  H52  C4   C5   109.51  3.000
 76J  H51  C4   C5   105.94  3.000
 76J  H52  C4   C3   110.38  3.000
 76J  H51  C4   C3   110.16  3.000
 76J  C5   C4   C3   114.37  3.000
 76J  H33  N6   H34  104.77  3.000
 76J  H33  N6   C7   108.98  3.000
 76J  H34  N6   C7   109.09  3.000
 76J  H33  N6   C5   109.89  3.000
 76J  H34  N6   C5   107.64  3.000
 76J  C7   N6   C5   115.89  3.000
 76J  H58  C9   H57  106.13  3.000
 76J  H58  C9   C10  109.18  3.000
 76J  H57  C9   C10  107.16  3.000
 76J  H58  C9   C8   108.60  3.000
 76J  H57  C9   C8   110.92  3.000
 76J  C10  C9   C8   114.51  3.000
 76J  H37  N11  H39  107.80  3.000
 76J  H37  N11  H38  105.93  3.000
 76J  H39  N11  H38  106.89  3.000
 76J  H37  N11  C10  110.99  3.000
 76J  H39  N11  C10  112.73  3.000
 76J  H38  N11  C10  112.15  3.000
 76J  H1   O14  C12  111.17  3.000
 76J  H41  C18  N23  106.99  3.000
 76J  H41  C18  C19  111.53  3.000
 76J  N23  C18  C19  112.80  3.000
 76J  H41  C18  O17  110.30  3.000
 76J  N23  C18  O17  108.97  3.000
 76J  C19  C18  O17  106.25  3.000
 76J  H61  O20  C19  108.94  3.000
 76J  H62  O22  C21  108.93  3.000
 76J  C32  N23  C18  124.13  3.000
 76J  C18  N23  C24  129.65  3.000
 76J  C32  N23  C24  106.21  3.000
 76J  C26  N25  C24  104.53  3.000
 76J  H65  N28  H64  118.33  3.000
 76J  H65  N28  C27  121.16  3.000
 76J  H64  N28  C27  120.22  3.000
 76J  C30  N29  C27  119.37  3.000
 76J  H66  C30  N31  116.16  3.000
 76J  H66  C30  N29  115.44  3.000
 76J  N31  C30  N29  128.39  3.000
 76J  C32  N31  C30  111.44  3.000
 76J  N31  C32  N23  127.81  3.000
 76J  N31  C32  C26  126.91  3.000
 76J  N23  C32  C26  105.28  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
 76J  CONST_01  C27  C26  N25  C24   180.00   0.0  0
 76J  CONST_02  C32  C26  N25  C24     0.00   0.0  0
 76J  CONST_03  C26  C32  N23  C24     0.00   0.0  0
 76J  CONST_04  N31  C32  N23  C24   180.00   0.0  0
 76J  CONST_05  N23  C24  N25  C26     0.00   0.0  0
 76J  CONST_06  C30  N29  C27  C26     0.00   0.0  0
 76J  CONST_07  C30  N31  C32  C26     0.00   0.0  0
 76J  CONST_08  N23  C32  C26  C27   180.00   0.0  0
 76J  CONST_09  N31  C32  C26  C27     0.00   0.0  0
 76J  CONST_10  N31  C30  N29  C27     0.00   0.0  0
 76J  CONST_11  N25  C26  C32  N23     0.00   0.0  0
 76J  CONST_12  C30  N31  C32  N23   180.00   0.0  0
 76J  CONST_13  C32  N23  C24  N25     0.00   0.0  0
 76J  CONST_14  N29  C27  C26  N25   180.00   0.0  0
 76J  CONST_15  N31  C32  C26  N25   180.00   0.0  0
 76J  CONST_16  C32  C26  C27  N29     0.00   0.0  0
 76J  CONST_17  C32  N31  C30  N29     0.00   0.0  0
 76J  CONST_18  C18  N23  C32  C26   180.00   0.0  0
 76J  CONST_19  N25  C24  N23  C18   180.00   0.0  0
 76J  CONST_20  N31  C32  N23  C18     0.00   0.0  0
 76J  CONST_21  N28  C27  C26  N25     0.00   0.0  0
 76J  CONST_22  C32  C26  C27  N28   180.00   0.0  0
 76J  CONST_23  C30  N29  C27  N28   180.00   0.0  0
 76J  CONST_24  H63  C24  N25  C26   180.00   0.0  0
 76J  CONST_25  H66  C30  N29  C27   180.00   0.0  0
 76J  CONST_26  H64  N28  C27  C26   180.00   0.0  0
 76J  CONST_27  H65  N28  C27  C26     0.00   0.0  0
 76J  CONST_28  H1   O14  C12  C10   180.00   0.0  0
 76J  Var_01    C4   C3   C2   C1     64.09  30.0  3
 76J  Var_02    C5   C4   C3   C2    179.68  30.0  3
 76J  Var_03    N6   C5   C4   C3    -66.64  30.0  3
 76J  Var_04    C4   C5   N6   C7   -179.14  30.0  1
 76J  Var_05    C10  C9   C8   C7    -63.80  30.0  3
 76J  Var_06    H44  C1   C2   C3    176.25  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
 76J  chir_01  C7   C15  N6   C8   negativ
 76J  chir_02  C10  N11  C9   C12  negativ
 76J  chir_03  C16  C21  C15  O17  negativ
 76J  chir_04  C19  O20  C21  C18  positiv
 76J  chir_05  C21  O22  C16  C19  positiv
 76J  chir_06  C18  O17  N23  C19  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
 76J  plan-1  C24  0.020
 76J  plan-1  C26  0.020
 76J  plan-1  C27  0.020
 76J  plan-1  C18  0.020
 76J  plan-1  N23  0.020
 76J  plan-1  N25  0.020
 76J  plan-1  N28  0.020
 76J  plan-1  N29  0.020
 76J  plan-1  C30  0.020
 76J  plan-1  N31  0.020
 76J  plan-1  C32  0.020
 76J  plan-1  H63  0.020
 76J  plan-1  H66  0.020
 76J  plan-2  C27  0.020
 76J  plan-2  N28  0.020
 76J  plan-2  H64  0.020
 76J  plan-2  H65  0.020
 76J  plan-3  C10  0.020
 76J  plan-3  C12  0.020
 76J  plan-3  O13  0.020
 76J  plan-3  O14  0.020
 76J  plan-3  H1   0.020

