# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 18:24:06 2021
#   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]-(3-oxidanylpropyl)azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[C@H](CC[C@@H]([NH3+])C(O)=O)[NH2+]CCCO)[C@@H](O)[C@H]3O
#
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
 76K  76K  '[(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]-(3-oxidanylpropyl)azanium'  ligand  62  31  .  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_76K
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
 76K  C2   C  CR6   0   0.459  17.8508  13.0241  37.1357
 76K  C6   C  CR56  0   0.487  17.4009  12.9582  34.8102
 76K  C8   C  CR15  0   0.101  15.8759  14.5164  34.6514
 76K  C10  C  CR56  0  -0.000  17.1229  13.5288  36.0414
 76K  C11  C  CH1   0   0.162  16.5384  13.3087  32.5007
 76K  C13  C  CH1   0   0.034  14.6991  13.9908  31.2353
 76K  C14  C  CH2   0  -0.494  13.6474  15.0757  31.3563
 76K  C15  C  CH1   0  -0.077  13.8314  16.2530  30.4044
 76K  C16  C  CH2   0  -0.497  15.1419  17.0248  30.5861
 76K  C25  C  CH2   0  -0.496  10.3079  17.8140  30.3488
 76K  C26  C  CH2   0  -0.161   8.8916  17.2939  30.1983
 76K  C28  C  CH1   0   0.019  14.3204  12.7075  31.9730
 76K  N1   N  NH2   0  -0.815  17.6833  13.4679  38.3820
 76K  N3   N  N     0  -0.473  18.7361  12.0489  36.9009
 76K  C4   C  CR16  0   0.042  18.8942  11.5965  35.6600
 76K  N5   N  N     0  -0.458  18.2746  11.9859  34.5587
 76K  N7   N  NR5   0  -0.535  16.5910  13.6041  33.9231
 76K  N9   N  N     0  -0.448  16.1668  14.5025  35.9192
 76K  O12  O  O2    0  -0.522  15.9372  14.3833  31.8342
 76K  C17  C  CH2   0  -0.467  16.2103  16.5766  29.5895
 76K  C18  C  CH1   0  -0.261  17.5848  17.1482  29.9126
 76K  N19  N  NT3   1  -0.789  18.1780  16.4468  31.0852
 76K  C20  C  C     0   0.595  18.5201  17.1075  28.7126
 76K  O21  O  OH1   0  -0.583  19.7136  16.6407  29.0146
 76K  O22  O  O     0  -0.411  18.1755  17.4957  27.6313
 76K  N23  N  NT2   1  -0.687  12.6937  17.2196  30.5798
 76K  O27  O  OH1   0  -0.671   8.7804  16.6252  28.9623
 76K  O29  O  OH1   0  -0.654  13.4181  11.9702  31.2138
 76K  C30  C  CH1   0  -0.067  15.6906  12.0644  32.1960
 76K  O31  O  OH1   0  -0.655  16.0928  11.4655  30.9991
 76K  H46  H  HCR5  0   0.295  15.1558  15.1783  34.1960
 76K  H32  H  HCH1  0   0.286  17.5715  13.1773  32.1650
 76K  H33  H  HCH1  0   0.259  14.8657  13.7539  30.1768
 76K  H47  H  HCH2  0   0.269  13.5965  15.4350  32.3892
 76K  H48  H  HCH2  0   0.293  12.6961  14.5868  31.1391
 76K  H34  H  HCH1  0   0.316  13.7401  15.9091  29.3712
 76K  H49  H  HCH2  0   0.262  15.4598  16.9445  31.6277
 76K  H50  H  HCH2  0   0.291  14.9742  18.0911  30.4133
 76K  H54  H  HCH2  0   0.292  11.1051  15.9679  31.1271
 76K  H53  H  HCH2  0   0.298  11.3484  16.1644  29.3854
 76K  H55  H  HCH2  0   0.257  10.5274  18.5292  29.5511
 76K  H56  H  HCH2  0   0.261  10.3657  18.3583  31.2948
 76K  H57  H  HCH2  0   0.220   8.2012  18.1429  30.2649
 76K  H58  H  HCH2  0   0.206   8.6607  16.6280  31.0393
 76K  H41  H  HCH1  0   0.242  13.9011  12.9713  32.9546
 76K  H43  H  HNH2  0   0.404  18.2829  13.1376  39.1188
 76K  H44  H  HNH2  0   0.412  17.0824  14.2498  38.5760
 76K  H45  H  HCR6  0   0.254  19.6274  10.8059  35.5426
 76K  H52  H  HCH2  0   0.304  15.9213  16.9366  28.6027
 76K  H51  H  HCH2  0   0.283  16.2850  15.4904  29.5086
 76K  H35  H  HCH1  0   0.366  17.4961  18.1976  30.2065
 76K  H36  H  HNT3  0   0.476  17.5259  16.4386  31.8697
 76K  H37  H  HNT3  0   0.475  18.4130  15.4744  30.8826
 76K  H38  H  HNT3  0   0.490  19.0268  16.9018  31.4252
 76K  H1   H  HOH1  0   0.504  20.2985  16.6450  28.2399
 76K  H39  H  HNT2  0   0.467  12.7342  17.6353  31.5135
 76K  H40  H  HNT2  0   0.471  12.8481  17.9966  29.9339
 76K  H59  H  HOH1  0   0.459   7.9173  16.2036  28.9237
 76K  H60  H  HOH1  0   0.466  13.0047  11.3082  31.7764
 76K  H42  H  HCH1  0   0.273  15.6991  11.3613  33.0363
 76K  H61  H  HOH1  0   0.463  16.9361  11.0238  31.1422
 76K  C24  C  CH2   0  -0.293  11.3222  16.6858  30.3400

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
 76K  O22  C20  double    1.199  0.020  1.199
 76K  C20  O21  single    1.317  0.020  1.317
 76K  C20  C18  single    1.522  0.020  1.522
 76K  C17  C18  single    1.523  0.020  1.523
 76K  C17  C16  single    1.528  0.020  1.528
 76K  O27  C26  single    1.410  0.020  1.410
 76K  C18  N19  single    1.490  0.020  1.490
 76K  C15  C16  single    1.532  0.020  1.532
 76K  C15  N23  single    1.503  0.020  1.503
 76K  C15  C14  single    1.525  0.020  1.525
 76K  C25  C26  single    1.516  0.020  1.516
 76K  C25  C24  single    1.517  0.020  1.517
 76K  N23  C24  single    1.491  0.020  1.491
 76K  O29  C28  single    1.391  0.020  1.391
 76K  O31  C30  single    1.397  0.020  1.397
 76K  C13  C14  single    1.516  0.020  1.516
 76K  C13  O12  single    1.430  0.020  1.430
 76K  C13  C28  single    1.528  0.020  1.528
 76K  O12  C11  single    1.400  0.020  1.400
 76K  C28  C30  single    1.530  0.020  1.530
 76K  C30  C11  single    1.536  0.020  1.536
 76K  C11  N7   single    1.454  0.020  1.454
 76K  N7   C8   aromatic  1.369  0.020  1.369
 76K  N7   C6   aromatic  1.364  0.020  1.364
 76K  C8   N9   aromatic  1.301  0.020  1.301
 76K  N5   C6   aromatic  1.331  0.020  1.331
 76K  N5   C4   aromatic  1.322  0.020  1.322
 76K  C6   C10  aromatic  1.385  0.020  1.385
 76K  N9   C10  aromatic  1.370  0.020  1.370
 76K  C10  C2   aromatic  1.408  0.020  1.408
 76K  C4   N3   aromatic  1.330  0.020  1.330
 76K  N3   C2   aromatic  1.338  0.020  1.338
 76K  C2   N1   single    1.334  0.020  1.334
 76K  C8   H46  single    0.930  0.020  1.080
 76K  C11  H32  single    0.970  0.020  1.090
 76K  C13  H33  single    0.970  0.020  1.090
 76K  C14  H47  single    0.970  0.020  1.090
 76K  C14  H48  single    0.970  0.020  1.090
 76K  C15  H34  single    0.970  0.020  1.090
 76K  C16  H49  single    0.970  0.020  1.090
 76K  C16  H50  single    0.970  0.020  1.090
 76K  C24  H54  single    0.970  0.020  1.090
 76K  C24  H53  single    0.970  0.020  1.090
 76K  C25  H55  single    0.970  0.020  1.090
 76K  C25  H56  single    0.970  0.020  1.090
 76K  C26  H57  single    0.970  0.020  1.090
 76K  C26  H58  single    0.970  0.020  1.090
 76K  C28  H41  single    0.970  0.020  1.090
 76K  N1   H43  single    0.860  0.020  1.020
 76K  N1   H44  single    0.860  0.020  1.020
 76K  C4   H45  single    0.930  0.020  1.080
 76K  C17  H52  single    0.970  0.020  1.090
 76K  C17  H51  single    0.970  0.020  1.090
 76K  C18  H35  single    0.970  0.020  1.090
 76K  N19  H36  single    0.890  0.020  1.040
 76K  N19  H37  single    0.890  0.020  1.040
 76K  N19  H38  single    0.890  0.020  1.040
 76K  O21  H1   single    0.850  0.020  0.980
 76K  N23  H39  single    0.890  0.020  1.040
 76K  N23  H40  single    0.890  0.020  1.040
 76K  O27  H59  single    0.850  0.020  0.980
 76K  O29  H60  single    0.850  0.020  0.980
 76K  C30  H42  single    0.970  0.020  1.090
 76K  O31  H61  single    0.850  0.020  0.980

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
 76K  N3   C2   N1   119.32  3.000
 76K  N1   C2   C10  122.84  3.000
 76K  N3   C2   C10  117.84  3.000
 76K  N7   C6   N5   127.79  3.000
 76K  N5   C6   C10  126.91  3.000
 76K  N7   C6   C10  105.30  3.000
 76K  H46  C8   N9   124.55  3.000
 76K  H46  C8   N7   122.20  3.000
 76K  N9   C8   N7   113.24  3.000
 76K  N9   C10  C6   110.71  3.000
 76K  N9   C10  C2   133.22  3.000
 76K  C6   C10  C2   116.07  3.000
 76K  H32  C11  C30  111.28  3.000
 76K  H32  C11  O12  110.58  3.000
 76K  C30  C11  O12  106.87  3.000
 76K  H32  C11  N7   106.89  3.000
 76K  C30  C11  N7   112.25  3.000
 76K  O12  C11  N7   108.98  3.000
 76K  H33  C13  O12  109.37  3.000
 76K  H33  C13  C28  108.78  3.000
 76K  O12  C13  C28  104.06  3.000
 76K  H33  C13  C14  109.68  3.000
 76K  C28  C13  C14  113.00  3.000
 76K  O12  C13  C14  111.76  3.000
 76K  H48  C14  H47  107.11  3.000
 76K  H48  C14  C15  109.07  3.000
 76K  H47  C14  C15  109.95  3.000
 76K  H48  C14  C13  105.56  3.000
 76K  H47  C14  C13  110.03  3.000
 76K  C15  C14  C13  114.77  3.000
 76K  H34  C15  N23  104.45  3.000
 76K  H34  C15  C16  110.02  3.000
 76K  N23  C15  C16  108.04  3.000
 76K  H34  C15  C14  109.70  3.000
 76K  N23  C15  C14  109.41  3.000
 76K  C16  C15  C14  114.71  3.000
 76K  H50  C16  H49  105.50  3.000
 76K  H50  C16  C17  106.87  3.000
 76K  H49  C16  C17  113.39  3.000
 76K  H50  C16  C15  109.97  3.000
 76K  H49  C16  C15  108.98  3.000
 76K  C17  C16  C15  111.90  3.000
 76K  H56  C25  H55  107.16  3.000
 76K  H56  C25  C26  107.82  3.000
 76K  H55  C25  C26  109.84  3.000
 76K  H56  C25  C24  109.88  3.000
 76K  H55  C25  C24  110.36  3.000
 76K  C26  C25  C24  111.65  3.000
 76K  H58  C26  H57  106.91  3.000
 76K  H58  C26  O27  111.56  3.000
 76K  H57  C26  O27  111.78  3.000
 76K  H58  C26  C25  109.18  3.000
 76K  H57  C26  C25  108.46  3.000
 76K  O27  C26  C25  108.87  3.000
 76K  H41  C28  C30  108.19  3.000
 76K  H41  C28  O29  111.54  3.000
 76K  C30  C28  O29  115.96  3.000
 76K  H41  C28  C13  108.90  3.000
 76K  C30  C28  C13  101.62  3.000
 76K  O29  C28  C13  110.03  3.000
 76K  H44  N1   H43  118.07  3.000
 76K  H44  N1   C2   120.95  3.000
 76K  H43  N1   C2   120.04  3.000
 76K  C4   N3   C2   119.36  3.000
 76K  H45  C4   N5   116.19  3.000
 76K  H45  C4   N3   115.41  3.000
 76K  N5   C4   N3   128.40  3.000
 76K  C4   N5   C6   111.43  3.000
 76K  C11  N7   C8   129.58  3.000
 76K  C8   N7   C6   106.25  3.000
 76K  C11  N7   C6   124.17  3.000
 76K  C10  N9   C8   104.51  3.000
 76K  C13  O12  C11  111.12  3.000
 76K  H51  C17  H52  106.25  3.000
 76K  H51  C17  C18  109.10  3.000
 76K  H52  C17  C18  107.91  3.000
 76K  H51  C17  C16  112.83  3.000
 76K  H52  C17  C16  107.96  3.000
 76K  C18  C17  C16  112.49  3.000
 76K  H35  C18  C20  106.70  3.000
 76K  H35  C18  N19  105.82  3.000
 76K  C20  C18  N19  111.31  3.000
 76K  H35  C18  C17  110.12  3.000
 76K  N19  C18  C17  110.47  3.000
 76K  C20  C18  C17  112.16  3.000
 76K  H38  N19  H37  107.41  3.000
 76K  H38  N19  H36  106.19  3.000
 76K  H37  N19  H36  106.99  3.000
 76K  H38  N19  C18  112.54  3.000
 76K  H37  N19  C18  112.58  3.000
 76K  H36  N19  C18  110.77  3.000
 76K  O22  C20  O21  125.59  3.000
 76K  O21  C20  C18  112.68  3.000
 76K  O22  C20  C18  121.71  3.000
 76K  H1   O21  C20  111.19  3.000
 76K  H40  N23  H39  105.18  3.000
 76K  H40  N23  C24  108.03  3.000
 76K  H39  N23  C24  109.19  3.000
 76K  H40  N23  C15  107.50  3.000
 76K  H39  N23  C15  109.75  3.000
 76K  C24  N23  C15  116.56  3.000
 76K  H59  O27  C26  108.31  3.000
 76K  H60  O29  C28  108.93  3.000
 76K  H42  C30  O31  112.31  3.000
 76K  H42  C30  C28  112.86  3.000
 76K  O31  C30  C28  108.24  3.000
 76K  H42  C30  C11  111.31  3.000
 76K  C28  C30  C11  100.53  3.000
 76K  O31  C30  C11  110.99  3.000
 76K  H61  O31  C30  108.75  3.000
 76K  H53  C24  H54  108.88  3.000
 76K  H53  C24  N23  106.89  3.000
 76K  H54  C24  N23  107.68  3.000
 76K  H53  C24  C25  112.18  3.000
 76K  H54  C24  C25  110.69  3.000
 76K  N23  C24  C25  110.35  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
 76K  CONST_01  N7   C6   C10  C2    180.00   0.0  0
 76K  CONST_02  N5   C6   C10  C2      0.00   0.0  0
 76K  CONST_03  C8   N9   C10  C2    180.00   0.0  0
 76K  CONST_04  N5   C4   N3   C2      0.00   0.0  0
 76K  CONST_05  N9   C8   N7   C6      0.00   0.0  0
 76K  CONST_06  N3   C4   N5   C6      0.00   0.0  0
 76K  CONST_07  C8   N9   C10  C6      0.00   0.0  0
 76K  CONST_08  N3   C2   C10  C6      0.00   0.0  0
 76K  CONST_09  N5   C6   N7   C8    180.00   0.0  0
 76K  CONST_10  C10  C6   N7   C8      0.00   0.0  0
 76K  CONST_11  C4   N5   C6   C10     0.00   0.0  0
 76K  CONST_12  N7   C8   N9   C10     0.00   0.0  0
 76K  CONST_13  C4   N3   C2   C10     0.00   0.0  0
 76K  CONST_14  N9   C10  C2   N3    180.00   0.0  0
 76K  CONST_15  N7   C6   N5   C4    180.00   0.0  0
 76K  CONST_16  N9   C10  C6   N5    180.00   0.0  0
 76K  CONST_17  N9   C10  C6   N7      0.00   0.0  0
 76K  CONST_18  C11  N7   C6   C10   180.00   0.0  0
 76K  CONST_19  N9   C8   N7   C11   180.00   0.0  0
 76K  CONST_20  N5   C6   N7   C11     0.00   0.0  0
 76K  CONST_21  N1   C2   C10  C6    180.00   0.0  0
 76K  CONST_22  N9   C10  C2   N1      0.00   0.0  0
 76K  CONST_23  C4   N3   C2   N1    180.00   0.0  0
 76K  CONST_24  H45  C4   N3   C2    180.00   0.0  0
 76K  CONST_25  H46  C8   N7   C6    180.00   0.0  0
 76K  CONST_26  H43  N1   C2   C10   180.00   0.0  0
 76K  CONST_27  H44  N1   C2   C10     0.00   0.0  0
 76K  CONST_28  H1   O21  C20  C18   180.00   0.0  0
 76K  Var_01    C18  C17  C16  C15  -169.75  30.0  1
 76K  Var_02    C25  C24  N23  C15  -171.49  30.0  3
 76K  Var_03    O27  C26  C25  C24   -61.15  30.0  3
 76K  Var_04    N23  C24  C25  C26  -176.26  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
 76K  chir_01  C11  O12  C30  N7   positiv
 76K  chir_02  C13  O12  C14  C28  positiv
 76K  chir_03  C15  N23  C14  C16  positiv
 76K  chir_04  C28  O29  C13  C30  positiv
 76K  chir_05  C18  C20  C17  N19  negativ
 76K  chir_06  C30  O31  C28  C11  positiv

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
 76K  plan-1  C2   0.020
 76K  plan-1  C6   0.020
 76K  plan-1  C8   0.020
 76K  plan-1  C10  0.020
 76K  plan-1  C11  0.020
 76K  plan-1  N1   0.020
 76K  plan-1  N3   0.020
 76K  plan-1  C4   0.020
 76K  plan-1  N5   0.020
 76K  plan-1  N7   0.020
 76K  plan-1  N9   0.020
 76K  plan-1  H46  0.020
 76K  plan-1  H45  0.020
 76K  plan-2  C2   0.020
 76K  plan-2  N1   0.020
 76K  plan-2  H43  0.020
 76K  plan-2  H44  0.020
 76K  plan-3  C18  0.020
 76K  plan-3  C20  0.020
 76K  plan-3  O21  0.020
 76K  plan-3  O22  0.020
 76K  plan-3  H1   0.020

