# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  9 16:00:43 2020
#   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  66  32  .  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_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  -0.663  -6.6777   5.4891   2.5708
 76J  C2   C  CH2    0  -0.421  -5.8498   5.1057   1.3525
 76J  C3   C  CH2    0  -0.416  -5.1761   3.7477   1.5086
 76J  C5   C  CH2    0  -0.289  -3.6937   2.0089   0.4755
 76J  C7   C  CH1    0  -0.087  -2.0756   0.4093  -0.6611
 76J  C8   C  CH2    0  -0.459  -2.8111  -0.8749  -0.2904
 76J  C10  C  CH1    0  -0.253  -2.3580  -3.2915   0.4375
 76J  C12  C  C      0   0.476  -1.2672  -4.3315   0.8311
 76J  C15  C  CH2    0  -0.508  -1.3164   0.2676  -1.9776
 76J  C16  C  CH1    0  -0.010  -0.1726   1.2568  -2.1608
 76J  O17  O  O2     0  -0.490   0.7277   1.1765  -1.0511
 76J  C19  C  CH1    0  -0.064   1.7197   0.0045  -2.8097
 76J  C21  C  CH1    0  -0.015   0.6629   0.9444  -3.3988
 76J  C24  C  CR15   0   0.111   2.0748  -1.4545  -0.0770
 76J  C26  C  CR56   0  -0.010   3.6738  -0.9932   1.2227
 76J  C27  C  CR6    0   0.461   4.6958  -0.9238   2.1878
 76J  C4   C  CH2    0  -0.463  -4.3866   3.3421   0.2697
 76J  N6   N  NT2    1  -0.689  -3.0160   1.5715  -0.7796
 76J  C9   C  CH2    0  -0.474  -1.8022  -1.9024   0.2155
 76J  N11  N  NT3    1  -0.798  -3.3988  -3.3200   1.5014
 76J  O13  O  O      0  -0.592  -1.6098  -5.1454   1.7119
 76J  O14  O  OC    -1  -0.556  -0.2005  -4.2608   0.2128
 76J  C18  C  CH1    0   0.221   1.9724   0.6687  -1.4591
 76J  O20  O  OH1    0  -0.651   2.9113  -0.0682  -3.5310
 76J  O22  O  OH1    0  -0.667   1.2501   2.1309  -3.8613
 76J  N23  N  NR5    0  -0.549   2.5056  -0.2054  -0.4510
 76J  N25  N  N      0  -0.441   2.7478  -1.9560   0.9127
 76J  N28  N  NH2    0  -0.816   4.9407  -1.9082   3.0523
 76J  N29  N  N      0  -0.474   5.4407   0.1869   2.2306
 76J  C30  C  CR16   0   0.047   5.1904   1.1687   1.3689
 76J  N31  N  N      0  -0.459   4.2687   1.2161   0.4223
 76J  C32  C  CR56   0   0.495   3.5376   0.1053   0.3922
 76J  H44  H  HCH3   0   0.229  -7.1427   6.4674   2.4450
 76J  H46  H  HCH3   0   0.218  -7.4749   4.7652   2.7490
 76J  H45  H  HCH3   0   0.218  -6.0618   5.5299   3.4711
 76J  H48  H  HCH2   0   0.217  -6.4884   5.0924   0.4644
 76J  H47  H  HCH2   0   0.217  -5.0877   5.8691   1.1706
 76J  H50  H  HCH2   0   0.224  -4.5120   3.7693   2.3785
 76J  H49  H  HCH2   0   0.224  -5.9349   2.9867   1.7161
 76J  H53  H  HCH2   0   0.294  -2.9279   2.0699   1.2474
 76J  H54  H  HCH2   0   0.290  -4.4070   1.2355   0.7498
 76J  H35  H  HCH1   0   0.309  -1.3942   0.6763   0.1488
 76J  H55  H  HCH2   0   0.271  -3.5589  -0.6827   0.4815
 76J  H56  H  HCH2   0   0.263  -3.3449  -1.2600  -1.1644
 76J  H36  H  HCH1   0   0.309  -2.8461  -3.6477  -0.4727
 76J  H59  H  HCH2   0   0.273  -0.9278  -0.7498  -2.0426
 76J  H60  H  HCH2   0   0.286  -2.0139   0.3660  -2.8146
 76J  H40  H  HCH1   0   0.267  -0.5561   2.2816  -2.2188
 76J  H42  H  HCH1   0   0.254   1.2742  -0.9891  -2.6706
 76J  H43  H  HCH1   0   0.257   0.0663   0.4525  -4.1780
 76J  H63  H  HCR5   0   0.287   1.2611  -1.9612  -0.5734
 76J  H51  H  HCH2   0   0.248  -5.0624   3.2771  -0.5880
 76J  H52  H  HCH2   0   0.247  -3.6415   4.1085   0.0360
 76J  H34  H  HNT2   0   0.464  -3.7222   1.3711  -1.4914
 76J  H33  H  HNT2   0   0.471  -2.4925   2.3686  -1.1471
 76J  H57  H  HCH2   0   0.265  -1.0011  -2.0248  -0.5106
 76J  H58  H  HCH2   0   0.263  -1.3344  -1.5392   1.1362
 76J  H38  H  HNT3   0   0.455  -3.2851  -4.2346   1.9673
 76J  H39  H  HNT3   0   0.460  -3.2586  -2.6031   2.2122
 76J  H37  H  HNT3   0   0.467  -4.3502  -3.2294   1.1523
 76J  H41  H  HCH1   0   0.263   2.7063   1.4731  -1.5709
 76J  H61  H  HOH1   0   0.472   2.8153  -0.7260  -4.2271
 76J  H62  H  HOH1   0   0.451   2.0366   1.8977  -4.3689
 76J  H64  H  HNH2   0   0.412   4.4280  -2.7716   3.0164
 76J  H65  H  HNH2   0   0.404   5.7071  -1.8353   3.6988
 76J  H66  H  HCR6   0   0.253   5.8280   2.0414   1.4589

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    1.522  0.020  1.522
 76J  C2   C3   single    1.524  0.020  1.524
 76J  C3   C4   single    1.524  0.020  1.524
 76J  C4   C5   single    1.517  0.020  1.517
 76J  O22  C21  single    1.402  0.020  1.402
 76J  C5   N6   single    1.492  0.020  1.492
 76J  C21  C16  single    1.526  0.020  1.526
 76J  C21  C19  single    1.532  0.020  1.532
 76J  C15  C16  single    1.523  0.020  1.523
 76J  C15  C7   single    1.526  0.020  1.526
 76J  N6   C7   single    1.500  0.020  1.500
 76J  C16  O17  single    1.431  0.020  1.431
 76J  C19  O20  single    1.395  0.020  1.395
 76J  C19  C18  single    1.526  0.020  1.526
 76J  C7   C8   single    1.526  0.020  1.526
 76J  N25  C24  aromatic  1.298  0.020  1.298
 76J  N25  C26  aromatic  1.371  0.020  1.371
 76J  N28  C27  single    1.333  0.020  1.333
 76J  C24  N23  aromatic  1.373  0.020  1.373
 76J  C26  C27  aromatic  1.407  0.020  1.407
 76J  C26  C32  aromatic  1.384  0.020  1.384
 76J  C27  N29  aromatic  1.338  0.020  1.338
 76J  N23  C32  aromatic  1.368  0.020  1.368
 76J  N23  C18  single    1.437  0.020  1.437
 76J  C32  N31  aromatic  1.330  0.020  1.330
 76J  N29  C30  aromatic  1.330  0.020  1.330
 76J  O17  C18  single    1.405  0.020  1.405
 76J  N31  C30  aromatic  1.322  0.020  1.322
 76J  C8   C9   single    1.526  0.020  1.526
 76J  C9   C10  single    1.513  0.020  1.513
 76J  C10  N11  single    1.489  0.020  1.489
 76J  C10  C12  single    1.558  0.020  1.558
 76J  O13  C12  deloc     1.247  0.020  1.247
 76J  C12  O14  deloc     1.235  0.020  1.235
 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  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  107.59  3.000
 76J  H45  C1   H44  107.60  3.000
 76J  H46  C1   H44  107.61  3.000
 76J  H45  C1   C2   111.26  3.000
 76J  H46  C1   C2   111.15  3.000
 76J  H44  C1   C2   111.44  3.000
 76J  H47  C2   H48  106.27  3.000
 76J  H47  C2   C3   109.32  3.000
 76J  H48  C2   C3   109.29  3.000
 76J  H47  C2   C1   109.65  3.000
 76J  H48  C2   C1   109.60  3.000
 76J  C3   C2   C1   112.52  3.000
 76J  H49  C3   H50  106.48  3.000
 76J  H49  C3   C4   109.16  3.000
 76J  H50  C3   C4   109.69  3.000
 76J  H49  C3   C2   109.42  3.000
 76J  H50  C3   C2   109.39  3.000
 76J  C4   C3   C2   112.52  3.000
 76J  H54  C5   H53  108.80  3.000
 76J  H54  C5   N6   107.56  3.000
 76J  H53  C5   N6   107.06  3.000
 76J  H54  C5   C4   111.09  3.000
 76J  H53  C5   C4   111.61  3.000
 76J  N6   C5   C4   110.56  3.000
 76J  H35  C7   N6   105.09  3.000
 76J  H35  C7   C15  110.62  3.000
 76J  N6   C7   C15  108.40  3.000
 76J  H35  C7   C8   109.06  3.000
 76J  N6   C7   C8   111.67  3.000
 76J  C15  C7   C8   111.79  3.000
 76J  H56  C8   H55  107.01  3.000
 76J  H56  C8   C9   110.51  3.000
 76J  H55  C8   C9   109.69  3.000
 76J  H56  C8   C7   109.72  3.000
 76J  H55  C8   C7   110.72  3.000
 76J  C9   C8   C7   109.18  3.000
 76J  H36  C10  N11  106.07  3.000
 76J  H36  C10  C9   109.95  3.000
 76J  N11  C10  C9   112.30  3.000
 76J  H36  C10  C12  107.80  3.000
 76J  N11  C10  C12  107.23  3.000
 76J  C9   C10  C12  113.14  3.000
 76J  O14  C12  O13  128.92  3.000
 76J  O14  C12  C10  116.11  3.000
 76J  O13  C12  C10  114.94  3.000
 76J  H60  C15  H59  105.39  3.000
 76J  H60  C15  C16  109.16  3.000
 76J  H59  C15  C16  109.32  3.000
 76J  H60  C15  C7   109.54  3.000
 76J  H59  C15  C7   108.37  3.000
 76J  C16  C15  C7   114.64  3.000
 76J  H40  C16  C21  109.88  3.000
 76J  H40  C16  O17  108.28  3.000
 76J  C21  C16  O17  105.85  3.000
 76J  H40  C16  C15  110.54  3.000
 76J  O17  C16  C15  110.04  3.000
 76J  C21  C16  C15  112.07  3.000
 76J  C18  O17  C16  110.64  3.000
 76J  H42  C19  O20  111.41  3.000
 76J  H42  C19  C18  110.43  3.000
 76J  O20  C19  C18  109.81  3.000
 76J  H42  C19  C21  108.91  3.000
 76J  C18  C19  C21  100.80  3.000
 76J  O20  C19  C21  114.98  3.000
 76J  H43  C21  O22  111.87  3.000
 76J  H43  C21  C19  111.89  3.000
 76J  O22  C21  C19  110.92  3.000
 76J  H43  C21  C16  111.72  3.000
 76J  C19  C21  C16  101.03  3.000
 76J  O22  C21  C16  108.88  3.000
 76J  H63  C24  N25  124.08  3.000
 76J  H63  C24  N23  122.56  3.000
 76J  N25  C24  N23  113.36  3.000
 76J  C32  C26  N25  110.80  3.000
 76J  C32  C26  C27  116.36  3.000
 76J  N25  C26  C27  132.84  3.000
 76J  N29  C27  N28  119.35  3.000
 76J  N29  C27  C26  117.84  3.000
 76J  N28  C27  C26  122.81  3.000
 76J  H52  C4   H51  107.16  3.000
 76J  H52  C4   C5   109.49  3.000
 76J  H51  C4   C5   109.66  3.000
 76J  H52  C4   C3   109.87  3.000
 76J  H51  C4   C3   109.46  3.000
 76J  C5   C4   C3   111.12  3.000
 76J  H33  N6   H34  104.85  3.000
 76J  H33  N6   C7   108.16  3.000
 76J  H34  N6   C7   109.64  3.000
 76J  H33  N6   C5   107.85  3.000
 76J  H34  N6   C5   109.23  3.000
 76J  C7   N6   C5   116.46  3.000
 76J  H58  C9   H57  106.49  3.000
 76J  H58  C9   C10  109.77  3.000
 76J  H57  C9   C10  105.38  3.000
 76J  H58  C9   C8   109.75  3.000
 76J  H57  C9   C8   109.95  3.000
 76J  C10  C9   C8   115.09  3.000
 76J  H37  N11  H39  107.78  3.000
 76J  H37  N11  H38  109.67  3.000
 76J  H39  N11  H38  107.05  3.000
 76J  H37  N11  C10  114.01  3.000
 76J  H39  N11  C10  112.87  3.000
 76J  H38  N11  C10  105.21  3.000
 76J  H41  C18  N23  105.65  3.000
 76J  H41  C18  C19  109.91  3.000
 76J  N23  C18  C19  114.68  3.000
 76J  H41  C18  O17  110.99  3.000
 76J  N23  C18  O17  110.18  3.000
 76J  C19  C18  O17  105.52  3.000
 76J  H61  O20  C19  108.93  3.000
 76J  H62  O22  C21  108.09  3.000
 76J  C32  N23  C18  125.03  3.000
 76J  C18  N23  C24  128.90  3.000
 76J  C32  N23  C24  105.98  3.000
 76J  C26  N25  C24  104.56  3.000
 76J  H65  N28  H64  118.31  3.000
 76J  H65  N28  C27  120.24  3.000
 76J  H64  N28  C27  121.18  3.000
 76J  C30  N29  C27  119.16  3.000
 76J  H66  C30  N31  116.13  3.000
 76J  H66  C30  N29  115.44  3.000
 76J  N31  C30  N29  128.43  3.000
 76J  C32  N31  C30  111.68  3.000
 76J  N31  C32  N23  128.18  3.000
 76J  N31  C32  C26  126.52  3.000
 76J  N23  C32  C26  105.30  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
 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     0.00   0.0  0
 76J  CONST_27  H65  N28  C27  C26   180.00   0.0  0
 76J  Var_01    C4   C3   C2   C1    178.01  30.0  3
 76J  Var_02    C5   C4   C3   C2    178.17  30.0  3
 76J  Var_03    N6   C5   C4   C3    175.45  30.0  3
 76J  Var_04    C4   C5   N6   C7    168.72  30.0  3
 76J  Var_05    C10  C9   C8   C7   -171.77  30.0  3
 76J  Var_06    H44  C1   C2   C3    179.38  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
 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

