# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  8 01:04:42 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-azaniumylethyl)-[(3~{S})-3-azaniumyl-4-oxidanyl-4-oxidanylidene-butyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[NH+](CC[NH3+])CC[C@H]([NH3+])C(O)=O)[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
 6L7  6L7  '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-azaniumylethyl)-[(3~{S})-3-azaniumyl-4-oxidanyl-4-oxidanylidene-butyl]azanium'  ligand  57  29  .  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_6L7
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
 6L7  C1    C  CR56   0   0.499   3.3938  -0.3731  -0.2843
 6L7  C2    C  CR56   0  -0.009   3.8360  -0.0806  -1.5626
 6L7  C3    C  CR6    0   0.466   4.8220  -0.9348  -2.0924
 6L7  C4    C  CR16   0   0.050   4.7213  -2.1104  -0.1164
 6L7  C5    C  CR15   0   0.106   2.3983   1.3952  -1.1055
 6L7  C6    C  CH1    0   0.213   1.6977   0.6757   1.2084
 6L7  C7    C  CH1    0  -0.047   1.6033   2.0732   1.8150
 6L7  N1    N  N      0  -0.439   3.1973   1.0281  -2.0583
 6L7  N2    N  NR5    0  -0.548   2.4672   0.5924   0.0050
 6L7  N3    N  N      0  -0.473   5.2423  -1.9501  -1.3292
 6L7  C8    C  CH1    0  -0.030   0.3311   1.9411   2.6615
 6L7  N4    N  N      0  -0.457   3.7995  -1.3774   0.4855
 6L7  N5    N  NH2    0  -0.814   5.3494  -0.7643  -3.3038
 6L7  C9    C  CH1    0  -0.027  -0.5304   1.0445   1.7740
 6L7  C10   C  CH2    0  -0.342  -1.4588   1.8456   0.8823
 6L7  O1    O  O2     0  -0.501   0.3613   0.3006   0.9469
 6L7  O2    O  OH1    0  -0.660   0.5863   1.2492   3.8506
 6L7  O3    O  OH1    0  -0.647   2.7584   2.3525   2.5400
 6L7  N6    N  NT1    1  -0.561  -2.1830   0.9448  -0.0770
 6L7  C11   C  CH2    0  -0.332  -2.5804   1.6636  -1.3223
 6L7  C12   C  CH2    0  -0.336  -1.3806   1.8616  -2.2315
 6L7  N7    N  NT3    1  -0.773  -1.8127   2.5025  -3.4903
 6L7  C13   C  CH2    0  -0.319  -3.3701   0.3068   0.5878
 6L7  C14   C  CH2    0  -0.508  -3.8220  -0.9527  -0.1293
 6L7  C15   C  CH1    0  -0.260  -5.0550  -1.5562   0.5156
 6L7  C16   C  C      0   0.484  -5.6355  -2.7699  -0.2766
 6L7  O4    O  OC    -1  -0.560  -5.6683  -2.6518  -1.5033
 6L7  O5    O  O      0  -0.586  -6.0317  -3.7113   0.4374
 6L7  N8    N  NT3    1  -0.804  -4.8039  -2.0321   1.9032
 6L7  HC4   H  HCR6   0   0.256   5.1054  -2.9531   0.4480
 6L7  HC5   H  HCR5   0   0.291   1.7454   2.2536  -1.1532
 6L7  HC6   H  HCH1   0   0.276   2.1626  -0.0136   1.9199
 6L7  HC7   H  HCH1   0   0.256   1.4289   2.8176   1.0278
 6L7  HC8   H  HCH1   0   0.272  -0.1414   2.9146   2.8449
 6L7  HN5A  H  HNH2   0   0.413   5.0103  -0.0483  -3.9219
 6L7  HN5B  H  HNH2   0   0.406   6.0224  -1.4207  -3.6605
 6L7  HC9   H  HCH1   0   0.296  -1.1034   0.3532   2.3998
 6L7  H10B  H  HCH2   0   0.341  -2.2132   2.3740   1.4642
 6L7  H10A  H  HCH2   0   0.306  -0.9085   2.5891   0.3068
 6L7  HO2   H  HOH1   0   0.457   1.3546   1.6509   4.2740
 6L7  HO3   H  HOH1   0   0.475   2.8601   3.3065   2.6167
 6L7  HN6   H  HNT1   0   0.462  -1.5396   0.1901  -0.3419
 6L7  H11B  H  HCH2   0   0.336  -3.3337   1.0641  -1.8281
 6L7  H11A  H  HCH2   0   0.341  -3.0295   2.6101  -1.0237
 6L7  H12B  H  HCH2   0   0.308  -0.6293   2.5151  -1.7972
 6L7  H12A  H  HCH2   0   0.330  -0.9233   0.9118  -2.4999
 6L7  HN7C  H  HNT3   0   0.483  -2.4966   1.9414  -3.9995
 6L7  HN7B  H  HNT3   0   0.483  -2.2207   3.4258  -3.3396
 6L7  HN7A  H  HNT3   0   0.495  -1.0168   2.6330  -4.1159
 6L7  H13B  H  HCH2   0   0.305  -3.0680   0.0902   1.6111
 6L7  H13A  H  HCH2   0   0.328  -4.1530   1.0643   0.6258
 6L7  H14A  H  HCH2   0   0.299  -4.0948  -0.7419  -1.1625
 6L7  H14B  H  HCH2   0   0.285  -3.0118  -1.6878  -0.1539
 6L7  HC15  H  HCH1   0   0.324  -5.8423  -0.8025   0.5902
 6L7  HN8B  H  HNT3   0   0.469  -5.0463  -1.3616   2.6295
 6L7  HN8C  H  HNT3   0   0.461  -5.4003  -2.8749   1.9922
 6L7  HN8A  H  HNT3   0   0.462  -3.8432  -2.3353   2.0612

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
 6L7  N5   C3    single    1.332  0.020  1.332
 6L7  C3   C2    aromatic  1.408  0.020  1.408
 6L7  C3   N3    aromatic  1.338  0.020  1.338
 6L7  N1   C2    aromatic  1.372  0.020  1.372
 6L7  N1   C5    aromatic  1.296  0.020  1.296
 6L7  C2   C1    aromatic  1.384  0.020  1.384
 6L7  N3   C4    aromatic  1.330  0.020  1.330
 6L7  C5   N2    aromatic  1.372  0.020  1.372
 6L7  C4   N4    aromatic  1.323  0.020  1.323
 6L7  C1   N2    aromatic  1.369  0.020  1.369
 6L7  C1   N4    aromatic  1.329  0.020  1.329
 6L7  N2   C6    single    1.431  0.020  1.431
 6L7  C6   C7    single    1.526  0.020  1.526
 6L7  C6   O1    single    1.412  0.020  1.412
 6L7  C7   O3    single    1.392  0.020  1.392
 6L7  C7   C8    single    1.534  0.020  1.534
 6L7  N7   C12   single    1.477  0.020  1.477
 6L7  O1   C9    single    1.426  0.020  1.426
 6L7  C10  C9    single    1.516  0.020  1.516
 6L7  C10  N6    single    1.502  0.020  1.502
 6L7  C12  C11   single    1.518  0.020  1.518
 6L7  C8   C9    single    1.528  0.020  1.528
 6L7  C8   O2    single    1.399  0.020  1.399
 6L7  C11  N6    single    1.492  0.020  1.492
 6L7  N6   C13   single    1.503  0.020  1.503
 6L7  C13  C14   single    1.518  0.020  1.518
 6L7  C14  C15   single    1.517  0.020  1.517
 6L7  N8   C15   single    1.488  0.020  1.488
 6L7  C15  C16   single    1.561  0.020  1.561
 6L7  O5   C16   deloc     1.246  0.020  1.246
 6L7  C16  O4    deloc     1.233  0.020  1.233
 6L7  C4   HC4   single    0.930  0.020  1.080
 6L7  C5   HC5   single    0.930  0.020  1.080
 6L7  C6   HC6   single    0.970  0.020  1.090
 6L7  C7   HC7   single    0.970  0.020  1.090
 6L7  C8   HC8   single    0.970  0.020  1.090
 6L7  N5   HN5A  single    0.860  0.020  1.020
 6L7  N5   HN5B  single    0.860  0.020  1.020
 6L7  C9   HC9   single    0.970  0.020  1.090
 6L7  C10  H10B  single    0.970  0.020  1.090
 6L7  C10  H10A  single    0.970  0.020  1.090
 6L7  O2   HO2   single    0.850  0.020  0.980
 6L7  O3   HO3   single    0.850  0.020  0.980
 6L7  N6   HN6   single    0.890  0.020  1.040
 6L7  C11  H11B  single    0.970  0.020  1.090
 6L7  C11  H11A  single    0.970  0.020  1.090
 6L7  C12  H12B  single    0.970  0.020  1.090
 6L7  C12  H12A  single    0.970  0.020  1.090
 6L7  N7   HN7C  single    0.890  0.020  1.040
 6L7  N7   HN7B  single    0.890  0.020  1.040
 6L7  N7   HN7A  single    0.890  0.020  1.040
 6L7  C13  H13B  single    0.970  0.020  1.090
 6L7  C13  H13A  single    0.970  0.020  1.090
 6L7  C14  H14A  single    0.970  0.020  1.090
 6L7  C14  H14B  single    0.970  0.020  1.090
 6L7  C15  HC15  single    0.970  0.020  1.090
 6L7  N8   HN8B  single    0.890  0.020  1.040
 6L7  N8   HN8C  single    0.890  0.020  1.040
 6L7  N8   HN8A  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
 6L7  N4    C1   N2    128.12  3.000
 6L7  N4    C1   C2    126.67  3.000
 6L7  N2    C1   C2    105.21  3.000
 6L7  N1    C2   C3    132.87  3.000
 6L7  N1    C2   C1    110.84  3.000
 6L7  C3    C2   C1    116.30  3.000
 6L7  N5    C3   N3    119.43  3.000
 6L7  N3    C3   C2    117.76  3.000
 6L7  N5    C3   C2    122.80  3.000
 6L7  HC4   C4   N4    116.14  3.000
 6L7  HC4   C4   N3    115.44  3.000
 6L7  N4    C4   N3    128.42  3.000
 6L7  HC5   C5   N2    122.09  3.000
 6L7  HC5   C5   N1    124.43  3.000
 6L7  N2    C5   N1    113.47  3.000
 6L7  HC6   C6   O1    110.80  3.000
 6L7  HC6   C6   N2    106.36  3.000
 6L7  O1    C6   N2    109.73  3.000
 6L7  HC6   C6   C7    110.15  3.000
 6L7  O1    C6   C7    104.97  3.000
 6L7  N2    C6   C7    114.88  3.000
 6L7  HC7   C7   O3    111.68  3.000
 6L7  HC7   C7   C8    108.82  3.000
 6L7  O3    C7   C8    114.71  3.000
 6L7  HC7   C7   C6    110.23  3.000
 6L7  C8    C7   C6    101.05  3.000
 6L7  O3    C7   C6    109.84  3.000
 6L7  C5    N1   C2    104.49  3.000
 6L7  C6    N2   C5    128.30  3.000
 6L7  C6    N2   C1    125.64  3.000
 6L7  C5    N2   C1    106.00  3.000
 6L7  C4    N3   C3    119.25  3.000
 6L7  HC8   C8   O2    112.03  3.000
 6L7  HC8   C8   C9    112.02  3.000
 6L7  O2    C8   C9    107.84  3.000
 6L7  HC8   C8   C7    111.89  3.000
 6L7  O2    C8   C7    111.12  3.000
 6L7  C9    C8   C7    101.40  3.000
 6L7  C4    N4   C1    111.59  3.000
 6L7  HN5B  N5   HN5A  118.22  3.000
 6L7  HN5B  N5   C3    120.27  3.000
 6L7  HN5A  N5   C3    121.13  3.000
 6L7  HC9   C9   O1    109.25  3.000
 6L7  HC9   C9   C10   110.45  3.000
 6L7  O1    C9   C10   108.51  3.000
 6L7  HC9   C9   C8    109.50  3.000
 6L7  C10   C9   C8    112.14  3.000
 6L7  O1    C9   C8    106.89  3.000
 6L7  H10A  C10  H10B  107.52  3.000
 6L7  H10A  C10  N6    108.39  3.000
 6L7  H10B  C10  N6    107.35  3.000
 6L7  H10A  C10  C9    111.22  3.000
 6L7  H10B  C10  C9    111.48  3.000
 6L7  N6    C10  C9    110.73  3.000
 6L7  C9    O1   C6    110.23  3.000
 6L7  HO2   O2   C8    108.20  3.000
 6L7  HO3   O3   C7    109.15  3.000
 6L7  HN6   N6   C13   107.28  3.000
 6L7  HN6   N6   C11   107.81  3.000
 6L7  C13   N6   C11   111.32  3.000
 6L7  HN6   N6   C10   107.67  3.000
 6L7  C13   N6   C10   110.67  3.000
 6L7  C11   N6   C10   111.88  3.000
 6L7  H11A  C11  H11B  108.72  3.000
 6L7  H11A  C11  C12   112.13  3.000
 6L7  H11B  C11  C12   109.92  3.000
 6L7  H11A  C11  N6    107.44  3.000
 6L7  H11B  C11  N6    107.89  3.000
 6L7  C12   C11  N6    110.62  3.000
 6L7  H12A  C12  H12B  109.46  3.000
 6L7  H12A  C12  N7    106.95  3.000
 6L7  H12B  C12  N7    106.38  3.000
 6L7  H12A  C12  C11   111.48  3.000
 6L7  H12B  C12  C11   112.67  3.000
 6L7  N7    C12  C11   109.61  3.000
 6L7  HN7A  N7   HN7B  106.65  3.000
 6L7  HN7A  N7   HN7C  106.67  3.000
 6L7  HN7B  N7   HN7C  107.64  3.000
 6L7  HN7A  N7   C12   110.47  3.000
 6L7  HN7B  N7   C12   112.56  3.000
 6L7  HN7C  N7   C12   112.50  3.000
 6L7  H13A  C13  H13B  107.74  3.000
 6L7  H13A  C13  C14   112.28  3.000
 6L7  H13B  C13  C14   111.19  3.000
 6L7  H13A  C13  N6    106.72  3.000
 6L7  H13B  C13  N6    106.33  3.000
 6L7  C14   C13  N6    112.24  3.000
 6L7  H14B  C14  H14A  107.11  3.000
 6L7  H14B  C14  C15   110.13  3.000
 6L7  H14A  C14  C15   106.06  3.000
 6L7  H14B  C14  C13   110.34  3.000
 6L7  H14A  C14  C13   111.23  3.000
 6L7  C15   C14  C13   111.79  3.000
 6L7  HC15  C15  N8    106.17  3.000
 6L7  HC15  C15  C16   107.63  3.000
 6L7  N8    C15  C16   106.69  3.000
 6L7  HC15  C15  C14   109.91  3.000
 6L7  C16   C15  C14   113.32  3.000
 6L7  N8    C15  C14   112.74  3.000
 6L7  O5    C16  O4    129.35  3.000
 6L7  O4    C16  C15   116.12  3.000
 6L7  O5    C16  C15   114.51  3.000
 6L7  HN8A  N8   HN8C  106.68  3.000
 6L7  HN8A  N8   HN8B  108.05  3.000
 6L7  HN8C  N8   HN8B  109.72  3.000
 6L7  HN8A  N8   C15   113.48  3.000
 6L7  HN8C  N8   C15   104.07  3.000
 6L7  HN8B  N8   C15   114.49  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
 6L7  CONST_01  N3    C3   C2   C1      0.00   0.0  0
 6L7  CONST_02  C5    N1   C2   C1      0.00   0.0  0
 6L7  CONST_03  N1    C5   N2   C1      0.00   0.0  0
 6L7  CONST_04  N3    C4   N4   C1      0.00   0.0  0
 6L7  CONST_05  C4    N3   C3   C2      0.00   0.0  0
 6L7  CONST_06  N2    C5   N1   C2      0.00   0.0  0
 6L7  CONST_07  C5    N2   C1   C2      0.00   0.0  0
 6L7  CONST_08  C4    N4   C1   C2      0.00   0.0  0
 6L7  CONST_09  C5    N1   C2   C3    180.00   0.0  0
 6L7  CONST_10  N2    C1   C2   C3    180.00   0.0  0
 6L7  CONST_11  N4    C1   C2   C3      0.00   0.0  0
 6L7  CONST_12  N4    C4   N3   C3      0.00   0.0  0
 6L7  CONST_13  N2    C1   N4   C4    180.00   0.0  0
 6L7  CONST_14  N4    C1   N2   C5    180.00   0.0  0
 6L7  CONST_15  N3    C3   C2   N1    180.00   0.0  0
 6L7  CONST_16  N2    C1   C2   N1      0.00   0.0  0
 6L7  CONST_17  N4    C1   C2   N1    180.00   0.0  0
 6L7  CONST_18  C6    N2   C1   C2    180.00   0.0  0
 6L7  CONST_19  N1    C5   N2   C6    180.00   0.0  0
 6L7  CONST_20  N4    C1   N2   C6      0.00   0.0  0
 6L7  CONST_21  N5    C3   C2   C1    180.00   0.0  0
 6L7  CONST_22  N5    C3   N3   C4    180.00   0.0  0
 6L7  CONST_23  N5    C3   C2   N1      0.00   0.0  0
 6L7  CONST_24  HC5   C5   N2   C1    180.00   0.0  0
 6L7  CONST_25  HC4   C4   N4   C1    180.00   0.0  0
 6L7  CONST_26  HN5A  N5   C3   C2      0.00   0.0  0
 6L7  CONST_27  HN5B  N5   C3   C2    180.00   0.0  0
 6L7  Var_01    N7    C12  C11  N6    176.67  30.0  1
 6L7  Var_02    C15   C14  C13  N6   -177.62  30.0  3
 6L7  Var_03    HN7C  N7   C12  C11   -60.33  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
 6L7  chir_01  C6   N2   C7   O1   negativ
 6L7  chir_02  C7   O3   C8   C6   positiv
 6L7  chir_03  C8   O2   C9   C7   positiv
 6L7  chir_04  C9   O1   C8   C10  negativ
 6L7  chir_05  N6   C10  C11  C13  positiv
 6L7  chir_06  C15  N8   C14  C16  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
 6L7  plan-1  C1    0.020
 6L7  plan-1  C2    0.020
 6L7  plan-1  C3    0.020
 6L7  plan-1  C4    0.020
 6L7  plan-1  C5    0.020
 6L7  plan-1  C6    0.020
 6L7  plan-1  N1    0.020
 6L7  plan-1  N2    0.020
 6L7  plan-1  N3    0.020
 6L7  plan-1  N4    0.020
 6L7  plan-1  N5    0.020
 6L7  plan-1  HC4   0.020
 6L7  plan-1  HC5   0.020
 6L7  plan-2  C3    0.020
 6L7  plan-2  N5    0.020
 6L7  plan-2  HN5A  0.020
 6L7  plan-2  HN5B  0.020
 6L7  plan-3  C15   0.020
 6L7  plan-3  C16   0.020
 6L7  plan-3  O4    0.020
 6L7  plan-3  O5    0.020

