# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 15:40:34 2021
#   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  58  29  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.496  50.3119  40.0088  127.8214
 6L7  C2    C  CR56  0  -0.011  50.0629  39.4757  126.5678
 6L7  C3    C  CR6   0   0.464  49.9337  40.3980  125.5126
 6L7  C4    C  CR16  0   0.048  50.3056  42.0645  127.0555
 6L7  C5    C  CR15  0   0.112  50.1869  37.8236  127.8760
 6L7  C6    C  CH1   0   0.198  50.6664  38.9693  130.0670
 6L7  C7    C  CH1   0  -0.008  49.6293  38.2563  130.9326
 6L7  N1    N  N     0  -0.445  49.9914  38.1065  126.6250
 6L7  N2    N  NR5   0  -0.542  50.3831  38.9311  128.6605
 6L7  N3    N  N     0  -0.473  50.0622  41.6985  125.8006
 6L7  C8    C  CH1   0  -0.061  50.4685  37.9097  132.1623
 6L7  N4    N  N     0  -0.458  50.4446  41.2967  128.1232
 6L7  N5    N  NH2   0  -0.815  49.6974  40.0278  124.2544
 6L7  C9    C  CH1   0  -0.038  51.7885  37.5015  131.4889
 6L7  C10   C  CH2   0  -0.362  51.8606  36.0328  131.0540
 6L7  O1    O  O2    0  -0.482  51.8809  38.3038  130.3194
 6L7  O2    O  OH1   0  -0.652  50.6090  39.0738  132.9218
 6L7  O3    O  OH1   0  -0.645  48.5370  39.0847  131.1369
 6L7  N6    N  NT1   1  -0.554  52.6587  35.1764  131.9912
 6L7  C11   C  CH2   0  -0.378  52.9752  33.8521  131.3707
 6L7  C12   C  CH2   0  -0.328  51.7638  32.9387  131.3083
 6L7  N7    N  NT3   1  -0.775  52.1037  31.7365  130.5192
 6L7  C13   C  CH2   0  -0.335  52.0382  35.0825  133.3495
 6L7  C14   C  CH2   0  -0.501  52.8958  34.2870  134.3213
 6L7  C15   C  CH1   0  -0.249  52.2306  34.1461  135.6885
 6L7  C16   C  C     0   0.591  52.9793  33.1763  136.5949
 6L7  O4    O  OH1   0  -0.571  53.0625  31.9900  136.0406
 6L7  O5    O  O     0  -0.408  53.4074  33.4879  137.6720
 6L7  N8    N  NT3   1  -0.783  52.1479  35.4444  136.3997
 6L7  HC4   H  HCR6  0   0.255  50.4003  43.1325  127.2199
 6L7  HC5   H  HCR5  0   0.295  50.2022  36.8235  128.2839
 6L7  HC6   H  HCH1  0   0.277  50.7324  40.0266  130.3402
 6L7  HC7   H  HCH1  0   0.248  49.3382  37.3141  130.4460
 6L7  HC8   H  HCH1  0   0.270  50.0212  37.0895  132.7393
 6L7  HN5A  H  HNH2  0   0.405  49.5707  40.7212  123.5374
 6L7  HN5B  H  HNH2  0   0.412  49.5611  39.0622  124.0125
 6L7  HC9   H  HCH1  0   0.296  52.6451  37.7327  132.1334
 6L7  H10B  H  HCH2  0   0.312  50.8780  35.5763  130.9405
 6L7  H10A  H  HCH2  0   0.343  52.3757  35.9794  130.0972
 6L7  HO2   H  HOH1  0   0.461  51.1521  38.8895  133.6947
 6L7  HO3   H  HOH1  0   0.468  47.8265  38.5750  131.5391
 6L7  HN6   H  HNT1  0   0.489  53.5648  35.6404  132.1037
 6L7  H11B  H  HCH2  0   0.348  53.7865  33.4054  131.9413
 6L7  H11A  H  HCH2  0   0.354  53.3612  34.0646  130.3748
 6L7  H12B  H  HCH2  0   0.335  50.9137  33.4028  130.8146
 6L7  H12A  H  HCH2  0   0.320  51.4483  32.5898  132.2884
 6L7  HN7C  H  HNT3  0   0.494  51.3132  31.0913  130.4987
 6L7  HN7B  H  HNT3  0   0.483  52.3248  31.9583  129.5478
 6L7  HN7A  H  HNT3  0   0.483  52.8939  31.2175  130.9046
 6L7  H13B  H  HCH2  0   0.307  51.9189  36.1095  133.6902
 6L7  H13A  H  HCH2  0   0.333  51.0430  34.6532  133.2337
 6L7  H14A  H  HCH2  0   0.311  53.0611  33.2770  133.9496
 6L7  H14B  H  HCH2  0   0.323  53.8801  34.7495  134.4313
 6L7  HC15  H  HCH1  0   0.376  51.2042  33.7872  135.5791
 6L7  H1    H  HOH1  0   0.506  53.5365  31.3680  136.6155
 6L7  HN8B  H  HNT3  0   0.492  51.7517  35.3378  137.3360
 6L7  HN8C  H  HNT3  0   0.483  53.0591  35.8927  136.5139
 6L7  HN8A  H  HNT3  0   0.483  51.5432  36.1108  135.9199

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    1.333  0.020  1.333
 6L7  C3   C2    aromatic  1.407  0.020  1.407
 6L7  C3   N3    aromatic  1.338  0.020  1.338
 6L7  N1   C2    aromatic  1.372  0.020  1.372
 6L7  N1   C5    aromatic  1.297  0.020  1.297
 6L7  C2   C1    aromatic  1.385  0.020  1.385
 6L7  N3   C4    aromatic  1.330  0.020  1.330
 6L7  C5   N2    aromatic  1.371  0.020  1.371
 6L7  C4   N4    aromatic  1.322  0.020  1.322
 6L7  C1   N2    aromatic  1.368  0.020  1.368
 6L7  C1   N4    aromatic  1.329  0.020  1.329
 6L7  N2   C6    single    1.435  0.020  1.435
 6L7  C6   C7    single    1.527  0.020  1.527
 6L7  C6   O1    single    1.408  0.020  1.408
 6L7  C7   O3    single    1.386  0.020  1.386
 6L7  C7   C8    single    1.529  0.020  1.529
 6L7  N7   C12   single    1.478  0.020  1.478
 6L7  O1   C9    single    1.421  0.020  1.421
 6L7  C10  C9    single    1.533  0.020  1.533
 6L7  C10  N6    single    1.500  0.020  1.500
 6L7  C12  C11   single    1.518  0.020  1.518
 6L7  C8   C9    single    1.537  0.020  1.537
 6L7  C8   O2    single    1.397  0.020  1.397
 6L7  C11  N6    single    1.496  0.020  1.496
 6L7  N6   C13   single    1.496  0.020  1.496
 6L7  C13  C14   single    1.521  0.020  1.521
 6L7  C14  C15   single    1.527  0.020  1.527
 6L7  N8   C15   single    1.483  0.020  1.483
 6L7  C15  C16   single    1.524  0.020  1.524
 6L7  O5   C16   double    1.200  0.020  1.200
 6L7  C16  O4    single    1.312  0.020  1.312
 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  O4   H1    single    0.850  0.020  0.980
 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    128.23  3.000
 6L7  N4    C1   C2    126.61  3.000
 6L7  N2    C1   C2    105.15  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    119.35  3.000
 6L7  N3    C3   C2    117.82  3.000
 6L7  N5    C3   C2    122.83  3.000
 6L7  HC4   C4   N4    116.11  3.000
 6L7  HC4   C4   N3    115.47  3.000
 6L7  N4    C4   N3    128.42  3.000
 6L7  HC5   C5   N2    121.98  3.000
 6L7  HC5   C5   N1    124.63  3.000
 6L7  N2    C5   N1    113.39  3.000
 6L7  HC6   C6   O1    111.10  3.000
 6L7  HC6   C6   N2    106.40  3.000
 6L7  O1    C6   N2    109.48  3.000
 6L7  HC6   C6   C7    110.52  3.000
 6L7  O1    C6   C7    105.28  3.000
 6L7  N2    C6   C7    114.13  3.000
 6L7  HC7   C7   O3    111.63  3.000
 6L7  HC7   C7   C8    107.88  3.000
 6L7  O3    C7   C8    116.71  3.000
 6L7  HC7   C7   C6    109.21  3.000
 6L7  C8    C7   C6    100.89  3.000
 6L7  O3    C7   C6    109.85  3.000
 6L7  C5    N1   C2    104.47  3.000
 6L7  C6    N2   C5    127.61  3.000
 6L7  C6    N2   C1    126.19  3.000
 6L7  C5    N2   C1    106.14  3.000
 6L7  C4    N3   C3    119.22  3.000
 6L7  HC8   C8   O2    112.19  3.000
 6L7  HC8   C8   C9    112.44  3.000
 6L7  O2    C8   C9    111.91  3.000
 6L7  HC8   C8   C7    111.62  3.000
 6L7  O2    C8   C7    107.68  3.000
 6L7  C9    C8   C7    100.32  3.000
 6L7  C4    N4   C1    111.64  3.000
 6L7  HN5B  N5   HN5A  118.30  3.000
 6L7  HN5B  N5   C3    121.22  3.000
 6L7  HN5A  N5   C3    120.27  3.000
 6L7  HC9   C9   O1    108.29  3.000
 6L7  HC9   C9   C10   109.38  3.000
 6L7  O1    C9   C10   107.71  3.000
 6L7  HC9   C9   C8    110.94  3.000
 6L7  C10   C9   C8    114.78  3.000
 6L7  O1    C9   C8    105.45  3.000
 6L7  H10A  C10  H10B  108.35  3.000
 6L7  H10A  C10  N6    105.64  3.000
 6L7  H10B  C10  N6    107.81  3.000
 6L7  H10A  C10  C9    108.59  3.000
 6L7  H10B  C10  C9    112.86  3.000
 6L7  N6    C10  C9    113.25  3.000
 6L7  C9    O1   C6    111.00  3.000
 6L7  HO2   O2   C8    109.49  3.000
 6L7  HO3   O3   C7    109.07  3.000
 6L7  HN6   N6   C13   107.19  3.000
 6L7  HN6   N6   C11   105.03  3.000
 6L7  C13   N6   C11   114.12  3.000
 6L7  HN6   N6   C10   106.31  3.000
 6L7  C13   N6   C10   112.49  3.000
 6L7  C11   N6   C10   111.03  3.000
 6L7  H11A  C11  H11B  107.18  3.000
 6L7  H11A  C11  C12   111.26  3.000
 6L7  H11B  C11  C12   111.69  3.000
 6L7  H11A  C11  N6    106.35  3.000
 6L7  H11B  C11  N6    107.68  3.000
 6L7  C12   C11  N6    112.38  3.000
 6L7  H12A  C12  H12B  108.64  3.000
 6L7  H12A  C12  N7    106.69  3.000
 6L7  H12B  C12  N7    106.54  3.000
 6L7  H12A  C12  C11   112.80  3.000
 6L7  H12B  C12  C11   112.69  3.000
 6L7  N7    C12  C11   109.14  3.000
 6L7  HN7A  N7   HN7B  107.59  3.000
 6L7  HN7A  N7   HN7C  106.60  3.000
 6L7  HN7B  N7   HN7C  106.62  3.000
 6L7  HN7A  N7   C12   112.96  3.000
 6L7  HN7B  N7   C12   112.41  3.000
 6L7  HN7C  N7   C12   110.29  3.000
 6L7  H13A  C13  H13B  107.74  3.000
 6L7  H13A  C13  C14   112.13  3.000
 6L7  H13B  C13  C14   110.81  3.000
 6L7  H13A  C13  N6    107.87  3.000
 6L7  H13B  C13  N6    105.69  3.000
 6L7  C14   C13  N6    112.28  3.000
 6L7  H14B  C14  H14A  106.87  3.000
 6L7  H14B  C14  C15   109.95  3.000
 6L7  H14A  C14  C15   106.63  3.000
 6L7  H14B  C14  C13   110.53  3.000
 6L7  H14A  C14  C13   110.65  3.000
 6L7  C15   C14  C13   112.01  3.000
 6L7  HC15  C15  N8    106.45  3.000
 6L7  HC15  C15  C16   108.18  3.000
 6L7  N8    C15  C16   107.42  3.000
 6L7  HC15  C15  C14   110.47  3.000
 6L7  C16   C15  C14   112.16  3.000
 6L7  N8    C15  C14   111.90  3.000
 6L7  O5    C16  O4    126.25  3.000
 6L7  O4    C16  C15   110.81  3.000
 6L7  O5    C16  C15   122.94  3.000
 6L7  H1    O4   C16   111.10  3.000
 6L7  HN8A  N8   HN8C  107.14  3.000
 6L7  HN8A  N8   HN8B  105.62  3.000
 6L7  HN8C  N8   HN8B  106.80  3.000
 6L7  HN8A  N8   C15   112.31  3.000
 6L7  HN8C  N8   C15   112.83  3.000
 6L7  HN8B  N8   C15   111.70  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    180.00   0.0  0
 6L7  CONST_27  HN5B  N5   C3   C2      0.00   0.0  0
 6L7  CONST_28  H1    O4   C16  C15   180.00   0.0  0
 6L7  Var_01    N7    C12  C11  N6    172.12  30.0  1
 6L7  Var_02    C15   C14  C13  N6   -177.65  30.0  3
 6L7  Var_03    HN7C  N7   C12  C11   177.63  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
 6L7  plan-3  H1    0.020

