# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 07:48:13 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [2-(aminooxy)ethyl]{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S+](CCON)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
 AAD  AAD  '[2-(aminooxy)ethyl]{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium (non-preferred name)'  ligand  45  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AAD
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
 AAD  C4'   C  CH1    0   0.008  -0.0574   2.7292  -0.3472
 AAD  O4'   O  O2     0  -0.495  -1.1766   2.7361   0.5325
 AAD  C3'   C  CH1    0  -0.025   1.0344   1.9876   0.4123
 AAD  O3'   O  OH1    0  -0.668   1.5785   2.7479   1.4577
 AAD  C2'   C  CH1    0  -0.040   0.1859   0.8715   1.0324
 AAD  O2'   O  OH1    0  -0.651   0.7573   0.2243   2.1192
 AAD  C1'   C  CH1    0   0.191  -1.1333   1.6092   1.3634
 AAD  N9    N  NR5    0  -0.537  -2.3129   0.8032   1.1591
 AAD  C8    C  CR15   0   0.116  -3.1843   0.3805   2.1255
 AAD  N7    N  N      0  -0.453  -4.1687  -0.3288   1.6621
 AAD  C5    C  CR56   0  -0.001  -3.9443  -0.3742   0.3101
 AAD  C6    C  CR6    0   0.461  -4.6490  -0.9685  -0.7541
 AAD  N6    N  NH2    0  -0.815  -5.7661  -1.6722  -0.5744
 AAD  N1    N  N      0  -0.474  -4.1612  -0.8165  -1.9908
 AAD  C2    C  CR16   0   0.047  -3.0440  -0.1179  -2.1659
 AAD  N3    N  N      0  -0.468  -2.3010   0.4853  -1.2532
 AAD  C4    C  CR56   0   0.501  -2.7967   0.3253  -0.0265
 AAD  N2    N  NH2    0  -0.532  -4.8239   5.8907  -3.1139
 AAD  O2    O  O2     0  -0.425  -3.8329   5.1202  -2.4716
 AAD  CG    C  CH2   -1  -0.628  -1.7994   3.9720  -2.6438
 AAD  SD    S  S3     1   0.395  -1.2901   4.9754  -1.2171
 AAD  CE    C  CH3    0  -0.772  -0.6599   6.4722  -1.9797
 AAD  C5'   C  CH2    0  -0.600   0.2515   4.1594  -0.7165
 AAD  HC4   H  HCH1   0   0.279  -0.2950   2.1545  -1.2500
 AAD  HC3   H  HCH1   0   0.282   1.7985   1.5930  -0.2622
 AAD  HO3   H  HOH1   0   0.476   2.4447   3.0771   1.2012
 AAD  HC2   H  HCH1   0   0.286  -0.0033   0.1166   0.2648
 AAD  HO2   H  HOH1   0   0.450   1.1875   0.8889   2.6721
 AAD  HC1   H  HCH1   0   0.280  -1.1522   1.9177   2.4129
 AAD  HC8   H  HCR5   0   0.302  -3.0293   0.6344   3.1640
 AAD  HN61  H  HNH2   0   0.413  -6.1811  -1.7650   0.3361
 AAD  HN62  H  HNH2   0   0.405  -6.2667  -2.0403  -1.3650
 AAD  HC2A  H  HCR6   0   0.255  -2.7021  -0.0319  -3.1917
 AAD  HN21  H  HNH2   0   0.373  -4.8706   6.7485  -2.5740
 AAD  HN22  H  HNH2   0   0.372  -5.6936   5.4006  -2.9313
 AAD  HCB1  H  HCH2   0   0.237  -2.4619   5.5398  -3.9695
 AAD  HCB2  H  HCH2   0   0.263  -3.3017   3.9973  -4.1470
 AAD  HCG2  H  HCH2   0   0.339  -0.9318   3.7833  -3.2765
 AAD  HCE1  H  HCH3   0   0.334  -0.1458   7.0316  -1.2012
 AAD  HCE2  H  HCH3   0   0.323  -1.5073   7.0551  -2.3315
 AAD  HCE3  H  HCH3   0   0.316   0.0202   6.2363  -2.7940
 AAD  HC51  H  HCH2   0   0.339   0.9636   4.2151  -1.5397
 AAD  HC52  H  HCH2   0   0.343   0.6170   4.7396   0.1317
 AAD  HCG1  H  HCH2   0   0.334  -2.1523   3.0294  -2.2206
 AAD  CB    C  CH2    0  -0.137  -2.8825   4.6954  -3.4137

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
 AAD  C4'  O4'   single    1.424  0.020  1.424
 AAD  C4'  C3'   single    1.523  0.020  1.523
 AAD  C4'  C5'   single    1.509  0.020  1.509
 AAD  C4'  HC4   single    0.970  0.020  1.090
 AAD  O4'  C1'   single    1.401  0.020  1.401
 AAD  C3'  O3'   single    1.403  0.020  1.403
 AAD  C3'  C2'   single    1.533  0.020  1.533
 AAD  C3'  HC3   single    0.970  0.020  1.090
 AAD  O3'  HO3   single    0.850  0.020  0.980
 AAD  C2'  O2'   single    1.388  0.020  1.388
 AAD  C2'  C1'   single    1.547  0.020  1.547
 AAD  C2'  HC2   single    0.970  0.020  1.090
 AAD  O2'  HO2   single    0.850  0.020  0.980
 AAD  C1'  N9    single    1.443  0.020  1.443
 AAD  C1'  HC1   single    0.970  0.020  1.090
 AAD  N9   C8    aromatic  1.368  0.020  1.368
 AAD  N9   C4    aromatic  1.367  0.020  1.367
 AAD  C8   N7    aromatic  1.299  0.020  1.299
 AAD  C8   HC8   single    0.930  0.020  1.080
 AAD  N7   C5    aromatic  1.371  0.020  1.371
 AAD  C5   C6    aromatic  1.408  0.020  1.408
 AAD  C5   C4    aromatic  1.385  0.020  1.385
 AAD  C6   N6    single    1.332  0.020  1.332
 AAD  C6   N1    aromatic  1.338  0.020  1.338
 AAD  N6   HN61  single    0.860  0.020  1.020
 AAD  N6   HN62  single    0.860  0.020  1.020
 AAD  N1   C2    aromatic  1.329  0.020  1.329
 AAD  C2   N3    aromatic  1.322  0.020  1.322
 AAD  C2   HC2A  single    0.930  0.020  1.080
 AAD  N3   C4    aromatic  1.333  0.020  1.333
 AAD  N2   O2    single    1.410  0.020  1.410
 AAD  N2   HN21  single    0.890  0.020  1.040
 AAD  N2   HN22  single    0.890  0.020  1.040
 AAD  O2   CB    single    1.404  0.020  1.404
 AAD  CB   CG    single    1.513  0.020  1.513
 AAD  CB   HCB1  single    0.970  0.020  1.090
 AAD  CB   HCB2  single    0.970  0.020  1.090
 AAD  CG   SD    single    1.817  0.020  1.817
 AAD  CG   HCG1  single    0.970  0.020  1.090
 AAD  CG   HCG2  single    0.970  0.020  1.090
 AAD  SD   CE    single    1.794  0.020  1.794
 AAD  SD   C5'   single    1.815  0.020  1.815
 AAD  CE   HCE1  single    0.970  0.020  1.090
 AAD  CE   HCE2  single    0.970  0.020  1.090
 AAD  CE   HCE3  single    0.970  0.020  1.090
 AAD  C5'  HC51  single    0.970  0.020  1.090
 AAD  C5'  HC52  single    0.970  0.020  1.090

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
 AAD  HC4   C4'  C5'   109.86  3.000
 AAD  HC4   C4'  C3'   108.11  3.000
 AAD  C5'   C4'  C3'   115.90  3.000
 AAD  HC4   C4'  O4'   109.95  3.000
 AAD  C5'   C4'  O4'   107.91  3.000
 AAD  C3'   C4'  O4'   104.94  3.000
 AAD  C1'   O4'  C4'   109.78  3.000
 AAD  HC3   C3'  C2'   111.94  3.000
 AAD  HC3   C3'  O3'   112.61  3.000
 AAD  C2'   C3'  O3'   107.93  3.000
 AAD  HC3   C3'  C4'   111.68  3.000
 AAD  C2'   C3'  C4'    99.18  3.000
 AAD  O3'   C3'  C4'   112.70  3.000
 AAD  HO3   O3'  C3'   109.65  3.000
 AAD  HC2   C2'  C1'   109.38  3.000
 AAD  HC2   C2'  O2'   107.41  3.000
 AAD  C1'   C2'  O2'   113.95  3.000
 AAD  HC2   C2'  C3'   108.33  3.000
 AAD  C1'   C2'  C3'   102.20  3.000
 AAD  O2'   C2'  C3'   115.36  3.000
 AAD  HO2   O2'  C2'   108.11  3.000
 AAD  HC1   C1'  N9    106.21  3.000
 AAD  HC1   C1'  C2'   110.75  3.000
 AAD  N9    C1'  C2'   113.60  3.000
 AAD  HC1   C1'  O4'   109.98  3.000
 AAD  N9    C1'  O4'   109.89  3.000
 AAD  C2'   C1'  O4'   106.44  3.000
 AAD  C4    N9   C8    106.21  3.000
 AAD  C4    N9   C1'   127.40  3.000
 AAD  C8    N9   C1'   126.38  3.000
 AAD  HC8   C8   N7    125.45  3.000
 AAD  HC8   C8   N9    121.00  3.000
 AAD  N7    C8   N9    113.55  3.000
 AAD  C5    N7   C8    104.22  3.000
 AAD  C4    C5   C6    116.36  3.000
 AAD  C4    C5   N7    111.01  3.000
 AAD  C6    C5   N7    132.63  3.000
 AAD  N1    C6   N6    119.36  3.000
 AAD  N1    C6   C5    117.92  3.000
 AAD  N6    C6   C5    122.73  3.000
 AAD  HN62  N6   HN61  118.23  3.000
 AAD  HN62  N6   C6    120.31  3.000
 AAD  HN61  N6   C6    121.14  3.000
 AAD  C2    N1   C6    119.20  3.000
 AAD  HC2A  C2   N3    116.07  3.000
 AAD  HC2A  C2   N1    115.54  3.000
 AAD  N3    C2   N1    128.39  3.000
 AAD  C4    N3   C2    111.81  3.000
 AAD  N3    C4   C5    126.33  3.000
 AAD  N3    C4   N9    128.66  3.000
 AAD  C5    C4   N9    105.01  3.000
 AAD  HN22  N2   HN21  105.85  3.000
 AAD  HN22  N2   O2    104.86  3.000
 AAD  HN21  N2   O2    104.60  3.000
 AAD  CB    O2   N2    109.60  3.000
 AAD  HCG2  CG   HCG1  109.43  3.000
 AAD  HCG2  CG   SD    109.16  3.000
 AAD  HCG1  CG   SD    105.25  3.000
 AAD  HCG2  CG   CB    110.92  3.000
 AAD  HCG1  CG   CB    112.25  3.000
 AAD  SD    CG   CB    109.64  3.000
 AAD  C5'   SD   CE    101.19  3.000
 AAD  C5'   SD   CG    101.91  3.000
 AAD  CE    SD   CG    103.03  3.000
 AAD  HCE3  CE   HCE2  111.20  3.000
 AAD  HCE3  CE   HCE1  110.62  3.000
 AAD  HCE2  CE   HCE1  108.92  3.000
 AAD  HCE3  CE   SD    110.93  3.000
 AAD  HCE2  CE   SD    108.13  3.000
 AAD  HCE1  CE   SD    106.91  3.000
 AAD  HC52  C5'  HC51  109.95  3.000
 AAD  HC52  C5'  SD    105.07  3.000
 AAD  HC51  C5'  SD    108.88  3.000
 AAD  HC52  C5'  C4'   112.49  3.000
 AAD  HC51  C5'  C4'   111.53  3.000
 AAD  SD    C5'  C4'   108.65  3.000
 AAD  HCB2  CB   HCB1  107.38  3.000
 AAD  HCB2  CB   CG    108.04  3.000
 AAD  HCB1  CB   CG    110.61  3.000
 AAD  HCB2  CB   O2    112.51  3.000
 AAD  HCB1  CB   O2    111.55  3.000
 AAD  CG    CB   O2    106.73  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
 AAD  CONST_01  C5    N7  C8  N9      0.00   0.0  0
 AAD  CONST_02  N7    C5  C4  N9      0.00   0.0  0
 AAD  CONST_03  C6    C5  C4  N9    180.00   0.0  0
 AAD  CONST_04  C2    N3  C4  N9    180.00   0.0  0
 AAD  CONST_05  C5    C4  N9  C8      0.00   0.0  0
 AAD  CONST_06  N3    C4  N9  C8    180.00   0.0  0
 AAD  CONST_07  C6    C5  N7  C8    180.00   0.0  0
 AAD  CONST_08  C4    C5  N7  C8      0.00   0.0  0
 AAD  CONST_09  C4    N9  C8  N7      0.00   0.0  0
 AAD  CONST_10  N1    C6  C5  N7    180.00   0.0  0
 AAD  CONST_11  N3    C4  C5  N7    180.00   0.0  0
 AAD  CONST_12  C2    N1  C6  C5      0.00   0.0  0
 AAD  CONST_13  C2    N3  C4  C5      0.00   0.0  0
 AAD  CONST_14  N3    C4  C5  C6      0.00   0.0  0
 AAD  CONST_15  N3    C2  N1  C6      0.00   0.0  0
 AAD  CONST_16  C4    C5  C6  N1      0.00   0.0  0
 AAD  CONST_17  C4    N3  C2  N1      0.00   0.0  0
 AAD  CONST_18  N7    C8  N9  C1'   180.00   0.0  0
 AAD  CONST_19  C5    C4  N9  C1'   180.00   0.0  0
 AAD  CONST_20  N3    C4  N9  C1'     0.00   0.0  0
 AAD  CONST_21  N6    C6  C5  N7      0.00   0.0  0
 AAD  CONST_22  C4    C5  C6  N6    180.00   0.0  0
 AAD  CONST_23  C2    N1  C6  N6    180.00   0.0  0
 AAD  CONST_24  HC8   C8  N9  C1'     0.00   0.0  0
 AAD  CONST_25  HC2A  C2  N1  C6    180.00   0.0  0
 AAD  CONST_26  HN61  N6  C6  C5      0.00   0.0  0
 AAD  CONST_27  HN62  N6  C6  C5    180.00   0.0  0
 AAD  Var_01    CG    CB  O2  N2    175.66  30.0  3
 AAD  Var_02    SD    CG  CB  O2    -48.22  30.0  3
 AAD  Var_03    HN21  N2  O2  CB   -127.86  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
 AAD  chir_01  C4'  O4'  C3'  C5'  positiv
 AAD  chir_02  C3'  O3'  C4'  C2'  positiv
 AAD  chir_03  C2'  O2'  C3'  C1'  positiv
 AAD  chir_04  C1'  O4'  N9   C2'  negativ
 AAD  chir_05  SD   CG   CE   C5'  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
 AAD  plan-1  C1'   0.020
 AAD  plan-1  N9    0.020
 AAD  plan-1  C8    0.020
 AAD  plan-1  N7    0.020
 AAD  plan-1  C5    0.020
 AAD  plan-1  C6    0.020
 AAD  plan-1  N6    0.020
 AAD  plan-1  N1    0.020
 AAD  plan-1  C2    0.020
 AAD  plan-1  N3    0.020
 AAD  plan-1  C4    0.020
 AAD  plan-1  HC8   0.020
 AAD  plan-1  HC2A  0.020
 AAD  plan-2  C6    0.020
 AAD  plan-2  N6    0.020
 AAD  plan-2  HN61  0.020
 AAD  plan-2  HN62  0.020

