# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:37:10 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 9-beta-D-erythro-pentofuranosyl-3-ulose-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)C(=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
 ADY  ADY  9-beta-D-erythro-pentofuranosyl-3-ulose-9H-purin-6-amine  ligand  30  19  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ADY
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
 ADY  O5'   O  OH1   0  -0.663  -3.9436   2.1719  -1.2322
 ADY  C5'   C  CH2   0  -0.147  -3.9888   1.2003  -0.2208
 ADY  C4'   C  CH1   0  -0.092  -3.0365   0.0837  -0.5927
 ADY  O4'   O  O2    0  -0.485  -1.6942   0.5459  -0.6092
 ADY  C3'   C  C     0   0.327  -3.0413  -1.0467   0.4177
 ADY  O3'   O  O     0  -0.354  -3.9712  -1.7520   0.6964
 ADY  C2'   C  CH1   0  -0.093  -1.6372  -1.1385   0.9864
 ADY  O2'   O  OH1   0  -0.644  -1.1848  -2.4218   1.2472
 ADY  C1'   C  CH1   0   0.185  -0.8480  -0.4769  -0.1382
 ADY  N9    N  NR5   0  -0.550   0.3979   0.1025   0.2526
 ADY  C8    C  CR15  0   0.114   0.6068   1.0664   1.2066
 ADY  N7    N  N     0  -0.445   1.8485   1.4288   1.3046
 ADY  C5    C  CR56  0  -0.010   2.5038   0.6718   0.3660
 ADY  C6    C  CR6   0   0.464   3.8525   0.5911  -0.0278
 ADY  N6    N  NH2   0  -0.815   4.8137   1.3238   0.5337
 ADY  N1    N  N     0  -0.474   4.1678  -0.2661  -1.0059
 ADY  C2    C  CR16  0   0.050   3.2078  -0.9993  -1.5612
 ADY  N3    N  N     0  -0.457   1.9162  -1.0124  -1.2771
 ADY  C4    C  CR56  0   0.495   1.6199  -0.1562  -0.3045
 ADY  HO5'  H  HOH1  0   0.462  -4.4885   2.9154  -0.9581
 ADY  H5'1  H  HCH2  0   0.217  -4.9872   0.7591  -0.1126
 ADY  H5'2  H  HCH2  0   0.214  -3.7042   1.6075   0.7576
 ADY  H4'   H  HCH1  0   0.291  -3.3165  -0.3271  -1.5739
 ADY  H2'   H  HCH1  0   0.283  -1.6183  -0.4851   1.8742
 ADY  HO2'  H  HOH1  0   0.472  -1.5784  -2.7347   2.0680
 ADY  H1'   H  HCH1  0   0.280  -0.6265  -1.2174  -0.9171
 ADY  H8    H  HCR5  0   0.302  -0.2027   1.4677   1.7980
 ADY  HN61  H  HNH2  0   0.405   5.7588   1.2654   0.1957
 ADY  HN62  H  HNH2  0   0.412   4.6021   2.0059   1.2402
 ADY  H2    H  HCR6  0   0.254   3.5308  -1.6714  -2.3492

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
 ADY  O5'  C5'   single    1.403  0.020  1.403
 ADY  O5'  HO5'  single    0.850  0.020  0.980
 ADY  C5'  C4'   single    1.514  0.020  1.514
 ADY  C5'  H5'1  single    0.970  0.020  1.090
 ADY  C5'  H5'2  single    0.970  0.020  1.090
 ADY  C4'  O4'   single    1.420  0.020  1.420
 ADY  C4'  C3'   single    1.516  0.020  1.516
 ADY  C4'  H4'   single    0.970  0.020  1.090
 ADY  O4'  C1'   single    1.409  0.020  1.409
 ADY  C3'  O3'   double    1.200  0.020  1.200
 ADY  C3'  C2'   single    1.518  0.020  1.518
 ADY  C2'  O2'   single    1.385  0.020  1.385
 ADY  C2'  C1'   single    1.525  0.020  1.525
 ADY  C2'  H2'   single    0.970  0.020  1.090
 ADY  O2'  HO2'  single    0.850  0.020  0.980
 ADY  C1'  N9    single    1.429  0.020  1.429
 ADY  C1'  H1'   single    0.970  0.020  1.090
 ADY  N9   C8    aromatic  1.372  0.020  1.372
 ADY  N9   C4    aromatic  1.368  0.020  1.368
 ADY  C8   N7    aromatic  1.297  0.020  1.297
 ADY  C8   H8    single    0.930  0.020  1.080
 ADY  N7   C5    aromatic  1.372  0.020  1.372
 ADY  C5   C6    aromatic  1.407  0.020  1.407
 ADY  C5   C4    aromatic  1.384  0.020  1.384
 ADY  C6   N6    single    1.333  0.020  1.333
 ADY  C6   N1    aromatic  1.338  0.020  1.338
 ADY  N6   HN61  single    0.860  0.020  1.020
 ADY  N6   HN62  single    0.860  0.020  1.020
 ADY  N1   C2    aromatic  1.330  0.020  1.330
 ADY  C2   N3    aromatic  1.323  0.020  1.323
 ADY  C2   H2    single    0.930  0.020  1.080
 ADY  N3   C4    aromatic  1.329  0.020  1.329

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
 ADY  HO5'  O5'  C5'   108.16  3.000
 ADY  H5'2  C5'  H5'1  107.30  3.000
 ADY  H5'2  C5'  C4'   109.24  3.000
 ADY  H5'1  C5'  C4'   107.47  3.000
 ADY  H5'2  C5'  O5'   112.17  3.000
 ADY  H5'1  C5'  O5'   112.27  3.000
 ADY  C4'   C5'  O5'   108.26  3.000
 ADY  H4'   C4'  C3'   108.37  3.000
 ADY  H4'   C4'  O4'   110.60  3.000
 ADY  C3'   C4'  O4'   104.68  3.000
 ADY  H4'   C4'  C5'   109.54  3.000
 ADY  C3'   C4'  C5'   112.59  3.000
 ADY  O4'   C4'  C5'   110.94  3.000
 ADY  C1'   O4'  C4'   109.13  3.000
 ADY  C2'   C3'  O3'   126.46  3.000
 ADY  C2'   C3'  C4'   106.97  3.000
 ADY  O3'   C3'  C4'   126.55  3.000
 ADY  H2'   C2'  C1'   109.14  3.000
 ADY  H2'   C2'  O2'   113.06  3.000
 ADY  C1'   C2'  O2'   111.82  3.000
 ADY  H2'   C2'  C3'   106.37  3.000
 ADY  C1'   C2'  C3'   100.15  3.000
 ADY  O2'   C2'  C3'   115.39  3.000
 ADY  HO2'  O2'  C2'   109.15  3.000
 ADY  H1'   C1'  N9    106.97  3.000
 ADY  H1'   C1'  C2'   109.59  3.000
 ADY  N9    C1'  C2'   115.19  3.000
 ADY  H1'   C1'  O4'   111.96  3.000
 ADY  N9    C1'  O4'   108.72  3.000
 ADY  C2'   C1'  O4'   104.52  3.000
 ADY  C4    N9   C8    106.27  3.000
 ADY  C4    N9   C1'   126.23  3.000
 ADY  C8    N9   C1'   127.43  3.000
 ADY  H8    C8   N7    124.91  3.000
 ADY  H8    C8   N9    121.85  3.000
 ADY  N7    C8   N9    113.23  3.000
 ADY  C5    N7   C8    104.55  3.000
 ADY  C4    C5   C6    116.24  3.000
 ADY  C4    C5   N7    110.87  3.000
 ADY  C6    C5   N7    132.89  3.000
 ADY  N1    C6   N6    119.35  3.000
 ADY  N1    C6   C5    117.84  3.000
 ADY  N6    C6   C5    122.81  3.000
 ADY  HN62  N6   HN61  118.28  3.000
 ADY  HN62  N6   C6    121.18  3.000
 ADY  HN61  N6   C6    120.29  3.000
 ADY  C2    N1   C6    119.24  3.000
 ADY  H2    C2   N3    116.15  3.000
 ADY  H2    C2   N1    115.47  3.000
 ADY  N3    C2   N1    128.38  3.000
 ADY  C4    N3   C2    111.62  3.000
 ADY  N3    C4   C5    126.68  3.000
 ADY  N3    C4   N9    128.25  3.000
 ADY  C5    C4   N9    105.07  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
 ADY  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 ADY  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 ADY  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 ADY  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 ADY  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 ADY  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 ADY  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 ADY  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 ADY  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 ADY  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 ADY  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 ADY  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 ADY  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 ADY  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 ADY  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 ADY  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 ADY  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 ADY  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 ADY  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 ADY  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 ADY  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 ADY  CONST_22  C4    C5  C6  N6   180.00  0.0  0
 ADY  CONST_23  C2    N1  C6  N6   180.00  0.0  0
 ADY  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 ADY  CONST_25  H2    C2  N1  C6   180.00  0.0  0
 ADY  CONST_26  HN61  N6  C6  C5   180.00  0.0  0
 ADY  CONST_27  HN62  N6  C6  C5     0.00  0.0  0

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
 ADY  chir_01  C4'  C5'  O4'  C3'  negativ
 ADY  chir_02  C2'  O2'  C3'  C1'  positiv
 ADY  chir_03  C1'  O4'  N9   C2'  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
 ADY  plan-1  C1'   0.020
 ADY  plan-1  N9    0.020
 ADY  plan-1  C8    0.020
 ADY  plan-1  N7    0.020
 ADY  plan-1  C5    0.020
 ADY  plan-1  C6    0.020
 ADY  plan-1  N6    0.020
 ADY  plan-1  N1    0.020
 ADY  plan-1  C2    0.020
 ADY  plan-1  N3    0.020
 ADY  plan-1  C4    0.020
 ADY  plan-1  H8    0.020
 ADY  plan-1  H2    0.020
 ADY  plan-2  C6    0.020
 ADY  plan-2  N6    0.020
 ADY  plan-2  HN61  0.020
 ADY  plan-2  HN62  0.020
 ADY  plan-3  C4'   0.020
 ADY  plan-3  C3'   0.020
 ADY  plan-3  O3'   0.020
 ADY  plan-3  C2'   0.020

