# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:04:40 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 6-amino-9-(2-deoxy-beta-L-erythro-pentofuranosyl)-1,2,7,9-tetrahydro-8H-purin-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C2NC(=O)N([C@@H]3C[C@@H](O)[C@H](CO)O3)C2=NCN1
#
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
 8DA  8DA  6-amino-9-(2-deoxy-beta-L-erythro-pentofuranosyl)-1,2,7,9-tetrahydro-8H-purin-8-one  ligand  34  19  .  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_8DA
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
 8DA  O19   O  OH1   0  -0.674  -3.1012  -2.0532  -1.8622
 8DA  C5'   C  CH2   0  -0.166  -2.8037  -1.7199  -0.5257
 8DA  C4'   C  CH1   0   0.027  -2.7886  -0.2192  -0.3713
 8DA  C3'   C  CH1   0   0.014  -2.5914   0.2135   1.0810
 8DA  O3'   O  OH1   0  -0.671  -3.8475   0.3326   1.7032
 8DA  O4'   O  O2    0  -0.501  -1.7121   0.3356  -1.1068
 8DA  C1'   C  CH1   0   0.207  -1.1032   1.4016  -0.4139
 8DA  C2'   C  CH2   0  -0.555  -1.8202   1.5223   0.9332
 8DA  N9    N  NR5   0  -0.612   0.3173   1.1783  -0.3377
 8DA  C4    C  CR5   0   0.487   0.9618   0.1758   0.3680
 8DA  N3    N  N     0  -0.472   0.4270  -0.7660   1.0555
 8DA  C5    C  CR5   0  -0.011   2.3540   0.3341   0.0896
 8DA  N7    N  NR15  0  -0.731   2.4662   1.4229  -0.8012
 8DA  C8    C  CR5   0   0.666   1.2422   1.9693  -1.0174
 8DA  O18   O  O     0  -0.506   0.9842   2.9704  -1.6617
 8DA  C6    C  C     0   0.554   3.1035  -0.8220   0.1247
 8DA  N6    N  NH2   0  -0.826   4.1938  -1.0723  -0.6239
 8DA  N1    N  NH1   0  -0.660   2.6387  -1.8017   0.9392
 8DA  C2    C  CH2   0  -0.180   1.4647  -1.4927   1.7521
 8DA  H19   H  HOH1  0   0.455  -3.0768  -3.0106  -1.9437
 8DA  H5'1  H  HCH2  0   0.203  -1.8270  -2.1086  -0.2102
 8DA  H5'2  H  HCH2  0   0.197  -3.5556  -2.1190   0.1687
 8DA  H4'   H  HCH1  0   0.217  -3.7400   0.1990  -0.7349
 8DA  H3'   H  HCH1  0   0.233  -1.9611  -0.5178   1.5960
 8DA  H1    H  HOH1  0   0.455  -3.7093   0.3569   2.6541
 8DA  H1'   H  HCH1  0   0.250  -1.2141   2.3230  -0.9887
 8DA  H2'1  H  HCH2  0   0.266  -1.1348   1.7175   1.7568
 8DA  H2'2  H  HCH2  0   0.259  -2.5302   2.3500   0.8804
 8DA  HN7   H  HNR5  0   0.410   3.2969   1.9807  -0.9211
 8DA  HN61  H  HNH2  0   0.403   4.5522  -0.3413  -1.2138
 8DA  HN62  H  HNH2  0   0.406   4.8860  -1.7164  -0.2781
 8DA  HN1   H  HNH1  0   0.398   2.7709  -2.7519   0.6255
 8DA  H21   H  HCH2  0   0.214   1.8127  -0.9043   2.6136
 8DA  H22   H  HCH2  0   0.245   1.0790  -2.4369   2.1299

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
 8DA  O19  C5'   single  1.409  0.020  1.409
 8DA  O19  H19   single  0.850  0.020  0.980
 8DA  C5'  C4'   single  1.509  0.020  1.509
 8DA  C5'  H5'1  single  0.970  0.020  1.090
 8DA  C5'  H5'2  single  0.970  0.020  1.090
 8DA  C4'  C3'   single  1.528  0.020  1.528
 8DA  C4'  O4'   single  1.417  0.020  1.417
 8DA  C4'  H4'   single  0.970  0.020  1.090
 8DA  C3'  O3'   single  1.407  0.020  1.407
 8DA  C3'  C2'   single  1.526  0.020  1.526
 8DA  C3'  H3'   single  0.970  0.020  1.090
 8DA  O3'  H1    single  0.850  0.020  0.980
 8DA  O4'  C1'   single  1.410  0.020  1.410
 8DA  C1'  C2'   single  1.531  0.020  1.531
 8DA  C1'  N9    single  1.440  0.020  1.440
 8DA  C1'  H1'   single  0.970  0.020  1.090
 8DA  C2'  H2'1  single  0.970  0.020  1.090
 8DA  C2'  H2'2  single  0.970  0.020  1.090
 8DA  N9   C4    single  1.385  0.020  1.385
 8DA  N9   C8    single  1.394  0.020  1.394
 8DA  C4   N3    double  1.283  0.020  1.283
 8DA  C4   C5    single  1.429  0.020  1.429
 8DA  N3   C2    single  1.446  0.020  1.446
 8DA  C5   N7    single  1.411  0.020  1.411
 8DA  C5   C6    double  1.378  0.020  1.378
 8DA  N7   C8    single  1.358  0.020  1.358
 8DA  N7   HN7   single  0.890  0.020  1.040
 8DA  C8   O18   double  1.218  0.020  1.218
 8DA  C6   N6    single  1.346  0.020  1.346
 8DA  C6   N1    single  1.356  0.020  1.356
 8DA  N6   HN61  single  0.890  0.020  1.040
 8DA  N6   HN62  single  0.890  0.020  1.040
 8DA  N1   C2    single  1.461  0.020  1.461
 8DA  N1   HN1   single  0.890  0.020  1.040
 8DA  C2   H21   single  0.970  0.020  1.090
 8DA  C2   H22   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
 8DA  H19   O19  C5'   108.10  3.000
 8DA  H5'2  C5'  H5'1  107.38  3.000
 8DA  H5'2  C5'  C4'   107.67  3.000
 8DA  H5'1  C5'  C4'   108.30  3.000
 8DA  H5'2  C5'  O19   111.66  3.000
 8DA  H5'1  C5'  O19   112.13  3.000
 8DA  C4'   C5'  O19   109.54  3.000
 8DA  H4'   C4'  O4'   109.66  3.000
 8DA  H4'   C4'  C3'   108.53  3.000
 8DA  O4'   C4'  C3'   106.53  3.000
 8DA  H4'   C4'  C5'   109.59  3.000
 8DA  O4'   C4'  C5'   110.12  3.000
 8DA  C3'   C4'  C5'   112.34  3.000
 8DA  H3'   C3'  C2'   109.13  3.000
 8DA  H3'   C3'  O3'   111.28  3.000
 8DA  C2'   C3'  O3'   114.92  3.000
 8DA  H3'   C3'  C4'   109.41  3.000
 8DA  C2'   C3'  C4'   102.47  3.000
 8DA  O3'   C3'  C4'   109.21  3.000
 8DA  H1    O3'  C3'   108.13  3.000
 8DA  C1'   O4'  C4'   111.66  3.000
 8DA  H1'   C1'  N9    105.02  3.000
 8DA  H1'   C1'  C2'   110.44  3.000
 8DA  N9    C1'  C2'   115.32  3.000
 8DA  H1'   C1'  O4'   109.61  3.000
 8DA  N9    C1'  O4'   109.56  3.000
 8DA  C2'   C1'  O4'   106.85  3.000
 8DA  H2'2  C2'  H2'1  108.05  3.000
 8DA  H2'2  C2'  C1'   108.77  3.000
 8DA  H2'1  C2'  C1'   112.64  3.000
 8DA  H2'2  C2'  C3'   109.04  3.000
 8DA  H2'1  C2'  C3'   113.48  3.000
 8DA  C1'   C2'  C3'   104.73  3.000
 8DA  C8    N9   C4    110.51  3.000
 8DA  C8    N9   C1'   122.73  3.000
 8DA  C4    N9   C1'   126.75  3.000
 8DA  C5    C4   N3    126.30  3.000
 8DA  C5    C4   N9    105.90  3.000
 8DA  N3    C4   N9    127.62  3.000
 8DA  C2    N3   C4    109.15  3.000
 8DA  C6    C5   N7    128.32  3.000
 8DA  C6    C5   C4    115.60  3.000
 8DA  N7    C5   C4    106.62  3.000
 8DA  HN7   N7   C8    120.09  3.000
 8DA  HN7   N7   C5    124.59  3.000
 8DA  C8    N7   C5    109.84  3.000
 8DA  O18   C8   N7    127.29  3.000
 8DA  O18   C8   N9    125.71  3.000
 8DA  N7    C8   N9    106.99  3.000
 8DA  N1    C6   N6    118.51  3.000
 8DA  N1    C6   C5    115.78  3.000
 8DA  N6    C6   C5    125.61  3.000
 8DA  HN62  N6   HN61  114.94  3.000
 8DA  HN62  N6   C6    119.00  3.000
 8DA  HN61  N6   C6    118.68  3.000
 8DA  HN1   N1   C2    118.51  3.000
 8DA  HN1   N1   C6    116.65  3.000
 8DA  C2    N1   C6    117.18  3.000
 8DA  H22   C2   H21   107.73  3.000
 8DA  H22   C2   N1    107.14  3.000
 8DA  H21   C2   N1    107.15  3.000
 8DA  H22   C2   N3    110.44  3.000
 8DA  H21   C2   N3    109.60  3.000
 8DA  N1    C2   N3    114.51  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
 8DA  CONST_01  N3    C4  N9  C1'    0.00   0.0  0
 8DA  CONST_02  C5    C4  N9  C1'  180.00   0.0  0
 8DA  CONST_03  N7    C8  N9  C1'  180.00   0.0  0
 8DA  CONST_04  C2    N3  C4  N9   180.00   0.0  0
 8DA  CONST_05  N7    C5  C4  N9     0.00   0.0  0
 8DA  CONST_06  C5    N7  C8  N9     0.00   0.0  0
 8DA  CONST_07  N7    C8  N9  C4     0.00   0.0  0
 8DA  CONST_08  C8    N7  C5  C4     0.00   0.0  0
 8DA  CONST_09  C8    N9  C4  N3   180.00   0.0  0
 8DA  CONST_10  C8    N9  C4  C5     0.00   0.0  0
 8DA  CONST_11  C2    N3  C4  C5     0.00   0.0  0
 8DA  CONST_12  C2    N1  C6  C5     0.00   0.0  0
 8DA  CONST_13  O18   C8  N9  C1'    0.00   0.0  0
 8DA  CONST_14  O18   C8  N9  C4   180.00   0.0  0
 8DA  CONST_15  O18   C8  N7  C5   180.00   0.0  0
 8DA  CONST_16  C2    N1  C6  N6   180.00   0.0  0
 8DA  CONST_19  HN61  N6  C6  C5     0.00   0.0  0
 8DA  Var_01    H21   C2  N3  C4    76.02  30.0  1

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
 8DA  chir_01  C4'  C5'  C3'  O4'  negativ
 8DA  chir_02  C3'  O3'  C2'  C4'  positiv
 8DA  chir_03  C1'  O4'  N9   C2'  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
 8DA  plan-1  C1'   0.020
 8DA  plan-1  N9    0.020
 8DA  plan-1  C4    0.020
 8DA  plan-1  N3    0.020
 8DA  plan-1  C5    0.020
 8DA  plan-1  N7    0.020
 8DA  plan-1  C8    0.020
 8DA  plan-1  O18   0.020
 8DA  plan-1  C6    0.020
 8DA  plan-1  N6    0.020
 8DA  plan-1  N1    0.020
 8DA  plan-1  C2    0.020
 8DA  plan-1  HN7   0.020
 8DA  plan-1  HN61  0.020
 8DA  plan-1  HN62  0.020
 8DA  plan-1  HN1   0.020

