# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 18:47:10 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 9-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1,9-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1CC[C@@H](O1)n2cnc3C(=O)NC=Nc23
#
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
 2DI  2DI  9-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1,9-dihydro-6H-purin-6-one  ligand  29  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2DI
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
 2DI  N9    N  NR5   0  -0.522   0.1796  -0.1313   0.4592
 2DI  C4    C  CR56  0   0.482  -1.1338  -0.3941   0.2353
 2DI  N3    N  N     0  -0.449  -1.7151  -1.6105   0.1632
 2DI  C2    C  CR16  0   0.158  -2.9876  -1.5416  -0.0535
 2DI  N1    N  NR16  0  -0.663  -3.6835  -0.3907  -0.1975
 2DI  C6    C  CR6   0   0.509  -3.1545   0.9020  -0.1338
 2DI  O6    O  O     0  -0.467  -3.8590   1.8858  -0.2748
 2DI  C5    C  CR56  0  -0.056  -1.7457   0.8396   0.1106
 2DI  N7    N  N     0  -0.446  -0.8353   1.8423   0.2652
 2DI  C8    C  CR15  0   0.099   0.2955   1.2285   0.4771
 2DI  C5'   C  CH2   0  -0.155   3.8841   0.8050  -0.4908
 2DI  O5'   O  OH1   0  -0.671   4.5948   1.3041   0.6153
 2DI  C4'   C  CH1   0   0.018   3.3214  -0.5537  -0.1511
 2DI  O4'   O  O2    0  -0.499   2.4221  -0.4703   0.9694
 2DI  C1'   C  CH1   0   0.196   1.2316  -1.1332   0.7048
 2DI  C2'   C  CH2   0  -0.508   1.4845  -1.9994  -0.5229
 2DI  C3'   C  CH2   0  -0.506   2.5096  -1.1700  -1.2818
 2DI  H2    H  HCR6  0   0.304  -3.5715  -2.4489  -0.1320
 2DI  HN1   H  HNR6  0   0.435  -4.6794  -0.4671  -0.3603
 2DI  H8    H  HCR5  0   0.295   1.2349   1.7204   0.6695
 2DI  H5'1  H  HCH2  0   0.194   3.0671   1.4753  -0.7919
 2DI  H5'2  H  HCH2  0   0.213   4.5290   0.6799  -1.3709
 2DI  H5'   H  HOH1  0   0.458   4.9414   2.1702   0.3835
 2DI  H4'   H  HCH1  0   0.240   4.1424  -1.2218   0.1348
 2DI  H1'   H  HCH1  0   0.280   0.9234  -1.7092   1.5798
 2DI  H2'1  H  HCH2  0   0.265   1.9173  -2.9465  -0.1954
 2DI  H2'2  H  HCH2  0   0.277   0.5820  -2.2230  -1.0877
 2DI  H3'1  H  HCH2  0   0.248   2.0186  -0.3973  -1.8806
 2DI  H3'2  H  HCH2  0   0.271   3.1286  -1.7658  -1.9499

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
 2DI  N9   C4    aromatic  1.358  0.020  1.358
 2DI  N9   C8    aromatic  1.365  0.020  1.365
 2DI  N9   C1'   single    1.473  0.020  1.473
 2DI  C4   N3    single    1.350  0.020  1.350
 2DI  C4   C5    aromatic  1.383  0.020  1.383
 2DI  N3   C2    double    1.293  0.020  1.293
 2DI  C2   N1    single    1.353  0.020  1.353
 2DI  C2   H2    single    0.930  0.020  1.080
 2DI  N1   C6    single    1.398  0.020  1.398
 2DI  N1   HN1   single    0.860  0.020  1.020
 2DI  C6   O6    double    1.218  0.020  1.218
 2DI  C6   C5    single    1.431  0.020  1.431
 2DI  C5   N7    aromatic  1.363  0.020  1.363
 2DI  N7   C8    aromatic  1.304  0.020  1.304
 2DI  C8   H8    single    0.930  0.020  1.080
 2DI  C5'  O5'   single    1.406  0.020  1.406
 2DI  C5'  C4'   single    1.509  0.020  1.509
 2DI  C5'  H5'1  single    0.970  0.020  1.090
 2DI  C5'  H5'2  single    0.970  0.020  1.090
 2DI  O5'  H5'   single    0.850  0.020  0.980
 2DI  C4'  O4'   single    1.439  0.020  1.439
 2DI  C4'  C3'   single    1.522  0.020  1.522
 2DI  C4'  H4'   single    0.970  0.020  1.090
 2DI  O4'  C1'   single    1.388  0.020  1.388
 2DI  C1'  C2'   single    1.524  0.020  1.524
 2DI  C1'  H1'   single    0.970  0.020  1.090
 2DI  C2'  C3'   single    1.521  0.020  1.521
 2DI  C2'  H2'1  single    0.970  0.020  1.090
 2DI  C2'  H2'2  single    0.970  0.020  1.090
 2DI  C3'  H3'1  single    0.970  0.020  1.090
 2DI  C3'  H3'2  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
 2DI  C1'   N9   C8    127.93  3.000
 2DI  C1'   N9   C4    125.90  3.000
 2DI  C8    N9   C4    106.09  3.000
 2DI  C5    C4   N3    127.48  3.000
 2DI  C5    C4   N9    105.67  3.000
 2DI  N3    C4   N9    126.84  3.000
 2DI  C2    N3   C4    112.63  3.000
 2DI  H2    C2   N1    115.35  3.000
 2DI  H2    C2   N3    119.92  3.000
 2DI  N1    C2   N3    124.73  3.000
 2DI  HN1   N1   C6    116.70  3.000
 2DI  HN1   N1   C2    117.34  3.000
 2DI  C6    N1   C2    125.96  3.000
 2DI  C5    C6   O6    128.62  3.000
 2DI  C5    C6   N1    109.86  3.000
 2DI  O6    C6   N1    121.51  3.000
 2DI  N7    C5   C6    130.14  3.000
 2DI  N7    C5   C4    110.52  3.000
 2DI  C6    C5   C4    119.34  3.000
 2DI  C8    N7   C5    104.56  3.000
 2DI  H8    C8   N7    124.76  3.000
 2DI  H8    C8   N9    122.08  3.000
 2DI  N7    C8   N9    113.15  3.000
 2DI  H5'2  C5'  H5'1  106.65  3.000
 2DI  H5'2  C5'  C4'   107.26  3.000
 2DI  H5'1  C5'  C4'   109.49  3.000
 2DI  H5'2  C5'  O5'   111.96  3.000
 2DI  H5'1  C5'  O5'   112.01  3.000
 2DI  C4'   C5'  O5'   109.32  3.000
 2DI  H5'   O5'  C5'   108.20  3.000
 2DI  H4'   C4'  C3'   110.26  3.000
 2DI  H4'   C4'  O4'   107.46  3.000
 2DI  C3'   C4'  O4'   105.57  3.000
 2DI  H4'   C4'  C5'   109.15  3.000
 2DI  C3'   C4'  C5'   113.34  3.000
 2DI  O4'   C4'  C5'   110.86  3.000
 2DI  C1'   O4'  C4'   111.09  3.000
 2DI  H1'   C1'  C2'   113.12  3.000
 2DI  H1'   C1'  O4'   109.95  3.000
 2DI  C2'   C1'  O4'   106.42  3.000
 2DI  H1'   C1'  N9    106.91  3.000
 2DI  C2'   C1'  N9    111.77  3.000
 2DI  O4'   C1'  N9    108.63  3.000
 2DI  H2'2  C2'  H2'1  107.84  3.000
 2DI  H2'2  C2'  C3'   114.33  3.000
 2DI  H2'1  C2'  C3'   110.83  3.000
 2DI  H2'2  C2'  C1'   113.42  3.000
 2DI  H2'1  C2'  C1'   108.50  3.000
 2DI  C3'   C2'  C1'   101.76  3.000
 2DI  H3'2  C3'  H3'1  107.82  3.000
 2DI  H3'2  C3'  C2'   113.01  3.000
 2DI  H3'1  C3'  C2'   110.83  3.000
 2DI  H3'2  C3'  C4'   111.98  3.000
 2DI  H3'1  C3'  C4'   111.10  3.000
 2DI  C2'   C3'  C4'   102.09  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
 2DI  CONST_01  N7   C5   C4   N9     0.00   0.0  0
 2DI  CONST_02  C5   N7   C8   N9     0.00   0.0  0
 2DI  CONST_03  N7   C8   N9   C4     0.00   0.0  0
 2DI  CONST_04  C8   N7   C5   C4     0.00   0.0  0
 2DI  CONST_05  C8   N9   C4   C5     0.00   0.0  0
 2DI  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 2DI  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 2DI  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 2DI  CONST_09  N1   C2   N3   C4     0.00   0.0  0
 2DI  CONST_10  C6   N1   C2   N3     0.00   0.0  0
 2DI  CONST_11  C5   C6   N1   C2     0.00   0.0  0
 2DI  CONST_12  O6   C6   N1   C2   180.00   0.0  0
 2DI  CONST_13  H8   C8   N9   C4   180.00   0.0  0
 2DI  CONST_14  H2   C2   N3   C4   180.00   0.0  0
 2DI  CONST_15  HN1  N1   C2   N3   180.00   0.0  0
 2DI  Var_01    C1'  C2'  C3'  C4'   35.14  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
 2DI  chir_01  C4'  C5'  O4'  C3'  negativ
 2DI  chir_02  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
 2DI  plan-1  N9   0.020
 2DI  plan-1  C4   0.020
 2DI  plan-1  N3   0.020
 2DI  plan-1  C2   0.020
 2DI  plan-1  N1   0.020
 2DI  plan-1  C6   0.020
 2DI  plan-1  O6   0.020
 2DI  plan-1  C5   0.020
 2DI  plan-1  N7   0.020
 2DI  plan-1  C8   0.020
 2DI  plan-1  C1'  0.020
 2DI  plan-1  H2   0.020
 2DI  plan-1  HN1  0.020
 2DI  plan-1  H8   0.020

