# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 09:57:44 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-beta-D-ribofuranosyl-3H-imidazo[4,5-b]pyridin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccnc2n(cnc12)[C@@H]3O[C@H](CO)[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
 1DA  1DA  3-beta-D-ribofuranosyl-3H-imidazo[4,5-b]pyridin-7-amine  ligand  33  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1DA
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
 1DA  O5'   O  OH1   0  -0.667  -1.9836   0.9385  -4.1854
 1DA  C5'   C  CH2   0  -0.156  -1.3752  -0.1736  -3.5787
 1DA  C4'   C  CH1   0   0.011  -0.0405   0.2400  -3.0110
 1DA  O4'   O  O2    0  -0.496  -0.2088   1.1963  -1.9637
 1DA  C3'   C  CH1   0  -0.044   0.7202  -0.9170  -2.3688
 1DA  O3'   O  OH1   0  -0.656   1.4575  -1.6084  -3.3367
 1DA  C2'   C  CH1   0  -0.037   1.5821  -0.1868  -1.3344
 1DA  O2'   O  OH1   0  -0.665   2.6786   0.4363  -1.9447
 1DA  C1'   C  CH1   0   0.174   0.6215   0.9106  -0.8787
 1DA  N9    N  NR5   0  -0.538  -0.1915   0.4788   0.2505
 1DA  C8    C  CR15  0   0.103  -1.4959   0.0811   0.2680
 1DA  N7    N  N     0  -0.461  -1.9220  -0.2431   1.4546
 1DA  C5    C  CR56  0   0.027  -0.8420  -0.0479   2.2777
 1DA  C6    C  CR6   0   0.356  -0.6959  -0.2302   3.6622
 1DA  N6    N  NH2   0  -0.844  -1.7198  -0.6372   4.4430
 1DA  C1    C  CR16  0  -0.428   0.5802   0.0839   4.1550
 1DA  C2    C  CR16  0  -0.097   1.5845   0.5351   3.3034
 1DA  N3    N  N     0  -0.462   1.4648   0.7088   1.9894
 1DA  C4    C  CR56  0   0.459   0.2533   0.4076   1.5452
 1DA  HO5'  H  HOH1  0   0.459  -2.8274   0.6573  -4.5504
 1DA  H5'1  H  HCH2  0   0.214  -1.1884  -0.9830  -4.2965
 1DA  H5'2  H  HCH2  0   0.198  -1.9963  -0.5982  -2.7780
 1DA  H4'   H  HCH1  0   0.245   0.5694   0.6829  -3.8084
 1DA  H3'   H  HCH1  0   0.243   0.0187  -1.5836  -1.8482
 1DA  HO3'  H  HOH1  0   0.469   1.6968  -2.4729  -2.9872
 1DA  H2'   H  HCH1  0   0.259   1.8892  -0.8343  -0.5046
 1DA  HO2'  H  HOH1  0   0.451   3.0179  -0.1599  -2.6240
 1DA  H1'   H  HCH1  0   0.279   1.1621   1.8065  -0.5610
 1DA  H8    H  HCR5  0   0.294  -2.1017   0.0597  -0.6240
 1DA  HN61  H  HNH2  0   0.396  -1.5187  -0.9709   5.3703
 1DA  HN62  H  HNH2  0   0.395  -2.5207  -1.0563   4.0020
 1DA  H1    H  HCR6  0   0.265   0.7942  -0.0228   5.2107
 1DA  H2    H  HCR6  0   0.254   2.5554   0.7662   3.7274

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
 1DA  O5'  C5'   single    1.405  0.020  1.405
 1DA  O5'  HO5'  single    0.850  0.020  0.980
 1DA  C5'  C4'   single    1.508  0.020  1.508
 1DA  C5'  H5'1  single    0.970  0.020  1.090
 1DA  C5'  H5'2  single    0.970  0.020  1.090
 1DA  C4'  O4'   single    1.428  0.020  1.428
 1DA  C4'  C3'   single    1.526  0.020  1.526
 1DA  C4'  H4'   single    0.970  0.020  1.090
 1DA  O4'  C1'   single    1.396  0.020  1.396
 1DA  C3'  O3'   single    1.400  0.020  1.400
 1DA  C3'  C2'   single    1.532  0.020  1.532
 1DA  C3'  H3'   single    0.970  0.020  1.090
 1DA  O3'  HO3'  single    0.850  0.020  0.980
 1DA  C2'  O2'   single    1.401  0.020  1.401
 1DA  C2'  C1'   single    1.528  0.020  1.528
 1DA  C2'  H2'   single    0.970  0.020  1.090
 1DA  O2'  HO2'  single    0.850  0.020  0.980
 1DA  C1'  N9    single    1.457  0.020  1.457
 1DA  C1'  H1'   single    0.970  0.020  1.090
 1DA  N9   C8    aromatic  1.364  0.020  1.364
 1DA  N9   C4    aromatic  1.371  0.020  1.371
 1DA  C8   N7    aromatic  1.302  0.020  1.302
 1DA  C8   H8    single    0.930  0.020  1.080
 1DA  N7   C5    aromatic  1.372  0.020  1.372
 1DA  C5   C6    aromatic  1.404  0.020  1.404
 1DA  C5   C4    aromatic  1.394  0.020  1.394
 1DA  C6   N6    single    1.350  0.020  1.350
 1DA  C6   C1    aromatic  1.403  0.020  1.403
 1DA  N6   HN61  single    0.890  0.020  1.040
 1DA  N6   HN62  single    0.890  0.020  1.040
 1DA  C1   C2    aromatic  1.392  0.020  1.392
 1DA  C1   H1    single    0.930  0.020  1.080
 1DA  C2   N3    aromatic  1.331  0.020  1.331
 1DA  C2   H2    single    0.930  0.020  1.080
 1DA  N3   C4    aromatic  1.325  0.020  1.325

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
 1DA  HO5'  O5'  C5'   108.20  3.000
 1DA  H5'2  C5'  H5'1  106.73  3.000
 1DA  H5'2  C5'  C4'   109.39  3.000
 1DA  H5'1  C5'  C4'   107.32  3.000
 1DA  H5'2  C5'  O5'   112.07  3.000
 1DA  H5'1  C5'  O5'   112.01  3.000
 1DA  C4'   C5'  O5'   109.18  3.000
 1DA  H4'   C4'  C3'   109.56  3.000
 1DA  H4'   C4'  O4'   109.15  3.000
 1DA  C3'   C4'  O4'   104.94  3.000
 1DA  H4'   C4'  C5'   109.21  3.000
 1DA  C3'   C4'  C5'   113.05  3.000
 1DA  O4'   C4'  C5'   110.82  3.000
 1DA  C1'   O4'  C4'   111.27  3.000
 1DA  H3'   C3'  C2'   109.18  3.000
 1DA  H3'   C3'  O3'   111.36  3.000
 1DA  C2'   C3'  O3'   113.96  3.000
 1DA  H3'   C3'  C4'   109.94  3.000
 1DA  C2'   C3'  C4'   101.73  3.000
 1DA  O3'   C3'  C4'   110.25  3.000
 1DA  HO3'  O3'  C3'   108.88  3.000
 1DA  H2'   C2'  C1'   111.99  3.000
 1DA  H2'   C2'  O2'   111.91  3.000
 1DA  C1'   C2'  O2'   107.61  3.000
 1DA  H2'   C2'  C3'   112.78  3.000
 1DA  C1'   C2'  C3'   100.95  3.000
 1DA  O2'   C2'  C3'   110.99  3.000
 1DA  HO2'  O2'  C2'   107.87  3.000
 1DA  H1'   C1'  N9    107.07  3.000
 1DA  H1'   C1'  C2'   111.36  3.000
 1DA  N9    C1'  C2'   111.66  3.000
 1DA  H1'   C1'  O4'   110.62  3.000
 1DA  N9    C1'  O4'   109.34  3.000
 1DA  C2'   C1'  O4'   106.81  3.000
 1DA  C4    N9   C8    106.44  3.000
 1DA  C4    N9   C1'   124.50  3.000
 1DA  C8    N9   C1'   129.06  3.000
 1DA  H8    C8   N7    124.41  3.000
 1DA  H8    C8   N9    122.17  3.000
 1DA  N7    C8   N9    113.42  3.000
 1DA  C5    N7   C8    104.70  3.000
 1DA  C4    C5   C6    118.60  3.000
 1DA  C4    C5   N7    110.47  3.000
 1DA  C6    C5   N7    130.93  3.000
 1DA  C1    C6   N6    123.63  3.000
 1DA  C1    C6   C5    114.31  3.000
 1DA  N6    C6   C5    122.03  3.000
 1DA  HN62  N6   HN61  115.16  3.000
 1DA  HN62  N6   C6    118.41  3.000
 1DA  HN61  N6   C6    118.78  3.000
 1DA  H1    C1   C2    119.08  3.000
 1DA  H1    C1   C6    120.01  3.000
 1DA  C2    C1   C6    120.92  3.000
 1DA  H2    C2   N3    116.03  3.000
 1DA  H2    C2   C1    118.42  3.000
 1DA  N3    C2   C1    125.55  3.000
 1DA  C4    N3   C2    112.55  3.000
 1DA  N3    C4   C5    128.06  3.000
 1DA  N3    C4   N9    126.97  3.000
 1DA  C5    C4   N9    104.97  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
 1DA  CONST_01  C5  N7  C8  N9     0.00  0.0  0
 1DA  CONST_02  N7  C5  C4  N9     0.00  0.0  0
 1DA  CONST_03  C6  C5  C4  N9   180.00  0.0  0
 1DA  CONST_04  C2  N3  C4  N9   180.00  0.0  0
 1DA  CONST_05  C5  C4  N9  C8     0.00  0.0  0
 1DA  CONST_06  N3  C4  N9  C8   180.00  0.0  0
 1DA  CONST_07  C6  C5  N7  C8   180.00  0.0  0
 1DA  CONST_08  C4  C5  N7  C8     0.00  0.0  0
 1DA  CONST_09  C4  N9  C8  N7     0.00  0.0  0
 1DA  CONST_10  C1  C6  C5  N7   180.00  0.0  0
 1DA  CONST_11  N3  C4  C5  N7   180.00  0.0  0
 1DA  CONST_12  C2  C1  C6  C5     0.00  0.0  0
 1DA  CONST_13  C2  N3  C4  C5     0.00  0.0  0
 1DA  CONST_14  N3  C4  C5  C6     0.00  0.0  0
 1DA  CONST_15  N3  C2  C1  C6     0.00  0.0  0
 1DA  CONST_16  C4  C5  C6  C1     0.00  0.0  0
 1DA  CONST_17  C4  N3  C2  C1     0.00  0.0  0
 1DA  CONST_18  N7  C8  N9  C1'  180.00  0.0  0
 1DA  CONST_19  C5  C4  N9  C1'  180.00  0.0  0
 1DA  CONST_20  N3  C4  N9  C1'    0.00  0.0  0
 1DA  CONST_21  N6  C6  C5  N7     0.00  0.0  0
 1DA  CONST_22  C4  C5  C6  N6   180.00  0.0  0
 1DA  CONST_23  C2  C1  C6  N6   180.00  0.0  0
 1DA  CONST_24  H8  C8  N9  C1'    0.00  0.0  0
 1DA  CONST_25  H1  C1  C6  C5   180.00  0.0  0
 1DA  CONST_26  H2  C2  C1  C6   180.00  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
 1DA  chir_01  C4'  C5'  O4'  C3'  negativ
 1DA  chir_02  C3'  O3'  C4'  C2'  positiv
 1DA  chir_03  C2'  O2'  C3'  C1'  positiv
 1DA  chir_04  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
 1DA  plan-1  C1'   0.020
 1DA  plan-1  N9    0.020
 1DA  plan-1  C8    0.020
 1DA  plan-1  N7    0.020
 1DA  plan-1  C5    0.020
 1DA  plan-1  C6    0.020
 1DA  plan-1  N6    0.020
 1DA  plan-1  C1    0.020
 1DA  plan-1  C2    0.020
 1DA  plan-1  N3    0.020
 1DA  plan-1  C4    0.020
 1DA  plan-1  H8    0.020
 1DA  plan-1  H1    0.020
 1DA  plan-1  H2    0.020
 1DA  plan-2  C6    0.020
 1DA  plan-2  N6    0.020
 1DA  plan-2  HN61  0.020
 1DA  plan-2  HN62  0.020

