# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:54:05 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 9-beta-D-ribofuranosyl-8,9-dihydro-7H-purin-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2CNc3c(O)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
 HPR  HPR  9-beta-D-ribofuranosyl-8,9-dihydro-7H-purin-6-ol  ligand  33  19  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HPR
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
 HPR  N1    N  N     0  -0.444  -0.8529  -0.1721  -4.0741
 HPR  C2    C  CR16  0   0.032  -1.7094   0.2559  -3.1744
 HPR  N3    N  N     0  -0.463  -1.4899   0.4242  -1.8678
 HPR  C4    C  CR56  0   0.511  -0.2616   0.1201  -1.4962
 HPR  C5    C  CR56  0   0.032   0.7418  -0.3254  -2.3562
 HPR  C6    C  CR6   0   0.449   0.3878  -0.4754  -3.6753
 HPR  O6    O  OH1   0  -0.603   1.2037  -0.8969  -4.6486
 HPR  N7    N  NR15  0  -0.695   1.8977  -0.5767  -1.6158
 HPR  C8    C  CH2   0  -0.098   1.6936   0.0531  -0.3057
 HPR  N9    N  NR5   0  -0.560   0.2374   0.1793  -0.2323
 HPR  C1'   C  CH1   0   0.182  -0.4189   0.9733   0.7954
 HPR  C2'   C  CH1   0  -0.034  -1.6232   0.2287   1.3600
 HPR  O2'   O  OH1   0  -0.669  -2.5024   1.1805   1.8977
 HPR  C3'   C  CH1   0  -0.035  -0.9618  -0.6003   2.4641
 HPR  O3'   O  OH1   0  -0.665  -1.8554  -0.9765   3.4771
 HPR  C4'   C  CH1   0   0.015   0.0996   0.3654   2.9880
 HPR  O4'   O  O2    0  -0.500   0.4656   1.1639   1.8643
 HPR  C5'   C  CH2   0  -0.155   1.3023  -0.3321   3.5712
 HPR  O5'   O  OH1   0  -0.670   2.2064   0.6291   4.0584
 HPR  H2    H  HCR6  0   0.255  -2.7050   0.4998  -3.5275
 HPR  HO6   H  HOH1  0   0.481   2.0465  -1.2046  -4.2957
 HPR  HN7   H  HNR5  0   0.389   2.7690  -0.3017  -2.0468
 HPR  H81   H  HCH2  0   0.231   2.1902   1.0307  -0.2421
 HPR  H82   H  HCH2  0   0.243   2.0814  -0.5806   0.4914
 HPR  H1'   H  HCH1  0   0.257  -0.7031   1.9493   0.3817
 HPR  H2'   H  HCH1  0   0.253  -2.1124  -0.3962   0.6054
 HPR  HO2'  H  HOH1  0   0.452  -3.0937   0.7243   2.5075
 HPR  H3'   H  HCH1  0   0.246  -0.4810  -1.4742   2.0085
 HPR  HO3'  H  HOH1  0   0.467  -2.0064  -1.9238   3.4286
 HPR  H4'   H  HCH1  0   0.234  -0.3488   1.0122   3.7531
 HPR  H5'1  H  HCH2  0   0.196   1.7607  -0.9727   2.8050
 HPR  H5'2  H  HCH2  0   0.209   0.9417  -0.9959   4.3680
 HPR  HO5'  H  HOH1  0   0.458   2.9303   0.1680   4.4917

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
 HPR  N1   C2    aromatic  1.314  0.020  1.314
 HPR  N1   C6    aromatic  1.338  0.020  1.338
 HPR  C2   N3    aromatic  1.336  0.020  1.336
 HPR  C2   H2    single    0.930  0.020  1.080
 HPR  N3   C4    aromatic  1.319  0.020  1.319
 HPR  C4   C5    aromatic  1.395  0.020  1.395
 HPR  C4   N9    single    1.360  0.020  1.360
 HPR  C5   C6    aromatic  1.374  0.020  1.374
 HPR  C5   N7    single    1.396  0.020  1.396
 HPR  C6   O6    single    1.338  0.020  1.338
 HPR  O6   HO6   single    0.850  0.020  0.980
 HPR  N7   C8    single    1.468  0.020  1.468
 HPR  N7   HN7   single    0.890  0.020  1.040
 HPR  C8   N9    single    1.463  0.020  1.463
 HPR  C8   H81   single    0.970  0.020  1.090
 HPR  C8   H82   single    0.970  0.020  1.090
 HPR  N9   C1'   single    1.455  0.020  1.455
 HPR  C1'  C2'   single    1.524  0.020  1.524
 HPR  C1'  O4'   single    1.400  0.020  1.400
 HPR  C1'  H1'   single    0.970  0.020  1.090
 HPR  C2'  O2'   single    1.403  0.020  1.403
 HPR  C2'  C3'   single    1.531  0.020  1.531
 HPR  C2'  H2'   single    0.970  0.020  1.090
 HPR  O2'  HO2'  single    0.850  0.020  0.980
 HPR  C3'  O3'   single    1.402  0.020  1.402
 HPR  C3'  C4'   single    1.528  0.020  1.528
 HPR  C3'  H3'   single    0.970  0.020  1.090
 HPR  O3'  HO3'  single    0.850  0.020  0.980
 HPR  C4'  O4'   single    1.426  0.020  1.426
 HPR  C4'  C5'   single    1.508  0.020  1.508
 HPR  C4'  H4'   single    0.970  0.020  1.090
 HPR  C5'  O5'   single    1.407  0.020  1.407
 HPR  C5'  H5'1  single    0.970  0.020  1.090
 HPR  C5'  H5'2  single    0.970  0.020  1.090
 HPR  O5'  HO5'  single    0.850  0.020  0.980

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
 HPR  C6    N1   C2    118.31  3.000
 HPR  H2    C2   N3    116.18  3.000
 HPR  H2    C2   N1    116.67  3.000
 HPR  N3    C2   N1    127.14  3.000
 HPR  C4    N3   C2    113.56  3.000
 HPR  N9    C4   C5    108.84  3.000
 HPR  N9    C4   N3    126.41  3.000
 HPR  C5    C4   N3    124.75  3.000
 HPR  N7    C5   C6    134.68  3.000
 HPR  N7    C5   C4    109.04  3.000
 HPR  C6    C5   C4    116.20  3.000
 HPR  O6    C6   C5    125.14  3.000
 HPR  O6    C6   N1    114.83  3.000
 HPR  C5    C6   N1    120.02  3.000
 HPR  HO6   O6   C6    111.55  3.000
 HPR  HN7   N7   C8    112.58  3.000
 HPR  HN7   N7   C5    116.04  3.000
 HPR  C8    N7   C5    106.32  3.000
 HPR  H82   C8   H81   108.32  3.000
 HPR  H82   C8   N9    111.57  3.000
 HPR  H81   C8   N9    111.73  3.000
 HPR  H82   C8   N7    110.73  3.000
 HPR  H81   C8   N7    111.76  3.000
 HPR  N9    C8   N7    102.72  3.000
 HPR  C1'   N9   C8    122.09  3.000
 HPR  C1'   N9   C4    120.97  3.000
 HPR  C8    N9   C4    108.34  3.000
 HPR  H1'   C1'  O4'   109.28  3.000
 HPR  H1'   C1'  C2'   111.68  3.000
 HPR  O4'   C1'  C2'   106.42  3.000
 HPR  H1'   C1'  N9    109.62  3.000
 HPR  O4'   C1'  N9    109.18  3.000
 HPR  C2'   C1'  N9    110.57  3.000
 HPR  H2'   C2'  C3'   112.39  3.000
 HPR  H2'   C2'  O2'   111.79  3.000
 HPR  C3'   C2'  O2'   111.21  3.000
 HPR  H2'   C2'  C1'   112.12  3.000
 HPR  C3'   C2'  C1'   100.98  3.000
 HPR  O2'   C2'  C1'   107.80  3.000
 HPR  HO2'  O2'  C2'   107.80  3.000
 HPR  H3'   C3'  C4'   109.97  3.000
 HPR  H3'   C3'  O3'   111.46  3.000
 HPR  C4'   C3'  O3'   111.39  3.000
 HPR  H3'   C3'  C2'   108.74  3.000
 HPR  C4'   C3'  C2'   101.84  3.000
 HPR  O3'   C3'  C2'   113.02  3.000
 HPR  HO3'  O3'  C3'   109.17  3.000
 HPR  H4'   C4'  C5'   109.20  3.000
 HPR  H4'   C4'  O4'   108.91  3.000
 HPR  C5'   C4'  O4'   111.05  3.000
 HPR  H4'   C4'  C3'   109.13  3.000
 HPR  C5'   C4'  C3'   113.24  3.000
 HPR  O4'   C4'  C3'   105.19  3.000
 HPR  C4'   O4'  C1'   111.29  3.000
 HPR  H5'2  C5'  H5'1  106.89  3.000
 HPR  H5'2  C5'  O5'   111.89  3.000
 HPR  H5'1  C5'  O5'   111.82  3.000
 HPR  H5'2  C5'  C4'   107.36  3.000
 HPR  H5'1  C5'  C4'   109.44  3.000
 HPR  O5'   C5'  C4'   109.31  3.000
 HPR  HO5'  O5'  C5'   108.20  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
 HPR  CONST_01  C4  N3  C2  N1     0.00   0.0  0
 HPR  CONST_02  C4  C5  C6  N1     0.00   0.0  0
 HPR  CONST_03  C5  C6  N1  C2     0.00   0.0  0
 HPR  CONST_04  C5  C4  N3  C2     0.00   0.0  0
 HPR  CONST_05  C6  N1  C2  N3     0.00   0.0  0
 HPR  CONST_06  C6  C5  C4  N3     0.00   0.0  0
 HPR  CONST_07  O6  C6  N1  C2   180.00   0.0  0
 HPR  CONST_08  O6  C6  C5  C4   180.00   0.0  0
 HPR  CONST_09  N7  C5  C6  O6     0.00   0.0  0
 HPR  CONST_10  H2  C2  N3  C4   180.00   0.0  0
 HPR  Var_01    C8  N9  C4  N3  -167.45  30.0  1
 HPR  Var_02    C8  N7  C5  C4   -14.26  30.0  1
 HPR  Var_03    N7  C8  N9  C4   -20.67  30.0  1
 HPR  Var_04    N9  C8  N7  C5    20.83  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
 HPR  chir_01  C1'  N9   C2'  O4'  negativ
 HPR  chir_02  C2'  O2'  C3'  C1'  positiv
 HPR  chir_03  C3'  O3'  C4'  C2'  positiv
 HPR  chir_04  C4'  O4'  C3'  C5'  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
 HPR  plan-1  N1  0.020
 HPR  plan-1  C2  0.020
 HPR  plan-1  N3  0.020
 HPR  plan-1  C4  0.020
 HPR  plan-1  C5  0.020
 HPR  plan-1  C6  0.020
 HPR  plan-1  O6  0.020
 HPR  plan-1  N7  0.020
 HPR  plan-1  N9  0.020
 HPR  plan-1  H2  0.020

