# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:17:02 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (6S)-6-hydroxy-9-beta-D-ribofuranosyl-6,9-dihydro-1H-purin-7-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c[nH+]c3[C@H](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
 PRH  PRH  (6S)-6-hydroxy-9-beta-D-ribofuranosyl-6,9-dihydro-1H-purin-7-ium  ligand  34  19  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PRH
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
 PRH  N1    N  NH1   0  -0.636  -4.0377  -0.7992  -0.0912
 PRH  C2    C  C1    0   0.166  -3.1553  -1.6655   0.4260
 PRH  N3    N  N     0  -0.474  -1.8874  -1.4551   0.5975
 PRH  C4    C  CR5   0   0.444  -1.5289  -0.2182   0.1774
 PRH  C5    C  CR5   0   0.213  -2.3450   0.7621  -0.2921
 PRH  C6    C  CH1   0   0.168  -3.8175   0.6215  -0.3272
 PRH  O6    O  OH1   0  -0.642  -4.3716   1.4279   0.6693
 PRH  N7    N  NR15  1  -0.615  -1.5475   1.8297  -0.5972
 PRH  C8    C  CR15  0   0.240  -0.2906   1.5264  -0.3332
 PRH  N9    N  NR5   0  -0.513  -0.2469   0.2817   0.1402
 PRH  C1'   C  CH1   0   0.216   0.9681  -0.4439   0.4888
 PRH  C2'   C  CH1   0   0.002   1.6151  -1.1304  -0.7139
 PRH  O2'   O  OH1   0  -0.645   0.9853  -2.3393  -0.9704
 PRH  C3'   C  CH1   0  -0.052   3.0748  -1.1842  -0.2572
 PRH  O3'   O  OH1   0  -0.665   3.2124  -2.2663   0.6213
 PRH  C4'   C  CH1   0  -0.043   3.2053   0.1723   0.4416
 PRH  O4'   O  O2    0  -0.494   1.8949   0.4853   0.9404
 PRH  C5'   C  CH2   0  -0.155   3.6870   1.2616  -0.4941
 PRH  O5'   O  OH1   0  -0.666   3.6432   2.4899   0.1849
 PRH  HN1   H  HNH1  0   0.431  -4.9820  -1.1332  -0.2146
 PRH  H2    H  H     0   0.297  -3.5639  -2.6333   0.6888
 PRH  H6    H  HCH1  0   0.279  -4.2418   0.8760  -1.3026
 PRH  HO6   H  HOH1  0   0.469  -5.2822   1.6415   0.4361
 PRH  HN7   H  HNR5  0   0.460  -1.8508   2.7277  -0.9492
 PRH  H8    H  HCR5  0   0.359   0.5491   2.1870  -0.4645
 PRH  H1'   H  HCH1  0   0.280   0.6886  -1.1743   1.2554
 PRH  H2'   H  HCH1  0   0.246   1.5592  -0.4476  -1.5736
 PRH  HO2'  H  HOH1  0   0.466   1.3225  -2.6969  -1.7980
 PRH  H3'   H  HCH1  0   0.261   3.7628  -1.2559  -1.1093
 PRH  HO3'  H  HOH1  0   0.460   4.1199  -2.2880   0.9412
 PRH  H4'   H  HCH1  0   0.267   3.8825   0.1094   1.2992
 PRH  H5'1  H  HCH2  0   0.200   3.0673   1.2788  -1.4013
 PRH  H5'2  H  HCH2  0   0.219   4.7039   0.9960  -0.8109
 PRH  HO5'  H  HOH1  0   0.460   3.9144   3.1798  -0.4272

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
 PRH  N1   C2    single    1.340  0.020  1.340
 PRH  N1   C6    single    1.457  0.020  1.457
 PRH  N1   HN1   single    0.860  0.020  1.020
 PRH  C2   N3    double    1.297  0.020  1.297
 PRH  C2   H2    single    0.930  0.020  1.080
 PRH  N3   C4    single    1.355  0.020  1.355
 PRH  C4   C5    aromatic  1.359  0.020  1.359
 PRH  C4   N9    aromatic  1.377  0.020  1.377
 PRH  C5   C6    single    1.480  0.020  1.480
 PRH  C5   N7    aromatic  1.367  0.020  1.367
 PRH  C6   O6    single    1.397  0.020  1.397
 PRH  C6   H6    single    0.970  0.020  1.090
 PRH  O6   HO6   single    0.850  0.020  0.980
 PRH  N7   C8    aromatic  1.320  0.020  1.320
 PRH  N7   HN7   single    0.860  0.020  1.020
 PRH  C8   N9    aromatic  1.332  0.020  1.332
 PRH  C8   H8    single    0.930  0.020  1.080
 PRH  N9   C1'   single    1.457  0.020  1.457
 PRH  C1'  C2'   single    1.529  0.020  1.529
 PRH  C1'  O4'   single    1.388  0.020  1.388
 PRH  C1'  H1'   single    0.970  0.020  1.090
 PRH  C2'  O2'   single    1.387  0.020  1.387
 PRH  C2'  C3'   single    1.530  0.020  1.530
 PRH  C2'  H2'   single    0.970  0.020  1.090
 PRH  O2'  HO2'  single    0.850  0.020  0.980
 PRH  C3'  O3'   single    1.401  0.020  1.401
 PRH  C3'  C4'   single    1.531  0.020  1.531
 PRH  C3'  H3'   single    0.970  0.020  1.090
 PRH  O3'  HO3'  single    0.850  0.020  0.980
 PRH  C4'  O4'   single    1.437  0.020  1.437
 PRH  C4'  C5'   single    1.515  0.020  1.515
 PRH  C4'  H4'   single    0.970  0.020  1.090
 PRH  C5'  O5'   single    1.404  0.020  1.404
 PRH  C5'  H5'1  single    0.970  0.020  1.090
 PRH  C5'  H5'2  single    0.970  0.020  1.090
 PRH  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
 PRH  HN1   N1   C6    116.38  3.000
 PRH  HN1   N1   C2    116.70  3.000
 PRH  C6    N1   C2    126.38  3.000
 PRH  H2    C2   N3    118.81  3.000
 PRH  H2    C2   N1    115.01  3.000
 PRH  N3    C2   N1    126.15  3.000
 PRH  C4    N3   C2    111.46  3.000
 PRH  N9    C4   C5    106.73  3.000
 PRH  N9    C4   N3    125.91  3.000
 PRH  C5    C4   N3    127.36  3.000
 PRH  N7    C5   C6    130.50  3.000
 PRH  N7    C5   C4    106.86  3.000
 PRH  C6    C5   C4    122.49  3.000
 PRH  H6    C6   O6    110.37  3.000
 PRH  H6    C6   C5    112.65  3.000
 PRH  O6    C6   C5    108.85  3.000
 PRH  H6    C6   N1    108.22  3.000
 PRH  O6    C6   N1    112.80  3.000
 PRH  C5    C6   N1    103.84  3.000
 PRH  HO6   O6   C6    109.28  3.000
 PRH  HN7   N7   C8    124.02  3.000
 PRH  HN7   N7   C5    126.61  3.000
 PRH  C8    N7   C5    109.36  3.000
 PRH  H8    C8   N9    126.23  3.000
 PRH  H8    C8   N7    125.28  3.000
 PRH  N9    C8   N7    108.48  3.000
 PRH  C1'   N9   C8    125.27  3.000
 PRH  C1'   N9   C4    126.09  3.000
 PRH  C8    N9   C4    108.56  3.000
 PRH  H1'   C1'  O4'   112.90  3.000
 PRH  H1'   C1'  C2'   111.06  3.000
 PRH  O4'   C1'  C2'   105.90  3.000
 PRH  H1'   C1'  N9    106.67  3.000
 PRH  O4'   C1'  N9    107.52  3.000
 PRH  C2'   C1'  N9    112.85  3.000
 PRH  H2'   C2'  C3'   107.68  3.000
 PRH  H2'   C2'  O2'   111.94  3.000
 PRH  C3'   C2'  O2'   117.24  3.000
 PRH  H2'   C2'  C1'   108.35  3.000
 PRH  C3'   C2'  C1'   100.64  3.000
 PRH  O2'   C2'  C1'   110.16  3.000
 PRH  HO2'  O2'  C2'   108.89  3.000
 PRH  H3'   C3'  C4'   111.02  3.000
 PRH  H3'   C3'  O3'   112.02  3.000
 PRH  C4'   C3'  O3'   112.94  3.000
 PRH  H3'   C3'  C2'   111.62  3.000
 PRH  C4'   C3'  C2'   100.74  3.000
 PRH  O3'   C3'  C2'   107.94  3.000
 PRH  HO3'  O3'  C3'   108.57  3.000
 PRH  H4'   C4'  C5'   109.19  3.000
 PRH  H4'   C4'  O4'   107.75  3.000
 PRH  C5'   C4'  O4'   110.36  3.000
 PRH  H4'   C4'  C3'   111.06  3.000
 PRH  C5'   C4'  C3'   112.47  3.000
 PRH  O4'   C4'  C3'   105.88  3.000
 PRH  C4'   O4'  C1'   110.50  3.000
 PRH  H5'2  C5'  H5'1  106.74  3.000
 PRH  H5'2  C5'  O5'   112.34  3.000
 PRH  H5'1  C5'  O5'   111.59  3.000
 PRH  H5'2  C5'  C4'   107.39  3.000
 PRH  H5'1  C5'  C4'   109.99  3.000
 PRH  O5'   C5'  C4'   108.69  3.000
 PRH  HO5'  O5'  C5'   108.13  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
 PRH  CONST_01  C8   N7  C5  C4    0.00  0.0  0
 PRH  CONST_02  N7   C8  N9  C4    0.00  0.0  0
 PRH  CONST_03  C8   N9  C4  C5    0.00  0.0  0
 PRH  CONST_04  N9   C8  N7  C5    0.00  0.0  0
 PRH  CONST_05  N9   C4  C5  N7    0.00  0.0  0
 PRH  CONST_06  C1'  N9  C4  N3    0.00  0.0  0
 PRH  CONST_07  C1'  N9  C4  C5  180.00  0.0  0
 PRH  CONST_08  C1'  N9  C8  N7  180.00  0.0  0
 PRH  CONST_09  C4   N3  C2  N1    0.00  0.0  0
 PRH  CONST_10  C6   N1  C2  N3    0.00  0.0  0
 PRH  CONST_11  HN7  N7  C5  C4  180.00  0.0  0
 PRH  CONST_12  H8   C8  N9  C4  180.00  0.0  0
 PRH  CONST_13  HN1  N1  C2  N3  180.00  0.0  0
 PRH  CONST_14  H2   C2  N3  C4  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
 PRH  chir_01  C6   N1   C5   O6   positiv
 PRH  chir_02  C1'  O4'  N9   C2'  negativ
 PRH  chir_03  C2'  O2'  C1'  C3'  negativ
 PRH  chir_04  C3'  O3'  C4'  C2'  positiv
 PRH  chir_05  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
 PRH  plan-1  N1   0.020
 PRH  plan-1  C2   0.020
 PRH  plan-1  N3   0.020
 PRH  plan-1  C4   0.020
 PRH  plan-1  C5   0.020
 PRH  plan-1  C6   0.020
 PRH  plan-1  N7   0.020
 PRH  plan-1  C8   0.020
 PRH  plan-1  N9   0.020
 PRH  plan-1  C1'  0.020
 PRH  plan-1  HN1  0.020
 PRH  plan-1  H2   0.020
 PRH  plan-1  HN7  0.020
 PRH  plan-1  H8   0.020

