# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:11:57 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 9-beta-D-ribofuranosyl-9H-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+]c3cncnc23
#
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
 PUR  PUR  9-beta-D-ribofuranosyl-9H-purin-7-ium  ligand  31  18  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PUR
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
 PUR  N1    N  N     0  -0.393  -4.3031  -0.0954  -0.3339
 PUR  C2    C  CR16  0   0.065  -3.5510  -1.1558  -0.0281
 PUR  N3    N  N     0  -0.392  -2.2510  -1.1683   0.2194
 PUR  C4    C  CR56  0   0.516  -1.6996   0.0217   0.1414
 PUR  C5    C  CR56  0   0.232  -2.3805   1.1943  -0.1598
 PUR  C6    C  CR16  0  -0.005  -3.7398   1.0973  -0.4044
 PUR  N7    N  NR15  1  -0.641  -1.4496   2.2012  -0.1215
 PUR  C8    C  CR15  0   0.282  -0.2753   1.6832   0.1844
 PUR  N9    N  NR5   0  -0.537  -0.3813   0.3667   0.3426
 PUR  C1'   C  CH1   0   0.211   0.7183  -0.5532   0.7058
 PUR  C2'   C  CH1   0  -0.019   1.2191  -1.3647  -0.5038
 PUR  O2'   O  OH1   0  -0.646   0.6360  -2.6251  -0.4973
 PUR  C3'   C  CH1   0  -0.017   2.7412  -1.3263  -0.2977
 PUR  O3'   O  OH1   0  -0.661   3.0770  -2.3508   0.5946
 PUR  C4'   C  CH1   0  -0.071   2.9183   0.0574   0.3190
 PUR  O4'   O  O2    0  -0.482   1.7704   0.2096   1.1677
 PUR  C5'   C  CH2   0  -0.183   3.0007   1.1604  -0.7203
 PUR  O5'   O  OH1   0  -0.659   2.8977   2.3994  -0.0608
 PUR  H2    H  HCR6  0   0.286  -4.0620  -2.1087   0.0218
 PUR  H6    H  HCR6  0   0.319  -4.3563   1.9538  -0.6483
 PUR  HN7   H  HNR5  0   0.471  -1.6127   3.1871  -0.2816
 PUR  H8    H  HCR5  0   0.374   0.6352   2.2572   0.2892
 PUR  H1'   H  HCH1  0   0.300   0.3167  -1.2013   1.4892
 PUR  H2'   H  HCH1  0   0.260   0.9827  -0.8204  -1.4266
 PUR  HO2'  H  HOH1  0   0.466   0.8090  -3.0470  -1.3446
 PUR  H3'   H  HCH1  0   0.259   3.2783  -1.4175  -1.2502
 PUR  HO3'  H  HOH1  0   0.460   4.0293  -2.3337   0.7337
 PUR  H4'   H  HCH1  0   0.281   3.7954   0.1103   0.9686
 PUR  H5'1  H  HCH2  0   0.206   2.2154   1.0445  -1.4800
 PUR  H5'2  H  HCH2  0   0.247   3.9576   1.0512  -1.2445
 PUR  HO5'  H  HOH1  0   0.468   3.0120   3.0978  -0.7127

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
 PUR  N1   C2    aromatic  1.335  0.020  1.335
 PUR  N1   C6    aromatic  1.321  0.020  1.321
 PUR  C2   N3    aromatic  1.323  0.020  1.323
 PUR  C2   H2    single    0.930  0.020  1.080
 PUR  N3   C4    aromatic  1.314  0.020  1.314
 PUR  C4   C5    aromatic  1.389  0.020  1.389
 PUR  C4   N9    aromatic  1.378  0.020  1.378
 PUR  C5   C6    aromatic  1.385  0.020  1.385
 PUR  C5   N7    aromatic  1.372  0.020  1.372
 PUR  C6   H6    single    0.930  0.020  1.080
 PUR  N7   C8    aromatic  1.319  0.020  1.319
 PUR  N7   HN7   single    0.860  0.020  1.020
 PUR  C8   N9    aromatic  1.330  0.020  1.330
 PUR  C8   H8    single    0.930  0.020  1.080
 PUR  N9   C1'   single    1.479  0.020  1.479
 PUR  C1'  C2'   single    1.540  0.020  1.540
 PUR  C1'  O4'   single    1.379  0.020  1.379
 PUR  C1'  H1'   single    0.970  0.020  1.090
 PUR  C2'  O2'   single    1.389  0.020  1.389
 PUR  C2'  C3'   single    1.537  0.020  1.537
 PUR  C2'  H2'   single    0.970  0.020  1.090
 PUR  O2'  HO2'  single    0.850  0.020  0.980
 PUR  C3'  O3'   single    1.399  0.020  1.399
 PUR  C3'  C4'   single    1.525  0.020  1.525
 PUR  C3'  H3'   single    0.970  0.020  1.090
 PUR  O3'  HO3'  single    0.850  0.020  0.980
 PUR  C4'  O4'   single    1.436  0.020  1.436
 PUR  C4'  C5'   single    1.518  0.020  1.518
 PUR  C4'  H4'   single    0.970  0.020  1.090
 PUR  C5'  O5'   single    1.407  0.020  1.407
 PUR  C5'  H5'1  single    0.970  0.020  1.090
 PUR  C5'  H5'2  single    0.970  0.020  1.090
 PUR  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
 PUR  C6    N1   C2    119.28  3.000
 PUR  H2    C2   N3    116.54  3.000
 PUR  H2    C2   N1    116.34  3.000
 PUR  N3    C2   N1    127.12  3.000
 PUR  C4    N3   C2    113.12  3.000
 PUR  N9    C4   C5    106.82  3.000
 PUR  N9    C4   N3    128.31  3.000
 PUR  C5    C4   N3    124.87  3.000
 PUR  N7    C5   C6    136.27  3.000
 PUR  N7    C5   C4    106.32  3.000
 PUR  C6    C5   C4    117.41  3.000
 PUR  H6    C6   C5    122.90  3.000
 PUR  H6    C6   N1    118.90  3.000
 PUR  C5    C6   N1    118.20  3.000
 PUR  HN7   N7   C8    124.23  3.000
 PUR  HN7   N7   C5    126.96  3.000
 PUR  C8    N7   C5    108.80  3.000
 PUR  H8    C8   N9    125.51  3.000
 PUR  H8    C8   N7    124.30  3.000
 PUR  N9    C8   N7    110.19  3.000
 PUR  C1'   N9   C8    125.85  3.000
 PUR  C1'   N9   C4    126.27  3.000
 PUR  C8    N9   C4    107.87  3.000
 PUR  H1'   C1'  O4'   111.60  3.000
 PUR  H1'   C1'  C2'   111.71  3.000
 PUR  O4'   C1'  C2'   107.84  3.000
 PUR  H1'   C1'  N9    105.76  3.000
 PUR  O4'   C1'  N9    107.78  3.000
 PUR  C2'   C1'  N9    112.12  3.000
 PUR  H2'   C2'  C3'   108.29  3.000
 PUR  H2'   C2'  O2'   111.33  3.000
 PUR  C3'   C2'  O2'   115.97  3.000
 PUR  H2'   C2'  C1'   109.22  3.000
 PUR  C3'   C2'  C1'   101.75  3.000
 PUR  O2'   C2'  C1'   109.75  3.000
 PUR  HO2'  O2'  C2'   108.56  3.000
 PUR  H3'   C3'  C4'   111.69  3.000
 PUR  H3'   C3'  O3'   112.03  3.000
 PUR  C4'   C3'  O3'   112.24  3.000
 PUR  H3'   C3'  C2'   111.49  3.000
 PUR  C4'   C3'  C2'   101.06  3.000
 PUR  O3'   C3'  C2'   107.75  3.000
 PUR  HO3'  O3'  C3'   108.45  3.000
 PUR  H4'   C4'  C5'   109.17  3.000
 PUR  H4'   C4'  O4'   106.57  3.000
 PUR  C5'   C4'  O4'   111.79  3.000
 PUR  H4'   C4'  C3'   112.18  3.000
 PUR  C5'   C4'  C3'   112.88  3.000
 PUR  O4'   C4'  C3'   104.02  3.000
 PUR  C4'   O4'  C1'   110.69  3.000
 PUR  H5'2  C5'  H5'1  106.42  3.000
 PUR  H5'2  C5'  O5'   112.06  3.000
 PUR  H5'1  C5'  O5'   111.38  3.000
 PUR  H5'2  C5'  C4'   107.60  3.000
 PUR  H5'1  C5'  C4'   110.98  3.000
 PUR  O5'   C5'  C4'   108.36  3.000
 PUR  HO5'  O5'  C5'   108.23  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
 PUR  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 PUR  CONST_02  C4   C5  C6  N1    0.00  0.0  0
 PUR  CONST_03  N7   C5  C6  N1  180.00  0.0  0
 PUR  CONST_04  C5   C6  N1  C2    0.00  0.0  0
 PUR  CONST_05  C5   C4  N3  C2    0.00  0.0  0
 PUR  CONST_06  N9   C4  N3  C2  180.00  0.0  0
 PUR  CONST_07  C6   N1  C2  N3    0.00  0.0  0
 PUR  CONST_08  C6   C5  C4  N3    0.00  0.0  0
 PUR  CONST_09  N7   C5  C4  N3  180.00  0.0  0
 PUR  CONST_10  C8   N9  C4  N3  180.00  0.0  0
 PUR  CONST_11  C8   N7  C5  C4    0.00  0.0  0
 PUR  CONST_12  N7   C8  N9  C4    0.00  0.0  0
 PUR  CONST_13  C8   N9  C4  C5    0.00  0.0  0
 PUR  CONST_14  N9   C8  N7  C5    0.00  0.0  0
 PUR  CONST_15  N9   C4  C5  C6  180.00  0.0  0
 PUR  CONST_16  C8   N7  C5  C6  180.00  0.0  0
 PUR  CONST_17  N9   C4  C5  N7    0.00  0.0  0
 PUR  CONST_18  C1'  N9  C4  N3    0.00  0.0  0
 PUR  CONST_19  C1'  N9  C4  C5  180.00  0.0  0
 PUR  CONST_20  C1'  N9  C8  N7  180.00  0.0  0
 PUR  CONST_21  H6   C6  N1  C2  180.00  0.0  0
 PUR  CONST_22  H2   C2  N3  C4  180.00  0.0  0
 PUR  CONST_23  HN7  N7  C5  C4  180.00  0.0  0
 PUR  CONST_24  H8   C8  N9  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
 PUR  chir_01  C1'  N9   C2'  O4'  negativ
 PUR  chir_02  C2'  O2'  C3'  C1'  positiv
 PUR  chir_03  C3'  O3'  C4'  C2'  positiv
 PUR  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
 PUR  plan-1  N1   0.020
 PUR  plan-1  C2   0.020
 PUR  plan-1  N3   0.020
 PUR  plan-1  C4   0.020
 PUR  plan-1  C5   0.020
 PUR  plan-1  C6   0.020
 PUR  plan-1  N7   0.020
 PUR  plan-1  C8   0.020
 PUR  plan-1  N9   0.020
 PUR  plan-1  C1'  0.020
 PUR  plan-1  H2   0.020
 PUR  plan-1  H6   0.020
 PUR  plan-1  HN7  0.020
 PUR  plan-1  H8   0.020

