# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:43:20 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (1S,2R,3S,4R)-4-(6-aminopurin-9-yl)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C[C@H](O)[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
 NRN  NRN  (1S,2R,3S,4R)-4-(6-aminopurin-9-yl)cyclopentane-1,2,3-triol  ligand  31  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NRN
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
 NRN  N6   N  NH2   0  -0.817  -4.7263   1.0702  -0.7139
 NRN  C6   C  CR6   0   0.457  -3.7521   0.3031  -0.2224
 NRN  N1   N  N     0  -0.476  -4.0674  -0.8457   0.3863
 NRN  C5   C  CR56  0  -0.011  -2.3910   0.6467  -0.3179
 NRN  N7   N  N     0  -0.451  -1.7356   1.7214  -0.8593
 NRN  C8   C  CR15  0   0.100  -0.4779   1.4735  -0.6347
 NRN  N9   N  NR5   0  -0.510  -0.2600   0.2976   0.0257
 NRN  C4   C  CR56  0   0.485  -1.4904  -0.2510   0.2354
 NRN  N3   N  N     0  -0.457  -1.7890  -1.3976   0.8430
 NRN  C2   C  CR16  0   0.044  -3.0924  -1.6108   0.8718
 NRN  C1A  C  CH1   0  -0.123   1.0136  -0.2834   0.3948
 NRN  C2A  C  CH1   0   0.008   1.9088  -0.6447  -0.8156
 NRN  O2A  O  OH1   0  -0.668   2.1368  -2.0314  -0.7787
 NRN  C5A  C  CH2   0  -0.501   1.8529   0.6226   1.3080
 NRN  C4A  C  CH1   0   0.032   3.2841   0.2620   0.9435
 NRN  O5A  O  OH1   0  -0.669   4.1814   1.2330   1.4156
 NRN  C3A  C  CH1   0   0.008   3.1933   0.1589  -0.5783
 NRN  O3A  O  OH1   0  -0.676   4.2868  -0.4541  -1.2077
 NRN  H1   H  HNH2  0   0.403  -5.6885   0.7989  -0.6082
 NRN  H2   H  HNH2  0   0.411  -4.5229   1.9448  -1.1644
 NRN  H3   H  HCR5  0   0.295   0.3395   2.1169  -0.9282
 NRN  H4   H  HCR6  0   0.251  -3.4165  -2.5278   1.3524
 NRN  H5   H  HCH1  0   0.297   0.7718  -1.2098   0.9163
 NRN  H6   H  HCH1  0   0.239   1.4345  -0.3517  -1.7612
 NRN  H7   H  HOH1  0   0.453   2.8222  -2.2393  -1.4234
 NRN  H8   H  HCH2  0   0.251   1.6801   1.6781   1.0767
 NRN  H9   H  HCH2  0   0.274   1.6155   0.4722   2.3604
 NRN  H10  H  HCH1  0   0.216   3.5264  -0.7310   1.3496
 NRN  H11  H  HOH1  0   0.453   5.0781   0.9054   1.2966
 NRN  H12  H  HCH1  0   0.221   3.0293   1.1759  -0.9640
 NRN  H13  H  HOH1  0   0.463   4.9396   0.2149  -1.4300

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
 NRN  O3A  C3A  single    1.403  0.020  1.403
 NRN  O5A  C4A  single    1.404  0.020  1.404
 NRN  C4A  C3A  single    1.528  0.020  1.528
 NRN  C4A  C5A  single    1.520  0.020  1.520
 NRN  C3A  C2A  single    1.534  0.020  1.534
 NRN  O2A  C2A  single    1.406  0.020  1.406
 NRN  C2A  C1A  single    1.548  0.020  1.548
 NRN  C5A  C1A  single    1.536  0.020  1.536
 NRN  C1A  N9   single    1.448  0.020  1.448
 NRN  N3   C2   aromatic  1.321  0.020  1.321
 NRN  N3   C4   aromatic  1.332  0.020  1.332
 NRN  C2   N1   aromatic  1.331  0.020  1.331
 NRN  N9   C4   aromatic  1.363  0.020  1.363
 NRN  N9   C8   aromatic  1.366  0.020  1.366
 NRN  C4   C5   aromatic  1.387  0.020  1.387
 NRN  N1   C6   aromatic  1.338  0.020  1.338
 NRN  C8   N7   aromatic  1.301  0.020  1.301
 NRN  C5   C6   aromatic  1.407  0.020  1.407
 NRN  C5   N7   aromatic  1.370  0.020  1.370
 NRN  C6   N6   single    1.334  0.020  1.334
 NRN  N6   H1   single    0.860  0.020  1.020
 NRN  N6   H2   single    0.860  0.020  1.020
 NRN  C8   H3   single    0.930  0.020  1.080
 NRN  C2   H4   single    0.930  0.020  1.080
 NRN  C1A  H5   single    0.970  0.020  1.090
 NRN  C2A  H6   single    0.970  0.020  1.090
 NRN  O2A  H7   single    0.850  0.020  0.980
 NRN  C5A  H8   single    0.970  0.020  1.090
 NRN  C5A  H9   single    0.970  0.020  1.090
 NRN  C4A  H10  single    0.970  0.020  1.090
 NRN  O5A  H11  single    0.850  0.020  0.980
 NRN  C3A  H12  single    0.970  0.020  1.090
 NRN  O3A  H13  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
 NRN  H2   N6   H1   118.42  3.000
 NRN  H2   N6   C6   121.20  3.000
 NRN  H1   N6   C6   120.34  3.000
 NRN  C5   C6   N1   117.95  3.000
 NRN  C5   C6   N6   122.76  3.000
 NRN  N1   C6   N6   119.30  3.000
 NRN  C2   N1   C6   119.14  3.000
 NRN  C4   C5   N7   110.77  3.000
 NRN  N7   C5   C6   132.93  3.000
 NRN  C4   C5   C6   116.30  3.000
 NRN  C8   N7   C5   104.17  3.000
 NRN  H3   C8   N9   121.54  3.000
 NRN  H3   C8   N7   124.79  3.000
 NRN  N9   C8   N7   113.67  3.000
 NRN  C1A  N9   C4   126.39  3.000
 NRN  C4   N9   C8   106.07  3.000
 NRN  C1A  N9   C8   127.51  3.000
 NRN  N3   C4   N9   128.24  3.000
 NRN  N9   C4   C5   105.32  3.000
 NRN  N3   C4   C5   126.43  3.000
 NRN  C2   N3   C4   111.72  3.000
 NRN  H4   C2   N3   116.15  3.000
 NRN  H4   C2   N1   115.38  3.000
 NRN  N3   C2   N1   128.46  3.000
 NRN  H5   C1A  C5A  109.76  3.000
 NRN  H5   C1A  C2A  107.69  3.000
 NRN  C5A  C1A  C2A  106.65  3.000
 NRN  H5   C1A  N9   105.53  3.000
 NRN  C5A  C1A  N9   113.30  3.000
 NRN  C2A  C1A  N9   113.77  3.000
 NRN  H6   C2A  C3A  110.81  3.000
 NRN  H6   C2A  O2A  110.86  3.000
 NRN  C3A  C2A  O2A  112.15  3.000
 NRN  H6   C2A  C1A  111.18  3.000
 NRN  O2A  C2A  C1A  107.67  3.000
 NRN  C3A  C2A  C1A  103.95  3.000
 NRN  H7   O2A  C2A  108.10  3.000
 NRN  H9   C5A  H8   107.64  3.000
 NRN  H9   C5A  C4A  113.83  3.000
 NRN  H8   C5A  C4A  109.07  3.000
 NRN  H9   C5A  C1A  111.96  3.000
 NRN  H8   C5A  C1A  110.92  3.000
 NRN  C4A  C5A  C1A  103.41  3.000
 NRN  H10  C4A  C3A  108.65  3.000
 NRN  H10  C4A  O5A  111.07  3.000
 NRN  C3A  C4A  O5A  114.81  3.000
 NRN  H10  C4A  C5A  109.45  3.000
 NRN  C3A  C4A  C5A  101.47  3.000
 NRN  O5A  C4A  C5A  110.92  3.000
 NRN  H11  O5A  C4A  108.58  3.000
 NRN  H12  C3A  O3A  111.28  3.000
 NRN  H12  C3A  C4A  107.20  3.000
 NRN  O3A  C3A  C4A  115.47  3.000
 NRN  H12  C3A  C2A  107.78  3.000
 NRN  C4A  C3A  C2A  103.84  3.000
 NRN  O3A  C3A  C2A  110.77  3.000
 NRN  H13  O3A  C3A  109.22  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
 NRN  CONST_01  N3   C2  N1  C6    0.00  0.0  0
 NRN  CONST_02  N3   C4  C5  C6    0.00  0.0  0
 NRN  CONST_03  N9   C4  C5  C6  180.00  0.0  0
 NRN  CONST_04  C8   N7  C5  C6  180.00  0.0  0
 NRN  CONST_05  C4   N3  C2  N1    0.00  0.0  0
 NRN  CONST_06  C4   C5  C6  N1    0.00  0.0  0
 NRN  CONST_07  N7   C5  C6  N1  180.00  0.0  0
 NRN  CONST_08  C2   N3  C4  C5    0.00  0.0  0
 NRN  CONST_09  C8   N9  C4  C5    0.00  0.0  0
 NRN  CONST_10  C2   N1  C6  C5    0.00  0.0  0
 NRN  CONST_11  N9   C8  N7  C5    0.00  0.0  0
 NRN  CONST_12  C4   N9  C8  N7    0.00  0.0  0
 NRN  CONST_13  N3   C4  C5  N7  180.00  0.0  0
 NRN  CONST_14  N9   C4  C5  N7    0.00  0.0  0
 NRN  CONST_15  N3   C4  N9  C8  180.00  0.0  0
 NRN  CONST_16  C4   C5  N7  C8    0.00  0.0  0
 NRN  CONST_17  C2   N3  C4  N9  180.00  0.0  0
 NRN  CONST_18  C1A  N9  C4  C5  180.00  0.0  0
 NRN  CONST_19  C1A  N9  C8  N7  180.00  0.0  0
 NRN  CONST_20  C1A  N9  C4  N3    0.00  0.0  0
 NRN  CONST_21  C2   N1  C6  N6  180.00  0.0  0
 NRN  CONST_22  C4   C5  C6  N6  180.00  0.0  0
 NRN  CONST_23  N7   C5  C6  N6    0.00  0.0  0
 NRN  CONST_24  H4   C2  N1  C6  180.00  0.0  0
 NRN  CONST_25  H3   C8  N7  C5  180.00  0.0  0
 NRN  CONST_26  H1   N6  C6  N1    0.00  0.0  0
 NRN  CONST_27  H2   N6  C6  N1  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
 NRN  chir_01  C1A  C2A  C5A  N9   negativ
 NRN  chir_02  C2A  O2A  C3A  C1A  positiv
 NRN  chir_03  C4A  O5A  C3A  C5A  positiv
 NRN  chir_04  C3A  O3A  C4A  C2A  positiv

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
 NRN  plan-1  N6   0.020
 NRN  plan-1  C6   0.020
 NRN  plan-1  N1   0.020
 NRN  plan-1  C5   0.020
 NRN  plan-1  N7   0.020
 NRN  plan-1  C8   0.020
 NRN  plan-1  N9   0.020
 NRN  plan-1  C4   0.020
 NRN  plan-1  N3   0.020
 NRN  plan-1  C2   0.020
 NRN  plan-1  C1A  0.020
 NRN  plan-1  H3   0.020
 NRN  plan-1  H4   0.020
 NRN  plan-2  N6   0.020
 NRN  plan-2  C6   0.020
 NRN  plan-2  H1   0.020
 NRN  plan-2  H2   0.020

