# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:12:02 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (1S,2R,5R)-5-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)cyclopent-3-ene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C=C(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
 6OS  6OS  (1S,2R,5R)-5-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)cyclopent-3-ene-1,2-diol  ligand  32  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6OS
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
 6OS  C2   C  CR16  0   0.039  -3.3587  -1.6054   0.6743
 6OS  C4   C  CR56  0   0.485  -1.6638  -0.2664   0.2824
 6OS  C5   C  CR56  0  -0.005  -2.4641   0.6528  -0.3785
 6OS  C6   C  CR6   0   0.455  -3.8318   0.3345  -0.4706
 6OS  O3'  O  OH1   0  -0.663   3.6841  -1.1448  -1.2528
 6OS  C3'  C  CR15  0  -0.035   2.5306  -0.4206  -0.8981
 6OS  C2'  C  CR15  0   0.018   1.4523  -1.3115  -0.2385
 6OS  O2'  O  OH1   0  -0.670   2.0560  -2.3628   0.4629
 6OS  C4'  C  CR5   0   0.055   2.8313   0.5948   0.1748
 6OS  C5'  C  CH2   0  -0.196   4.0480   1.4438   0.0968
 6OS  O5'  O  OH1   0  -0.663   4.0279   2.4034   1.1200
 6OS  C6'  C  CR15  0  -0.277   1.8622   0.6343   1.0833
 6OS  C1'  C  CR15  0  -0.169   0.7896  -0.3754   0.7894
 6OS  N9   N  NR5   0  -0.505  -0.4070   0.2603   0.2513
 6OS  N3   N  N     0  -0.459  -2.0603  -1.4154   0.8277
 6OS  N1   N  N     0  -0.475  -4.2453  -0.8164   0.0714
 6OS  C8   C  CR15  0   0.111  -0.5095   1.4436  -0.4239
 6OS  N7   N  N     0  -0.453  -1.7213   1.7179  -0.8145
 6OS  N6   N  NH2   0  -0.817  -4.7204   1.1325  -1.0650
 6OS  H1   H  HCR6  0   0.251  -3.7606  -2.5226   1.0914
 6OS  H2   H  HOH1  0   0.470   3.5735  -1.4899  -2.1447
 6OS  H3   H  HCR5  0   0.256   2.1161   0.0921  -1.7759
 6OS  H4   H  HCR5  0   0.233   0.7263  -1.6892  -0.9703
 6OS  H5   H  HOH1  0   0.447   2.8975  -2.5511   0.0263
 6OS  H6   H  HCH2  0   0.227   4.9323   0.7958   0.1587
 6OS  H7   H  HCH2  0   0.217   4.0841   1.9040  -0.9023
 6OS  H8   H  HOH1  0   0.462   4.8745   2.8586   1.1209
 6OS  H9   H  HCR5  0   0.267   1.7975   1.3132   1.9221
 6OS  H10  H  HCR5  0   0.287   0.4698  -0.9306   1.6737
 6OS  H11  H  HCR5  0   0.295   0.3509   2.0731  -0.5923
 6OS  H12  H  HNH2  0   0.411  -4.4355   1.9851  -1.5137
 6OS  H13  H  HNH2  0   0.403  -5.6826   0.8517  -1.1418

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
 6OS  C5'  C4'  single    1.486  0.020  1.486
 6OS  C5'  O5'  single    1.403  0.020  1.403
 6OS  C3'  C4'  single    1.507  0.020  1.507
 6OS  C3'  O3'  single    1.407  0.020  1.407
 6OS  C3'  C2'  single    1.546  0.020  1.546
 6OS  C8   N7   aromatic  1.302  0.020  1.302
 6OS  C8   N9   aromatic  1.366  0.020  1.366
 6OS  C4'  C6'  double    1.329  0.020  1.329
 6OS  N7   C5   aromatic  1.370  0.020  1.370
 6OS  C2'  C1'  single    1.540  0.020  1.540
 6OS  C2'  O2'  single    1.401  0.020  1.401
 6OS  C6'  C1'  single    1.502  0.020  1.502
 6OS  N9   C1'  single    1.458  0.020  1.458
 6OS  N9   C4   aromatic  1.363  0.020  1.363
 6OS  C5   C4   aromatic  1.386  0.020  1.386
 6OS  C5   C6   aromatic  1.407  0.020  1.407
 6OS  C4   N3   aromatic  1.332  0.020  1.332
 6OS  N6   C6   single    1.334  0.020  1.334
 6OS  C6   N1   aromatic  1.338  0.020  1.338
 6OS  N3   C2   aromatic  1.321  0.020  1.321
 6OS  N1   C2   aromatic  1.331  0.020  1.331
 6OS  C2   H1   single    0.930  0.020  1.080
 6OS  O3'  H2   single    0.850  0.020  0.980
 6OS  C3'  H3   single    0.970  0.020  1.090
 6OS  C2'  H4   single    0.970  0.020  1.090
 6OS  O2'  H5   single    0.850  0.020  0.980
 6OS  C5'  H6   single    0.970  0.020  1.090
 6OS  C5'  H7   single    0.970  0.020  1.090
 6OS  O5'  H8   single    0.850  0.020  0.980
 6OS  C6'  H9   single    0.930  0.020  1.080
 6OS  C1'  H10  single    0.970  0.020  1.090
 6OS  C8   H11  single    0.930  0.020  1.080
 6OS  N6   H12  single    0.860  0.020  1.020
 6OS  N6   H13  single    0.860  0.020  1.020

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
 6OS  H1   C2   N1   115.37  3.000
 6OS  H1   C2   N3   116.17  3.000
 6OS  N1   C2   N3   128.46  3.000
 6OS  N3   C4   N9   128.10  3.000
 6OS  N3   C4   C5   126.53  3.000
 6OS  N9   C4   C5   105.38  3.000
 6OS  N7   C5   C6   133.01  3.000
 6OS  C6   C5   C4   116.25  3.000
 6OS  N7   C5   C4   110.75  3.000
 6OS  N6   C6   N1   119.30  3.000
 6OS  N1   C6   C5   117.94  3.000
 6OS  N6   C6   C5   122.76  3.000
 6OS  H2   O3'  C3'  108.89  3.000
 6OS  H3   C3'  C4'  109.26  3.000
 6OS  H3   C3'  C2'  110.29  3.000
 6OS  C4'  C3'  C2'  102.91  3.000
 6OS  H3   C3'  O3'  110.38  3.000
 6OS  C2'  C3'  O3'  112.49  3.000
 6OS  C4'  C3'  O3'  111.25  3.000
 6OS  H4   C2'  C1'  111.68  3.000
 6OS  H4   C2'  O2'  111.14  3.000
 6OS  C1'  C2'  O2'  107.91  3.000
 6OS  H4   C2'  C3'  112.03  3.000
 6OS  O2'  C2'  C3'  110.21  3.000
 6OS  C1'  C2'  C3'  103.57  3.000
 6OS  H5   O2'  C2'  107.17  3.000
 6OS  C6'  C4'  C5'  128.03  3.000
 6OS  C6'  C4'  C3'  111.17  3.000
 6OS  C5'  C4'  C3'  120.72  3.000
 6OS  H7   C5'  H6   105.75  3.000
 6OS  H7   C5'  O5'  112.12  3.000
 6OS  H6   C5'  O5'  111.97  3.000
 6OS  H7   C5'  C4'  108.27  3.000
 6OS  H6   C5'  C4'  108.62  3.000
 6OS  O5'  C5'  C4'  109.93  3.000
 6OS  H8   O5'  C5'  108.18  3.000
 6OS  H9   C6'  C1'  122.09  3.000
 6OS  H9   C6'  C4'  126.35  3.000
 6OS  C1'  C6'  C4'  111.53  3.000
 6OS  H10  C1'  N9   106.28  3.000
 6OS  H10  C1'  C6'  113.11  3.000
 6OS  N9   C1'  C6'  111.42  3.000
 6OS  H10  C1'  C2'  110.94  3.000
 6OS  N9   C1'  C2'  111.83  3.000
 6OS  C6'  C1'  C2'  103.40  3.000
 6OS  C8   N9   C1'  128.44  3.000
 6OS  C1'  N9   C4   125.44  3.000
 6OS  C8   N9   C4   106.07  3.000
 6OS  C4   N3   C2   111.65  3.000
 6OS  C6   N1   C2   119.18  3.000
 6OS  H11  C8   N7   124.90  3.000
 6OS  H11  C8   N9   121.50  3.000
 6OS  N7   C8   N9   113.60  3.000
 6OS  C8   N7   C5   104.20  3.000
 6OS  H13  N6   H12  118.32  3.000
 6OS  H13  N6   C6   120.29  3.000
 6OS  H12  N6   C6   121.18  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
 6OS  CONST_01  N9   C4   N3   C2   180.00   0.0  0
 6OS  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 6OS  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 6OS  CONST_04  N7   C8   N9   C4     0.00   0.0  0
 6OS  CONST_05  C8   N7   C5   C4     0.00   0.0  0
 6OS  CONST_06  N1   C6   C5   C4     0.00   0.0  0
 6OS  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 6OS  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 6OS  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 6OS  CONST_10  C8   N7   C5   C6   180.00   0.0  0
 6OS  CONST_11  N9   C4   C5   C6   180.00   0.0  0
 6OS  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 6OS  CONST_13  N3   C2   N1   C6     0.00   0.0  0
 6OS  CONST_14  N7   C5   C4   N9     0.00   0.0  0
 6OS  CONST_15  C8   N9   C4   N3   180.00   0.0  0
 6OS  CONST_16  N7   C5   C4   N3   180.00   0.0  0
 6OS  CONST_17  N7   C5   C6   N1   180.00   0.0  0
 6OS  CONST_18  C1'  N9   C4   C5   180.00   0.0  0
 6OS  CONST_19  N7   C8   N9   C1'  180.00   0.0  0
 6OS  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 6OS  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 6OS  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 6OS  CONST_23  N6   C6   C5   N7     0.00   0.0  0
 6OS  CONST_24  H11  C8   N9   C4   180.00   0.0  0
 6OS  CONST_25  H1   C2   N3   C4   180.00   0.0  0
 6OS  CONST_26  H12  N6   C6   C5     0.00   0.0  0
 6OS  CONST_27  H13  N6   C6   C5   180.00   0.0  0
 6OS  Var_01    C1'  C6'  C4'  C3'    1.95  30.0  1
 6OS  Var_02    O5'  C5'  C4'  C3'  173.39  30.0  3

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
 6OS  chir_01  C3'  C4'  O3'  C2'  negativ
 6OS  chir_02  C2'  O2'  C3'  C1'  positiv
 6OS  chir_03  C1'  N9   C6'  C2'  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
 6OS  plan-1  C2   0.020
 6OS  plan-1  C4   0.020
 6OS  plan-1  C5   0.020
 6OS  plan-1  C6   0.020
 6OS  plan-1  C1'  0.020
 6OS  plan-1  N9   0.020
 6OS  plan-1  N3   0.020
 6OS  plan-1  N1   0.020
 6OS  plan-1  C8   0.020
 6OS  plan-1  N7   0.020
 6OS  plan-1  N6   0.020
 6OS  plan-1  H1   0.020
 6OS  plan-1  H11  0.020
 6OS  plan-2  C6   0.020
 6OS  plan-2  N6   0.020
 6OS  plan-2  H12  0.020
 6OS  plan-2  H13  0.020

