# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:14:57 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 7-beta-D-ribofuranosyl-1,7-dihydroimidazo[4,5-c][1,2,6]thiadiazin-4(3H)-one 2,2-dioxide
#   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)N[S](=O)(=O)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
 13A  13A  '7-beta-D-ribofuranosyl-1,7-dihydroimidazo[4,5-c][1,2,6]thiadiazin-4(3H)-one 2,2-dioxide'  ligand  33  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_13A
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
 13A  O21  O  OS    0  -0.608  -3.1815   0.7313  -1.6045
 13A  S16  S  S     0   1.515  -2.9762   0.9651  -0.1977
 13A  O20  O  OS    0  -0.613  -3.5722   2.1005   0.4560
 13A  N17  N  NC1   0  -0.836  -3.4104  -0.4068   0.6539
 13A  C18  C  C     0   0.553  -2.7381  -1.6251   0.5444
 13A  O19  O  O     0  -0.419  -3.2653  -2.6653   0.8627
 13A  C13  C  CR5   0  -0.038  -1.3638  -1.4704   0.1023
 13A  N12  N  N     0  -0.436  -0.4653  -2.4682  -0.1370
 13A  C11  C  CR15  0   0.102   0.6559  -1.8655  -0.4043
 13A  N15  N  NC1   0  -0.827  -1.3357   1.0010   0.0574
 13A  C14  C  CR5   0   0.549  -0.7533  -0.2510  -0.0427
 13A  N10  N  NR5   0  -0.499   0.5309  -0.5033  -0.3730
 13A  C5   C  CH1   0   0.212   1.5733   0.5028  -0.5524
 13A  O1   O  O2    0  -0.486   2.6544  -0.0765  -1.1956
 13A  C4   C  CH1   0  -0.023   2.0810   1.0460   0.7907
 13A  O7   O  OH1   0  -0.656   1.3212   2.1559   1.1569
 13A  C3   C  CH1   0  -0.023   3.5605   1.2859   0.4845
 13A  O6   O  OH1   0  -0.664   3.6654   2.5050  -0.1968
 13A  C2   C  CH1   0  -0.069   3.8489   0.0871  -0.4192
 13A  C8   C  CH2   0  -0.163   4.1770  -1.1733   0.3593
 13A  O9   O  OH1   0  -0.664   4.2675  -2.2438  -0.5468
 13A  H17  H  HNC1  0   0.452  -4.3648  -0.4214   1.0036
 13A  H11  H  HCR5  0   0.300   1.5907  -2.3490  -0.6420
 13A  H15  H  HNC1  0   0.446  -1.0123   1.6176   0.8009
 13A  H5   H  HCH1  0   0.280   1.1358   1.3068  -1.1557
 13A  H4   H  HCH1  0   0.260   2.0104   0.2555   1.5474
 13A  HO7  H  HOH1  0   0.471   1.4701   2.3434   2.0894
 13A  H3   H  HCH1  0   0.258   4.1772   1.2659   1.3917
 13A  HO6  H  HOH1  0   0.460   4.5925   2.6633  -0.4023
 13A  H2   H  HCH1  0   0.272   4.6621   0.2940  -1.1204
 13A  H81  H  HCH2  0   0.202   3.4124  -1.3597   1.1256
 13A  H82  H  HCH2  0   0.229   5.1214  -1.0015   0.8912
 13A  HO9  H  HOH1  0   0.462   4.4722  -3.0400  -0.0483

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
 13A  O21  S16  double    1.441  0.020  1.441
 13A  S16  O20  double    1.439  0.020  1.439
 13A  S16  N17  single    1.672  0.020  1.672
 13A  S16  N15  single    1.661  0.020  1.661
 13A  N17  C18  single    1.396  0.020  1.396
 13A  N17  H17  single    0.890  0.020  1.040
 13A  C18  O19  double    1.209  0.020  1.209
 13A  C18  C13  single    1.452  0.020  1.452
 13A  C13  N12  aromatic  1.364  0.020  1.364
 13A  C13  C14  aromatic  1.371  0.020  1.371
 13A  N12  C11  aromatic  1.301  0.020  1.301
 13A  C11  N10  aromatic  1.368  0.020  1.368
 13A  C11  H11  single    0.930  0.020  1.080
 13A  N15  C14  single    1.385  0.020  1.385
 13A  N15  H15  single    0.890  0.020  1.040
 13A  C14  N10  aromatic  1.350  0.020  1.350
 13A  N10  C5   single    1.460  0.020  1.460
 13A  C5   O1   single    1.385  0.020  1.385
 13A  C5   C4   single    1.535  0.020  1.535
 13A  C5   H5   single    0.970  0.020  1.090
 13A  O1   C2   single    1.434  0.020  1.434
 13A  C4   O7   single    1.394  0.020  1.394
 13A  C4   C3   single    1.530  0.020  1.530
 13A  C4   H4   single    0.970  0.020  1.090
 13A  O7   HO7  single    0.850  0.020  0.980
 13A  C3   O6   single    1.400  0.020  1.400
 13A  C3   C2   single    1.529  0.020  1.529
 13A  C3   H3   single    0.970  0.020  1.090
 13A  O6   HO6  single    0.850  0.020  0.980
 13A  C2   C8   single    1.517  0.020  1.517
 13A  C2   H2   single    0.970  0.020  1.090
 13A  C8   O9   single    1.405  0.020  1.405
 13A  C8   H81  single    0.970  0.020  1.090
 13A  C8   H82  single    0.970  0.020  1.090
 13A  O9   HO9  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
 13A  N15  S16  N17  101.31  3.000
 13A  N15  S16  O20  108.80  3.000
 13A  N17  S16  O20  107.96  3.000
 13A  N15  S16  O21  107.11  3.000
 13A  N17  S16  O21  109.10  3.000
 13A  O20  S16  O21  120.83  3.000
 13A  H17  N17  C18  117.82  3.000
 13A  H17  N17  S16  115.52  3.000
 13A  C18  N17  S16  123.45  3.000
 13A  C13  C18  O19  125.78  3.000
 13A  C13  C18  N17  112.75  3.000
 13A  O19  C18  N17  121.36  3.000
 13A  C14  C13  N12  109.80  3.000
 13A  C14  C13  C18  123.25  3.000
 13A  N12  C13  C18  126.80  3.000
 13A  C11  N12  C13  105.36  3.000
 13A  H11  C11  N10  122.03  3.000
 13A  H11  C11  N12  125.76  3.000
 13A  N10  C11  N12  112.20  3.000
 13A  H15  N15  C14  117.81  3.000
 13A  H15  N15  S16  116.03  3.000
 13A  C14  N15  S16  112.64  3.000
 13A  N10  C14  N15  125.94  3.000
 13A  N10  C14  C13  106.45  3.000
 13A  N15  C14  C13  127.53  3.000
 13A  C5   N10  C14  125.50  3.000
 13A  C5   N10  C11  128.17  3.000
 13A  C14  N10  C11  106.18  3.000
 13A  H5   C5   C4   110.72  3.000
 13A  H5   C5   O1   111.27  3.000
 13A  C4   C5   O1   107.22  3.000
 13A  H5   C5   N10  106.74  3.000
 13A  C4   C5   N10  111.87  3.000
 13A  O1   C5   N10  109.04  3.000
 13A  C2   O1   C5   110.56  3.000
 13A  H4   C4   C3   108.27  3.000
 13A  H4   C4   O7   110.95  3.000
 13A  C3   C4   O7   117.06  3.000
 13A  H4   C4   C5   109.10  3.000
 13A  C3   C4   C5   101.55  3.000
 13A  O7   C4   C5   109.35  3.000
 13A  HO7  O7   C4   108.98  3.000
 13A  H3   C3   C2   111.62  3.000
 13A  H3   C3   O6   112.08  3.000
 13A  C2   C3   O6   112.39  3.000
 13A  H3   C3   C4   112.04  3.000
 13A  C2   C3   C4   100.24  3.000
 13A  O6   C3   C4   107.84  3.000
 13A  HO6  O6   C3   108.62  3.000
 13A  H2   C2   C8   108.98  3.000
 13A  H2   C2   C3   111.78  3.000
 13A  C8   C2   C3   112.88  3.000
 13A  H2   C2   O1   107.09  3.000
 13A  C8   C2   O1   111.29  3.000
 13A  C3   C2   O1   104.62  3.000
 13A  H82  C8   H81  106.71  3.000
 13A  H82  C8   O9   112.10  3.000
 13A  H81  C8   O9   111.43  3.000
 13A  H82  C8   C2   107.74  3.000
 13A  H81  C8   C2   110.39  3.000
 13A  O9   C8   C2   108.41  3.000
 13A  HO9  O9   C8   108.08  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
 13A  CONST_01  N10  C11  N12  C13     0.00   0.0  0
 13A  CONST_02  C11  N10  C14  C13     0.00   0.0  0
 13A  CONST_03  N10  C14  C13  N12     0.00   0.0  0
 13A  CONST_04  C14  N10  C11  N12     0.00   0.0  0
 13A  CONST_05  C14  C13  N12  C11     0.00   0.0  0
 13A  CONST_06  C5   N10  C14  C13   180.00   0.0  0
 13A  CONST_07  C5   N10  C11  N12   180.00   0.0  0
 13A  CONST_08  C5   N10  C14  N15     0.00   0.0  0
 13A  CONST_11  H11  C11  N12  C13   180.00   0.0  0
 13A  CONST_12  H17  N17  C18  C13   180.00   0.0  0
 13A  Var_01    C13  C14  N15  S16   -22.28  30.0  1
 13A  Var_02    C14  N15  S16  N17    42.11  30.0  1
 13A  Var_03    N12  C13  C18  N17  -177.95  30.0  1
 13A  Var_04    N15  S16  N17  C18   -47.49  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
 13A  chir_01  C5  N10  O1  C4  positiv
 13A  chir_02  C4  O7   C5  C3  negativ
 13A  chir_03  C3  O6   C2  C4  positiv
 13A  chir_04  C2  O1   C3  C8  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
 13A  plan-1  S16  0.020
 13A  plan-1  N17  0.020
 13A  plan-1  C18  0.020
 13A  plan-1  O19  0.020
 13A  plan-1  C13  0.020
 13A  plan-1  H17  0.020
 13A  plan-2  C18  0.020
 13A  plan-2  C13  0.020
 13A  plan-2  N12  0.020
 13A  plan-2  C11  0.020
 13A  plan-2  N15  0.020
 13A  plan-2  C14  0.020
 13A  plan-2  N10  0.020
 13A  plan-2  C5   0.020
 13A  plan-2  H11  0.020
 13A  plan-3  S16  0.020
 13A  plan-3  N15  0.020
 13A  plan-3  C14  0.020
 13A  plan-3  H15  0.020

