# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 11:26:49 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-O-(L-threonylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 TSB  TSB  5'-O-(L-threonylsulfamoyl)adenosine  ligand  51  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TSB
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
 TSB  CG2   C  CH3   0  -0.703   3.4636  -1.8567   4.3640
 TSB  N     N  NH2   0  -0.776   2.5236  -1.1298   1.5517
 TSB  CA    C  CH1   0  -0.258   1.7467  -0.9220   2.7493
 TSB  CB    C  CH1   0   0.026   2.5354  -0.6926   4.0629
 TSB  OG1   O  OH1   0  -0.658   3.2092   0.5451   4.0390
 TSB  S1    S  S     0   1.627  -1.4874   1.4110   3.2603
 TSB  O1S   O  OS    0  -0.631  -2.4988   0.9428   4.1736
 TSB  O2S   O  OS    0  -0.608  -0.9552   2.7403   3.3559
 TSB  O5'   O  OC2   0  -0.565  -1.9873   1.2930   1.7616
 TSB  C5'   C  CH2   0  -0.198  -2.4601   0.0258   1.2731
 TSB  C4'   C  CH1   0  -0.022  -2.7938   0.2100  -0.1905
 TSB  O4'   O  O2    0  -0.484  -1.6627   0.7193  -0.8928
 TSB  C3'   C  CH1   0  -0.051  -3.1519  -1.1294  -0.8393
 TSB  O3'   O  OH1   0  -0.663  -4.1462  -0.9066  -1.8017
 TSB  C2'   C  CH1   0  -0.036  -1.8197  -1.5119  -1.4989
 TSB  O2'   O  OH1   0  -0.651  -1.9308  -2.3712  -2.5903
 TSB  C1'   C  CH1   0   0.214  -1.3357  -0.1406  -1.9537
 TSB  N9    N  NR5   0  -0.549   0.0657  -0.0457  -2.2367
 TSB  C8    C  CR15  0   0.119   1.1245  -0.3526  -1.4190
 TSB  N7    N  N     0  -0.454   2.2779  -0.1114  -1.9654
 TSB  C5    C  CR56  0  -0.011   1.9762   0.3854  -3.2079
 TSB  C6    C  CR6   0   0.459   2.7706   0.8320  -4.2795
 TSB  N6    N  NH2   0  -0.817   4.1035   0.8299  -4.2390
 TSB  N1    N  N     0  -0.474   2.1489   1.2721  -5.3798
 TSB  C2    C  CR16  0   0.046   0.8194   1.2689  -5.4170
 TSB  N3    N  N     0  -0.458  -0.0275   0.8740  -4.4819
 TSB  C4    C  CR56  0   0.489   0.6063   0.4405  -3.3957
 TSB  HG21  H  HCH3  0   0.240   2.9092  -2.7946   4.4071
 TSB  HG22  H  HCH3  0   0.227   4.2434  -1.9642   3.6068
 TSB  HG23  H  HCH3  0   0.253   3.9528  -1.7122   5.3269
 TSB  HN11  H  HNH2  0   0.351   3.1191  -0.3392   1.3422
 TSB  HN12  H  HNH2  0   0.369   3.1149  -1.9440   1.6475
 TSB  HA    H  HCH1  0   0.282   1.1221  -1.8088   2.9018
 TSB  HB    H  HCH1  0   0.241   1.8094  -0.6164   4.8783
 TSB  HG1   H  HOH1  0   0.445   3.9782   0.4723   3.4634
 TSB  HN8   H  HNC1  0   0.458  -0.4552  -0.5013   3.9747
 TSB  H5'1  H  HCH2  0   0.248  -1.6889  -0.7372   1.4093
 TSB  H5'2  H  HCH2  0   0.281  -3.3559  -0.2808   1.8163
 TSB  H4'   H  HCH1  0   0.278  -3.6280   0.9122  -0.2841
 TSB  H3'   H  HCH1  0   0.261  -3.4672  -1.8739  -0.0963
 TSB  HO3'  H  HOH1  0   0.452  -4.1653  -1.6696  -2.3911
 TSB  H2'   H  HCH1  0   0.249  -1.1430  -1.9112  -0.7319
 TSB  HO2'  H  HOH1  0   0.471  -1.9342  -3.2803  -2.2744
 TSB  H1'   H  HCH1  0   0.260  -1.8492   0.1442  -2.8790
 TSB  H8    H  HCR5  0   0.294   1.0045  -0.7481  -0.4207
 TSB  HN61  H  HNH2  0   0.404   4.6372   1.1664  -5.0218
 TSB  HN62  H  HNH2  0   0.411   4.5988   0.5175  -3.4227
 TSB  H2    H  HCR6  0   0.252   0.3778   1.6393  -6.3359
 TSB  C     C  C     0   0.592   0.8325   0.2675   2.5217
 TSB  O     O  O     0  -0.398   1.0264   1.1363   1.7112
 TSB  N8    N  NC1   0  -0.837  -0.2774   0.2750   3.3476

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
 TSB  CG2  CB    single    1.519  0.020  1.519
 TSB  CG2  HG21  single    0.970  0.020  1.090
 TSB  CG2  HG22  single    0.970  0.020  1.090
 TSB  CG2  HG23  single    0.970  0.020  1.090
 TSB  N    CA    single    1.443  0.020  1.443
 TSB  N    HN11  single    0.890  0.020  1.040
 TSB  N    HN12  single    0.890  0.020  1.040
 TSB  CA   CB    single    1.549  0.020  1.549
 TSB  CA   C     single    1.517  0.020  1.517
 TSB  CA   HA    single    0.970  0.020  1.090
 TSB  CB   OG1   single    1.409  0.020  1.409
 TSB  CB   HB    single    0.970  0.020  1.090
 TSB  OG1  HG1   single    0.850  0.020  0.980
 TSB  C    O     double    1.204  0.020  1.204
 TSB  C    N8    single    1.383  0.020  1.383
 TSB  N8   S1    single    1.662  0.020  1.662
 TSB  N8   HN8   single    0.860  0.020  1.020
 TSB  S1   O1S   deloc     1.441  0.020  1.441
 TSB  S1   O2S   deloc     1.435  0.020  1.435
 TSB  S1   O5'   single    1.584  0.020  1.584
 TSB  O5'  C5'   single    1.438  0.020  1.438
 TSB  C5'  C4'   single    1.512  0.020  1.512
 TSB  C5'  H5'1  single    0.970  0.020  1.090
 TSB  C5'  H5'2  single    0.970  0.020  1.090
 TSB  C4'  O4'   single    1.425  0.020  1.425
 TSB  C4'  C3'   single    1.531  0.020  1.531
 TSB  C4'  H4'   single    0.970  0.020  1.090
 TSB  O4'  C1'   single    1.404  0.020  1.404
 TSB  C3'  O3'   single    1.402  0.020  1.402
 TSB  C3'  C2'   single    1.535  0.020  1.535
 TSB  C3'  H3'   single    0.970  0.020  1.090
 TSB  O3'  HO3'  single    0.850  0.020  0.980
 TSB  C2'  O2'   single    1.394  0.020  1.394
 TSB  C2'  C1'   single    1.524  0.020  1.524
 TSB  C2'  H2'   single    0.970  0.020  1.090
 TSB  O2'  HO2'  single    0.850  0.020  0.980
 TSB  C1'  N9    single    1.433  0.020  1.433
 TSB  C1'  H1'   single    0.970  0.020  1.090
 TSB  N9   C8    aromatic  1.373  0.020  1.373
 TSB  N9   C4    aromatic  1.368  0.020  1.368
 TSB  C8   N7    aromatic  1.299  0.020  1.299
 TSB  C8   H8    single    0.930  0.020  1.080
 TSB  N7   C5    aromatic  1.372  0.020  1.372
 TSB  C5   C6    aromatic  1.407  0.020  1.407
 TSB  C5   C4    aromatic  1.384  0.020  1.384
 TSB  C6   N6    single    1.333  0.020  1.333
 TSB  C6   N1    aromatic  1.338  0.020  1.338
 TSB  N6   HN61  single    0.860  0.020  1.020
 TSB  N6   HN62  single    0.860  0.020  1.020
 TSB  N1   C2    aromatic  1.330  0.020  1.330
 TSB  C2   N3    aromatic  1.322  0.020  1.322
 TSB  C2   H2    single    0.930  0.020  1.080
 TSB  N3   C4    aromatic  1.330  0.020  1.330

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
 TSB  HG23  CG2  HG22  107.77  3.000
 TSB  HG23  CG2  HG21  107.90  3.000
 TSB  HG22  CG2  HG21  107.80  3.000
 TSB  HG23  CG2  CB    110.36  3.000
 TSB  HG22  CG2  CB    111.98  3.000
 TSB  HG21  CG2  CB    110.88  3.000
 TSB  HN12  N    HN11  107.74  3.000
 TSB  HN12  N    CA    110.64  3.000
 TSB  HN11  N    CA    112.11  3.000
 TSB  HA    CA   C     108.18  3.000
 TSB  HA    CA   CB    106.99  3.000
 TSB  C     CA   CB    108.53  3.000
 TSB  HA    CA   N     107.82  3.000
 TSB  C     CA   N     108.23  3.000
 TSB  CB    CA   N     116.81  3.000
 TSB  HB    CB   OG1   105.59  3.000
 TSB  HB    CB   CA    107.72  3.000
 TSB  OG1   CB   CA    111.04  3.000
 TSB  HB    CB   CG2   108.12  3.000
 TSB  OG1   CB   CG2   112.59  3.000
 TSB  CA    CB   CG2   111.45  3.000
 TSB  HG1   OG1  CB    109.00  3.000
 TSB  O5'   S1   O2S   104.42  3.000
 TSB  O5'   S1   O1S   110.72  3.000
 TSB  O2S   S1   O1S   121.27  3.000
 TSB  O5'   S1   N8    103.21  3.000
 TSB  O2S   S1   N8    111.08  3.000
 TSB  O1S   S1   N8    104.81  3.000
 TSB  C5'   O5'  S1    119.39  3.000
 TSB  H5'2  C5'  H5'1  108.71  3.000
 TSB  H5'2  C5'  C4'   109.56  3.000
 TSB  H5'1  C5'  C4'   111.17  3.000
 TSB  H5'2  C5'  O5'   110.38  3.000
 TSB  H5'1  C5'  O5'   109.92  3.000
 TSB  C4'   C5'  O5'   107.10  3.000
 TSB  H4'   C4'  C3'   110.30  3.000
 TSB  H4'   C4'  O4'   109.48  3.000
 TSB  C3'   C4'  O4'   106.82  3.000
 TSB  H4'   C4'  C5'   109.21  3.000
 TSB  C3'   C4'  C5'   110.81  3.000
 TSB  O4'   C4'  C5'   110.19  3.000
 TSB  C1'   O4'  C4'   109.77  3.000
 TSB  H3'   C3'  C2'   111.78  3.000
 TSB  H3'   C3'  O3'   111.63  3.000
 TSB  C2'   C3'  O3'   111.12  3.000
 TSB  H3'   C3'  C4'   111.94  3.000
 TSB  C2'   C3'  C4'   101.37  3.000
 TSB  O3'   C3'  C4'   108.53  3.000
 TSB  HO3'  O3'  C3'   107.93  3.000
 TSB  H2'   C2'  C1'   109.87  3.000
 TSB  H2'   C2'  O2'   111.84  3.000
 TSB  C1'   C2'  O2'   110.27  3.000
 TSB  H2'   C2'  C3'   108.99  3.000
 TSB  C1'   C2'  C3'   100.35  3.000
 TSB  O2'   C2'  C3'   114.90  3.000
 TSB  HO2'  O2'  C2'   109.00  3.000
 TSB  H1'   C1'  N9    105.92  3.000
 TSB  H1'   C1'  C2'   109.70  3.000
 TSB  N9    C1'  C2'   115.42  3.000
 TSB  H1'   C1'  O4'   111.69  3.000
 TSB  N9    C1'  O4'   109.66  3.000
 TSB  C2'   C1'  O4'   104.58  3.000
 TSB  C4    N9   C8    106.22  3.000
 TSB  C4    N9   C1'   125.26  3.000
 TSB  C8    N9   C1'   128.46  3.000
 TSB  H8    C8   N7    123.73  3.000
 TSB  H8    C8   N9    123.13  3.000
 TSB  N7    C8   N9    113.13  3.000
 TSB  C5    N7   C8    104.66  3.000
 TSB  C4    C5   C6    116.30  3.000
 TSB  C4    C5   N7    110.80  3.000
 TSB  C6    C5   N7    132.90  3.000
 TSB  N1    C6   N6    119.33  3.000
 TSB  N1    C6   C5    117.93  3.000
 TSB  N6    C6   C5    122.74  3.000
 TSB  HN62  N6   HN61  118.36  3.000
 TSB  HN62  N6   C6    121.19  3.000
 TSB  HN61  N6   C6    120.43  3.000
 TSB  C2    N1   C6    119.12  3.000
 TSB  H2    C2   N3    116.13  3.000
 TSB  H2    C2   N1    115.46  3.000
 TSB  N3    C2   N1    128.41  3.000
 TSB  C4    N3   C2    111.70  3.000
 TSB  N3    C4   C5    126.54  3.000
 TSB  N3    C4   N9    128.27  3.000
 TSB  C5    C4   N9    105.19  3.000
 TSB  N8    C    O     121.82  3.000
 TSB  N8    C    CA    113.45  3.000
 TSB  O     C    CA    124.73  3.000
 TSB  HN8   N8   S1    115.36  3.000
 TSB  HN8   N8   C     120.39  3.000
 TSB  S1    N8   C     123.81  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
 TSB  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 TSB  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 TSB  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 TSB  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 TSB  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 TSB  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 TSB  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 TSB  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 TSB  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 TSB  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 TSB  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 TSB  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 TSB  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 TSB  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 TSB  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 TSB  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 TSB  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 TSB  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 TSB  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 TSB  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 TSB  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 TSB  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 TSB  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 TSB  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 TSB  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 TSB  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 TSB  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 TSB  CONST_28  S1    N8   C    CA    180.00   0.0  0
 TSB  CONST_29  S1    N8   C    O       0.00   0.0  0
 TSB  CONST_30  HN8   N8   C    CA      0.00   0.0  0
 TSB  Var_01    C4'   C5'  O5'  S1   -177.09  30.0  3
 TSB  Var_02    O1S   S1   N8   C     173.10  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
 TSB  chir_01  CA   N    CB   C    negativ
 TSB  chir_02  CB   OG1  CA   CG2  negativ
 TSB  chir_03  C4'  C5'  O4'  C3'  negativ
 TSB  chir_04  C3'  O3'  C4'  C2'  positiv
 TSB  chir_05  C2'  O2'  C3'  C1'  positiv
 TSB  chir_06  C1'  O4'  N9   C2'  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
 TSB  plan-1  C1'   0.020
 TSB  plan-1  N9    0.020
 TSB  plan-1  C8    0.020
 TSB  plan-1  N7    0.020
 TSB  plan-1  C5    0.020
 TSB  plan-1  C6    0.020
 TSB  plan-1  N6    0.020
 TSB  plan-1  N1    0.020
 TSB  plan-1  C2    0.020
 TSB  plan-1  N3    0.020
 TSB  plan-1  C4    0.020
 TSB  plan-1  H8    0.020
 TSB  plan-1  H2    0.020
 TSB  plan-2  C6    0.020
 TSB  plan-2  N6    0.020
 TSB  plan-2  HN61  0.020
 TSB  plan-2  HN62  0.020
 TSB  plan-3  CA    0.020
 TSB  plan-3  S1    0.020
 TSB  plan-3  HN8   0.020
 TSB  plan-3  C     0.020
 TSB  plan-3  O     0.020
 TSB  plan-3  N8    0.020

