# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:55:59 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: 5'-O-{[(2R)-2-hydroxy-3,3-dimethylbutanoyl]sulfamoyl}adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)[C@@H](O)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
 52H  52H  5'-O-{[(2R)-2-hydroxy-3,3-dimethylbutanoyl]sulfamoyl}adenosine  ligand  55  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_52H
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
 52H  C4    C  CR56  0   0.491   3.5216   0.2407   0.3867
 52H  C5    C  CR56  0  -0.009   3.4191  -1.0944   0.7468
 52H  C6    C  CR6   0   0.459   4.6227  -1.8216   0.7965
 52H  C8    C  CR15  0   0.102   1.4521  -0.3326   0.8081
 52H  N1    N  N     0  -0.474   5.7562  -1.1771   0.4997
 52H  N3    N  N     0  -0.451   4.6413   0.8958   0.0888
 52H  CBB   C  CT    0  -0.122  -2.0084  -2.8753  -1.4368
 52H  CAB   C  CH3   0  -0.677  -0.6366  -3.3610  -0.9651
 52H  CAC   C  CH3   0  -0.667  -1.8472  -1.5605  -2.2006
 52H  CAX   C  CH1   0  -0.030  -2.9959  -2.6836  -0.2554
 52H  OAH   O  OH1   0  -0.647  -3.1207  -3.8114   0.5611
 52H  CAT   C  C     0   0.554  -2.6449  -1.4840   0.6240
 52H  OAE   O  O     0  -0.415  -1.8098  -1.5273   1.4959
 52H  NAQ   N  NC1   0  -0.831  -3.3702  -0.3411   0.3641
 52H  SBE   S  S     0   1.623  -3.3545   1.0167   1.3354
 52H  OAF   O  OS    0  -0.622  -4.3334   1.8975   0.7533
 52H  OAG   O  OS    0  -0.601  -3.4071   0.6454   2.7197
 52H  O5'   O  OC2   0  -0.563  -1.8934   1.5967   1.1377
 52H  C4'   C  CH1   0  -0.041  -0.3058   3.0032   0.0608
 52H  O4'   O  O2    0  -0.488   0.7000   2.3800   0.8553
 52H  C3'   C  CH1   0  -0.031   0.3602   3.3481  -1.2642
 52H  O3'   O  OH1   0  -0.662   1.0013   4.5854  -1.1288
 52H  C2'   C  CH1   0  -0.040   1.3802   2.2085  -1.3765
 52H  O2'   O  OH1   0  -0.646   2.4814   2.4868  -2.1828
 52H  C1'   C  CH1   0   0.223   1.8195   2.0553   0.0821
 52H  N9    N  NR5   0  -0.541   2.2430   0.7177   0.4267
 52H  N7    N  N     0  -0.444   2.1176  -1.4309   1.0096
 52H  C2    C  CR16  0   0.041   5.7019   0.1124   0.1742
 52H  N6    N  NH2   0  -0.816   4.6693  -3.1150   1.1189
 52H  H8    H  HCR5  0   0.285   0.3901  -0.2224   0.9617
 52H  HAA   H  HCH3  0   0.236  -2.7616  -4.8780  -1.8679
 52H  HAAA  H  HCH3  0   0.230  -3.5773  -3.5973  -2.7703
 52H  HAAB  H  HCH3  0   0.235  -1.9494  -4.0974  -3.2222
 52H  HAB   H  HCH3  0   0.242   0.0167  -3.4950  -1.8288
 52H  HABA  H  HCH3  0   0.246  -0.1384  -2.6612  -0.2942
 52H  HABB  H  HCH3  0   0.230  -0.6914  -4.3308  -0.4668
 52H  HAC   H  HCH3  0   0.240  -2.8077  -1.1309  -2.4932
 52H  HACA  H  HCH3  0   0.212  -1.3022  -0.8094  -1.6239
 52H  HACB  H  HCH3  0   0.254  -1.2752  -1.7289  -3.1136
 52H  HAX   H  HCH1  0   0.271  -3.9881  -2.5151  -0.6871
 52H  HOAH  H  HOH1  0   0.455  -2.2838  -3.9700   1.0125
 52H  HNAQ  H  HNC1  0   0.458  -4.0888  -0.3445  -0.3506
 52H  H5'   H  HCH2  0   0.241  -1.2317   1.2221  -0.7867
 52H  H5'A  H  HCH2  0   0.292  -2.2902   2.6341  -0.6407
 52H  H4'   H  HCH1  0   0.289  -0.6496   3.9002   0.5822
 52H  H3'   H  HCH1  0   0.264  -0.3527   3.3432  -2.0995
 52H  HO3'  H  HOH1  0   0.453   1.6827   4.6451  -1.8088
 52H  H2'   H  HCH1  0   0.241   0.8666   1.2928  -1.6975
 52H  HO2'  H  HOH1  0   0.471   2.2597   2.2828  -3.0970
 52H  H1'   H  HCH1  0   0.269   2.6638   2.7195   0.2958
 52H  H2    H  HCR6  0   0.252   6.6569   0.5760  -0.0494
 52H  HN6   H  HNH2  0   0.411   3.8396  -3.6089   1.3971
 52H  HN6A  H  HNH2  0   0.404   5.5550  -3.5810   1.2144
 52H  C5'   C  CH2   0  -0.208  -1.4870   2.0772  -0.1552
 52H  CAA   C  CH3   0  -0.645  -2.6133  -3.9239  -2.3738

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
 52H  C4   C5    aromatic  1.387  0.020  1.387
 52H  C4   N3    aromatic  1.331  0.020  1.331
 52H  C4   N9    aromatic  1.365  0.020  1.365
 52H  C5   C6    aromatic  1.407  0.020  1.407
 52H  C5   N7    aromatic  1.370  0.020  1.370
 52H  C6   N1    aromatic  1.337  0.020  1.337
 52H  C6   N6    single    1.334  0.020  1.334
 52H  C8   N9    aromatic  1.369  0.020  1.369
 52H  C8   N7    aromatic  1.300  0.020  1.300
 52H  N1   C2    aromatic  1.331  0.020  1.331
 52H  N3   C2    aromatic  1.321  0.020  1.321
 52H  CAA  CBB   single    1.531  0.020  1.531
 52H  CBB  CAB   single    1.530  0.020  1.530
 52H  CBB  CAC   single    1.529  0.020  1.529
 52H  CBB  CAX   single    1.552  0.020  1.552
 52H  CAX  OAH   single    1.398  0.020  1.398
 52H  CAX  CAT   single    1.528  0.020  1.528
 52H  CAT  OAE   double    1.208  0.020  1.208
 52H  CAT  NAQ   single    1.378  0.020  1.378
 52H  NAQ  SBE   single    1.670  0.020  1.670
 52H  SBE  OAF   deloc     1.440  0.020  1.440
 52H  SBE  OAG   deloc     1.434  0.020  1.434
 52H  SBE  O5'   single    1.584  0.020  1.584
 52H  O5'  C5'   single    1.438  0.020  1.438
 52H  C5'  C4'   single    1.516  0.020  1.516
 52H  C4'  O4'   single    1.425  0.020  1.425
 52H  C4'  C3'   single    1.523  0.020  1.523
 52H  O4'  C1'   single    1.399  0.020  1.399
 52H  C3'  O3'   single    1.400  0.020  1.400
 52H  C3'  C2'   single    1.533  0.020  1.533
 52H  C2'  O2'   single    1.393  0.020  1.393
 52H  C2'  C1'   single    1.531  0.020  1.531
 52H  C1'  N9    single    1.445  0.020  1.445
 52H  C8   H8    single    0.930  0.020  1.080
 52H  CAA  HAA   single    0.970  0.020  1.090
 52H  CAA  HAAA  single    0.970  0.020  1.090
 52H  CAA  HAAB  single    0.970  0.020  1.090
 52H  CAB  HAB   single    0.970  0.020  1.090
 52H  CAB  HABA  single    0.970  0.020  1.090
 52H  CAB  HABB  single    0.970  0.020  1.090
 52H  CAC  HAC   single    0.970  0.020  1.090
 52H  CAC  HACA  single    0.970  0.020  1.090
 52H  CAC  HACB  single    0.970  0.020  1.090
 52H  CAX  HAX   single    0.970  0.020  1.090
 52H  OAH  HOAH  single    0.850  0.020  0.980
 52H  NAQ  HNAQ  single    0.860  0.020  1.020
 52H  C5'  H5'   single    0.970  0.020  1.090
 52H  C5'  H5'A  single    0.970  0.020  1.090
 52H  C4'  H4'   single    0.970  0.020  1.090
 52H  C3'  H3'   single    0.970  0.020  1.090
 52H  O3'  HO3'  single    0.850  0.020  0.980
 52H  C2'  H2'   single    0.970  0.020  1.090
 52H  O2'  HO2'  single    0.850  0.020  0.980
 52H  C1'  H1'   single    0.970  0.020  1.090
 52H  C2   H2    single    0.930  0.020  1.080
 52H  N6   HN6   single    0.860  0.020  1.020
 52H  N6   HN6A  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
 52H  N9    C4   N3    128.49  3.000
 52H  N9    C4   C5    105.05  3.000
 52H  N3    C4   C5    126.46  3.000
 52H  N7    C5   C6    132.76  3.000
 52H  N7    C5   C4    110.89  3.000
 52H  C6    C5   C4    116.33  3.000
 52H  N6    C6   N1    119.44  3.000
 52H  N6    C6   C5    122.66  3.000
 52H  N1    C6   C5    117.91  3.000
 52H  H8    C8   N7    124.63  3.000
 52H  H8    C8   N9    122.01  3.000
 52H  N7    C8   N9    113.31  3.000
 52H  C2    N1   C6    119.12  3.000
 52H  C2    N3   C4    111.65  3.000
 52H  CAX   CBB  CAC   109.95  3.000
 52H  CAX   CBB  CAB   112.04  3.000
 52H  CAC   CBB  CAB   109.42  3.000
 52H  CAX   CBB  CAA   107.41  3.000
 52H  CAC   CBB  CAA   108.96  3.000
 52H  CAB   CBB  CAA   109.00  3.000
 52H  HABB  CAB  HABA  108.20  3.000
 52H  HABB  CAB  HAB   106.40  3.000
 52H  HABA  CAB  HAB   107.00  3.000
 52H  HABB  CAB  CBB   112.19  3.000
 52H  HABA  CAB  CBB   113.32  3.000
 52H  HAB   CAB  CBB   109.38  3.000
 52H  HACB  CAC  HACA  106.64  3.000
 52H  HACB  CAC  HAC   107.33  3.000
 52H  HACA  CAC  HAC   108.04  3.000
 52H  HACB  CAC  CBB   109.92  3.000
 52H  HACA  CAC  CBB   112.34  3.000
 52H  HAC   CAC  CBB   112.30  3.000
 52H  HAX   CAX  CAT   108.31  3.000
 52H  HAX   CAX  OAH   105.87  3.000
 52H  CAT   CAX  OAH   108.52  3.000
 52H  HAX   CAX  CBB   107.19  3.000
 52H  CAT   CAX  CBB   112.89  3.000
 52H  OAH   CAX  CBB   113.69  3.000
 52H  HOAH  OAH  CAX   109.19  3.000
 52H  NAQ   CAT  OAE   121.97  3.000
 52H  NAQ   CAT  CAX   114.93  3.000
 52H  OAE   CAT  CAX   123.09  3.000
 52H  HNAQ  NAQ  SBE   114.81  3.000
 52H  HNAQ  NAQ  CAT   120.22  3.000
 52H  SBE   NAQ  CAT   124.04  3.000
 52H  O5'   SBE  OAG   104.42  3.000
 52H  O5'   SBE  OAF   110.64  3.000
 52H  OAG   SBE  OAF   121.58  3.000
 52H  O5'   SBE  NAQ   103.52  3.000
 52H  OAG   SBE  NAQ   110.52  3.000
 52H  OAF   SBE  NAQ   104.83  3.000
 52H  C5'   O5'  SBE   119.68  3.000
 52H  H4'   C4'  C3'   111.52  3.000
 52H  H4'   C4'  O4'   108.36  3.000
 52H  C3'   C4'  O4'   105.99  3.000
 52H  H4'   C4'  C5'   108.91  3.000
 52H  C3'   C4'  C5'   110.80  3.000
 52H  O4'   C4'  C5'   111.23  3.000
 52H  C1'   O4'  C4'   110.99  3.000
 52H  H3'   C3'  C2'   111.89  3.000
 52H  H3'   C3'  O3'   112.01  3.000
 52H  C2'   C3'  O3'   111.06  3.000
 52H  H3'   C3'  C4'   112.15  3.000
 52H  C2'   C3'  C4'   100.74  3.000
 52H  O3'   C3'  C4'   108.44  3.000
 52H  HO3'  O3'  C3'   108.06  3.000
 52H  H2'   C2'  C1'   109.23  3.000
 52H  H2'   C2'  O2'   111.55  3.000
 52H  C1'   C2'  O2'   110.16  3.000
 52H  H2'   C2'  C3'   109.28  3.000
 52H  C1'   C2'  C3'   101.27  3.000
 52H  O2'   C2'  C3'   114.82  3.000
 52H  HO2'  O2'  C2'   108.99  3.000
 52H  H1'   C1'  N9    106.80  3.000
 52H  H1'   C1'  C2'   110.27  3.000
 52H  N9    C1'  C2'   113.83  3.000
 52H  H1'   C1'  O4'   111.61  3.000
 52H  N9    C1'  O4'   108.52  3.000
 52H  C2'   C1'  O4'   105.88  3.000
 52H  C1'   N9   C8    127.40  3.000
 52H  C1'   N9   C4    126.23  3.000
 52H  C8    N9   C4    106.33  3.000
 52H  C8    N7   C5    104.43  3.000
 52H  H2    C2   N3    116.10  3.000
 52H  H2    C2   N1    115.37  3.000
 52H  N3    C2   N1    128.53  3.000
 52H  HN6A  N6   HN6   118.25  3.000
 52H  HN6A  N6   C6    120.21  3.000
 52H  HN6   N6   C6    120.98  3.000
 52H  H5'A  C5'  H5'   108.30  3.000
 52H  H5'A  C5'  C4'   108.97  3.000
 52H  H5'   C5'  C4'   112.21  3.000
 52H  H5'A  C5'  O5'   111.25  3.000
 52H  H5'   C5'  O5'   108.91  3.000
 52H  C4'   C5'  O5'   107.23  3.000
 52H  HAAB  CAA  HAAA  107.59  3.000
 52H  HAAB  CAA  HAA   107.72  3.000
 52H  HAAA  CAA  HAA   108.06  3.000
 52H  HAAB  CAA  CBB   110.15  3.000
 52H  HAAA  CAA  CBB   111.48  3.000
 52H  HAA   CAA  CBB   111.67  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
 52H  CONST_01  N1    C6   C5   C4      0.00   0.0  0
 52H  CONST_02  C8    N7   C5   C4      0.00   0.0  0
 52H  CONST_03  N1    C2   N3   C4      0.00   0.0  0
 52H  CONST_04  N7    C8   N9   C4      0.00   0.0  0
 52H  CONST_05  C2    N3   C4   C5      0.00   0.0  0
 52H  CONST_06  C8    N9   C4   C5      0.00   0.0  0
 52H  CONST_07  C2    N1   C6   C5      0.00   0.0  0
 52H  CONST_08  N9    C8   N7   C5      0.00   0.0  0
 52H  CONST_09  N3    C4   C5   C6      0.00   0.0  0
 52H  CONST_10  N9    C4   C5   C6    180.00   0.0  0
 52H  CONST_11  C8    N7   C5   C6    180.00   0.0  0
 52H  CONST_12  N3    C2   N1   C6      0.00   0.0  0
 52H  CONST_13  N3    C4   N9   C8    180.00   0.0  0
 52H  CONST_14  N7    C5   C6   N1    180.00   0.0  0
 52H  CONST_15  N7    C5   C4   N3    180.00   0.0  0
 52H  CONST_16  N7    C5   C4   N9      0.00   0.0  0
 52H  CONST_17  C2    N3   C4   N9    180.00   0.0  0
 52H  CONST_18  C1'   N9   C4   C5    180.00   0.0  0
 52H  CONST_19  C1'   N9   C4   N3      0.00   0.0  0
 52H  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 52H  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 52H  CONST_22  N6    C6   C5   N7      0.00   0.0  0
 52H  CONST_23  N6    C6   N1   C2    180.00   0.0  0
 52H  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 52H  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 52H  CONST_26  HN6   N6   C6   C5      0.00   0.0  0
 52H  CONST_27  HN6A  N6   C6   C5    180.00   0.0  0
 52H  CONST_28  SBE   NAQ  CAT  CAX   180.00   0.0  0
 52H  CONST_29  SBE   NAQ  CAT  OAE     0.00   0.0  0
 52H  CONST_30  HNAQ  NAQ  CAT  CAX     0.00   0.0  0
 52H  Var_01    C4'   C5'  O5'  SBE   159.54  30.0  3
 52H  Var_02    OAF   SBE  NAQ  CAT  -174.99  30.0  3
 52H  Var_03    HAB   CAB  CBB  CAA    60.44  30.0  3
 52H  Var_04    HAC   CAC  CBB  CAA    65.33  30.0  3
 52H  Var_05    HAA   CAA  CBB  CAB    61.51  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
 52H  chir_01  CAX  CBB  OAH  CAT  negativ
 52H  chir_02  C4'  O4'  C5'  C3'  positiv
 52H  chir_03  C3'  O3'  C4'  C2'  positiv
 52H  chir_04  C2'  O2'  C3'  C1'  positiv
 52H  chir_05  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
 52H  plan-1  C4    0.020
 52H  plan-1  C5    0.020
 52H  plan-1  C6    0.020
 52H  plan-1  C8    0.020
 52H  plan-1  N1    0.020
 52H  plan-1  N3    0.020
 52H  plan-1  C1'   0.020
 52H  plan-1  N9    0.020
 52H  plan-1  N7    0.020
 52H  plan-1  C2    0.020
 52H  plan-1  N6    0.020
 52H  plan-1  H8    0.020
 52H  plan-1  H2    0.020
 52H  plan-2  C6    0.020
 52H  plan-2  N6    0.020
 52H  plan-2  HN6   0.020
 52H  plan-2  HN6A  0.020
 52H  plan-3  CAX   0.020
 52H  plan-3  CAT   0.020
 52H  plan-3  OAE   0.020
 52H  plan-3  NAQ   0.020
 52H  plan-3  SBE   0.020
 52H  plan-3  HNAQ  0.020

