# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 15:08:18 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2R,3S,4R,5S,6S)-6-{[(2R,3R,4R,5R,6R)-4,6-dihydroxy-5-(sulfoamino)-2-(sulfooxy)tetrahydro-2H-pyran-3-yl]oxy}-3,4-dihydroxy-5-(sulfooxy)tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](O[S](O)(=O)=O)[C@H](O[C@H]2O[C@H]([C@@H](O)[C@@H](O)[C@@H]2O[S](O)(=O)=O)C(O)=O)[C@H](O)[C@H]1N[S](O)(=O)=O
#
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
 M7J  M7J  '(2R,3S,4R,5S,6S)-6-{[(2R,3R,4R,5R,6R)-4,6-dihydroxy-5-(sulfoamino)-2-(sulfooxy)tetrahydro-2H-pyran-3-yl]oxy}-3,4-dihydroxy-5-(sulfooxy)tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  saccharide  50  35  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M7J
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
 M7J  C4   C  CH1    0  -0.010   4.1159  -1.6248  -0.0246
 M7J  C5   C  CH1    0  -0.151   3.6729  -0.7694   1.1646
 M7J  C6   C  C      0   0.450   4.1948  -1.2913   2.5233
 M7J  C3   C  CH1    0   0.028   3.4600  -1.0882  -1.2979
 M7J  CAS  C  CH1    0  -0.049  -0.2086   0.7358   1.2942
 M7J  CAT  C  CH1    0   0.087  -1.4716   0.0953   1.8697
 M7J  CAU  C  CH1    0  -0.212  -2.5555  -0.0034   0.7848
 M7J  CAW  C  CH1    0   0.302  -0.6040   2.0887   0.7096
 M7J  CAY  C  CH1    0   0.280  -2.7849   1.4021   0.2221
 M7J  NAM  N  NC1    0  -0.781  -3.8059  -0.4899   1.3734
 M7J  OAA  O  OC    -1  -0.607   4.1984  -2.5421   2.6665
 M7J  OAB  O  OS    -1  -0.764  -3.0641  -2.8438   1.6772
 M7J  OAF  O  OS     0  -0.747  -5.4626  -2.2781   1.8377
 M7J  OAH  O  OS     0  -0.733  -4.3445  -2.3387  -0.3494
 M7J  OAL  O  OH1    0  -0.706  -1.1428  -1.1206   2.4702
 M7J  OAX  O  O2     0  -0.479  -1.5844   1.9348  -0.2742
 M7J  OAZ  O  OH1    0  -0.650  -3.6959   1.3397  -0.8094
 M7J  SAG  S  S      0   1.520  -4.2110  -2.1053   1.0932
 M7J  OBA  O  OS    -1  -0.716  -0.8053  -1.6493  -2.1339
 M7J  OBC  O  OS     0  -0.747   0.9053  -2.3183  -3.7430
 M7J  OBD  O  OC2    0  -0.623   0.4928   2.6972   0.1082
 M7J  OBE  O  OS     0  -0.747  -0.2222  -0.1514  -4.0087
 M7J  OBF  O  OS    -1  -0.736   0.8256   4.5483   1.7247
 M7J  OBH  O  OS     0  -0.724   1.8931   4.5444  -0.4956
 M7J  OBI  O  OS     0  -0.729  -0.5304   4.9372  -0.2820
 M7J  SBB  S  S      0   1.569   0.2070  -1.2065  -3.0911
 M7J  SBG  S  S      0   1.565   0.6774   4.3387   0.2834
 M7J  C1   C  CH1    0   0.317   1.6581  -0.1788   0.1288
 M7J  O1   O  O2     0  -0.482   0.2989  -0.1386   0.3171
 M7J  C2   C  CH1    0  -0.002   1.9487  -1.0240  -1.1139
 M7J  O2   O  OC2    0  -0.625   1.3569  -0.3962  -2.2366
 M7J  O3   O  OH1    0  -0.658   3.7508  -1.8702  -2.4246
 M7J  O4   O  OH1    0  -0.707   3.7724  -2.9726   0.1479
 M7J  O5   O  O2     0  -0.502   2.2586  -0.7706   1.2553
 M7J  O6   O  O      0  -0.570   4.5464  -0.4553   3.3625
 M7J  H1   H  HCH1   0   0.204   5.2089  -1.4983  -0.1284
 M7J  H2   H  HCH1   0   0.207   4.0403   0.2564   1.0113
 M7J  H5   H  HCH1   0   0.201   3.8220  -0.0559  -1.4369
 M7J  H6   H  HCH1   0   0.248   0.5096   0.9040   2.1066
 M7J  H7   H  HCH1   0   0.189  -1.8639   0.7912   2.6315
 M7J  H8   H  HCH1   0   0.300  -2.2112  -0.6400  -0.0407
 M7J  H9   H  HCH1   0   0.200  -0.9931   2.6995   1.5437
 M7J  H10  H  HCH1   0   0.189  -3.1543   2.0496   1.0394
 M7J  HAM  H  HNC1   0   0.386  -4.5989   0.0876   1.1104
 M7J  HAL  H  HOH1   0   0.450  -1.8064  -1.7968   2.2304
 M7J  HAZ  H  HOH1   0   0.466  -4.1033   2.2042  -0.9266
 M7J  H12  H  HCH1   0   0.183   2.0866   0.8278  -0.0128
 M7J  H13  H  HCH1   0   0.235   1.5530  -2.0329  -0.9534
 M7J  H3   H  HOH1   0   0.446   4.7007  -1.8287  -2.5747
 M7J  H4   H  HOH1   0   0.438   3.8832  -3.1139   1.1182

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
 M7J  OBC  SBB  deloc   1.466  0.020  1.466
 M7J  OBI  SBG  deloc   1.462  0.020  1.462
 M7J  OBE  SBB  deloc   1.463  0.020  1.463
 M7J  SBB  OBA  deloc   1.462  0.020  1.462
 M7J  SBB  O2   single  1.646  0.020  1.646
 M7J  OBD  SBG  single  1.661  0.020  1.661
 M7J  OBD  CAW  single  1.391  0.020  1.391
 M7J  SBG  OBH  deloc   1.458  0.020  1.458
 M7J  SBG  OBF  deloc   1.464  0.020  1.464
 M7J  OAL  CAT  single  1.395  0.020  1.395
 M7J  O2   C2   single  1.416  0.020  1.416
 M7J  OAX  CAW  single  1.397  0.020  1.397
 M7J  OAX  CAY  single  1.404  0.020  1.404
 M7J  OAZ  CAY  single  1.378  0.020  1.378
 M7J  CAW  CAS  single  1.526  0.020  1.526
 M7J  CAT  CAU  single  1.537  0.020  1.537
 M7J  CAT  CAS  single  1.529  0.020  1.529
 M7J  CAY  CAU  single  1.531  0.020  1.531
 M7J  OAF  SAG  deloc   1.466  0.020  1.466
 M7J  CAU  NAM  single  1.465  0.020  1.465
 M7J  O1   CAS  single  1.406  0.020  1.406
 M7J  O1   C1   single  1.373  0.020  1.373
 M7J  C2   C1   single  1.531  0.020  1.531
 M7J  C2   C3   single  1.524  0.020  1.524
 M7J  O3   C3   single  1.402  0.020  1.402
 M7J  C1   O5   single  1.407  0.020  1.407
 M7J  C3   C4   single  1.530  0.020  1.530
 M7J  SAG  NAM  single  1.689  0.020  1.689
 M7J  SAG  OAH  deloc   1.467  0.020  1.467
 M7J  SAG  OAB  deloc   1.484  0.020  1.484
 M7J  O4   C4   single  1.402  0.020  1.402
 M7J  O5   C5   single  1.417  0.020  1.417
 M7J  C4   C5   single  1.530  0.020  1.530
 M7J  C5   C6   single  1.546  0.020  1.546
 M7J  C6   O6   deloc   1.236  0.020  1.236
 M7J  C6   OAA  deloc   1.259  0.020  1.259
 M7J  C4   H1   single  0.970  0.020  1.090
 M7J  C5   H2   single  0.970  0.020  1.090
 M7J  C3   H5   single  0.970  0.020  1.090
 M7J  CAS  H6   single  0.970  0.020  1.090
 M7J  CAT  H7   single  0.970  0.020  1.090
 M7J  CAU  H8   single  0.970  0.020  1.090
 M7J  CAW  H9   single  0.970  0.020  1.090
 M7J  CAY  H10  single  0.970  0.020  1.090
 M7J  NAM  HAM  single  0.890  0.020  1.040
 M7J  OAL  HAL  single  0.850  0.020  0.980
 M7J  OAZ  HAZ  single  0.850  0.020  0.980
 M7J  C1   H12  single  0.970  0.020  1.090
 M7J  C2   H13  single  0.970  0.020  1.090
 M7J  O3   H3   single  0.850  0.020  0.980
 M7J  O4   H4   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
 M7J  H1   C4   O4   111.35  3.000
 M7J  H1   C4   C3   107.80  3.000
 M7J  O4   C4   C3   109.56  3.000
 M7J  H1   C4   C5   107.17  3.000
 M7J  O4   C4   C5   111.77  3.000
 M7J  C3   C4   C5   109.07  3.000
 M7J  H2   C5   O5   110.06  3.000
 M7J  H2   C5   C6   108.93  3.000
 M7J  O5   C5   C6   106.28  3.000
 M7J  H2   C5   C4   108.43  3.000
 M7J  C6   C5   C4   113.35  3.000
 M7J  O5   C5   C4   109.76  3.000
 M7J  O6   C6   OAA  126.45  3.000
 M7J  OAA  C6   C5   115.87  3.000
 M7J  O6   C6   C5   117.68  3.000
 M7J  H5   C3   O3   110.65  3.000
 M7J  H5   C3   C2   107.54  3.000
 M7J  O3   C3   C2   109.04  3.000
 M7J  H5   C3   C4   107.01  3.000
 M7J  O3   C3   C4   112.61  3.000
 M7J  C2   C3   C4   109.85  3.000
 M7J  H6   CAS  O1   111.93  3.000
 M7J  H6   CAS  CAW  108.50  3.000
 M7J  O1   CAS  CAW  112.25  3.000
 M7J  H6   CAS  CAT  109.05  3.000
 M7J  O1   CAS  CAT  107.42  3.000
 M7J  CAW  CAS  CAT  107.56  3.000
 M7J  H7   CAT  OAL  109.64  3.000
 M7J  H7   CAT  CAU  106.08  3.000
 M7J  OAL  CAT  CAU  114.46  3.000
 M7J  H7   CAT  CAS  106.81  3.000
 M7J  CAU  CAT  CAS  110.11  3.000
 M7J  OAL  CAT  CAS  109.42  3.000
 M7J  H8   CAU  NAM  112.16  3.000
 M7J  H8   CAU  CAY  107.63  3.000
 M7J  NAM  CAU  CAY  108.94  3.000
 M7J  H8   CAU  CAT  110.30  3.000
 M7J  NAM  CAU  CAT  109.85  3.000
 M7J  CAY  CAU  CAT  107.83  3.000
 M7J  H9   CAW  OBD  111.24  3.000
 M7J  H9   CAW  OAX  110.20  3.000
 M7J  OBD  CAW  OAX  107.28  3.000
 M7J  H9   CAW  CAS  106.99  3.000
 M7J  OAX  CAW  CAS  110.72  3.000
 M7J  OBD  CAW  CAS  110.43  3.000
 M7J  H10  CAY  OAZ  111.03  3.000
 M7J  H10  CAY  OAX  108.94  3.000
 M7J  OAZ  CAY  OAX  108.54  3.000
 M7J  H10  CAY  CAU  108.41  3.000
 M7J  OAZ  CAY  CAU  109.43  3.000
 M7J  OAX  CAY  CAU  110.49  3.000
 M7J  HAM  NAM  SAG  108.27  3.000
 M7J  HAM  NAM  CAU  111.93  3.000
 M7J  SAG  NAM  CAU  117.11  3.000
 M7J  HAL  OAL  CAT  109.71  3.000
 M7J  CAY  OAX  CAW  113.13  3.000
 M7J  HAZ  OAZ  CAY  109.28  3.000
 M7J  OAH  SAG  OAF  113.75  3.000
 M7J  OAH  SAG  OAB  112.21  3.000
 M7J  OAF  SAG  OAB  113.66  3.000
 M7J  OAB  SAG  NAM  103.02  3.000
 M7J  OAH  SAG  NAM  109.70  3.000
 M7J  OAF  SAG  NAM  103.49  3.000
 M7J  SBG  OBD  CAW  118.31  3.000
 M7J  O2   SBB  OBE  100.11  3.000
 M7J  O2   SBB  OBC  105.75  3.000
 M7J  OBE  SBB  OBC  114.07  3.000
 M7J  O2   SBB  OBA  107.03  3.000
 M7J  OBE  SBB  OBA  115.22  3.000
 M7J  OBC  SBB  OBA  113.04  3.000
 M7J  OBI  SBG  OBH  115.11  3.000
 M7J  OBH  SBG  OBF  114.92  3.000
 M7J  OBI  SBG  OBF  113.94  3.000
 M7J  OBF  SBG  OBD  104.87  3.000
 M7J  OBH  SBG  OBD  100.12  3.000
 M7J  OBI  SBG  OBD  105.78  3.000
 M7J  H12  C1   O5   108.71  3.000
 M7J  H12  C1   C2   109.02  3.000
 M7J  O5   C1   C2   109.68  3.000
 M7J  H12  C1   O1   112.05  3.000
 M7J  O5   C1   O1   108.97  3.000
 M7J  C2   C1   O1   108.39  3.000
 M7J  C1   O1   CAS  118.10  3.000
 M7J  H13  C2   O2   111.93  3.000
 M7J  H13  C2   C1   108.72  3.000
 M7J  O2   C2   C1   108.64  3.000
 M7J  H13  C2   C3   109.70  3.000
 M7J  C1   C2   C3   108.03  3.000
 M7J  O2   C2   C3   109.73  3.000
 M7J  C2   O2   SBB  119.04  3.000
 M7J  H3   O3   C3   107.82  3.000
 M7J  H4   O4   C4   103.37  3.000
 M7J  C1   O5   C5   111.98  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
 M7J  Var_01  OAF  SAG  NAM  CAU  178.21  30.0  2
 M7J  Var_02  OBI  SBG  OBD  CAW  -59.17  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
 M7J  chir_01  C4   C3   O4   C5   positiv
 M7J  chir_02  C5   O5   C4   C6   positiv
 M7J  chir_03  C3   O3   C4   C2   positiv
 M7J  chir_04  CAS  O1   CAT  CAW  positiv
 M7J  chir_05  CAT  OAL  CAU  CAS  positiv
 M7J  chir_06  CAU  NAM  CAT  CAY  positiv
 M7J  chir_07  CAW  OAX  OBD  CAS  positiv
 M7J  chir_08  CAY  OAZ  OAX  CAU  positiv
 M7J  chir_09  C1   O5   O1   C2   positiv
 M7J  chir_10  C2   O2   C3   C1   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
 M7J  plan-1  C5   0.020
 M7J  plan-1  C6   0.020
 M7J  plan-1  OAA  0.020
 M7J  plan-1  O6   0.020

