# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Nov 18 20:00:51 2022
#   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  "heparin"  saccharide  54  35  .  2023-02-15  2023-02-16
;
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  -0.024   3.2059  113.1079  292.5878
 M7J  C5   C  CH1   0  -0.089   1.8732  112.7115  293.2124
 M7J  C6   C  C     0   0.527   2.0795  111.7993  294.4079
 M7J  C3   C  CH1   0   0.017   2.9116  113.9315  291.3333
 M7J  CAS  C  CH1   0  -0.087  -0.0758  110.4809  290.5515
 M7J  CAT  C  CH1   0   0.007   1.0952  109.7056  289.9518
 M7J  CAU  C  CH1   0  -0.170   0.9332  108.2186  290.3386
 M7J  CAW  C  CH1   0   0.289  -1.4084  109.9698  289.9917
 M7J  CAY  C  CH1   0   0.308  -0.5306  107.8514  290.6192
 M7J  NAM  N  NC1   0  -0.783   1.7088  107.8335  291.5051
 M7J  OAA  O  OH1   0  -0.587   2.7537  112.4269  295.3569
 M7J  OAB  O  OS    0  -0.705   3.3304  105.9993  292.1591
 M7J  OAF  O  OS    0  -0.638   3.5996  107.2195  290.0081
 M7J  OAH  O  OS    0  -0.638   4.1060  108.2458  292.2420
 M7J  OAL  O  OH1   0  -0.657   1.1505  109.7792  288.5534
 M7J  OAX  O  O2    0  -0.488  -1.3731  108.6039  289.7602
 M7J  OAZ  O  OH1   0  -0.640  -0.7104  106.5227  290.3406
 M7J  SAG  S  S     0   1.589   3.2836  107.4056  291.4060
 M7J  OBA  O  OS    0  -0.733   3.5383  114.9677  288.2554
 M7J  OBC  O  OS    0  -0.616   1.4270  114.8554  287.0833
 M7J  OBD  O  OC2   0  -0.575  -1.6378  110.5759  288.7242
 M7J  OBE  O  OS    0  -0.633   2.7061  112.7575  287.5277
 M7J  OBF  O  OS    0  -0.700  -3.3529  112.3619  288.9033
 M7J  OBH  O  OS    0  -0.621  -4.0568  109.9879  288.7691
 M7J  OBI  O  OS    0  -0.610  -2.9806  111.1882  286.8413
 M7J  SBB  S  S     0   1.649   2.2904  114.0806  287.9271
 M7J  SBG  S  S     0   1.649  -3.1132  110.9413  288.2458
 M7J  C1   C  CH1   0   0.312   0.7473  112.6828  291.1441
 M7J  O1   O  O2    0  -0.509  -0.0516  111.8738  290.3388
 M7J  C2   C  CH1   0  -0.070   2.0110  113.1438  290.3942
 M7J  O2   O  OC2   0  -0.589   1.5319  113.9924  289.3359
 M7J  O3   O  OH1   0  -0.690   4.1194  114.2404  290.6504
 M7J  O4   O  OH1   0  -0.654   3.8984  111.9253  292.3019
 M7J  O5   O  O2    0  -0.495   1.0935  111.9916  292.2977
 M7J  O6   O  O     0  -0.406   1.6764  110.6721  294.4802
 M7J  H1   H  HCH1  0   0.277   3.7491  113.7475  293.2955
 M7J  H2   H  HCH1  0   0.301   1.3525  113.6211  293.5477
 M7J  H5   H  HCH1  0   0.276   2.3958  114.8514  291.6355
 M7J  H6   H  HCH1  0   0.281  -0.0998  110.2620  291.6243
 M7J  H7   H  HCH1  0   0.256   2.0252  110.0671  290.4108
 M7J  H8   H  HCH1  0   0.309   1.2641  107.6196  289.4894
 M7J  H9   H  HCH1  0   0.264  -2.2160  110.2328  290.6889
 M7J  H10  H  HCH1  0   0.221  -0.7886  108.0768  291.6659
 M7J  HAM  H  HNC1  0   0.428   1.4680  108.2825  292.3832
 M7J  H11  H  HOH1  0   0.491   2.8966  111.8404  296.1160
 M7J  HAL  H  HOH1  0   0.449   1.2751  110.6957  288.2843
 M7J  HAZ  H  HOH1  0   0.470  -1.5026  106.1989  290.7839
 M7J  H12  H  HCH1  0   0.259   0.1509  113.5756  291.3913
 M7J  H13  H  HCH1  0   0.300   2.5467  112.2809  289.9875
 M7J  H3   H  HOH1  0   0.495   4.6040  114.9160  291.1446
 M7J  H4   H  HOH1  0   0.464   4.7750  112.1446  291.9682
 M7J  H14  H  H     0   0.499   2.7695  105.3327  291.7280
 M7J  H15  H  H     0   0.506   3.9378  114.7267  289.1529
 M7J  H16  H  H     0   0.512  -3.7021  112.3126  289.8102

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  double  1.435  0.020  1.435
 M7J  OBI  SBG  double  1.432  0.020  1.432
 M7J  OBE  SBB  double  1.443  0.020  1.443
 M7J  SBB  OBA  single  1.566  0.020  1.566
 M7J  SBB  O2   single  1.602  0.020  1.602
 M7J  OBD  SBG  single  1.593  0.020  1.593
 M7J  OBD  CAW  single  1.424  0.020  1.424
 M7J  SBG  OBH  double  1.440  0.020  1.440
 M7J  SBG  OBF  single  1.584  0.020  1.584
 M7J  OAL  CAT  single  1.401  0.020  1.401
 M7J  O2   C2   single  1.439  0.020  1.439
 M7J  OAX  CAW  single  1.386  0.020  1.386
 M7J  OAX  CAY  single  1.419  0.020  1.419
 M7J  OAZ  CAY  single  1.369  0.020  1.369
 M7J  CAW  CAS  single  1.533  0.020  1.533
 M7J  CAT  CAU  single  1.545  0.020  1.545
 M7J  CAT  CAS  single  1.527  0.020  1.527
 M7J  CAY  CAU  single  1.535  0.020  1.535
 M7J  OAF  SAG  double  1.445  0.020  1.445
 M7J  CAU  NAM  single  1.453  0.020  1.453
 M7J  O1   CAS  single  1.409  0.020  1.409
 M7J  O1   C1   single  1.393  0.020  1.393
 M7J  C2   C1   single  1.540  0.020  1.540
 M7J  C2   C3   single  1.521  0.020  1.521
 M7J  O3   C3   single  1.421  0.020  1.421
 M7J  C1   O5   single  1.389  0.020  1.389
 M7J  C3   C4   single  1.529  0.020  1.529
 M7J  SAG  NAM  single  1.635  0.020  1.635
 M7J  SAG  OAH  double  1.443  0.020  1.443
 M7J  SAG  OAB  single  1.596  0.020  1.596
 M7J  O4   C4   single  1.400  0.020  1.400
 M7J  O5   C5   single  1.401  0.020  1.401
 M7J  C4   C5   single  1.524  0.020  1.524
 M7J  C5   C6   single  1.518  0.020  1.518
 M7J  C6   O6   double  1.199  0.020  1.199
 M7J  C6   OAA  single  1.323  0.020  1.323
 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  OAA  H11  single  0.850  0.020  0.980
 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
 M7J  OAB  H14  single  0.850  0.020  0.980
 M7J  OBA  H15  single  0.850  0.020  0.980
 M7J  OBF  H16  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   112.29  3.000
 M7J  H1   C4   C3   108.07  3.000
 M7J  O4   C4   C3   112.50  3.000
 M7J  H1   C4   C5   108.66  3.000
 M7J  O4   C4   C5   107.25  3.000
 M7J  C3   C4   C5   107.93  3.000
 M7J  H2   C5   O5   111.11  3.000
 M7J  H2   C5   C6   108.73  3.000
 M7J  O5   C5   C6   106.32  3.000
 M7J  H2   C5   C4   108.89  3.000
 M7J  C6   C5   C4   111.11  3.000
 M7J  O5   C5   C4   110.66  3.000
 M7J  O6   C6   OAA  125.04  3.000
 M7J  OAA  C6   C5   110.44  3.000
 M7J  O6   C6   C5   124.52  3.000
 M7J  H5   C3   O3   110.47  3.000
 M7J  H5   C3   C2   109.02  3.000
 M7J  O3   C3   C2   108.60  3.000
 M7J  H5   C3   C4   108.43  3.000
 M7J  O3   C3   C4   110.34  3.000
 M7J  C2   C3   C4   109.97  3.000
 M7J  H6   CAS  O1   110.23  3.000
 M7J  H6   CAS  CAW  105.79  3.000
 M7J  O1   CAS  CAW  106.81  3.000
 M7J  H6   CAS  CAT  107.46  3.000
 M7J  O1   CAS  CAT  115.43  3.000
 M7J  CAW  CAS  CAT  110.72  3.000
 M7J  H7   CAT  OAL  111.49  3.000
 M7J  H7   CAT  CAU  107.52  3.000
 M7J  OAL  CAT  CAU  107.73  3.000
 M7J  H7   CAT  CAS  108.55  3.000
 M7J  CAU  CAT  CAS  108.06  3.000
 M7J  OAL  CAT  CAS  113.29  3.000
 M7J  H8   CAU  NAM  108.52  3.000
 M7J  H8   CAU  CAY  107.47  3.000
 M7J  NAM  CAU  CAY  107.39  3.000
 M7J  H8   CAU  CAT  107.57  3.000
 M7J  NAM  CAU  CAT  113.59  3.000
 M7J  CAY  CAU  CAT  112.08  3.000
 M7J  H9   CAW  OBD  110.16  3.000
 M7J  H9   CAW  OAX  111.14  3.000
 M7J  OBD  CAW  OAX  105.96  3.000
 M7J  H9   CAW  CAS  109.10  3.000
 M7J  OAX  CAW  CAS  111.56  3.000
 M7J  OBD  CAW  CAS  108.87  3.000
 M7J  H10  CAY  OAZ  111.18  3.000
 M7J  H10  CAY  OAX  109.13  3.000
 M7J  OAZ  CAY  OAX  108.26  3.000
 M7J  H10  CAY  CAU  110.38  3.000
 M7J  OAZ  CAY  CAU  108.67  3.000
 M7J  OAX  CAY  CAU  109.18  3.000
 M7J  HAM  NAM  SAG  113.37  3.000
 M7J  HAM  NAM  CAU  116.79  3.000
 M7J  SAG  NAM  CAU  122.34  3.000
 M7J  H11  OAA  C6   110.47  3.000
 M7J  H14  OAB  SAG  112.22  3.000
 M7J  HAL  OAL  CAT  109.50  3.000
 M7J  CAY  OAX  CAW  115.89  3.000
 M7J  HAZ  OAZ  CAY  109.90  3.000
 M7J  OAH  SAG  OAF  120.72  3.000
 M7J  OAH  SAG  OAB  102.89  3.000
 M7J  OAF  SAG  OAB  109.66  3.000
 M7J  OAB  SAG  NAM  103.31  3.000
 M7J  OAH  SAG  NAM  111.20  3.000
 M7J  OAF  SAG  NAM  107.63  3.000
 M7J  H15  OBA  SBB  111.46  3.000
 M7J  SBG  OBD  CAW  120.94  3.000
 M7J  H16  OBF  SBG  113.31  3.000
 M7J  O2   SBB  OBE  109.22  3.000
 M7J  O2   SBB  OBC  105.18  3.000
 M7J  OBE  SBB  OBC  120.38  3.000
 M7J  O2   SBB  OBA  102.95  3.000
 M7J  OBE  SBB  OBA  110.36  3.000
 M7J  OBC  SBB  OBA  107.28  3.000
 M7J  OBI  SBG  OBH  122.09  3.000
 M7J  OBH  SBG  OBF  110.11  3.000
 M7J  OBI  SBG  OBF  105.46  3.000
 M7J  OBF  SBG  OBD  102.78  3.000
 M7J  OBH  SBG  OBD  110.23  3.000
 M7J  OBI  SBG  OBD  104.37  3.000
 M7J  H12  C1   O5   110.60  3.000
 M7J  H12  C1   C2   108.11  3.000
 M7J  O5   C1   C2   110.43  3.000
 M7J  H12  C1   O1   106.84  3.000
 M7J  O5   C1   O1   109.52  3.000
 M7J  C2   C1   O1   111.27  3.000
 M7J  C1   O1   CAS  119.77  3.000
 M7J  H13  C2   O2   110.79  3.000
 M7J  H13  C2   C1   110.28  3.000
 M7J  O2   C2   C1   105.16  3.000
 M7J  H13  C2   C3   110.37  3.000
 M7J  C1   C2   C3   109.89  3.000
 M7J  O2   C2   C3   110.24  3.000
 M7J  C2   O2   SBB  121.43  3.000
 M7J  H3   O3   C3   109.39  3.000
 M7J  H4   O4   C4   109.18  3.000
 M7J  C1   O5   C5   115.17  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  CONST_01  H11  OAA  C6   C5    180.00   0.0  0
 M7J  CONST_02  H11  OAA  C6   O6      0.00   0.0  0
 M7J  Var_01    OAF  SAG  NAM  CAU   -11.91  30.0  3
 M7J  Var_02    OAH  SAG  NAM  CAU   122.38  30.0  3
 M7J  Var_03    OAB  SAG  NAM  CAU  -127.89  30.0  3
 M7J  Var_04    OBI  SBG  OBD  CAW  -165.40  30.0  3
 M7J  Var_05    OBH  SBG  OBD  CAW   -32.64  30.0  3
 M7J  Var_06    OBF  SBG  OBD  CAW    84.71  30.0  3
 M7J  Var_07    C2   O2   SBB  OBA   -75.92  30.0  3
 M7J  Var_08    C2   O2   SBB  OBC   171.86  30.0  3
 M7J  Var_09    C2   O2   SBB  OBE    41.35  30.0  3
 M7J  Var_10    HAM  NAM  SAG  OAB    83.39  30.0  3
 M7J  Var_11    HAM  NAM  SAG  OAF  -160.63  30.0  3
 M7J  Var_12    HAM  NAM  SAG  OAH   -26.34  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  OAX  OAZ  CAU  negativ
 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
 M7J  plan-1  H11  0.020

