# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:17:29 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: (2R,3S,5S)-2-(hydroxymethyl)-5-[(2-sulfoethyl)carbamoyl]pyrrolidinium-3-yl 2-(acetylamino)-2-deoxy-4-O-sulfo-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O[S](O)(=O)=O)[C@@H](CO)O[C@H]1O[C@H]2C[C@H]([NH2+][C@@H]2CO)C(=O)NCC[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
 BLG  BLG  '(2R,3S,5S)-2-(hydroxymethyl)-5-[(2-sulfoethyl)carbamoyl]pyrrolidinium-3-yl 2-(acetylamino)-2-deoxy-4-O-sulfo-beta-D-glucopyranoside'  ligand  63  35  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BLG
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
 BLG  C1    C  CH1    0   0.329  -2.0609   0.9097   0.2610
 BLG  C2    C  CH1    0  -0.177  -3.3517   1.1285  -0.5200
 BLG  C3    C  CH1    0   0.051  -4.4016   0.1234  -0.0379
 BLG  C4    C  CH1    0  -0.016  -3.8346  -1.3005  -0.0407
 BLG  C5    C  CH1    0  -0.029  -2.4678  -1.3625   0.6458
 BLG  O5    O  O2     0  -0.468  -1.6172  -0.4012   0.0630
 BLG  O1    O  O2     0  -0.492  -1.0901   1.7712  -0.2089
 BLG  N2    N  NH1    0  -0.631  -3.8308   2.4747  -0.3688
 BLG  C7    C  C      0   0.445  -3.7829   3.4110  -1.3357
 BLG  O7    O  O      0  -0.428  -3.3770   3.1896  -2.4670
 BLG  C8    C  CH3    0  -0.760  -4.2814   4.7728  -0.9185
 BLG  O3    O  OH1    0  -0.627  -5.5283   0.2710  -0.8541
 BLG  O4    O  OC2    0  -0.612  -4.7064  -2.1498   0.7043
 BLG  S4    S  S      0   1.530  -5.6984  -3.1824  -0.0996
 BLG  O41   O  OS     0  -0.735  -6.5838  -2.3080  -0.8924
 BLG  O42   O  OS     0  -0.556  -6.3571  -3.8548   1.0117
 BLG  O43   O  OS    -1  -0.841  -4.8313  -4.0232  -0.9217
 BLG  C6    C  CH2    0  -0.168  -1.8053  -2.7144   0.4915
 BLG  O6    O  OH1    0  -0.654  -0.5778  -2.6831   1.1799
 BLG  CA    C  CH1    0  -0.106   0.7383   3.1934   0.3009
 BLG  CB    C  CH1    0  -0.023   0.0553   1.8588   0.5897
 BLG  CG    C  CH2    0  -0.427   1.1465   0.8338   0.2930
 BLG  CD    C  CH1    0  -0.281   2.3811   1.4862   0.9043
 BLG  N     N  NT2    1  -0.685   2.1565   2.9581   0.7350
 BLG  C9    C  CH2    0  -0.169   0.1304   4.3845   1.0015
 BLG  O9    O  OH1    0  -0.659   0.8989   5.5142   0.6805
 BLG  C10   C  C      0   0.597   3.6859   1.1204   0.2095
 BLG  O10   O  O      0  -0.467   4.2544   1.9393  -0.4983
 BLG  N3    N  NH1    0  -0.620   4.0936  -0.1275   0.4180
 BLG  C11   C  CH2    0  -0.234   5.3334  -0.6589  -0.1131
 BLG  C12   C  CH2    0  -0.679   6.5079  -0.3597   0.8092
 BLG  S     S  S      0   1.325   8.0559  -1.0307   0.1737
 BLG  OS1   O  OS     0  -0.869   8.2637  -0.3680  -1.1279
 BLG  OS2   O  OS     0  -0.691   7.8383  -2.4860   0.0494
 BLG  OS3   O  OS    -1  -0.683   9.0719  -0.6750   1.1814
 BLG  H1    H  HCH1   0   0.202  -2.2398   1.0826   1.3386
 BLG  H2    H  HCH1   0   0.267  -3.1480   0.9552  -1.5792
 BLG  H3    H  HCH1   0   0.190  -4.6395   0.3628   1.0133
 BLG  H4    H  HCH1   0   0.257  -3.7282  -1.6441  -1.0781
 BLG  H5    H  HCH1   0   0.183  -2.6051  -1.1469   1.7180
 BLG  HN2   H  HNH1   0   0.374  -4.1596   2.7514   0.5429
 BLG  H81   H  HCH3   0   0.260  -3.4747   5.4988  -1.0211
 BLG  H82   H  HCH3   0   0.247  -5.0893   5.0875  -1.5779
 BLG  H83   H  HCH3   0   0.279  -4.6392   4.8055   0.1090
 BLG  HO3   H  HOH1   0   0.447  -6.0509  -0.5501  -0.8421
 BLG  H61   H  HCH2   0   0.246  -2.4773  -3.4793   0.8927
 BLG  H62   H  HCH2   0   0.193  -1.6713  -2.9281  -0.5777
 BLG  HO6   H  HOH1   0   0.443  -0.2104  -3.5714   1.1740
 BLG  HA    H  HCH1   0   0.305   0.7652   3.3533  -0.7786
 BLG  HB    H  HCH1   0   0.257  -0.2163   1.8063   1.6538
 BLG  HG1   H  HCH2   0   0.308   0.9457  -0.1433   0.7279
 BLG  HG2   H  HCH2   0   0.287   1.2572   0.7148  -0.7876
 BLG  HD    H  HCH1   0   0.364   2.4447   1.2884   1.9742
 BLG  HN1   H  HNT2   0   0.478   2.3818   3.4547   1.5990
 BLG  HN2A  H  HNT2   0   0.474   2.8311   3.3013   0.0384
 BLG  H91   H  HCH2   0   0.237  -0.9095   4.4701   0.6627
 BLG  H92   H  HCH2   0   0.249   0.1035   4.1973   2.0826
 BLG  HO9   H  HOH1   0   0.459   0.6278   6.2418   1.2481
 BLG  HN3   H  HNH1   0   0.441   3.5861  -0.7065   1.0693
 BLG  H111  H  HCH2   0   0.215   5.2084  -1.7344  -0.2228
 BLG  H112  H  HCH2   0   0.281   5.5082  -0.2427  -1.1035
 BLG  H121  H  HCH2   0   0.329   6.6460   0.7171   0.9227
 BLG  H122  H  HCH2   0   0.237   6.3387  -0.7891   1.7983

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
 BLG  C1   C2    single  1.524  0.020  1.524
 BLG  C1   O5    single  1.398  0.020  1.398
 BLG  C1   O1    single  1.380  0.020  1.380
 BLG  C1   H1    single  0.970  0.020  1.090
 BLG  C2   C3    single  1.531  0.020  1.531
 BLG  C2   N2    single  1.437  0.020  1.437
 BLG  C2   H2    single  0.970  0.020  1.090
 BLG  C3   C4    single  1.533  0.020  1.533
 BLG  C3   O3    single  1.399  0.020  1.399
 BLG  C3   H3    single  0.970  0.020  1.090
 BLG  C4   C5    single  1.531  0.020  1.531
 BLG  C4   O4    single  1.427  0.020  1.427
 BLG  C4   H4    single  0.970  0.020  1.090
 BLG  C5   O5    single  1.410  0.020  1.410
 BLG  C5   C6    single  1.513  0.020  1.513
 BLG  C5   H5    single  0.970  0.020  1.090
 BLG  O1   CB    single  1.399  0.020  1.399
 BLG  N2   C7    single  1.347  0.020  1.347
 BLG  N2   HN2   single  0.860  0.020  1.020
 BLG  C7   O7    double  1.222  0.020  1.222
 BLG  C7   C8    single  1.509  0.020  1.509
 BLG  C8   H81   single  0.970  0.020  1.090
 BLG  C8   H82   single  0.970  0.020  1.090
 BLG  C8   H83   single  0.970  0.020  1.090
 BLG  O3   HO3   single  0.850  0.020  0.980
 BLG  O4   S4    single  1.642  0.020  1.642
 BLG  S4   O41   deloc   1.475  0.020  1.475
 BLG  S4   O42   deloc   1.456  0.020  1.456
 BLG  S4   O43   deloc   1.461  0.020  1.461
 BLG  C6   O6    single  1.408  0.020  1.408
 BLG  C6   H61   single  0.970  0.020  1.090
 BLG  C6   H62   single  0.970  0.020  1.090
 BLG  O6   HO6   single  0.850  0.020  0.980
 BLG  CA   CB    single  1.527  0.020  1.527
 BLG  CA   N     single  1.502  0.020  1.502
 BLG  CA   C9    single  1.510  0.020  1.510
 BLG  CA   HA    single  0.970  0.020  1.090
 BLG  CB   CG    single  1.526  0.020  1.526
 BLG  CB   HB    single  0.970  0.020  1.090
 BLG  CG   CD    single  1.524  0.020  1.524
 BLG  CG   HG1   single  0.970  0.020  1.090
 BLG  CG   HG2   single  0.970  0.020  1.090
 BLG  CD   N     single  1.499  0.020  1.499
 BLG  CD   C10   single  1.523  0.020  1.523
 BLG  CD   HD    single  0.970  0.020  1.090
 BLG  N    HN1   single  0.890  0.020  1.040
 BLG  N    HN2A  single  0.890  0.020  1.040
 BLG  C9   O9    single  1.403  0.020  1.403
 BLG  C9   H91   single  0.970  0.020  1.090
 BLG  C9   H92   single  0.970  0.020  1.090
 BLG  O9   HO9   single  0.850  0.020  0.980
 BLG  C10  O10   double  1.223  0.020  1.223
 BLG  C10  N3    single  1.329  0.020  1.329
 BLG  N3   C11   single  1.450  0.020  1.450
 BLG  N3   HN3   single  0.860  0.020  1.020
 BLG  C11  C12   single  1.523  0.020  1.523
 BLG  C11  H111  single  0.970  0.020  1.090
 BLG  C11  H112  single  0.970  0.020  1.090
 BLG  C12  S     single  1.803  0.020  1.803
 BLG  C12  H121  single  0.970  0.020  1.090
 BLG  C12  H122  single  0.970  0.020  1.090
 BLG  S    OS1   deloc   1.475  0.020  1.475
 BLG  S    OS2   deloc   1.477  0.020  1.477
 BLG  S    OS3   deloc   1.475  0.020  1.475

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
 BLG  H1    C1   O1    110.36  3.000
 BLG  H1    C1   O5    109.63  3.000
 BLG  O1    C1   O5    108.29  3.000
 BLG  H1    C1   C2    109.86  3.000
 BLG  O1    C1   C2    109.36  3.000
 BLG  O5    C1   C2    109.31  3.000
 BLG  H2    C2   N2    108.23  3.000
 BLG  H2    C2   C3    109.20  3.000
 BLG  N2    C2   C3    110.68  3.000
 BLG  H2    C2   C1    108.42  3.000
 BLG  N2    C2   C1    111.28  3.000
 BLG  C3    C2   C1    108.97  3.000
 BLG  H3    C3   O3    111.04  3.000
 BLG  H3    C3   C4    106.43  3.000
 BLG  O3    C3   C4    113.26  3.000
 BLG  H3    C3   C2    107.77  3.000
 BLG  O3    C3   C2    107.42  3.000
 BLG  C4    C3   C2    110.83  3.000
 BLG  H4    C4   O4    111.48  3.000
 BLG  H4    C4   C5    108.94  3.000
 BLG  O4    C4   C5    106.70  3.000
 BLG  H4    C4   C3    109.16  3.000
 BLG  O4    C4   C3    109.02  3.000
 BLG  C5    C4   C3    111.54  3.000
 BLG  H5    C5   C6    109.17  3.000
 BLG  H5    C5   O5    110.12  3.000
 BLG  C6    C5   O5    107.63  3.000
 BLG  H5    C5   C4    108.49  3.000
 BLG  C6    C5   C4    112.41  3.000
 BLG  O5    C5   C4    109.01  3.000
 BLG  C5    O5   C1    112.92  3.000
 BLG  CB    O1   C1    114.87  3.000
 BLG  HN2   N2   C7    118.05  3.000
 BLG  HN2   N2   C2    117.46  3.000
 BLG  C7    N2   C2    124.32  3.000
 BLG  C8    C7   O7    121.95  3.000
 BLG  C8    C7   N2    114.65  3.000
 BLG  O7    C7   N2    123.40  3.000
 BLG  H83   C8   H82   108.60  3.000
 BLG  H83   C8   H81   108.18  3.000
 BLG  H82   C8   H81   107.43  3.000
 BLG  H83   C8   C7    113.37  3.000
 BLG  H82   C8   C7    109.78  3.000
 BLG  H81   C8   C7    109.30  3.000
 BLG  HO3   O3   C3    109.65  3.000
 BLG  S4    O4   C4    119.19  3.000
 BLG  O43   S4   O42   115.60  3.000
 BLG  O43   S4   O41   113.25  3.000
 BLG  O42   S4   O41   114.34  3.000
 BLG  O43   S4   O4    106.19  3.000
 BLG  O42   S4   O4    100.95  3.000
 BLG  O41   S4   O4    104.65  3.000
 BLG  H62   C6   H61   107.20  3.000
 BLG  H62   C6   O6    111.96  3.000
 BLG  H61   C6   O6    111.82  3.000
 BLG  H62   C6   C5    109.05  3.000
 BLG  H61   C6   C5    108.55  3.000
 BLG  O6    C6   C5    108.18  3.000
 BLG  HO6   O6   C6    108.05  3.000
 BLG  HA    CA   C9    110.69  3.000
 BLG  HA    CA   N     106.59  3.000
 BLG  C9    CA   N     111.69  3.000
 BLG  HA    CA   CB    109.04  3.000
 BLG  C9    CA   CB    114.94  3.000
 BLG  N     CA   CB    103.35  3.000
 BLG  HB    CB   CG    109.43  3.000
 BLG  HB    CB   CA    109.59  3.000
 BLG  CG    CB   CA    103.32  3.000
 BLG  HB    CB   O1    110.32  3.000
 BLG  CG    CB   O1    115.61  3.000
 BLG  CA    CB   O1    108.24  3.000
 BLG  HG2   CG   HG1   108.43  3.000
 BLG  HG2   CG   CD    111.17  3.000
 BLG  HG1   CG   CD    111.93  3.000
 BLG  HG2   CG   CB    109.74  3.000
 BLG  HG1   CG   CB    113.17  3.000
 BLG  CD    CG   CB    102.34  3.000
 BLG  HD    CD   C10   110.75  3.000
 BLG  HD    CD   N     107.33  3.000
 BLG  C10   CD   N     108.23  3.000
 BLG  HD    CD   CG    111.30  3.000
 BLG  C10   CD   CG    114.09  3.000
 BLG  N     CD   CG    104.70  3.000
 BLG  HN2A  N    HN1   105.42  3.000
 BLG  HN2A  N    CD    107.81  3.000
 BLG  HN1   N    CD    110.42  3.000
 BLG  HN2A  N    CA    111.79  3.000
 BLG  HN1   N    CA    112.12  3.000
 BLG  CD    N    CA    109.15  3.000
 BLG  H92   C9   H91   107.11  3.000
 BLG  H92   C9   O9    112.09  3.000
 BLG  H91   C9   O9    112.68  3.000
 BLG  H92   C9   CA    109.42  3.000
 BLG  H91   C9   CA    107.45  3.000
 BLG  O9    C9   CA    107.97  3.000
 BLG  HO9   O9   C9    108.64  3.000
 BLG  N3    C10  O10   125.25  3.000
 BLG  N3    C10  CD    114.63  3.000
 BLG  O10   C10  CD    120.10  3.000
 BLG  HN3   N3   C11   117.16  3.000
 BLG  HN3   N3   C10   119.08  3.000
 BLG  C11   N3   C10   123.30  3.000
 BLG  H112  C11  H111  107.73  3.000
 BLG  H112  C11  C12   110.62  3.000
 BLG  H111  C11  C12   110.11  3.000
 BLG  H112  C11  N3    109.30  3.000
 BLG  H111  C11  N3    107.51  3.000
 BLG  C12   C11  N3    111.45  3.000
 BLG  H122  C12  H121  108.27  3.000
 BLG  H122  C12  S     107.83  3.000
 BLG  H121  C12  S     107.17  3.000
 BLG  H122  C12  C11   110.60  3.000
 BLG  H121  C12  C11   110.75  3.000
 BLG  S     C12  C11   112.06  3.000
 BLG  OS3   S    OS2   113.38  3.000
 BLG  OS3   S    OS1   113.42  3.000
 BLG  OS2   S    OS1   112.90  3.000
 BLG  OS3   S    C12   105.13  3.000
 BLG  OS2   S    C12   105.66  3.000
 BLG  OS1   S    C12   105.35  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
 BLG  CONST_01  O7   C7   N2   C2     0.00   0.0  0
 BLG  CONST_02  C8   C7   N2   C2   180.00   0.0  0
 BLG  CONST_03  C11  N3   C10  CD   180.00   0.0  0
 BLG  CONST_04  HN3  N3   C10  CD     0.00   0.0  0
 BLG  CONST_05  C11  N3   C10  O10    0.00   0.0  0
 BLG  CONST_06  HN2  N2   C7   O7   180.00   0.0  0
 BLG  Var_01    O41  S4   O4   C4   -62.50  30.0  3
 BLG  Var_02    C12  C11  N3   C10   86.04  30.0  3
 BLG  Var_03    S    C12  C11  N3   179.32  30.0  3
 BLG  Var_04    OS1  S    C12  C11   60.74  30.0  3
 BLG  Var_05    H81  C8   C7   N2   119.24  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
 BLG  chir_01  C1  C2  O5  O1   negativ
 BLG  chir_02  C2  N2  C3  C1   positiv
 BLG  chir_03  C3  O3  C2  C4   positiv
 BLG  chir_04  C4  O4  C3  C5   negativ
 BLG  chir_05  C5  O5  C4  C6   negativ
 BLG  chir_06  CA  N   CB  C9   negativ
 BLG  chir_07  CB  O1  CG  CA   negativ
 BLG  chir_08  CD  N   CG  C10  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
 BLG  plan-1  C2   0.020
 BLG  plan-1  N2   0.020
 BLG  plan-1  C7   0.020
 BLG  plan-1  O7   0.020
 BLG  plan-1  C8   0.020
 BLG  plan-1  HN2  0.020
 BLG  plan-2  CD   0.020
 BLG  plan-2  C10  0.020
 BLG  plan-2  O10  0.020
 BLG  plan-2  N3   0.020
 BLG  plan-2  C11  0.020
 BLG  plan-2  HN3  0.020

