# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 23:38:51 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](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
 YJM  YJM  2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose  D-saccharide  33  20  .  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_YJM
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
 YJM  C01   C  CH1   0   0.275   0.7623   0.9492  -0.6524
 YJM  C02   C  CH1   0  -0.152   1.7436  -0.0512  -0.0369
 YJM  C03   C  CH1   0   0.037   1.2750  -1.4820  -0.2736
 YJM  C04   C  CH1   0  -0.011  -0.1575  -1.6302   0.2380
 YJM  C05   C  CH1   0  -0.022  -1.0543  -0.5608  -0.3956
 YJM  C06   C  CH2   0  -0.203  -2.4389  -0.5997   0.2056
 YJM  N07   N  NC1   0  -0.763   3.0754   0.1790  -0.5665
 YJM  O08   O  OH1   0  -0.654   2.1515  -2.3465   0.3934
 YJM  O09   O  OH1   0  -0.671  -0.6055  -2.9235  -0.0947
 YJM  O10   O  O2    0  -0.498  -0.5278   0.7279  -0.1489
 YJM  O11   O  OC2   0  -0.572  -3.2337   0.3629  -0.5184
 YJM  S12   S  S     0   1.580   4.3070   0.6939   0.3324
 YJM  O13   O  OS    0  -0.650   5.3980   1.0236  -0.5563
 YJM  O14   O  OS    0  -0.653   3.8283   1.6791   1.2786
 YJM  O15   O  OS    0  -0.709   4.7010  -0.6242   1.1559
 YJM  S16   S  S     0   1.666  -4.7143   0.6642  -0.0529
 YJM  O17   O  OS    0  -0.634  -5.4191  -0.5641   0.2140
 YJM  O18   O  OS    0  -0.709  -4.4911   1.4512   1.3065
 YJM  O19   O  OS    0  -0.620  -5.2003   1.6211  -1.0041
 YJM  O20   O  OH1   0  -0.662   0.8296   0.8241  -2.0318
 YJM  H01   H  HCH1  0   0.250   1.0247   1.9599  -0.3242
 YJM  H02   H  HCH1  0   0.296   1.7572   0.1307   1.0411
 YJM  H03   H  HCH1  0   0.226   1.2710  -1.6860  -1.3561
 YJM  H04   H  HCH1  0   0.240  -0.1456  -1.4820   1.3271
 YJM  H05   H  HCH1  0   0.249  -1.1307  -0.7588  -1.4733
 YJM  H06   H  HCH2  0   0.271  -2.8704  -1.5938   0.0914
 YJM  H06A  H  HCH2  0   0.257  -2.4009  -0.3386   1.2666
 YJM  HN07  H  HNC1  0   0.432   3.3323  -0.2684  -1.4375
 YJM  HO08  H  HOH1  0   0.453   1.8833  -3.2497   0.1941
 YJM  HO09  H  HOH1  0   0.467  -1.0844  -3.2952   0.6508
 YJM  HO15  H  H     0   0.499   5.3529  -0.4236   1.8488
 YJM  HO18  H  H     0   0.515  -4.6722   0.9075   2.0911
 YJM  HO20  H  HOH1  0   0.469   0.4238   1.5948  -2.4436

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
 YJM  O10  C01   single  1.402  0.020  1.402
 YJM  C02  C01   single  1.531  0.020  1.531
 YJM  C01  O20   single  1.387  0.020  1.387
 YJM  C01  H01   single  0.970  0.020  1.090
 YJM  C03  C02   single  1.524  0.020  1.524
 YJM  C02  N07   single  1.452  0.020  1.452
 YJM  C02  H02   single  0.970  0.020  1.090
 YJM  C04  C03   single  1.528  0.020  1.528
 YJM  C03  O08   single  1.400  0.020  1.400
 YJM  C03  H03   single  0.970  0.020  1.090
 YJM  O09  C04   single  1.409  0.020  1.409
 YJM  C04  C05   single  1.533  0.020  1.533
 YJM  C04  H04   single  0.970  0.020  1.090
 YJM  C06  C05   single  1.510  0.020  1.510
 YJM  C05  O10   single  1.414  0.020  1.414
 YJM  C05  H05   single  0.970  0.020  1.090
 YJM  C06  O11   single  1.443  0.020  1.443
 YJM  C06  H06   single  0.970  0.020  1.090
 YJM  C06  H06A  single  0.970  0.020  1.090
 YJM  N07  S12   single  1.609  0.020  1.609
 YJM  N07  HN07  single  0.890  0.020  1.040
 YJM  O08  HO08  single  0.850  0.020  0.980
 YJM  O09  HO09  single  0.850  0.020  0.980
 YJM  S16  O11   single  1.581  0.020  1.581
 YJM  O13  S12   double  1.445  0.020  1.445
 YJM  O14  S12   double  1.447  0.020  1.447
 YJM  S12  O15   single  1.603  0.020  1.603
 YJM  O15  HO15  single  0.850  0.020  0.980
 YJM  O19  S16   double  1.434  0.020  1.434
 YJM  S16  O17   double  1.441  0.020  1.441
 YJM  S16  O18   single  1.587  0.020  1.587
 YJM  O18  HO18  single  0.850  0.020  0.980
 YJM  O20  HO20  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
 YJM  H01   C01  O20  111.71  3.000
 YJM  H01   C01  O10  104.98  3.000
 YJM  O20   C01  O10  112.80  3.000
 YJM  H01   C01  C02  109.22  3.000
 YJM  O20   C01  C02  108.06  3.000
 YJM  O10   C01  C02  110.02  3.000
 YJM  H02   C02  N07  108.78  3.000
 YJM  H02   C02  C03  108.25  3.000
 YJM  N07   C02  C03  111.98  3.000
 YJM  H02   C02  C01  107.20  3.000
 YJM  N07   C02  C01  109.75  3.000
 YJM  C03   C02  C01  110.73  3.000
 YJM  H03   C03  O08  110.86  3.000
 YJM  H03   C03  C04  107.91  3.000
 YJM  O08   C03  C04  111.55  3.000
 YJM  H03   C03  C02  109.12  3.000
 YJM  O08   C03  C02  108.25  3.000
 YJM  C04   C03  C02  109.10  3.000
 YJM  H04   C04  O09  111.17  3.000
 YJM  H04   C04  C05  108.77  3.000
 YJM  O09   C04  C05  110.91  3.000
 YJM  H04   C04  C03  107.97  3.000
 YJM  C05   C04  C03  110.02  3.000
 YJM  O09   C04  C03  107.94  3.000
 YJM  H05   C05  O10  111.19  3.000
 YJM  H05   C05  C06  108.80  3.000
 YJM  O10   C05  C06  107.19  3.000
 YJM  H05   C05  C04  108.69  3.000
 YJM  O10   C05  C04  110.24  3.000
 YJM  C06   C05  C04  110.73  3.000
 YJM  H06A  C06  H06  109.47  3.000
 YJM  H06A  C06  O11  110.29  3.000
 YJM  H06   C06  O11  109.75  3.000
 YJM  H06A  C06  C05  110.38  3.000
 YJM  H06   C06  C05  110.18  3.000
 YJM  O11   C06  C05  106.74  3.000
 YJM  HN07  N07  S12  115.33  3.000
 YJM  HN07  N07  C02  118.47  3.000
 YJM  S12   N07  C02  123.30  3.000
 YJM  HO08  O08  C03  107.82  3.000
 YJM  HO09  O09  C04  109.30  3.000
 YJM  C05   O10  C01  115.07  3.000
 YJM  S16   O11  C06  119.68  3.000
 YJM  O15   S12  O14  107.76  3.000
 YJM  O15   S12  O13  108.53  3.000
 YJM  O14   S12  O13  119.76  3.000
 YJM  O15   S12  N07  102.23  3.000
 YJM  O14   S12  N07  109.26  3.000
 YJM  O13   S12  N07  107.90  3.000
 YJM  HO15  O15  S12  111.17  3.000
 YJM  O19   S16  O18  106.56  3.000
 YJM  O18   S16  O17  109.45  3.000
 YJM  O19   S16  O17  121.72  3.000
 YJM  O18   S16  O11  102.42  3.000
 YJM  O17   S16  O11  110.50  3.000
 YJM  O19   S16  O11  104.43  3.000
 YJM  HO18  O18  S16  112.83  3.000
 YJM  HO20  O20  C01  109.43  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
 YJM  Var_01  O13  S12  N07  C02  -170.48  30.0  3
 YJM  Var_02  O19  S16  O11  C06  -178.50  30.0  2
 YJM  Var_03  H06  C06  O11  S16    65.94  30.0  1

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
 YJM  chir_01  C01  O10  C02  O20  negativ
 YJM  chir_02  C02  N07  C03  C01  positiv
 YJM  chir_03  C03  O08  C02  C04  positiv
 YJM  chir_04  C04  O09  C05  C03  positiv
 YJM  chir_05  C05  O10  C04  C06  negativ

