# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:16:25 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: 2,3,4-tri-O-propanoyl-6-O-sulfamoyl-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)O[C@H]1[C@@H](O)O[C@H](CO[S](N)(=O)=O)[C@@H](OC(=O)CC)[C@@H]1OC(=O)CC
#
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
 SG5  SG5  2,3,4-tri-O-propanoyl-6-O-sulfamoyl-alpha-D-glucopyranose  D-saccharide  53  28  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SG5
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
 SG5  C1    C  CH1   0   0.249  16.8539  -0.0100  11.7963
 SG5  O5    O  O2    0  -0.488  16.7722   0.2062  13.1682
 SG5  C2    C  CH1   0  -0.035  16.3665   1.2385  11.0407
 SG5  C3    C  CH1   0  -0.012  17.1028   2.4785  11.5246
 SG5  C4    C  CH1   0   0.006  16.9458   2.5814  13.0334
 SG5  C5    C  CH1   0  -0.029  17.5209   1.3068  13.6540
 SG5  O1    O  OH1   0  -0.654  18.1710  -0.3358  11.4829
 SG5  O2    O  O2    0  -0.484  16.6455   1.0434   9.6623
 SG5  C2B   C  C     0   0.603  15.7563   1.4193   8.7299
 SG5  O2C   O  O     0  -0.427  14.6644   1.8490   8.9838
 SG5  C2D   C  CH2   0  -0.578  16.3239   1.2184   7.3517
 SG5  C2E   C  CH3   0  -0.662  15.4335   1.7622   6.2497
 SG5  O3    O  O2    0  -0.476  16.5222   3.6241  10.9202
 SG5  C3B   C  C     0   0.602  17.2912   4.4810  10.2325
 SG5  O3C   O  O     0  -0.430  18.4694   4.3269  10.0536
 SG5  C3D   C  CH2   0  -0.582  16.4729   5.6333   9.7212
 SG5  C3E   C  CH3   0  -0.664  17.3051   6.7171   9.0617
 SG5  O4    O  O2    0  -0.476  17.6814   3.7024  13.4947
 SG5  C4B   C  C     0   0.577  17.0308   4.7538  14.0208
 SG5  O4C   O  O     0  -0.424  15.8376   4.8007  14.1530
 SG5  C4D   C  CH2   0  -0.552  17.9905   5.8508  14.3833
 SG5  C4E   C  CH3   0  -0.678  18.5600   6.5392  13.1418
 SG5  C6    C  CH2   0  -0.214  17.4969   1.2844  15.1616
 SG5  O6    O  OC2   0  -0.582  16.1700   1.5994  15.6061
 SG5  S5C   S  S     0   1.583  15.8801   1.6484  17.1746
 SG5  O5D   O  OS    0  -0.626  14.5308   2.1531  17.2430
 SG5  O5E   O  OS    0  -0.649  16.9497   2.3365  17.8607
 SG5  N5F   N  NC2   0  -0.899  16.0081   0.0611  17.5624
 SG5  H1    H  HCH1  0   0.254  16.1714  -0.8412  11.5823
 SG5  H2    H  HCH1  0   0.280  15.2922   1.3501  11.2117
 SG5  H3    H  HCH1  0   0.278  18.1629   2.4061  11.2661
 SG5  H4    H  HCH1  0   0.283  15.8886   2.6785  13.2928
 SG5  H5    H  HCH1  0   0.273  18.5796   1.2145  13.3788
 SG5  HO1   H  HOH1  0   0.465  18.2253  -0.6176  10.5631
 SG5  H2D   H  HCH2  0   0.274  17.3121   1.6842   7.3181
 SG5  H2DA  H  HCH2  0   0.280  16.5022   0.1476   7.2144
 SG5  H2E   H  HCH3  0   0.240  15.8948   1.5833   5.2796
 SG5  H2EA  H  HCH3  0   0.232  14.4561   1.2823   6.2460
 SG5  H2EB  H  HCH3  0   0.232  15.2825   2.8365   6.3508
 SG5  H3D   H  HCH2  0   0.280  15.7338   5.2296   9.0223
 SG5  H3DA  H  HCH2  0   0.274  15.8935   6.0395  10.5543
 SG5  H3E   H  HCH3  0   0.240  16.6573   7.5184   8.7093
 SG5  H3EA  H  HCH3  0   0.233  18.0204   7.1525   9.7592
 SG5  H3EB  H  HCH3  0   0.232  17.8588   6.3375   8.2040
 SG5  H4D   H  HCH2  0   0.264  17.4586   6.5722  15.0020
 SG5  H4DA  H  HCH2  0   0.267  18.8053   5.4370  14.9810
 SG5  H4E   H  HCH3  0   0.251  19.2166   7.3537  13.4431
 SG5  H4EA  H  HCH3  0   0.237  19.1393   5.8520  12.5279
 SG5  H4EB  H  HCH3  0   0.239  17.7672   6.9643  12.5252
 SG5  H61   H  HCH2  0   0.277  17.7934   0.2951  15.5182
 SG5  H62   H  HCH2  0   0.270  18.2082   2.0180  15.5428
 SG5  HN5F  H  HNC2  0   0.427  16.2538  -0.0873  18.5350
 SG5  HN5A  H  HNC2  0   0.423  15.2000  -0.4914  17.2950

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
 SG5  C1   O5    single  1.391  0.020  1.391
 SG5  C1   C2    single  1.539  0.020  1.539
 SG5  C1   O1    single  1.393  0.020  1.393
 SG5  O5   C5    single  1.417  0.020  1.417
 SG5  C2   C3    single  1.521  0.020  1.521
 SG5  C2   O2    single  1.420  0.020  1.420
 SG5  C3   C4    single  1.520  0.020  1.520
 SG5  C3   O3    single  1.419  0.020  1.419
 SG5  C4   C5    single  1.530  0.020  1.530
 SG5  C4   O4    single  1.418  0.020  1.418
 SG5  C5   C6    single  1.508  0.020  1.508
 SG5  O2   C2B   single  1.342  0.020  1.342
 SG5  C2B  O2C   double  1.201  0.020  1.201
 SG5  C2B  C2D   single  1.504  0.020  1.504
 SG5  C2D  C2E   single  1.518  0.020  1.518
 SG5  O3   C3B   single  1.341  0.020  1.341
 SG5  C3B  O3C   double  1.202  0.020  1.202
 SG5  C3B  C3D   single  1.503  0.020  1.503
 SG5  C3D  C3E   single  1.517  0.020  1.517
 SG5  O4   C4B   single  1.344  0.020  1.344
 SG5  C4B  O4C   double  1.201  0.020  1.201
 SG5  C4B  C4D   single  1.502  0.020  1.502
 SG5  C4D  C4E   single  1.530  0.020  1.530
 SG5  C6   O6    single  1.434  0.020  1.434
 SG5  O6   S5C   single  1.596  0.020  1.596
 SG5  S5C  O5D   deloc   1.442  0.020  1.442
 SG5  S5C  O5E   deloc   1.445  0.020  1.445
 SG5  S5C  N5F   single  1.639  0.020  1.639
 SG5  C1   H1    single  0.970  0.020  1.090
 SG5  C2   H2    single  0.970  0.020  1.090
 SG5  C3   H3    single  0.970  0.020  1.090
 SG5  C4   H4    single  0.970  0.020  1.090
 SG5  C5   H5    single  0.970  0.020  1.090
 SG5  O1   HO1   single  0.850  0.020  0.980
 SG5  C2D  H2D   single  0.970  0.020  1.090
 SG5  C2D  H2DA  single  0.970  0.020  1.090
 SG5  C2E  H2E   single  0.970  0.020  1.090
 SG5  C2E  H2EA  single  0.970  0.020  1.090
 SG5  C2E  H2EB  single  0.970  0.020  1.090
 SG5  C3D  H3D   single  0.970  0.020  1.090
 SG5  C3D  H3DA  single  0.970  0.020  1.090
 SG5  C3E  H3E   single  0.970  0.020  1.090
 SG5  C3E  H3EA  single  0.970  0.020  1.090
 SG5  C3E  H3EB  single  0.970  0.020  1.090
 SG5  C4D  H4D   single  0.970  0.020  1.090
 SG5  C4D  H4DA  single  0.970  0.020  1.090
 SG5  C4E  H4E   single  0.970  0.020  1.090
 SG5  C4E  H4EA  single  0.970  0.020  1.090
 SG5  C4E  H4EB  single  0.970  0.020  1.090
 SG5  C6   H61   single  0.970  0.020  1.090
 SG5  C6   H62   single  0.970  0.020  1.090
 SG5  N5F  HN5F  single  0.890  0.020  1.040
 SG5  N5F  HN5A  single  0.890  0.020  1.040

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
 SG5  H1    C1   O1    111.55  3.000
 SG5  H1    C1   C2    108.79  3.000
 SG5  O1    C1   C2    112.27  3.000
 SG5  H1    C1   O5    105.88  3.000
 SG5  O1    C1   O5    108.29  3.000
 SG5  C2    C1   O5    109.85  3.000
 SG5  C5    O5   C1    115.33  3.000
 SG5  H2    C2   O2    111.03  3.000
 SG5  H2    C2   C3    110.04  3.000
 SG5  O2    C2   C3    109.01  3.000
 SG5  H2    C2   C1    108.49  3.000
 SG5  O2    C2   C1    107.64  3.000
 SG5  C3    C2   C1    110.61  3.000
 SG5  H3    C3   O3    110.44  3.000
 SG5  H3    C3   C4    109.83  3.000
 SG5  O3    C3   C4    109.01  3.000
 SG5  H3    C3   C2    109.88  3.000
 SG5  O3    C3   C2    108.93  3.000
 SG5  C4    C3   C2    108.72  3.000
 SG5  H4    C4   O4    110.76  3.000
 SG5  H4    C4   C5    109.96  3.000
 SG5  O4    C4   C5    109.37  3.000
 SG5  H4    C4   C3    109.97  3.000
 SG5  O4    C4   C3    108.83  3.000
 SG5  C5    C4   C3    107.90  3.000
 SG5  H5    C5   C6    105.35  3.000
 SG5  H5    C5   C4    109.32  3.000
 SG5  C6    C5   C4    114.33  3.000
 SG5  H5    C5   O5    111.00  3.000
 SG5  C6    C5   O5    108.84  3.000
 SG5  C4    C5   O5    108.02  3.000
 SG5  HO1   O1   C1    109.67  3.000
 SG5  C2B   O2   C2    120.38  3.000
 SG5  C2D   C2B  O2C   125.79  3.000
 SG5  C2D   C2B  O2    110.44  3.000
 SG5  O2C   C2B  O2    123.77  3.000
 SG5  H2DA  C2D  H2D   105.42  3.000
 SG5  H2DA  C2D  C2E   110.80  3.000
 SG5  H2D   C2D  C2E   110.83  3.000
 SG5  H2DA  C2D  C2B   107.88  3.000
 SG5  H2D   C2D  C2B   108.21  3.000
 SG5  C2E   C2D  C2B   113.34  3.000
 SG5  H2EB  C2E  H2EA  108.09  3.000
 SG5  H2EB  C2E  H2E   107.65  3.000
 SG5  H2EA  C2E  H2E   107.75  3.000
 SG5  H2EB  C2E  C2D   111.55  3.000
 SG5  H2EA  C2E  C2D   111.79  3.000
 SG5  H2E   C2E  C2D   109.85  3.000
 SG5  C3B   O3   C3    119.97  3.000
 SG5  C3D   C3B  O3C   125.56  3.000
 SG5  C3D   C3B  O3    110.62  3.000
 SG5  O3C   C3B  O3    123.82  3.000
 SG5  H3DA  C3D  H3D   105.42  3.000
 SG5  H3DA  C3D  C3E   110.89  3.000
 SG5  H3D   C3D  C3E   110.87  3.000
 SG5  H3DA  C3D  C3B   108.32  3.000
 SG5  H3D   C3D  C3B   107.58  3.000
 SG5  C3E   C3D  C3B   113.38  3.000
 SG5  H3EB  C3E  H3EA  108.03  3.000
 SG5  H3EB  C3E  H3E   107.70  3.000
 SG5  H3EA  C3E  H3E   107.67  3.000
 SG5  H3EB  C3E  C3D   111.85  3.000
 SG5  H3EA  C3E  C3D   111.54  3.000
 SG5  H3E   C3E  C3D   109.88  3.000
 SG5  C4B   O4   C4    119.66  3.000
 SG5  C4D   C4B  O4C   125.42  3.000
 SG5  C4D   C4B  O4    110.89  3.000
 SG5  O4C   C4B  O4    123.68  3.000
 SG5  H4DA  C4D  H4D   107.73  3.000
 SG5  H4DA  C4D  C4E   109.70  3.000
 SG5  H4D   C4D  C4E   110.17  3.000
 SG5  H4DA  C4D  C4B   109.39  3.000
 SG5  H4D   C4D  C4B   107.99  3.000
 SG5  C4E   C4D  C4B   111.76  3.000
 SG5  H4EB  C4E  H4EA  108.31  3.000
 SG5  H4EB  C4E  H4E   107.65  3.000
 SG5  H4EA  C4E  H4E   107.90  3.000
 SG5  H4EB  C4E  C4D   111.32  3.000
 SG5  H4EA  C4E  C4D   111.83  3.000
 SG5  H4E   C4E  C4D   109.67  3.000
 SG5  H62   C6   H61   108.54  3.000
 SG5  H62   C6   O6    110.32  3.000
 SG5  H61   C6   O6    110.41  3.000
 SG5  H62   C6   C5    109.21  3.000
 SG5  H61   C6   C5    109.60  3.000
 SG5  O6    C6   C5    108.74  3.000
 SG5  S5C   O6   C6    118.64  3.000
 SG5  N5F   S5C  O5E   106.91  3.000
 SG5  N5F   S5C  O5D   113.63  3.000
 SG5  O5E   S5C  O5D   120.22  3.000
 SG5  N5F   S5C  O6    100.87  3.000
 SG5  O5E   S5C  O6    110.29  3.000
 SG5  O5D   S5C  O6    103.14  3.000
 SG5  HN5A  N5F  HN5F  111.47  3.000
 SG5  HN5A  N5F  S5C   113.75  3.000
 SG5  HN5F  N5F  S5C   112.81  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
 SG5  Var_01  O2C   C2B  O2   C2     -5.01  30.0  3
 SG5  Var_02  O3C   C3B  O3   C3      2.15  30.0  3
 SG5  Var_03  O4C   C4B  O4   C4      1.43  30.0  3
 SG5  Var_04  C2E   C2D  C2B  O2   -173.73  30.0  3
 SG5  Var_05  C3E   C3D  C3B  O3    173.80  30.0  3
 SG5  Var_06  C4E   C4D  C4B  O4     71.30  30.0  3
 SG5  Var_07  O5D   S5C  O6   C6    172.88  30.0  3
 SG5  Var_08  H2E   C2E  C2D  C2B  -179.75  30.0  3
 SG5  Var_09  H3E   C3E  C3D  C3B   179.72  30.0  3
 SG5  Var_10  H4E   C4E  C4D  C4B   177.61  30.0  3
 SG5  Var_11  HN5F  N5F  S5C  O6    155.09  30.0  3
 SG5  Var_12  H61   C6   O6   S5C    60.03  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
 SG5  chir_01  C1  O5  C2  O1  negativ
 SG5  chir_02  C2  O2  C3  C1  positiv
 SG5  chir_03  C3  O3  C4  C2  negativ
 SG5  chir_04  C4  O4  C5  C3  positiv
 SG5  chir_05  C5  O5  C4  C6  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
 SG5  plan-1  O2   0.020
 SG5  plan-1  C2B  0.020
 SG5  plan-1  O2C  0.020
 SG5  plan-1  C2D  0.020
 SG5  plan-2  O3   0.020
 SG5  plan-2  C3B  0.020
 SG5  plan-2  O3C  0.020
 SG5  plan-2  C3D  0.020
 SG5  plan-3  O4   0.020
 SG5  plan-3  C4B  0.020
 SG5  plan-3  O4C  0.020
 SG5  plan-3  C4D  0.020

