# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 05:59:11 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 3,4-di-O-acetyl-6-O-sulfamoyl-alpha-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)O[C@@H]1[C@H](O)[C@@H](O)O[C@H](CO[S](N)(=O)=O)[C@H]1OC(C)=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
 SG7  SG7  3,4-di-O-acetyl-6-O-sulfamoyl-alpha-D-mannopyranose  D-saccharide  39  22  .  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_SG7
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
 SG7  C1    C  CH1   0   0.246  16.9534  2.0312  11.3472
 SG7  O5    O  O2    0  -0.488  16.7985  2.0703  12.7303
 SG7  C2    C  CH1   0  -0.058  16.4196  3.3114  10.6926
 SG7  C3    C  CH1   0  -0.010  17.0791  4.5231  11.3533
 SG7  C4    C  CH1   0   0.021  16.8558  4.4691  12.8543
 SG7  C5    C  CH1   0  -0.020  17.4349  3.1528  13.3804
 SG7  O1    O  OH1   0  -0.658  18.3090  1.8388  11.0721
 SG7  O2    O  OH1   0  -0.659  15.0276  3.3077  10.8734
 SG7  O3    O  O2    0  -0.471  16.4958  5.7363  10.8872
 SG7  C3B   C  C     0   0.566  17.0319  6.3520   9.8268
 SG7  C3C   C  CH3   0  -0.772  16.3207  7.6394   9.5424
 SG7  O3D   O  O     0  -0.435  17.9616  5.9104   9.2048
 SG7  O4    O  O2    0  -0.473  17.5619  5.5380  13.4692
 SG7  C4B   C  CH3   0  -0.775  17.8311  7.5568  14.6117
 SG7  C4C   C  C     0   0.563  16.8860  6.5474  14.0361
 SG7  O4D   O  O     0  -0.431  15.6869  6.6136  14.0754
 SG7  C6    C  CH2   0  -0.213  17.2824  2.9715  14.8710
 SG7  O6    O  OC2   0  -0.582  15.9030  3.1670  15.2171
 SG7  S5C   S  S     0   1.582  15.4493  2.9093  16.7241
 SG7  O5D   O  OS    0  -0.627  14.0933  3.3996  16.7455
 SG7  O5E   O  OS    0  -0.650  16.4284  3.4403  17.6453
 SG7  N5F   N  NC2   0  -0.899  15.5571  1.2761  16.8087
 SG7  H1    H  HCH1  0   0.245  16.3474  1.1820  11.0073
 SG7  H2    H  HCH1  0   0.256  16.6811  3.2929   9.6254
 SG7  H3    H  HCH1  0   0.267  18.1523  4.5147  11.1423
 SG7  H4    H  HCH1  0   0.276  15.7896  4.5306  13.0774
 SG7  H5    H  HCH1  0   0.265  18.5176  3.1412  13.1976
 SG7  HO1   H  HOH1  0   0.463  18.4371  1.7580  10.1207
 SG7  HO2   H  HOH1  0   0.459  14.6396  4.0079  10.3393
 SG7  H3C   H  HCH3  0   0.263  16.7495  8.1264   8.6714
 SG7  H3CA  H  HCH3  0   0.274  15.2604  7.4579   9.3646
 SG7  H3CB  H  HCH3  0   0.275  16.3942  8.3095  10.3996
 SG7  H4B   H  HCH3  0   0.263  17.2808  8.3935  15.0312
 SG7  H4BA  H  HCH3  0   0.275  18.4369  7.1005  15.3957
 SG7  H4BB  H  HCH3  0   0.273  18.5152  7.9234  13.8465
 SG7  H61   H  HCH2  0   0.275  17.6089  1.9667  15.1501
 SG7  H62   H  HCH2  0   0.269  17.9078  3.6966  15.3929
 SG7  HN5F  H  HNC2  0   0.427  15.7133  0.9438  17.7540
 SG7  HN5A  H  HNC2  0   0.422  14.7834  0.7895  16.3683

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
 SG7  C1   O5    single  1.392  0.020  1.392
 SG7  C1   C2    single  1.534  0.020  1.534
 SG7  C1   O1    single  1.397  0.020  1.397
 SG7  O5   C5    single  1.414  0.020  1.414
 SG7  C2   C3    single  1.530  0.020  1.530
 SG7  C2   O2    single  1.404  0.020  1.404
 SG7  C3   C4    single  1.518  0.020  1.518
 SG7  C3   O3    single  1.425  0.020  1.425
 SG7  C4   C5    single  1.531  0.020  1.531
 SG7  C4   O4    single  1.421  0.020  1.421
 SG7  C5   C6    single  1.509  0.020  1.509
 SG7  O3   C3B   single  1.338  0.020  1.338
 SG7  C3B  C3C   single  1.498  0.020  1.498
 SG7  C3B  O3D   double  1.203  0.020  1.203
 SG7  O4   C4C   single  1.341  0.020  1.341
 SG7  C4B  C4C   single  1.498  0.020  1.498
 SG7  C4C  O4D   double  1.202  0.020  1.202
 SG7  C6   O6    single  1.435  0.020  1.435
 SG7  O6   S5C   single  1.595  0.020  1.595
 SG7  S5C  O5D   deloc   1.442  0.020  1.442
 SG7  S5C  O5E   deloc   1.445  0.020  1.445
 SG7  S5C  N5F   single  1.639  0.020  1.639
 SG7  C1   H1    single  0.970  0.020  1.090
 SG7  C2   H2    single  0.970  0.020  1.090
 SG7  C3   H3    single  0.970  0.020  1.090
 SG7  C4   H4    single  0.970  0.020  1.090
 SG7  C5   H5    single  0.970  0.020  1.090
 SG7  O1   HO1   single  0.850  0.020  0.980
 SG7  O2   HO2   single  0.850  0.020  0.980
 SG7  C3C  H3C   single  0.970  0.020  1.090
 SG7  C3C  H3CA  single  0.970  0.020  1.090
 SG7  C3C  H3CB  single  0.970  0.020  1.090
 SG7  C4B  H4B   single  0.970  0.020  1.090
 SG7  C4B  H4BA  single  0.970  0.020  1.090
 SG7  C4B  H4BB  single  0.970  0.020  1.090
 SG7  C6   H61   single  0.970  0.020  1.090
 SG7  C6   H62   single  0.970  0.020  1.090
 SG7  N5F  HN5F  single  0.890  0.020  1.040
 SG7  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
 SG7  H1    C1   O1    111.62  3.000
 SG7  H1    C1   C2    108.76  3.000
 SG7  O1    C1   C2    111.64  3.000
 SG7  H1    C1   O5    105.54  3.000
 SG7  O1    C1   O5    107.91  3.000
 SG7  C2    C1   O5    111.21  3.000
 SG7  C5    O5   C1    115.35  3.000
 SG7  H2    C2   O2    111.17  3.000
 SG7  H2    C2   C3    109.28  3.000
 SG7  O2    C2   C3    111.96  3.000
 SG7  H2    C2   C1    108.52  3.000
 SG7  O2    C2   C1    106.73  3.000
 SG7  C3    C2   C1    109.07  3.000
 SG7  H3    C3   O3    110.20  3.000
 SG7  H3    C3   C4    109.56  3.000
 SG7  O3    C3   C4    107.07  3.000
 SG7  H3    C3   C2    109.48  3.000
 SG7  O3    C3   C2    110.90  3.000
 SG7  C4    C3   C2    109.60  3.000
 SG7  H4    C4   O4    110.78  3.000
 SG7  H4    C4   C5    110.35  3.000
 SG7  O4    C4   C5    108.06  3.000
 SG7  H4    C4   C3    110.11  3.000
 SG7  O4    C4   C3    109.14  3.000
 SG7  C5    C4   C3    108.34  3.000
 SG7  H5    C5   C6    105.23  3.000
 SG7  H5    C5   C4    108.95  3.000
 SG7  C6    C5   C4    113.85  3.000
 SG7  H5    C5   O5    111.04  3.000
 SG7  C6    C5   O5    108.46  3.000
 SG7  C4    C5   O5    109.27  3.000
 SG7  HO1   O1   C1    109.58  3.000
 SG7  HO2   O2   C2    109.05  3.000
 SG7  C3B   O3   C3    119.14  3.000
 SG7  O3D   C3B  C3C   125.76  3.000
 SG7  O3D   C3B  O3    123.41  3.000
 SG7  C3C   C3B  O3    110.83  3.000
 SG7  H3CB  C3C  H3CA  107.22  3.000
 SG7  H3CB  C3C  H3C   109.16  3.000
 SG7  H3CA  C3C  H3C   109.13  3.000
 SG7  H3CB  C3C  C3B   110.30  3.000
 SG7  H3CA  C3C  C3B   110.46  3.000
 SG7  H3C   C3C  C3B   110.50  3.000
 SG7  C4C   O4   C4    119.93  3.000
 SG7  H4BB  C4B  H4BA  107.26  3.000
 SG7  H4BB  C4B  H4B   109.27  3.000
 SG7  H4BA  C4B  H4B   109.04  3.000
 SG7  H4BB  C4B  C4C   110.66  3.000
 SG7  H4BA  C4B  C4C   110.17  3.000
 SG7  H4B   C4B  C4C   110.37  3.000
 SG7  O4D   C4C  C4B   125.45  3.000
 SG7  O4D   C4C  O4    123.95  3.000
 SG7  C4B   C4C  O4    110.60  3.000
 SG7  H62   C6   H61   108.52  3.000
 SG7  H62   C6   O6    110.19  3.000
 SG7  H61   C6   O6    110.53  3.000
 SG7  H62   C6   C5    109.56  3.000
 SG7  H61   C6   C5    109.42  3.000
 SG7  O6    C6   C5    108.59  3.000
 SG7  S5C   O6   C6    118.63  3.000
 SG7  N5F   S5C  O5E   106.78  3.000
 SG7  N5F   S5C  O5D   113.57  3.000
 SG7  O5E   S5C  O5D   120.17  3.000
 SG7  N5F   S5C  O6    101.02  3.000
 SG7  O5E   S5C  O6    110.50  3.000
 SG7  O5D   S5C  O6    103.09  3.000
 SG7  HN5A  N5F  HN5F  111.41  3.000
 SG7  HN5A  N5F  S5C   113.91  3.000
 SG7  HN5F  N5F  S5C   112.63  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
 SG7  Var_01  C3C   C3B  O3   C3   -177.05  30.0  3
 SG7  Var_02  C4B   C4C  O4   C4   -179.72  30.0  3
 SG7  Var_03  O5D   S5C  O6   C6    171.21  30.0  3
 SG7  Var_04  H3C   C3C  C3B  O3   -179.08  30.0  3
 SG7  Var_05  H4B   C4B  C4C  O4    177.53  30.0  3
 SG7  Var_06  HN5F  N5F  S5C  O6    154.31  30.0  3
 SG7  Var_07  H61   C6   O6   S5C    54.87  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
 SG7  chir_01  C1  O5  C2  O1  negativ
 SG7  chir_02  C2  O2  C3  C1  negativ
 SG7  chir_03  C3  O3  C4  C2  negativ
 SG7  chir_04  C4  O4  C5  C3  positiv
 SG7  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
 SG7  plan-1  O3   0.020
 SG7  plan-1  C3B  0.020
 SG7  plan-1  C3C  0.020
 SG7  plan-1  O3D  0.020
 SG7  plan-2  O4   0.020
 SG7  plan-2  C4B  0.020
 SG7  plan-2  C4C  0.020
 SG7  plan-2  O4D  0.020

