# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 25 01:24:10 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](OC(C)=O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)COC(C)=O)C(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
 SIO  SIO  'methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  52  28  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SIO
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
 SIO  OA4   O  O      0  -0.455   4.9810   0.4209   1.0957
 SIO  CA4   C  C      0   0.565   4.7836  -0.3166   0.1624
 SIO  CM4   C  CH3    0  -0.772   5.8266  -1.1803  -0.4839
 SIO  O4    O  O2     0  -0.462   3.6002  -0.4797  -0.4187
 SIO  C4    C  CH1    0   0.060   2.4540   0.2187   0.0942
 SIO  C5    C  CH1    0  -0.135   1.2609  -0.6821  -0.1929
 SIO  N5    N  NH1    0  -0.637   1.3396  -1.8828   0.6005
 SIO  C10   C  C      0   0.525   1.4961  -3.1265   0.1054
 SIO  O10   O  O      0  -0.497   1.5485  -3.3747  -1.0898
 SIO  C11   C  CH3    0  -0.782   1.5800  -4.2162   1.1455
 SIO  C3    C  CH2    0  -0.547   2.3126   1.5596  -0.6054
 SIO  C2    C  CT     0   0.416   0.9519   2.2318  -0.3852
 SIO  O2    O  O2     0  -0.498   0.7233   3.2595  -1.2840
 SIO  CM2   C  CH3    0  -0.431   0.8183   2.9784  -2.6663
 SIO  C1    C  C      0   0.401   0.7794   2.8332   1.0459
 SIO  O1    O  OC    -1  -0.588   1.3348   2.2000   1.9657
 SIO  O3    O  O      0  -0.586   0.0785   3.8482   1.1504
 SIO  O6    O  O2     0  -0.535  -0.0942   1.2879  -0.5944
 SIO  C6    C  CH1    0   0.040  -0.0425   0.0686   0.1082
 SIO  C7    C  CH1    0  -0.018  -1.2746  -0.7192  -0.3412
 SIO  O7    O  OH1    0  -0.662  -1.3257  -0.8342  -1.7420
 SIO  C8    C  CH1    0  -0.038  -2.5689  -0.1131   0.2328
 SIO  O8    O  OH1    0  -0.655  -2.5414  -0.1041   1.6397
 SIO  C9    C  CH2    0  -0.180  -3.7844  -0.8532  -0.3013
 SIO  O9    O  O2     0  -0.450  -4.9389  -0.2172   0.2515
 SIO  CA9   C  C      0   0.573  -6.1286  -0.7268  -0.0362
 SIO  OA9   O  O      0  -0.462  -6.2846  -1.7018  -0.7305
 SIO  CM9   C  CH3    0  -0.774  -7.2495   0.0534   0.5852
 SIO  HM4   H  HCH3   0   0.273   5.6401  -2.2279  -0.2416
 SIO  HM4A  H  HCH3   0   0.268   5.7953  -1.0889  -1.5689
 SIO  HM4B  H  HCH3   0   0.260   6.8171  -0.9134  -0.1268
 SIO  H4    H  HCH1   0   0.257   2.5591   0.3620   1.1682
 SIO  H5    H  HCH1   0   0.266   1.2695  -0.9721  -1.2453
 SIO  HN5   H  HNH1   0   0.398   1.3342  -1.7709   1.6028
 SIO  H11   H  HCH3   0   0.248   1.5834  -3.8458   2.1687
 SIO  H11A  H  HCH3   0   0.268   0.7316  -4.8905   1.0277
 SIO  H11B  H  HCH3   0   0.265   2.4846  -4.8026   0.9878
 SIO  H3    H  HCH2   0   0.257   3.1042   2.2373  -0.2795
 SIO  H3A   H  HCH2   0   0.253   2.4622   1.3817  -1.6744
 SIO  HM2   H  HCH3   0   0.215   0.3366   2.0393  -2.9472
 SIO  HM2A  H  HCH3   0   0.239   0.3084   3.7881  -3.1871
 SIO  HM2B  H  HCH3   0   0.213   1.8531   2.9538  -3.0198
 SIO  H6    H  HCH1   0   0.231  -0.1064   0.2333   1.1904
 SIO  H7    H  HCH1   0   0.246  -1.1844  -1.7406   0.0451
 SIO  HO7   H  HOH1   0   0.446  -1.2487   0.0521  -2.1137
 SIO  H8    H  HCH1   0   0.245  -2.6392   0.9371  -0.0692
 SIO  HO8   H  HOH1   0   0.446  -2.5067  -1.0135   1.9577
 SIO  H9    H  HCH2   0   0.248  -3.8188  -0.8086  -1.3902
 SIO  H9A   H  HCH2   0   0.234  -3.7550  -1.9079  -0.0073
 SIO  HM9   H  HCH3   0   0.260  -6.9036   0.8068   1.2875
 SIO  HM9A  H  HCH3   0   0.277  -7.8182   0.5483  -0.2031
 SIO  HM9B  H  HCH3   0   0.272  -7.9303  -0.6277   1.0935

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
 SIO  CA4  OA4   double  1.206  0.020  1.206
 SIO  O4   CA4   single  1.328  0.020  1.328
 SIO  CA4  CM4   single  1.501  0.020  1.501
 SIO  CM4  HM4   single  0.970  0.020  1.090
 SIO  CM4  HM4A  single  0.970  0.020  1.090
 SIO  CM4  HM4B  single  0.970  0.020  1.090
 SIO  C4   O4    single  1.437  0.020  1.437
 SIO  C5   C4    single  1.522  0.020  1.522
 SIO  C3   C4    single  1.519  0.020  1.519
 SIO  C4   H4    single  0.970  0.020  1.090
 SIO  C6   C5    single  1.534  0.020  1.534
 SIO  C5   N5    single  1.441  0.020  1.441
 SIO  C5   H5    single  0.970  0.020  1.090
 SIO  N5   C10   single  1.348  0.020  1.348
 SIO  N5   HN5   single  0.860  0.020  1.020
 SIO  O10  C10   double  1.222  0.020  1.222
 SIO  C10  C11   single  1.509  0.020  1.509
 SIO  C11  H11   single  0.970  0.020  1.090
 SIO  C11  H11A  single  0.970  0.020  1.090
 SIO  C11  H11B  single  0.970  0.020  1.090
 SIO  C2   C3    single  1.534  0.020  1.534
 SIO  C3   H3    single  0.970  0.020  1.090
 SIO  C3   H3A   single  0.970  0.020  1.090
 SIO  O2   C2    single  1.384  0.020  1.384
 SIO  O6   C2    single  1.424  0.020  1.424
 SIO  C2   C1    single  1.562  0.020  1.562
 SIO  CM2  O2    single  1.414  0.020  1.414
 SIO  CM2  HM2   single  0.970  0.020  1.090
 SIO  CM2  HM2A  single  0.970  0.020  1.090
 SIO  CM2  HM2B  single  0.970  0.020  1.090
 SIO  O3   C1    deloc   1.238  0.020  1.238
 SIO  C1   O1    deloc   1.247  0.020  1.247
 SIO  O6   C6    single  1.408  0.020  1.408
 SIO  C7   C6    single  1.530  0.020  1.530
 SIO  C6   H6    single  0.970  0.020  1.090
 SIO  O7   C7    single  1.406  0.020  1.406
 SIO  C8   C7    single  1.540  0.020  1.540
 SIO  C7   H7    single  0.970  0.020  1.090
 SIO  O7   HO7   single  0.850  0.020  0.980
 SIO  C9   C8    single  1.520  0.020  1.520
 SIO  C8   O8    single  1.407  0.020  1.407
 SIO  C8   H8    single  0.970  0.020  1.090
 SIO  O8   HO8   single  0.850  0.020  0.980
 SIO  C9   O9    single  1.429  0.020  1.429
 SIO  C9   H9    single  0.970  0.020  1.090
 SIO  C9   H9A   single  0.970  0.020  1.090
 SIO  CA9  O9    single  1.326  0.020  1.326
 SIO  OA9  CA9   double  1.207  0.020  1.207
 SIO  CA9  CM9   single  1.500  0.020  1.500
 SIO  CM9  HM9   single  0.970  0.020  1.090
 SIO  CM9  HM9A  single  0.970  0.020  1.090
 SIO  CM9  HM9B  single  0.970  0.020  1.090

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
 SIO  O4    CA4  CM4   111.11  3.000
 SIO  CM4   CA4  OA4   124.87  3.000
 SIO  O4    CA4  OA4   124.02  3.000
 SIO  HM4B  CM4  HM4A  109.46  3.000
 SIO  HM4B  CM4  HM4   108.59  3.000
 SIO  HM4A  CM4  HM4   107.27  3.000
 SIO  HM4B  CM4  CA4   110.53  3.000
 SIO  HM4A  CM4  CA4   111.14  3.000
 SIO  HM4   CM4  CA4   109.76  3.000
 SIO  C4    O4   CA4   119.66  3.000
 SIO  H4    C4   C3    110.32  3.000
 SIO  H4    C4   C5    109.85  3.000
 SIO  C3    C4   C5    111.26  3.000
 SIO  H4    C4   O4    109.82  3.000
 SIO  C3    C4   O4    109.81  3.000
 SIO  C5    C4   O4    105.68  3.000
 SIO  H5    C5   C6    109.03  3.000
 SIO  H5    C5   N5    108.00  3.000
 SIO  C6    C5   N5    110.24  3.000
 SIO  H5    C5   C4    109.44  3.000
 SIO  N5    C5   C4    110.26  3.000
 SIO  C6    C5   C4    109.84  3.000
 SIO  HN5   N5   C10   117.92  3.000
 SIO  HN5   N5   C5    117.02  3.000
 SIO  C10   N5   C5    124.95  3.000
 SIO  C11   C10  O10   121.68  3.000
 SIO  C11   C10  N5    114.82  3.000
 SIO  O10   C10  N5    123.49  3.000
 SIO  H11B  C11  H11A  107.32  3.000
 SIO  H11B  C11  H11   108.46  3.000
 SIO  H11A  C11  H11   108.33  3.000
 SIO  H11B  C11  C10   109.58  3.000
 SIO  H11A  C11  C10   109.21  3.000
 SIO  H11   C11  C10   113.74  3.000
 SIO  H3A   C3   H3    107.07  3.000
 SIO  H3A   C3   C2    109.44  3.000
 SIO  H3    C3   C2    109.16  3.000
 SIO  H3A   C3   C4    107.08  3.000
 SIO  H3    C3   C4    110.06  3.000
 SIO  C2    C3   C4    113.79  3.000
 SIO  O6    C2   C1    107.97  3.000
 SIO  C1    C2   O2    106.91  3.000
 SIO  O6    C2   O2    105.98  3.000
 SIO  C1    C2   C3    113.48  3.000
 SIO  O6    C2   C3    109.88  3.000
 SIO  O2    C2   C3    112.26  3.000
 SIO  CM2   O2   C2    118.43  3.000
 SIO  HM2B  CM2  HM2A  107.76  3.000
 SIO  HM2B  CM2  HM2   108.34  3.000
 SIO  HM2A  CM2  HM2   108.05  3.000
 SIO  HM2B  CM2  O2    112.58  3.000
 SIO  HM2A  CM2  O2    106.75  3.000
 SIO  HM2   CM2  O2    113.13  3.000
 SIO  O3    C1   O1    127.32  3.000
 SIO  O1    C1   C2    115.53  3.000
 SIO  O3    C1   C2    117.10  3.000
 SIO  C6    O6   C2    118.26  3.000
 SIO  H6    C6   C7    108.68  3.000
 SIO  H6    C6   O6    111.12  3.000
 SIO  C7    C6   O6    105.65  3.000
 SIO  H6    C6   C5    108.47  3.000
 SIO  C7    C6   C5    112.00  3.000
 SIO  O6    C6   C5    110.92  3.000
 SIO  H7    C7   C8    107.73  3.000
 SIO  H7    C7   O7    106.13  3.000
 SIO  C8    C7   O7    111.89  3.000
 SIO  H7    C7   C6    108.07  3.000
 SIO  C8    C7   C6    111.39  3.000
 SIO  O7    C7   C6    111.34  3.000
 SIO  HO7   O7   C7    107.81  3.000
 SIO  H8    C8   C9    108.58  3.000
 SIO  H8    C8   O8    105.72  3.000
 SIO  C9    C8   O8    111.72  3.000
 SIO  H8    C8   C7    109.19  3.000
 SIO  O8    C8   C7    111.02  3.000
 SIO  C9    C8   C7    110.45  3.000
 SIO  HO8   O8   C8    108.94  3.000
 SIO  H9A   C9   H9    107.95  3.000
 SIO  H9A   C9   O9    110.27  3.000
 SIO  H9    C9   O9    110.03  3.000
 SIO  H9A   C9   C8    110.68  3.000
 SIO  H9    C9   C8    110.87  3.000
 SIO  O9    C9   C8    107.06  3.000
 SIO  CA9   O9   C9    118.02  3.000
 SIO  CM9   CA9  OA9   124.17  3.000
 SIO  CM9   CA9  O9    112.37  3.000
 SIO  OA9   CA9  O9    123.45  3.000
 SIO  HM9B  CM9  HM9A  107.17  3.000
 SIO  HM9B  CM9  HM9   109.33  3.000
 SIO  HM9A  CM9  HM9   108.57  3.000
 SIO  HM9B  CM9  CA9   109.59  3.000
 SIO  HM9A  CM9  CA9   109.03  3.000
 SIO  HM9   CM9  CA9   112.98  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
 SIO  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 SIO  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 SIO  CONST_03  HN5  N5   C10  O10  180.00   0.0  0
 SIO  Var_01    HM2  CM2  O2   C2    43.61  30.0  3
 SIO  Var_02    OA9  CA9  O9   C9     0.54  30.0  2
 SIO  Var_03    HM4  CM4  CA4  OA4  108.88  30.0  3
 SIO  Var_04    H11  C11  C10  N5    -4.68  30.0  3
 SIO  Var_05    HM9  CM9  CA9  O9    -8.90  30.0  3
 SIO  Var_06    H9   C9   O9   CA9   61.93  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
 SIO  chir_01  C4  O4  C5  C3  positiv
 SIO  chir_02  C5  N5  C6  C4  negativ
 SIO  chir_03  C2  O6  C1  C3  negativ
 SIO  chir_04  C6  O6  C5  C7  positiv
 SIO  chir_05  C7  O7  C6  C8  negativ
 SIO  chir_06  C8  O8  C7  C9  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
 SIO  plan-1  C5   0.020
 SIO  plan-1  N5   0.020
 SIO  plan-1  C10  0.020
 SIO  plan-1  O10  0.020
 SIO  plan-1  C11  0.020
 SIO  plan-1  HN5  0.020
 SIO  plan-2  C2   0.020
 SIO  plan-2  C1   0.020
 SIO  plan-2  O1   0.020
 SIO  plan-2  O3   0.020
 SIO  plan-3  OA4  0.020
 SIO  plan-3  CA4  0.020
 SIO  plan-3  CM4  0.020
 SIO  plan-3  O4   0.020
 SIO  plan-4  O9   0.020
 SIO  plan-4  CA9  0.020
 SIO  plan-4  OA9  0.020
 SIO  plan-4  CM9  0.020

