# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:01:03 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: methyl 9-S-acetyl-5-(acetylamino)-3,5-dideoxy-9-thio-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](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CSC(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
 SID  SID  'methyl 9-S-acetyl-5-(acetylamino)-3,5-dideoxy-9-thio-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  47  25  .  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_SID
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
 SID  C1    C  C      0   0.373   1.9911   2.4849   1.1069
 SID  O1    O  O      0  -0.582   0.9055   2.5883   1.6977
 SID  C2    C  CT     0   0.415   1.9353   1.9289  -0.3572
 SID  O2    O  O2     0  -0.518   1.7216   3.0748  -1.1196
 SID  C3    C  CH2    0  -0.541   3.1881   1.1520  -0.7490
 SID  O3    O  OC    -1  -0.590   3.1185   2.8154   1.5161
 SID  C4    C  CH1    0   0.069   3.2914  -0.1429   0.0438
 SID  O4    O  OH1    0  -0.666   4.3855  -0.9305  -0.3644
 SID  C5    C  CH1    0  -0.118   2.0263  -0.9662  -0.1649
 SID  N5    N  NH1    0  -0.633   2.0326  -2.1440   0.6676
 SID  C6    C  CH1    0   0.028   0.7886  -0.1127   0.1517
 SID  O6    O  O2     0  -0.522   0.8072   1.1029  -0.5570
 SID  C7    C  CH1    0   0.001  -0.5126  -0.8070  -0.2533
 SID  O7    O  OH1    0  -0.665  -0.6190  -0.9092  -1.6513
 SID  C8    C  CH1    0   0.011  -1.7333  -0.1048   0.3709
 SID  O8    O  OH1    0  -0.655  -1.7069  -0.2104   1.7753
 SID  C9    C  CH2    0  -0.584  -3.0311  -0.6599  -0.2032
 SID  S9    S  S2     0   0.008  -4.4168   0.0928   0.6954
 SID  C10   C  C      0   0.522   2.1028  -3.4086   0.2120
 SID  O10   O  O      0  -0.502   2.1186  -3.6991  -0.9758
 SID  C11   C  CH3    0  -0.782   2.1381  -4.4694   1.2844
 SID  CA9   C  C      0   0.255  -5.7710  -0.2418  -0.3848
 SID  OA9   O  O      0  -0.395  -5.6556  -0.8284  -1.4320
 SID  CM2   C  CH3    0  -0.423   1.7526   2.9525  -2.5286
 SID  CM9   C  CH3    0  -0.750  -7.0835   0.2499   0.1583
 SID  H3    H  HCH2   0   0.241   3.1616   0.8925  -1.8121
 SID  H3A   H  HCH2   0   0.246   4.0714   1.7704  -0.5814
 SID  H4    H  HCH1   0   0.202   3.3761   0.1000   1.1140
 SID  HO4   H  HOH1   0   0.451   5.1912  -0.4347  -0.1879
 SID  H5    H  HCH1   0   0.257   1.9857  -1.2929  -1.2062
 SID  HN5   H  HNH1   0   0.396   2.0635  -2.0012   1.6654
 SID  H6    H  HCH1   0   0.228   0.7634   0.0731   1.2336
 SID  H7    H  HCH1   0   0.242  -0.4939  -1.8342   0.1272
 SID  HO7   H  HOH1   0   0.446  -0.4539  -0.0350  -2.0238
 SID  H8    H  HCH1   0   0.251  -1.6835   0.9666   0.1563
 SID  HO8   H  HOH1   0   0.446  -1.7707  -1.1412   2.0192
 SID  H9    H  HCH2   0   0.293  -3.1285  -0.4189  -1.2596
 SID  H9A   H  HCH2   0   0.278  -3.0821  -1.7459  -0.0935
 SID  H11   H  HCH3   0   0.248   2.1471  -4.0699   2.2967
 SID  H11A  H  HCH3   0   0.266   1.2680  -5.1174   1.1787
 SID  H11B  H  HCH3   0   0.265   3.0230  -5.0912   1.1515
 SID  HM2   H  HCH3   0   0.214   2.7662   2.8119  -2.9136
 SID  HM2A  H  HCH3   0   0.215   1.1257   2.1375  -2.8981
 SID  HM2B  H  HCH3   0   0.239   1.3667   3.8876  -2.9323
 SID  HM9   H  HCH3   0   0.260  -6.9652   1.0004   0.9373
 SID  HM9A  H  HCH3   0   0.276  -7.6871   0.6605  -0.6499
 SID  HM9B  H  HCH3   0   0.283  -7.6256  -0.5969   0.5834

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
 SID  O1   C1    deloc   1.240  0.020  1.240
 SID  O3   C1    deloc   1.244  0.020  1.244
 SID  C1   C2    single  1.567  0.020  1.567
 SID  C3   C2    single  1.525  0.020  1.525
 SID  O6   C2    single  1.412  0.020  1.412
 SID  C2   O2    single  1.393  0.020  1.393
 SID  O2   CM2   single  1.415  0.020  1.415
 SID  C4   C3    single  1.522  0.020  1.522
 SID  C3   H3    single  0.970  0.020  1.090
 SID  C3   H3A   single  0.970  0.020  1.090
 SID  C5   C4    single  1.524  0.020  1.524
 SID  C4   O4    single  1.409  0.020  1.409
 SID  C4   H4    single  0.970  0.020  1.090
 SID  O4   HO4   single  0.850  0.020  0.980
 SID  N5   C5    single  1.442  0.020  1.442
 SID  C5   C6    single  1.536  0.020  1.536
 SID  C5   H5    single  0.970  0.020  1.090
 SID  C10  N5    single  1.346  0.020  1.346
 SID  N5   HN5   single  0.860  0.020  1.020
 SID  C6   C7    single  1.529  0.020  1.529
 SID  C6   O6    single  1.407  0.020  1.407
 SID  C6   H6    single  0.970  0.020  1.090
 SID  C7   C8    single  1.540  0.020  1.540
 SID  C7   O7    single  1.406  0.020  1.406
 SID  C7   H7    single  0.970  0.020  1.090
 SID  O7   HO7   single  0.850  0.020  0.980
 SID  O8   C8    single  1.409  0.020  1.409
 SID  C8   C9    single  1.524  0.020  1.524
 SID  C8   H8    single  0.970  0.020  1.090
 SID  O8   HO8   single  0.850  0.020  0.980
 SID  S9   C9    single  1.815  0.020  1.815
 SID  C9   H9    single  0.970  0.020  1.090
 SID  C9   H9A   single  0.970  0.020  1.090
 SID  CA9  S9    single  1.764  0.020  1.764
 SID  C11  C10   single  1.509  0.020  1.509
 SID  C10  O10   double  1.223  0.020  1.223
 SID  C11  H11   single  0.970  0.020  1.090
 SID  C11  H11A  single  0.970  0.020  1.090
 SID  C11  H11B  single  0.970  0.020  1.090
 SID  CM9  CA9   single  1.503  0.020  1.503
 SID  CA9  OA9   double  1.206  0.020  1.206
 SID  CM2  HM2   single  0.970  0.020  1.090
 SID  CM2  HM2A  single  0.970  0.020  1.090
 SID  CM2  HM2B  single  0.970  0.020  1.090
 SID  CM9  HM9   single  0.970  0.020  1.090
 SID  CM9  HM9A  single  0.970  0.020  1.090
 SID  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
 SID  O3    C1   C2    115.71  3.000
 SID  C2    C1   O1    116.33  3.000
 SID  O3    C1   O1    127.90  3.000
 SID  O6    C2   C3    108.77  3.000
 SID  O6    C2   O2    106.33  3.000
 SID  C3    C2   O2    113.86  3.000
 SID  O2    C2   C1    103.00  3.000
 SID  O6    C2   C1    111.60  3.000
 SID  C3    C2   C1    113.04  3.000
 SID  CM2   O2   C2    118.08  3.000
 SID  H3A   C3   H3    107.65  3.000
 SID  H3A   C3   C4    110.32  3.000
 SID  H3    C3   C4    107.81  3.000
 SID  H3A   C3   C2    109.68  3.000
 SID  H3    C3   C2    110.50  3.000
 SID  C4    C3   C2    110.81  3.000
 SID  H4    C4   C5    108.44  3.000
 SID  H4    C4   O4    110.21  3.000
 SID  C5    C4   O4    107.65  3.000
 SID  H4    C4   C3    108.90  3.000
 SID  O4    C4   C3    112.18  3.000
 SID  C5    C4   C3    109.39  3.000
 SID  HO4   O4   C4    108.01  3.000
 SID  H5    C5   C6    109.44  3.000
 SID  H5    C5   N5    107.83  3.000
 SID  C6    C5   N5    109.76  3.000
 SID  H5    C5   C4    108.85  3.000
 SID  C6    C5   C4    109.90  3.000
 SID  N5    C5   C4    111.01  3.000
 SID  HN5   N5   C10   117.79  3.000
 SID  HN5   N5   C5    117.11  3.000
 SID  C10   N5   C5    124.90  3.000
 SID  H6    C6   C7    108.55  3.000
 SID  H6    C6   O6    110.51  3.000
 SID  C7    C6   O6    105.66  3.000
 SID  H6    C6   C5    108.40  3.000
 SID  O6    C6   C5    111.43  3.000
 SID  C7    C6   C5    112.25  3.000
 SID  C6    O6   C2    116.39  3.000
 SID  H7    C7   C8    107.47  3.000
 SID  H7    C7   O7    106.17  3.000
 SID  C8    C7   O7    112.09  3.000
 SID  H7    C7   C6    108.61  3.000
 SID  O7    C7   C6    111.15  3.000
 SID  C8    C7   C6    111.10  3.000
 SID  HO7   O7   C7    107.77  3.000
 SID  H8    C8   C9    108.76  3.000
 SID  H8    C8   O8    105.55  3.000
 SID  C9    C8   O8    111.36  3.000
 SID  H8    C8   C7    109.33  3.000
 SID  C9    C8   C7    110.87  3.000
 SID  O8    C8   C7    110.79  3.000
 SID  HO8   O8   C8    108.86  3.000
 SID  H9A   C9   H9    108.27  3.000
 SID  H9A   C9   S9    109.07  3.000
 SID  H9    C9   S9    108.69  3.000
 SID  H9A   C9   C8    111.34  3.000
 SID  H9    C9   C8    111.19  3.000
 SID  S9    C9   C8    108.22  3.000
 SID  CA9   S9   C9    101.79  3.000
 SID  C11   C10  O10   121.53  3.000
 SID  O10   C10  N5    123.54  3.000
 SID  C11   C10  N5    114.91  3.000
 SID  H11B  C11  H11A  107.29  3.000
 SID  H11B  C11  H11   108.44  3.000
 SID  H11A  C11  H11   108.37  3.000
 SID  H11B  C11  C10   109.48  3.000
 SID  H11A  C11  C10   109.29  3.000
 SID  H11   C11  C10   113.77  3.000
 SID  CM9   CA9  OA9   123.81  3.000
 SID  OA9   CA9  S9    123.40  3.000
 SID  CM9   CA9  S9    112.76  3.000
 SID  HM2B  CM2  HM2A  108.17  3.000
 SID  HM2B  CM2  HM2   107.96  3.000
 SID  HM2A  CM2  HM2   108.48  3.000
 SID  HM2B  CM2  O2    106.69  3.000
 SID  HM2A  CM2  O2    112.88  3.000
 SID  HM2   CM2  O2    112.46  3.000
 SID  HM9B  CM9  HM9A  107.83  3.000
 SID  HM9B  CM9  HM9   108.08  3.000
 SID  HM9A  CM9  HM9   109.36  3.000
 SID  HM9B  CM9  CA9   108.69  3.000
 SID  HM9A  CM9  CA9   109.83  3.000
 SID  HM9   CM9  CA9   112.92  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
 SID  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 SID  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 SID  CONST_03  HN5  N5   C10  O10  180.00   0.0  0
 SID  Var_01    HM2  CM2  O2   C2   -73.24  30.0  3
 SID  Var_02    CM9  CA9  S9   C9   178.11  30.0  1
 SID  Var_03    H11  C11  C10  N5    -2.61  30.0  3
 SID  Var_04    HM9  CM9  CA9  S9    18.96  30.0  3
 SID  Var_05    H9   C9   S9   CA9   42.22  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
 SID  chir_01  C2  C3  O6  O2  positiv
 SID  chir_02  C4  O4  C5  C3  positiv
 SID  chir_03  C5  N5  C6  C4  negativ
 SID  chir_04  C6  O6  C7  C5  negativ
 SID  chir_05  C7  O7  C6  C8  negativ
 SID  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
 SID  plan-1  C5   0.020
 SID  plan-1  N5   0.020
 SID  plan-1  C10  0.020
 SID  plan-1  O10  0.020
 SID  plan-1  C11  0.020
 SID  plan-1  HN5  0.020
 SID  plan-2  C1   0.020
 SID  plan-2  O1   0.020
 SID  plan-2  C2   0.020
 SID  plan-2  O3   0.020
 SID  plan-3  S9   0.020
 SID  plan-3  CA9  0.020
 SID  plan-3  OA9  0.020
 SID  plan-3  CM9  0.020

