# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:14:36 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 1,6-dithio-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H]1O[C@H](CS)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 MSX  MSX  'methyl 1,6-dithio-alpha-D-mannopyranoside'  D-saccharide  27  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MSX
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
 MSX  O3    O  OH1   0  -0.664  -0.5578   1.6849  -1.7945
 MSX  C6    C  CH1   0  -0.041  -0.1659   2.0305  -0.4897
 MSX  C     C  CH1   0   0.027  -1.3068   1.6685   0.4700
 MSX  O     O  OH1   0  -0.669  -1.0953   2.2778   1.7229
 MSX  C5    C  CH1   0   0.038   1.1254   1.3174  -0.0816
 MSX  O2    O  OH1   0  -0.667   2.0781   1.5822  -1.0771
 MSX  C3    C  CH1   0  -0.137   0.8546  -0.1786   0.0771
 MSX  S1    S  S2    0  -0.016   2.3685  -1.0063   0.6115
 MSX  C4    C  CH3   0  -0.767   2.1351  -2.6407  -0.1273
 MSX  O1    O  O2    0  -0.469  -0.1326  -0.3849   1.0562
 MSX  C1    C  CH1   0  -0.005  -1.3984   0.1631   0.7343
 MSX  C2    C  CH2   0  -0.603  -2.0920  -0.6045  -0.3848
 MSX  S     S  S2    0  -0.238  -1.9245  -2.3875  -0.0341
 MSX  H3    H  HOH1  0   0.455   0.1973   1.8178  -2.3782
 MSX  H6    H  HCH1  0   0.241   0.0078   3.1160  -0.4206
 MSX  H     H  HCH1  0   0.240  -2.2545   2.0007   0.0234
 MSX  H5    H  HCH1  0   0.227   1.4365   1.7122   0.8959
 MSX  HA    H  HOH1  0   0.456  -1.0892   3.2329   1.6026
 MSX  H1    H  HCH1  0   0.270  -1.9961   0.0269   1.6401
 MSX  H2    H  HOH1  0   0.448   2.8431   1.0129  -0.9285
 MSX  HB    H  HCH1  0   0.262   0.5700  -0.6154  -0.8894
 MSX  H41C  H  HCH3  0   0.272   1.2038  -3.0872   0.2139
 MSX  H42C  H  HCH3  0   0.270   2.1388  -2.5821  -1.2136
 MSX  H43C  H  HCH3  0   0.280   2.9663  -3.2637   0.1967
 MSX  H21C  H  HCH2  0   0.290  -3.1481  -0.3357  -0.3831
 MSX  H22C  H  HCH2  0   0.283  -1.6886  -0.3785  -1.3684
 MSX  HS    H  HSH1  0   0.220  -2.8752  -2.8020  -0.8787

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
 MSX  O3  C6    single  1.406  0.020  1.406
 MSX  C6  C     single  1.534  0.020  1.534
 MSX  C6  C5    single  1.530  0.020  1.530
 MSX  C   O     single  1.409  0.020  1.409
 MSX  C   C1    single  1.531  0.020  1.531
 MSX  C5  O2    single  1.403  0.020  1.403
 MSX  C5  C3    single  1.529  0.020  1.529
 MSX  C3  S1    single  1.806  0.020  1.806
 MSX  C3  O1    single  1.406  0.020  1.406
 MSX  S1  C4    single  1.809  0.020  1.809
 MSX  O1  C1    single  1.416  0.020  1.416
 MSX  C1  C2    single  1.524  0.020  1.524
 MSX  C2  S     single  1.825  0.020  1.825
 MSX  O3  H3    single  0.850  0.020  0.980
 MSX  C6  H6    single  0.970  0.020  1.090
 MSX  C   H     single  0.970  0.020  1.090
 MSX  C5  H5    single  0.970  0.020  1.090
 MSX  O   HA    single  0.850  0.020  0.980
 MSX  C1  H1    single  0.970  0.020  1.090
 MSX  O2  H2    single  0.850  0.020  0.980
 MSX  C3  HB    single  0.970  0.020  1.090
 MSX  C4  H41C  single  0.970  0.020  1.090
 MSX  C4  H42C  single  0.970  0.020  1.090
 MSX  C4  H43C  single  0.970  0.020  1.090
 MSX  C2  H21C  single  0.970  0.020  1.090
 MSX  C2  H22C  single  0.970  0.020  1.090
 MSX  S   HS    single  1.200  0.020  1.300

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
 MSX  H3    O3  C6    108.05  3.000
 MSX  H6    C6  C5    108.02  3.000
 MSX  H6    C6  C     108.09  3.000
 MSX  C5    C6  C     110.53  3.000
 MSX  H6    C6  O3    110.15  3.000
 MSX  C5    C6  O3    111.61  3.000
 MSX  C     C6  O3    108.38  3.000
 MSX  H     C   C1    108.40  3.000
 MSX  H     C   O     111.10  3.000
 MSX  C1    C   O     106.29  3.000
 MSX  H     C   C6    108.41  3.000
 MSX  C1    C   C6    112.61  3.000
 MSX  O     C   C6    110.03  3.000
 MSX  HA    O   C     108.59  3.000
 MSX  H5    C5  C3    108.02  3.000
 MSX  H5    C5  O2    111.78  3.000
 MSX  C3    C5  O2    112.25  3.000
 MSX  H5    C5  C6    107.98  3.000
 MSX  C3    C5  C6    109.53  3.000
 MSX  O2    C5  C6    107.20  3.000
 MSX  H2    O2  C5    108.52  3.000
 MSX  HB    C3  O1    111.87  3.000
 MSX  HB    C3  S1    107.18  3.000
 MSX  O1    C3  S1    108.38  3.000
 MSX  HB    C3  C5    110.11  3.000
 MSX  O1    C3  C5    109.90  3.000
 MSX  S1    C3  C5    109.32  3.000
 MSX  C4    S1  C3    100.67  3.000
 MSX  H43C  C4  H42C  109.00  3.000
 MSX  H43C  C4  H41C  109.00  3.000
 MSX  H42C  C4  H41C  109.77  3.000
 MSX  H43C  C4  S1    107.29  3.000
 MSX  H42C  C4  S1    111.02  3.000
 MSX  H41C  C4  S1    110.69  3.000
 MSX  C1    O1  C3    114.37  3.000
 MSX  H1    C1  C2    107.26  3.000
 MSX  H1    C1  O1    104.60  3.000
 MSX  C2    C1  O1    112.25  3.000
 MSX  H1    C1  C     107.35  3.000
 MSX  C2    C1  C     113.31  3.000
 MSX  O1    C1  C     111.48  3.000
 MSX  H22C  C2  H21C  108.04  3.000
 MSX  H22C  C2  S     110.06  3.000
 MSX  H21C  C2  S     109.25  3.000
 MSX  H22C  C2  C1    113.01  3.000
 MSX  H21C  C2  C1    108.40  3.000
 MSX  S     C2  C1    108.02  3.000
 MSX  HS    S   C2     96.68  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
 MSX  Var_01  H41C  C4  S1  C3  -56.90  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
 MSX  chir_01  C6  O3  C   C5  negativ
 MSX  chir_02  C   O   C1  C6  positiv
 MSX  chir_03  C5  O2  C6  C3  negativ
 MSX  chir_04  C3  S1  O1  C5  negativ
 MSX  chir_05  C1  O1  C2  C   positiv

