# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 09:40:32 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](C)[C@@H](NC(=O)[C@H](O)CCO)[C@H](O)[C@@H]1OC
#
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
 MGS  MGS  'methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranoside'  D-saccharide  43  20  .  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_MGS
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
 MGS  C1    C  CH1   0   0.262   0.1886  -0.5111   3.1992
 MGS  O1    O  O2    0  -0.499   0.3769  -1.8874   3.1296
 MGS  C7    C  CH3   0  -0.410   1.3878  -2.3834   3.9826
 MGS  C2    C  CH1   0  -0.024  -1.0712  -0.1788   2.3929
 MGS  O2    O  O2    0  -0.490  -1.4216   1.1670   2.5766
 MGS  C8    C  CH3   0  -0.406  -2.1866   1.4160   3.7305
 MGS  C3    C  CH1   0   0.051  -0.8028  -0.4000   0.9057
 MGS  O3    O  OH1   0  -0.655  -1.8874  -0.0186   0.1041
 MGS  C4    C  CH1   0  -0.127   0.4246   0.4052   0.4806
 MGS  N4    N  NH1   0  -0.632   0.7310   0.1427  -0.9044
 MGS  C9    C  C     0   0.525   0.4321   0.9732  -1.9134
 MGS  O9    O  O     0  -0.489   0.0681   2.1312  -1.7778
 MGS  C5    C  CH1   0   0.046   1.6248   0.0504   1.3681
 MGS  O5    O  O2    0  -0.497   1.2891   0.2169   2.7376
 MGS  C6    C  CH3   0  -0.681   2.8309   0.9248   1.0967
 MGS  O12   O  OH1   0  -0.674  -1.9413  -1.7665  -5.1456
 MGS  C11   C  CH2   0  -0.482  -0.7613  -0.3917  -3.6103
 MGS  C10   C  CH1   0  -0.092   0.5392   0.3609  -3.3086
 MGS  O10   O  OH1   0  -0.657   0.8254   1.3539  -4.2525
 MGS  HC1   H  HCH1  0   0.232   0.0717  -0.1972   4.2466
 MGS  HC71  H  HCH3  0   0.238   1.3429  -3.4702   3.9428
 MGS  HC72  H  HCH3  0   0.219   2.3874  -2.0666   3.6746
 MGS  HC73  H  HCH3  0   0.214   1.2293  -2.0655   5.0188
 MGS  HC2   H  HCH1  0   0.235  -1.8860  -0.8420   2.7212
 MGS  HC81  H  HCH3  0   0.238  -2.4345   2.4767   3.7395
 MGS  HC82  H  HCH3  0   0.209  -3.1206   0.8423   3.7303
 MGS  HC83  H  HCH3  0   0.208  -1.6515   1.1863   4.6581
 MGS  HC3   H  HCH1  0   0.224  -0.5712  -1.4647   0.7651
 MGS  HO3   H  HOH1  0   0.453  -2.5161  -0.7448   0.0719
 MGS  HC4   H  HCH1  0   0.267   0.2159   1.4724   0.5782
 MGS  HN4   H  HNH1  0   0.396   0.9982  -0.8018  -1.1404
 MGS  HC5   H  HCH1  0   0.216   1.9009  -0.9966   1.1740
 MGS  HC61  H  HCH3  0   0.243   3.6637   0.6375   1.7394
 MGS  HC62  H  HCH3  0   0.237   3.1589   0.8160   0.0642
 MGS  HC63  H  HCH3  0   0.229   2.6057   1.9777   1.2745
 MGS  H121  H  HCH2  0   0.200  -0.5941  -0.3030  -5.7511
 MGS  H122  H  HCH2  0   0.189   0.1362  -1.7335  -5.0226
 MGS  HO12  H  HOH1  0   0.454  -1.9334  -2.1649  -6.0204
 MGS  H112  H  HCH2  0   0.239  -1.6057   0.3035  -3.5534
 MGS  HC10  H  HCH1  0   0.252   1.3737  -0.3492  -3.3355
 MGS  HO10  H  HOH1  0   0.442   0.2702   2.1169  -4.0484
 MGS  H111  H  HCH2  0   0.237  -0.9219  -1.1498  -2.8386
 MGS  C12   C  CH2   0  -0.138  -0.7312  -1.0605  -4.9714

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
 MGS  C1   O1    single  1.391  0.020  1.391
 MGS  C1   C2    single  1.532  0.020  1.532
 MGS  C1   O5    single  1.398  0.020  1.398
 MGS  C1   HC1   single  0.970  0.020  1.090
 MGS  O1   C7    single  1.413  0.020  1.413
 MGS  C7   HC71  single  0.970  0.020  1.090
 MGS  C7   HC72  single  0.970  0.020  1.090
 MGS  C7   HC73  single  0.970  0.020  1.090
 MGS  C2   O2    single  1.403  0.020  1.403
 MGS  C2   C3    single  1.527  0.020  1.527
 MGS  C2   HC2   single  0.970  0.020  1.090
 MGS  O2   C8    single  1.407  0.020  1.407
 MGS  C8   HC81  single  0.970  0.020  1.090
 MGS  C8   HC82  single  0.970  0.020  1.090
 MGS  C8   HC83  single  0.970  0.020  1.090
 MGS  C3   O3    single  1.402  0.020  1.402
 MGS  C3   C4    single  1.528  0.020  1.528
 MGS  C3   HC3   single  0.970  0.020  1.090
 MGS  O3   HO3   single  0.850  0.020  0.980
 MGS  C4   N4    single  1.443  0.020  1.443
 MGS  C4   C5    single  1.534  0.020  1.534
 MGS  C4   HC4   single  0.970  0.020  1.090
 MGS  N4   C9    single  1.341  0.020  1.341
 MGS  N4   HN4   single  0.860  0.020  1.020
 MGS  C9   O9    double  1.221  0.020  1.221
 MGS  C9   C10   single  1.527  0.020  1.527
 MGS  C5   O5    single  1.420  0.020  1.420
 MGS  C5   C6    single  1.514  0.020  1.514
 MGS  C5   HC5   single  0.970  0.020  1.090
 MGS  C6   HC61  single  0.970  0.020  1.090
 MGS  C6   HC62  single  0.970  0.020  1.090
 MGS  C6   HC63  single  0.970  0.020  1.090
 MGS  C12  O12   single  1.412  0.020  1.412
 MGS  C12  C11   single  1.517  0.020  1.517
 MGS  C12  H121  single  0.970  0.020  1.090
 MGS  C12  H122  single  0.970  0.020  1.090
 MGS  O12  HO12  single  0.850  0.020  0.980
 MGS  C11  C10   single  1.533  0.020  1.533
 MGS  C11  H111  single  0.970  0.020  1.090
 MGS  C11  H112  single  0.970  0.020  1.090
 MGS  C10  O10   single  1.400  0.020  1.400
 MGS  C10  HC10  single  0.970  0.020  1.090
 MGS  O10  HO10  single  0.850  0.020  0.980

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
 MGS  HC1   C1   O5    104.45  3.000
 MGS  HC1   C1   C2    110.60  3.000
 MGS  O5    C1   C2    111.14  3.000
 MGS  HC1   C1   O1    110.15  3.000
 MGS  O5    C1   O1    113.09  3.000
 MGS  C2    C1   O1    107.43  3.000
 MGS  C7    O1   C1    114.46  3.000
 MGS  HC73  C7   HC72  108.35  3.000
 MGS  HC73  C7   HC71  108.57  3.000
 MGS  HC72  C7   HC71  108.47  3.000
 MGS  HC73  C7   O1    111.46  3.000
 MGS  HC72  C7   O1    112.49  3.000
 MGS  HC71  C7   O1    107.40  3.000
 MGS  HC2   C2   C3    109.47  3.000
 MGS  HC2   C2   O2    110.74  3.000
 MGS  C3    C2   O2    108.08  3.000
 MGS  HC2   C2   C1    108.73  3.000
 MGS  C3    C2   C1    109.66  3.000
 MGS  O2    C2   C1    110.16  3.000
 MGS  C8    O2   C2    114.40  3.000
 MGS  HC83  C8   HC82  107.86  3.000
 MGS  HC83  C8   HC81  107.97  3.000
 MGS  HC82  C8   HC81  108.41  3.000
 MGS  HC83  C8   O2    113.07  3.000
 MGS  HC82  C8   O2    111.76  3.000
 MGS  HC81  C8   O2    107.63  3.000
 MGS  HC3   C3   C4    107.80  3.000
 MGS  HC3   C3   O3    110.71  3.000
 MGS  C4    C3   O3    108.60  3.000
 MGS  HC3   C3   C2    107.58  3.000
 MGS  C4    C3   C2    109.61  3.000
 MGS  O3    C3   C2    112.43  3.000
 MGS  HO3   O3   C3    108.65  3.000
 MGS  HC4   C4   C5    108.89  3.000
 MGS  HC4   C4   N4    107.72  3.000
 MGS  C5    C4   N4    110.31  3.000
 MGS  HC4   C4   C3    109.67  3.000
 MGS  C5    C4   C3    110.21  3.000
 MGS  N4    C4   C3    109.99  3.000
 MGS  HN4   N4   C9    117.56  3.000
 MGS  HN4   N4   C4    116.80  3.000
 MGS  C9    N4   C4    124.23  3.000
 MGS  C10   C9   O9    120.15  3.000
 MGS  C10   C9   N4    115.06  3.000
 MGS  O9    C9   N4    124.77  3.000
 MGS  HC5   C5   C6    108.54  3.000
 MGS  HC5   C5   O5    109.94  3.000
 MGS  C6    C5   O5    107.07  3.000
 MGS  HC5   C5   C4    108.32  3.000
 MGS  C6    C5   C4    112.70  3.000
 MGS  O5    C5   C4    110.24  3.000
 MGS  C5    O5   C1    116.33  3.000
 MGS  HC63  C6   HC62  108.24  3.000
 MGS  HC63  C6   HC61  108.41  3.000
 MGS  HC62  C6   HC61  107.61  3.000
 MGS  HC63  C6   C5    111.32  3.000
 MGS  HC62  C6   C5    110.62  3.000
 MGS  HC61  C6   C5    110.52  3.000
 MGS  HO12  O12  C12   108.21  3.000
 MGS  H112  C11  H111  106.86  3.000
 MGS  H112  C11  C10   109.41  3.000
 MGS  H111  C11  C10   109.03  3.000
 MGS  H112  C11  C12   109.98  3.000
 MGS  H111  C11  C12   109.30  3.000
 MGS  C10   C11  C12   112.11  3.000
 MGS  HC10  C10  O10   106.70  3.000
 MGS  HC10  C10  C11   108.85  3.000
 MGS  O10   C10  C11   112.91  3.000
 MGS  HC10  C10  C9    109.60  3.000
 MGS  O10   C10  C9    110.24  3.000
 MGS  C11   C10  C9    108.50  3.000
 MGS  HO10  O10  C10   107.49  3.000
 MGS  H122  C12  H121  106.95  3.000
 MGS  H122  C12  C11   109.11  3.000
 MGS  H121  C12  C11   109.65  3.000
 MGS  H122  C12  O12   111.37  3.000
 MGS  H121  C12  O12   111.42  3.000
 MGS  C11   C12  O12   108.31  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
 MGS  CONST_01  O9    C9   N4   C4      0.00   0.0  0
 MGS  CONST_02  C10   C9   N4   C4    180.00   0.0  0
 MGS  CONST_03  HN4   N4   C9   O9    180.00   0.0  0
 MGS  Var_01    HC71  C7   O1   C1    172.15  30.0  3
 MGS  Var_02    HC81  C8   O2   C2   -177.38  30.0  3
 MGS  Var_03    C10   C11  C12  O12   177.91  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
 MGS  chir_01  C1   O1   C2  O5   positiv
 MGS  chir_02  C2   O2   C3  C1   negativ
 MGS  chir_03  C3   O3   C2  C4   positiv
 MGS  chir_04  C4   N4   C5  C3   positiv
 MGS  chir_05  C5   O5   C4  C6   negativ
 MGS  chir_06  C10  O10  C9  C11  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
 MGS  plan-1  C4   0.020
 MGS  plan-1  N4   0.020
 MGS  plan-1  C9   0.020
 MGS  plan-1  O9   0.020
 MGS  plan-1  C10  0.020
 MGS  plan-1  HN4  0.020

