# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 23:26:08 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: methyl 3-O-alpha-D-mannopyranosyl-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O)[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
 MDM  MDM  'methyl 3-O-alpha-D-mannopyranosyl-alpha-D-mannopyranoside'  D-saccharide  48  24  .  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_MDM
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
 MDM  C1    C  CH1   0   0.226  -0.7057   0.9631  -1.3491
 MDM  C2    C  CH1   0  -0.029  -1.6312   0.6546  -2.5301
 MDM  C3    C  CH1   0   0.000  -1.0949  -0.5573  -3.2869
 MDM  C4    C  CH1   0   0.038   0.3606  -0.3414  -3.6870
 MDM  C5    C  CH1   0  -0.016   1.1809  -0.0016  -2.4411
 MDM  C6    C  CH2   0  -0.160   2.6107   0.3565  -2.7861
 MDM  O2    O  OH1   0  -0.669  -1.6757   1.7458  -3.4142
 MDM  O3    O  OH1   0  -0.674  -1.8250  -0.8277  -4.4605
 MDM  O4    O  OH1   0  -0.677   0.9079  -1.5077  -4.2554
 MDM  O5    O  O2    0  -0.499   0.6187   1.1143  -1.7706
 MDM  O6    O  OH1   0  -0.665   3.3317   0.5565  -1.5926
 MDM  C1'   C  CH1   0   0.258   1.3230  -0.3825   2.6185
 MDM  C2'   C  CH1   0  -0.029   0.9174  -0.5653   1.1538
 MDM  C3'   C  CH1   0   0.020  -0.3726   0.2023   0.8820
 MDM  C4'   C  CH1   0   0.016  -1.4583  -0.1763   1.8817
 MDM  C5'   C  CH1   0  -0.016  -0.9198  -0.0124   3.3096
 MDM  C6'   C  CH2   0  -0.163  -1.9015  -0.5246   4.3406
 MDM  O1'   O  O2    0  -0.499   1.7344   0.9368   2.7794
 MDM  O2'   O  OH1   0  -0.672   0.6780  -1.9242   0.8835
 MDM  O3'   O  O2    0  -0.505  -0.8599  -0.0549  -0.4163
 MDM  O4'   O  OH1   0  -0.669  -2.5567   0.6796   1.6693
 MDM  O5'   O  O2    0  -0.499   0.2858  -0.7384   3.4821
 MDM  O6'   O  OH1   0  -0.668  -1.4179  -0.2170   5.6262
 MDM  H1    H  HCH1  0   0.238  -0.9743   1.9342  -0.9094
 MDM  H2    H  HCH1  0   0.230  -2.6292   0.4229  -2.1328
 MDM  H3    H  HCH1  0   0.228  -1.1267  -1.4175  -2.6042
 MDM  H4    H  HCH1  0   0.211   0.4214   0.5020  -4.3908
 MDM  H5    H  HCH1  0   0.227   1.1878  -0.8823  -1.7830
 MDM  H61   H  HCH2  0   0.211   3.0372  -0.4572  -3.3816
 MDM  H62   H  HCH2  0   0.194   2.6122   1.2557  -3.4185
 MDM  HO2   H  HOH1  0   0.455  -2.1530   2.4646  -2.9887
 MDM  HO3   H  HOH1  0   0.457  -2.6354  -1.2872  -4.2213
 MDM  HO4   H  HOH1  0   0.452   0.3508  -1.7634  -4.9982
 MDM  HO6   H  HOH1  0   0.456   4.2530   0.7047  -1.8234
 MDM  H1'   H  HCH1  0   0.232   2.1450  -1.0716   2.8658
 MDM  H2'   H  HCH1  0   0.245   1.7199  -0.1680   0.5203
 MDM  H3'   H  HCH1  0   0.236  -0.1602   1.2734   1.0058
 MDM  H4'   H  HCH1  0   0.229  -1.7392  -1.2261   1.7238
 MDM  H5'   H  HCH1  0   0.223  -0.7566   1.0606   3.4877
 MDM  H6'1  H  HCH2  0   0.203  -2.8747  -0.0549   4.1559
 MDM  H6'2  H  HCH2  0   0.196  -2.0344  -1.6069   4.2008
 MDM  H7'1  H  HCH3  0   0.237   2.7042   2.2265   4.0025
 MDM  H7'2  H  HCH3  0   0.219   1.5327   1.1994   4.8441
 MDM  H7'3  H  HCH3  0   0.211   3.0824   0.5218   4.3089
 MDM  HO2'  H  HOH1  0   0.456   1.5224  -2.3832   0.8464
 MDM  HO4'  H  HOH1  0   0.459  -3.3691   0.1832   1.7946
 MDM  HO6'  H  HOH1  0   0.455  -2.0808  -0.4922   6.2655
 MDM  C7'   C  CH3   0  -0.409   2.2826   1.2240   4.0493

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
 MDM  C1   C2    single  1.532  0.020  1.532
 MDM  C1   O5    single  1.398  0.020  1.398
 MDM  C1   O3'   single  1.389  0.020  1.389
 MDM  C1   H1    single  0.970  0.020  1.090
 MDM  C2   C3    single  1.526  0.020  1.526
 MDM  C2   O2    single  1.405  0.020  1.405
 MDM  C2   H2    single  0.970  0.020  1.090
 MDM  C3   C4    single  1.525  0.020  1.525
 MDM  C3   O3    single  1.408  0.020  1.408
 MDM  C3   H3    single  0.970  0.020  1.090
 MDM  C4   C5    single  1.530  0.020  1.530
 MDM  C4   O4    single  1.408  0.020  1.408
 MDM  C4   H4    single  0.970  0.020  1.090
 MDM  C5   C6    single  1.514  0.020  1.514
 MDM  C5   O5    single  1.418  0.020  1.418
 MDM  C5   H5    single  0.970  0.020  1.090
 MDM  C6   O6    single  1.409  0.020  1.409
 MDM  C6   H61   single  0.970  0.020  1.090
 MDM  C6   H62   single  0.970  0.020  1.090
 MDM  O2   HO2   single  0.850  0.020  0.980
 MDM  O3   HO3   single  0.850  0.020  0.980
 MDM  O4   HO4   single  0.850  0.020  0.980
 MDM  O6   HO6   single  0.850  0.020  0.980
 MDM  C1'  C2'   single  1.531  0.020  1.531
 MDM  C1'  O1'   single  1.391  0.020  1.391
 MDM  C1'  O5'   single  1.396  0.020  1.396
 MDM  C1'  H1'   single  0.970  0.020  1.090
 MDM  C2'  C3'   single  1.525  0.020  1.525
 MDM  C2'  O2'   single  1.406  0.020  1.406
 MDM  C2'  H2'   single  0.970  0.020  1.090
 MDM  C3'  C4'   single  1.524  0.020  1.524
 MDM  C3'  O3'   single  1.410  0.020  1.410
 MDM  C3'  H3'   single  0.970  0.020  1.090
 MDM  C4'  C5'   single  1.535  0.020  1.535
 MDM  C4'  O4'   single  1.409  0.020  1.409
 MDM  C4'  H4'   single  0.970  0.020  1.090
 MDM  C5'  C6'   single  1.513  0.020  1.513
 MDM  C5'  O5'   single  1.418  0.020  1.418
 MDM  C5'  H5'   single  0.970  0.020  1.090
 MDM  C6'  O6'   single  1.408  0.020  1.408
 MDM  C6'  H6'1  single  0.970  0.020  1.090
 MDM  C6'  H6'2  single  0.970  0.020  1.090
 MDM  C7'  O1'   single  1.413  0.020  1.413
 MDM  C7'  H7'1  single  0.970  0.020  1.090
 MDM  C7'  H7'2  single  0.970  0.020  1.090
 MDM  C7'  H7'3  single  0.970  0.020  1.090
 MDM  O2'  HO2'  single  0.850  0.020  0.980
 MDM  O4'  HO4'  single  0.850  0.020  0.980
 MDM  O6'  HO6'  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
 MDM  H1    C1   O3'   110.58  3.000
 MDM  H1    C1   O5    104.86  3.000
 MDM  O3'   C1   O5    112.75  3.000
 MDM  H1    C1   C2    109.80  3.000
 MDM  O3'   C1   C2    107.64  3.000
 MDM  O5    C1   C2    111.20  3.000
 MDM  H2    C2   O2    111.25  3.000
 MDM  H2    C2   C3    109.32  3.000
 MDM  O2    C2   C3    108.41  3.000
 MDM  H2    C2   C1    108.21  3.000
 MDM  O2    C2   C1    110.36  3.000
 MDM  C3    C2   C1    109.26  3.000
 MDM  H3    C3   O3    110.64  3.000
 MDM  H3    C3   C4    107.55  3.000
 MDM  O3    C3   C4    107.66  3.000
 MDM  H3    C3   C2    107.66  3.000
 MDM  O3    C3   C2    112.55  3.000
 MDM  C4    C3   C2    110.68  3.000
 MDM  H4    C4   O4    110.81  3.000
 MDM  H4    C4   C5    108.73  3.000
 MDM  O4    C4   C5    107.71  3.000
 MDM  H4    C4   C3    109.22  3.000
 MDM  O4    C4   C3    111.08  3.000
 MDM  C5    C4   C3    109.24  3.000
 MDM  H5    C5   O5    110.47  3.000
 MDM  H5    C5   C6    108.66  3.000
 MDM  O5    C5   C6    107.22  3.000
 MDM  H5    C5   C4    108.24  3.000
 MDM  O5    C5   C4    110.32  3.000
 MDM  C6    C5   C4    111.93  3.000
 MDM  H62   C6   H61   107.12  3.000
 MDM  H62   C6   O6    111.75  3.000
 MDM  H61   C6   O6    111.53  3.000
 MDM  H62   C6   C5    109.02  3.000
 MDM  H61   C6   C5    108.43  3.000
 MDM  O6    C6   C5    108.90  3.000
 MDM  HO2   O2   C2    108.52  3.000
 MDM  HO3   O3   C3    108.74  3.000
 MDM  HO4   O4   C4    107.84  3.000
 MDM  C5    O5   C1    115.66  3.000
 MDM  HO6   O6   C6    107.99  3.000
 MDM  H1'   C1'  O5'   104.85  3.000
 MDM  H1'   C1'  O1'   110.29  3.000
 MDM  O5'   C1'  O1'   112.95  3.000
 MDM  H1'   C1'  C2'   109.76  3.000
 MDM  O5'   C1'  C2'   111.38  3.000
 MDM  O1'   C1'  C2'   107.59  3.000
 MDM  H2'   C2'  O2'   111.32  3.000
 MDM  H2'   C2'  C3'   109.48  3.000
 MDM  O2'   C2'  C3'   107.94  3.000
 MDM  H2'   C2'  C1'   108.39  3.000
 MDM  O2'   C2'  C1'   110.15  3.000
 MDM  C3'   C2'  C1'   109.54  3.000
 MDM  H3'   C3'  O3'   110.37  3.000
 MDM  H3'   C3'  C4'   107.82  3.000
 MDM  O3'   C3'  C4'   108.21  3.000
 MDM  H3'   C3'  C2'   107.87  3.000
 MDM  O3'   C3'  C2'   111.37  3.000
 MDM  C4'   C3'  C2'   111.14  3.000
 MDM  H4'   C4'  O4'   111.08  3.000
 MDM  H4'   C4'  C5'   109.00  3.000
 MDM  O4'   C4'  C5'   110.42  3.000
 MDM  H4'   C4'  C3'   109.00  3.000
 MDM  O4'   C4'  C3'   107.80  3.000
 MDM  C5'   C4'  C3'   109.50  3.000
 MDM  H5'   C5'  O5'   110.71  3.000
 MDM  H5'   C5'  C6'   108.43  3.000
 MDM  O5'   C5'  C6'   107.18  3.000
 MDM  H5'   C5'  C4'   107.87  3.000
 MDM  O5'   C5'  C4'   110.91  3.000
 MDM  C6'   C5'  C4'   111.73  3.000
 MDM  H6'2  C6'  H6'1  107.04  3.000
 MDM  H6'2  C6'  O6'   111.89  3.000
 MDM  H6'1  C6'  O6'   111.42  3.000
 MDM  H6'2  C6'  C5'   108.97  3.000
 MDM  H6'1  C6'  C5'   108.43  3.000
 MDM  O6'   C6'  C5'   109.00  3.000
 MDM  C7'   O1'  C1'   114.30  3.000
 MDM  HO2'  O2'  C2'   108.61  3.000
 MDM  C3'   O3'  C1    116.50  3.000
 MDM  HO4'  O4'  C4'   109.02  3.000
 MDM  C5'   O5'  C1'   115.22  3.000
 MDM  HO6'  O6'  C6'   107.94  3.000
 MDM  H7'3  C7'  H7'2  108.31  3.000
 MDM  H7'3  C7'  H7'1  108.53  3.000
 MDM  H7'2  C7'  H7'1  108.53  3.000
 MDM  H7'3  C7'  O1'   111.47  3.000
 MDM  H7'2  C7'  O1'   112.51  3.000
 MDM  H7'1  C7'  O1'   107.39  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
 MDM  Var_01  H7'1  C7'  O1'  C1'  171.35  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
 MDM  chir_01  C1   C2   O5   O3'  positiv
 MDM  chir_02  C2   O2   C1   C3   positiv
 MDM  chir_03  C3   O3   C2   C4   positiv
 MDM  chir_04  C4   O4   C5   C3   positiv
 MDM  chir_05  C5   O5   C4   C6   negativ
 MDM  chir_06  C1'  O5'  O1'  C2'  positiv
 MDM  chir_07  C2'  O2'  C1'  C3'  positiv
 MDM  chir_08  C3'  O3'  C4'  C2'  negativ
 MDM  chir_09  C4'  O4'  C3'  C5'  negativ
 MDM  chir_10  C5'  O5'  C4'  C6'  negativ

