# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 08:49:19 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: methyl 3-O-alpha-D-mannopyranosyl-beta-D-altropyranoside
#   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
 M13  M13  'methyl 3-O-alpha-D-mannopyranosyl-beta-D-altropyranoside'  ligand  48  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M13
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
 M13  O10   O  OH1   0  -0.665  -1.9050  -2.1697  -3.2081
 M13  C12   C  CH2   0  -0.172  -1.7659  -1.1651  -2.2331
 M13  C11   C  CH1   0  -0.031  -1.5154  -1.7303  -0.8459
 M13  O11   O  O2    0  -0.513  -0.3071  -2.4654  -0.9139
 M13  C7    C  CH1   0   0.316  -0.0081  -3.1459   0.2782
 M13  O7    O  O2    0  -0.501   1.1473  -3.8738   0.0900
 M13  CM    C  CH3   0  -0.407   1.0256  -4.9679  -0.7984
 M13  C10   C  CH1   0   0.035  -1.3771  -0.6363   0.2169
 M13  O9    O  OH1   0  -0.659  -2.5733   0.0884   0.3686
 M13  C9    C  CH1   0  -0.044  -0.9927  -1.2449   1.5640
 M13  C8    C  CH1   0  -0.025   0.2310  -2.1556   1.4159
 M13  O8    O  OH1   0  -0.669   1.3358  -1.3238   1.1699
 M13  O1    O  O2    0  -0.511  -2.1010  -1.9901   2.0263
 M13  C1    C  CH1   0   0.260  -2.1824  -2.2035   3.4056
 M13  O6    O  O2    0  -0.497  -2.2541  -1.0222   4.1371
 M13  C2    C  CH1   0  -0.049  -3.4139  -3.0774   3.6369
 M13  O2    O  OH1   0  -0.678  -3.4642  -3.5008   4.9811
 M13  C3    C  CH1   0   0.011  -4.6901  -2.2854   3.3622
 M13  O3    O  OH1   0  -0.667  -5.8339  -3.0565   3.6271
 M13  C4    C  CH1   0   0.003  -4.6877  -0.9683   4.1384
 M13  O4    O  OH1   0  -0.669  -5.8019  -0.2191   3.7098
 M13  C5    C  CH1   0  -0.028  -3.3836  -0.2033   3.8727
 M13  C6    C  CH2   0  -0.163  -3.2545   1.0111   4.7669
 M13  O5    O  OH1   0  -0.667  -2.1023   1.7307   4.3997
 M13  HO10  H  HOH1  0   0.446  -1.0842  -2.6714  -3.2354
 M13  H121  H  HCH2  0   0.199  -0.9609  -0.4606  -2.4870
 M13  H122  H  HCH2  0   0.229  -2.6997  -0.6006  -2.2239
 M13  H11   H  HCH1  0   0.222  -2.3506  -2.3986  -0.5834
 M13  H7    H  HCH1  0   0.190  -0.8522  -3.8086   0.5435
 M13  HM1   H  HCH3  0   0.239   1.9361  -5.5578  -0.7125
 M13  HM2   H  HCH3  0   0.221   0.9134  -4.6494  -1.8369
 M13  HM3   H  HCH3  0   0.213   0.1733  -5.6024  -0.5350
 M13  H10   H  HCH1  0   0.234  -0.5526   0.0233  -0.0815
 M13  HO9   H  HOH1  0   0.459  -2.5403   0.8597  -0.2036
 M13  H9    H  HCH1  0   0.262  -0.7530  -0.4326   2.2610
 M13  H8    H  HCH1  0   0.236   0.3695  -2.7314   2.3430
 M13  HO8   H  HOH1  0   0.454   2.1096  -1.8769   1.0200
 M13  H1    H  HCH1  0   0.235  -1.2873  -2.7158   3.7845
 M13  H2    H  HCH1  0   0.245  -3.3730  -3.9357   2.9548
 M13  HO2   H  HOH1  0   0.463  -2.8943  -4.2677   5.0891
 M13  H3    H  HCH1  0   0.247  -4.7175  -2.0494   2.2935
 M13  HO3   H  HOH1  0   0.440  -5.7395  -3.4253   4.5131
 M13  H4    H  HCH1  0   0.217  -4.7549  -1.1863   5.2147
 M13  HO4   H  HOH1  0   0.455  -6.0646   0.3800   4.4131
 M13  H5    H  HCH1  0   0.240  -3.3815   0.1276   2.8265
 M13  H61   H  HCH2  0   0.197  -3.2156   0.6811   5.8149
 M13  H62   H  HCH2  0   0.196  -4.1571   1.6244   4.6576
 M13  HO5   H  HOH1  0   0.455  -2.0431   2.5055   4.9655

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
 M13  O10  C12   single  1.407  0.020  1.407
 M13  O10  HO10  single  0.850  0.020  0.980
 M13  C12  C11   single  1.519  0.020  1.519
 M13  C12  H121  single  0.970  0.020  1.090
 M13  C12  H122  single  0.970  0.020  1.090
 M13  C11  C10   single  1.531  0.020  1.531
 M13  C11  O11   single  1.416  0.020  1.416
 M13  C11  H11   single  0.970  0.020  1.090
 M13  O11  C7    single  1.405  0.020  1.405
 M13  C7   O7    single  1.379  0.020  1.379
 M13  C7   C8    single  1.527  0.020  1.527
 M13  C7   H7    single  0.970  0.020  1.090
 M13  O7   CM    single  1.415  0.020  1.415
 M13  CM   HM1   single  0.970  0.020  1.090
 M13  CM   HM2   single  0.970  0.020  1.090
 M13  CM   HM3   single  0.970  0.020  1.090
 M13  C10  O9    single  1.407  0.020  1.407
 M13  C10  C9    single  1.527  0.020  1.527
 M13  C10  H10   single  0.970  0.020  1.090
 M13  O9   HO9   single  0.850  0.020  0.980
 M13  C9   C8    single  1.533  0.020  1.533
 M13  C9   O1    single  1.413  0.020  1.413
 M13  C9   H9    single  0.970  0.020  1.090
 M13  C8   O8    single  1.405  0.020  1.405
 M13  C8   H8    single  0.970  0.020  1.090
 M13  O8   HO8   single  0.850  0.020  0.980
 M13  O1   C1    single  1.398  0.020  1.398
 M13  C1   O6    single  1.391  0.020  1.391
 M13  C1   C2    single  1.528  0.020  1.528
 M13  C1   H1    single  0.970  0.020  1.090
 M13  O6   C5    single  1.420  0.020  1.420
 M13  C2   O2    single  1.410  0.020  1.410
 M13  C2   C3    single  1.527  0.020  1.527
 M13  C2   H2    single  0.970  0.020  1.090
 M13  O2   HO2   single  0.850  0.020  0.980
 M13  C3   C4    single  1.529  0.020  1.529
 M13  C3   O3    single  1.405  0.020  1.405
 M13  C3   H3    single  0.970  0.020  1.090
 M13  O3   HO3   single  0.850  0.020  0.980
 M13  C4   C5    single  1.535  0.020  1.535
 M13  C4   O4    single  1.409  0.020  1.409
 M13  C4   H4    single  0.970  0.020  1.090
 M13  O4   HO4   single  0.850  0.020  0.980
 M13  C5   C6    single  1.514  0.020  1.514
 M13  C5   H5    single  0.970  0.020  1.090
 M13  C6   O5    single  1.407  0.020  1.407
 M13  C6   H61   single  0.970  0.020  1.090
 M13  C6   H62   single  0.970  0.020  1.090
 M13  O5   HO5   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
 M13  HO10  O10  C12   107.92  3.000
 M13  H122  C12  H121  107.28  3.000
 M13  H122  C12  C11   109.02  3.000
 M13  H121  C12  C11   109.18  3.000
 M13  H122  C12  O10   106.90  3.000
 M13  H121  C12  O10   111.71  3.000
 M13  C11   C12  O10   112.55  3.000
 M13  H11   C11  C10   109.67  3.000
 M13  H11   C11  O11   110.09  3.000
 M13  C10   C11  O11   109.10  3.000
 M13  H11   C11  C12   108.57  3.000
 M13  O11   C11  C12   106.86  3.000
 M13  C10   C11  C12   112.51  3.000
 M13  C7    O11  C11   113.10  3.000
 M13  H7    C7   C8    109.24  3.000
 M13  H7    C7   O7    110.87  3.000
 M13  C8    C7   O7    108.23  3.000
 M13  H7    C7   O11   109.36  3.000
 M13  C8    C7   O11   110.57  3.000
 M13  O7    C7   O11   108.56  3.000
 M13  CM    O7   C7    114.96  3.000
 M13  HM3   CM   HM2   108.54  3.000
 M13  HM3   CM   HM1   108.55  3.000
 M13  HM2   CM   HM1   108.61  3.000
 M13  HM3   CM   O7    111.36  3.000
 M13  HM2   CM   O7    112.36  3.000
 M13  HM1   CM   O7    107.31  3.000
 M13  H10   C10  C9    106.87  3.000
 M13  H10   C10  O9    111.02  3.000
 M13  C9    C10  O9    108.92  3.000
 M13  H10   C10  C11   107.97  3.000
 M13  C9    C10  C11   110.49  3.000
 M13  O9    C10  C11   111.47  3.000
 M13  HO9   O9   C10   108.66  3.000
 M13  H9    C9   O1    110.73  3.000
 M13  H9    C9   C8    109.09  3.000
 M13  O1    C9   C8    110.15  3.000
 M13  H9    C9   C10   108.68  3.000
 M13  O1    C9   C10   107.53  3.000
 M13  C8    C9   C10   110.64  3.000
 M13  H8    C8   O8    111.01  3.000
 M13  H8    C8   C9    109.28  3.000
 M13  O8    C8   C9    107.04  3.000
 M13  H8    C8   C7    107.95  3.000
 M13  O8    C8   C7    112.13  3.000
 M13  C9    C8   C7    109.41  3.000
 M13  HO8   O8   C8    108.61  3.000
 M13  C1    O1   C9    116.67  3.000
 M13  H1    C1   C2    109.75  3.000
 M13  H1    C1   O6    104.86  3.000
 M13  C2    C1   O6    111.38  3.000
 M13  H1    C1   O1    111.34  3.000
 M13  C2    C1   O1    106.47  3.000
 M13  O6    C1   O1    113.09  3.000
 M13  C5    O6   C1    115.64  3.000
 M13  H2    C2   C3    108.97  3.000
 M13  H2    C2   O2    111.04  3.000
 M13  C3    C2   O2    107.30  3.000
 M13  H2    C2   C1    108.87  3.000
 M13  C3    C2   C1    110.48  3.000
 M13  O2    C2   C1    110.17  3.000
 M13  HO2   O2   C2    108.99  3.000
 M13  H3    C3   C4    108.05  3.000
 M13  H3    C3   O3    106.38  3.000
 M13  C4    C3   O3    112.24  3.000
 M13  H3    C3   C2    107.96  3.000
 M13  O3    C3   C2    111.22  3.000
 M13  C4    C3   C2    110.75  3.000
 M13  HO3   O3   C3    107.67  3.000
 M13  H4    C4   C5    108.66  3.000
 M13  H4    C4   O4    110.76  3.000
 M13  C5    C4   O4    110.73  3.000
 M13  H4    C4   C3    109.02  3.000
 M13  O4    C4   C3    107.60  3.000
 M13  C5    C4   C3    110.05  3.000
 M13  HO4   O4   C4    108.97  3.000
 M13  H5    C5   C6    108.74  3.000
 M13  H5    C5   C4    108.48  3.000
 M13  C6    C5   C4    111.72  3.000
 M13  H5    C5   O6    110.49  3.000
 M13  C6    C5   O6    106.55  3.000
 M13  C4    C5   O6    110.86  3.000
 M13  H62   C6   H61   106.98  3.000
 M13  H62   C6   O5    111.21  3.000
 M13  H61   C6   O5    111.92  3.000
 M13  H62   C6   C5    108.64  3.000
 M13  H61   C6   C5    108.99  3.000
 M13  O5    C6   C5    109.02  3.000
 M13  HO5   O5   C6    108.00  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
 M13  Var_01  HM1  CM  O7  C7  -169.52  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
 M13  chir_01  C11  C12  C10  O11  positiv
 M13  chir_02  C7   O7   O11  C8   positiv
 M13  chir_03  C10  O9   C11  C9   positiv
 M13  chir_04  C9   O1   C8   C10  negativ
 M13  chir_05  C8   O8   C9   C7   negativ
 M13  chir_06  C1   O6   O1   C2   positiv
 M13  chir_07  C2   O2   C1   C3   positiv
 M13  chir_08  C3   O3   C2   C4   positiv
 M13  chir_09  C4   O4   C3   C5   negativ
 M13  chir_10  C5   O6   C4   C6   negativ

