# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:14:37 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: methyl 7-deoxy-L-glycero-alpha-D-manno-heptopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H]([C@H](C)O)[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
 2M5  2M5  'methyl 7-deoxy-L-glycero-alpha-D-manno-heptopyranoside'  D-saccharide  30  14  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2M5
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
 2M5  C1    C  CH1   0   0.260  48.7967  -24.8584  39.6176
 2M5  O1    O  O2    0  -0.494  49.1529  -26.1016  40.1293
 2M5  C2    C  CH1   0  -0.013  49.9641  -24.3699  38.7625
 2M5  O2    O  OH1   0  -0.668  49.4877  -23.2856  38.0040
 2M5  C3    C  CH1   0  -0.000  51.1324  -23.9619  39.6563
 2M5  O3    O  OH1   0  -0.673  52.1273  -23.4198  38.8199
 2M5  C4    C  CH1   0   0.014  50.6662  -22.9703  40.7145
 2M5  O4    O  OH1   0  -0.674  51.7751  -22.6920  41.5422
 2M5  C5    C  CH1   0   0.012  49.5122  -23.6007  41.5028
 2M5  O5    O  O2    0  -0.502  48.4613  -23.9358  40.6109
 2M5  C6    C  CH1   0   0.010  48.9477  -22.7083  42.5987
 2M5  O6    O  OH1   0  -0.671  48.5363  -21.4898  42.0157
 2M5  CAI   C  CH3   0  -0.688  47.8191  -23.3889  43.3619
 2M5  CAN   C  CH3   0  -0.409  48.1110  -26.7760  40.8020
 2M5  H1    H  HCH1  0   0.232  47.8934  -24.9427  38.9959
 2M5  H2    H  HCH1  0   0.230  50.2812  -25.1964  38.1110
 2M5  HO2   H  HOH1  0   0.450  50.2471  -22.8655  37.5856
 2M5  H3    H  HCH1  0   0.214  51.5029  -24.8610  40.1713
 2M5  HO3   H  HOH1  0   0.451  52.7957  -23.0046  39.3759
 2M5  H4    H  HCH1  0   0.224  50.3108  -22.0614  40.2156
 2M5  HO4   H  HOH1  0   0.459  51.6655  -21.8176  41.9264
 2M5  H5    H  HCH1  0   0.225  49.8936  -24.5004  42.0072
 2M5  H61   H  HCH1  0   0.208  49.7702  -22.5400  43.3086
 2M5  HO6   H  HOH1  0   0.451  48.2521  -20.8997  42.7202
 2M5  HAI   H  HCH3  0   0.234  47.4867  -22.7608  44.1906
 2M5  HAIA  H  HCH3  0   0.230  46.9589  -23.5873  42.7233
 2M5  HAIB  H  HCH3  0   0.225  48.1552  -24.3356  43.7878
 2M5  HAN   H  HCH3  0   0.236  48.4532  -27.7911  40.9958
 2M5  HANA  H  HCH3  0   0.218  47.8561  -26.3094  41.7574
 2M5  HANB  H  HCH3  0   0.211  47.2030  -26.8261  40.1913

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
 2M5  C1   O1    single  1.391  0.020  1.391
 2M5  C1   C2    single  1.527  0.020  1.527
 2M5  C1   O5    single  1.397  0.020  1.397
 2M5  O1   CAN   single  1.412  0.020  1.412
 2M5  C2   O2    single  1.406  0.020  1.406
 2M5  C2   C3    single  1.527  0.020  1.527
 2M5  C3   O3    single  1.408  0.020  1.408
 2M5  C3   C4    single  1.523  0.020  1.523
 2M5  C4   O4    single  1.411  0.020  1.411
 2M5  C4   C5    single  1.533  0.020  1.533
 2M5  C5   O5    single  1.419  0.020  1.419
 2M5  C5   C6    single  1.522  0.020  1.522
 2M5  C6   O6    single  1.412  0.020  1.412
 2M5  C6   CAI   single  1.523  0.020  1.523
 2M5  C1   H1    single  0.970  0.020  1.090
 2M5  C2   H2    single  0.970  0.020  1.090
 2M5  O2   HO2   single  0.850  0.020  0.980
 2M5  C3   H3    single  0.970  0.020  1.090
 2M5  O3   HO3   single  0.850  0.020  0.980
 2M5  C4   H4    single  0.970  0.020  1.090
 2M5  O4   HO4   single  0.850  0.020  0.980
 2M5  C5   H5    single  0.970  0.020  1.090
 2M5  C6   H61   single  0.970  0.020  1.090
 2M5  O6   HO6   single  0.850  0.020  0.980
 2M5  CAI  HAI   single  0.970  0.020  1.090
 2M5  CAI  HAIA  single  0.970  0.020  1.090
 2M5  CAI  HAIB  single  0.970  0.020  1.090
 2M5  CAN  HAN   single  0.970  0.020  1.090
 2M5  CAN  HANA  single  0.970  0.020  1.090
 2M5  CAN  HANB  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
 2M5  H1    C1   O5    104.80  3.000
 2M5  H1    C1   C2    109.63  3.000
 2M5  O5    C1   C2    111.75  3.000
 2M5  H1    C1   O1    110.48  3.000
 2M5  O5    C1   O1    112.97  3.000
 2M5  C2    C1   O1    107.23  3.000
 2M5  CAN   O1   C1    114.41  3.000
 2M5  H2    C2   C3    109.10  3.000
 2M5  H2    C2   O2    110.96  3.000
 2M5  C3    C2   O2    111.65  3.000
 2M5  H2    C2   C1    108.17  3.000
 2M5  C3    C2   C1    110.04  3.000
 2M5  O2    C2   C1    106.84  3.000
 2M5  HO2   O2   C2    107.67  3.000
 2M5  H3    C3   C4    108.05  3.000
 2M5  H3    C3   O3    110.77  3.000
 2M5  C4    C3   O3    112.23  3.000
 2M5  H3    C3   C2    108.26  3.000
 2M5  C4    C3   C2    110.27  3.000
 2M5  O3    C3   C2    107.21  3.000
 2M5  HO3   O3   C3    108.25  3.000
 2M5  H4    C4   C5    109.33  3.000
 2M5  H4    C4   O4    110.99  3.000
 2M5  C5    C4   O4    111.77  3.000
 2M5  H4    C4   C3    108.83  3.000
 2M5  C5    C4   C3    108.66  3.000
 2M5  O4    C4   C3    107.17  3.000
 2M5  HO4   O4   C4    108.91  3.000
 2M5  H5    C5   C6    106.15  3.000
 2M5  H5    C5   O5    110.61  3.000
 2M5  C6    C5   O5    108.45  3.000
 2M5  H5    C5   C4    108.13  3.000
 2M5  C6    C5   C4    114.10  3.000
 2M5  O5    C5   C4    109.36  3.000
 2M5  C5    O5   C1    115.17  3.000
 2M5  H61   C6   CAI   107.40  3.000
 2M5  H61   C6   O6    110.64  3.000
 2M5  CAI   C6   O6    112.13  3.000
 2M5  H61   C6   C5    106.10  3.000
 2M5  CAI   C6   C5    111.94  3.000
 2M5  O6    C6   C5    108.47  3.000
 2M5  HO6   O6   C6    108.25  3.000
 2M5  HAIB  CAI  HAIA  108.30  3.000
 2M5  HAIB  CAI  HAI   107.26  3.000
 2M5  HAIA  CAI  HAI   108.02  3.000
 2M5  HAIB  CAI  C6    110.80  3.000
 2M5  HAIA  CAI  C6    111.88  3.000
 2M5  HAI   CAI  C6    110.42  3.000
 2M5  HANB  CAN  HANA  108.27  3.000
 2M5  HANB  CAN  HAN   108.49  3.000
 2M5  HANA  CAN  HAN   108.40  3.000
 2M5  HANB  CAN  O1    111.59  3.000
 2M5  HANA  CAN  O1    112.62  3.000
 2M5  HAN   CAN  O1    107.35  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
 2M5  Var_01  HAN  CAN  O1  C1  170.12  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
 2M5  chir_01  C1  O1  C2  O5   positiv
 2M5  chir_02  C2  O2  C1  C3   positiv
 2M5  chir_03  C3  O3  C2  C4   positiv
 2M5  chir_04  C4  O4  C5  C3   positiv
 2M5  chir_05  C5  O5  C6  C4   positiv
 2M5  chir_06  C6  O6  C5  CAI  positiv

