# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:54:50 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 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]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
 MMA  MMA  'methyl alpha-D-mannopyranoside'  D-saccharide  27  13  .  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_MMA
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
 MMA  C1   C  CH1   0   0.262  27.9879  130.6400  -21.4761
 MMA  C2   C  CH1   0  -0.017  27.0956  129.5176  -22.0021
 MMA  C3   C  CH1   0   0.003  26.2741  128.9229  -20.8621
 MMA  C4   C  CH1   0   0.011  27.1899  128.5099  -19.7178
 MMA  C5   C  CH1   0  -0.010  28.0183  129.7232  -19.2795
 MMA  C6   C  CH2   0  -0.194  28.9979  129.4309  -18.1639
 MMA  O1   O  O2    0  -0.495  27.1636  131.7198  -21.1795
 MMA  O2   O  OH1   0  -0.668  27.9488  128.5600  -22.5803
 MMA  O3   O  OH1   0  -0.672  25.5562  127.8308  -21.3860
 MMA  O4   O  OH1   0  -0.674  26.3676  128.0375  -18.6721
 MMA  O5   O  O2    0  -0.499  28.7552  130.2269  -20.3844
 MMA  O6   O  OH1   0  -0.667  29.8819  128.4093  -18.5560
 MMA  H1   H  HCH1  0   0.232  28.7224  130.9161  -22.2466
 MMA  H2   H  HCH1  0   0.232  26.4152  129.9440  -22.7527
 MMA  H3   H  HCH1  0   0.213  25.5874  129.6980  -20.4896
 MMA  H4   H  HCH1  0   0.224  27.8620  127.7208  -20.0737
 MMA  H5   H  HCH1  0   0.226  27.3310  130.4881  -18.8896
 MMA  H61  H  HCH2  0   0.215  29.5303  130.3598  -17.9191
 MMA  H62  H  HCH2  0   0.206  28.4212  129.1593  -17.2713
 MMA  H71  H  HCH3  0   0.236  27.1187  133.7089  -20.8113
 MMA  H72  H  HCH3  0   0.217  28.3376  132.8454  -19.8638
 MMA  H73  H  HCH3  0   0.211  28.6123  133.1569  -21.5890
 MMA  HO2  H  HOH1  0   0.450  27.4191  127.7829  -22.7880
 MMA  HO3  H  HOH1  0   0.450  25.1657  127.3495  -20.6484
 MMA  HO4  H  HOH1  0   0.459  26.8630  127.4015  -18.1478
 MMA  HO6  H  HOH1  0   0.456  30.4314  128.1805  -17.8015
 MMA  C7   C  CH3   0  -0.406  27.8521  132.9049  -20.8416

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
 MMA  C1  C2   single  1.527  0.020  1.527
 MMA  C1  O1   single  1.390  0.020  1.390
 MMA  C1  O5   single  1.397  0.020  1.397
 MMA  C1  H1   single  0.970  0.020  1.090
 MMA  C2  C3   single  1.526  0.020  1.526
 MMA  C2  O2   single  1.407  0.020  1.407
 MMA  C2  H2   single  0.970  0.020  1.090
 MMA  C3  C4   single  1.523  0.020  1.523
 MMA  C3  O3   single  1.408  0.020  1.408
 MMA  C3  H3   single  0.970  0.020  1.090
 MMA  C4  C5   single  1.533  0.020  1.533
 MMA  C4  O4   single  1.412  0.020  1.412
 MMA  C4  H4   single  0.970  0.020  1.090
 MMA  C5  C6   single  1.513  0.020  1.513
 MMA  C5  O5   single  1.420  0.020  1.420
 MMA  C5  H5   single  0.970  0.020  1.090
 MMA  C6  O6   single  1.407  0.020  1.407
 MMA  C6  H61  single  0.970  0.020  1.090
 MMA  C6  H62  single  0.970  0.020  1.090
 MMA  C7  O1   single  1.412  0.020  1.412
 MMA  C7  H71  single  0.970  0.020  1.090
 MMA  C7  H72  single  0.970  0.020  1.090
 MMA  C7  H73  single  0.970  0.020  1.090
 MMA  O2  HO2  single  0.850  0.020  0.980
 MMA  O3  HO3  single  0.850  0.020  0.980
 MMA  O4  HO4  single  0.850  0.020  0.980
 MMA  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
 MMA  H1   C1  O5   104.77  3.000
 MMA  H1   C1  O1   110.51  3.000
 MMA  O5   C1  O1   112.87  3.000
 MMA  H1   C1  C2   109.47  3.000
 MMA  O5   C1  C2   111.89  3.000
 MMA  O1   C1  C2   107.33  3.000
 MMA  H2   C2  O2   111.02  3.000
 MMA  H2   C2  C3   109.16  3.000
 MMA  O2   C2  C3   111.61  3.000
 MMA  H2   C2  C1   108.16  3.000
 MMA  O2   C2  C1   106.70  3.000
 MMA  C3   C2  C1   110.10  3.000
 MMA  H3   C3  O3   110.74  3.000
 MMA  H3   C3  C4   108.17  3.000
 MMA  O3   C3  C4   112.08  3.000
 MMA  H3   C3  C2   108.32  3.000
 MMA  O3   C3  C2   107.39  3.000
 MMA  C4   C3  C2   110.08  3.000
 MMA  H4   C4  O4   110.90  3.000
 MMA  H4   C4  C5   109.34  3.000
 MMA  O4   C4  C5   111.58  3.000
 MMA  H4   C4  C3   108.67  3.000
 MMA  O4   C4  C3   107.29  3.000
 MMA  C5   C4  C3   108.98  3.000
 MMA  H5   C5  O5   110.70  3.000
 MMA  H5   C5  C6   106.12  3.000
 MMA  O5   C5  C6   107.83  3.000
 MMA  H5   C5  C4   108.30  3.000
 MMA  O5   C5  C4   109.79  3.000
 MMA  C6   C5  C4   114.06  3.000
 MMA  H62  C6  H61  106.43  3.000
 MMA  H62  C6  O6   112.18  3.000
 MMA  H61  C6  O6   111.83  3.000
 MMA  H62  C6  C5   107.90  3.000
 MMA  H61  C6  C5   108.34  3.000
 MMA  O6   C6  C5   109.98  3.000
 MMA  C7   O1  C1   114.45  3.000
 MMA  HO2  O2  C2   107.72  3.000
 MMA  HO3  O3  C3   108.02  3.000
 MMA  HO4  O4  C4   108.98  3.000
 MMA  C5   O5  C1   115.33  3.000
 MMA  HO6  O6  C6   108.27  3.000
 MMA  H73  C7  H72  108.33  3.000
 MMA  H73  C7  H71  108.46  3.000
 MMA  H72  C7  H71  108.33  3.000
 MMA  H73  C7  O1   111.61  3.000
 MMA  H72  C7  O1   112.64  3.000
 MMA  H71  C7  O1   107.34  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
 MMA  Var_01  H71  C7  O1  C1  169.88  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
 MMA  chir_01  C1  C2  O1  O5  negativ
 MMA  chir_02  C2  O2  C1  C3  positiv
 MMA  chir_03  C3  O3  C2  C4  positiv
 MMA  chir_04  C4  O4  C5  C3  positiv
 MMA  chir_05  C5  O5  C4  C6  negativ

