# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 15:10:49 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: L-glycero-alpha-D-manno-heptopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@H]1O[C@H](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
 GMH  GMH  L-glycero-alpha-D-manno-heptopyranose  D-saccharide  28  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 PERFECT
;

data_comp_GMH
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
 GMH  C1   C  CH1   0   0.230  58.5628  63.4147  56.5314
 GMH  C2   C  CH1   0  -0.011  58.5275  61.9287  56.1865
 GMH  C3   C  CH1   0   0.000  57.5112  61.2136  57.0713
 GMH  C4   C  CH1   0   0.008  57.7980  61.4987  58.5403
 GMH  C5   C  CH1   0   0.010  57.8227  63.0168  58.7599
 GMH  C6   C  CH1   0  -0.017  58.1503  63.4118  60.1904
 GMH  C7   C  CH2   0  -0.165  58.1258  64.9208  60.3797
 GMH  O1   O  OH1   0  -0.663  57.3679  63.9730  56.0864
 GMH  O2   O  OH1   0  -0.668  59.8293  61.4330  56.3824
 GMH  O3   O  OH1   0  -0.672  57.5880  59.8393  56.7751
 GMH  O4   O  OH1   0  -0.674  56.7730  60.8841  59.2916
 GMH  O5   O  O2    0  -0.504  58.7783  63.6146  57.9007
 GMH  O6   O  OH1   0  -0.672  59.3992  62.8693  60.5488
 GMH  O7   O  OH1   0  -0.672  58.3301  65.1729  61.7545
 GMH  H1   H  HCH1  0   0.235  59.4276  63.8812  56.0446
 GMH  H2   H  HCH1  0   0.232  58.2229  61.8262  55.1350
 GMH  H3   H  HCH1  0   0.214  56.5109  61.6078  56.8365
 GMH  H4   H  HCH1  0   0.226  58.7776  61.0791  58.7958
 GMH  H5   H  HCH1  0   0.225  56.8159  63.4060  58.5510
 GMH  H6   H  HCH1  0   0.211  57.3468  62.9956  60.8186
 GMH  H71  H  HCH2  0   0.209  58.9063  65.3864  59.7694
 GMH  H72  H  HCH2  0   0.194  57.1591  65.3125  60.0363
 GMH  HO1  H  HOH1  0   0.460  57.4253  64.9325  56.1519
 GMH  HO2  H  HOH1  0   0.450  59.7926  60.4734  56.3080
 GMH  HO3  H  HOH1  0   0.450  57.0698  59.3624  57.4326
 GMH  HO4  H  HOH1  0   0.459  57.1133  60.6601  60.1625
 GMH  HO6  H  HOH1  0   0.447  59.6132  63.1925  61.4304
 GMH  HO7  H  HOH1  0   0.457  58.6089  66.0863  61.8614

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
 GMH  C1  C2   single  1.526  0.020  1.526
 GMH  C1  O1   single  1.392  0.020  1.392
 GMH  C1  O5   single  1.401  0.020  1.401
 GMH  C1  H1   single  0.970  0.020  1.090
 GMH  C2  C3   single  1.525  0.020  1.525
 GMH  C2  O2   single  1.407  0.020  1.407
 GMH  C2  H2   single  0.970  0.020  1.090
 GMH  C3  C4   single  1.524  0.020  1.524
 GMH  C3  O3   single  1.408  0.020  1.408
 GMH  C3  H3   single  0.970  0.020  1.090
 GMH  C4  C5   single  1.534  0.020  1.534
 GMH  C4  O4   single  1.412  0.020  1.412
 GMH  C4  H4   single  0.970  0.020  1.090
 GMH  C5  C6   single  1.520  0.020  1.520
 GMH  C5  O5   single  1.417  0.020  1.417
 GMH  C5  H5   single  0.970  0.020  1.090
 GMH  C6  C7   single  1.521  0.020  1.521
 GMH  C6  O6   single  1.408  0.020  1.408
 GMH  C6  H6   single  0.970  0.020  1.090
 GMH  C7  O7   single  1.413  0.020  1.413
 GMH  C7  H71  single  0.970  0.020  1.090
 GMH  C7  H72  single  0.970  0.020  1.090
 GMH  O1  HO1  single  0.850  0.020  0.980
 GMH  O2  HO2  single  0.850  0.020  0.980
 GMH  O3  HO3  single  0.850  0.020  0.980
 GMH  O4  HO4  single  0.850  0.020  0.980
 GMH  O6  HO6  single  0.850  0.020  0.980
 GMH  O7  HO7  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
 GMH  H1   C1  O5   104.59  3.000
 GMH  H1   C1  O1   111.37  3.000
 GMH  O5   C1  O1   112.80  3.000
 GMH  H1   C1  C2   109.40  3.000
 GMH  O5   C1  C2   111.32  3.000
 GMH  O1   C1  C2   107.37  3.000
 GMH  H2   C2  O2   110.90  3.000
 GMH  H2   C2  C3   109.05  3.000
 GMH  O2   C2  C3   111.75  3.000
 GMH  H2   C2  C1   108.27  3.000
 GMH  O2   C2  C1   106.88  3.000
 GMH  C3   C2  C1   109.93  3.000
 GMH  H3   C3  O3   110.75  3.000
 GMH  H3   C3  C4   108.04  3.000
 GMH  O3   C3  C4   112.04  3.000
 GMH  H3   C3  C2   108.29  3.000
 GMH  O3   C3  C2   107.41  3.000
 GMH  C4   C3  C2   110.25  3.000
 GMH  H4   C4  O4   111.00  3.000
 GMH  H4   C4  C5   109.34  3.000
 GMH  O4   C4  C5   111.49  3.000
 GMH  H4   C4  C3   108.74  3.000
 GMH  O4   C4  C3   107.15  3.000
 GMH  C5   C4  C3   109.04  3.000
 GMH  H5   C5  O5   110.66  3.000
 GMH  H5   C5  C6   106.52  3.000
 GMH  O5   C5  C6   108.40  3.000
 GMH  H5   C5  C4   107.96  3.000
 GMH  O5   C5  C4   109.97  3.000
 GMH  C6   C5  C4   113.29  3.000
 GMH  H6   C6  O6   110.88  3.000
 GMH  H6   C6  C7   106.98  3.000
 GMH  O6   C6  C7   111.40  3.000
 GMH  H6   C6  C5   106.34  3.000
 GMH  O6   C6  C5   109.31  3.000
 GMH  C7   C6  C5   111.81  3.000
 GMH  H72  C7  H71  107.56  3.000
 GMH  H72  C7  O7   111.59  3.000
 GMH  H71  C7  O7   111.32  3.000
 GMH  H72  C7  C6   109.22  3.000
 GMH  H71  C7  C6   109.94  3.000
 GMH  O7   C7  C6   107.21  3.000
 GMH  HO1  O1  C1   109.06  3.000
 GMH  HO2  O2  C2   107.76  3.000
 GMH  HO3  O3  C3   108.07  3.000
 GMH  HO4  O4  C4   109.06  3.000
 GMH  C5   O5  C1   115.39  3.000
 GMH  HO6  O6  C6   107.51  3.000
 GMH  HO7  O7  C7   108.65  3.000

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
 GMH  chir_01  C1  C2  O1  O5  negativ
 GMH  chir_02  C2  O2  C1  C3  positiv
 GMH  chir_03  C3  O3  C2  C4  positiv
 GMH  chir_04  C4  O4  C5  C3  positiv
 GMH  chir_05  C5  O5  C6  C4  positiv
 GMH  chir_06  C6  O6  C5  C7  positiv

