# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 22:03:16 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl alpha-D-glucopyranoside
#   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
 GYP  GYP  'methyl alpha-D-glucopyranoside'  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_GYP
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
 GYP  C1    C  CH1   0   0.243  -15.6182  48.0009  -16.0080
 GYP  C2    C  CH1   0   0.004  -14.3555  48.2838  -15.1827
 GYP  C3    C  CH1   0   0.015  -13.2839  47.2509  -15.4956
 GYP  C4    C  CH1   0   0.000  -13.8666  45.8563  -15.2851
 GYP  C5    C  CH1   0  -0.008  -15.1330  45.6799  -16.1256
 GYP  C6    C  CH2   0  -0.197  -15.8110  44.3399  -15.9389
 GYP  O1    O  O2    0  -0.487  -15.3395  48.2625  -17.3418
 GYP  O2    O  OH1   0  -0.659  -13.8435  49.5661  -15.4264
 GYP  O3    O  OH1   0  -0.666  -12.1818  47.4766  -14.6523
 GYP  O4    O  OH1   0  -0.673  -12.8753  44.9240  -15.6567
 GYP  O5    O  O2    0  -0.502  -16.0707  46.6937  -15.7943
 GYP  O6    O  OH1   0  -0.667  -16.0896  44.1258  -14.5761
 GYP  H1    H  HCH1  0   0.228  -16.4411  48.6422  -15.6567
 GYP  H2    H  HCH1  0   0.220  -14.6410  48.1649  -14.1265
 GYP  H3    H  HCH1  0   0.208  -12.9884  47.3467  -16.5525
 GYP  H4    H  HCH1  0   0.225  -14.1223  45.7547  -14.2222
 GYP  H5    H  HCH1  0   0.227  -14.8569  45.7407  -17.1878
 GYP  H61   H  HCH2  0   0.217  -16.7229  44.3286  -16.5508
 GYP  H62   H  HCH2  0   0.206  -15.1516  43.5663  -16.3507
 GYP  H7C1  H  HCH3  0   0.215  -16.9093  47.2779  -18.3116
 GYP  H7C2  H  HCH3  0   0.210  -17.2475  48.9458  -17.8124
 GYP  H7C3  H  HCH3  0   0.235  -16.1436  48.6278  -19.1622
 GYP  HO2   H  HOH1  0   0.452  -14.4661  50.2147  -15.0830
 GYP  HO3   H  HOH1  0   0.445  -11.5428  46.7755  -14.8197
 GYP  HO4   H  HOH1  0   0.459  -12.9920  44.1221  -15.1395
 GYP  HO6   H  HOH1  0   0.456  -16.4676  43.2473  -14.4805
 GYP  C7    C  CH3   0  -0.406  -16.4694  48.2711  -18.1864

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
 GYP  C1  C2    single  1.535  0.020  1.535
 GYP  C1  O1    single  1.387  0.020  1.387
 GYP  C1  O5    single  1.400  0.020  1.400
 GYP  C1  H1    single  0.970  0.020  1.090
 GYP  C2  C3    single  1.521  0.020  1.521
 GYP  C2  O2    single  1.402  0.020  1.402
 GYP  C2  H2    single  0.970  0.020  1.090
 GYP  C3  C4    single  1.526  0.020  1.526
 GYP  C3  O3    single  1.406  0.020  1.406
 GYP  C3  H3    single  0.970  0.020  1.090
 GYP  C4  C5    single  1.530  0.020  1.530
 GYP  C4  O4    single  1.411  0.020  1.411
 GYP  C4  H4    single  0.970  0.020  1.090
 GYP  C5  C6    single  1.513  0.020  1.513
 GYP  C5  O5    single  1.420  0.020  1.420
 GYP  C5  H5    single  0.970  0.020  1.090
 GYP  C6  O6    single  1.407  0.020  1.407
 GYP  C6  H61   single  0.970  0.020  1.090
 GYP  C6  H62   single  0.970  0.020  1.090
 GYP  C7  O1    single  1.411  0.020  1.411
 GYP  C7  H7C1  single  0.970  0.020  1.090
 GYP  C7  H7C2  single  0.970  0.020  1.090
 GYP  C7  H7C3  single  0.970  0.020  1.090
 GYP  O2  HO2   single  0.850  0.020  0.980
 GYP  O3  HO3   single  0.850  0.020  0.980
 GYP  O4  HO4   single  0.850  0.020  0.980
 GYP  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
 GYP  H1    C1  O5    104.70  3.000
 GYP  H1    C1  O1    110.31  3.000
 GYP  O5    C1  O1    112.82  3.000
 GYP  H1    C1  C2    109.63  3.000
 GYP  O5    C1  C2    110.86  3.000
 GYP  O1    C1  C2    108.48  3.000
 GYP  H2    C2  O2    111.12  3.000
 GYP  H2    C2  C3    107.87  3.000
 GYP  O2    C2  C3    109.15  3.000
 GYP  H2    C2  C1    106.42  3.000
 GYP  O2    C2  C1    112.06  3.000
 GYP  C3    C2  C1    110.11  3.000
 GYP  H3    C3  O3    110.57  3.000
 GYP  H3    C3  C4    108.32  3.000
 GYP  O3    C3  C4    111.30  3.000
 GYP  H3    C3  C2    109.11  3.000
 GYP  O3    C3  C2    108.65  3.000
 GYP  C4    C3  C2    108.85  3.000
 GYP  H4    C4  O4    110.94  3.000
 GYP  H4    C4  C5    109.17  3.000
 GYP  O4    C4  C5    111.14  3.000
 GYP  H4    C4  C3    107.89  3.000
 GYP  O4    C4  C3    107.41  3.000
 GYP  C5    C4  C3    110.22  3.000
 GYP  H5    C5  O5    110.60  3.000
 GYP  H5    C5  C6    106.31  3.000
 GYP  O5    C5  C6    107.91  3.000
 GYP  H5    C5  C4    108.46  3.000
 GYP  O5    C5  C4    109.64  3.000
 GYP  C6    C5  C4    113.90  3.000
 GYP  H62   C6  H61   106.43  3.000
 GYP  H62   C6  O6    112.04  3.000
 GYP  H61   C6  O6    111.94  3.000
 GYP  H62   C6  C5    107.99  3.000
 GYP  H61   C6  C5    108.21  3.000
 GYP  O6    C6  C5    110.05  3.000
 GYP  C7    O1  C1    114.57  3.000
 GYP  HO2   O2  C2    108.54  3.000
 GYP  HO3   O3  C3    107.39  3.000
 GYP  HO4   O4  C4    108.92  3.000
 GYP  C5    O5  C1    114.68  3.000
 GYP  HO6   O6  C6    108.25  3.000
 GYP  H7C3  C7  H7C2  108.46  3.000
 GYP  H7C3  C7  H7C1  108.39  3.000
 GYP  H7C2  C7  H7C1  108.22  3.000
 GYP  H7C3  C7  O1    107.39  3.000
 GYP  H7C2  C7  O1    111.60  3.000
 GYP  H7C1  C7  O1    112.66  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
 GYP  Var_01  H7C1  C7  O1  C1  -68.89  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
 GYP  chir_01  C1  C2  O1  O5  negativ
 GYP  chir_02  C2  O2  C1  C3  negativ
 GYP  chir_03  C3  O3  C2  C4  positiv
 GYP  chir_04  C4  O4  C5  C3  positiv
 GYP  chir_05  C5  O5  C4  C6  negativ

