# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:52:51 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl beta-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
 YZ0  YZ0  'methyl beta-D-mannopyranoside'  D-saccharide  27  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YZ0
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
 YZ0  C1    C  CR16  0   0.308  21.8811  68.6879  13.4329
 YZ0  C1M   C  CH3   0  -0.410  23.2451  70.4479  14.1732
 YZ0  C2    C  CR16  0  -0.087  20.8019  68.3623  12.3864
 YZ0  C3    C  CR16  0   0.017  20.7910  66.8559  12.1753
 YZ0  C4    C  CR16  0  -0.013  22.1232  66.4111  11.5844
 YZ0  C5    C  CR16  0  -0.031  23.3006  67.0261  12.3741
 YZ0  C6    C  CH2   0  -0.175  24.1828  67.8774  11.4757
 YZ0  O1    O  O2    0  -0.485  22.3971  69.9441  13.1629
 YZ0  O2    O  OH1   0  -0.657  21.0494  69.0512  11.1859
 YZ0  O3    O  OH1   0  -0.673  19.7136  66.5463  11.3231
 YZ0  O4    O  OH1   0  -0.677  22.1273  64.9976  11.6009
 YZ0  O5    O  O     0  -0.502  22.8653  67.6966  13.5433
 YZ0  O6    O  OH1   0  -0.668  25.2971  68.3244  12.2092
 YZ0  H1    H  HCR6  0   0.227  21.4019  68.6831  14.4229
 YZ0  H1M1  H  HCH3  0   0.232  23.4827  71.4779  13.9118
 YZ0  H1M2  H  HCH3  0   0.219  24.1763  69.8839  14.2468
 YZ0  H1M3  H  HCH3  0   0.205  22.7538  70.4449  15.1531
 YZ0  H2    H  HCR6  0   0.246  19.8340  68.6679  12.8071
 YZ0  HO2   H  HOH1  0   0.452  20.4071  68.7406  10.5384
 YZ0  H3    H  HCR6  0   0.222  20.6605  66.3720  13.1551
 YZ0  HO3   H  HOH1  0   0.453  19.7924  65.6229  11.0600
 YZ0  H4    H  HCR6  0   0.227  22.1629  66.7651  10.5463
 YZ0  HO4   H  HOH1  0   0.456  22.7682  64.6837  10.9563
 YZ0  H5    H  HCR6  0   0.248  23.9075  66.1988  12.7556
 YZ0  H62   H  HCH2  0   0.215  23.6083  68.7079  11.0562
 YZ0  H61   H  HCH2  0   0.197  24.4873  67.2440  10.6287
 YZ0  HO6   H  HOH1  0   0.455  25.7171  69.0324  11.7141

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
 YZ0  C1   O5    single  1.401  0.020  1.401
 YZ0  C1   O1    single  1.385  0.020  1.385
 YZ0  C1   C2    single  1.538  0.020  1.538
 YZ0  C1   H1    single  0.970  0.020  1.090
 YZ0  C1M  O1    single  1.412  0.020  1.412
 YZ0  C1M  H1M1  single  0.970  0.020  1.090
 YZ0  C1M  H1M3  single  0.970  0.020  1.090
 YZ0  C1M  H1M2  single  0.970  0.020  1.090
 YZ0  C2   O2    single  1.406  0.020  1.406
 YZ0  C2   C3    single  1.521  0.020  1.521
 YZ0  C2   H2    single  0.970  0.020  1.090
 YZ0  C3   O3    single  1.408  0.020  1.408
 YZ0  C3   H3    single  0.970  0.020  1.090
 YZ0  C3   C4    single  1.524  0.020  1.524
 YZ0  C4   H4    single  0.970  0.020  1.090
 YZ0  C4   O4    single  1.414  0.020  1.414
 YZ0  C4   C5    single  1.545  0.020  1.545
 YZ0  C5   O5    single  1.416  0.020  1.416
 YZ0  C5   H5    single  0.970  0.020  1.090
 YZ0  C5   C6    single  1.520  0.020  1.520
 YZ0  C6   H61   single  0.970  0.020  1.090
 YZ0  C6   H62   single  0.970  0.020  1.090
 YZ0  C6   O6    single  1.407  0.020  1.407
 YZ0  O2   HO2   single  0.850  0.020  0.980
 YZ0  O3   HO3   single  0.850  0.020  0.980
 YZ0  O4   HO4   single  0.850  0.020  0.980
 YZ0  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
 YZ0  H1    C1   O5    103.41  3.000
 YZ0  H1    C1   O1    109.99  3.000
 YZ0  O5    C1   O1    113.29  3.000
 YZ0  H1    C1   C2    107.81  3.000
 YZ0  O1    C1   C2    108.72  3.000
 YZ0  O5    C1   C2    113.37  3.000
 YZ0  H1M3  C1M  H1M2  108.71  3.000
 YZ0  H1M2  C1M  H1M1  108.60  3.000
 YZ0  H1M3  C1M  H1M1  108.36  3.000
 YZ0  H1M2  C1M  O1    112.11  3.000
 YZ0  H1M3  C1M  O1    111.68  3.000
 YZ0  H1M1  C1M  O1    107.26  3.000
 YZ0  H2    C2   O2    110.23  3.000
 YZ0  H2    C2   C3    108.80  3.000
 YZ0  O2    C2   C3    111.59  3.000
 YZ0  H2    C2   C1    107.37  3.000
 YZ0  C3    C2   C1    108.00  3.000
 YZ0  O2    C2   C1    110.71  3.000
 YZ0  H3    C3   O3    110.57  3.000
 YZ0  H3    C3   C4    108.70  3.000
 YZ0  O3    C3   C4    111.72  3.000
 YZ0  C4    C3   C2    109.67  3.000
 YZ0  H3    C3   C2    108.23  3.000
 YZ0  O3    C3   C2    107.89  3.000
 YZ0  H4    C4   O4    109.48  3.000
 YZ0  O4    C4   C5    112.94  3.000
 YZ0  H4    C4   C5    109.11  3.000
 YZ0  C5    C4   C3    110.60  3.000
 YZ0  O4    C4   C3    106.85  3.000
 YZ0  H4    C4   C3    107.71  3.000
 YZ0  H5    C5   O5    103.92  3.000
 YZ0  H5    C5   C6    107.91  3.000
 YZ0  O5    C5   C6    113.65  3.000
 YZ0  C6    C5   C4    111.29  3.000
 YZ0  H5    C5   C4    107.44  3.000
 YZ0  O5    C5   C4    112.09  3.000
 YZ0  H61   C6   H62   106.69  3.000
 YZ0  H62   C6   O6    112.01  3.000
 YZ0  H61   C6   O6    111.40  3.000
 YZ0  O6    C6   C5    109.24  3.000
 YZ0  H62   C6   C5    110.32  3.000
 YZ0  H61   C6   C5    107.04  3.000
 YZ0  C1M   O1   C1    114.08  3.000
 YZ0  HO2   O2   C2    107.37  3.000
 YZ0  HO3   O3   C3    108.26  3.000
 YZ0  HO4   O4   C4    108.69  3.000
 YZ0  C5    O5   C1    119.06  3.000
 YZ0  HO6   O6   C6    108.17  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
 YZ0  Var_01  H1M1  C1M  O1  C1  -172.93  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
 YZ0  chir_01  C1  O5  O1  C2  negativ
 YZ0  chir_02  C2  O2  C1  C3  positiv
 YZ0  chir_03  C3  O3  C2  C4  positiv
 YZ0  chir_04  C4  O4  C5  C3  positiv
 YZ0  chir_05  C5  O5  C4  C6  negativ

