# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:46:08 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 7-deoxy-L-glycero-alpha-D-manno-heptopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 YYH  YYH  7-deoxy-L-glycero-alpha-D-manno-heptopyranose  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 PERFECT
;

data_comp_YYH
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
 YYH  O6    O  OH1   0  -0.676  15.8358   -8.0769  -58.5709
 YYH  C1    C  CH1   0   0.246  12.5943  -10.6361  -58.7142
 YYH  C2    C  CH1   0  -0.046  11.5443   -9.5707  -58.3836
 YYH  C3    C  CH1   0   0.009  11.6509   -8.4053  -59.3613
 YYH  C4    C  CH1   0   0.009  13.0812   -7.8839  -59.3864
 YYH  C5    C  CH1   0   0.018  14.0139   -9.0399  -59.7615
 YYH  C6    C  CH1   0   0.010  15.4820   -8.6465  -59.8150
 YYH  C6M   C  CH3   0  -0.688  16.3826   -9.8188  -60.1772
 YYH  O1    O  OH1   0  -0.666  12.2979  -11.2945  -59.9152
 YYH  O2    O  OH1   0  -0.670  11.7828   -9.1643  -57.0584
 YYH  O3    O  OH1   0  -0.677  10.7313   -7.4203  -58.9526
 YYH  O4    O  OH1   0  -0.679  13.1427   -6.8433  -60.3392
 YYH  O5    O  O2    0  -0.498  13.8666  -10.0943  -58.8223
 YYH  H1    H  HCH1  0   0.230  12.6481  -11.3477  -57.8794
 YYH  HO1   H  HOH1  0   0.459  11.4097  -11.6633  -59.8635
 YYH  H2    H  HCH1  0   0.233  10.5449  -10.0241  -58.4739
 YYH  HO2   H  HOH1  0   0.452  11.2030   -8.4193  -56.8683
 YYH  H3    H  HCH1  0   0.212  11.4029   -8.7758  -60.3674
 YYH  HO3   H  HOH1  0   0.452  10.9030   -6.6234  -59.4662
 YYH  H4    H  HCH1  0   0.229  13.3409   -7.5160  -58.3880
 YYH  HO4   H  HOH1  0   0.460  13.7982   -6.2006  -60.0542
 YYH  H5    H  HCH1  0   0.228  13.7463   -9.3799  -60.7715
 YYH  H61   H  HCH1  0   0.212  15.5668   -7.9024  -60.6190
 YYH  H6M1  H  HCH3  0   0.226  16.0850  -10.2593  -61.1300
 YYH  H6M2  H  HCH3  0   0.232  16.3572  -10.5985  -59.4168
 YYH  H6M3  H  HCH3  0   0.233  17.4154   -9.4820  -60.2841
 YYH  HO6   H  HOH1  0   0.453  16.7354   -7.7436  -58.6400

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
 YYH  O6   C6    single  1.413  0.020  1.413
 YYH  O6   HO6   single  0.850  0.020  0.980
 YYH  C1   O5    single  1.387  0.020  1.387
 YYH  C1   H1    single  0.970  0.020  1.090
 YYH  C1   O1    single  1.401  0.020  1.401
 YYH  C1   C2    single  1.532  0.020  1.532
 YYH  C2   H2    single  0.970  0.020  1.090
 YYH  C2   C3    single  1.525  0.020  1.525
 YYH  C2   O2    single  1.407  0.020  1.407
 YYH  C3   C4    single  1.523  0.020  1.523
 YYH  C3   H3    single  0.970  0.020  1.090
 YYH  C3   O3    single  1.408  0.020  1.408
 YYH  C4   O4    single  1.412  0.020  1.412
 YYH  C4   C5    single  1.532  0.020  1.532
 YYH  C4   H4    single  0.970  0.020  1.090
 YYH  C5   O5    single  1.420  0.020  1.420
 YYH  C5   C6    single  1.521  0.020  1.521
 YYH  C5   H5    single  0.970  0.020  1.090
 YYH  C6   C6M   single  1.522  0.020  1.522
 YYH  C6   H61   single  0.970  0.020  1.090
 YYH  C6M  H6M1  single  0.970  0.020  1.090
 YYH  C6M  H6M3  single  0.970  0.020  1.090
 YYH  C6M  H6M2  single  0.970  0.020  1.090
 YYH  O1   HO1   single  0.850  0.020  0.980
 YYH  O2   HO2   single  0.850  0.020  0.980
 YYH  O3   HO3   single  0.850  0.020  0.980
 YYH  O4   HO4   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
 YYH  HO6   O6   C6    108.09  3.000
 YYH  H1    C1   O5    105.51  3.000
 YYH  H1    C1   O1    110.94  3.000
 YYH  O5    C1   O1    108.11  3.000
 YYH  O1    C1   C2    111.51  3.000
 YYH  H1    C1   C2    108.67  3.000
 YYH  O5    C1   C2    111.95  3.000
 YYH  H2    C2   O2    110.50  3.000
 YYH  O2    C2   C3    111.80  3.000
 YYH  H2    C2   C3    109.00  3.000
 YYH  O2    C2   C1    106.74  3.000
 YYH  C3    C2   C1    110.20  3.000
 YYH  H2    C2   C1    108.54  3.000
 YYH  H3    C3   O3    110.71  3.000
 YYH  O3    C3   C4    112.26  3.000
 YYH  H3    C3   C4    108.17  3.000
 YYH  O3    C3   C2    107.63  3.000
 YYH  H3    C3   C2    108.25  3.000
 YYH  C4    C3   C2    109.75  3.000
 YYH  H4    C4   O4    110.93  3.000
 YYH  H4    C4   C5    109.41  3.000
 YYH  O4    C4   C5    111.36  3.000
 YYH  H4    C4   C3    108.83  3.000
 YYH  C5    C4   C3    108.51  3.000
 YYH  O4    C4   C3    107.72  3.000
 YYH  H5    C5   O5    110.67  3.000
 YYH  H5    C5   C6    106.43  3.000
 YYH  O5    C5   C6    108.39  3.000
 YYH  H5    C5   C4    108.08  3.000
 YYH  C6    C5   C4    113.65  3.000
 YYH  O5    C5   C4    109.59  3.000
 YYH  H61   C6   C6M   107.56  3.000
 YYH  H61   C6   C5    105.99  3.000
 YYH  C6M   C6   C5    112.35  3.000
 YYH  H61   C6   O6    110.61  3.000
 YYH  C6M   C6   O6    111.83  3.000
 YYH  C5    C6   O6    108.36  3.000
 YYH  H6M3  C6M  H6M2  108.13  3.000
 YYH  H6M2  C6M  H6M1  108.32  3.000
 YYH  H6M3  C6M  H6M1  107.28  3.000
 YYH  H6M2  C6M  C6    111.80  3.000
 YYH  H6M3  C6M  C6    110.21  3.000
 YYH  H6M1  C6M  C6    110.94  3.000
 YYH  HO1   O1   C1    109.21  3.000
 YYH  HO2   O2   C2    107.90  3.000
 YYH  HO3   O3   C3    107.90  3.000
 YYH  HO4   O4   C4    108.80  3.000
 YYH  C5    O5   C1    115.90  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
 YYH  chir_01  C1  O5  O1  C2   positiv
 YYH  chir_02  C2  O2  C1  C3   positiv
 YYH  chir_03  C3  O3  C2  C4   positiv
 YYH  chir_04  C4  O4  C3  C5   negativ
 YYH  chir_05  C5  O5  C6  C4   positiv
 YYH  chir_06  C6  O6  C5  C6M  positiv

