# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:02:55 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)C[C@](C)(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
 MDA  MDA  2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose  D-saccharide  25  11  .  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_MDA
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
 MDA  C1    C  CH1   0   0.304  6.3212  6.3765  16.4705
 MDA  C2    C  CH2   0  -0.502  6.2288  7.6955  15.7300
 MDA  C3    C  CT    0   0.150  6.4627  7.5048  14.2282
 MDA  C4    C  CH1   0   0.077  7.7860  6.7416  14.0407
 MDA  C5    C  CH1   0   0.028  7.8217  5.4599  14.8816
 MDA  C6    C  CH3   0  -0.680  9.1679  4.7654  14.8173
 MDA  C3'   C  CH3   0  -0.682  6.5144  8.8603  13.5294
 MDA  O1    O  OH1   0  -0.658  6.2025  6.6138  17.8284
 MDA  O5    O  O2    0  -0.503  7.5778  5.7799  16.2383
 MDA  O3    O  OH1   0  -0.672  5.4430  6.6970  13.6671
 MDA  O4    O  OH1   0  -0.672  8.0157  6.3836  12.7004
 MDA  H1    H  HCH1  0   0.175  5.5332  5.6924  16.1162
 MDA  H2    H  HCH2  0   0.236  6.9746  8.3851  16.1369
 MDA  H22   H  HCH2  0   0.245  5.2467  8.1508  15.8932
 MDA  H4    H  HCH1  0   0.207  8.5872  7.3950  14.4191
 MDA  H5    H  HCH1  0   0.207  7.0462  4.7707  14.5142
 MDA  H61   H  HCH3  0   0.235  9.1748  3.8829  15.4580
 MDA  H62   H  HCH3  0   0.234  9.3877  4.4391  13.8029
 MDA  H63   H  HCH3  0   0.221  9.9699  5.4309  15.1430
 MDA  H3'1  H  HCH3  0   0.234  6.6414  8.7510  12.4514
 MDA  H3'2  H  HCH3  0   0.235  5.5880  9.4148  13.6971
 MDA  H3'3  H  HCH3  0   0.227  7.3346  9.4696  13.9109
 MDA  HO1   H  HOH1  0   0.455  6.0525  5.7781  18.2835
 MDA  HO3   H  HOH1  0   0.445  4.5993  7.1402  13.8068
 MDA  HO4   H  HOH1  0   0.453  8.3478  7.1500  12.2248

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
 MDA  C1   C2    single  1.515  0.020  1.515
 MDA  C1   O1    single  1.384  0.020  1.384
 MDA  C1   O5    single  1.410  0.020  1.410
 MDA  C1   H1    single  0.970  0.020  1.090
 MDA  C2   C3    single  1.532  0.020  1.532
 MDA  C2   H2    single  0.970  0.020  1.090
 MDA  C2   H22   single  0.970  0.020  1.090
 MDA  C3   C4    single  1.539  0.020  1.539
 MDA  C3   C3'   single  1.526  0.020  1.526
 MDA  C3   O3    single  1.417  0.020  1.417
 MDA  C4   C5    single  1.533  0.020  1.533
 MDA  C4   O4    single  1.406  0.020  1.406
 MDA  C4   H4    single  0.970  0.020  1.090
 MDA  C5   C6    single  1.516  0.020  1.516
 MDA  C5   O5    single  1.415  0.020  1.415
 MDA  C5   H5    single  0.970  0.020  1.090
 MDA  C6   H61   single  0.970  0.020  1.090
 MDA  C6   H62   single  0.970  0.020  1.090
 MDA  C6   H63   single  0.970  0.020  1.090
 MDA  C3'  H3'1  single  0.970  0.020  1.090
 MDA  C3'  H3'2  single  0.970  0.020  1.090
 MDA  C3'  H3'3  single  0.970  0.020  1.090
 MDA  O1   HO1   single  0.850  0.020  0.980
 MDA  O3   HO3   single  0.850  0.020  0.980
 MDA  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
 MDA  H1    C1   O5    108.76  3.000
 MDA  H1    C1   O1    111.14  3.000
 MDA  O5    C1   O1    108.09  3.000
 MDA  H1    C1   C2    109.85  3.000
 MDA  O5    C1   C2    110.00  3.000
 MDA  O1    C1   C2    108.97  3.000
 MDA  H22   C2   H2    107.09  3.000
 MDA  H22   C2   C3    109.57  3.000
 MDA  H2    C2   C3    109.81  3.000
 MDA  H22   C2   C1    110.11  3.000
 MDA  H2    C2   C1    108.98  3.000
 MDA  C3    C2   C1    111.19  3.000
 MDA  O3    C3   C3'   110.46  3.000
 MDA  O3    C3   C4    106.73  3.000
 MDA  C3'   C3   C4    110.83  3.000
 MDA  O3    C3   C2    110.45  3.000
 MDA  C3'   C3   C2    110.10  3.000
 MDA  C4    C3   C2    108.21  3.000
 MDA  H4    C4   O4    111.09  3.000
 MDA  H4    C4   C5    106.90  3.000
 MDA  O4    C4   C5    107.82  3.000
 MDA  H4    C4   C3    106.83  3.000
 MDA  O4    C4   C3    112.51  3.000
 MDA  C5    C4   C3    111.58  3.000
 MDA  H5    C5   O5    109.89  3.000
 MDA  H5    C5   C6    108.94  3.000
 MDA  O5    C5   C6    107.29  3.000
 MDA  H5    C5   C4    108.91  3.000
 MDA  O5    C5   C4    109.43  3.000
 MDA  C6    C5   C4    112.36  3.000
 MDA  H63   C6   H62   108.21  3.000
 MDA  H63   C6   H61   108.26  3.000
 MDA  H62   C6   H61   107.68  3.000
 MDA  H63   C6   C5    111.12  3.000
 MDA  H62   C6   C5    110.87  3.000
 MDA  H61   C6   C5    110.58  3.000
 MDA  H3'3  C3'  H3'2  107.48  3.000
 MDA  H3'3  C3'  H3'1  108.31  3.000
 MDA  H3'2  C3'  H3'1  107.53  3.000
 MDA  H3'3  C3'  C3    111.19  3.000
 MDA  H3'2  C3'  C3    110.60  3.000
 MDA  H3'1  C3'  C3    111.56  3.000
 MDA  HO1   O1   C1    109.17  3.000
 MDA  C5    O5   C1    114.02  3.000
 MDA  HO3   O3   C3    108.09  3.000
 MDA  HO4   O4   C4    108.97  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
 MDA  chir_01  C1  C2  O1  O5   positiv
 MDA  chir_02  C3  C2  C4  C3'  positiv
 MDA  chir_03  C4  O4  C3  C5   negativ
 MDA  chir_04  C5  O5  C4  C6   negativ

