# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:11:50 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: 2,4-dideoxy-3-O-methyl-4-(propan-2-ylamino)-alpha-L-threo-pentopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1C[C@H](O)OC[C@@H]1NC(C)C
#
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
 MAT  MAT  2,4-dideoxy-3-O-methyl-4-(propan-2-ylamino)-alpha-L-threo-pentopyranose  L-saccharide  32  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 OK
;

data_comp_MAT
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
 MAT  C1   C  CH1   0   0.251  -4.0629   9.2319  4.7571
 MAT  C2   C  CH2   0  -0.509  -3.5974  10.0845  5.9260
 MAT  C3   C  CH1   0   0.061  -2.2205  10.6852  5.6598
 MAT  C4   C  CH1   0  -0.108  -2.2392  11.4528  4.3401
 MAT  C5   C  CH2   0  -0.175  -2.7509  10.5133  3.2467
 MAT  C7   C  CH3   0  -0.679  -1.7717  14.0178  2.9492
 MAT  C8   C  CH3   0  -0.650  -0.4638  12.3178  1.6317
 MAT  O1   O  OH1   0  -0.665  -3.2719   8.0816  4.7164
 MAT  O3   O  O2    0  -0.494  -1.8276  11.5801  6.6774
 MAT  N4   N  NH1   0  -0.620  -0.8952  11.9177  4.0494
 MAT  O5   O  O2    0  -0.492  -4.0134   9.9559  3.5559
 MAT  H1   H  HCH1  0   0.225  -5.1214   8.9738  4.8779
 MAT  H2   H  HCH2  0   0.239  -4.3212  10.8905  6.0739
 MAT  H22  H  HCH2  0   0.251  -3.6015   9.4802  6.8359
 MAT  H3   H  HCH1  0   0.205  -1.4765   9.8782  5.5744
 MAT  H4   H  HCH1  0   0.210  -2.9682  12.2726  4.4519
 MAT  H51  H  HCH2  0   0.233  -2.8954  11.0563  2.3134
 MAT  H52  H  HCH2  0   0.202  -1.9960   9.7392  3.0630
 MAT  H6   H  HCH1  0   0.223   0.2392  13.4247  3.2862
 MAT  H71  H  HCH3  0   0.227  -1.9367  14.4700  3.9288
 MAT  H72  H  HCH3  0   0.231  -1.4684  14.8110  2.2642
 MAT  H73  H  HCH3  0   0.219  -2.7282  13.6302  2.5921
 MAT  H81  H  HCH3  0   0.224   0.3030  11.5446  1.6793
 MAT  H82  H  HCH3  0   0.217  -1.3673  11.8721  1.2147
 MAT  H83  H  HCH3  0   0.221  -0.1297  13.0831  0.9294
 MAT  H91  H  HCH3  0   0.234  -0.9848  11.7362  8.5112
 MAT  H92  H  HCH3  0   0.208  -2.1419  10.4064  8.3786
 MAT  H93  H  HCH3  0   0.205  -0.5397  10.2592  7.6372
 MAT  HO1  H  HOH1  0   0.454  -3.6322   7.4774  4.0582
 MAT  HN4  H  HNH1  0   0.348  -0.5193  12.2893  4.9114
 MAT  C6   C  CH1   0  -0.091  -0.6978  12.9329  3.0089
 MAT  C9   C  CH3   0  -0.403  -1.3584  10.9572  7.8476

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
 MAT  C1  C2   single  1.520  0.020  1.520
 MAT  C1  O1   single  1.397  0.020  1.397
 MAT  C1  O5   single  1.403  0.020  1.403
 MAT  C1  H1   single  0.970  0.020  1.090
 MAT  C2  C3   single  1.526  0.020  1.526
 MAT  C2  H2   single  0.970  0.020  1.090
 MAT  C2  H22  single  0.970  0.020  1.090
 MAT  C3  C4   single  1.527  0.020  1.527
 MAT  C3  O3   single  1.411  0.020  1.411
 MAT  C3  H3   single  0.970  0.020  1.090
 MAT  C4  C5   single  1.530  0.020  1.530
 MAT  C4  N4   single  1.452  0.020  1.452
 MAT  C4  H4   single  0.970  0.020  1.090
 MAT  C5  O5   single  1.414  0.020  1.414
 MAT  C5  H51  single  0.970  0.020  1.090
 MAT  C5  H52  single  0.970  0.020  1.090
 MAT  C6  C7   single  1.528  0.020  1.528
 MAT  C6  C8   single  1.526  0.020  1.526
 MAT  C6  N4   single  1.467  0.020  1.467
 MAT  C6  H6   single  0.970  0.020  1.090
 MAT  C7  H71  single  0.970  0.020  1.090
 MAT  C7  H72  single  0.970  0.020  1.090
 MAT  C7  H73  single  0.970  0.020  1.090
 MAT  C8  H81  single  0.970  0.020  1.090
 MAT  C8  H82  single  0.970  0.020  1.090
 MAT  C8  H83  single  0.970  0.020  1.090
 MAT  C9  O3   single  1.406  0.020  1.406
 MAT  C9  H91  single  0.970  0.020  1.090
 MAT  C9  H92  single  0.970  0.020  1.090
 MAT  C9  H93  single  0.970  0.020  1.090
 MAT  O1  HO1  single  0.850  0.020  0.980
 MAT  N4  HN4  single  0.890  0.020  1.040

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
 MAT  H1   C1  O5   104.46  3.000
 MAT  H1   C1  O1   110.87  3.000
 MAT  O5   C1  O1   112.34  3.000
 MAT  H1   C1  C2   110.07  3.000
 MAT  O5   C1  C2   110.98  3.000
 MAT  O1   C1  C2   108.12  3.000
 MAT  H22  C2  H2   107.02  3.000
 MAT  H22  C2  C3   111.51  3.000
 MAT  H2   C2  C3   109.32  3.000
 MAT  H22  C2  C1   109.21  3.000
 MAT  H2   C2  C1   108.35  3.000
 MAT  C3   C2  C1   111.29  3.000
 MAT  H3   C3  O3   109.43  3.000
 MAT  H3   C3  C4   108.05  3.000
 MAT  O3   C3  C4   107.94  3.000
 MAT  H3   C3  C2   109.56  3.000
 MAT  O3   C3  C2   112.04  3.000
 MAT  C4   C3  C2   109.74  3.000
 MAT  H4   C4  N4   113.22  3.000
 MAT  H4   C4  C5   107.93  3.000
 MAT  N4   C4  C5   111.30  3.000
 MAT  H4   C4  C3   107.11  3.000
 MAT  N4   C4  C3   108.83  3.000
 MAT  C5   C4  C3   108.25  3.000
 MAT  H52  C5  H51  107.44  3.000
 MAT  H52  C5  O5   111.89  3.000
 MAT  H51  C5  O5   105.39  3.000
 MAT  H52  C5  C4   108.84  3.000
 MAT  H51  C5  C4   110.53  3.000
 MAT  O5   C5  C4   112.61  3.000
 MAT  H73  C7  H72  107.23  3.000
 MAT  H73  C7  H71  107.95  3.000
 MAT  H72  C7  H71  107.72  3.000
 MAT  H73  C7  C6   112.11  3.000
 MAT  H72  C7  C6   110.21  3.000
 MAT  H71  C7  C6   111.43  3.000
 MAT  H83  C8  H82  107.12  3.000
 MAT  H83  C8  H81  108.07  3.000
 MAT  H82  C8  H81  108.05  3.000
 MAT  H83  C8  C6   110.18  3.000
 MAT  H82  C8  C6   112.50  3.000
 MAT  H81  C8  C6   110.75  3.000
 MAT  HO1  O1  C1   108.94  3.000
 MAT  C9   O3  C3   114.34  3.000
 MAT  HN4  N4  C6   107.48  3.000
 MAT  HN4  N4  C4   106.92  3.000
 MAT  C6   N4  C4   119.23  3.000
 MAT  C5   O5  C1   114.96  3.000
 MAT  H6   C6  N4   104.28  3.000
 MAT  H6   C6  C8   106.18  3.000
 MAT  N4   C6  C8   112.44  3.000
 MAT  H6   C6  C7   107.02  3.000
 MAT  N4   C6  C7   115.13  3.000
 MAT  C8   C6  C7   111.02  3.000
 MAT  H93  C9  H92  107.89  3.000
 MAT  H93  C9  H91  108.43  3.000
 MAT  H92  C9  H91  108.03  3.000
 MAT  H93  C9  O3   111.81  3.000
 MAT  H92  C9  O3   112.80  3.000
 MAT  H91  C9  O3   107.73  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
 MAT  Var_01  C4   C5  O5  C1   -57.85  30.0  1
 MAT  Var_02  C7   C6  N4  C4    37.97  30.0  1
 MAT  Var_03  H91  C9  O3  C3   173.86  30.0  3
 MAT  Var_04  H81  C8  C6  C7   179.99  30.0  3
 MAT  Var_05  H71  C7  C6  C8  -179.38  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
 MAT  chir_01  C1  C2  O1  O5  positiv
 MAT  chir_02  C3  O3  C2  C4  negativ
 MAT  chir_03  C4  N4  C3  C5  positiv

