# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 05:30:29 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: pentan-3-yl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)O[C@@H]1OC(=C[C@H](O)[C@H]1NC(C)=O)C(O)=O
#
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
 0HX  0HX  'pentan-3-yl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid'  L-saccharide  40  20  .  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_0HX
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
 0HX  C4   C  CH2    0  -0.432   0.8136   3.3731  -1.0782
 0HX  C5   C  CH3    0  -0.658   1.8345   2.6051  -1.9054
 0HX  C6   C  CH1    0   0.331   0.1063   0.2282   0.2553
 0HX  C11  C  CH1    0  -0.188  -0.8698  -0.9136  -0.0361
 0HX  C7   C  C      0   0.179   1.8822  -1.2992   0.1156
 0HX  C8   C  C      0   0.373   3.3915  -1.4330  -0.0697
 0HX  C9   C  C1     0  -0.416   1.1028  -2.2765   0.5814
 0HX  C10  C  CH1    0   0.062  -0.3878  -2.1590   0.7002
 0HX  C13  C  CH3    0  -0.784  -4.4652   0.2535   0.1497
 0HX  N1   N  NH1    0  -0.632  -2.2120  -0.5759   0.3523
 0HX  C3   C  CH1    0   0.047   0.2295   2.6060   0.1027
 0HX  C2   C  CH2    0  -0.417  -0.8527   3.4168   0.8055
 0HX  O1   O  O2     0  -0.494  -0.3261   1.3714  -0.3579
 0HX  O2   O  O2     0  -0.469   1.3907  -0.0926  -0.2480
 0HX  O3   O  OC    -1  -0.585   3.9797  -0.4340  -0.5130
 0HX  O4   O  O      0  -0.591   3.8823  -2.5345   0.2387
 0HX  O5   O  OH1    0  -0.664  -1.0590  -3.2700   0.1456
 0HX  O6   O  O      0  -0.501  -3.0092  -0.1014  -1.7106
 0HX  H1   H  HCH2   0   0.220   1.2762   4.2783  -0.6753
 0HX  H2   H  HCH2   0   0.214  -0.0027   3.7146  -1.7234
 0HX  H3   H  HCH3   0   0.217   2.3025   3.2670  -2.6353
 0HX  H4   H  HCH3   0   0.225   2.6219   2.1720  -1.2883
 0HX  H5   H  HCH3   0   0.217   1.3701   1.7863  -2.4531
 0HX  H6   H  HCH1   0   0.198   0.1983   0.3591   1.3486
 0HX  H7   H  HCH1   0   0.274  -0.8592  -1.1071  -1.1117
 0HX  H8   H  H      0   0.252   1.5668  -3.2040   0.8891
 0HX  H9   H  HCH1   0   0.218  -0.6542  -2.0562   1.7641
 0HX  H10  H  HCH3   0   0.267  -4.6048   1.3277   0.0211
 0HX  H11  H  HCH3   0   0.266  -5.2964  -0.2432  -0.3488
 0HX  H12  H  HCH3   0   0.249  -4.5144   0.0305   1.2140
 0HX  H13  H  HNH1   0   0.398  -2.4214  -0.5785   1.3380
 0HX  H14  H  HCH1   0   0.213   1.0382   2.4012   0.8175
 0HX  H15  H  HCH3   0   0.219  -0.6173   2.5832   2.7994
 0HX  H16  H  HCH3   0   0.234  -2.1406   3.4257   2.5443
 0HX  H17  H  HCH3   0   0.216  -1.9028   1.8277   1.8577
 0HX  H18  H  HCH2   0   0.220  -0.4289   4.3941   1.0525
 0HX  H19  H  HCH2   0   0.219  -1.6663   3.6059   0.0985
 0HX  H21  H  HOH1   0   0.454  -0.8767  -4.0355   0.6994
 0HX  C12  C  C      0   0.526  -3.1662  -0.1541  -0.4997
 0HX  C1   C  CH3    0  -0.676  -1.4063   2.7744   2.0695

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
 0HX  C13  C12  single  1.508  0.020  1.508
 0HX  C1   C2   single  1.522  0.020  1.522
 0HX  C2   C3   single  1.524  0.020  1.524
 0HX  N1   C12  single  1.347  0.020  1.347
 0HX  N1   C11  single  1.437  0.020  1.437
 0HX  C12  O6   double  1.222  0.020  1.222
 0HX  C3   O1   single  1.430  0.020  1.430
 0HX  C3   C4   single  1.525  0.020  1.525
 0HX  C6   O1   single  1.367  0.020  1.367
 0HX  C6   C11  single  1.530  0.020  1.530
 0HX  C6   O2   single  1.416  0.020  1.416
 0HX  C11  C10  single  1.525  0.020  1.525
 0HX  C10  O5   single  1.411  0.020  1.411
 0HX  C10  C9   single  1.500  0.020  1.500
 0HX  C4   C5   single  1.522  0.020  1.522
 0HX  O2   C7   single  1.353  0.020  1.353
 0HX  C9   C7   double  1.334  0.020  1.334
 0HX  C7   C8   single  1.527  0.020  1.527
 0HX  C8   O4   deloc   1.245  0.020  1.245
 0HX  C8   O3   deloc   1.241  0.020  1.241
 0HX  C4   H1   single  0.970  0.020  1.090
 0HX  C4   H2   single  0.970  0.020  1.090
 0HX  C5   H3   single  0.970  0.020  1.090
 0HX  C5   H4   single  0.970  0.020  1.090
 0HX  C5   H5   single  0.970  0.020  1.090
 0HX  C6   H6   single  0.970  0.020  1.090
 0HX  C11  H7   single  0.970  0.020  1.090
 0HX  C9   H8   single  0.930  0.020  1.080
 0HX  C10  H9   single  0.970  0.020  1.090
 0HX  C13  H10  single  0.970  0.020  1.090
 0HX  C13  H11  single  0.970  0.020  1.090
 0HX  C13  H12  single  0.970  0.020  1.090
 0HX  N1   H13  single  0.860  0.020  1.020
 0HX  C3   H14  single  0.970  0.020  1.090
 0HX  C1   H15  single  0.970  0.020  1.090
 0HX  C1   H16  single  0.970  0.020  1.090
 0HX  C1   H17  single  0.970  0.020  1.090
 0HX  C2   H18  single  0.970  0.020  1.090
 0HX  C2   H19  single  0.970  0.020  1.090
 0HX  O5   H21  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
 0HX  H2   C4   H1   105.92  3.000
 0HX  H2   C4   C3   109.13  3.000
 0HX  H1   C4   C3   107.05  3.000
 0HX  H2   C4   C5   109.71  3.000
 0HX  H1   C4   C5   109.52  3.000
 0HX  C3   C4   C5   115.09  3.000
 0HX  H5   C5   H4   107.10  3.000
 0HX  H5   C5   H3   107.62  3.000
 0HX  H4   C5   H3   108.06  3.000
 0HX  H5   C5   C4   111.51  3.000
 0HX  H4   C5   C4   112.16  3.000
 0HX  H3   C5   C4   110.20  3.000
 0HX  H6   C6   O2   107.63  3.000
 0HX  H6   C6   O1   111.77  3.000
 0HX  O2   C6   O1   108.47  3.000
 0HX  H6   C6   C11  109.27  3.000
 0HX  O2   C6   C11  109.99  3.000
 0HX  O1   C6   C11  109.67  3.000
 0HX  H7   C11  N1   108.45  3.000
 0HX  H7   C11  C10  109.11  3.000
 0HX  N1   C11  C10  110.89  3.000
 0HX  H7   C11  C6   108.26  3.000
 0HX  C10  C11  C6   108.41  3.000
 0HX  N1   C11  C6   111.65  3.000
 0HX  O2   C7   C9   122.35  3.000
 0HX  C9   C7   C8   123.77  3.000
 0HX  O2   C7   C8   113.88  3.000
 0HX  O4   C8   O3   127.88  3.000
 0HX  O3   C8   C7   116.19  3.000
 0HX  O4   C8   C7   115.93  3.000
 0HX  H8   C9   C10  118.09  3.000
 0HX  H8   C9   C7   118.48  3.000
 0HX  C10  C9   C7   123.43  3.000
 0HX  H9   C10  O5   109.75  3.000
 0HX  H9   C10  C9   108.91  3.000
 0HX  O5   C10  C9   112.32  3.000
 0HX  H9   C10  C11  108.28  3.000
 0HX  C9   C10  C11  109.87  3.000
 0HX  O5   C10  C11  107.63  3.000
 0HX  H12  C13  H11  108.64  3.000
 0HX  H12  C13  H10  108.13  3.000
 0HX  H11  C13  H10  107.31  3.000
 0HX  H12  C13  C12  113.86  3.000
 0HX  H11  C13  C12  109.69  3.000
 0HX  H10  C13  C12  109.00  3.000
 0HX  H13  N1   C12  118.19  3.000
 0HX  H13  N1   C11  117.24  3.000
 0HX  C12  N1   C11  124.34  3.000
 0HX  H14  C3   O1   109.55  3.000
 0HX  H14  C3   C2   108.77  3.000
 0HX  O1   C3   C2   109.38  3.000
 0HX  H14  C3   C4   108.41  3.000
 0HX  O1   C3   C4   109.50  3.000
 0HX  C2   C3   C4   111.20  3.000
 0HX  H19  C2   H18  106.24  3.000
 0HX  H19  C2   C1   109.82  3.000
 0HX  H18  C2   C1   109.30  3.000
 0HX  H19  C2   C3   108.78  3.000
 0HX  H18  C2   C3   107.73  3.000
 0HX  C1   C2   C3   114.63  3.000
 0HX  C3   O1   C6   117.03  3.000
 0HX  C7   O2   C6   115.85  3.000
 0HX  H21  O5   C10  108.06  3.000
 0HX  O6   C12  N1   123.32  3.000
 0HX  O6   C12  C13  121.70  3.000
 0HX  N1   C12  C13  114.98  3.000
 0HX  H17  C1   H16  107.26  3.000
 0HX  H17  C1   H15  107.88  3.000
 0HX  H16  C1   H15  107.47  3.000
 0HX  H17  C1   C2   111.78  3.000
 0HX  H16  C1   C2   110.76  3.000
 0HX  H15  C1   C2   111.49  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
 0HX  CONST_01  C13  C12  N1   C11   180.00   0.0  0
 0HX  CONST_02  O6   C12  N1   C11     0.00   0.0  0
 0HX  CONST_03  H13  N1   C12  C13     0.00   0.0  0
 0HX  Var_01    C9   C7   O2   C6     18.42  30.0  1
 0HX  Var_02    O2   C7   C9   C10     2.38  30.0  1
 0HX  Var_03    O4   C8   C7   C9      0.26  30.0  2
 0HX  Var_04    C2   C3   O1   C6   -111.77  30.0  2
 0HX  Var_05    C1   C2   C3   C4   -174.98  30.0  1
 0HX  Var_06    H10  C13  C12  N1    113.09  30.0  3
 0HX  Var_07    H15  C1   C2   C3     57.80  30.0  3
 0HX  Var_08    H3   C5   C4   C3   -171.97  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
 0HX  chir_01  C6   O1  C11  O2  negativ
 0HX  chir_02  C11  N1  C10  C6  positiv
 0HX  chir_03  C10  O5  C11  C9  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 0HX  plan-1  C11  0.020
 0HX  plan-1  C13  0.020
 0HX  plan-1  N1   0.020
 0HX  plan-1  O6   0.020
 0HX  plan-1  H13  0.020
 0HX  plan-1  C12  0.020
 0HX  plan-2  C7   0.020
 0HX  plan-2  C8   0.020
 0HX  plan-2  O3   0.020
 0HX  plan-2  O4   0.020

