# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:17:39 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  41  20  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.431   0.8231   3.3748  -1.0654
 0HX  C5   C  CH3   0  -0.657   2.0346   2.7206  -1.7122
 0HX  C6   C  CH1   0   0.324   0.1270   0.2089   0.2467
 0HX  C11  C  CH1   0  -0.182  -0.8748  -0.9171  -0.0322
 0HX  C7   C  C     0   0.237   1.8460  -1.3791   0.0883
 0HX  C8   C  C     0   0.505   3.3088  -1.5928  -0.0927
 0HX  C9   C  C1    0  -0.365   1.0606  -2.3478   0.5561
 0HX  C10  C  CH1   0   0.052  -0.4231  -2.1767   0.7015
 0HX  C13  C  CH3   0  -0.789  -4.4366   0.3178   0.1898
 0HX  N1   N  NH1   0  -0.631  -2.2044  -0.5495   0.3635
 0HX  C3   C  CH1   0   0.040   0.2241   2.6006   0.1015
 0HX  C2   C  CH2   0  -0.417  -0.9090   3.3773   0.7610
 0HX  O1   O  O2    0  -0.488  -0.2737   1.3469  -0.3832
 0HX  O2   O  O2    0  -0.477   1.4096  -0.1562  -0.2662
 0HX  O3   O  OH1   0  -0.578   3.9207  -0.5163  -0.5500
 0HX  O4   O  O     0  -0.432   3.8602  -2.6386   0.1474
 0HX  O5   O  OH1   0  -0.656  -1.1312  -3.2674   0.1668
 0HX  O6   O  O     0  -0.489  -2.9940  -0.0463  -1.6949
 0HX  H1   H  HCH2  0   0.222   1.1025   4.3626  -0.6901
 0HX  H2   H  HCH2  0   0.220   0.0440   3.5448  -1.8152
 0HX  H3   H  HCH3  0   0.223   2.4471   3.3678  -2.4870
 0HX  H4   H  HCH3  0   0.216   2.8228   2.5337  -0.9816
 0HX  H5   H  HCH3  0   0.224   1.7859   1.7675  -2.1745
 0HX  H6   H  HCH1  0   0.214   0.2391   0.3494   1.3350
 0HX  H7   H  HCH1  0   0.284  -0.8749  -1.1129  -1.1077
 0HX  H8   H  H     0   0.283   1.4996  -3.2924   0.8484
 0HX  H9   H  HCH1  0   0.239  -0.6508  -2.0585   1.7718
 0HX  H10  H  HCH3  0   0.263  -5.1225   0.7492  -0.5343
 0HX  H11  H  HCH3  0   0.271  -4.9183  -0.5416   0.6582
 0HX  H12  H  HCH3  0   0.258  -4.2498   1.0519   0.9750
 0HX  H13  H  HNH1  0   0.402  -2.4142  -0.5536   1.3500
 0HX  H14  H  HCH1  0   0.216   1.0109   2.4210   0.8473
 0HX  H15  H  HCH3  0   0.222  -0.6850   2.5818   2.7711
 0HX  H16  H  HCH3  0   0.236  -2.2262   3.3776   2.4766
 0HX  H17  H  HCH3  0   0.213  -1.9336   1.7759   1.8237
 0HX  H18  H  HCH2  0   0.223  -0.5278   4.3731   1.0024
 0HX  H19  H  HCH2  0   0.222  -1.7102   3.5242   0.0304
 0HX  H20  H  HOH1  0   0.489   4.8660  -0.6996  -0.6605
 0HX  H21  H  HOH1  0   0.460  -1.0283  -4.0181   0.7604
 0HX  C12  C  C     0   0.514  -3.1524  -0.0967  -0.4864
 0HX  C1   C  CH3   0  -0.678  -1.4664   2.7392   2.0252

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  1.509  0.020  1.509
 0HX  C1   C2   single  1.522  0.020  1.522
 0HX  C2   C3   single  1.524  0.020  1.524
 0HX  N1   C12  single  1.351  0.020  1.351
 0HX  N1   C11  single  1.435  0.020  1.435
 0HX  C12  O6   double  1.220  0.020  1.220
 0HX  C3   O1   single  1.433  0.020  1.433
 0HX  C3   C4   single  1.523  0.020  1.523
 0HX  C6   O1   single  1.361  0.020  1.361
 0HX  C6   C11  single  1.533  0.020  1.533
 0HX  C6   O2   single  1.429  0.020  1.429
 0HX  C11  C10  single  1.526  0.020  1.526
 0HX  C10  O5   single  1.406  0.020  1.406
 0HX  C10  C9   single  1.501  0.020  1.501
 0HX  C4   C5   single  1.521  0.020  1.521
 0HX  O2   C7   single  1.346  0.020  1.346
 0HX  C9   C7   double  1.332  0.020  1.332
 0HX  C7   C8   single  1.489  0.020  1.489
 0HX  C8   O4   double  1.206  0.020  1.206
 0HX  C8   O3   single  1.320  0.020  1.320
 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  O3   H20  single  0.850  0.020  0.980
 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   106.07  3.000
 0HX  H2   C4   C3   108.89  3.000
 0HX  H1   C4   C3   107.27  3.000
 0HX  H2   C4   C5   110.02  3.000
 0HX  H1   C4   C5   109.33  3.000
 0HX  C3   C4   C5   114.86  3.000
 0HX  H5   C5   H4   107.43  3.000
 0HX  H5   C5   H3   107.73  3.000
 0HX  H4   C5   H3   107.71  3.000
 0HX  H5   C5   C4   112.05  3.000
 0HX  H4   C5   C4   111.37  3.000
 0HX  H3   C5   C4   110.37  3.000
 0HX  H6   C6   O2   107.19  3.000
 0HX  H6   C6   O1   112.34  3.000
 0HX  O2   C6   O1   108.17  3.000
 0HX  H6   C6   C11  109.85  3.000
 0HX  O2   C6   C11  109.49  3.000
 0HX  O1   C6   C11  109.73  3.000
 0HX  H7   C11  N1   108.49  3.000
 0HX  H7   C11  C10  108.98  3.000
 0HX  N1   C11  C10  110.67  3.000
 0HX  H7   C11  C6   108.10  3.000
 0HX  C10  C11  C6   108.99  3.000
 0HX  N1   C11  C6   111.54  3.000
 0HX  O2   C7   C9   124.21  3.000
 0HX  C9   C7   C8   121.16  3.000
 0HX  O2   C7   C8   114.63  3.000
 0HX  O4   C8   O3   124.34  3.000
 0HX  O3   C8   C7   112.36  3.000
 0HX  O4   C8   C7   123.30  3.000
 0HX  H8   C9   C10  118.33  3.000
 0HX  H8   C9   C7   119.38  3.000
 0HX  C10  C9   C7   122.28  3.000
 0HX  H9   C10  O5   110.43  3.000
 0HX  H9   C10  C9   108.12  3.000
 0HX  O5   C10  C9   111.88  3.000
 0HX  H9   C10  C11  108.52  3.000
 0HX  C9   C10  C11  109.89  3.000
 0HX  O5   C10  C11  107.96  3.000
 0HX  H12  C13  H11  107.25  3.000
 0HX  H12  C13  H10  108.70  3.000
 0HX  H11  C13  H10  108.67  3.000
 0HX  H12  C13  C12  111.20  3.000
 0HX  H11  C13  C12  110.59  3.000
 0HX  H10  C13  C12  110.34  3.000
 0HX  H13  N1   C12  118.07  3.000
 0HX  H13  N1   C11  117.48  3.000
 0HX  C12  N1   C11  124.22  3.000
 0HX  H14  C3   O1   109.59  3.000
 0HX  H14  C3   C2   108.78  3.000
 0HX  O1   C3   C2   109.51  3.000
 0HX  H14  C3   C4   108.76  3.000
 0HX  O1   C3   C4   108.79  3.000
 0HX  C2   C3   C4   111.40  3.000
 0HX  H19  C2   H18  106.29  3.000
 0HX  H19  C2   C1   110.04  3.000
 0HX  H18  C2   C1   109.04  3.000
 0HX  H19  C2   C3   108.90  3.000
 0HX  H18  C2   C3   107.49  3.000
 0HX  C1   C2   C3   114.72  3.000
 0HX  C3   O1   C6   118.20  3.000
 0HX  C7   O2   C6   115.38  3.000
 0HX  H20  O3   C8   109.72  3.000
 0HX  H21  O5   C10  108.46  3.000
 0HX  O6   C12  N1   123.09  3.000
 0HX  O6   C12  C13  122.88  3.000
 0HX  N1   C12  C13  114.02  3.000
 0HX  H17  C1   H16  107.18  3.000
 0HX  H17  C1   H15  107.81  3.000
 0HX  H16  C1   H15  107.48  3.000
 0HX  H17  C1   C2   111.98  3.000
 0HX  H16  C1   C2   110.71  3.000
 0HX  H15  C1   C2   111.45  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  H20  O3   C8   C7    180.00   0.0  0
 0HX  CONST_04  H13  N1   C12  C13     0.00   0.0  0
 0HX  Var_01    C9   C7   O2   C6     18.03  30.0  1
 0HX  Var_02    O2   C7   C9   C10     1.69  30.0  1
 0HX  Var_03    O4   C8   C7   C9      1.16  30.0  2
 0HX  Var_04    C2   C3   O1   C6   -110.21  30.0  1
 0HX  Var_05    C1   C2   C3   C4   -173.94  30.0  2
 0HX  Var_06    H10  C13  C12  N1    175.19  30.0  3
 0HX  Var_07    H15  C1   C2   C3     56.80  30.0  3
 0HX  Var_08    H3   C5   C4   C3   -175.85  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
 0HX  plan-2  H20  0.020

