# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:55:59 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-(acetylamino)-2,4-dideoxy-alpha-L-erythro-hex-4-enopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@H](O)OC(=C[C@@H]1O)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
 49V  49V  '2-(acetylamino)-2,4-dideoxy-alpha-L-erythro-hex-4-enopyranuronic acid'  L-saccharide  25  15  .  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 (reasonable std)
;

data_comp_49V
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
 49V  C1   C  CH1    0   0.299   0.2135   0.6983  -1.3643
 49V  O5   O  O2     0  -0.485  -0.8717   1.0323  -0.5093
 49V  C5   C  C      0   0.168  -1.6378  -0.0027  -0.0861
 49V  C6   C  C      0   0.377  -2.9591   0.4280   0.5453
 49V  O6   O  O      0  -0.589  -3.6927  -0.4892   0.9553
 49V  O9   O  OC    -1  -0.594  -3.1688   1.6506   0.5902
 49V  C4   C  C1     0  -0.420  -1.2538  -1.2766  -0.1980
 49V  C3   C  CH1    0   0.072   0.0688  -1.6822  -0.7838
 49V  O3   O  OH1    0  -0.663   0.6882  -2.7202  -0.0622
 49V  C2   C  CH1    0  -0.235   1.0033  -0.4721  -0.7883
 49V  N2   N  NH1    0  -0.608   1.4893  -0.1731   0.5334
 49V  C7   C  C      0   0.524   2.7758   0.0909   0.8215
 49V  O7   O  O      0  -0.508   3.6661   0.1043  -0.0178
 49V  C8   C  CH3    0  -0.781   3.0576   0.3804   2.2751
 49V  H1   H  HCH1   0   0.215  -0.2042   0.3980  -2.3380
 49V  H4   H  H      0   0.253  -1.9332  -2.0470   0.1425
 49V  H5   H  HCH1   0   0.234  -0.0727  -1.9865  -1.8309
 49V  H6   H  HOH1   0   0.455   0.1414  -3.5075  -0.1476
 49V  H7   H  HCH1   0   0.283   1.8595  -0.6709  -1.4330
 49V  H8   H  HNH1   0   0.402   0.8267  -0.1915   1.2928
 49V  H9   H  HCH3   0   0.248   2.1977   0.2384   2.9269
 49V  H10  H  HCH3   0   0.264   3.8670  -0.2607   2.6226
 49V  H11  H  HCH3   0   0.267   3.3956   1.4122   2.3767
 49V  O1   O  OH1    0  -0.646   1.0258   1.8004  -1.4693
 49V  H2   H  HOH1   0   0.466   0.6040   2.4551  -2.0364

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
 49V  O6  C6   deloc   1.244  0.020  1.244
 49V  C6  O9   deloc   1.241  0.020  1.241
 49V  C6  C5   single  1.526  0.020  1.526
 49V  O5  C5   single  1.355  0.020  1.355
 49V  O5  C1   single  1.421  0.020  1.421
 49V  C5  C4   double  1.335  0.020  1.335
 49V  C1  C2   single  1.525  0.020  1.525
 49V  C4  C3   single  1.502  0.020  1.502
 49V  C2  C3   single  1.529  0.020  1.529
 49V  C2  N2   single  1.440  0.020  1.440
 49V  C3  O3   single  1.408  0.020  1.408
 49V  N2  C7   single  1.345  0.020  1.345
 49V  O7  C7   double  1.224  0.020  1.224
 49V  C7  C8   single  1.509  0.020  1.509
 49V  C1  H1   single  0.970  0.020  1.090
 49V  C4  H4   single  0.930  0.020  1.080
 49V  C3  H5   single  0.970  0.020  1.090
 49V  O3  H6   single  0.850  0.020  0.980
 49V  C2  H7   single  0.970  0.020  1.090
 49V  N2  H8   single  0.860  0.020  1.020
 49V  C8  H9   single  0.970  0.020  1.090
 49V  C8  H10  single  0.970  0.020  1.090
 49V  C8  H11  single  0.970  0.020  1.090
 49V  C1  O1   single  1.373  0.020  1.373
 49V  O1  H2   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
 49V  O1   C1  H1   112.06  3.000
 49V  O1   C1  C2   109.79  3.000
 49V  H1   C1  C2   108.73  3.000
 49V  O1   C1  O5   108.01  3.000
 49V  H1   C1  O5   107.84  3.000
 49V  C2   C1  O5   110.40  3.000
 49V  C5   O5  C1   116.10  3.000
 49V  C4   C5  C6   123.56  3.000
 49V  C4   C5  O5   122.67  3.000
 49V  C6   C5  O5   113.76  3.000
 49V  O9   C6  O6   127.93  3.000
 49V  O9   C6  C5   116.05  3.000
 49V  O6   C6  C5   116.03  3.000
 49V  H4   C4  C3   118.90  3.000
 49V  H4   C4  C5   118.18  3.000
 49V  C3   C4  C5   122.92  3.000
 49V  H5   C3  C2   107.15  3.000
 49V  H5   C3  O3   109.91  3.000
 49V  C2   C3  O3   108.43  3.000
 49V  H5   C3  C4   109.44  3.000
 49V  O3   C3  C4   112.74  3.000
 49V  C2   C3  C4   109.00  3.000
 49V  H6   O3  C3   107.92  3.000
 49V  H7   C2  N2   108.40  3.000
 49V  H7   C2  C3   109.73  3.000
 49V  N2   C2  C3   111.59  3.000
 49V  H7   C2  C1   108.87  3.000
 49V  N2   C2  C1   111.24  3.000
 49V  C3   C2  C1   106.98  3.000
 49V  H8   N2  C7   118.10  3.000
 49V  H8   N2  C2   117.78  3.000
 49V  C7   N2  C2   124.09  3.000
 49V  C8   C7  O7   121.52  3.000
 49V  C8   C7  N2   115.02  3.000
 49V  O7   C7  N2   123.46  3.000
 49V  H11  C8  H10  107.27  3.000
 49V  H11  C8  H9   108.21  3.000
 49V  H10  C8  H9   108.61  3.000
 49V  H11  C8  C7   109.23  3.000
 49V  H10  C8  C7   109.46  3.000
 49V  H9   C8  C7   113.85  3.000
 49V  H2   O1  C1   109.36  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
 49V  CONST_01  O7  C7  N2  C2     0.00   0.0  0
 49V  CONST_02  C8  C7  N2  C2   180.00   0.0  0
 49V  CONST_03  H8  N2  C7  O7   180.00   0.0  0
 49V  Var_01    C4  C5  O5  C1    14.57  30.0  1
 49V  Var_02    C3  C4  C5  O5     0.91  30.0  1
 49V  Var_03    O6  C6  C5  O5  -179.63  30.0  3
 49V  Var_04    H9  C8  C7  N2     5.96  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
 49V  chir_01  C1  O5  C2  O1  positiv
 49V  chir_02  C3  O3  C4  C2  negativ
 49V  chir_03  C2  N2  C3  C1  negativ

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
 49V  plan-1  C2  0.020
 49V  plan-1  N2  0.020
 49V  plan-1  C7  0.020
 49V  plan-1  O7  0.020
 49V  plan-1  C8  0.020
 49V  plan-1  H8  0.020
 49V  plan-2  C5  0.020
 49V  plan-2  C6  0.020
 49V  plan-2  O6  0.020
 49V  plan-2  O9  0.020

