# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:01:48 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: methyl 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](OC(C)=O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CO)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
 ANA  ANA  'methyl 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  D-saccharide  47  25  .  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_ANA
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
 ANA  C1    C  C      0   0.345   2.7165  -0.9361   0.3123
 ANA  C2    C  CT     0   0.432   2.1091   0.5081   0.2559
 ANA  C3    C  CH2    0  -0.506   1.7386   0.9165  -1.1663
 ANA  C4    C  CH1    0   0.035   0.5612   0.0888  -1.6394
 ANA  C5    C  CH1    0  -0.102  -0.6190   0.2581  -0.6864
 ANA  C6    C  CH1    0   0.023  -0.1751  -0.0740   0.7467
 ANA  C7    C  CH1    0  -0.014  -1.2397   0.3261   1.7690
 ANA  C8    C  CH1    0  -0.021  -0.9280  -0.2370   3.1678
 ANA  C9    C  CH2    0  -0.161  -1.9475   0.2443   4.1886
 ANA  C11   C  CH3    0  -0.787  -3.7934  -1.2480  -2.0868
 ANA  CM4   C  CH3    0  -0.772  -0.6709   0.4218  -5.1050
 ANA  N5    N  NH1    0  -0.629  -1.7285  -0.5788  -1.0655
 ANA  O1A   O  O      0  -0.570   2.3511  -1.6802   1.2341
 ANA  O1B   O  OC    -1  -0.594   3.5485  -1.1827  -0.5806
 ANA  O2    O  O2     0  -0.508   3.0410   1.4426   0.6991
 ANA  O4    O  O2     0  -0.466   0.1784   0.5557  -2.9366
 ANA  O6    O  O2     0  -0.518   0.9810   0.6510   1.0908
 ANA  O7    O  OH1    0  -0.666  -1.4171   1.7235   1.7887
 ANA  O8    O  OH1    0  -0.658  -0.8601  -1.6446   3.1287
 ANA  O9    O  OH1    0  -0.671  -1.6019  -0.2739   5.4528
 ANA  O10   O  O      0  -0.490  -3.0226   1.0251  -2.0029
 ANA  OA4   O  O      0  -0.449  -0.2316  -1.5016  -3.7338
 ANA  H31   H  HCH2   0   0.242   1.4693   1.9777  -1.1738
 ANA  H32   H  HCH2   0   0.259   2.5913   0.7774  -1.8296
 ANA  H4    H  HCH1   0   0.248   0.8438  -0.9661  -1.6981
 ANA  H5    H  HCH1   0   0.262  -0.9522   1.2972  -0.7288
 ANA  H6    H  HCH1   0   0.239   0.0033  -1.1527   0.8242
 ANA  H7    H  HCH1   0   0.238  -2.1978  -0.0978   1.4458
 ANA  H8    H  HCH1   0   0.234   0.0675   0.1000   3.4764
 ANA  H91   H  HCH2   0   0.206  -1.9666   1.3384   4.1938
 ANA  H92   H  HCH2   0   0.185  -2.9499  -0.0893   3.8756
 ANA  H111  H  HCH3   0   0.261  -4.6517  -0.8421  -2.6151
 ANA  H112  H  HCH3   0   0.262  -3.3110  -1.9920  -2.7226
 ANA  H113  H  HCH3   0   0.266  -4.1426  -1.7648  -1.1920
 ANA  H121  H  HCH3   0   0.232   4.2543   2.0732   2.1784
 ANA  H122  H  HCH3   0   0.217   2.9169   1.0680   2.7545
 ANA  H123  H  HCH3   0   0.210   4.3055   0.3249   1.9373
 ANA  HM41  H  HCH3   0   0.260  -1.0170  -0.2816  -5.8569
 ANA  HM42  H  HCH3   0   0.269  -1.4767   1.1167  -4.8665
 ANA  HM43  H  HCH3   0   0.273   0.1495   1.0091  -5.5184
 ANA  HN5   H  HNH1   0   0.398  -1.6156  -1.5743  -0.9470
 ANA  HO7   H  HOH1   0   0.443  -0.5472   2.1262   1.8960
 ANA  HO8   H  HOH1   0   0.441  -1.7425  -1.9886   2.9505
 ANA  HO9   H  HOH1   0   0.454  -2.2329   0.0660   6.0929
 ANA  C10   C  C      0   0.504  -2.8252  -0.1478  -1.7255
 ANA  C12   C  CH3    0  -0.419   3.6467   1.1979   1.9530
 ANA  CA4   C  C      0   0.562  -0.2279  -0.3045  -3.8699

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
 ANA  C1   C2    single  1.568  0.020  1.568
 ANA  C1   O1A   deloc   1.240  0.020  1.240
 ANA  C1   O1B   deloc   1.245  0.020  1.245
 ANA  C2   C3    single  1.525  0.020  1.525
 ANA  C2   O2    single  1.392  0.020  1.392
 ANA  C2   O6    single  1.411  0.020  1.411
 ANA  C3   C4    single  1.515  0.020  1.515
 ANA  C3   H31   single  0.970  0.020  1.090
 ANA  C3   H32   single  0.970  0.020  1.090
 ANA  C4   C5    single  1.526  0.020  1.526
 ANA  C4   O4    single  1.431  0.020  1.431
 ANA  C4   H4    single  0.970  0.020  1.090
 ANA  C5   C6    single  1.537  0.020  1.537
 ANA  C5   N5    single  1.441  0.020  1.441
 ANA  C5   H5    single  0.970  0.020  1.090
 ANA  C6   C7    single  1.529  0.020  1.529
 ANA  C6   O6    single  1.407  0.020  1.407
 ANA  C6   H6    single  0.970  0.020  1.090
 ANA  C7   C8    single  1.540  0.020  1.540
 ANA  C7   O7    single  1.409  0.020  1.409
 ANA  C7   H7    single  0.970  0.020  1.090
 ANA  C8   C9    single  1.521  0.020  1.521
 ANA  C8   O8    single  1.410  0.020  1.410
 ANA  C8   H8    single  0.970  0.020  1.090
 ANA  C9   O9    single  1.409  0.020  1.409
 ANA  C9   H91   single  0.970  0.020  1.090
 ANA  C9   H92   single  0.970  0.020  1.090
 ANA  C10  C11   single  1.509  0.020  1.509
 ANA  C10  N5    single  1.351  0.020  1.351
 ANA  C10  O10   double  1.221  0.020  1.221
 ANA  C11  H111  single  0.970  0.020  1.090
 ANA  C11  H112  single  0.970  0.020  1.090
 ANA  C11  H113  single  0.970  0.020  1.090
 ANA  C12  O2    single  1.414  0.020  1.414
 ANA  C12  H121  single  0.970  0.020  1.090
 ANA  C12  H122  single  0.970  0.020  1.090
 ANA  C12  H123  single  0.970  0.020  1.090
 ANA  CA4  CM4   single  1.500  0.020  1.500
 ANA  CA4  O4    single  1.333  0.020  1.333
 ANA  CA4  OA4   double  1.205  0.020  1.205
 ANA  CM4  HM41  single  0.970  0.020  1.090
 ANA  CM4  HM42  single  0.970  0.020  1.090
 ANA  CM4  HM43  single  0.970  0.020  1.090
 ANA  N5   HN5   single  0.860  0.020  1.020
 ANA  O7   HO7   single  0.850  0.020  0.980
 ANA  O8   HO8   single  0.850  0.020  0.980
 ANA  O9   HO9   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
 ANA  O1B   C1   O1A   127.68  3.000
 ANA  O1B   C1   C2    114.56  3.000
 ANA  O1A   C1   C2    117.74  3.000
 ANA  O6    C2   O2    106.20  3.000
 ANA  O6    C2   C3    109.30  3.000
 ANA  O2    C2   C3    106.24  3.000
 ANA  O6    C2   C1    112.45  3.000
 ANA  O2    C2   C1    110.34  3.000
 ANA  C3    C2   C1    111.98  3.000
 ANA  H32   C3   H31   108.19  3.000
 ANA  H32   C3   C4    110.39  3.000
 ANA  H31   C3   C4    109.64  3.000
 ANA  H32   C3   C2    110.09  3.000
 ANA  H31   C3   C2    109.00  3.000
 ANA  C4    C3   C2    109.49  3.000
 ANA  H4    C4   O4    109.59  3.000
 ANA  H4    C4   C5    109.89  3.000
 ANA  O4    C4   C5    108.85  3.000
 ANA  H4    C4   C3    110.06  3.000
 ANA  O4    C4   C3    108.23  3.000
 ANA  C5    C4   C3    110.20  3.000
 ANA  H5    C5   N5    107.91  3.000
 ANA  H5    C5   C6    109.26  3.000
 ANA  N5    C5   C6    110.03  3.000
 ANA  H5    C5   C4    108.50  3.000
 ANA  N5    C5   C4    111.52  3.000
 ANA  C6    C5   C4    109.57  3.000
 ANA  H6    C6   O6    110.86  3.000
 ANA  H6    C6   C7    108.87  3.000
 ANA  O6    C6   C7    105.89  3.000
 ANA  H6    C6   C5    109.00  3.000
 ANA  O6    C6   C5    110.73  3.000
 ANA  C7    C6   C5    111.46  3.000
 ANA  H7    C7   O7    106.12  3.000
 ANA  H7    C7   C8    107.66  3.000
 ANA  O7    C7   C8    112.06  3.000
 ANA  H7    C7   C6    108.07  3.000
 ANA  O7    C7   C6    110.89  3.000
 ANA  C8    C7   C6    111.76  3.000
 ANA  H8    C8   O8    105.73  3.000
 ANA  H8    C8   C9    108.83  3.000
 ANA  O8    C8   C9    111.53  3.000
 ANA  H8    C8   C7    109.11  3.000
 ANA  O8    C8   C7    110.47  3.000
 ANA  C9    C8   C7    111.00  3.000
 ANA  H92   C9   H91   106.76  3.000
 ANA  H92   C9   O9    111.50  3.000
 ANA  H91   C9   O9    111.57  3.000
 ANA  H92   C9   C8    108.87  3.000
 ANA  H91   C9   C8    109.35  3.000
 ANA  O9    C9   C8    108.74  3.000
 ANA  H113  C11  H112  107.25  3.000
 ANA  H113  C11  H111  108.84  3.000
 ANA  H112  C11  H111  108.71  3.000
 ANA  H113  C11  C10   110.75  3.000
 ANA  H112  C11  C10   110.67  3.000
 ANA  H111  C11  C10   110.53  3.000
 ANA  HM43  CM4  HM42  107.20  3.000
 ANA  HM43  CM4  HM41  109.03  3.000
 ANA  HM42  CM4  HM41  109.19  3.000
 ANA  HM43  CM4  CA4   110.53  3.000
 ANA  HM42  CM4  CA4   110.29  3.000
 ANA  HM41  CM4  CA4   110.52  3.000
 ANA  HN5   N5   C10   117.59  3.000
 ANA  HN5   N5   C5    117.14  3.000
 ANA  C10   N5   C5    124.66  3.000
 ANA  C12   O2   C2    116.93  3.000
 ANA  CA4   O4   C4    120.39  3.000
 ANA  C6    O6   C2    117.39  3.000
 ANA  HO7   O7   C7    107.59  3.000
 ANA  HO8   O8   C8    108.51  3.000
 ANA  HO9   O9   C9    107.84  3.000
 ANA  O10   C10  N5    123.28  3.000
 ANA  O10   C10  C11   122.81  3.000
 ANA  N5    C10  C11   113.91  3.000
 ANA  H123  C12  H122  108.56  3.000
 ANA  H123  C12  H121  107.96  3.000
 ANA  H122  C12  H121  108.45  3.000
 ANA  H123  C12  O2    112.55  3.000
 ANA  H122  C12  O2    112.66  3.000
 ANA  H121  C12  O2    106.47  3.000
 ANA  OA4   CA4  O4    124.27  3.000
 ANA  OA4   CA4  CM4   124.98  3.000
 ANA  O4    CA4  CM4   110.75  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
 ANA  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 ANA  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 ANA  CONST_03  HN5   N5   C10  C11     0.00   0.0  0
 ANA  Var_01    CM4   CA4  O4   C4    175.78  30.0  1
 ANA  Var_02    H121  C12  O2   C2   -174.08  30.0  3
 ANA  Var_03    H111  C11  C10  N5   -179.93  30.0  3
 ANA  Var_04    HM41  CM4  CA4  O4   -179.05  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
 ANA  chir_01  C2  C3  O2  O6  negativ
 ANA  chir_02  C4  O4  C5  C3  positiv
 ANA  chir_03  C5  N5  C6  C4  negativ
 ANA  chir_04  C6  O6  C7  C5  negativ
 ANA  chir_05  C7  O7  C6  C8  negativ
 ANA  chir_06  C8  O8  C7  C9  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
 ANA  plan-1  C5   0.020
 ANA  plan-1  C11  0.020
 ANA  plan-1  N5   0.020
 ANA  plan-1  O10  0.020
 ANA  plan-1  HN5  0.020
 ANA  plan-1  C10  0.020
 ANA  plan-2  C1   0.020
 ANA  plan-2  C2   0.020
 ANA  plan-2  O1A  0.020
 ANA  plan-2  O1B  0.020
 ANA  plan-3  CM4  0.020
 ANA  plan-3  O4   0.020
 ANA  plan-3  OA4  0.020
 ANA  plan-3  CA4  0.020

