# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 22:18:54 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](C)[C@@H](NC(=O)[C@H](O)CCO)[C@H](O)[C@@H]1O
#
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
 ZD0  ZD0  'methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-alpha-D-mannopyranoside'  D-saccharide  40  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZD0
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
 ZD0  C1    C  CH1   0   0.249  42.1587  36.7390   -7.9117
 ZD0  C1M   C  CH3   0  -0.432  43.2737  38.1764   -6.2753
 ZD0  C2    C  CH1   0  -0.041  41.6764  35.7461   -6.8433
 ZD0  C3    C  CH1   0   0.016  42.8179  34.9585   -6.2055
 ZD0  C4    C  CH1   0  -0.124  43.7049  34.3527   -7.2906
 ZD0  C5    C  CH1   0   0.042  44.2238  35.4646   -8.2091
 ZD0  C6    C  CH3   0  -0.679  45.0224  34.9320   -9.3811
 ZD0  C8    C  CH1   0  -0.064  46.3772  31.8240   -6.3042
 ZD0  C9    C  CH2   0  -0.486  47.5052  31.7464   -7.3305
 ZD0  C10   C  CH2   0  -0.159  48.7716  31.1042   -6.7981
 ZD0  N4    N  NH1   0  -0.650  44.7904  33.6220   -6.6818
 ZD0  O1    O  O2    0  -0.488  42.5007  38.0077   -7.4451
 ZD0  O2    O  OH1   0  -0.672  40.7938  34.8765   -7.5139
 ZD0  O3    O  OH1   0  -0.667  42.2345  33.9796   -5.3822
 ZD0  O5    O  O2    0  -0.495  43.1294  36.1879   -8.7566
 ZD0  O7    O  O     0  -0.489  44.5104  31.6615   -7.7912
 ZD0  O8    O  OH1   0  -0.664  46.8011  32.6318   -5.2328
 ZD0  O10   O  OH1   0  -0.675  48.4848  29.7762   -6.4169
 ZD0  H101  H  HCH2  0   0.209  49.5313  31.1397   -7.5887
 ZD0  H102  H  HCH2  0   0.201  49.1608  31.6909   -5.9585
 ZD0  H10O  H  HOH1  0   0.455  49.2812  29.3910   -6.0411
 ZD0  H1    H  HCH1  0   0.246  41.3083  36.9279   -8.5715
 ZD0  H1M1  H  HCH3  0   0.254  43.4224  39.2482   -6.1530
 ZD0  H1M2  H  HCH3  0   0.219  42.7665  37.8101   -5.3777
 ZD0  H1M3  H  HCH3  0   0.217  44.8758  36.1302   -7.6243
 ZD0  H2    H  HCH1  0   0.245  41.1457  36.3072   -6.0605
 ZD0  HO2   H  HOH1  0   0.454  40.5619  34.1650   -6.9068
 ZD0  H3    H  HCH1  0   0.222  43.4328  35.6427   -5.6044
 ZD0  HO3   H  HOH1  0   0.455  42.9311  33.4001   -5.0555
 ZD0  H4    H  HCH1  0   0.264  43.1235  33.6452   -7.8857
 ZD0  H4N   H  HNH1  0   0.402  45.4085  34.1130   -6.0506
 ZD0  H5    H  HCH1  0   0.216  44.2600  37.7101   -6.3353
 ZD0  H61   H  HCH3  0   0.247  45.3585  35.7520  -10.0160
 ZD0  H62   H  HCH3  0   0.233  45.9101  34.4024   -9.0376
 ZD0  H63   H  HCH3  0   0.232  44.4275  34.2462   -9.9862
 ZD0  H8    H  HCH1  0   0.255  46.1321  30.8117   -5.9646
 ZD0  H8O   H  HOH1  0   0.464  46.2967  32.4011   -4.4466
 ZD0  H91   H  HCH2  0   0.251  47.1539  31.1919   -8.2031
 ZD0  H92   H  HCH2  0   0.243  47.7520  32.7545   -7.6779
 ZD0  C7    C  C     0   0.496  45.1241  32.3578   -6.9969

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
 ZD0  C1   O1    single  1.394  0.020  1.394
 ZD0  C1   O5    single  1.400  0.020  1.400
 ZD0  C1   C2    single  1.536  0.020  1.536
 ZD0  O1   C1M   single  1.412  0.020  1.412
 ZD0  C1   H1    single  0.970  0.020  1.090
 ZD0  C1M  H1M1  single  0.970  0.020  1.090
 ZD0  C1M  H1M2  single  0.970  0.020  1.090
 ZD0  C1M  H1M3  single  0.970  0.020  1.090
 ZD0  C2   O2    single  1.409  0.020  1.409
 ZD0  C2   H2    single  0.970  0.020  1.090
 ZD0  O2   HO2   single  0.850  0.020  0.980
 ZD0  C2   C3    single  1.526  0.020  1.526
 ZD0  C3   O3    single  1.406  0.020  1.406
 ZD0  C3   H3    single  0.970  0.020  1.090
 ZD0  O3   HO3   single  0.850  0.020  0.980
 ZD0  C3   C4    single  1.527  0.020  1.527
 ZD0  C4   H4    single  0.970  0.020  1.090
 ZD0  C4   N4    single  1.443  0.020  1.443
 ZD0  N4   H4N   single  0.860  0.020  1.020
 ZD0  C4   C5    single  1.533  0.020  1.533
 ZD0  C5   O5    single  1.421  0.020  1.421
 ZD0  C5   C6    single  1.515  0.020  1.515
 ZD0  C5   H5    single  0.970  0.020  1.090
 ZD0  C6   H61   single  0.970  0.020  1.090
 ZD0  C6   H62   single  0.970  0.020  1.090
 ZD0  C6   H63   single  0.970  0.020  1.090
 ZD0  N4   C7    single  1.345  0.020  1.345
 ZD0  C7   O7    double  1.222  0.020  1.222
 ZD0  C7   C8    single  1.528  0.020  1.528
 ZD0  C8   H8    single  0.970  0.020  1.090
 ZD0  C8   O8    single  1.407  0.020  1.407
 ZD0  O8   H8O   single  0.850  0.020  0.980
 ZD0  C8   C9    single  1.527  0.020  1.527
 ZD0  C9   H91   single  0.970  0.020  1.090
 ZD0  C9   H92   single  0.970  0.020  1.090
 ZD0  C9   C10   single  1.516  0.020  1.516
 ZD0  C10  H101  single  0.970  0.020  1.090
 ZD0  C10  H102  single  0.970  0.020  1.090
 ZD0  C10  O10   single  1.411  0.020  1.411
 ZD0  O10  H10O  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
 ZD0  H1    C1   O5    104.08  3.000
 ZD0  H1    C1   O1    103.63  3.000
 ZD0  O5    C1   O1    112.96  3.000
 ZD0  H1    C1   C2    106.70  3.000
 ZD0  O5    C1   C2    112.52  3.000
 ZD0  O1    C1   C2    115.62  3.000
 ZD0  H1M3  C1M  H1M2  113.43  3.000
 ZD0  H1M3  C1M  H1M1  131.67  3.000
 ZD0  H1M2  C1M  H1M1  107.50  3.000
 ZD0  H1M3  C1M  O1     80.47  3.000
 ZD0  H1M2  C1M  O1    112.70  3.000
 ZD0  H1M1  C1M  O1    106.58  3.000
 ZD0  H2    C2   O2    110.58  3.000
 ZD0  H2    C2   C3    109.07  3.000
 ZD0  O2    C2   C3    110.42  3.000
 ZD0  C3    C2   C1    112.91  3.000
 ZD0  H2    C2   C1    108.47  3.000
 ZD0  O2    C2   C1    105.34  3.000
 ZD0  H3    C3   O3    110.20  3.000
 ZD0  H3    C3   C4    108.10  3.000
 ZD0  O3    C3   C4    112.40  3.000
 ZD0  C4    C3   C2    110.01  3.000
 ZD0  H3    C3   C2    109.01  3.000
 ZD0  O3    C3   C2    107.07  3.000
 ZD0  H4    C4   N4    107.60  3.000
 ZD0  N4    C4   C5    111.44  3.000
 ZD0  H4    C4   C5    108.89  3.000
 ZD0  C5    C4   C3    109.56  3.000
 ZD0  N4    C4   C3    109.75  3.000
 ZD0  H4    C4   C3    109.57  3.000
 ZD0  H5    C5   O5     82.28  3.000
 ZD0  H5    C5   C6    139.38  3.000
 ZD0  O5    C5   C6    106.66  3.000
 ZD0  H5    C5   C4    100.21  3.000
 ZD0  C6    C5   C4    112.77  3.000
 ZD0  O5    C5   C4    109.83  3.000
 ZD0  H63   C6   H62   108.29  3.000
 ZD0  H63   C6   H61   108.54  3.000
 ZD0  H62   C6   H61   107.34  3.000
 ZD0  H63   C6   C5    111.26  3.000
 ZD0  H62   C6   C5    110.89  3.000
 ZD0  H61   C6   C5    110.40  3.000
 ZD0  H8    C8   O8    111.21  3.000
 ZD0  O8    C8   C9    108.56  3.000
 ZD0  H8    C8   C9    109.07  3.000
 ZD0  C9    C8   C7    108.60  3.000
 ZD0  O8    C8   C7    113.06  3.000
 ZD0  H8    C8   C7    106.25  3.000
 ZD0  H92   C9   H91   106.65  3.000
 ZD0  H92   C9   C10   108.26  3.000
 ZD0  H91   C9   C10   109.52  3.000
 ZD0  C10   C9   C8    113.73  3.000
 ZD0  H92   C9   C8    109.46  3.000
 ZD0  H91   C9   C8    108.98  3.000
 ZD0  H102  C10  H101  106.79  3.000
 ZD0  H102  C10  O10   111.67  3.000
 ZD0  H101  C10  O10   111.46  3.000
 ZD0  O10   C10  C9    108.89  3.000
 ZD0  H102  C10  C9    109.81  3.000
 ZD0  H101  C10  C9    108.16  3.000
 ZD0  H4N   N4   C7    116.82  3.000
 ZD0  C7    N4   C4    124.31  3.000
 ZD0  H4N   N4   C4    118.52  3.000
 ZD0  C1M   O1   C1    121.34  3.000
 ZD0  HO2   O2   C2    107.85  3.000
 ZD0  HO3   O3   C3    108.50  3.000
 ZD0  C5    O5   C1    120.11  3.000
 ZD0  H8O   O8   C8    109.06  3.000
 ZD0  H10O  O10  C10   108.32  3.000
 ZD0  O7    C7   N4    124.30  3.000
 ZD0  O7    C7   C8    120.50  3.000
 ZD0  N4    C7   C8    115.19  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
 ZD0  CONST_01  O7    C7   N4  C4    0.00   0.0  0
 ZD0  CONST_02  C8    C7   N4  C4  180.00   0.0  0
 ZD0  CONST_03  H4N   N4   C7  C8    0.00   0.0  0
 ZD0  Var_01    H1M1  C1M  O1  C1  178.24  30.0  3
 ZD0  Var_02    O10   C10  C9  C8   61.44  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
 ZD0  chir_01  C1  O1  O5  C2  negativ
 ZD0  chir_02  C2  O2  C1  C3  positiv
 ZD0  chir_03  C3  O3  C2  C4  positiv
 ZD0  chir_04  C4  N4  C5  C3  positiv
 ZD0  chir_05  C5  O5  C4  C6  negativ
 ZD0  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
 ZD0  plan-1  C4   0.020
 ZD0  plan-1  C8   0.020
 ZD0  plan-1  N4   0.020
 ZD0  plan-1  O7   0.020
 ZD0  plan-1  H4N  0.020
 ZD0  plan-1  C7   0.020

