# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 14:39:17 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: methyl 9-(alpha-D-mannopyranosyloxy)nonanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[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
 XNS  XNS  'methyl 9-(alpha-D-mannopyranosyloxy)nonanoate'  ligand  54  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XNS
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
 XNS  C14   C  CH2   0  -0.581   -7.2789   0.5210  -0.4974
 XNS  O7    O  O     0  -0.453   -8.6719  -0.9221   0.8408
 XNS  C15   C  C     0   0.600   -8.5732  -0.0612   0.0024
 XNS  O8    O  O2    0  -0.457   -9.6210   0.4935  -0.5974
 XNS  C16   C  CH3   0  -0.423  -10.9182   0.0389  -0.2141
 XNS  C13   C  CH2   0  -0.418   -6.0451  -0.0610   0.1731
 XNS  C12   C  CH2   0  -0.416   -4.7628   0.5701  -0.3541
 XNS  C11   C  CH2   0  -0.413   -3.5111   0.0169   0.3142
 XNS  C10   C  CH2   0  -0.412   -2.2274   0.6535  -0.2022
 XNS  C9    C  CH2   0  -0.426   -0.9761   0.1194   0.4829
 XNS  C8    C  CH2   0  -0.463    0.3031   0.7668  -0.0334
 XNS  C7    C  CH2   0  -0.133    1.5265   0.2538   0.6979
 XNS  O1    O  O2    0  -0.507    2.6811   0.8745   0.1588
 XNS  C1    C  CH1   0   0.242    3.8209   0.7836   0.9493
 XNS  C2    C  CH1   0  -0.030    4.9109   1.6356   0.2913
 XNS  O2    O  OH1   0  -0.668    6.0179   1.7625   1.1466
 XNS  C3    C  CH1   0   0.002    5.3708   0.9551  -0.9948
 XNS  O3    O  OH1   0  -0.673    6.4612   1.6119  -1.5966
 XNS  C4    C  CH1   0   0.032    5.7973  -0.4826  -0.7207
 XNS  O4    O  OH1   0  -0.677    6.0795  -1.1654  -1.9199
 XNS  C5    C  CH1   0  -0.010    4.6598  -1.2279  -0.0210
 XNS  O5    O  O2    0  -0.499    4.2502  -0.5316   1.1429
 XNS  C6    C  CH2   0  -0.160    5.0849  -2.6137   0.4172
 XNS  O6    O  OH1   0  -0.670    3.9709  -3.2800   0.9628
 XNS  H141  H  HCH2  0   0.273   -7.2330   0.3718  -1.5810
 XNS  H142  H  HCH2  0   0.272   -7.3148   1.6059  -0.3554
 XNS  H131  H  HCH2  0   0.224   -6.1050   0.0903   1.2542
 XNS  H132  H  HCH2  0   0.224   -6.0099  -1.1423   0.0146
 XNS  H161  H  HCH3  0   0.250  -11.6240   0.6109  -0.8091
 XNS  H162  H  HCH3  0   0.237  -11.0485  -1.0226  -0.4236
 XNS  H163  H  HCH3  0   0.237  -11.1084   0.2202   0.8435
 XNS  H121  H  HCH2  0   0.213   -4.6965   0.4156  -1.4367
 XNS  H122  H  HCH2  0   0.212   -4.8030   1.6548  -0.2058
 XNS  H111  H  HCH2  0   0.210   -3.5814   0.1694   1.3968
 XNS  H112  H  HCH2  0   0.210   -3.4662  -1.0673   0.1639
 XNS  H101  H  HCH2  0   0.211   -2.1489   0.4909  -1.2826
 XNS  H102  H  HCH2  0   0.210   -2.2801   1.7388  -0.0629
 XNS  H91C  H  HCH2  0   0.214   -1.0588   0.2831   1.5629
 XNS  H92C  H  HCH2  0   0.215   -0.9199  -0.9655   0.3441
 XNS  H81C  H  HCH2  0   0.224    0.4063   0.5704  -1.1051
 XNS  H82C  H  HCH2  0   0.221    0.2381   1.8527   0.0854
 XNS  H71C  H  HCH2  0   0.201    1.4414   0.4786   1.7700
 XNS  H72C  H  HCH2  0   0.209    1.5931  -0.8363   0.6032
 XNS  H1    H  HCH1  0   0.232    3.6129   1.1596   1.9629
 XNS  H2    H  HCH1  0   0.230    4.4812   2.6177   0.0472
 XNS  HA    H  HOH1  0   0.455    5.7538   2.2768   1.9158
 XNS  H3    H  HCH1  0   0.227    4.5118   0.9211  -1.6784
 XNS  HB    H  HOH1  0   0.457    6.1411   2.4043  -2.0384
 XNS  H4    H  HCH1  0   0.211    6.6768  -0.4760  -0.0591
 XNS  HC    H  HOH1  0   0.452    6.7442  -0.6584  -2.3980
 XNS  H5    H  HCH1  0   0.223    3.8247  -1.3230  -0.7305
 XNS  H61C  H  HCH2  0   0.210    5.4888  -3.1446  -0.4513
 XNS  H62C  H  HCH2  0   0.194    5.9016  -2.5187   1.1463
 XNS  H6    H  HOH1  0   0.455    4.2477  -4.1673   1.2081

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
 XNS  C14  C15   single  1.505  0.020  1.505
 XNS  C14  C13   single  1.520  0.020  1.520
 XNS  O7   C15   double  1.206  0.020  1.206
 XNS  C15  O8    single  1.329  0.020  1.329
 XNS  O8   C16   single  1.427  0.020  1.427
 XNS  C13  C12   single  1.523  0.020  1.523
 XNS  C12  C11   single  1.523  0.020  1.523
 XNS  C11  C10   single  1.523  0.020  1.523
 XNS  C10  C9    single  1.523  0.020  1.523
 XNS  C9   C8    single  1.524  0.020  1.524
 XNS  C8   C7    single  1.515  0.020  1.515
 XNS  C7   O1    single  1.417  0.020  1.417
 XNS  O1   C1    single  1.390  0.020  1.390
 XNS  C1   C2    single  1.532  0.020  1.532
 XNS  C1   O5    single  1.397  0.020  1.397
 XNS  C2   O2    single  1.405  0.020  1.405
 XNS  C2   C3    single  1.526  0.020  1.526
 XNS  C3   O3    single  1.408  0.020  1.408
 XNS  C3   C4    single  1.524  0.020  1.524
 XNS  C4   O4    single  1.409  0.020  1.409
 XNS  C4   C5    single  1.529  0.020  1.529
 XNS  C5   O5    single  1.417  0.020  1.417
 XNS  C5   C6    single  1.514  0.020  1.514
 XNS  C6   O6    single  1.408  0.020  1.408
 XNS  C14  H141  single  0.970  0.020  1.090
 XNS  C14  H142  single  0.970  0.020  1.090
 XNS  C13  H131  single  0.970  0.020  1.090
 XNS  C13  H132  single  0.970  0.020  1.090
 XNS  C16  H161  single  0.970  0.020  1.090
 XNS  C16  H162  single  0.970  0.020  1.090
 XNS  C16  H163  single  0.970  0.020  1.090
 XNS  C12  H121  single  0.970  0.020  1.090
 XNS  C12  H122  single  0.970  0.020  1.090
 XNS  C11  H111  single  0.970  0.020  1.090
 XNS  C11  H112  single  0.970  0.020  1.090
 XNS  C10  H101  single  0.970  0.020  1.090
 XNS  C10  H102  single  0.970  0.020  1.090
 XNS  C9   H91C  single  0.970  0.020  1.090
 XNS  C9   H92C  single  0.970  0.020  1.090
 XNS  C8   H81C  single  0.970  0.020  1.090
 XNS  C8   H82C  single  0.970  0.020  1.090
 XNS  C7   H71C  single  0.970  0.020  1.090
 XNS  C7   H72C  single  0.970  0.020  1.090
 XNS  C1   H1    single  0.970  0.020  1.090
 XNS  C2   H2    single  0.970  0.020  1.090
 XNS  O2   HA    single  0.850  0.020  0.980
 XNS  C3   H3    single  0.970  0.020  1.090
 XNS  O3   HB    single  0.850  0.020  0.980
 XNS  C4   H4    single  0.970  0.020  1.090
 XNS  O4   HC    single  0.850  0.020  0.980
 XNS  C5   H5    single  0.970  0.020  1.090
 XNS  C6   H61C  single  0.970  0.020  1.090
 XNS  C6   H62C  single  0.970  0.020  1.090
 XNS  O6   H6    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
 XNS  H142  C14  H141  105.35  3.000
 XNS  H142  C14  C13   110.42  3.000
 XNS  H141  C14  C13   110.51  3.000
 XNS  H142  C14  C15   108.19  3.000
 XNS  H141  C14  C15   108.18  3.000
 XNS  C13   C14  C15   113.80  3.000
 XNS  O8    C15  O7    123.19  3.000
 XNS  O8    C15  C14   111.52  3.000
 XNS  O7    C15  C14   125.28  3.000
 XNS  C16   O8   C15   117.55  3.000
 XNS  H163  C16  H162  109.14  3.000
 XNS  H163  C16  H161  109.31  3.000
 XNS  H162  C16  H161  109.27  3.000
 XNS  H163  C16  O8    111.49  3.000
 XNS  H162  C16  O8    111.56  3.000
 XNS  H161  C16  O8    106.01  3.000
 XNS  H132  C13  H131  106.38  3.000
 XNS  H132  C13  C12   109.42  3.000
 XNS  H131  C13  C12   109.33  3.000
 XNS  H132  C13  C14   109.93  3.000
 XNS  H131  C13  C14   109.80  3.000
 XNS  C12   C13  C14   111.84  3.000
 XNS  H122  C12  H121  106.00  3.000
 XNS  H122  C12  C11   109.29  3.000
 XNS  H121  C12  C11   109.43  3.000
 XNS  H122  C12  C13   109.42  3.000
 XNS  H121  C12  C13   109.54  3.000
 XNS  C11   C12  C13   112.92  3.000
 XNS  H112  C11  H111  106.02  3.000
 XNS  H112  C11  C10   109.43  3.000
 XNS  H111  C11  C10   109.33  3.000
 XNS  H112  C11  C12   109.44  3.000
 XNS  H111  C11  C12   109.29  3.000
 XNS  C10   C11  C12   113.09  3.000
 XNS  H102  C10  H101  106.02  3.000
 XNS  H102  C10  C9    109.25  3.000
 XNS  H101  C10  C9    109.43  3.000
 XNS  H102  C10  C11   109.29  3.000
 XNS  H101  C10  C11   109.43  3.000
 XNS  C9    C10  C11   113.16  3.000
 XNS  H92C  C9   H91C  106.07  3.000
 XNS  H92C  C9   C8    109.56  3.000
 XNS  H91C  C9   C8    109.50  3.000
 XNS  H92C  C9   C10   109.42  3.000
 XNS  H91C  C9   C10   109.21  3.000
 XNS  C8    C9   C10   112.85  3.000
 XNS  H82C  C8   H81C  106.85  3.000
 XNS  H82C  C8   C7    109.36  3.000
 XNS  H81C  C8   C7    109.63  3.000
 XNS  H82C  C8   C9    109.57  3.000
 XNS  H81C  C8   C9    109.55  3.000
 XNS  C7    C8   C9    111.75  3.000
 XNS  H72C  C7   H71C  107.00  3.000
 XNS  H72C  C7   O1    110.68  3.000
 XNS  H71C  C7   O1    110.16  3.000
 XNS  H72C  C7   C8    110.12  3.000
 XNS  H71C  C7   C8    109.83  3.000
 XNS  O1    C7   C8    109.02  3.000
 XNS  C1    O1   C7    115.02  3.000
 XNS  H1    C1   O5    104.60  3.000
 XNS  H1    C1   C2    109.87  3.000
 XNS  O5    C1   C2    111.37  3.000
 XNS  H1    C1   O1    110.27  3.000
 XNS  O5    C1   O1    113.10  3.000
 XNS  C2    C1   O1    107.63  3.000
 XNS  H2    C2   C3    109.21  3.000
 XNS  H2    C2   O2    111.25  3.000
 XNS  C3    C2   O2    108.42  3.000
 XNS  H2    C2   C1    108.30  3.000
 XNS  C3    C2   C1    109.17  3.000
 XNS  O2    C2   C1    110.46  3.000
 XNS  HA    O2   C2    108.59  3.000
 XNS  H3    C3   C4    107.55  3.000
 XNS  H3    C3   O3    110.74  3.000
 XNS  C4    C3   O3    107.46  3.000
 XNS  H3    C3   C2    107.62  3.000
 XNS  C4    C3   C2    110.69  3.000
 XNS  O3    C3   C2    112.68  3.000
 XNS  HB    O3   C3    108.83  3.000
 XNS  H4    C4   C5    108.80  3.000
 XNS  H4    C4   O4    110.77  3.000
 XNS  C5    C4   O4    107.60  3.000
 XNS  H4    C4   C3    109.03  3.000
 XNS  C5    C4   C3    109.50  3.000
 XNS  O4    C4   C3    111.11  3.000
 XNS  HC    O4   C4    107.81  3.000
 XNS  H5    C5   C6    108.70  3.000
 XNS  H5    C5   O5    110.67  3.000
 XNS  C6    C5   O5    107.05  3.000
 XNS  H5    C5   C4    108.16  3.000
 XNS  C6    C5   C4    111.69  3.000
 XNS  O5    C5   C4    110.57  3.000
 XNS  C5    O5   C1    115.96  3.000
 XNS  H62C  C6   H61C  107.10  3.000
 XNS  H62C  C6   O6    111.83  3.000
 XNS  H61C  C6   O6    111.70  3.000
 XNS  H62C  C6   C5    108.75  3.000
 XNS  H61C  C6   C5    108.52  3.000
 XNS  O6    C6   C5    108.85  3.000
 XNS  H6    O6   C6    107.93  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
 XNS  Var_01  H71C  C7   O1   C1     42.83  30.0  2
 XNS  Var_02  C11   C12  C13  C14   179.27  30.0  3
 XNS  Var_03  C13   C14  C15  O7     -0.95  30.0  2
 XNS  Var_04  C12   C13  C14  C15  -179.35  30.0  3
 XNS  Var_05  C10   C11  C12  C13  -179.53  30.0  3
 XNS  Var_06  C9    C10  C11  C12   178.97  30.0  3
 XNS  Var_07  C8    C9   C10  C11  -179.67  30.0  3
 XNS  Var_08  C7    C8   C9   C10   177.98  30.0  3
 XNS  Var_09  O1    C7   C8   C9    179.02  30.0  3
 XNS  Var_10  H161  C16  O8   C15   179.82  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
 XNS  chir_01  C1  O1  C2  O5  positiv
 XNS  chir_02  C2  O2  C1  C3  positiv
 XNS  chir_03  C3  O3  C2  C4  positiv
 XNS  chir_04  C4  O4  C5  C3  positiv
 XNS  chir_05  C5  O5  C4  C6  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
 XNS  plan-1  C14  0.020
 XNS  plan-1  O7   0.020
 XNS  plan-1  C15  0.020
 XNS  plan-1  O8   0.020

