# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 08:34:03 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-(propylsulfanyl)propyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCSCCCO[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
 FK9  FK9  '3-(propylsulfanyl)propyl alpha-D-mannopyranoside'  D-saccharide  43  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 OK
;

data_comp_FK9
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
 FK9  O6    O  OH1   0  -0.669  -1.9032   3.3686   0.8375
 FK9  C6    C  CH2   0  -0.160  -3.0361   2.6745   0.3717
 FK9  C5    C  CH1   0  -0.010  -2.6276   1.2656  -0.0042
 FK9  O5    O  O2    0  -0.499  -2.1878   0.6285   1.1826
 FK9  C4    C  CH1   0   0.031  -3.7876   0.4916  -0.6331
 FK9  O4    O  OH1   0  -0.676  -4.0988   1.1098  -1.8596
 FK9  C3    C  CH1   0   0.003  -3.3789  -0.9626  -0.8394
 FK9  O3    O  OH1   0  -0.673  -4.4898  -1.6425  -1.3740
 FK9  C2    C  CH1   0  -0.032  -2.8892  -1.5743   0.4698
 FK9  O2    O  OH1   0  -0.669  -3.9712  -1.6353   1.3639
 FK9  C1    C  CH1   0   0.243  -1.7724  -0.6981   1.0464
 FK9  O1    O  O2    0  -0.505  -0.6602  -0.8380   0.2225
 FK9  C7    C  CH2   0  -0.130   0.5204  -0.2199   0.6992
 FK9  C8    C  CH2   0  -0.469   1.6950  -0.7586  -0.0956
 FK9  C9    C  CH2   0  -0.551   2.9989  -0.1230   0.3645
 FK9  C13   C  CH2   0  -0.533   5.7689   0.0949   0.1576
 FK9  C14   C  CH2   0  -0.427   7.0873  -0.3887  -0.4289
 FK9  C15   C  CH3   0  -0.660   8.2733   0.3630   0.1604
 FK9  S1    S  S2    0  -0.039   4.3840  -0.8196  -0.5772
 FK9  H6    H  HOH1  0   0.455  -2.1755   4.2634   1.0594
 FK9  H61C  H  HCH2  0   0.195  -3.8255   2.6228   1.1343
 FK9  H62C  H  HCH2  0   0.210  -3.4711   3.1570  -0.5100
 FK9  H5    H  HCH1  0   0.223  -1.8116   1.3216  -0.7398
 FK9  H4    H  HCH1  0   0.212  -4.6488   0.5275   0.0512
 FK9  H1    H  HCH1  0   0.235  -1.5319  -1.0215   2.0704
 FK9  HA    H  HOH1  0   0.452  -4.7793   0.5819  -2.2906
 FK9  H3    H  HCH1  0   0.227  -2.5393  -0.9745  -1.5473
 FK9  HB    H  HOH1  0   0.457  -4.1872  -2.4588  -1.7835
 FK9  H2    H  HCH1  0   0.232  -2.4785  -2.5744   0.2716
 FK9  HC    H  HOH1  0   0.456  -3.7057  -2.1488   2.1331
 FK9  H71C  H  HCH2  0   0.214   0.4615   0.8695   0.5944
 FK9  H72C  H  HCH2  0   0.208   0.6567  -0.4364   1.7672
 FK9  H81C  H  HCH2  0   0.240   1.7493  -1.8434   0.0270
 FK9  H82C  H  HCH2  0   0.242   1.5424  -0.5574  -1.1591
 FK9  H91C  H  HCH2  0   0.261   2.9723   0.9588   0.2165
 FK9  H92C  H  HCH2  0   0.260   3.1610  -0.3103   1.4285
 FK9  H151  H  HCH3  0   0.234   9.2118   0.0088  -0.2659
 FK9  H152  H  HCH3  0   0.222   8.2016   1.4334  -0.0384
 FK9  H153  H  HCH3  0   0.222   8.3284   0.2299   1.2421
 FK9  H141  H  HCH2  0   0.229   7.1979  -1.4597  -0.2413
 FK9  H142  H  HCH2  0   0.229   7.0739  -0.2617  -1.5144
 FK9  H131  H  HCH2  0   0.255   5.7568  -0.0543   1.2399
 FK9  H132  H  HCH2  0   0.255   5.6365   1.1625  -0.0322

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
 FK9  O6   C6    single  1.408  0.020  1.408
 FK9  C6   C5    single  1.514  0.020  1.514
 FK9  C5   O5    single  1.417  0.020  1.417
 FK9  C5   C4    single  1.530  0.020  1.530
 FK9  O5   C1    single  1.397  0.020  1.397
 FK9  C4   O4    single  1.408  0.020  1.408
 FK9  C4   C3    single  1.525  0.020  1.525
 FK9  C3   O3    single  1.408  0.020  1.408
 FK9  C3   C2    single  1.526  0.020  1.526
 FK9  C2   O2    single  1.405  0.020  1.405
 FK9  C2   C1    single  1.532  0.020  1.532
 FK9  C1   O1    single  1.391  0.020  1.391
 FK9  O1   C7    single  1.415  0.020  1.415
 FK9  C7   C8    single  1.517  0.020  1.517
 FK9  C8   C9    single  1.522  0.020  1.522
 FK9  C9   S1    single  1.814  0.020  1.814
 FK9  C15  C14   single  1.523  0.020  1.523
 FK9  C14  C13   single  1.522  0.020  1.522
 FK9  C13  S1    single  1.815  0.020  1.815
 FK9  O6   H6    single  0.850  0.020  0.980
 FK9  C6   H61C  single  0.970  0.020  1.090
 FK9  C6   H62C  single  0.970  0.020  1.090
 FK9  C5   H5    single  0.970  0.020  1.090
 FK9  C4   H4    single  0.970  0.020  1.090
 FK9  C1   H1    single  0.970  0.020  1.090
 FK9  O4   HA    single  0.850  0.020  0.980
 FK9  C3   H3    single  0.970  0.020  1.090
 FK9  O3   HB    single  0.850  0.020  0.980
 FK9  C2   H2    single  0.970  0.020  1.090
 FK9  O2   HC    single  0.850  0.020  0.980
 FK9  C7   H71C  single  0.970  0.020  1.090
 FK9  C7   H72C  single  0.970  0.020  1.090
 FK9  C8   H81C  single  0.970  0.020  1.090
 FK9  C8   H82C  single  0.970  0.020  1.090
 FK9  C9   H91C  single  0.970  0.020  1.090
 FK9  C9   H92C  single  0.970  0.020  1.090
 FK9  C15  H151  single  0.970  0.020  1.090
 FK9  C15  H152  single  0.970  0.020  1.090
 FK9  C15  H153  single  0.970  0.020  1.090
 FK9  C14  H141  single  0.970  0.020  1.090
 FK9  C14  H142  single  0.970  0.020  1.090
 FK9  C13  H131  single  0.970  0.020  1.090
 FK9  C13  H132  single  0.970  0.020  1.090

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
 FK9  H6    O6   C6    107.90  3.000
 FK9  H62C  C6   H61C  107.11  3.000
 FK9  H62C  C6   C5    108.49  3.000
 FK9  H61C  C6   C5    108.80  3.000
 FK9  H62C  C6   O6    111.65  3.000
 FK9  H61C  C6   O6    111.81  3.000
 FK9  C5    C6   O6    108.89  3.000
 FK9  H5    C5   C4    108.26  3.000
 FK9  H5    C5   O5    110.66  3.000
 FK9  C4    C5   O5    110.62  3.000
 FK9  H5    C5   C6    108.58  3.000
 FK9  C4    C5   C6    111.60  3.000
 FK9  O5    C5   C6    107.11  3.000
 FK9  C1    O5   C5    115.95  3.000
 FK9  H4    C4   C3    108.97  3.000
 FK9  H4    C4   O4    110.75  3.000
 FK9  C3    C4   O4    111.10  3.000
 FK9  H4    C4   C5    108.74  3.000
 FK9  C3    C4   C5    109.57  3.000
 FK9  O4    C4   C5    107.67  3.000
 FK9  HA    O4   C4    107.78  3.000
 FK9  H3    C3   C2    107.66  3.000
 FK9  H3    C3   O3    110.68  3.000
 FK9  C2    C3   O3    112.67  3.000
 FK9  H3    C3   C4    107.61  3.000
 FK9  C2    C3   C4    110.63  3.000
 FK9  O3    C3   C4    107.48  3.000
 FK9  HB    O3   C3    108.86  3.000
 FK9  H2    C2   C1    108.41  3.000
 FK9  H2    C2   O2    111.29  3.000
 FK9  C1    C2   O2    110.28  3.000
 FK9  H2    C2   C3    109.27  3.000
 FK9  C1    C2   C3    109.12  3.000
 FK9  O2    C2   C3    108.44  3.000
 FK9  HC    O2   C2    108.63  3.000
 FK9  H1    C1   O1    110.29  3.000
 FK9  H1    C1   C2    109.97  3.000
 FK9  O1    C1   C2    107.60  3.000
 FK9  H1    C1   O5    104.67  3.000
 FK9  O1    C1   O5    113.02  3.000
 FK9  C2    C1   O5    111.29  3.000
 FK9  C7    O1   C1    115.06  3.000
 FK9  H72C  C7   H71C  107.19  3.000
 FK9  H72C  C7   C8    110.08  3.000
 FK9  H71C  C7   C8    110.15  3.000
 FK9  H72C  C7   O1    110.18  3.000
 FK9  H71C  C7   O1    110.92  3.000
 FK9  C8    C7   O1    108.32  3.000
 FK9  H82C  C8   H81C  107.38  3.000
 FK9  H82C  C8   C9    109.69  3.000
 FK9  H81C  C8   C9    109.76  3.000
 FK9  H82C  C8   C7    109.65  3.000
 FK9  H81C  C8   C7    109.40  3.000
 FK9  C9    C8   C7    110.90  3.000
 FK9  H92C  C9   H91C  107.78  3.000
 FK9  H92C  C9   S1    109.06  3.000
 FK9  H91C  C9   S1    109.18  3.000
 FK9  H92C  C9   C8    110.49  3.000
 FK9  H91C  C9   C8    110.60  3.000
 FK9  S1    C9   C8    109.69  3.000
 FK9  H132  C13  H131  107.71  3.000
 FK9  H132  C13  S1    109.24  3.000
 FK9  H131  C13  S1    108.89  3.000
 FK9  H132  C13  C14   110.40  3.000
 FK9  H131  C13  C14   110.36  3.000
 FK9  S1    C13  C14   110.17  3.000
 FK9  H142  C14  H141  106.59  3.000
 FK9  H142  C14  C15   109.66  3.000
 FK9  H141  C14  C15   109.79  3.000
 FK9  H142  C14  C13   109.59  3.000
 FK9  H141  C14  C13   109.45  3.000
 FK9  C15   C14  C13   111.63  3.000
 FK9  H153  C15  H152  107.68  3.000
 FK9  H153  C15  H151  107.73  3.000
 FK9  H152  C15  H151  107.70  3.000
 FK9  H153  C15  C14   111.27  3.000
 FK9  H152  C15  C14   111.26  3.000
 FK9  H151  C15  C14   111.03  3.000
 FK9  C13   S1   C9    100.31  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
 FK9  Var_01  C8    C7   O1   C1   165.30  30.0  3
 FK9  Var_02  C9    C8   C7   O1   179.61  30.0  3
 FK9  Var_03  S1    C9   C8   C7   178.60  30.0  3
 FK9  Var_04  C14   C13  S1   C9   176.59  30.0  1
 FK9  Var_05  S1    C13  C14  C15  179.70  30.0  3
 FK9  Var_06  H151  C15  C14  C13  179.98  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
 FK9  chir_01  C5  C6  O5  C4  negativ
 FK9  chir_02  C4  O4  C5  C3  positiv
 FK9  chir_03  C3  O3  C2  C4  positiv
 FK9  chir_04  C2  O2  C3  C1  negativ
 FK9  chir_05  C1  O1  O5  C2  negativ

