# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 09:45:15 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: octyl 4-O-beta-D-allopyranosyl-1-thio-beta-D-altropyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@@H](O)[C@H]2O)[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
 OOC  OOC  'octyl 4-O-beta-D-allopyranosyl-1-thio-beta-D-altropyranoside'  ligand  69  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OOC
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
 OOC  C2    C  CR16  0  -0.034  -4.9518  -1.7017   0.5813
 OOC  C4    C  CR16  0   0.047  -6.7493   0.0315   0.4971
 OOC  C5    C  CR16  0  -0.009  -5.6990   1.0177  -0.0202
 OOC  C6    C  CH2   0  -0.155  -5.9604   2.4308   0.4551
 OOC  O2    O  OH1   0  -0.671  -4.6151  -2.9887   0.1267
 OOC  O4    O  OH1   0  -0.669  -8.0010   0.4052  -0.0169
 OOC  C1    C  CR16  0   0.304  -4.0110  -0.6325   0.0326
 OOC  C3    C  CR16  0  -0.064  -6.3739  -1.4001   0.1117
 OOC  O1    O  O2    0  -0.516  -2.7434  -0.8642   0.5255
 OOC  O3    O  OH1   0  -0.666  -6.4953  -1.5274  -1.2845
 OOC  O5    O  O     0  -0.495  -4.4346   0.6288   0.4772
 OOC  O6    O  OH1   0  -0.665  -4.9633   3.2757  -0.0695
 OOC  C1'   C  CH1   0  -0.105   1.0454   0.6448  -0.0482
 OOC  C2'   C  CH1   0  -0.010  -0.0497   1.7064  -0.0260
 OOC  C3'   C  CH1   0  -0.023  -1.3171   1.1010   0.5906
 OOC  C4'   C  CH1   0   0.029  -1.6822  -0.1972  -0.1301
 OOC  C5'   C  CH1   0  -0.003  -0.4866  -1.1552  -0.1854
 OOC  C6'   C  CH2   0  -0.155  -0.7840  -2.3566  -1.0590
 OOC  O3'   O  OH1   0  -0.667  -1.1019   0.7860   1.9446
 OOC  O5'   O  O2    0  -0.476   0.6264  -0.4935  -0.7566
 OOC  O6'   O  OH1   0  -0.668   0.3037  -3.2467  -1.0016
 OOC  O2'   O  OH1   0  -0.670  -0.3647   2.1543  -1.3222
 OOC  CB    C  CH2   0  -0.425   5.1725   0.6804  -0.5884
 OOC  CC    C  CH2   0  -0.411   6.2841  -0.1315   0.0670
 OOC  CD    C  CH2   0  -0.413   7.6738   0.3080  -0.3768
 OOC  CF    C  CH2   0  -0.413   8.7945  -0.4575   0.3147
 OOC  CG    C  CH2   0  -0.406  10.1838  -0.0166  -0.1285
 OOC  CH    C  CH2   0  -0.421  11.3085  -0.7664   0.5746
 OOC  CI    C  CH3   0  -0.661  12.6915  -0.3163   0.1244
 OOC  H2    H  HCR6  0   0.229  -4.9292  -1.6434   1.6791
 OOC  HA    H  HOH1  0   0.462  -3.7826  -3.2530   0.5298
 OOC  H1    H  HCR6  0   0.192  -4.0117  -0.6615  -1.0712
 OOC  H3    H  HCR6  0   0.240  -7.0599  -2.0914   0.6259
 OOC  H4    H  HCR6  0   0.218  -6.7400   0.0830   1.5966
 OOC  H5    H  HCR6  0   0.225  -5.6962   1.0047  -1.1206
 OOC  HB    H  HOH1  0   0.456  -8.6735  -0.1667   0.3665
 OOC  H61C  H  HCH2  0   0.212  -6.9600   2.7281   0.1217
 OOC  H62C  H  HCH2  0   0.193  -5.9680   2.4441   1.5543
 OOC  H6    H  HOH1  0   0.455  -5.1766   4.1774   0.1862
 OOC  HC    H  HOH1  0   0.453  -6.1851  -2.4041  -1.5346
 OOC  H4'   H  HCH1  0   0.241  -1.9699   0.0574  -1.1592
 OOC  H1'   H  HCH1  0   0.250   1.3139   0.3868   0.9851
 OOC  H2'   H  HCH1  0   0.247   0.2826   2.5362   0.6121
 OOC  H3'   H  HCH1  0   0.248  -2.1364   1.8213   0.4729
 OOC  HD    H  HOH1  0   0.461   0.2025   2.8974  -1.5463
 OOC  HE    H  HOH1  0   0.457  -0.9400   1.6036   2.4254
 OOC  H5'   H  HCH1  0   0.225  -0.2486  -1.4982   0.8334
 OOC  H6'1  H  HCH2  0   0.200  -1.7073  -2.8273  -0.7052
 OOC  H6'2  H  HCH2  0   0.198  -0.9757  -2.0078  -2.0835
 OOC  H6'   H  HOH1  0   0.456   0.0778  -4.0219  -1.5231
 OOC  HA1C  H  HCH2  0   0.261   3.7197   0.2802   0.9582
 OOC  HA2C  H  HCH2  0   0.265   3.6067  -0.8032  -0.4334
 OOC  HB1C  H  HCH2  0   0.230   5.2465   0.5962  -1.6767
 OOC  HB2C  H  HCH2  0   0.228   5.3077   1.7389  -0.3462
 OOC  HC1C  H  HCH2  0   0.214   6.2039  -0.0384   1.1553
 OOC  HC2C  H  HCH2  0   0.216   6.1475  -1.1939  -0.1597
 OOC  HD1C  H  HCH2  0   0.210   7.7641   0.1865  -1.4618
 OOC  HD2C  H  HCH2  0   0.209   7.7927   1.3793  -0.1810
 OOC  HF1C  H  HCH2  0   0.207   8.7029  -0.3315   1.3993
 OOC  HF2C  H  HCH2  0   0.208   8.6762  -1.5299   0.1241
 OOC  HG1C  H  HCH2  0   0.206  10.2792  -0.1522  -1.2117
 OOC  HG2C  H  HCH2  0   0.206  10.2969   1.0583   0.0519
 OOC  HH1C  H  HCH2  0   0.210  11.2122  -0.6298   1.6563
 OOC  HH2C  H  HCH2  0   0.210  11.1955  -1.8401   0.3946
 OOC  HI1C  H  HCH3  0   0.216  12.8431   0.7464   0.3223
 OOC  HI2C  H  HCH3  0   0.225  13.4809  -0.8643   0.6401
 OOC  HI3C  H  HCH3  0   0.215  12.8266  -0.4726  -0.9475
 OOC  S1    S  S2    0  -0.018   2.5193   1.3064  -0.8487
 OOC  CA    C  CH2   0  -0.543   3.7950   0.2274  -0.1300

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
 OOC  C2   O2    single  1.406  0.020  1.406
 OOC  C2   C1    single  1.526  0.020  1.526
 OOC  C2   C3    single  1.528  0.020  1.528
 OOC  C4   C5    single  1.531  0.020  1.531
 OOC  C4   O4    single  1.404  0.020  1.404
 OOC  C4   C3    single  1.529  0.020  1.529
 OOC  C5   C6    single  1.514  0.020  1.514
 OOC  C5   O5    single  1.413  0.020  1.413
 OOC  C6   O6    single  1.408  0.020  1.408
 OOC  C1   O1    single  1.380  0.020  1.380
 OOC  C1   O5    single  1.403  0.020  1.403
 OOC  C3   O3    single  1.407  0.020  1.407
 OOC  O1   C4'   single  1.414  0.020  1.414
 OOC  C1'  C2'   single  1.525  0.020  1.525
 OOC  C1'  S1    single  1.803  0.020  1.803
 OOC  C1'  O5'   single  1.405  0.020  1.405
 OOC  C2'  C3'   single  1.534  0.020  1.534
 OOC  C2'  O2'   single  1.407  0.020  1.407
 OOC  C3'  C4'   single  1.529  0.020  1.529
 OOC  C3'  O3'   single  1.407  0.020  1.407
 OOC  C4'  C5'   single  1.533  0.020  1.533
 OOC  C5'  C6'   single  1.515  0.020  1.515
 OOC  C5'  O5'   single  1.415  0.020  1.415
 OOC  C6'  O6'   single  1.407  0.020  1.407
 OOC  S1   CA    single  1.819  0.020  1.819
 OOC  CA   CB    single  1.521  0.020  1.521
 OOC  CB   CC    single  1.525  0.020  1.525
 OOC  CC   CD    single  1.524  0.020  1.524
 OOC  CD   CF    single  1.523  0.020  1.523
 OOC  CF   CG    single  1.524  0.020  1.524
 OOC  CG   CH    single  1.524  0.020  1.524
 OOC  C2   H2    single  0.970  0.020  1.090
 OOC  O2   HA    single  0.850  0.020  0.980
 OOC  C1   H1    single  0.970  0.020  1.090
 OOC  C3   H3    single  0.970  0.020  1.090
 OOC  C4   H4    single  0.970  0.020  1.090
 OOC  C5   H5    single  0.970  0.020  1.090
 OOC  O4   HB    single  0.850  0.020  0.980
 OOC  C6   H61C  single  0.970  0.020  1.090
 OOC  C6   H62C  single  0.970  0.020  1.090
 OOC  O6   H6    single  0.850  0.020  0.980
 OOC  O3   HC    single  0.850  0.020  0.980
 OOC  C4'  H4'   single  0.970  0.020  1.090
 OOC  C1'  H1'   single  0.970  0.020  1.090
 OOC  C2'  H2'   single  0.970  0.020  1.090
 OOC  C3'  H3'   single  0.970  0.020  1.090
 OOC  O2'  HD    single  0.850  0.020  0.980
 OOC  O3'  HE    single  0.850  0.020  0.980
 OOC  C5'  H5'   single  0.970  0.020  1.090
 OOC  C6'  H6'1  single  0.970  0.020  1.090
 OOC  C6'  H6'2  single  0.970  0.020  1.090
 OOC  O6'  H6'   single  0.850  0.020  0.980
 OOC  CA   HA1C  single  0.970  0.020  1.090
 OOC  CA   HA2C  single  0.970  0.020  1.090
 OOC  CB   HB1C  single  0.970  0.020  1.090
 OOC  CB   HB2C  single  0.970  0.020  1.090
 OOC  CC   HC1C  single  0.970  0.020  1.090
 OOC  CC   HC2C  single  0.970  0.020  1.090
 OOC  CD   HD1C  single  0.970  0.020  1.090
 OOC  CD   HD2C  single  0.970  0.020  1.090
 OOC  CF   HF1C  single  0.970  0.020  1.090
 OOC  CF   HF2C  single  0.970  0.020  1.090
 OOC  CG   HG1C  single  0.970  0.020  1.090
 OOC  CG   HG2C  single  0.970  0.020  1.090
 OOC  CH   HH1C  single  0.970  0.020  1.090
 OOC  CH   HH2C  single  0.970  0.020  1.090
 OOC  CI   HI1C  single  0.970  0.020  1.090
 OOC  CI   HI2C  single  0.970  0.020  1.090
 OOC  CI   HI3C  single  0.970  0.020  1.090
 OOC  CI   CH    single  1.522  0.020  1.522

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
 OOC  H2    C2   C3    108.40  3.000
 OOC  H2    C2   C1    108.01  3.000
 OOC  C3    C2   C1    108.97  3.000
 OOC  H2    C2   O2    111.50  3.000
 OOC  C3    C2   O2    107.71  3.000
 OOC  C1    C2   O2    112.18  3.000
 OOC  H4    C4   C3    107.07  3.000
 OOC  H4    C4   O4    111.15  3.000
 OOC  C3    C4   O4    112.07  3.000
 OOC  H4    C4   C5    107.55  3.000
 OOC  C3    C4   C5    110.46  3.000
 OOC  O4    C4   C5    108.45  3.000
 OOC  H5    C5   O5    110.27  3.000
 OOC  H5    C5   C6    108.99  3.000
 OOC  O5    C5   C6    107.51  3.000
 OOC  H5    C5   C4    109.39  3.000
 OOC  O5    C5   C4    108.52  3.000
 OOC  C6    C5   C4    112.14  3.000
 OOC  H62C  C6   H61C  107.15  3.000
 OOC  H62C  C6   O6    111.73  3.000
 OOC  H61C  C6   O6    111.72  3.000
 OOC  H62C  C6   C5    109.05  3.000
 OOC  H61C  C6   C5    108.39  3.000
 OOC  O6    C6   C5    108.72  3.000
 OOC  HA    O2   C2    108.86  3.000
 OOC  HB    O4   C4    108.61  3.000
 OOC  H1    C1   O5    109.89  3.000
 OOC  H1    C1   O1    110.69  3.000
 OOC  O5    C1   O1    108.37  3.000
 OOC  H1    C1   C2    109.91  3.000
 OOC  O5    C1   C2    109.25  3.000
 OOC  O1    C1   C2    108.68  3.000
 OOC  H3    C3   O3    110.66  3.000
 OOC  H3    C3   C4    108.48  3.000
 OOC  O3    C3   C4    108.27  3.000
 OOC  H3    C3   C2    108.20  3.000
 OOC  O3    C3   C2    111.56  3.000
 OOC  C4    C3   C2    109.62  3.000
 OOC  C4'   O1   C1    116.40  3.000
 OOC  HC    O3   C3    108.20  3.000
 OOC  C1    O5   C5    113.96  3.000
 OOC  H6    O6   C6    107.86  3.000
 OOC  H1'   C1'  O5'   110.92  3.000
 OOC  H1'   C1'  S1    107.70  3.000
 OOC  O5'   C1'  S1    108.50  3.000
 OOC  H1'   C1'  C2'   108.98  3.000
 OOC  O5'   C1'  C2'   110.93  3.000
 OOC  S1    C1'  C2'   109.75  3.000
 OOC  H2'   C2'  O2'   111.25  3.000
 OOC  H2'   C2'  C3'   108.34  3.000
 OOC  O2'   C2'  C3'   108.12  3.000
 OOC  H2'   C2'  C1'   108.48  3.000
 OOC  O2'   C2'  C1'   111.65  3.000
 OOC  C3'   C2'  C1'   108.93  3.000
 OOC  H3'   C3'  O3'   111.38  3.000
 OOC  H3'   C3'  C4'   109.18  3.000
 OOC  O3'   C3'  C4'   107.46  3.000
 OOC  H3'   C3'  C2'   108.34  3.000
 OOC  O3'   C3'  C2'   110.42  3.000
 OOC  C4'   C3'  C2'   110.05  3.000
 OOC  H4'   C4'  C5'   108.38  3.000
 OOC  H4'   C4'  C3'   107.89  3.000
 OOC  C5'   C4'  C3'   111.18  3.000
 OOC  H4'   C4'  O1    110.30  3.000
 OOC  C5'   C4'  O1    107.89  3.000
 OOC  C3'   C4'  O1    111.16  3.000
 OOC  H5'   C5'  O5'   110.43  3.000
 OOC  H5'   C5'  C6'   109.21  3.000
 OOC  O5'   C5'  C6'   107.00  3.000
 OOC  H5'   C5'  C4'   109.26  3.000
 OOC  O5'   C5'  C4'   109.62  3.000
 OOC  C6'   C5'  C4'   111.30  3.000
 OOC  H6'2  C6'  H6'1  106.89  3.000
 OOC  H6'2  C6'  O6'   111.94  3.000
 OOC  H6'1  C6'  O6'   111.52  3.000
 OOC  H6'2  C6'  C5'   108.67  3.000
 OOC  H6'1  C6'  C5'   108.67  3.000
 OOC  O6'   C6'  C5'   109.05  3.000
 OOC  HE    O3'  C3'   108.45  3.000
 OOC  C5'   O5'  C1'   114.20  3.000
 OOC  H6'   O6'  C6'   107.84  3.000
 OOC  HD    O2'  C2'   109.20  3.000
 OOC  HB2C  CB   HB1C  106.64  3.000
 OOC  HB2C  CB   CC    109.26  3.000
 OOC  HB1C  CB   CC    109.71  3.000
 OOC  HB2C  CB   CA    109.48  3.000
 OOC  HB1C  CB   CA    109.76  3.000
 OOC  CC    CB   CA    111.85  3.000
 OOC  HC2C  CC   HC1C  106.21  3.000
 OOC  HC2C  CC   CD    109.48  3.000
 OOC  HC1C  CC   CD    109.37  3.000
 OOC  HC2C  CC   CB    109.68  3.000
 OOC  HC1C  CC   CB    109.18  3.000
 OOC  CD    CC   CB    112.71  3.000
 OOC  HD2C  CD   HD1C  106.06  3.000
 OOC  HD2C  CD   CF    109.30  3.000
 OOC  HD1C  CD   CF    109.46  3.000
 OOC  HD2C  CD   CC    109.21  3.000
 OOC  HD1C  CD   CC    109.37  3.000
 OOC  CF    CD   CC    113.19  3.000
 OOC  HF2C  CF   HF1C  106.01  3.000
 OOC  HF2C  CF   CG    109.34  3.000
 OOC  HF1C  CF   CG    109.32  3.000
 OOC  HF2C  CF   CD    109.49  3.000
 OOC  HF1C  CF   CD    109.27  3.000
 OOC  CG    CF   CD    113.17  3.000
 OOC  HG2C  CG   HG1C  105.97  3.000
 OOC  HG2C  CG   CH    109.30  3.000
 OOC  HG1C  CG   CH    109.33  3.000
 OOC  HG2C  CG   CF    109.28  3.000
 OOC  HG1C  CG   CF    109.34  3.000
 OOC  CH    CG   CF    113.36  3.000
 OOC  HH2C  CH   HH1C  106.01  3.000
 OOC  HH2C  CH   CI    109.58  3.000
 OOC  HH1C  CH   CI    109.59  3.000
 OOC  CI    CH   CG    112.87  3.000
 OOC  HH2C  CH   CG    109.31  3.000
 OOC  HH1C  CH   CG    109.25  3.000
 OOC  HI3C  CI   HI2C  107.63  3.000
 OOC  HI3C  CI   HI1C  107.47  3.000
 OOC  HI2C  CI   HI1C  107.64  3.000
 OOC  HI3C  CI   CH    111.13  3.000
 OOC  HI2C  CI   CH    111.67  3.000
 OOC  HI1C  CI   CH    111.12  3.000
 OOC  CA    S1   C1'   100.38  3.000
 OOC  HA2C  CA   HA1C  108.11  3.000
 OOC  HA2C  CA   CB    110.73  3.000
 OOC  HA1C  CA   CB    110.39  3.000
 OOC  HA2C  CA   S1    109.24  3.000
 OOC  HA1C  CA   S1    108.46  3.000
 OOC  CB    CA   S1    109.84  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
 OOC  Var_01  CB    CA  S1  C1'  -175.51  30.0  3
 OOC  Var_02  CC    CB  CA  S1    175.92  30.0  3
 OOC  Var_03  CD    CC  CB  CA   -179.90  30.0  3
 OOC  Var_04  CF    CD  CC  CB    177.63  30.0  3
 OOC  Var_05  CG    CF  CD  CC   -179.94  30.0  3
 OOC  Var_06  CH    CG  CF  CD    179.21  30.0  3
 OOC  Var_07  CI    CH  CG  CF   -179.95  30.0  3
 OOC  Var_08  HI1C  CI  CH  CG     59.75  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
 OOC  chir_01  C2   O2   C1   C3   negativ
 OOC  chir_02  C4   O4   C3   C5   negativ
 OOC  chir_03  C5   O5   C4   C6   negativ
 OOC  chir_04  C1   O1   O5   C2   positiv
 OOC  chir_05  C3   O3   C2   C4   negativ
 OOC  chir_06  C1'  C2'  S1   O5'  positiv
 OOC  chir_07  C2'  O2'  C1'  C3'  positiv
 OOC  chir_08  C3'  O3'  C2'  C4'  negativ
 OOC  chir_09  C4'  O1   C5'  C3'  positiv
 OOC  chir_10  C5'  O5'  C4'  C6'  negativ

