# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 08:05:34 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: methyl 4-O-(4-thio-beta-D-glucopyranosyl)-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[C@@H](S)[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
 VAM  VAM  'methyl 4-O-(4-thio-beta-D-glucopyranosyl)-beta-D-glucopyranoside'  ligand  48  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 PERFECT
;

data_comp_VAM
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
 VAM  O10   O  OH1   0  -0.667   2.7232   3.0464   1.1422
 VAM  C12   C  CH2   0  -0.166   1.7520   2.0412   0.9835
 VAM  C11   C  CH1   0  -0.005   2.2909   0.9974   0.0281
 VAM  O11   O  O2    0  -0.493   3.4576   0.4543   0.6052
 VAM  C7    C  CH1   0   0.302   4.1411  -0.4244  -0.2510
 VAM  O7    O  O2    0  -0.495   5.2984  -0.8346   0.3710
 VAM  CM    C  CH3   0  -0.412   6.3282   0.1360   0.3963
 VAM  C10   C  CH1   0   0.014   1.2875  -0.1350  -0.2429
 VAM  O9    O  O2    0  -0.513   0.1566   0.3759  -0.9253
 VAM  C9    C  CH1   0   0.010   1.9408  -1.1915  -1.1250
 VAM  C8    C  CH1   0  -0.035   3.2682  -1.6435  -0.5217
 VAM  O8    O  OH1   0  -0.670   3.8646  -2.5206  -1.4447
 VAM  O1    O  OH1   0  -0.654   1.0521  -2.2636  -1.2790
 VAM  O6    O  OH1   0  -0.663  -4.2200   2.2700  -0.8857
 VAM  C2    C  CH2   0  -0.147  -3.2554  -2.2785   0.6745
 VAM  O2    O  OH1   0  -0.662  -2.2691  -3.0293   1.3345
 VAM  C3    C  CH1   0   0.022  -2.7981  -0.8355   0.5989
 VAM  O3    O  O2    0  -0.470  -1.6173  -0.8040  -0.1716
 VAM  C4    C  CH1   0  -0.438  -3.8481   0.0803  -0.0444
 VAM  C5    C  CH1   0   0.066  -3.2826   1.4878  -0.1928
 VAM  C6    C  CH1   0  -0.026  -1.9448   1.4431  -0.9257
 VAM  C70   C  CH1   0   0.285  -1.0212   0.4621  -0.2108
 VAM  O5    O  OH1   0  -0.664  -1.4245   2.7486  -0.9259
 VAM  S10   S  S2    0  -0.234  -5.3463   0.0896   1.0030
 VAM  H10   H  HOH1  0   0.457   2.3392   3.7455   1.6785
 VAM  H121  H  HCH2  0   0.199   1.4997   1.5575   1.9379
 VAM  H122  H  HCH2  0   0.204   0.8223   2.4495   0.5735
 VAM  H11   H  HCH1  0   0.226   2.5322   1.4822  -0.9327
 VAM  HA    H  HCH1  0   0.245   0.9941  -0.5942   0.7109
 VAM  H7    H  HCH1  0   0.185   4.3670   0.0887  -1.2063
 VAM  H8    H  HCH1  0   0.225   3.0691  -2.1438   0.4383
 VAM  HMC1  H  HCH3  0   0.215   6.5857   0.4707  -0.6135
 VAM  HMC2  H  HCH3  0   0.221   6.0581   1.0100   0.9931
 VAM  HMC3  H  HCH3  0   0.240   7.2044  -0.3313   0.8412
 VAM  H9    H  HCH1  0   0.211   2.1617  -0.7184  -2.0976
 VAM  H70   H  HCH1  0   0.191  -0.8408   0.8172   0.8217
 VAM  H1    H  HOH1  0   0.449   1.4815  -2.9226  -1.8349
 VAM  HB    H  HOH1  0   0.459   4.5884  -2.9811  -1.0090
 VAM  H6    H  HOH1  0   0.458  -3.9278   3.1868  -0.8633
 VAM  H2C1  H  HCH2  0   0.202  -3.4439  -2.6440  -0.3445
 VAM  H2C2  H  HCH2  0   0.209  -4.2124  -2.3160   1.2081
 VAM  H2    H  HOH1  0   0.457  -2.5936  -3.9298   1.4220
 VAM  H3    H  HCH1  0   0.227  -2.5957  -0.4715   1.6199
 VAM  H4    H  HCH1  0   0.288  -4.1069  -0.3151  -1.0318
 VAM  HC    H  HSH1  0   0.237  -5.9829   1.0744   0.3621
 VAM  HD    H  HCH1  0   0.229  -2.1139   1.0740  -1.9485
 VAM  HE    H  HOH1  0   0.460  -0.6933   2.7905  -1.5502
 VAM  H5    H  HCH1  0   0.221  -3.1052   1.8892   0.8176

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
 VAM  O10  C12   single  1.407  0.020  1.407
 VAM  C12  C11   single  1.514  0.020  1.514
 VAM  C11  O11   single  1.410  0.020  1.410
 VAM  C11  C10   single  1.537  0.020  1.537
 VAM  O11  C7    single  1.404  0.020  1.404
 VAM  C7   O7    single  1.376  0.020  1.376
 VAM  C7   C8    single  1.524  0.020  1.524
 VAM  O7   CM    single  1.415  0.020  1.415
 VAM  C10  O9    single  1.416  0.020  1.416
 VAM  C10  C9    single  1.523  0.020  1.523
 VAM  O9   C70   single  1.380  0.020  1.380
 VAM  C9   C8    single  1.526  0.020  1.526
 VAM  C9   O1    single  1.401  0.020  1.401
 VAM  C8   O8    single  1.406  0.020  1.406
 VAM  O6   C5    single  1.404  0.020  1.404
 VAM  C2   O2    single  1.404  0.020  1.404
 VAM  C2   C3    single  1.516  0.020  1.516
 VAM  C3   O3    single  1.410  0.020  1.410
 VAM  C3   C4    single  1.535  0.020  1.535
 VAM  O3   C70   single  1.400  0.020  1.400
 VAM  C4   C5    single  1.524  0.020  1.524
 VAM  C4   S10   single  1.828  0.020  1.828
 VAM  C5   C6    single  1.526  0.020  1.526
 VAM  C6   C70   single  1.525  0.020  1.525
 VAM  C6   O5    single  1.405  0.020  1.405
 VAM  O10  H10   single  0.850  0.020  0.980
 VAM  C12  H121  single  0.970  0.020  1.090
 VAM  C12  H122  single  0.970  0.020  1.090
 VAM  C11  H11   single  0.970  0.020  1.090
 VAM  C10  HA    single  0.970  0.020  1.090
 VAM  C7   H7    single  0.970  0.020  1.090
 VAM  C8   H8    single  0.970  0.020  1.090
 VAM  CM   HMC1  single  0.970  0.020  1.090
 VAM  CM   HMC2  single  0.970  0.020  1.090
 VAM  CM   HMC3  single  0.970  0.020  1.090
 VAM  C9   H9    single  0.970  0.020  1.090
 VAM  C70  H70   single  0.970  0.020  1.090
 VAM  O1   H1    single  0.850  0.020  0.980
 VAM  O8   HB    single  0.850  0.020  0.980
 VAM  O6   H6    single  0.850  0.020  0.980
 VAM  C5   H5    single  0.970  0.020  1.090
 VAM  C2   H2C1  single  0.970  0.020  1.090
 VAM  C2   H2C2  single  0.970  0.020  1.090
 VAM  O2   H2    single  0.850  0.020  0.980
 VAM  C3   H3    single  0.970  0.020  1.090
 VAM  C4   H4    single  0.970  0.020  1.090
 VAM  S10  HC    single  1.200  0.020  1.300
 VAM  C6   HD    single  0.970  0.020  1.090
 VAM  O5   HE    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
 VAM  H10   O10  C12   107.87  3.000
 VAM  H122  C12  H121  107.12  3.000
 VAM  H122  C12  C11   108.84  3.000
 VAM  H121  C12  C11   109.04  3.000
 VAM  H122  C12  O10   111.22  3.000
 VAM  H121  C12  O10   112.02  3.000
 VAM  C11   C12  O10   108.55  3.000
 VAM  H11   C11  C10   108.25  3.000
 VAM  H11   C11  O11   110.16  3.000
 VAM  C10   C11  O11   109.18  3.000
 VAM  H11   C11  C12   108.94  3.000
 VAM  C10   C11  C12   112.76  3.000
 VAM  O11   C11  C12   107.56  3.000
 VAM  C7    O11  C11   113.21  3.000
 VAM  H7    C7   C8    109.52  3.000
 VAM  H7    C7   O7    110.87  3.000
 VAM  C8    C7   O7    108.88  3.000
 VAM  H7    C7   O11   109.59  3.000
 VAM  C8    C7   O11   109.27  3.000
 VAM  O7    C7   O11   108.67  3.000
 VAM  CM    O7   C7    114.55  3.000
 VAM  HMC3  CM   HMC2  108.62  3.000
 VAM  HMC3  CM   HMC1  108.61  3.000
 VAM  HMC2  CM   HMC1  108.52  3.000
 VAM  HMC3  CM   O7    107.38  3.000
 VAM  HMC2  CM   O7    112.25  3.000
 VAM  HMC1  CM   O7    111.37  3.000
 VAM  HA    C10  C9    109.11  3.000
 VAM  HA    C10  O9    110.85  3.000
 VAM  C9    C10  O9    108.28  3.000
 VAM  HA    C10  C11   109.22  3.000
 VAM  C9    C10  C11   109.45  3.000
 VAM  O9    C10  C11   109.90  3.000
 VAM  C70   O9   C10   117.03  3.000
 VAM  H9    C9   O1    110.98  3.000
 VAM  H9    C9   C8    107.52  3.000
 VAM  O1    C9   C8    111.62  3.000
 VAM  H9    C9   C10   107.38  3.000
 VAM  O1    C9   C10   108.80  3.000
 VAM  C8    C9   C10   110.45  3.000
 VAM  H8    C8   O8    111.45  3.000
 VAM  H8    C8   C9    108.79  3.000
 VAM  O8    C8   C9    107.11  3.000
 VAM  H8    C8   C7    108.20  3.000
 VAM  O8    C8   C7    111.88  3.000
 VAM  C9    C8   C7    109.36  3.000
 VAM  HB    O8   C8    108.69  3.000
 VAM  H1    O1   C9    107.71  3.000
 VAM  H6    O6   C5    108.45  3.000
 VAM  H2C2  C2   H2C1  106.87  3.000
 VAM  H2C2  C2   C3    108.68  3.000
 VAM  H2C1  C2   C3    108.79  3.000
 VAM  H2C2  C2   O2    111.47  3.000
 VAM  H2C1  C2   O2    112.23  3.000
 VAM  C3    C2   O2    108.69  3.000
 VAM  H2    O2   C2    107.85  3.000
 VAM  H3    C3   C4    108.46  3.000
 VAM  H3    C3   O3    110.17  3.000
 VAM  C4    C3   O3    109.30  3.000
 VAM  H3    C3   C2    108.88  3.000
 VAM  C4    C3   C2    112.49  3.000
 VAM  O3    C3   C2    107.53  3.000
 VAM  C70   O3   C3    113.08  3.000
 VAM  H4    C4   S10   108.96  3.000
 VAM  H4    C4   C5    109.48  3.000
 VAM  S10   C4   C5    110.81  3.000
 VAM  H4    C4   C3    108.93  3.000
 VAM  S10   C4   C3    108.88  3.000
 VAM  C5    C4   C3    109.76  3.000
 VAM  H5    C5   C6    108.06  3.000
 VAM  H5    C5   C4    107.88  3.000
 VAM  C6    C5   C4    110.18  3.000
 VAM  H5    C5   O6    110.93  3.000
 VAM  C6    C5   O6    111.38  3.000
 VAM  C4    C5   O6    108.35  3.000
 VAM  HD    C6   O5    111.62  3.000
 VAM  HD    C6   C70   108.24  3.000
 VAM  O5    C6   C70   111.92  3.000
 VAM  HD    C6   C5    108.75  3.000
 VAM  O5    C6   C5    107.30  3.000
 VAM  C70   C6   C5    108.94  3.000
 VAM  H70   C70  C6    109.24  3.000
 VAM  H70   C70  O3    109.48  3.000
 VAM  C6    C70  O3    109.69  3.000
 VAM  H70   C70  O9    111.34  3.000
 VAM  C6    C70  O9    108.31  3.000
 VAM  O3    C70  O9    108.75  3.000
 VAM  HE    O5   C6    108.77  3.000
 VAM  HC    S10  C4     96.85  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
 VAM  Var_01  HMC1  CM  O7  C7  -56.98  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
 VAM  chir_01  C11  C12  O11  C10  negativ
 VAM  chir_02  C7   O7   O11  C8   positiv
 VAM  chir_03  C10  O9   C11  C9   positiv
 VAM  chir_04  C9   O1   C10  C8   negativ
 VAM  chir_05  C8   O8   C9   C7   positiv
 VAM  chir_06  C3   C2   O3   C4   negativ
 VAM  chir_07  C4   S10  C3   C5   positiv
 VAM  chir_08  C5   O6   C4   C6   negativ
 VAM  chir_09  C6   O5   C5   C70  positiv
 VAM  chir_10  C70  O3   O9   C6   negativ

