# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 21:24:59 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: methyl alpha-D-mannopyranosyl-(1->3)-[6-thio-alpha-D-mannopyranosyl-(1->6)]-beta-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO[C@H]2O[C@H](CS)[C@@H](O)[C@H](O)[C@@H]2O)[C@@H](O)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[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
 WZ3  WZ3  'methyl alpha-D-mannopyranosyl-(1->3)-[6-thio-alpha-D-mannopyranosyl-(1->6)]-beta-D-mannopyranoside'  ligand  69  35  .  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_WZ3
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
 WZ3  O21   O  OH1   0  -0.669   6.1276   2.0332   1.0783
 WZ3  C21   C  CH1   0  -0.029   5.0798   1.7699   0.1795
 WZ3  C31   C  CH1   0   0.003   5.6500   1.0128  -1.0149
 WZ3  O31   O  OH1   0  -0.673   6.7315   1.6848  -1.6157
 WZ3  C41   C  CH1   0   0.037   6.1403  -0.3683  -0.5930
 WZ3  O41   O  OH1   0  -0.677   6.5322  -1.1300  -1.7109
 WZ3  C51   C  CH1   0  -0.017   4.9996  -1.1153   0.1004
 WZ3  C61   C  CH2   0  -0.160   5.4531  -2.4456   0.6622
 WZ3  O61   O  OH1   0  -0.665   4.3384  -3.1165   1.2013
 WZ3  O51   O  O2    0  -0.498   4.4971  -0.3513   1.1853
 WZ3  C11   C  CH1   0   0.223   4.0040   0.9138   0.8554
 WZ3  O11   O  O2    0  -0.504   2.9070   0.8575   0.0035
 WZ3  C32   C  CH1   0   0.013   1.6824   0.4716   0.5823
 WZ3  C42   C  CH1   0   0.018   0.6036   1.4450   0.1174
 WZ3  O42   O  OH1   0  -0.668   0.9337   2.7212   0.6108
 WZ3  C22   C  CH1   0  -0.032   1.3207  -0.9716   0.2471
 WZ3  O22   O  OH1   0  -0.667   1.3563  -1.1237  -1.1473
 WZ3  C12   C  CH1   0   0.311  -0.0689  -1.2550   0.8186
 WZ3  O12   O  O2    0  -0.499  -0.4382  -2.5289   0.4488
 WZ3  C72   C  CH3   0  -0.415  -1.6236  -3.0126   1.0520
 WZ3  O52   O  O2    0  -0.482  -1.0085  -0.3492   0.3099
 WZ3  C52   C  CH1   0  -0.028  -0.7488   0.9852   0.6773
 WZ3  C62   C  CH2   0  -0.161  -1.9031   1.8216   0.1697
 WZ3  O62   O  O2    0  -0.503  -3.0501   1.4289   0.8934
 WZ3  C13   C  CH1   0   0.245  -4.2845   1.7847   0.3633
 WZ3  O53   O  O2    0  -0.501  -4.5182   1.2286  -0.8984
 WZ3  C53   C  CH1   0   0.023  -4.4797  -0.1877  -0.9508
 WZ3  C63   C  CH2   0  -0.584  -4.7376  -0.5743  -2.3926
 WZ3  S63   S  S2    0  -0.239  -3.5546   0.3138  -3.4632
 WZ3  C43   C  CH1   0   0.048  -5.5158  -0.7902  -0.0010
 WZ3  O43   O  OH1   0  -0.674  -5.3326  -2.1854  -0.0184
 WZ3  C33   C  CH1   0  -0.007  -5.3257  -0.2192   1.4010
 WZ3  O33   O  OH1   0  -0.674  -6.3454  -0.7505   2.2158
 WZ3  C23   C  CH1   0  -0.027  -5.3381   1.3082   1.3687
 WZ3  O23   O  OH1   0  -0.668  -6.6184   1.7367   0.9846
 WZ3  HO21  H  HOH1  0   0.455   5.7941   2.6011   1.7799
 WZ3  H21   H  HCH1  0   0.230   4.6100   2.7010  -0.1680
 WZ3  H31   H  HCH1  0   0.226   4.8345   0.8664  -1.7362
 WZ3  HO31  H  HOH1  0   0.457   6.3877   2.4082  -2.1483
 WZ3  H41   H  HCH1  0   0.211   6.9744  -0.2564   0.1153
 WZ3  HO41  H  HOH1  0   0.452   7.2099  -0.6348  -2.1828
 WZ3  H51   H  HCH1  0   0.229   4.2084  -1.2939  -0.6409
 WZ3  H61   H  HCH2  0   0.211   5.9195  -3.0208  -0.1442
 WZ3  H61A  H  HCH2  0   0.194   6.2275  -2.2661   1.4211
 WZ3  HO61  H  HOH1  0   0.456   4.6287  -3.9821   1.5022
 WZ3  H11   H  HCH1  0   0.239   3.7211   1.3674   1.8157
 WZ3  H32   H  HCH1  0   0.232   1.7426   0.5454   1.6792
 WZ3  H42   H  HCH1  0   0.233   0.5593   1.4385  -0.9792
 WZ3  HO42  H  HOH1  0   0.460   0.6872   3.3828  -0.0403
 WZ3  H22   H  HCH1  0   0.239   2.0335  -1.6439   0.7440
 WZ3  HO22  H  HOH1  0   0.450   1.0821  -2.0213  -1.3616
 WZ3  H12   H  HCH1  0   0.182  -0.0291  -1.1631   1.9221
 WZ3  H72   H  HCH3  0   0.238  -1.6517  -4.0886   0.8889
 WZ3  H72A  H  HCH3  0   0.211  -1.6275  -2.8262   2.1310
 WZ3  H72B  H  HCH3  0   0.225  -2.5260  -2.5730   0.6214
 WZ3  H52   H  HCH1  0   0.217  -0.7063   1.0818   1.7752
 WZ3  H62   H  HCH2  0   0.227  -1.7006   2.8872   0.3275
 WZ3  H62A  H  HCH2  0   0.225  -2.0235   1.6561  -0.9067
 WZ3  H13   H  HCH1  0   0.236  -4.3566   2.8717   0.2107
 WZ3  H53   H  HCH1  0   0.255  -3.4852  -0.5525  -0.6631
 WZ3  H63   H  HCH2  0   0.285  -4.5910  -1.6452  -2.5147
 WZ3  H63A  H  HCH2  0   0.264  -5.7597  -0.3281  -2.6858
 WZ3  HS63  H  HSH1  0   0.218  -3.5966  -0.5385  -4.4928
 WZ3  H43   H  HCH1  0   0.215  -6.5216  -0.5238  -0.3603
 WZ3  HO43  H  HOH1  0   0.451  -5.9022  -2.5673   0.6579
 WZ3  H33   H  HCH1  0   0.233  -4.3386  -0.5365   1.7616
 WZ3  HO33  H  HOH1  0   0.457  -6.0518  -0.7279   3.1313
 WZ3  H23   H  HCH1  0   0.232  -5.0688   1.6935   2.3623
 WZ3  HO23  H  HOH1  0   0.455  -6.6666   2.6922   1.0868

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
 WZ3  O21  C21   single  1.405  0.020  1.405
 WZ3  C21  C31   single  1.525  0.020  1.525
 WZ3  C21  C11   single  1.532  0.020  1.532
 WZ3  C31  O31   single  1.408  0.020  1.408
 WZ3  C31  C41   single  1.525  0.020  1.525
 WZ3  C41  O41   single  1.408  0.020  1.408
 WZ3  C41  C51   single  1.530  0.020  1.530
 WZ3  C51  C61   single  1.514  0.020  1.514
 WZ3  C51  O51   single  1.419  0.020  1.419
 WZ3  C61  O61   single  1.408  0.020  1.408
 WZ3  O51  C11   single  1.397  0.020  1.397
 WZ3  C11  O11   single  1.390  0.020  1.390
 WZ3  O11  C32   single  1.408  0.020  1.408
 WZ3  C32  C42   single  1.526  0.020  1.526
 WZ3  C32  C22   single  1.525  0.020  1.525
 WZ3  C42  O42   single  1.407  0.020  1.407
 WZ3  C42  C52   single  1.534  0.020  1.534
 WZ3  C22  O22   single  1.403  0.020  1.403
 WZ3  C22  C12   single  1.529  0.020  1.529
 WZ3  C12  O12   single  1.377  0.020  1.377
 WZ3  C12  O52   single  1.401  0.020  1.401
 WZ3  O12  C72   single  1.415  0.020  1.415
 WZ3  O52  C52   single  1.408  0.020  1.408
 WZ3  C52  C62   single  1.513  0.020  1.513
 WZ3  C62  O62   single  1.412  0.020  1.412
 WZ3  O62  C13   single  1.390  0.020  1.390
 WZ3  C13  O53   single  1.398  0.020  1.398
 WZ3  C13  C23   single  1.532  0.020  1.532
 WZ3  O53  C53   single  1.418  0.020  1.418
 WZ3  C53  C63   single  1.515  0.020  1.515
 WZ3  C53  C43   single  1.529  0.020  1.529
 WZ3  C63  S63   single  1.826  0.020  1.826
 WZ3  C43  O43   single  1.407  0.020  1.407
 WZ3  C43  C33   single  1.526  0.020  1.526
 WZ3  C33  O33   single  1.409  0.020  1.409
 WZ3  C33  C23   single  1.528  0.020  1.528
 WZ3  C23  O23   single  1.404  0.020  1.404
 WZ3  O21  HO21  single  0.850  0.020  0.980
 WZ3  C21  H21   single  0.970  0.020  1.090
 WZ3  C31  H31   single  0.970  0.020  1.090
 WZ3  O31  HO31  single  0.850  0.020  0.980
 WZ3  C41  H41   single  0.970  0.020  1.090
 WZ3  O41  HO41  single  0.850  0.020  0.980
 WZ3  C51  H51   single  0.970  0.020  1.090
 WZ3  C61  H61   single  0.970  0.020  1.090
 WZ3  C61  H61A  single  0.970  0.020  1.090
 WZ3  O61  HO61  single  0.850  0.020  0.980
 WZ3  C11  H11   single  0.970  0.020  1.090
 WZ3  C32  H32   single  0.970  0.020  1.090
 WZ3  C42  H42   single  0.970  0.020  1.090
 WZ3  O42  HO42  single  0.850  0.020  0.980
 WZ3  C22  H22   single  0.970  0.020  1.090
 WZ3  O22  HO22  single  0.850  0.020  0.980
 WZ3  C12  H12   single  0.970  0.020  1.090
 WZ3  C72  H72   single  0.970  0.020  1.090
 WZ3  C72  H72A  single  0.970  0.020  1.090
 WZ3  C72  H72B  single  0.970  0.020  1.090
 WZ3  C52  H52   single  0.970  0.020  1.090
 WZ3  C62  H62   single  0.970  0.020  1.090
 WZ3  C62  H62A  single  0.970  0.020  1.090
 WZ3  C13  H13   single  0.970  0.020  1.090
 WZ3  C53  H53   single  0.970  0.020  1.090
 WZ3  C63  H63   single  0.970  0.020  1.090
 WZ3  C63  H63A  single  0.970  0.020  1.090
 WZ3  S63  HS63  single  1.200  0.020  1.300
 WZ3  C43  H43   single  0.970  0.020  1.090
 WZ3  O43  HO43  single  0.850  0.020  0.980
 WZ3  C33  H33   single  0.970  0.020  1.090
 WZ3  O33  HO33  single  0.850  0.020  0.980
 WZ3  C23  H23   single  0.970  0.020  1.090
 WZ3  O23  HO23  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
 WZ3  HO21  O21  C21   108.57  3.000
 WZ3  H21   C21  C11   108.22  3.000
 WZ3  H21   C21  C31   109.44  3.000
 WZ3  C11   C21  C31   109.31  3.000
 WZ3  H21   C21  O21   111.23  3.000
 WZ3  C11   C21  O21   110.25  3.000
 WZ3  C31   C21  O21   108.37  3.000
 WZ3  H31   C31  C41   107.44  3.000
 WZ3  H31   C31  O31   110.71  3.000
 WZ3  C41   C31  O31   107.66  3.000
 WZ3  H31   C31  C21   107.63  3.000
 WZ3  C41   C31  C21   110.69  3.000
 WZ3  O31   C31  C21   112.61  3.000
 WZ3  HO31  O31  C31   108.71  3.000
 WZ3  H41   C41  C51   108.85  3.000
 WZ3  H41   C41  O41   110.81  3.000
 WZ3  C51   C41  O41   107.65  3.000
 WZ3  H41   C41  C31   109.26  3.000
 WZ3  C51   C41  C31   109.14  3.000
 WZ3  O41   C41  C31   111.08  3.000
 WZ3  HO41  O41  C41   107.86  3.000
 WZ3  H51   C51  O51   110.38  3.000
 WZ3  H51   C51  C61   108.86  3.000
 WZ3  O51   C51  C61   107.19  3.000
 WZ3  H51   C51  C41   108.09  3.000
 WZ3  O51   C51  C41   110.35  3.000
 WZ3  C61   C51  C41   111.96  3.000
 WZ3  H61A  C61  H61   107.11  3.000
 WZ3  H61A  C61  O61   111.79  3.000
 WZ3  H61   C61  O61   111.65  3.000
 WZ3  H61A  C61  C51   108.90  3.000
 WZ3  H61   C61  C51   108.42  3.000
 WZ3  O61   C61  C51   108.88  3.000
 WZ3  HO61  O61  C61   108.04  3.000
 WZ3  C11   O51  C51   115.60  3.000
 WZ3  H11   C11  O11   110.43  3.000
 WZ3  H11   C11  O51   104.97  3.000
 WZ3  O11   C11  O51   112.73  3.000
 WZ3  H11   C11  C21   109.61  3.000
 WZ3  O11   C11  C21   107.84  3.000
 WZ3  O51   C11  C21   111.24  3.000
 WZ3  C32   O11  C11   116.45  3.000
 WZ3  H32   C32  C22   107.18  3.000
 WZ3  H32   C32  C42   107.43  3.000
 WZ3  C22   C32  C42   111.66  3.000
 WZ3  H32   C32  O11   110.09  3.000
 WZ3  C22   C32  O11   112.03  3.000
 WZ3  C42   C32  O11   108.35  3.000
 WZ3  H42   C42  C52   109.11  3.000
 WZ3  H42   C42  O42   111.41  3.000
 WZ3  C52   C42  O42   110.52  3.000
 WZ3  H42   C42  C32   109.22  3.000
 WZ3  C52   C42  C32   108.72  3.000
 WZ3  O42   C42  C32   107.81  3.000
 WZ3  HO42  O42  C42   109.07  3.000
 WZ3  H22   C22  C12   107.89  3.000
 WZ3  H22   C22  O22   111.51  3.000
 WZ3  C12   C22  O22   111.98  3.000
 WZ3  H22   C22  C32   109.02  3.000
 WZ3  C12   C22  C32   107.98  3.000
 WZ3  O22   C22  C32   108.36  3.000
 WZ3  HO22  O22  C22   108.36  3.000
 WZ3  H12   C12  O52   109.40  3.000
 WZ3  H12   C12  O12   110.72  3.000
 WZ3  O52   C12  O12   108.71  3.000
 WZ3  H12   C12  C22   108.92  3.000
 WZ3  O52   C12  C22   110.74  3.000
 WZ3  O12   C12  C22   108.35  3.000
 WZ3  C72   O12  C12   115.24  3.000
 WZ3  H72B  C72  H72A  108.49  3.000
 WZ3  H72B  C72  H72   108.51  3.000
 WZ3  H72A  C72  H72   108.41  3.000
 WZ3  H72B  C72  O12   112.73  3.000
 WZ3  H72A  C72  O12   111.39  3.000
 WZ3  H72   C72  O12   107.19  3.000
 WZ3  C52   O52  C12   113.22  3.000
 WZ3  H52   C52  C62   108.36  3.000
 WZ3  H52   C52  O52   110.47  3.000
 WZ3  C62   C52  O52   107.19  3.000
 WZ3  H52   C52  C42   107.65  3.000
 WZ3  C62   C52  C42   112.60  3.000
 WZ3  O52   C52  C42   110.57  3.000
 WZ3  H62A  C62  H62   107.98  3.000
 WZ3  H62A  C62  O62   111.85  3.000
 WZ3  H62   C62  O62   110.28  3.000
 WZ3  H62A  C62  C52   109.27  3.000
 WZ3  H62   C62  C52   110.38  3.000
 WZ3  O62   C62  C52   107.10  3.000
 WZ3  C13   O62  C62   117.05  3.000
 WZ3  H13   C13  C23   110.68  3.000
 WZ3  H13   C13  O53   104.88  3.000
 WZ3  C23   C13  O53   110.69  3.000
 WZ3  H13   C13  O62   111.35  3.000
 WZ3  C23   C13  O62   106.31  3.000
 WZ3  O53   C13  O62   113.01  3.000
 WZ3  C53   O53  C13   115.22  3.000
 WZ3  H53   C53  C43   108.67  3.000
 WZ3  H53   C53  C63   108.60  3.000
 WZ3  C43   C53  C63   112.04  3.000
 WZ3  H53   C53  O53   110.30  3.000
 WZ3  C43   C53  O53   110.62  3.000
 WZ3  C63   C53  O53   106.59  3.000
 WZ3  H63A  C63  H63   108.55  3.000
 WZ3  H63A  C63  S63   109.84  3.000
 WZ3  H63   C63  S63   109.00  3.000
 WZ3  H63A  C63  C53   110.96  3.000
 WZ3  H63   C63  C53   109.58  3.000
 WZ3  S63   C63  C53   108.88  3.000
 WZ3  HS63  S63  C63    96.96  3.000
 WZ3  H43   C43  C33   108.85  3.000
 WZ3  H43   C43  O43   110.79  3.000
 WZ3  C33   C43  O43   111.48  3.000
 WZ3  H43   C43  C53   108.72  3.000
 WZ3  C33   C43  C53   109.81  3.000
 WZ3  O43   C43  C53   107.14  3.000
 WZ3  HO43  O43  C43   107.91  3.000
 WZ3  H33   C33  C23   107.65  3.000
 WZ3  H33   C33  O33   110.60  3.000
 WZ3  C23   C33  O33   112.54  3.000
 WZ3  H33   C33  C43   107.80  3.000
 WZ3  C23   C33  C43   110.71  3.000
 WZ3  O33   C33  C43   107.46  3.000
 WZ3  HO33  O33  C33   108.70  3.000
 WZ3  H23   C23  O23   111.34  3.000
 WZ3  H23   C23  C33   109.23  3.000
 WZ3  O23   C23  C33   108.57  3.000
 WZ3  H23   C23  C13   108.40  3.000
 WZ3  O23   C23  C13   110.65  3.000
 WZ3  C33   C23  C13   108.61  3.000
 WZ3  HO23  O23  C23   108.65  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
 WZ3  Var_01  H72  C72  O12  C12  -165.22  30.0  3
 WZ3  Var_02  H62  C62  O62  C13    77.02  30.0  2

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
 WZ3  chir_01  C21  O21  C31  C11  negativ
 WZ3  chir_02  C31  O31  C21  C41  positiv
 WZ3  chir_03  C41  O41  C51  C31  positiv
 WZ3  chir_04  C51  O51  C41  C61  negativ
 WZ3  chir_05  C11  O51  O11  C21  positiv
 WZ3  chir_06  C32  O11  C22  C42  positiv
 WZ3  chir_07  C42  O42  C32  C52  negativ
 WZ3  chir_08  C22  O22  C32  C12  negativ
 WZ3  chir_09  C12  O12  O52  C22  positiv
 WZ3  chir_10  C52  O52  C42  C62  negativ
 WZ3  chir_11  C13  O62  O53  C23  negativ
 WZ3  chir_12  C53  O53  C63  C43  positiv
 WZ3  chir_13  C43  O43  C53  C33  positiv
 WZ3  chir_14  C33  O33  C23  C43  positiv
 WZ3  chir_15  C23  O23  C13  C33  positiv

