# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 17:27:03 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](S[C@@H]2CO[C@@H](S[C@@H]3CO[C@@H](S[C@@H]4CO[C@@H](O)[C@H](O)[C@H]4O)[C@H](O)[C@H]3O)[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
 X4S  X4S  beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranosyl-(1->4)-4-thio-beta-D-xylopyranose  saccharide  71  37  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X4S
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
 X4S  O21   O  OH1   0  -0.655   -5.9885   2.3522   0.9622
 X4S  C21   C  CH1   0   0.029   -7.1309   1.6169   0.6242
 X4S  C31   C  CH1   0   0.019   -7.9964   1.4679   1.8660
 X4S  O31   O  OH1   0  -0.667   -8.4011   2.7446   2.2863
 X4S  C41   C  CH1   0  -0.008   -9.1840   0.5668   1.5473
 X4S  O41   O  OH1   0  -0.670   -9.8957   0.3626   2.7458
 X4S  C51   C  CH2   0  -0.225   -8.6899  -0.7565   0.9715
 X4S  O51   O  O2    0  -0.465   -7.8950  -0.5418  -0.1795
 X4S  C11   C  CH1   0  -0.127   -6.7556   0.2173   0.1165
 X4S  S42   S  S2    0   0.026   -5.7551   0.3527  -1.3884
 X4S  C42   C  CH1   0  -0.457   -4.3048  -0.6506  -0.9393
 X4S  C32   C  CH1   0   0.065   -3.5358  -1.0041  -2.2042
 X4S  O32   O  OH1   0  -0.655   -4.3560  -1.7767  -3.0353
 X4S  C22   C  CH1   0   0.012   -2.2559  -1.7514  -1.8199
 X4S  O22   O  OH1   0  -0.660   -1.5144  -1.9254  -2.9971
 X4S  C52   C  CH2   0  -0.168   -3.3883   0.1211   0.0017
 X4S  O52   O  O2    0  -0.457   -2.2564  -0.6522   0.3415
 X4S  C12   C  CH1   0  -0.134   -1.4678  -0.9462  -0.7786
 X4S  S43   S  S2    0   0.031   -0.0564  -1.9338  -0.2402
 X4S  C43   C  CH1   0  -0.457    1.1401  -0.6373   0.2011
 X4S  C33   C  CH1   0   0.063    2.0945  -1.1756   1.2584
 X4S  O33   O  OH1   0  -0.655    1.3655  -1.4535   2.4213
 X4S  C23   C  CH1   0   0.021    3.1904  -0.1391   1.5086
 X4S  O23   O  OH1   0  -0.660    4.1144  -0.7111   2.3933
 X4S  C53   C  CH2   0  -0.160    1.9158  -0.1988  -1.0356
 X4S  O53   O  O2    0  -0.461    2.9028   0.7610  -0.7123
 X4S  C13   C  CH1   0  -0.127    3.8514   0.2464   0.1816
 X4S  S13   S  S2    0   0.026    5.1151   1.5116   0.4705
 X4S  C44   C  CH1   0  -0.455    6.5618   0.7696  -0.3455
 X4S  C54   C  CH2   0  -0.169    7.1407  -0.3593   0.5010
 X4S  O54   O  O2    0  -0.485    8.2870  -0.9019  -0.1099
 X4S  C14   C  CH1   0   0.266    9.3300   0.0402  -0.2149
 X4S  O14   O  OH1   0  -0.660   10.4153  -0.5693  -0.8067
 X4S  C24   C  CH1   0  -0.027    8.8890   1.2064  -1.0988
 X4S  O24   O  OH1   0  -0.669    9.8687   2.2133  -1.1455
 X4S  C34   C  CH1   0   0.057    7.6206   1.8462  -0.5362
 X4S  O34   O  OH1   0  -0.659    7.1134   2.8368  -1.3874
 X4S  HO21  H  HOH1  0   0.449   -5.4763   2.4833   0.1548
 X4S  H21   H  HCH1  0   0.229   -7.7223   2.1194  -0.1567
 X4S  H31   H  HCH1  0   0.209   -7.3915   0.9680   2.6423
 X4S  HO31  H  HOH1  0   0.451   -8.9839   2.6345   3.0453
 X4S  H41   H  HCH1  0   0.225   -9.8087   1.0714   0.7967
 X4S  HO41  H  HOH1  0   0.462  -10.7811   0.0541   2.5306
 X4S  H51   H  HCH2  0   0.218   -8.1246  -1.3031   1.7398
 X4S  H51A  H  HCH2  0   0.254   -9.5302  -1.3811   0.6640
 X4S  H11   H  HCH1  0   0.260   -6.1431  -0.2831   0.8820
 X4S  H42   H  HCH1  0   0.302   -4.6573  -1.5666  -0.4555
 X4S  H32   H  HCH1  0   0.224   -3.2345  -0.0672  -2.7019
 X4S  HO32  H  HOH1  0   0.456   -3.8832  -1.9442  -3.8571
 X4S  H22   H  HCH1  0   0.233   -2.5453  -2.7147  -1.3712
 X4S  HO22  H  HOH1  0   0.454   -0.7453  -2.4718  -2.8004
 X4S  H52   H  HCH2  0   0.222   -3.0930   1.0679  -0.4719
 X4S  H52A  H  HCH2  0   0.260   -3.8933   0.3623   0.9364
 X4S  H12   H  HCH1  0   0.262   -1.0985  -0.0227  -1.2489
 X4S  H43   H  HCH1  0   0.303    0.5852   0.2075   0.6191
 X4S  H33   H  HCH1  0   0.223    2.5801  -2.0852   0.8671
 X4S  HO33  H  HOH1  0   0.456    1.9567  -1.8661   3.0591
 X4S  H23   H  HCH1  0   0.231    2.7215   0.7616   1.9334
 X4S  HO23  H  HOH1  0   0.454    4.7564  -0.0325   2.6346
 X4S  H53   H  HCH2  0   0.223    2.3683  -1.0759  -1.5175
 X4S  H53A  H  HCH2  0   0.261    1.2490   0.2707  -1.7595
 X4S  H13   H  HCH1  0   0.262    4.3489  -0.6378  -0.2440
 X4S  H44   H  HCH1  0   0.300    6.2490   0.3880  -1.3220
 X4S  H54   H  HCH2  0   0.218    7.3674   0.0222   1.5069
 X4S  H54A  H  HCH2  0   0.257    6.4219  -1.1712   0.6121
 X4S  H14   H  HCH1  0   0.193    9.5765   0.4229   0.7910
 X4S  HO14  H  HOH1  0   0.468   10.9091  -1.0645  -0.1445
 X4S  H24   H  HCH1  0   0.227    8.6656   0.8124  -2.1020
 X4S  HO24  H  HOH1  0   0.459   10.6107   1.8998  -1.6720
 X4S  H34   H  HCH1  0   0.219    7.8694   2.2651   0.4541
 X4S  HO34  H  HOH1  0   0.454    7.7965   3.5039  -1.5137

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
 X4S  O21  C21   single  1.400  0.020  1.400
 X4S  O21  HO21  single  0.850  0.020  0.980
 X4S  C21  C11   single  1.536  0.020  1.536
 X4S  C21  C31   single  1.521  0.020  1.521
 X4S  C21  H21   single  0.970  0.020  1.090
 X4S  C31  O31   single  1.404  0.020  1.404
 X4S  C31  C41   single  1.524  0.020  1.524
 X4S  C31  H31   single  0.970  0.020  1.090
 X4S  O31  HO31  single  0.850  0.020  0.980
 X4S  C51  C41   single  1.525  0.020  1.525
 X4S  C41  O41   single  1.409  0.020  1.409
 X4S  C41  H41   single  0.970  0.020  1.090
 X4S  O41  HO41  single  0.850  0.020  0.980
 X4S  O51  C51   single  1.415  0.020  1.415
 X4S  C51  H51   single  0.970  0.020  1.090
 X4S  C51  H51A  single  0.970  0.020  1.090
 X4S  C11  O51   single  1.401  0.020  1.401
 X4S  S42  C11   single  1.812  0.020  1.812
 X4S  C11  H11   single  0.970  0.020  1.090
 X4S  C42  S42   single  1.820  0.020  1.820
 X4S  C52  C42   single  1.523  0.020  1.523
 X4S  C42  C32   single  1.522  0.020  1.522
 X4S  C42  H42   single  0.970  0.020  1.090
 X4S  C22  C32   single  1.531  0.020  1.531
 X4S  C32  O32   single  1.400  0.020  1.400
 X4S  C32  H32   single  0.970  0.020  1.090
 X4S  O32  HO32  single  0.850  0.020  0.980
 X4S  C12  C22   single  1.534  0.020  1.534
 X4S  O22  C22   single  1.402  0.020  1.402
 X4S  C22  H22   single  0.970  0.020  1.090
 X4S  O22  HO22  single  0.850  0.020  0.980
 X4S  O52  C52   single  1.412  0.020  1.412
 X4S  C52  H52   single  0.970  0.020  1.090
 X4S  C52  H52A  single  0.970  0.020  1.090
 X4S  C12  O52   single  1.401  0.020  1.401
 X4S  S43  C12   single  1.805  0.020  1.805
 X4S  C12  H12   single  0.970  0.020  1.090
 X4S  C43  S43   single  1.819  0.020  1.819
 X4S  C53  C43   single  1.524  0.020  1.524
 X4S  C33  C43   single  1.523  0.020  1.523
 X4S  C43  H43   single  0.970  0.020  1.090
 X4S  C23  C33   single  1.529  0.020  1.529
 X4S  C33  O33   single  1.400  0.020  1.400
 X4S  C33  H33   single  0.970  0.020  1.090
 X4S  O33  HO33  single  0.850  0.020  0.980
 X4S  C13  C23   single  1.532  0.020  1.532
 X4S  O23  C23   single  1.401  0.020  1.401
 X4S  C23  H23   single  0.970  0.020  1.090
 X4S  O23  HO23  single  0.850  0.020  0.980
 X4S  O53  C53   single  1.414  0.020  1.414
 X4S  C53  H53   single  0.970  0.020  1.090
 X4S  C53  H53A  single  0.970  0.020  1.090
 X4S  C13  O53   single  1.401  0.020  1.401
 X4S  S13  C13   single  1.811  0.020  1.811
 X4S  C13  H13   single  0.970  0.020  1.090
 X4S  C44  S13   single  1.819  0.020  1.819
 X4S  C54  C44   single  1.525  0.020  1.525
 X4S  C34  C44   single  1.522  0.020  1.522
 X4S  C44  H44   single  0.970  0.020  1.090
 X4S  O54  C54   single  1.408  0.020  1.408
 X4S  C54  H54   single  0.970  0.020  1.090
 X4S  C54  H54A  single  0.970  0.020  1.090
 X4S  C14  O54   single  1.409  0.020  1.409
 X4S  O14  C14   single  1.378  0.020  1.378
 X4S  C14  C24   single  1.528  0.020  1.528
 X4S  C14  H14   single  0.970  0.020  1.090
 X4S  O14  HO14  single  0.850  0.020  0.980
 X4S  O24  C24   single  1.406  0.020  1.406
 X4S  C24  C34   single  1.528  0.020  1.528
 X4S  C24  H24   single  0.970  0.020  1.090
 X4S  O24  HO24  single  0.850  0.020  0.980
 X4S  C34  O34   single  1.401  0.020  1.401
 X4S  C34  H34   single  0.970  0.020  1.090
 X4S  O34  HO34  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
 X4S  HO21  O21  C21  107.61  3.000
 X4S  H21   C21  C11  108.22  3.000
 X4S  H21   C21  C31  108.55  3.000
 X4S  C11   C21  C31  108.65  3.000
 X4S  H21   C21  O21  111.71  3.000
 X4S  C31   C21  O21  108.59  3.000
 X4S  C11   C21  O21  111.04  3.000
 X4S  H31   C31  C41  107.83  3.000
 X4S  H31   C31  O31  111.06  3.000
 X4S  C41   C31  O31  112.07  3.000
 X4S  H31   C31  C21  107.86  3.000
 X4S  C41   C31  C21  109.30  3.000
 X4S  O31   C31  C21  108.63  3.000
 X4S  HO31  O31  C31  107.84  3.000
 X4S  H41   C41  C51  108.94  3.000
 X4S  H41   C41  O41  111.12  3.000
 X4S  C51   C41  O41  111.04  3.000
 X4S  H41   C41  C31  108.31  3.000
 X4S  O41   C41  C31  107.54  3.000
 X4S  C51   C41  C31  109.84  3.000
 X4S  HO41  O41  C41  108.74  3.000
 X4S  H51A  C51  H51  107.96  3.000
 X4S  H51A  C51  O51  106.87  3.000
 X4S  H51   C51  O51  110.79  3.000
 X4S  H51A  C51  C41  110.70  3.000
 X4S  H51   C51  C41  109.52  3.000
 X4S  O51   C51  C41  110.94  3.000
 X4S  C11   O51  C51  111.55  3.000
 X4S  H11   C11  S42  107.72  3.000
 X4S  H11   C11  O51  110.69  3.000
 X4S  S42   C11  O51  108.31  3.000
 X4S  H11   C11  C21  108.68  3.000
 X4S  S42   C11  C21  109.96  3.000
 X4S  O51   C11  C21  111.41  3.000
 X4S  C42   S42  C11  101.18  3.000
 X4S  H42   C42  C52  110.17  3.000
 X4S  H42   C42  C32  109.62  3.000
 X4S  C52   C42  C32  109.09  3.000
 X4S  H42   C42  S42  108.29  3.000
 X4S  C32   C42  S42  109.00  3.000
 X4S  C52   C42  S42  110.65  3.000
 X4S  H32   C32  C22  107.43  3.000
 X4S  H32   C32  O32  111.16  3.000
 X4S  C22   C32  O32  111.67  3.000
 X4S  H32   C32  C42  108.41  3.000
 X4S  O32   C32  C42  109.00  3.000
 X4S  C22   C32  C42  109.10  3.000
 X4S  HO32  O32  C32  108.36  3.000
 X4S  H22   C22  C12  108.51  3.000
 X4S  H22   C22  O22  111.87  3.000
 X4S  C12   C22  O22  111.30  3.000
 X4S  H22   C22  C32  108.03  3.000
 X4S  O22   C22  C32  106.98  3.000
 X4S  C12   C22  C32  110.09  3.000
 X4S  HO22  O22  C22  108.73  3.000
 X4S  H52A  C52  H52  107.67  3.000
 X4S  H52A  C52  O52  106.64  3.000
 X4S  H52   C52  O52  111.11  3.000
 X4S  H52A  C52  C42  111.29  3.000
 X4S  H52   C52  C42  109.38  3.000
 X4S  O52   C52  C42  110.70  3.000
 X4S  C12   O52  C52  111.94  3.000
 X4S  H12   C12  S43  108.92  3.000
 X4S  H12   C12  O52  110.77  3.000
 X4S  S43   C12  O52  108.45  3.000
 X4S  H12   C12  C22  108.84  3.000
 X4S  S43   C12  C22  108.48  3.000
 X4S  O52   C12  C22  111.32  3.000
 X4S  C43   S43  C12  101.35  3.000
 X4S  H43   C43  C53  110.25  3.000
 X4S  H43   C43  C33  109.01  3.000
 X4S  C53   C43  C33  110.25  3.000
 X4S  H43   C43  S43  108.03  3.000
 X4S  C33   C43  S43  109.20  3.000
 X4S  C53   C43  S43  110.06  3.000
 X4S  H33   C33  C23  107.55  3.000
 X4S  H33   C33  O33  111.11  3.000
 X4S  C23   C33  O33  111.82  3.000
 X4S  H33   C33  C43  108.73  3.000
 X4S  O33   C33  C43  108.70  3.000
 X4S  C23   C33  C43  108.86  3.000
 X4S  HO33  O33  C33  108.40  3.000
 X4S  H23   C23  C13  108.19  3.000
 X4S  H23   C23  O23  111.80  3.000
 X4S  C13   C23  O23  111.41  3.000
 X4S  H23   C23  C33  108.21  3.000
 X4S  O23   C23  C33  107.41  3.000
 X4S  C13   C23  C33  109.76  3.000
 X4S  HO23  O23  C23  108.03  3.000
 X4S  H53A  C53  H53  107.73  3.000
 X4S  H53A  C53  O53  106.64  3.000
 X4S  H53   C53  O53  110.78  3.000
 X4S  H53A  C53  C43  110.57  3.000
 X4S  H53   C53  C43  109.63  3.000
 X4S  O53   C53  C43  111.40  3.000
 X4S  C13   O53  C53  111.66  3.000
 X4S  H13   C13  S13  107.91  3.000
 X4S  H13   C13  O53  110.76  3.000
 X4S  S13   C13  O53  108.51  3.000
 X4S  H13   C13  C23  109.15  3.000
 X4S  S13   C13  C23  109.79  3.000
 X4S  O53   C13  C23  110.66  3.000
 X4S  C44   S13  C13  101.44  3.000
 X4S  H44   C44  C34  109.50  3.000
 X4S  H44   C44  C54  110.22  3.000
 X4S  C34   C44  C54  109.21  3.000
 X4S  H44   C44  S13  108.38  3.000
 X4S  C34   C44  S13  108.72  3.000
 X4S  C54   C44  S13  110.78  3.000
 X4S  H54A  C54  H54  107.53  3.000
 X4S  H54A  C54  O54  107.11  3.000
 X4S  H54   C54  O54  111.28  3.000
 X4S  H54A  C54  C44  110.95  3.000
 X4S  H54   C54  C44  109.22  3.000
 X4S  O54   C54  C44  110.70  3.000
 X4S  C14   O54  C54  112.17  3.000
 X4S  H14   C14  C24  109.08  3.000
 X4S  H14   C14  O14  111.63  3.000
 X4S  C24   C14  O14  108.44  3.000
 X4S  H14   C14  O54  109.21  3.000
 X4S  C24   C14  O54  109.85  3.000
 X4S  O14   C14  O54  108.61  3.000
 X4S  HO14  O14  C14  109.63  3.000
 X4S  H24   C24  C34  108.48  3.000
 X4S  H24   C24  O24  111.57  3.000
 X4S  C34   C24  O24  106.91  3.000
 X4S  H24   C24  C14  108.21  3.000
 X4S  C34   C24  C14  110.25  3.000
 X4S  O24   C24  C14  111.39  3.000
 X4S  HO24  O24  C24  108.80  3.000
 X4S  H34   C34  O34  111.00  3.000
 X4S  H34   C34  C24  107.59  3.000
 X4S  O34   C34  C24  111.89  3.000
 X4S  H34   C34  C44  108.23  3.000
 X4S  O34   C34  C44  108.93  3.000
 X4S  C24   C34  C44  109.11  3.000
 X4S  HO34  O34  C34  108.21  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
 X4S  Var_01  H51  C51  O51  C11  -60.60  30.0  1
 X4S  Var_02  H53  C53  O53  C13  -60.85  30.0  1
 X4S  Var_03  H54  C54  O54  C14  -58.31  30.0  1

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
 X4S  chir_01  C21  O21  C11  C31  negativ
 X4S  chir_02  C31  O31  C21  C41  positiv
 X4S  chir_03  C41  O41  C31  C51  negativ
 X4S  chir_04  C11  S42  O51  C21  positiv
 X4S  chir_05  C42  S42  C52  C32  positiv
 X4S  chir_06  C32  O32  C42  C22  negativ
 X4S  chir_07  C22  O22  C32  C12  positiv
 X4S  chir_08  C12  S43  O52  C22  positiv
 X4S  chir_09  C43  S43  C53  C33  positiv
 X4S  chir_10  C33  O33  C43  C23  negativ
 X4S  chir_11  C23  O23  C33  C13  positiv
 X4S  chir_12  C13  S13  O53  C23  positiv
 X4S  chir_13  C44  S13  C54  C34  positiv
 X4S  chir_14  C14  O54  O14  C24  negativ
 X4S  chir_15  C24  O24  C14  C34  negativ
 X4S  chir_16  C34  O34  C24  C44  positiv

