# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 18:12:58 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: [(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] (1~{E})-~{N}-sulfooxybut-3-enimidothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](SC(/CC=C)=N/O[S](O)(=O)=O)[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
 SZZ  SZZ  '[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] (1~{E})-~{N}-sulfooxybut-3-enimidothioate'  D-saccharide  39  22  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZZ
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
 SZZ  O15  O  OS    0  -0.637   2.0572   2.4559  -1.1184
 SZZ  S12  S  S     0   1.659   2.8786   1.6196  -0.2819
 SZZ  O14  O  OS    0  -0.634   4.2926   1.8534  -0.1684
 SZZ  O13  O  OS    0  -0.743   2.2745   1.4779   1.1383
 SZZ  O11  O  OC2   0  -0.491   2.8277   0.0895  -0.8263
 SZZ  N10  N  N     0  -0.132   1.4952  -0.3544  -0.8457
 SZZ  C09  C  C     0   0.130   1.4208  -1.5957  -0.5928
 SZZ  C16  C  CH2   0  -0.588   2.5461  -2.5453  -0.2848
 SZZ  C17  C  C1    0  -0.156   2.9105  -2.4442   1.1699
 SZZ  C18  C  C2    0  -0.510   2.6907  -3.4118   2.0498
 SZZ  S08  S  S2    0   0.104  -0.1717  -2.3098  -0.4888
 SZZ  C07  C  CH1   0  -0.149  -1.2367  -0.8474  -0.5609
 SZZ  O06  O  O2    0  -0.465  -1.0122  -0.0832   0.5860
 SZZ  C19  C  CH1   0   0.009  -2.6972  -1.3031  -0.6126
 SZZ  O20  O  OH1   0  -0.662  -2.9692  -2.0135  -1.7928
 SZZ  C21  C  CH1   0  -0.003  -3.5757  -0.0534  -0.5891
 SZZ  O22  O  OH1   0  -0.668  -4.9357  -0.3794  -0.4514
 SZZ  C23  C  CH1   0   0.033  -3.2104   0.8727   0.5681
 SZZ  O24  O  OH1   0  -0.668  -3.8800   2.1030   0.4619
 SZZ  C05  C  CH1   0  -0.017  -1.7063   1.1492   0.5459
 SZZ  C04  C  CH2   0  -0.151  -1.2688   1.9745   1.7339
 SZZ  O03  O  OH1   0  -0.695   0.0358   2.5048   1.5026
 SZZ  H1   H  HCH2  0   0.287   2.2377  -3.5637  -0.5253
 SZZ  H2   H  HCH2  0   0.303   3.4060  -2.3109  -0.9143
 SZZ  H3   H  H     0   0.259   3.3658  -1.5140   1.4915
 SZZ  H4   H  H     0   0.244   2.2317  -4.3509   1.7641
 SZZ  H5   H  H     0   0.248   2.9663  -3.2982   3.0898
 SZZ  H6   H  HCH1  0   0.279  -0.9814  -0.2882  -1.4711
 SZZ  H7   H  HCH1  0   0.248  -2.9110  -1.9041   0.2814
 SZZ  H8   H  HOH1  0   0.465  -2.9439  -2.9573  -1.6134
 SZZ  H9   H  HCH1  0   0.224  -3.3978   0.4991  -1.5254
 SZZ  H10  H  HOH1  0   0.459  -5.2490  -0.7520  -1.2814
 SZZ  H11  H  HCH1  0   0.222  -3.4565   0.3670   1.5152
 SZZ  H12  H  HOH1  0   0.458  -4.8277   1.9338   0.4860
 SZZ  H13  H  HCH1  0   0.240  -1.4584   1.6946  -0.3782
 SZZ  H14  H  HCH2  0   0.255  -1.9627   2.8044   1.8655
 SZZ  H15  H  HCH2  0   0.235  -1.2881   1.3650   2.6426
 SZZ  H16  H  HOH1  0   0.496   0.2026   3.2129   2.1360
 SZZ  H17  H  H     0   0.513   1.2964   1.8115   1.2489

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
 SZZ  O03  C04  single  1.427  0.020  1.427
 SZZ  C04  C05  single  1.511  0.020  1.511
 SZZ  S08  C09  single  1.748  0.020  1.748
 SZZ  S08  C07  single  1.810  0.020  1.810
 SZZ  C05  O06  single  1.415  0.020  1.415
 SZZ  C05  C23  single  1.530  0.020  1.530
 SZZ  O06  C07  single  1.396  0.020  1.396
 SZZ  N10  C09  double  1.269  0.020  1.269
 SZZ  N10  O11  single  1.405  0.020  1.405
 SZZ  C09  C16  single  1.504  0.020  1.504
 SZZ  O14  S12  double  1.438  0.020  1.438
 SZZ  O11  S12  single  1.625  0.020  1.625
 SZZ  C07  C19  single  1.531  0.020  1.531
 SZZ  C23  O24  single  1.405  0.020  1.405
 SZZ  C23  C21  single  1.526  0.020  1.526
 SZZ  C16  C17  single  1.503  0.020  1.503
 SZZ  S12  O15  double  1.440  0.020  1.440
 SZZ  S12  O13  single  1.550  0.020  1.550
 SZZ  C19  C21  single  1.528  0.020  1.528
 SZZ  C19  O20  single  1.404  0.020  1.404
 SZZ  C21  O22  single  1.405  0.020  1.405
 SZZ  C17  C18  double  1.326  0.020  1.326
 SZZ  C16  H1   single  0.970  0.020  1.090
 SZZ  C16  H2   single  0.970  0.020  1.090
 SZZ  C17  H3   single  0.930  0.020  1.080
 SZZ  C18  H4   single  0.930  0.020  1.080
 SZZ  C18  H5   single  0.930  0.020  1.080
 SZZ  C07  H6   single  0.970  0.020  1.090
 SZZ  C19  H7   single  0.970  0.020  1.090
 SZZ  O20  H8   single  0.850  0.020  0.980
 SZZ  C21  H9   single  0.970  0.020  1.090
 SZZ  O22  H10  single  0.850  0.020  0.980
 SZZ  C23  H11  single  0.970  0.020  1.090
 SZZ  O24  H12  single  0.850  0.020  0.980
 SZZ  C05  H13  single  0.970  0.020  1.090
 SZZ  C04  H14  single  0.970  0.020  1.090
 SZZ  C04  H15  single  0.970  0.020  1.090
 SZZ  O03  H16  single  0.850  0.020  0.980
 SZZ  O13  H17  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
 SZZ  O11  S12  O13  102.05  3.000
 SZZ  O13  S12  O14  109.02  3.000
 SZZ  O11  S12  O14  102.15  3.000
 SZZ  O13  S12  O15  111.29  3.000
 SZZ  O11  S12  O15  109.53  3.000
 SZZ  O14  S12  O15  120.82  3.000
 SZZ  H17  O13  S12  115.79  3.000
 SZZ  N10  O11  S12  109.38  3.000
 SZZ  C09  N10  O11  111.22  3.000
 SZZ  S08  C09  C16  114.29  3.000
 SZZ  C16  C09  N10  127.91  3.000
 SZZ  S08  C09  N10  117.70  3.000
 SZZ  H2   C16  H1   107.23  3.000
 SZZ  H2   C16  C17  110.66  3.000
 SZZ  H1   C16  C17  110.16  3.000
 SZZ  H2   C16  C09  109.62  3.000
 SZZ  H1   C16  C09  109.43  3.000
 SZZ  C17  C16  C09  109.70  3.000
 SZZ  H3   C17  C18  119.91  3.000
 SZZ  H3   C17  C16  116.52  3.000
 SZZ  C18  C17  C16  123.57  3.000
 SZZ  H5   C18  H4   116.90  3.000
 SZZ  H5   C18  C17  121.26  3.000
 SZZ  H4   C18  C17  121.84  3.000
 SZZ  C07  S08  C09  101.74  3.000
 SZZ  H6   C07  C19  110.20  3.000
 SZZ  H6   C07  O06  111.38  3.000
 SZZ  C19  C07  O06  110.12  3.000
 SZZ  H6   C07  S08  107.92  3.000
 SZZ  C19  C07  S08  108.79  3.000
 SZZ  O06  C07  S08  108.35  3.000
 SZZ  C05  O06  C07  112.00  3.000
 SZZ  H7   C19  C21  108.85  3.000
 SZZ  H7   C19  O20  111.70  3.000
 SZZ  C21  C19  O20  108.39  3.000
 SZZ  H7   C19  C07  108.73  3.000
 SZZ  O20  C19  C07  111.33  3.000
 SZZ  C21  C19  C07  107.73  3.000
 SZZ  H8   O20  C19  109.56  3.000
 SZZ  H9   C21  C23  107.54  3.000
 SZZ  H9   C21  O22  110.85  3.000
 SZZ  C23  C21  O22  107.34  3.000
 SZZ  H9   C21  C19  107.72  3.000
 SZZ  O22  C21  C19  111.61  3.000
 SZZ  C23  C21  C19  111.74  3.000
 SZZ  H10  O22  C21  108.68  3.000
 SZZ  H11  C23  C05  108.37  3.000
 SZZ  H11  C23  O24  111.14  3.000
 SZZ  C05  C23  O24  108.02  3.000
 SZZ  H11  C23  C21  108.65  3.000
 SZZ  O24  C23  C21  111.10  3.000
 SZZ  C05  C23  C21  109.51  3.000
 SZZ  H12  O24  C23  108.26  3.000
 SZZ  H13  C05  C04  108.91  3.000
 SZZ  H13  C05  C23  108.84  3.000
 SZZ  C04  C05  C23  111.84  3.000
 SZZ  H13  C05  O06  110.16  3.000
 SZZ  C23  C05  O06  108.93  3.000
 SZZ  C04  C05  O06  108.14  3.000
 SZZ  H15  C04  H14  108.22  3.000
 SZZ  H15  C04  O03  110.95  3.000
 SZZ  H14  C04  O03  108.58  3.000
 SZZ  H15  C04  C05  110.09  3.000
 SZZ  H14  C04  C05  109.06  3.000
 SZZ  O03  C04  C05  109.88  3.000
 SZZ  H16  O03  C04  108.93  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
 SZZ  Var_01  S08  C09  N10  O11  176.79   0.0  2
 SZZ  Var_02  C17  C16  C09  N10   82.72  30.0  3
 SZZ  Var_03  C18  C17  C16  C09  111.38  30.0  3
 SZZ  Var_04  H4   C18  C17  C16    0.33   0.0  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
 SZZ  chir_01  C07  S08  O06  C19  positiv
 SZZ  chir_02  C19  O20  C07  C21  negativ
 SZZ  chir_03  C21  O22  C19  C23  positiv
 SZZ  chir_04  C23  O24  C05  C21  positiv
 SZZ  chir_05  C05  O06  C23  C04  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SZZ  plan-1  O11  0.020
 SZZ  plan-1  N10  0.020
 SZZ  plan-1  C09  0.020
 SZZ  plan-1  C16  0.020
 SZZ  plan-1  S08  0.020
 SZZ  plan-2  C16  0.020
 SZZ  plan-2  C17  0.020
 SZZ  plan-2  C18  0.020
 SZZ  plan-2  H3   0.020
 SZZ  plan-2  H4   0.020
 SZZ  plan-2  H5   0.020

