# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 15 09:54:36 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: ~{N}-[(1~{R},2~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-methylsulfanyl-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanyl-propyl]-4-nitro-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H]1O[C@@H]([C@H](O)[C@H](O)[C@H]1O)[C@H](NC(=O)c2ccc(cc2)[N+]([O-])=O)[C@@H](C)O
#
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
 95H  95H  ~{N}-[(1~{R},2~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-methylsulfanyl-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanyl-propyl]-4-nitro-benzamide  ligand  49  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_95H
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
 95H  O17  O  OH1    0  -0.649  -2.3901  -3.0302  -1.1089
 95H  O14  O  OH1    0  -0.674  -2.0868   3.2488   0.8278
 95H  C5   C  CH1    0  -0.144  -4.1651   0.1509   0.3378
 95H  C8   C  CH1    0   0.060  -1.0510  -2.6097  -1.0029
 95H  O10  O  OH1    0  -0.661  -1.0579   0.8248   1.7359
 95H  C4   C  CH1    0   0.008  -3.8055   1.5361   0.8965
 95H  C3   C  CH1    0   0.018  -2.5315   2.0494   0.2432
 95H  C2   C  CH1    0   0.005  -1.4148   1.0196   0.3917
 95H  C1   C  CH1    0   0.040  -1.8870  -0.3107  -0.1856
 95H  C18  C  CR6    0  -0.018   2.7345  -0.4039   0.5093
 95H  C19  C  CR16   0  -0.266   3.4816   0.1232   1.5592
 95H  C20  C  CR16   0  -0.254   4.7110   0.7102   1.3245
 95H  C21  C  CR6    0   0.254   5.1978   0.7432   0.0261
 95H  C22  C  CR16   0  -0.250   4.4858   0.2053  -1.0337
 95H  C23  C  CR16   0  -0.287   3.2494  -0.3652  -0.7836
 95H  C7   C  CH1    0  -0.142  -0.8671  -1.4516   0.0004
 95H  C9   C  CH3    0  -0.688  -0.1353  -3.7822  -0.6754
 95H  N13  N  NH1    0  -0.662   0.4828  -0.9527  -0.1306
 95H  N24  N  N      1   0.331   6.4946   1.3573  -0.2295
 95H  O11  O  O      0  -0.468   1.2343  -1.5615   1.9203
 95H  O15  O  OH1    0  -0.659  -4.8138   2.4870   0.6788
 95H  O26  O  O      0  -0.373   6.9081   1.3561  -1.3642
 95H  O27  O  O     -1  -0.373   7.0879   1.8367   0.7067
 95H  O6   O  O2     0  -0.470  -3.0826  -0.7256   0.4493
 95H  H1   H  HOH1   0   0.444  -2.7089  -3.2824  -0.2359
 95H  H2   H  HOH1   0   0.454  -2.8165   3.8773   0.8308
 95H  H3   H  HCH1   0   0.284  -4.9619  -0.2945   0.9404
 95H  H4   H  HCH1   0   0.226  -0.7917  -2.2250  -1.9957
 95H  H5   H  HOH1   0   0.452  -0.7471   1.6641   2.0901
 95H  H6   H  HCH1   0   0.244  -3.6153   1.4021   1.9697
 95H  H7   H  HCH1   0   0.215  -2.7163   2.1862  -0.8338
 95H  H8   H  HCH1   0   0.232  -0.5601   1.3709  -0.2026
 95H  H9   H  HCH1   0   0.237  -2.0664  -0.1552  -1.2596
 95H  H10  H  HCR6   0   0.281   3.0998   0.0840   2.5697
 95H  H11  H  HCR6   0   0.303   5.2728   1.1280   2.1468
 95H  H12  H  HCR6   0   0.305   4.8744   0.2222  -2.0411
 95H  H13  H  HCR6   0   0.280   2.7095  -0.7990  -1.6150
 95H  H14  H  HCH3   0   0.258  -6.1505  -1.6291  -0.8584
 95H  H15  H  HCH3   0   0.271  -5.9103  -1.3788  -2.5918
 95H  H16  H  HCH3   0   0.277  -4.6027  -2.0738  -1.6200
 95H  H17  H  HCH1   0   0.267  -0.9694  -1.8328   1.0190
 95H  H18  H  HCH3   0   0.242  -0.2812  -4.5823  -1.4014
 95H  H19  H  HCH3   0   0.229   0.9167  -3.5013  -0.7050
 95H  H20  H  HCH3   0   0.225  -0.3500  -4.1816   0.3188
 95H  H21  H  HNH1   0   0.410   0.7152  -0.4765  -0.9885
 95H  H22  H  HOH1   0   0.460  -5.5619   2.2877   1.2506
 95H  S16  S  S2     0  -0.051  -4.8171   0.3246  -1.3611
 95H  C12  C  C      0   0.553   1.4114  -1.0304   0.8372
 95H  C25  C  CH3    0  -0.778  -5.4198  -1.3590  -1.6202

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
 95H  O10  C2   single    1.404  0.020  1.404
 95H  O14  C3   single    1.406  0.020  1.406
 95H  C4   O15  single    1.403  0.020  1.403
 95H  C4   C3   single    1.521  0.020  1.521
 95H  C4   C5   single    1.536  0.020  1.536
 95H  C3   C2   single    1.526  0.020  1.526
 95H  C5   O6   single    1.397  0.020  1.397
 95H  C5   S16  single    1.828  0.020  1.828
 95H  C2   C1   single    1.525  0.020  1.525
 95H  O6   C1   single    1.416  0.020  1.416
 95H  C1   C7   single    1.542  0.020  1.542
 95H  O11  C12  double    1.219  0.020  1.219
 95H  C7   C8   single    1.543  0.020  1.543
 95H  C7   N13  single    1.445  0.020  1.445
 95H  C25  S16  single    1.807  0.020  1.807
 95H  C8   O17  single    1.408  0.020  1.408
 95H  C8   C9   single    1.523  0.020  1.523
 95H  C12  N13  single    1.344  0.020  1.344
 95H  C12  C18  single    1.500  0.020  1.500
 95H  C18  C19  aromatic  1.392  0.020  1.392
 95H  C18  C23  aromatic  1.392  0.020  1.392
 95H  C19  C20  aromatic  1.382  0.020  1.382
 95H  C23  C22  aromatic  1.384  0.020  1.384
 95H  C20  C21  aromatic  1.387  0.020  1.387
 95H  C22  C21  aromatic  1.386  0.020  1.386
 95H  C21  N24  single    1.457  0.020  1.457
 95H  N24  O27  single    1.208  0.020  1.208
 95H  N24  O26  double    1.208  0.020  1.208
 95H  O17  H1   single    0.850  0.020  0.980
 95H  O14  H2   single    0.850  0.020  0.980
 95H  C5   H3   single    0.970  0.020  1.090
 95H  C8   H4   single    0.970  0.020  1.090
 95H  O10  H5   single    0.850  0.020  0.980
 95H  C4   H6   single    0.970  0.020  1.090
 95H  C3   H7   single    0.970  0.020  1.090
 95H  C2   H8   single    0.970  0.020  1.090
 95H  C1   H9   single    0.970  0.020  1.090
 95H  C19  H10  single    0.930  0.020  1.080
 95H  C20  H11  single    0.930  0.020  1.080
 95H  C22  H12  single    0.930  0.020  1.080
 95H  C23  H13  single    0.930  0.020  1.080
 95H  C25  H14  single    0.970  0.020  1.090
 95H  C25  H15  single    0.970  0.020  1.090
 95H  C25  H16  single    0.970  0.020  1.090
 95H  C7   H17  single    0.970  0.020  1.090
 95H  C9   H18  single    0.970  0.020  1.090
 95H  C9   H19  single    0.970  0.020  1.090
 95H  C9   H20  single    0.970  0.020  1.090
 95H  N13  H21  single    0.860  0.020  1.020
 95H  O15  H22  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
 95H  H1   O17  C8   108.96  3.000
 95H  H2   O14  C3   108.56  3.000
 95H  H3   C5   S16  106.91  3.000
 95H  H3   C5   O6   105.36  3.000
 95H  S16  C5   O6   114.21  3.000
 95H  H3   C5   C4   109.72  3.000
 95H  S16  C5   C4   109.62  3.000
 95H  O6   C5   C4   110.80  3.000
 95H  H4   C8   C9   108.83  3.000
 95H  H4   C8   C7   107.30  3.000
 95H  C9   C8   C7   111.48  3.000
 95H  H4   C8   O17  105.17  3.000
 95H  C9   C8   O17  110.98  3.000
 95H  C7   C8   O17  112.74  3.000
 95H  H5   O10  C2   108.27  3.000
 95H  H6   C4   O15  111.03  3.000
 95H  H6   C4   C3   108.41  3.000
 95H  O15  C4   C3   107.86  3.000
 95H  H6   C4   C5   106.61  3.000
 95H  C3   C4   C5   110.13  3.000
 95H  O15  C4   C5   112.73  3.000
 95H  H7   C3   C2   107.56  3.000
 95H  H7   C3   C4   108.75  3.000
 95H  C2   C3   C4   110.08  3.000
 95H  H7   C3   O14  110.71  3.000
 95H  C2   C3   O14  107.68  3.000
 95H  C4   C3   O14  111.97  3.000
 95H  H8   C2   C1   108.36  3.000
 95H  H8   C2   C3   107.50  3.000
 95H  C1   C2   C3   108.98  3.000
 95H  H8   C2   O10  111.37  3.000
 95H  C1   C2   O10  108.67  3.000
 95H  C3   C2   O10  111.88  3.000
 95H  H9   C1   O6   109.97  3.000
 95H  H9   C1   C7   109.29  3.000
 95H  O6   C1   C7   106.72  3.000
 95H  H9   C1   C2   107.26  3.000
 95H  C7   C1   C2   113.27  3.000
 95H  O6   C1   C2   110.32  3.000
 95H  C23  C18  C19  119.43  3.000
 95H  C23  C18  C12  122.74  3.000
 95H  C19  C18  C12  117.81  3.000
 95H  H10  C19  C20  119.22  3.000
 95H  H10  C19  C18  120.11  3.000
 95H  C20  C19  C18  120.66  3.000
 95H  H11  C20  C21  121.40  3.000
 95H  H11  C20  C19  119.84  3.000
 95H  C21  C20  C19  118.76  3.000
 95H  N24  C21  C22  119.12  3.000
 95H  N24  C21  C20  119.11  3.000
 95H  C22  C21  C20  121.77  3.000
 95H  H12  C22  C23  119.76  3.000
 95H  H12  C22  C21  121.51  3.000
 95H  C23  C22  C21  118.73  3.000
 95H  H13  C23  C22  118.16  3.000
 95H  H13  C23  C18  121.19  3.000
 95H  C22  C23  C18  120.63  3.000
 95H  H17  C7   N13  107.01  3.000
 95H  H17  C7   C1   107.98  3.000
 95H  N13  C7   C1   110.58  3.000
 95H  H17  C7   C8   109.46  3.000
 95H  N13  C7   C8   108.14  3.000
 95H  C1   C7   C8   113.46  3.000
 95H  H20  C9   H19  107.99  3.000
 95H  H20  C9   H18  108.15  3.000
 95H  H19  C9   H18  107.48  3.000
 95H  H20  C9   C8   111.03  3.000
 95H  H19  C9   C8   112.10  3.000
 95H  H18  C9   C8   109.95  3.000
 95H  H21  N13  C7   117.10  3.000
 95H  H21  N13  C12  118.74  3.000
 95H  C7   N13  C12  124.08  3.000
 95H  O27  N24  O26  124.10  3.000
 95H  O26  N24  C21  117.97  3.000
 95H  O27  N24  C21  117.93  3.000
 95H  H22  O15  C4   109.04  3.000
 95H  C1   O6   C5   115.76  3.000
 95H  C25  S16  C5    99.42  3.000
 95H  O11  C12  N13  124.38  3.000
 95H  N13  C12  C18  115.34  3.000
 95H  O11  C12  C18  120.28  3.000
 95H  H16  C25  H15  109.10  3.000
 95H  H16  C25  H14  109.96  3.000
 95H  H15  C25  H14  108.50  3.000
 95H  H16  C25  S16  111.25  3.000
 95H  H15  C25  S16  107.17  3.000
 95H  H14  C25  S16  110.76  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
 95H  CONST_01  C21  C20  C19  C18    0.00   0.0  0
 95H  CONST_02  C21  C22  C23  C18    0.00   0.0  0
 95H  CONST_03  C22  C23  C18  C19    0.00   0.0  0
 95H  CONST_04  C22  C21  C20  C19    0.00   0.0  0
 95H  CONST_05  C23  C18  C19  C20    0.00   0.0  0
 95H  CONST_06  C23  C22  C21  C20    0.00   0.0  0
 95H  CONST_07  C20  C19  C18  C12  180.00   0.0  0
 95H  CONST_08  C22  C23  C18  C12  180.00   0.0  0
 95H  CONST_09  N24  C21  C20  C19  180.00   0.0  0
 95H  CONST_10  N24  C21  C22  C23  180.00   0.0  0
 95H  CONST_11  H11  C20  C19  C18  180.00   0.0  0
 95H  CONST_12  H12  C22  C23  C18  180.00   0.0  0
 95H  CONST_13  H13  C23  C18  C19  180.00   0.0  0
 95H  CONST_14  H10  C19  C20  C21  180.00   0.0  0
 95H  CONST_15  O27  N24  C21  C20    0.00   0.0  0
 95H  CONST_16  O26  N24  C21  C20  180.00   0.0  0
 95H  CONST_17  O27  N24  C21  C22  180.00   0.0  0
 95H  CONST_18  O26  N24  C21  C22    0.00   0.0  0
 95H  CONST_19  C7   N13  C12  C18  180.00   0.0  0
 95H  CONST_20  H21  N13  C12  C18    0.00   0.0  0
 95H  CONST_21  O11  C12  N13  C7     0.00   0.0  0
 95H  Var_01    O11  C12  C18  C19  -29.88  30.0  2
 95H  Var_02    H14  C25  S16  C5    57.76  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
 95H  chir_01  C5  C4   O6  S16  positiv
 95H  chir_02  C8  O17  C7  C9   negativ
 95H  chir_03  C4  O15  C3  C5   positiv
 95H  chir_04  C3  O14  C4  C2   positiv
 95H  chir_05  C2  O10  C3  C1   positiv
 95H  chir_06  C1  O6   C7  C2   positiv
 95H  chir_07  C7  N13  C8  C1   positiv

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
 95H  plan-1  C18  0.020
 95H  plan-1  C19  0.020
 95H  plan-1  C20  0.020
 95H  plan-1  C21  0.020
 95H  plan-1  C22  0.020
 95H  plan-1  C23  0.020
 95H  plan-1  N24  0.020
 95H  plan-1  H10  0.020
 95H  plan-1  H11  0.020
 95H  plan-1  H12  0.020
 95H  plan-1  H13  0.020
 95H  plan-1  C12  0.020
 95H  plan-2  C21  0.020
 95H  plan-2  N24  0.020
 95H  plan-2  O26  0.020
 95H  plan-2  O27  0.020
 95H  plan-3  C18  0.020
 95H  plan-3  C7   0.020
 95H  plan-3  N13  0.020
 95H  plan-3  O11  0.020
 95H  plan-3  H21  0.020
 95H  plan-3  C12  0.020

