# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 12:53:10 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-nitrophenyl 1-thio-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Sc2ccccc2[N+]([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
 OTN  OTN  '2-nitrophenyl 1-thio-beta-D-galactopyranoside'  D-saccharide  36  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OTN
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
 OTN  O2'  O  O     -1  -0.376  -4.6451  -1.8631   0.2431
 OTN  N1'  N  N      1   0.332  -3.6881  -1.3731  -0.3086
 OTN  O3'  O  O      0  -0.374  -3.0882  -1.8983  -1.2197
 OTN  C2'  C  CR6    0   0.263  -3.2270  -0.0748   0.1311
 OTN  C3'  C  CR16   0  -0.267  -4.1604   0.7663   0.7241
 OTN  C4'  C  CR16   0  -0.261  -3.7808   2.0296   1.1307
 OTN  C5'  C  CR16   0  -0.219  -2.4679   2.4385   0.9388
 OTN  C6'  C  CR16   0  -0.240  -1.5402   1.5957   0.3512
 OTN  C1'  C  CR6    0  -0.147  -1.8917   0.3060  -0.0535
 OTN  S01  S  S2     0   0.123  -0.6881  -0.7892  -0.7367
 OTN  C1   C  CH1    0  -0.163   0.8231  -0.2402   0.0973
 OTN  O5   O  O2     0  -0.473   1.3902   0.8141  -0.6232
 OTN  C5   C  CH1    0  -0.017   2.5570   1.3253   0.0018
 OTN  C6   C  CH2    0  -0.156   2.9682   2.5815  -0.7325
 OTN  O6   O  OH1    0  -0.666   1.9794   3.5602  -0.5152
 OTN  C4   C  CH1    0   0.003   3.6442   0.2623   0.0392
 OTN  O4   O  OH1    0  -0.670   4.0278  -0.0411  -1.2781
 OTN  C3   C  CH1    0   0.011   3.1019  -0.9607   0.7749
 OTN  O3   O  OH1    0  -0.670   4.0894  -1.9585   0.7327
 OTN  C2   C  CH1    0   0.018   1.7852  -1.4355   0.1631
 OTN  O2   O  OH1    0  -0.661   1.2899  -2.4557   0.9901
 OTN  H1   H  HCR6   0   0.301  -5.1824   0.4391   0.8509
 OTN  H2   H  HCR6   0   0.281  -4.5059   2.6923   1.5814
 OTN  H3   H  HCR6   0   0.282  -2.1609   3.4317   1.2376
 OTN  H4   H  HCR6   0   0.298  -0.5370   1.9621   0.1851
 OTN  H5   H  HCH1   0   0.272   0.5607   0.0635   1.1218
 OTN  H6   H  HCH1   0   0.236   2.3317   1.5968   1.0451
 OTN  H7   H  HCH2   0   0.204   3.9454   2.8958  -0.3433
 OTN  H8   H  HCH2   0   0.211   3.0994   2.3647  -1.7985
 OTN  H9   H  HOH1   0   0.458   2.1916   4.3247  -1.0579
 OTN  H10  H  HCH1   0   0.238   4.4887   0.6609   0.6211
 OTN  H11  H  HOH1   0   0.454   4.6507  -0.7750  -1.2478
 OTN  H12  H  HCH1   0   0.221   2.8947  -0.6519   1.8117
 OTN  H13  H  HOH1   0   0.457   3.7471  -2.7530   1.1563
 OTN  H14  H  HCH1   0   0.238   1.9765  -1.7953  -0.8577
 OTN  H15  H  HOH1   0   0.458   0.6055  -2.9424   0.5197

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
 OTN  O2'  N1'  single    1.208  0.020  1.208
 OTN  C3'  C4'  aromatic  1.380  0.020  1.380
 OTN  C3'  C2'  aromatic  1.389  0.020  1.389
 OTN  N1'  C2'  single    1.446  0.020  1.446
 OTN  N1'  O3'  double    1.211  0.020  1.211
 OTN  C4'  C5'  aromatic  1.388  0.020  1.388
 OTN  C2'  C1'  aromatic  1.401  0.020  1.401
 OTN  C5'  C6'  aromatic  1.384  0.020  1.384
 OTN  C1'  C6'  aromatic  1.397  0.020  1.397
 OTN  C1'  S01  single    1.765  0.020  1.765
 OTN  S01  C1   single    1.811  0.020  1.811
 OTN  O2   C2   single    1.404  0.020  1.404
 OTN  C1   C2   single    1.536  0.020  1.536
 OTN  C1   O5   single    1.397  0.020  1.397
 OTN  C2   C3   single    1.528  0.020  1.528
 OTN  O5   C5   single    1.419  0.020  1.419
 OTN  C3   O3   single    1.404  0.020  1.404
 OTN  C3   C4   single    1.527  0.020  1.527
 OTN  C5   C4   single    1.521  0.020  1.521
 OTN  C5   C6   single    1.512  0.020  1.512
 OTN  O6   C6   single    1.408  0.020  1.408
 OTN  C4   O4   single    1.405  0.020  1.405
 OTN  C3'  H1   single    0.930  0.020  1.080
 OTN  C4'  H2   single    0.930  0.020  1.080
 OTN  C5'  H3   single    0.930  0.020  1.080
 OTN  C6'  H4   single    0.930  0.020  1.080
 OTN  C1   H5   single    0.970  0.020  1.090
 OTN  C5   H6   single    0.970  0.020  1.090
 OTN  C6   H7   single    0.970  0.020  1.090
 OTN  C6   H8   single    0.970  0.020  1.090
 OTN  O6   H9   single    0.850  0.020  0.980
 OTN  C4   H10  single    0.970  0.020  1.090
 OTN  O4   H11  single    0.850  0.020  0.980
 OTN  C3   H12  single    0.970  0.020  1.090
 OTN  O3   H13  single    0.850  0.020  0.980
 OTN  C2   H14  single    0.970  0.020  1.090
 OTN  O2   H15  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
 OTN  C2'  N1'  O3'  117.41  3.000
 OTN  O3'  N1'  O2'  124.06  3.000
 OTN  C2'  N1'  O2'  118.53  3.000
 OTN  C1'  C2'  C3'  122.15  3.000
 OTN  C1'  C2'  N1'  120.52  3.000
 OTN  C3'  C2'  N1'  117.32  3.000
 OTN  H1   C3'  C4'  120.18  3.000
 OTN  H1   C3'  C2'  120.15  3.000
 OTN  C4'  C3'  C2'  119.67  3.000
 OTN  H2   C4'  C5'  120.77  3.000
 OTN  H2   C4'  C3'  119.96  3.000
 OTN  C5'  C4'  C3'  119.27  3.000
 OTN  H3   C5'  C6'  119.08  3.000
 OTN  H3   C5'  C4'  120.04  3.000
 OTN  C6'  C5'  C4'  120.87  3.000
 OTN  H4   C6'  C1'  120.14  3.000
 OTN  H4   C6'  C5'  118.75  3.000
 OTN  C1'  C6'  C5'  121.10  3.000
 OTN  S01  C1'  C6'  120.90  3.000
 OTN  S01  C1'  C2'  122.17  3.000
 OTN  C6'  C1'  C2'  116.92  3.000
 OTN  C1   S01  C1'  101.69  3.000
 OTN  H5   C1   C2   108.93  3.000
 OTN  H5   C1   O5   111.63  3.000
 OTN  C2   C1   O5   110.80  3.000
 OTN  H5   C1   S01  108.26  3.000
 OTN  O5   C1   S01  109.26  3.000
 OTN  C2   C1   S01  107.85  3.000
 OTN  C5   O5   C1   112.24  3.000
 OTN  H6   C5   C4   107.17  3.000
 OTN  H6   C5   C6   108.11  3.000
 OTN  C4   C5   C6   113.47  3.000
 OTN  H6   C5   O5   109.74  3.000
 OTN  C6   C5   O5   108.00  3.000
 OTN  C4   C5   O5   110.29  3.000
 OTN  H8   C6   H7   107.15  3.000
 OTN  H8   C6   O6   111.83  3.000
 OTN  H7   C6   O6   111.80  3.000
 OTN  H8   C6   C5   109.91  3.000
 OTN  H7   C6   C5   107.92  3.000
 OTN  O6   C6   C5   108.15  3.000
 OTN  H9   O6   C6   108.10  3.000
 OTN  H10  C4   C3   107.94  3.000
 OTN  H10  C4   O4   111.38  3.000
 OTN  C3   C4   O4   112.07  3.000
 OTN  H10  C4   C5   107.97  3.000
 OTN  O4   C4   C5   108.84  3.000
 OTN  C3   C4   C5   108.53  3.000
 OTN  H11  O4   C4   108.16  3.000
 OTN  H12  C3   C2   107.58  3.000
 OTN  H12  C3   O3   111.09  3.000
 OTN  C2   C3   O3   111.91  3.000
 OTN  H12  C3   C4   107.21  3.000
 OTN  O3   C3   C4   107.75  3.000
 OTN  C2   C3   C4   111.23  3.000
 OTN  H13  O3   C3   108.84  3.000
 OTN  H14  C2   O2   111.76  3.000
 OTN  H14  C2   C3   108.89  3.000
 OTN  O2   C2   C3   107.10  3.000
 OTN  H14  C2   C1   108.91  3.000
 OTN  C3   C2   C1   108.38  3.000
 OTN  O2   C2   C1   111.71  3.000
 OTN  H15  O2   C2   109.29  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
 OTN  CONST_01  C5'  C4'  C3'  C2'    0.00  0.0  0
 OTN  CONST_02  C5'  C6'  C1'  C2'    0.00  0.0  0
 OTN  CONST_03  C6'  C5'  C4'  C3'    0.00  0.0  0
 OTN  CONST_04  C6'  C1'  C2'  C3'    0.00  0.0  0
 OTN  CONST_05  C1'  C2'  C3'  C4'    0.00  0.0  0
 OTN  CONST_06  C1'  C6'  C5'  C4'    0.00  0.0  0
 OTN  CONST_07  C4'  C3'  C2'  N1'  180.00  0.0  0
 OTN  CONST_08  C6'  C1'  C2'  N1'  180.00  0.0  0
 OTN  CONST_09  S01  C1'  C2'  C3'  180.00  0.0  0
 OTN  CONST_10  S01  C1'  C6'  C5'  180.00  0.0  0
 OTN  CONST_11  H2   C4'  C3'  C2'  180.00  0.0  0
 OTN  CONST_12  H4   C6'  C1'  C2'  180.00  0.0  0
 OTN  CONST_13  H3   C5'  C4'  C3'  180.00  0.0  0
 OTN  CONST_14  H1   C3'  C4'  C5'  180.00  0.0  0

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
 OTN  chir_01  C1  S01  C2  O5  negativ
 OTN  chir_02  C5  O5   C6  C4  positiv
 OTN  chir_03  C4  O4   C5  C3  negativ
 OTN  chir_04  C3  O3   C4  C2  negativ
 OTN  chir_05  C2  O2   C3  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
 OTN  plan-1  N1'  0.020
 OTN  plan-1  C2'  0.020
 OTN  plan-1  C3'  0.020
 OTN  plan-1  C4'  0.020
 OTN  plan-1  C5'  0.020
 OTN  plan-1  C6'  0.020
 OTN  plan-1  C1'  0.020
 OTN  plan-1  S01  0.020
 OTN  plan-1  H1   0.020
 OTN  plan-1  H2   0.020
 OTN  plan-1  H3   0.020
 OTN  plan-1  H4   0.020
 OTN  plan-2  O2'  0.020
 OTN  plan-2  N1'  0.020
 OTN  plan-2  O3'  0.020
 OTN  plan-2  C2'  0.020

