# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:57:19 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl 1-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Sc2ccc(cc2)[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
 PSG  PSG  '4-nitrophenyl 1-thio-beta-D-glucopyranoside'  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 PERFECT
;

data_comp_PSG
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
 PSG  C7    C  CR16   0  -0.241   1.3453  -1.8829  -5.1385
 PSG  C8    C  CR16   0  -0.248   1.5973  -1.7727  -6.4935
 PSG  C9    C  CR6    0   0.238   2.5703  -2.5702  -7.0763
 PSG  C10   C  CR16   0  -0.251   3.2971  -3.4820  -6.3206
 PSG  C11   C  CR16   0  -0.258   3.0324  -3.5975  -4.9723
 PSG  C12   C  CR6    0  -0.094   2.0518  -2.8056  -4.3656
 PSG  N1    N  N      1   0.328   2.8336  -2.4511  -8.4954
 PSG  O11   O  O      0  -0.383   2.1861  -1.6512  -9.1312
 PSG  O12   O  O     -1  -0.383   3.6882  -3.1588  -8.9774
 PSG  S1    S  S2     0   0.129   1.8240  -3.0616  -2.6467
 PSG  C1    C  CH1    0  -0.184   0.3469  -2.1064  -2.2554
 PSG  C2    C  CH1    0   0.026  -0.1495  -2.5312  -0.8656
 PSG  C3    C  CH1    0  -0.001  -1.3616  -1.6685  -0.5152
 PSG  C4    C  CH1    0  -0.004  -1.0405  -0.1802  -0.6822
 PSG  C5    C  CH1    0  -0.053  -0.4682   0.0829  -2.0736
 PSG  C6    C  CH2    0  -0.166  -0.0112   1.5162  -2.2751
 PSG  O2    O  OH1    0  -0.644  -0.4131  -3.9016  -0.7937
 PSG  O3    O  OH1    0  -0.660  -1.7442  -1.9724   0.7984
 PSG  O4    O  OH1    0  -0.657  -2.1662   0.6171  -0.4016
 PSG  O5    O  O2     0  -0.480   0.6700  -0.7461  -2.2620
 PSG  O6    O  OH1    0  -0.662   0.4888   1.7381  -3.5710
 PSG  H7    H  HCR6   0   0.281   0.5998  -1.2334  -4.7056
 PSG  H8    H  HCR6   0   0.302   1.0374  -1.0574  -7.0780
 PSG  H10   H  HCR6   0   0.302   4.0573  -4.1052  -6.7683
 PSG  H11   H  HCR6   0   0.286   3.5886  -4.3186  -4.3874
 PSG  H1    H  HCH1   0   0.275  -0.4249  -2.3298  -3.0090
 PSG  H2    H  HCH1   0   0.264   0.6460  -2.3303  -0.1388
 PSG  H3    H  HCH1   0   0.209  -2.1691  -1.9197  -1.2286
 PSG  H4    H  HCH1   0   0.249  -0.2842   0.0955   0.0616
 PSG  H5    H  HCH1   0   0.231  -1.2278  -0.1567  -2.8370
 PSG  H62   H  HCH2   0   0.209   0.7255   1.7747  -1.5028
 PSG  H61   H  HCH2   0   0.237  -0.8665   2.1786  -2.1419
 PSG  H2O1  H  HOH1   0   0.452  -1.1442  -4.1172  -1.3841
 PSG  H3O1  H  HOH1   0   0.453  -2.4783  -1.3951   1.0354
 PSG  H4O1  H  HOH1   0   0.452  -2.8555   0.4329  -1.0510
 PSG  H6O1  H  HOH1   0   0.448   1.2990   1.2293  -3.6702

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
 PSG  C7   C8    aromatic  1.383  0.020  1.383
 PSG  C7   C12   aromatic  1.396  0.020  1.396
 PSG  C7   H7    single    0.930  0.020  1.080
 PSG  C8   C9    aromatic  1.387  0.020  1.387
 PSG  C8   H8    single    0.930  0.020  1.080
 PSG  C9   C10   aromatic  1.389  0.020  1.389
 PSG  C9   N1    single    1.448  0.020  1.448
 PSG  C10  C11   aromatic  1.379  0.020  1.379
 PSG  C10  H10   single    0.930  0.020  1.080
 PSG  C11  C12   aromatic  1.399  0.020  1.399
 PSG  C11  H11   single    0.930  0.020  1.080
 PSG  C12  S1    single    1.753  0.020  1.753
 PSG  N1   O11   double    1.210  0.020  1.210
 PSG  N1   O12   single    1.210  0.020  1.210
 PSG  S1   C1    single    1.802  0.020  1.802
 PSG  C1   C2    single    1.536  0.020  1.536
 PSG  C1   O5    single    1.398  0.020  1.398
 PSG  C1   H1    single    0.970  0.020  1.090
 PSG  C2   C3    single    1.528  0.020  1.528
 PSG  C2   O2    single    1.397  0.020  1.397
 PSG  C2   H2    single    0.970  0.020  1.090
 PSG  C3   C4    single    1.532  0.020  1.532
 PSG  C3   O3    single    1.402  0.020  1.402
 PSG  C3   H3    single    0.970  0.020  1.090
 PSG  C4   C5    single    1.527  0.020  1.527
 PSG  C4   O4    single    1.408  0.020  1.408
 PSG  C4   H4    single    0.970  0.020  1.090
 PSG  C5   C6    single    1.518  0.020  1.518
 PSG  C5   O5    single    1.421  0.020  1.421
 PSG  C5   H5    single    0.970  0.020  1.090
 PSG  C6   O6    single    1.407  0.020  1.407
 PSG  C6   H62   single    0.970  0.020  1.090
 PSG  C6   H61   single    0.970  0.020  1.090
 PSG  O2   H2O1  single    0.850  0.020  0.980
 PSG  O3   H3O1  single    0.850  0.020  0.980
 PSG  O4   H4O1  single    0.850  0.020  0.980
 PSG  O6   H6O1  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
 PSG  H7    C7   C12  121.69  3.000
 PSG  H7    C7   C8   118.10  3.000
 PSG  C12   C7   C8   120.21  3.000
 PSG  H8    C8   C9   121.14  3.000
 PSG  H8    C8   C7   119.25  3.000
 PSG  C9    C8   C7   119.60  3.000
 PSG  N1    C9   C10  119.46  3.000
 PSG  N1    C9   C8   119.49  3.000
 PSG  C10   C9   C8   121.06  3.000
 PSG  H10   C10  C11  119.48  3.000
 PSG  H10   C10  C9   121.42  3.000
 PSG  C11   C10  C9   119.10  3.000
 PSG  H11   C11  C12  120.20  3.000
 PSG  H11   C11  C10  119.05  3.000
 PSG  C12   C11  C10  120.75  3.000
 PSG  S1    C12  C11  115.71  3.000
 PSG  S1    C12  C7   125.02  3.000
 PSG  C11   C12  C7   119.27  3.000
 PSG  O12   N1   O11  123.75  3.000
 PSG  O12   N1   C9   118.08  3.000
 PSG  O11   N1   C9   118.17  3.000
 PSG  C1    S1   C12  104.01  3.000
 PSG  H1    C1   O5   110.85  3.000
 PSG  H1    C1   C2   109.66  3.000
 PSG  O5    C1   C2   110.37  3.000
 PSG  H1    C1   S1   108.56  3.000
 PSG  O5    C1   S1   108.98  3.000
 PSG  C2    C1   S1   108.35  3.000
 PSG  H2    C2   O2   106.41  3.000
 PSG  H2    C2   C3   108.66  3.000
 PSG  O2    C2   C3   113.09  3.000
 PSG  H2    C2   C1   108.35  3.000
 PSG  O2    C2   C1   112.26  3.000
 PSG  C3    C2   C1   107.92  3.000
 PSG  H3    C3   O3   110.85  3.000
 PSG  H3    C3   C4   107.65  3.000
 PSG  O3    C3   C4   111.72  3.000
 PSG  H3    C3   C2   107.62  3.000
 PSG  O3    C3   C2   108.00  3.000
 PSG  C4    C3   C2   110.93  3.000
 PSG  H4    C4   O4   105.91  3.000
 PSG  H4    C4   C5   108.44  3.000
 PSG  O4    C4   C5   112.57  3.000
 PSG  H4    C4   C3   108.36  3.000
 PSG  O4    C4   C3   111.16  3.000
 PSG  C5    C4   C3   110.20  3.000
 PSG  H5    C5   O5   109.46  3.000
 PSG  H5    C5   C6   108.69  3.000
 PSG  O5    C5   C6   106.99  3.000
 PSG  H5    C5   C4   109.57  3.000
 PSG  O5    C5   C4   108.70  3.000
 PSG  C6    C5   C4   113.35  3.000
 PSG  H61   C6   H62  107.31  3.000
 PSG  H61   C6   O6   107.19  3.000
 PSG  H62   C6   O6   111.86  3.000
 PSG  H61   C6   C5   108.75  3.000
 PSG  H62   C6   C5   109.32  3.000
 PSG  O6    C6   C5   112.23  3.000
 PSG  H2O1  O2   C2   109.32  3.000
 PSG  H3O1  O3   C3   107.97  3.000
 PSG  H4O1  O4   C4   109.20  3.000
 PSG  C5    O5   C1   112.46  3.000
 PSG  H6O1  O6   C6   108.11  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
 PSG  CONST_01  C10  C9   C8   C7     0.00  0.0  0
 PSG  CONST_02  C10  C11  C12  C7     0.00  0.0  0
 PSG  CONST_03  C11  C12  C7   C8     0.00  0.0  0
 PSG  CONST_04  C11  C10  C9   C8     0.00  0.0  0
 PSG  CONST_05  C12  C7   C8   C9     0.00  0.0  0
 PSG  CONST_06  C12  C11  C10  C9     0.00  0.0  0
 PSG  CONST_07  N1   C9   C8   C7   180.00  0.0  0
 PSG  CONST_08  S1   C12  C7   C8   180.00  0.0  0
 PSG  CONST_09  S1   C12  C11  C10  180.00  0.0  0
 PSG  CONST_10  N1   C9   C10  C11  180.00  0.0  0
 PSG  CONST_11  H11  C11  C12  C7   180.00  0.0  0
 PSG  CONST_12  H10  C10  C9   C8   180.00  0.0  0
 PSG  CONST_13  H7   C7   C8   C9   180.00  0.0  0
 PSG  CONST_14  H8   C8   C9   C10  180.00  0.0  0
 PSG  CONST_15  O11  N1   C9   C8     0.00  0.0  0
 PSG  CONST_16  O12  N1   C9   C8   180.00  0.0  0
 PSG  CONST_17  O11  N1   C9   C10  180.00  0.0  0
 PSG  CONST_18  O12  N1   C9   C10    0.00  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
 PSG  chir_01  C1  S1  C2  O5  negativ
 PSG  chir_02  C2  O2  C1  C3  negativ
 PSG  chir_03  C3  O3  C2  C4  positiv
 PSG  chir_04  C4  O4  C5  C3  positiv
 PSG  chir_05  C5  O5  C4  C6  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
 PSG  plan-1  C7   0.020
 PSG  plan-1  C8   0.020
 PSG  plan-1  C9   0.020
 PSG  plan-1  C10  0.020
 PSG  plan-1  C11  0.020
 PSG  plan-1  C12  0.020
 PSG  plan-1  N1   0.020
 PSG  plan-1  S1   0.020
 PSG  plan-1  H7   0.020
 PSG  plan-1  H8   0.020
 PSG  plan-1  H10  0.020
 PSG  plan-1  H11  0.020
 PSG  plan-2  C9   0.020
 PSG  plan-2  N1   0.020
 PSG  plan-2  O11  0.020
 PSG  plan-2  O12  0.020

