# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:48:56 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-phenylethyl 1-thio-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](SCCc2ccccc2)[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
 PTQ  PTQ  '2-phenylethyl 1-thio-beta-D-galactopyranoside'  D-saccharide  40  20  .  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_PTQ
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
 PTQ  C1   C  CH1   0  -0.126  -1.2627   0.4163   0.0255
 PTQ  O1   O  O2    0  -0.469  -1.5483  -0.8691  -0.4501
 PTQ  S1   S  S2    0  -0.019  -0.0001   1.1660  -1.0221
 PTQ  C2   C  CH1   0   0.016  -2.5097   1.3096   0.0068
 PTQ  O2   O  OH1   0  -0.664  -2.2646   2.5514   0.6167
 PTQ  C3   C  CH1   0   0.011  -3.6196   0.6305   0.8033
 PTQ  O3   O  OH1   0  -0.672  -4.8430   1.3142   0.6972
 PTQ  C4   C  CH1   0  -0.002  -3.8424  -0.7971   0.3127
 PTQ  O4   O  OH1   0  -0.671  -4.3512  -0.8297  -0.9977
 PTQ  C5   C  CH1   0  -0.013  -2.5120  -1.5371   0.3436
 PTQ  C6   C  CH2   0  -0.156  -2.6303  -2.9641  -0.1458
 PTQ  C7   C  CH2   0  -0.539   1.5125   0.4661  -0.2950
 PTQ  C8   C  CH2   0  -0.514   2.7330   1.1074  -0.9485
 PTQ  C9   C  CR6   0   0.126   3.9997   0.5424  -0.3667
 PTQ  C10  C  CR16  0  -0.304   4.5723  -0.6116  -0.8972
 PTQ  C11  C  CR16  0  -0.239   5.7199  -1.1574  -0.3376
 PTQ  C12  C  CR16  0  -0.271   6.3117  -0.5554   0.7655
 PTQ  C13  C  CR16  0  -0.239   5.7482   0.5946   1.3035
 PTQ  C14  C  CR16  0  -0.305   4.6001   1.1368   0.7409
 PTQ  H1   H  HCH1  0   0.252  -0.8712   0.3749   1.0545
 PTQ  H2   H  HCH1  0   0.228  -2.8415   1.4290  -1.0349
 PTQ  HO2  H  HOH1  0   0.451  -1.6111   3.0296   0.0940
 PTQ  H3   H  HCH1  0   0.217  -3.2892   0.5694   1.8525
 PTQ  HO3  H  HOH1  0   0.457  -4.7084   2.2338   0.9489
 PTQ  H4   H  HCH1  0   0.235  -4.5233  -1.2992   1.0165
 PTQ  HO4  H  HOH1  0   0.453  -5.1361  -0.2719  -1.0278
 PTQ  H5   H  HCH1  0   0.228  -2.1825  -1.5602   1.3953
 PTQ  HO5  H  HOH1  0   0.457  -1.4992  -4.5318  -0.2085
 PTQ  H6   H  HCH2  0   0.203  -3.4720  -3.4296   0.3833
 PTQ  H6A  H  HCH2  0   0.208  -2.8768  -2.9724  -1.2135
 PTQ  H7   H  HCH2  0   0.278   1.5086   0.6577   0.7794
 PTQ  H7A  H  HCH2  0   0.277   1.5196  -0.6133  -0.4503
 PTQ  H8   H  HCH2  0   0.260   2.7059   0.9325  -2.0265
 PTQ  H8A  H  HCH2  0   0.259   2.7004   2.1887  -0.7982
 PTQ  H10  H  HCR6  0   0.249   4.1176  -1.0873  -1.7588
 PTQ  H11  H  HCR6  0   0.254   6.1540  -2.0521  -0.7655
 PTQ  H12  H  HCR6  0   0.255   7.2079  -0.9778   1.2014
 PTQ  H13  H  HCR6  0   0.254   6.2053   1.0736   2.1601
 PTQ  H14  H  HCR6  0   0.248   4.1677   2.0361   1.1647
 PTQ  O5   O  OH1   0  -0.670  -1.4181  -3.6306   0.1156

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
 PTQ  C1   O1   single    1.400  0.020  1.400
 PTQ  C1   S1   single    1.804  0.020  1.804
 PTQ  C1   C2   single    1.534  0.020  1.534
 PTQ  O1   C5   single    1.416  0.020  1.416
 PTQ  S1   C7   single    1.818  0.020  1.818
 PTQ  C2   O2   single    1.405  0.020  1.405
 PTQ  C2   C3   single    1.526  0.020  1.526
 PTQ  C3   O3   single    1.405  0.020  1.405
 PTQ  C3   C4   single    1.526  0.020  1.526
 PTQ  C4   O4   single    1.406  0.020  1.406
 PTQ  C4   C5   single    1.523  0.020  1.523
 PTQ  C5   C6   single    1.513  0.020  1.513
 PTQ  O5   C6   single    1.408  0.020  1.408
 PTQ  C7   C8   single    1.526  0.020  1.526
 PTQ  C8   C9   single    1.504  0.020  1.504
 PTQ  C9   C10  aromatic  1.393  0.020  1.393
 PTQ  C9   C14  aromatic  1.393  0.020  1.393
 PTQ  C10  C11  aromatic  1.389  0.020  1.389
 PTQ  C11  C12  aromatic  1.389  0.020  1.389
 PTQ  C12  C13  aromatic  1.389  0.020  1.389
 PTQ  C13  C14  aromatic  1.389  0.020  1.389
 PTQ  C1   H1   single    0.970  0.020  1.090
 PTQ  C2   H2   single    0.970  0.020  1.090
 PTQ  O2   HO2  single    0.850  0.020  0.980
 PTQ  C3   H3   single    0.970  0.020  1.090
 PTQ  O3   HO3  single    0.850  0.020  0.980
 PTQ  C4   H4   single    0.970  0.020  1.090
 PTQ  O4   HO4  single    0.850  0.020  0.980
 PTQ  C5   H5   single    0.970  0.020  1.090
 PTQ  O5   HO5  single    0.850  0.020  0.980
 PTQ  C6   H6   single    0.970  0.020  1.090
 PTQ  C6   H6A  single    0.970  0.020  1.090
 PTQ  C7   H7   single    0.970  0.020  1.090
 PTQ  C7   H7A  single    0.970  0.020  1.090
 PTQ  C8   H8   single    0.970  0.020  1.090
 PTQ  C8   H8A  single    0.970  0.020  1.090
 PTQ  C10  H10  single    0.930  0.020  1.080
 PTQ  C11  H11  single    0.930  0.020  1.080
 PTQ  C12  H12  single    0.930  0.020  1.080
 PTQ  C13  H13  single    0.930  0.020  1.080
 PTQ  C14  H14  single    0.930  0.020  1.080

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
 PTQ  H1   C1   C2   108.80  3.000
 PTQ  H1   C1   S1   108.02  3.000
 PTQ  C2   C1   S1   108.66  3.000
 PTQ  H1   C1   O1   110.81  3.000
 PTQ  C2   C1   O1   111.38  3.000
 PTQ  S1   C1   O1   109.09  3.000
 PTQ  C5   O1   C1   112.43  3.000
 PTQ  C7   S1   C1   100.95  3.000
 PTQ  H2   C2   C3   108.87  3.000
 PTQ  H2   C2   O2   111.58  3.000
 PTQ  C3   C2   O2   107.08  3.000
 PTQ  H2   C2   C1   108.66  3.000
 PTQ  C3   C2   C1   109.01  3.000
 PTQ  O2   C2   C1   111.56  3.000
 PTQ  HO2  O2   C2   108.75  3.000
 PTQ  H3   C3   C4   107.35  3.000
 PTQ  H3   C3   O3   111.09  3.000
 PTQ  C4   C3   O3   107.68  3.000
 PTQ  H3   C3   C2   107.68  3.000
 PTQ  C4   C3   C2   110.79  3.000
 PTQ  O3   C3   C2   112.16  3.000
 PTQ  HO3  O3   C3   108.86  3.000
 PTQ  H4   C4   C5   107.81  3.000
 PTQ  H4   C4   O4   111.20  3.000
 PTQ  C5   C4   O4   108.90  3.000
 PTQ  H4   C4   C3   108.15  3.000
 PTQ  C5   C4   C3   108.69  3.000
 PTQ  O4   C4   C3   111.97  3.000
 PTQ  HO4  O4   C4   108.09  3.000
 PTQ  H5   C5   C6   108.20  3.000
 PTQ  H5   C5   C4   106.90  3.000
 PTQ  C6   C5   C4   112.54  3.000
 PTQ  H5   C5   O1   109.96  3.000
 PTQ  C6   C5   O1   108.47  3.000
 PTQ  C4   C5   O1   110.73  3.000
 PTQ  H6A  C6   H6   107.09  3.000
 PTQ  H6A  C6   O5   111.78  3.000
 PTQ  H6   C6   O5   111.71  3.000
 PTQ  H6A  C6   C5   109.87  3.000
 PTQ  H6   C6   C5   107.69  3.000
 PTQ  O5   C6   C5   108.60  3.000
 PTQ  H7A  C7   H7   108.30  3.000
 PTQ  H7A  C7   C8   110.47  3.000
 PTQ  H7   C7   C8   110.54  3.000
 PTQ  H7A  C7   S1   109.23  3.000
 PTQ  H7   C7   S1   108.85  3.000
 PTQ  C8   C7   S1   109.41  3.000
 PTQ  H8A  C8   H8   107.07  3.000
 PTQ  H8A  C8   C9   110.11  3.000
 PTQ  H8   C8   C9   110.02  3.000
 PTQ  H8A  C8   C7   109.47  3.000
 PTQ  H8   C8   C7   109.61  3.000
 PTQ  C9   C8   C7   110.49  3.000
 PTQ  C14  C9   C10  118.63  3.000
 PTQ  C14  C9   C8   120.68  3.000
 PTQ  C10  C9   C8   120.66  3.000
 PTQ  H10  C10  C11  119.63  3.000
 PTQ  H10  C10  C9   119.58  3.000
 PTQ  C11  C10  C9   120.79  3.000
 PTQ  H11  C11  C12  120.08  3.000
 PTQ  H11  C11  C10  119.80  3.000
 PTQ  C12  C11  C10  120.11  3.000
 PTQ  H12  C12  C13  120.20  3.000
 PTQ  H12  C12  C11  120.22  3.000
 PTQ  C13  C12  C11  119.58  3.000
 PTQ  H13  C13  C14  119.79  3.000
 PTQ  H13  C13  C12  120.10  3.000
 PTQ  C14  C13  C12  120.11  3.000
 PTQ  H14  C14  C13  119.68  3.000
 PTQ  H14  C14  C9   119.53  3.000
 PTQ  C13  C14  C9   120.78  3.000
 PTQ  HO5  O5   C6   107.97  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
 PTQ  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 PTQ  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 PTQ  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 PTQ  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 PTQ  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 PTQ  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 PTQ  CONST_07  C11  C10  C9   C8    180.00   0.0  0
 PTQ  CONST_08  C13  C14  C9   C8    180.00   0.0  0
 PTQ  CONST_09  H11  C11  C10  C9    180.00   0.0  0
 PTQ  CONST_10  H13  C13  C14  C9    180.00   0.0  0
 PTQ  CONST_11  H14  C14  C9   C10   180.00   0.0  0
 PTQ  CONST_12  H12  C12  C11  C10   180.00   0.0  0
 PTQ  CONST_13  H10  C10  C11  C12   180.00   0.0  0
 PTQ  Var_01    C10  C9   C8   C7     87.52  30.0  2
 PTQ  Var_02    C8   C7   S1   C1   -173.61  30.0  3
 PTQ  Var_03    C9   C8   C7   S1   -179.84  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
 PTQ  chir_01  C1  O1  S1  C2  negativ
 PTQ  chir_02  C2  O2  C1  C3  negativ
 PTQ  chir_03  C3  O3  C2  C4  positiv
 PTQ  chir_04  C4  O4  C5  C3  negativ
 PTQ  chir_05  C5  O1  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
 PTQ  plan-1  C8   0.020
 PTQ  plan-1  C9   0.020
 PTQ  plan-1  C10  0.020
 PTQ  plan-1  C11  0.020
 PTQ  plan-1  C12  0.020
 PTQ  plan-1  C13  0.020
 PTQ  plan-1  C14  0.020
 PTQ  plan-1  H10  0.020
 PTQ  plan-1  H11  0.020
 PTQ  plan-1  H12  0.020
 PTQ  plan-1  H13  0.020
 PTQ  plan-1  H14  0.020

