# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 12:27:27 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[SH](C)CCC(O)=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
 DQY  DQY  '3-(dimethyl-lambda~4~-sulfanyl)propanoic acid'  ligand  20  8  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DQY
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
 DQY  S     S  SH1   0   0.250  -1.8652   0.1931   0.5041
 DQY  C1    C  C     0   0.545   2.3886  -0.1495   0.0632
 DQY  O1    O  O     0  -0.448   2.7109  -1.2531  -0.3007
 DQY  C2    C  CH2   0  -0.552   0.9802   0.3849   0.1148
 DQY  O2    O  OH1   0  -0.601   3.2766   0.7591   0.4683
 DQY  C3    C  CH2   0  -0.683  -0.1071  -0.6116  -0.2089
 DQY  CM1   C  CH3   0  -0.733  -1.8686   1.4495  -0.8084
 DQY  CM2   C  CH3   0  -0.721  -2.7737  -1.2713  -0.0321
 DQY  H2    H  HCH2  0   0.256   0.8268   0.8111   1.1155
 DQY  H2A   H  HCH2  0   0.270   0.9492   1.2452  -0.5636
 DQY  HO2   H  HOH1  0   0.476   4.1715   0.3927   0.4126
 DQY  H3    H  HCH2  0   0.221   0.0278  -1.5301   0.3688
 DQY  H3A   H  HCH2  0   0.218  -0.1262  -0.8756  -1.2694
 DQY  HM1   H  HCH3  0   0.280  -1.1689   1.1843  -1.5951
 DQY  HM1A  H  HCH3  0   0.286  -2.8736   1.5348  -1.2098
 DQY  HM1B  H  HCH3  0   0.285  -1.5812   2.3948  -0.3504
 DQY  HM2   H  HCH3  0   0.275  -2.1078  -2.1296  -0.0487
 DQY  HM2A  H  HCH3  0   0.274  -3.5980  -1.4205   0.6620
 DQY  HM2B  H  HCH3  0   0.282  -3.1725  -1.1033  -1.0305
 DQY  HS    H  HSH1  0  -0.181  -3.2436   0.7733   0.8682

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
 DQY  CM1  S     single  1.817  0.020  1.817
 DQY  CM2  S     single  1.805  0.020  1.805
 DQY  S    C3    single  2.061  0.020  2.061
 DQY  C2   C1    single  1.507  0.020  1.507
 DQY  C1   O1    double  1.206  0.020  1.206
 DQY  C1   O2    single  1.334  0.020  1.334
 DQY  C3   C2    single  1.510  0.020  1.510
 DQY  C2   H2    single  0.970  0.020  1.090
 DQY  C2   H2A   single  0.970  0.020  1.090
 DQY  O2   HO2   single  0.850  0.020  0.980
 DQY  C3   H3    single  0.970  0.020  1.090
 DQY  C3   H3A   single  0.970  0.020  1.090
 DQY  CM1  HM1   single  0.970  0.020  1.090
 DQY  CM1  HM1A  single  0.970  0.020  1.090
 DQY  CM1  HM1B  single  0.970  0.020  1.090
 DQY  CM2  HM2   single  0.970  0.020  1.090
 DQY  CM2  HM2A  single  0.970  0.020  1.090
 DQY  CM2  HM2B  single  0.970  0.020  1.090
 DQY  S    HS    single  1.200  0.020  1.300

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
 DQY  HS    S    CM2    85.72  3.000
 DQY  HS    S    CM1    84.75  3.000
 DQY  CM2   S    CM1   110.21  3.000
 DQY  HS    S    C3    173.22  3.000
 DQY  CM2   S    C3     90.56  3.000
 DQY  CM1   S    C3     91.24  3.000
 DQY  O2    C1   C2    111.73  3.000
 DQY  O2    C1   O1    122.49  3.000
 DQY  C2    C1   O1    125.77  3.000
 DQY  H2A   C2   H2    104.80  3.000
 DQY  H2A   C2   C3    111.40  3.000
 DQY  H2    C2   C3    110.54  3.000
 DQY  H2A   C2   C1    106.47  3.000
 DQY  H2    C2   C1    107.42  3.000
 DQY  C3    C2   C1    115.56  3.000
 DQY  HO2   O2   C1    109.88  3.000
 DQY  H3A   C3   H3    108.17  3.000
 DQY  H3A   C3   C2    112.34  3.000
 DQY  H3    C3   C2    110.63  3.000
 DQY  H3A   C3   S     114.53  3.000
 DQY  H3    C3   S     104.50  3.000
 DQY  C2    C3   S     106.40  3.000
 DQY  HM1B  CM1  HM1A  109.37  3.000
 DQY  HM1B  CM1  HM1   110.29  3.000
 DQY  HM1A  CM1  HM1   110.36  3.000
 DQY  HM1B  CM1  S     107.21  3.000
 DQY  HM1A  CM1  S     108.85  3.000
 DQY  HM1   CM1  S     110.69  3.000
 DQY  HM2B  CM2  HM2A  109.20  3.000
 DQY  HM2B  CM2  HM2   109.43  3.000
 DQY  HM2A  CM2  HM2   111.46  3.000
 DQY  HM2B  CM2  S     109.38  3.000
 DQY  HM2A  CM2  S     107.64  3.000
 DQY  HM2   CM2  S     109.69  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
 DQY  CONST_01  HO2  O2   C1  O1    0.00   0.0  0
 DQY  Var_01    C1   C2   C3  S   162.56  30.0  3
 DQY  Var_02    C3   C2   C1  O1    5.60  30.0  2
 DQY  Var_03    CM1  S    C3  C2   71.38  30.0  2
 DQY  Var_04    HM1  CM1  S   C3   14.97  30.0  3
 DQY  Var_05    HM2  CM2  S   C3   26.85  30.0  3

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
 DQY  plan-1  C1   0.020
 DQY  plan-1  O1   0.020
 DQY  plan-1  C2   0.020
 DQY  plan-1  O2   0.020
 DQY  plan-1  HO2  0.020

