# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 03:48:47 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R)-2-(trimethylsilyl)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Si](C)(C)[C@H](CC(O)=O)C(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
 SIF  SIF  '(2R)-2-(trimethylsilyl)butanedioic acid'  ligand  26  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SIF
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
 SIF  C1   C   C     0   0.563   0.5481   0.0206  -2.4055
 SIF  O1   O   O     0  -0.439  -0.3640  -0.6723  -2.7818
 SIF  O2   O   OH1   0  -0.594   1.3578   0.6729  -3.2305
 SIF  C2   C   CH2   0  -0.599   0.9167   0.2485  -0.9620
 SIF  C3   C   CH1   0  -0.638  -0.0350  -0.4394   0.0068
 SIF  SI   SI  SI    0   1.081   0.4958  -0.1197   1.8322
 SIF  C4   C   C     0   0.549  -1.4665  -0.0622  -0.1659
 SIF  O3   O   O     0  -0.460  -2.4060  -0.7860   0.0704
 SIF  O4   O   OH1   0  -0.597  -1.6207   1.2042  -0.5509
 SIF  C5   C   CH3   0  -0.970  -0.6937  -1.0202   2.9733
 SIF  C6   C   CH3   0  -0.983   0.4752   1.7290   2.1739
 SIF  C7   C   CH3   0  -0.982   2.2350  -0.8089   2.0252
 SIF  HO2  H   HOH1  0   0.482   1.1043   0.5037  -4.1503
 SIF  H21  H   HCH2  0   0.288   0.9843   1.3254  -0.7889
 SIF  H22  H   HCH2  0   0.301   1.9329  -0.1305  -0.8189
 SIF  H3   H   HCH1  0   0.293   0.0284  -1.5246  -0.1144
 SIF  HO4  H   HOH1  0   0.477  -2.5639   1.4133  -0.6179
 SIF  H51  H   HCH3  0   0.245  -0.3643  -0.9315   4.0102
 SIF  H52  H   HCH3  0   0.248  -1.7046  -0.6153   2.9127
 SIF  H53  H   HCH3  0   0.247  -0.7459  -2.0831   2.7322
 SIF  H61  H   HCH3  0   0.248  -0.5183   2.1553   2.0303
 SIF  H62  H   HCH3  0   0.247   0.7747   1.9256   3.2050
 SIF  H63  H   HCH3  0   0.245   1.1668   2.2695   1.5256
 SIF  H71  H   HCH3  0   0.249   2.2793  -1.8649   1.7528
 SIF  H72  H   HCH3  0   0.249   2.9626  -0.2755   1.4114
 SIF  H73  H   HCH3  0   0.250   2.5597  -0.7227   3.0640

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
 SIF  C1  O1   double  1.206  0.020  1.206
 SIF  C1  O2   single  1.327  0.020  1.327
 SIF  C1  C2   single  1.507  0.020  1.507
 SIF  O2  HO2  single  0.850  0.020  0.980
 SIF  C2  C3   single  1.522  0.020  1.522
 SIF  C2  H21  single  0.970  0.020  1.090
 SIF  C2  H22  single  0.970  0.020  1.090
 SIF  C3  SI   single  1.928  0.020  1.928
 SIF  C3  C4   single  1.490  0.020  1.490
 SIF  C3  H3   single  0.970  0.020  1.090
 SIF  SI  C5   single  1.878  0.020  1.878
 SIF  SI  C6   single  1.880  0.020  1.880
 SIF  SI  C7   single  1.881  0.020  1.881
 SIF  C4  O3   double  1.209  0.020  1.209
 SIF  C4  O4   single  1.333  0.020  1.333
 SIF  O4  HO4  single  0.850  0.020  0.980
 SIF  C5  H51  single  0.970  0.020  1.090
 SIF  C5  H52  single  0.970  0.020  1.090
 SIF  C5  H53  single  0.970  0.020  1.090
 SIF  C6  H61  single  0.970  0.020  1.090
 SIF  C6  H62  single  0.970  0.020  1.090
 SIF  C6  H63  single  0.970  0.020  1.090
 SIF  C7  H71  single  0.970  0.020  1.090
 SIF  C7  H72  single  0.970  0.020  1.090
 SIF  C7  H73  single  0.970  0.020  1.090

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
 SIF  C2   C1  O2   111.82  3.000
 SIF  C2   C1  O1   124.81  3.000
 SIF  O2   C1  O1   123.36  3.000
 SIF  HO2  O2  C1   110.15  3.000
 SIF  H22  C2  H21  105.26  3.000
 SIF  H22  C2  C3   109.94  3.000
 SIF  H21  C2  C3   112.53  3.000
 SIF  H22  C2  C1   107.46  3.000
 SIF  H21  C2  C1   108.41  3.000
 SIF  C3   C2  C1   112.85  3.000
 SIF  H3   C3  C4   107.09  3.000
 SIF  H3   C3  SI   104.69  3.000
 SIF  C4   C3  SI   109.40  3.000
 SIF  H3   C3  C2   109.97  3.000
 SIF  C4   C3  C2   114.35  3.000
 SIF  SI   C3  C2   110.82  3.000
 SIF  C7   SI  C6   110.60  3.000
 SIF  C7   SI  C5   110.34  3.000
 SIF  C6   SI  C5   110.73  3.000
 SIF  C7   SI  C3   106.92  3.000
 SIF  C6   SI  C3   109.40  3.000
 SIF  C5   SI  C3   108.74  3.000
 SIF  O4   C4  O3   122.37  3.000
 SIF  O4   C4  C3   112.65  3.000
 SIF  O3   C4  C3   124.90  3.000
 SIF  HO4  O4  C4   109.74  3.000
 SIF  H53  C5  H52  107.76  3.000
 SIF  H53  C5  H51  107.66  3.000
 SIF  H52  C5  H51  107.60  3.000
 SIF  H53  C5  SI   111.28  3.000
 SIF  H52  C5  SI   112.04  3.000
 SIF  H51  C5  SI   110.31  3.000
 SIF  H63  C6  H62  107.34  3.000
 SIF  H63  C6  H61  107.79  3.000
 SIF  H62  C6  H61  107.69  3.000
 SIF  H63  C6  SI   111.85  3.000
 SIF  H62  C6  SI   110.23  3.000
 SIF  H61  C6  SI   111.75  3.000
 SIF  H73  C7  H72  107.36  3.000
 SIF  H73  C7  H71  107.56  3.000
 SIF  H72  C7  H71  107.79  3.000
 SIF  H73  C7  SI   110.11  3.000
 SIF  H72  C7  SI   112.32  3.000
 SIF  H71  C7  SI   111.50  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
 SIF  CONST_01  HO2  O2  C1  O1    0.00   0.0  0
 SIF  CONST_02  HO4  O4  C4  C3  180.00   0.0  0
 SIF  Var_01    C3   C2  C1  O1   -2.91  30.0  3
 SIF  Var_02    H51  C5  SI  C3  174.86  30.0  3
 SIF  Var_03    H61  C6  SI  C3   60.33  30.0  3
 SIF  Var_04    H71  C7  SI  C3  -56.42  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
 SIF  chir_01  C3  C2  SI  C4  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
 SIF  plan-1  C1   0.020
 SIF  plan-1  O1   0.020
 SIF  plan-1  O2   0.020
 SIF  plan-1  C2   0.020
 SIF  plan-1  HO2  0.020
 SIF  plan-2  C3   0.020
 SIF  plan-2  C4   0.020
 SIF  plan-2  O3   0.020
 SIF  plan-2  O4   0.020
 SIF  plan-2  HO4  0.020

