# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:01:48 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  24  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   0.408   0.6662   0.2323  -2.5025
 SIF  O1   O   O      0  -0.608   0.0204  -0.7695  -2.8669
 SIF  O2   O   OC    -1  -0.641   1.1637   1.0986  -3.2571
 SIF  C2   C   CH2    0  -0.583   0.9160   0.4264  -0.9967
 SIF  C3   C   CH1    0  -0.582   0.0331  -0.4079  -0.0787
 SIF  SI   SI  SI     0   1.066   0.4794  -0.0979   1.7366
 SIF  C4   C   C      0   0.418  -1.4582  -0.1355  -0.2685
 SIF  O3   O   O      0  -0.634  -2.2452  -1.0967  -0.1235
 SIF  O4   O   OC    -1  -0.627  -1.7936   1.0473  -0.5037
 SIF  C5   C   CH3    0  -0.963  -0.8177  -0.8524   2.8821
 SIF  C6   C   CH3    0  -0.979   0.5983   1.7548   2.0843
 SIF  C7   C   CH3    0  -0.975   2.1536  -0.8981   2.1072
 SIF  H21  H   HCH2   0   0.210   0.8087   1.4897  -0.7699
 SIF  H22  H   HCH2   0   0.211   1.9752   0.2000  -0.8132
 SIF  H3   H   HCH1   0   0.197   0.2207  -1.4716  -0.2624
 SIF  H51  H   HCH3   0   0.224  -0.5154  -0.7677   3.9280
 SIF  H52  H   HCH3   0   0.234  -1.7835  -0.3569   2.7733
 SIF  H53  H   HCH3   0   0.232  -0.9690  -1.9105   2.6626
 SIF  H61  H   HCH3   0   0.236  -0.3275   2.2581   1.8018
 SIF  H62  H   HCH3   0   0.229   0.7853   1.9525   3.1416
 SIF  H63  H   HCH3   0   0.230   1.4070   2.2150   1.5136
 SIF  H71  H   HCH3   0   0.233   2.1235  -1.9757   1.9325
 SIF  H72  H   HCH3   0   0.233   2.9441  -0.4864   1.4760
 SIF  H73  H   HCH3   0   0.231   2.4499  -0.7419   3.1467

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   deloc   1.246  0.020  1.246
 SIF  C1  O2   deloc   1.252  0.020  1.252
 SIF  C1  C2   single  1.539  0.020  1.539
 SIF  C2  C3   single  1.523  0.020  1.523
 SIF  C2  H21  single  0.970  0.020  1.090
 SIF  C2  H22  single  0.970  0.020  1.090
 SIF  C3  SI   single  1.895  0.020  1.895
 SIF  C3  C4   single  1.528  0.020  1.528
 SIF  C3  H3   single  0.970  0.020  1.090
 SIF  SI  C5   single  1.888  0.020  1.888
 SIF  SI  C6   single  1.889  0.020  1.889
 SIF  SI  C7   single  1.892  0.020  1.892
 SIF  C4  O3   deloc   1.251  0.020  1.251
 SIF  C4  O4   deloc   1.252  0.020  1.252
 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   115.98  3.000
 SIF  C2   C1  O1   118.14  3.000
 SIF  O2   C1  O1   125.86  3.000
 SIF  H22  C2  H21  105.11  3.000
 SIF  H22  C2  C3   110.21  3.000
 SIF  H21  C2  C3   110.56  3.000
 SIF  H22  C2  C1   107.10  3.000
 SIF  H21  C2  C1   108.06  3.000
 SIF  C3   C2  C1   115.26  3.000
 SIF  H3   C3  C4   108.63  3.000
 SIF  H3   C3  SI   106.20  3.000
 SIF  C4   C3  SI   108.65  3.000
 SIF  H3   C3  C2   109.37  3.000
 SIF  C4   C3  C2   113.17  3.000
 SIF  SI   C3  C2   110.57  3.000
 SIF  C7   SI  C6   108.85  3.000
 SIF  C7   SI  C5   108.67  3.000
 SIF  C6   SI  C5   108.88  3.000
 SIF  C7   SI  C3   109.08  3.000
 SIF  C6   SI  C3   110.59  3.000
 SIF  C5   SI  C3   110.74  3.000
 SIF  O4   C4  O3   125.41  3.000
 SIF  O4   C4  C3   116.96  3.000
 SIF  O3   C4  C3   117.57  3.000
 SIF  H53  C5  H52  107.31  3.000
 SIF  H53  C5  H51  107.84  3.000
 SIF  H52  C5  H51  107.78  3.000
 SIF  H53  C5  SI   111.14  3.000
 SIF  H52  C5  SI   111.48  3.000
 SIF  H51  C5  SI   111.10  3.000
 SIF  H63  C6  H62  107.64  3.000
 SIF  H63  C6  H61  107.39  3.000
 SIF  H62  C6  H61  108.22  3.000
 SIF  H63  C6  SI   111.34  3.000
 SIF  H62  C6  SI   111.51  3.000
 SIF  H61  C6  SI   110.57  3.000
 SIF  H73  C7  H72  107.45  3.000
 SIF  H73  C7  H71  107.51  3.000
 SIF  H72  C7  H71  107.42  3.000
 SIF  H73  C7  SI   111.47  3.000
 SIF  H72  C7  SI   111.58  3.000
 SIF  H71  C7  SI   111.19  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  Var_01  C3   C2  C1  O1  -16.17  30.0  3
 SIF  Var_02  H51  C5  SI  C3  174.16  30.0  3
 SIF  Var_03  H61  C6  SI  C3   55.53  30.0  3
 SIF  Var_04  H71  C7  SI  C3  -60.09  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-2  C3  0.020
 SIF  plan-2  C4  0.020
 SIF  plan-2  O3  0.020
 SIF  plan-2  O4  0.020

