# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 19:03:57 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2~{R})-4-methyl-2-[(1~{S})-1-sulfanylethyl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H]([C@H](C)S)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
 O2S  O2S  '(2~{R})-4-methyl-2-[(1~{S})-1-sulfanylethyl]pentanoic acid'  ligand  27  11  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_O2S
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
 O2S  O01  O  OH1   0  -0.585  -0.0895   1.9730  -1.0524
 O2S  C02  C  C     0   0.552  -0.1957   1.2901   0.0791
 O2S  O03  O  O     0  -0.445  -0.3225   1.8159   1.1582
 O2S  C04  C  CH1   0  -0.330  -0.1008  -0.2071  -0.1188
 O2S  C05  C  CH2   0  -0.411   1.1934  -0.7177   0.5318
 O2S  C06  C  CH1   0  -0.249   2.4872  -0.0786   0.0189
 O2S  C07  C  CH3   0  -0.650   3.6717  -0.6318   0.8057
 O2S  C08  C  CH3   0  -0.657   2.6905  -0.3035  -1.4763
 O2S  C09  C  CH1   0  -0.369  -1.3478  -0.8753   0.4764
 O2S  S10  S  S2    0  -0.224  -2.8685  -0.1163  -0.2115
 O2S  C11  C  CH3   0  -0.642  -1.3680  -2.3834   0.2908
 O2S  H1   H  HOH1  0   0.477  -0.1322   2.9244  -0.8700
 O2S  H2   H  HCH1  0   0.265  -0.0783  -0.4285  -1.1898
 O2S  H3   H  HCH2  0   0.235   1.1225  -0.5736   1.6145
 O2S  H4   H  HCH2  0   0.240   1.2619  -1.7966   0.3690
 O2S  H5   H  HCH1  0   0.223   2.4475   1.0019   0.2013
 O2S  H6   H  HCH3  0   0.215   3.7666  -1.7108   0.6591
 O2S  H7   H  HCH3  0   0.228   4.6074  -0.1712   0.4847
 O2S  H8   H  HCH3  0   0.227   3.5609  -0.4509   1.8761
 O2S  H9   H  HCH3  0   0.229   1.9061   0.1555  -2.0783
 O2S  H10  H  HCH3  0   0.230   3.6399   0.1221  -1.8047
 O2S  H11  H  HCH3  0   0.215   2.7081  -1.3711  -1.7096
 O2S  H12  H  HCH1  0   0.286  -1.4059  -0.6403   1.5422
 O2S  H13  H  HSH1  0   0.217  -2.6854  -0.5116  -1.4782
 O2S  H14  H  HCH3  0   0.243  -0.5357  -2.8585   0.8102
 O2S  H15  H  HCH3  0   0.249  -2.2895  -2.8047   0.6895
 O2S  H16  H  HCH3  0   0.230  -1.3028  -2.6518  -0.7654

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
 O2S  O03  C02  double  1.207  0.020  1.207
 O2S  O01  C02  single  1.326  0.020  1.326
 O2S  C02  C04  single  1.513  0.020  1.513
 O2S  C08  C06  single  1.526  0.020  1.526
 O2S  S10  C09  single  1.834  0.020  1.834
 O2S  C06  C05  single  1.532  0.020  1.532
 O2S  C06  C07  single  1.526  0.020  1.526
 O2S  C04  C09  single  1.535  0.020  1.535
 O2S  C04  C05  single  1.536  0.020  1.536
 O2S  C09  C11  single  1.520  0.020  1.520
 O2S  O01  H1   single  0.850  0.020  0.980
 O2S  C04  H2   single  0.970  0.020  1.090
 O2S  C05  H3   single  0.970  0.020  1.090
 O2S  C05  H4   single  0.970  0.020  1.090
 O2S  C06  H5   single  0.970  0.020  1.090
 O2S  C07  H6   single  0.970  0.020  1.090
 O2S  C07  H7   single  0.970  0.020  1.090
 O2S  C07  H8   single  0.970  0.020  1.090
 O2S  C08  H9   single  0.970  0.020  1.090
 O2S  C08  H10  single  0.970  0.020  1.090
 O2S  C08  H11  single  0.970  0.020  1.090
 O2S  C09  H12  single  0.970  0.020  1.090
 O2S  S10  H13  single  1.200  0.020  1.300
 O2S  C11  H14  single  0.970  0.020  1.090
 O2S  C11  H15  single  0.970  0.020  1.090
 O2S  C11  H16  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
 O2S  H1   O01  C02  109.96  3.000
 O2S  C04  C02  O03  123.68  3.000
 O2S  C04  C02  O01  113.14  3.000
 O2S  O03  C02  O01  123.16  3.000
 O2S  H2   C04  C09  107.96  3.000
 O2S  H2   C04  C05  109.28  3.000
 O2S  C09  C04  C05  112.06  3.000
 O2S  H2   C04  C02  109.25  3.000
 O2S  C05  C04  C02  109.05  3.000
 O2S  C09  C04  C02  109.21  3.000
 O2S  H4   C05  H3   106.34  3.000
 O2S  H4   C05  C06  108.00  3.000
 O2S  H3   C05  C06  109.33  3.000
 O2S  H4   C05  C04  108.53  3.000
 O2S  H3   C05  C04  108.71  3.000
 O2S  C06  C05  C04  115.55  3.000
 O2S  H5   C06  C08  108.25  3.000
 O2S  H5   C06  C07  107.44  3.000
 O2S  C08  C06  C07  110.40  3.000
 O2S  H5   C06  C05  108.95  3.000
 O2S  C07  C06  C05  109.38  3.000
 O2S  C08  C06  C05  112.29  3.000
 O2S  H8   C07  H7   107.79  3.000
 O2S  H8   C07  H6   107.70  3.000
 O2S  H7   C07  H6   107.63  3.000
 O2S  H8   C07  C06  111.52  3.000
 O2S  H7   C07  C06  111.16  3.000
 O2S  H6   C07  C06  110.86  3.000
 O2S  H11  C08  H10  107.63  3.000
 O2S  H11  C08  H9   107.76  3.000
 O2S  H10  C08  H9   107.20  3.000
 O2S  H11  C08  C06  110.82  3.000
 O2S  H10  C08  C06  110.69  3.000
 O2S  H9   C08  C06  112.53  3.000
 O2S  H12  C09  C11  109.38  3.000
 O2S  H12  C09  S10  103.46  3.000
 O2S  C11  C09  S10  110.73  3.000
 O2S  H12  C09  C04  109.13  3.000
 O2S  C11  C09  C04  113.30  3.000
 O2S  S10  C09  C04  110.37  3.000
 O2S  H13  S10  C09   96.85  3.000
 O2S  H16  C11  H15  108.04  3.000
 O2S  H16  C11  H14  107.96  3.000
 O2S  H15  C11  H14  107.64  3.000
 O2S  H16  C11  C09  111.18  3.000
 O2S  H15  C11  C09  110.51  3.000
 O2S  H14  C11  C09  111.36  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
 O2S  CONST_01  H1   O01  C02  O03    0.00   0.0  0
 O2S  Var_01    C08  C06  C05  C04  -59.99  30.0  1
 O2S  Var_02    H9   C08  C06  C05   62.65  30.0  3
 O2S  Var_03    H6   C07  C06  C05   62.14  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
 O2S  chir_01  C04  C02  C09  C05  positiv
 O2S  chir_02  C09  S10  C04  C11  positiv

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
 O2S  plan-1  O01  0.020
 O2S  plan-1  C02  0.020
 O2S  plan-1  O03  0.020
 O2S  plan-1  C04  0.020
 O2S  plan-1  H1   0.020

