# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:06:35 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  26  11  .  2021-08-17  2021-08-17  
;
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  OC    -1  -0.613  -0.0846   2.0129  -1.1450
 O2S  C02  C  C      0   0.427  -0.2182   1.3556  -0.0940
 O2S  O03  O  O      0  -0.619  -0.3815   1.8234   1.0529
 O2S  C04  C  CH1    0  -0.300  -0.1383  -0.1812  -0.1943
 O2S  C05  C  CH2    0  -0.400   1.1441  -0.6782   0.4852
 O2S  C06  C  CH1    0  -0.234   2.4445  -0.0447  -0.0161
 O2S  C07  C  CH3    0  -0.650   3.6285  -0.6199   0.7562
 O2S  C08  C  CH3    0  -0.660   2.6382  -0.2399  -1.5164
 O2S  C09  C  CH1    0  -0.361  -1.3772  -0.8318   0.4258
 O2S  S10  S  S2     0  -0.249  -2.9084  -0.1743  -0.3448
 O2S  C11  C  CH3    0  -0.638  -1.3823  -2.3520   0.3677
 O2S  H2   H  HCH1   0   0.202  -0.1083  -0.4688  -1.2516
 O2S  H3   H  HCH2   0   0.210   1.0592  -0.5074   1.5638
 O2S  H4   H  HCH2   0   0.210   1.2342  -1.7620   0.3559
 O2S  H5   H  HCH1   0   0.214   2.4078   1.0321   0.1832
 O2S  H6   H  HCH3   0   0.209   3.7161  -1.6971   0.5909
 O2S  H7   H  HCH3   0   0.221   4.5684  -0.1610   0.4434
 O2S  H8   H  HCH3   0   0.221   3.5216  -0.4590   1.8308
 O2S  H9   H  HCH3   0   0.231   1.8600   0.2636  -2.0891
 O2S  H10  H  HCH3   0   0.219   3.6001   0.1616  -1.8413
 O2S  H11  H  HCH3   0   0.205   2.6189  -1.3013  -1.7790
 O2S  H12  H  HCH1   0   0.261  -1.4624  -0.5060   1.4654
 O2S  H13  H  HSH1   0   0.204  -2.6721  -0.6331  -1.5808
 O2S  H14  H  HCH3   0   0.233  -0.5504  -2.7740   0.9326
 O2S  H15  H  HCH3   0   0.236  -2.3038  -2.7560   0.7857
 O2S  H16  H  HCH3   0   0.220  -1.2976  -2.7039  -0.6627

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  deloc   1.249  0.020  1.249
 O2S  O01  C02  deloc   1.247  0.020  1.247
 O2S  C02  C04  single  1.542  0.020  1.542
 O2S  C08  C06  single  1.525  0.020  1.525
 O2S  S10  C09  single  1.836  0.020  1.836
 O2S  C06  C05  single  1.531  0.020  1.531
 O2S  C06  C07  single  1.526  0.020  1.526
 O2S  C04  C09  single  1.531  0.020  1.531
 O2S  C04  C05  single  1.534  0.020  1.534
 O2S  C09  C11  single  1.521  0.020  1.521
 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  C04  C02  O03  116.08  3.000
 O2S  C04  C02  O01  117.71  3.000
 O2S  O03  C02  O01  126.19  3.000
 O2S  H2   C04  C09  107.54  3.000
 O2S  H2   C04  C05  108.62  3.000
 O2S  C09  C04  C05  111.07  3.000
 O2S  H2   C04  C02  109.00  3.000
 O2S  C05  C04  C02  109.72  3.000
 O2S  C09  C04  C02  110.82  3.000
 O2S  H4   C05  H3   106.08  3.000
 O2S  H4   C05  C06  107.51  3.000
 O2S  H3   C05  C06  108.89  3.000
 O2S  H4   C05  C04  109.70  3.000
 O2S  H3   C05  C04  108.72  3.000
 O2S  C06  C05  C04  115.53  3.000
 O2S  H5   C06  C08  108.00  3.000
 O2S  H5   C06  C07  107.71  3.000
 O2S  C08  C06  C07  110.55  3.000
 O2S  H5   C06  C05  108.58  3.000
 O2S  C07  C06  C05  109.72  3.000
 O2S  C08  C06  C05  112.15  3.000
 O2S  H8   C07  H7   107.71  3.000
 O2S  H8   C07  H6   107.57  3.000
 O2S  H7   C07  H6   107.57  3.000
 O2S  H8   C07  C06  111.51  3.000
 O2S  H7   C07  C06  111.38  3.000
 O2S  H6   C07  C06  110.91  3.000
 O2S  H11  C08  H10  107.51  3.000
 O2S  H11  C08  H9   108.04  3.000
 O2S  H10  C08  H9   107.63  3.000
 O2S  H11  C08  C06  110.99  3.000
 O2S  H10  C08  C06  110.95  3.000
 O2S  H9   C08  C06  111.55  3.000
 O2S  H12  C09  C11  109.51  3.000
 O2S  H12  C09  S10  103.15  3.000
 O2S  C11  C09  S10  109.82  3.000
 O2S  H12  C09  C04  108.77  3.000
 O2S  C11  C09  C04  114.33  3.000
 O2S  S10  C09  C04  110.66  3.000
 O2S  H13  S10  C09   96.75  3.000
 O2S  H16  C11  H15  107.95  3.000
 O2S  H16  C11  H14  107.75  3.000
 O2S  H15  C11  H14  107.63  3.000
 O2S  H16  C11  C09  110.96  3.000
 O2S  H15  C11  C09  111.03  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  Var_01  C08  C06  C05  C04  -57.38  30.0  1
 O2S  Var_02  H9   C08  C06  C05   63.69  30.0  3
 O2S  Var_03  H6   C07  C06  C05   62.17  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

