# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 20:10:04 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S)-4-methyl-2-[(1R)-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
 O2V  O2V  '(2S)-4-methyl-2-[(1R)-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_O2V
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
 O2V  O01   O  OH1   0  -0.583   0.4096   1.9088  -1.0631
 O2V  C02   C  C     0   0.548   0.3165   1.2563   0.0874
 O2V  O03   O  O     0  -0.442   0.3323   1.8043   1.1623
 O2V  C04   C  CH1   0  -0.347   0.1627  -0.2403  -0.0915
 O2V  C05   C  CH2   0  -0.406  -1.1990  -0.6791   0.4644
 O2V  C06   C  CH1   0  -0.251  -2.4159   0.0296  -0.1370
 O2V  C07   C  CH3   0  -0.656  -2.5298  -0.1898  -1.6420
 O2V  C08   C  CH3   0  -0.649  -3.6805  -0.4501   0.5691
 O2V  C09   C  CH1   0  -0.355   1.3227  -0.9551   0.6173
 O2V  S10   S  S2    0  -0.241   2.8724  -0.3428  -0.1594
 O2V  C11   C  CH3   0  -0.643   1.2430  -2.4692   0.5250
 O2V  H01   H  HOH1  0   0.479   0.4895   2.8612  -0.8993
 O2V  H04   H  HCH1  0   0.272   0.2135  -0.4840  -1.1574
 O2V  H051  H  HCH2  0   0.243  -1.3105  -1.7528   0.2936
 O2V  H052  H  HCH2  0   0.236  -1.1987  -0.5377   1.5497
 O2V  H09   H  HCH1  0   0.282   1.3419  -0.6466   1.6642
 O2V  H06   H  HCH1  0   0.223  -2.3263   1.1067   0.0473
 O2V  H071  H  HCH3  0   0.230  -3.4208   0.3014  -2.0367
 O2V  H072  H  HCH3  0   0.228  -1.6732   0.2066  -2.1878
 O2V  H073  H  HCH3  0   0.216  -2.6089  -1.2545  -1.8748
 O2V  H081  H  HCH3  0   0.227  -3.6314  -0.2675   1.6439
 O2V  H082  H  HCH3  0   0.228  -4.5645   0.0597   0.1830
 O2V  H083  H  HCH3  0   0.215  -3.8249  -1.5232   0.4208
 O2V  H111  H  HCH3  0   0.241   0.3804  -2.8553   1.0694
 O2V  H112  H  HCH3  0   0.232   1.1684  -2.7965  -0.5129
 O2V  H113  H  HCH3  0   0.246   2.1320  -2.9256   0.9593
 O2V  H10   H  HSH1  0   0.228   3.7170  -0.7890   0.7768

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
 O2V  O01  C02   single  1.326  0.020  1.326
 O2V  C02  O03   double  1.207  0.020  1.207
 O2V  C02  C04   single  1.515  0.020  1.515
 O2V  C04  C05   single  1.535  0.020  1.535
 O2V  C04  C09   single  1.536  0.020  1.536
 O2V  C05  C06   single  1.531  0.020  1.531
 O2V  C06  C07   single  1.525  0.020  1.525
 O2V  C06  C08   single  1.526  0.020  1.526
 O2V  C09  S10   single  1.838  0.020  1.838
 O2V  C09  C11   single  1.519  0.020  1.519
 O2V  O01  H01   single  0.850  0.020  0.980
 O2V  C04  H04   single  0.970  0.020  1.090
 O2V  C05  H051  single  0.970  0.020  1.090
 O2V  C05  H052  single  0.970  0.020  1.090
 O2V  C09  H09   single  0.970  0.020  1.090
 O2V  C06  H06   single  0.970  0.020  1.090
 O2V  C07  H071  single  0.970  0.020  1.090
 O2V  C07  H072  single  0.970  0.020  1.090
 O2V  C07  H073  single  0.970  0.020  1.090
 O2V  C08  H081  single  0.970  0.020  1.090
 O2V  C08  H082  single  0.970  0.020  1.090
 O2V  C08  H083  single  0.970  0.020  1.090
 O2V  C11  H111  single  0.970  0.020  1.090
 O2V  C11  H112  single  0.970  0.020  1.090
 O2V  C11  H113  single  0.970  0.020  1.090
 O2V  S10  H10   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
 O2V  H01   O01  C02   110.03  3.000
 O2V  C04   C02  O03   123.72  3.000
 O2V  C04   C02  O01   113.00  3.000
 O2V  O03   C02  O01   123.27  3.000
 O2V  H04   C04  C09   108.10  3.000
 O2V  H04   C04  C05   109.29  3.000
 O2V  C09   C04  C05   111.71  3.000
 O2V  H04   C04  C02   109.28  3.000
 O2V  C09   C04  C02   109.18  3.000
 O2V  C05   C04  C02   109.25  3.000
 O2V  H052  C05  H051  106.37  3.000
 O2V  H052  C05  C06   109.26  3.000
 O2V  H051  C05  C06   108.19  3.000
 O2V  H052  C05  C04   108.78  3.000
 O2V  H051  C05  C04   108.35  3.000
 O2V  C06   C05  C04   115.50  3.000
 O2V  H06   C06  C08   107.39  3.000
 O2V  H06   C06  C07   108.25  3.000
 O2V  C08   C06  C07   110.46  3.000
 O2V  H06   C06  C05   108.89  3.000
 O2V  C08   C06  C05   109.36  3.000
 O2V  C07   C06  C05   112.35  3.000
 O2V  H073  C07  H072  107.72  3.000
 O2V  H073  C07  H071  107.61  3.000
 O2V  H072  C07  H071  107.27  3.000
 O2V  H073  C07  C06   110.84  3.000
 O2V  H072  C07  C06   112.52  3.000
 O2V  H071  C07  C06   110.68  3.000
 O2V  H083  C08  H082  107.68  3.000
 O2V  H083  C08  H081  107.69  3.000
 O2V  H082  C08  H081  107.86  3.000
 O2V  H083  C08  C06   110.82  3.000
 O2V  H082  C08  C06   111.15  3.000
 O2V  H081  C08  C06   111.46  3.000
 O2V  H09   C09  C11   109.93  3.000
 O2V  H09   C09  S10   107.23  3.000
 O2V  C11   C09  S10   110.52  3.000
 O2V  H09   C09  C04   108.93  3.000
 O2V  C11   C09  C04   113.34  3.000
 O2V  S10   C09  C04   106.66  3.000
 O2V  H10   S10  C09    97.20  3.000
 O2V  H113  C11  H112  108.01  3.000
 O2V  H113  C11  H111  107.34  3.000
 O2V  H112  C11  H111  108.34  3.000
 O2V  H113  C11  C09   110.52  3.000
 O2V  H112  C11  C09   111.13  3.000
 O2V  H111  C11  C09   111.35  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
 O2V  CONST_01  H01   O01  C02  O03    0.00   0.0  0
 O2V  Var_01    C07   C06  C05  C04   60.28  30.0  3
 O2V  Var_02    H071  C07  C06  C05  178.32  30.0  3
 O2V  Var_03    H081  C08  C06  C05   57.92  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
 O2V  chir_01  C04  C02  C05  C09  positiv
 O2V  chir_02  C09  S10  C04  C11  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
 O2V  plan-1  O01  0.020
 O2V  plan-1  C02  0.020
 O2V  plan-1  O03  0.020
 O2V  plan-1  C04  0.020
 O2V  plan-1  H01  0.020

