# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:54:36 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: (3R)-4-[(4-carboxybutanoyl)oxy]-N-[(1E)-3-oxoprop-1-en-1-yl]-3-sulfino-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](COC(=O)CCCC(O)=O)([C@@H](N\C=C\C=O)C(O)=O)[S@@](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
 SA2  SA2  (3R)-4-[(4-carboxybutanoyl)oxy]-N-[(1E)-3-oxoprop-1-en-1-yl]-3-sulfino-D-valine  ligand  41  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SA2
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
 SA2  O23   O  OC    -1  -0.633   8.3485  -0.8561   0.6628
 SA2  C20   C  C      0   0.413   7.4246  -0.2470   0.0828
 SA2  O22   O  O      0  -0.608   7.5551   0.6497  -0.7730
 SA2  C19   C  CH2    0  -0.586   5.9964  -0.6576   0.4827
 SA2  C18   C  CH2    0  -0.409   4.8725   0.0733  -0.2330
 SA2  C17   C  CH2    0  -0.581   3.5117  -0.3946   0.2592
 SA2  C16   C  C      0   0.608   2.3498   0.2864  -0.4102
 SA2  O24   O  O      0  -0.458   2.4224   1.0090  -1.3739
 SA2  O15   O  O2     0  -0.446   1.2035  -0.0166   0.1867
 SA2  C14   C  CH2    0  -0.139   0.0092   0.5439  -0.3446
 SA2  C2    C  CT     0  -0.349  -1.1775   0.1450   0.5244
 SA2  S1    S  S3     0   0.998  -1.6012  -1.6539   0.3018
 SA2  O13   O  OH1    0  -0.745  -1.8647  -1.5379  -1.3239
 SA2  O12   O  O      0  -0.711  -0.3500  -2.4232   0.5036
 SA2  C21   C  CH3    0  -0.676  -0.8858   0.2754   2.0182
 SA2  C3    C  CH1    0  -0.184  -2.4166   0.9755   0.0907
 SA2  C9    C  C      0   0.446  -2.3458   2.4229   0.6725
 SA2  O10   O  OC    -1  -0.579  -1.5712   3.2043   0.0950
 SA2  O11   O  O      0  -0.582  -3.0604   2.6466   1.6624
 SA2  N4    N  NH1    0  -0.588  -3.6463   0.3391   0.5047
 SA2  C5    C  C1     0   0.061  -4.5837  -0.0966  -0.3316
 SA2  C6    C  C1     0  -0.464  -5.8233  -0.5580   0.0083
 SA2  C7    C  C1     0   0.113  -6.6907  -1.0011  -1.0335
 SA2  O8    O  O      0  -0.477  -7.8249  -1.4410  -0.8952
 SA2  H191  H  HCH2   0   0.221   5.8949  -0.5213   1.5659
 SA2  H192  H  HCH2   0   0.221   5.8941  -1.7377   0.3254
 SA2  H181  H  HCH2   0   0.217   4.9525  -0.0866  -1.3098
 SA2  H182  H  HCH2   0   0.217   4.9704   1.1492  -0.0743
 SA2  H171  H  HCH2   0   0.263   3.4211  -0.2530   1.3402
 SA2  H172  H  HCH2   0   0.271   3.3972  -1.4729   0.1007
 SA2  H141  H  HCH2   0   0.256  -0.1371   0.2275  -1.3803
 SA2  H142  H  HCH2   0   0.266   0.0698   1.6337  -0.3418
 SA2  HO13  H  HOH1   0   0.491  -2.4858  -2.2329  -1.5874
 SA2  H211  H  HCH3   0   0.264  -0.5068   1.2718   2.2446
 SA2  H212  H  HCH3   0   0.249  -1.7818   0.1176   2.6192
 SA2  H213  H  HCH3   0   0.263  -0.1346  -0.4395   2.3479
 SA2  H3    H  HCH1   0   0.276  -2.4279   1.0401  -0.9994
 SA2  HN4   H  HNH1   0   0.398  -3.9053   0.4898   1.4704
 SA2  H52   H  H      0   0.287  -4.3041  -0.0785  -1.3811
 SA2  H62   H  H      0   0.253  -6.1478  -0.5967   1.0422
 SA2  H7    H  H      0   0.160  -6.2525  -0.9201  -2.0489

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
 SA2  O23  C20   deloc   1.249  0.020  1.249
 SA2  C20  O22   deloc   1.246  0.020  1.246
 SA2  C20  C19   single  1.539  0.020  1.539
 SA2  C19  C18   single  1.520  0.020  1.520
 SA2  C19  H191  single  0.970  0.020  1.090
 SA2  C19  H192  single  0.970  0.020  1.090
 SA2  C18  C17   single  1.521  0.020  1.521
 SA2  C18  H181  single  0.970  0.020  1.090
 SA2  C18  H182  single  0.970  0.020  1.090
 SA2  C17  C16   single  1.504  0.020  1.504
 SA2  C17  H171  single  0.970  0.020  1.090
 SA2  C17  H172  single  0.970  0.020  1.090
 SA2  C16  O24   double  1.207  0.020  1.207
 SA2  C16  O15   single  1.327  0.020  1.327
 SA2  O15  C14   single  1.422  0.020  1.422
 SA2  C14  C2    single  1.524  0.020  1.524
 SA2  C14  H141  single  0.970  0.020  1.090
 SA2  C14  H142  single  0.970  0.020  1.090
 SA2  C2   S1    single  1.862  0.020  1.862
 SA2  C2   C21   single  1.528  0.020  1.528
 SA2  C2   C3    single  1.553  0.020  1.553
 SA2  S1   O13   single  1.651  0.020  1.651
 SA2  S1   O12   double  1.483  0.020  1.483
 SA2  O13  HO13  single  0.850  0.020  0.980
 SA2  C21  H211  single  0.970  0.020  1.090
 SA2  C21  H212  single  0.970  0.020  1.090
 SA2  C21  H213  single  0.970  0.020  1.090
 SA2  C3   C9    single  1.562  0.020  1.562
 SA2  C3   N4    single  1.445  0.020  1.445
 SA2  C3   H3    single  0.970  0.020  1.090
 SA2  C9   O10   deloc   1.243  0.020  1.243
 SA2  C9   O11   deloc   1.241  0.020  1.241
 SA2  N4   C5    single  1.330  0.020  1.330
 SA2  N4   HN4   single  0.860  0.020  1.020
 SA2  C5   C6    double  1.366  0.020  1.366
 SA2  C5   H52   single  0.930  0.020  1.080
 SA2  C6   C7    single  1.426  0.020  1.426
 SA2  C6   H62   single  0.930  0.020  1.080
 SA2  C7   O8    double  1.224  0.020  1.224
 SA2  C7   H7    single  0.930  0.020  1.080

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
 SA2  C19   C20  O22   117.87  3.000
 SA2  C19   C20  O23   115.82  3.000
 SA2  O22   C20  O23   126.30  3.000
 SA2  H192  C19  H191  104.81  3.000
 SA2  H192  C19  C18   109.71  3.000
 SA2  H191  C19  C18   109.69  3.000
 SA2  H192  C19  C20   108.19  3.000
 SA2  H191  C19  C20   108.02  3.000
 SA2  C18   C19  C20   115.83  3.000
 SA2  H182  C18  H181  106.33  3.000
 SA2  H182  C18  C17   109.65  3.000
 SA2  H181  C18  C17   109.86  3.000
 SA2  H182  C18  C19   109.83  3.000
 SA2  H181  C18  C19   109.87  3.000
 SA2  C17   C18  C19   111.18  3.000
 SA2  H172  C17  H171  105.16  3.000
 SA2  H172  C17  C16   107.49  3.000
 SA2  H171  C17  C16   108.50  3.000
 SA2  H172  C17  C18   110.45  3.000
 SA2  H171  C17  C18   110.73  3.000
 SA2  C16   C17  C18   114.08  3.000
 SA2  O15   C16  O24   123.22  3.000
 SA2  O15   C16  C17   111.32  3.000
 SA2  O24   C16  C17   125.46  3.000
 SA2  C14   O15  C16   117.85  3.000
 SA2  H142  C14  H141  107.39  3.000
 SA2  H142  C14  C2    107.65  3.000
 SA2  H141  C14  C2    111.13  3.000
 SA2  H142  C14  O15   110.24  3.000
 SA2  H141  C14  O15   110.63  3.000
 SA2  C2    C14  O15   109.74  3.000
 SA2  C3    C2   C21   112.31  3.000
 SA2  C3    C2   S1    107.56  3.000
 SA2  C21   C2   S1    104.06  3.000
 SA2  C3    C2   C14   108.78  3.000
 SA2  C21   C2   C14   112.74  3.000
 SA2  S1    C2   C14   111.22  3.000
 SA2  O12   S1   O13   107.77  3.000
 SA2  O12   S1   C2    107.04  3.000
 SA2  O13   S1   C2     94.94  3.000
 SA2  HO13  O13  S1    108.65  3.000
 SA2  H213  C21  H212  107.77  3.000
 SA2  H213  C21  H211  107.32  3.000
 SA2  H212  C21  H211  107.68  3.000
 SA2  H213  C21  C2    111.84  3.000
 SA2  H212  C21  C2    111.70  3.000
 SA2  H211  C21  C2    110.34  3.000
 SA2  H3    C3   N4    107.65  3.000
 SA2  H3    C3   C9    108.51  3.000
 SA2  N4    C3   C9    109.88  3.000
 SA2  H3    C3   C2    108.58  3.000
 SA2  N4    C3   C2    111.30  3.000
 SA2  C9    C3   C2    110.81  3.000
 SA2  O11   C9   O10   128.04  3.000
 SA2  O11   C9   C3    115.98  3.000
 SA2  O10   C9   C3    115.98  3.000
 SA2  HN4   N4   C5    117.97  3.000
 SA2  HN4   N4   C3    115.21  3.000
 SA2  C5    N4   C3    124.33  3.000
 SA2  H52   C5   C6    118.66  3.000
 SA2  H52   C5   N4    114.88  3.000
 SA2  C6    C5   N4    126.45  3.000
 SA2  H62   C6   C7    120.22  3.000
 SA2  H62   C6   C5    121.40  3.000
 SA2  C7    C6   C5    118.38  3.000
 SA2  H7    C7   O8    119.72  3.000
 SA2  H7    C7   C6    113.94  3.000
 SA2  O8    C7   C6    126.34  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
 SA2  Var_01  C7   C6   C5   N4   -179.21   0.0  2
 SA2  Var_02  C18  C19  C20  O23  -179.40  30.0  3
 SA2  Var_03  C17  C18  C19  C20  -178.95  30.0  3
 SA2  Var_04  C16  C17  C18  C19  -179.87  30.0  3
 SA2  Var_05  O24  C16  C17  C18     9.64  30.0  3
 SA2  Var_06  C2   C14  O15  C16  -176.66  30.0  3
 SA2  Var_07  C6   C5   N4   C3   -171.74  30.0  2
 SA2  Var_08  O8   C7   C6   C5    179.92  30.0  2

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
 SA2  chir_01  C2  S1  C21  C3  positiv
 SA2  chir_03  C3  N4  C2   C9  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
 SA2  plan-1  O23  0.020
 SA2  plan-1  C20  0.020
 SA2  plan-1  O22  0.020
 SA2  plan-1  C19  0.020
 SA2  plan-2  C3   0.020
 SA2  plan-2  C9   0.020
 SA2  plan-2  O10  0.020
 SA2  plan-2  O11  0.020
 SA2  plan-3  C17  0.020
 SA2  plan-3  C16  0.020
 SA2  plan-3  O24  0.020
 SA2  plan-3  O15  0.020
 SA2  plan-4  C2   0.020
 SA2  plan-4  S1   0.020
 SA2  plan-4  O13  0.020
 SA2  plan-4  O12  0.020
 SA2  plan-5  N4   0.020
 SA2  plan-5  C5   0.020
 SA2  plan-5  C6   0.020
 SA2  plan-5  C7   0.020
 SA2  plan-5  H52  0.020
 SA2  plan-5  H62  0.020
 SA2  plan-6  C6   0.020
 SA2  plan-6  C7   0.020
 SA2  plan-6  O8   0.020
 SA2  plan-6  H7   0.020

