# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jan 24 20:32:06 2023
#   Inital geometry file: a 97 line input string
#   Ligand name: (2S,3R)-4-(2-amino-2-oxoethoxy)-3-(dihydroxy-lambda~4~-sulfanyl)-3-methyl-4-oxo-2-{[(1E)-3-oxoprop-1-en-1-yl]amino}butanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]([C@@H](N\C=C\C=O)C(O)=O)([SH](O)O)C(=O)OCC(N)=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
 SR3  SR3  "(2S,3R)-4-(2-amino-2-oxoethoxy)-3-(dihydroxy-lambda~4~-sulfanyl)-3-methyl-4-oxo-2-{[(1E)-3-oxoprop-1-en-1-yl]amino}butanoic acid"  ligand  37  21  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SR3
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
 SR3  C     C  C     0   0.546  -2.0645  -2.1256   0.7761
 SR3  N     N  NH1   0  -0.579  -1.8641   0.0704  -0.1202
 SR3  O     O  O     0  -0.441  -2.1014  -2.7247  -0.2724
 SR3  CA    C  CH1   0  -0.157  -1.3455  -0.7926   0.9210
 SR3  CB    C  CT    0  -0.467   0.1743  -1.0147   0.8578
 SR3  CG    C  C     0   0.640   0.8809   0.2429   1.0592
 SR3  CAA   C  CH3   0  -0.682   0.6553  -2.1718   1.7159
 SR3  NAB   N  NH2   0  -0.776   3.4331   3.0135  -0.2859
 SR3  OAC   O  O     0  -0.479  -3.8598   4.2516  -1.1532
 SR3  OAD   O  O     0  -0.528   2.7397   1.0527  -1.1322
 SR3  CAJ   C  C1    0   0.114  -3.4169   3.3712  -0.4261
 SR3  CAK   C  C1    0  -0.479  -2.8567   2.1307  -0.8483
 SR3  CAL   C  C1    0   0.103  -2.4009   1.2636   0.1026
 SR3  CAM   C  CH2   0  -0.306   2.9916   1.2249   1.2589
 SR3  CAP   C  C     0   0.545   3.0260   1.7606  -0.1616
 SR3  SAT   S  SH1   0   0.729   0.5467  -1.6745  -1.2604
 SR3  OD1   O  O     0  -0.467   0.4243   1.3628   0.9402
 SR3  OD2   O  O2    0  -0.470   2.1923   0.0730   1.3466
 SR3  OXT   O  OH1   0  -0.571  -2.6292  -2.5416   1.8907
 SR3  HN    H  HNH1  0   0.403  -1.7333  -0.2176  -1.0784
 SR3  HA    H  HCH1  0   0.294  -1.6262  -0.3428   1.8786
 SR3  HAA   H  HCH3  0   0.229   0.2239  -3.1266   1.4006
 SR3  HAAA  H  HCH3  0   0.264   1.7343  -2.2952   1.6500
 SR3  HAAB  H  HCH3  0   0.248   0.4014  -2.0533   2.7737
 SR3  HNAB  H  HNH2  0   0.418   3.5575   3.4268  -1.1968
 SR3  HNAA  H  HNH2  0   0.423   3.6402   3.5872   0.5149
 SR3  HOAG  H  HOH1  0   0.501   2.3493  -0.4407  -1.0831
 SR3  HOAH  H  HOH1  0   0.457   0.5037  -1.9452  -3.4620
 SR3  HAJ   H  H     0   0.160  -3.4308   3.5077   0.6740
 SR3  HAK   H  H     0   0.252  -2.7916   1.8935  -1.9047
 SR3  HAL   H  H     0   0.284  -2.4849   1.5392   1.1493
 SR3  HAM   H  HCH2  0   0.304   4.0020   0.9141   1.5310
 SR3  HAMA  H  HCH2  0   0.270   2.6842   2.0047   1.9589
 SR3  HOXT  H  HOH1  0   0.489  -3.0591  -3.4011   1.7547
 SR3  HSAT  H  HSH1  0   0.266   0.4184  -2.8619  -0.6601
 SR3  OAG   O  OH1   0  -0.743   2.1262  -1.4288  -1.1214
 SR3  OAH   O  OH1   0  -0.798   0.6841  -2.5637  -2.7415

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
 SR3  O    C     double  1.208  0.020  1.208
 SR3  C    CA    single  1.522  0.020  1.522
 SR3  C    OXT   single  1.317  0.020  1.317
 SR3  CA   N     single  1.448  0.020  1.448
 SR3  N    CAL   single  1.327  0.020  1.327
 SR3  N    HN    single  0.860  0.020  1.020
 SR3  CB   CA    single  1.537  0.020  1.537
 SR3  CA   HA    single  0.970  0.020  1.090
 SR3  SAT  CB    single  2.250  0.020  2.250
 SR3  CG   CB    single  1.456  0.020  1.456
 SR3  CB   CAA   single  1.519  0.020  1.519
 SR3  OD1  CG    double  1.215  0.020  1.215
 SR3  CG   OD2   single  1.353  0.020  1.353
 SR3  CAA  HAA   single  0.970  0.020  1.090
 SR3  CAA  HAAA  single  0.970  0.020  1.090
 SR3  CAA  HAAB  single  0.970  0.020  1.090
 SR3  NAB  CAP   single  1.323  0.020  1.323
 SR3  NAB  HNAB  single  0.860  0.020  1.020
 SR3  NAB  HNAA  single  0.860  0.020  1.020
 SR3  CAJ  OAC   double  1.225  0.020  1.225
 SR3  OAD  CAP   double  1.235  0.020  1.235
 SR3  SAT  OAG   single  1.604  0.020  1.604
 SR3  OAG  HOAG  single  0.850  0.020  0.980
 SR3  OAH  SAT   single  1.733  0.020  1.733
 SR3  OAH  HOAH  single  0.850  0.020  0.980
 SR3  CAK  CAJ   single  1.425  0.020  1.425
 SR3  CAJ  HAJ   single  0.930  0.020  1.080
 SR3  CAL  CAK   double  1.365  0.020  1.365
 SR3  CAK  HAK   single  0.930  0.020  1.080
 SR3  CAL  HAL   single  0.930  0.020  1.080
 SR3  CAP  CAM   single  1.518  0.020  1.518
 SR3  CAM  OD2   single  1.405  0.020  1.405
 SR3  CAM  HAM   single  0.970  0.020  1.090
 SR3  CAM  HAMA  single  0.970  0.020  1.090
 SR3  OXT  HOXT  single  0.850  0.020  0.980
 SR3  SAT  HSAT  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
 SR3  OXT   C    CA    113.50  3.000
 SR3  OXT   C    O     124.39  3.000
 SR3  CA    C    O     122.11  3.000
 SR3  HN    N    CAL   117.93  3.000
 SR3  HN    N    CA    117.79  3.000
 SR3  CAL   N    CA    124.04  3.000
 SR3  HA    CA   CB    110.41  3.000
 SR3  HA    CA   N     107.00  3.000
 SR3  CB    CA   N     114.24  3.000
 SR3  HA    CA   C     108.80  3.000
 SR3  CB    CA   C     109.68  3.000
 SR3  N     CA   C     106.52  3.000
 SR3  SAT   CB   CAA   104.84  3.000
 SR3  CAA   CB   CG    115.22  3.000
 SR3  SAT   CB   CG    107.65  3.000
 SR3  CAA   CB   CA    113.58  3.000
 SR3  CG    CB   CA    110.44  3.000
 SR3  SAT   CB   CA    104.17  3.000
 SR3  OD2   CG   OD1   120.04  3.000
 SR3  OD2   CG   CB    113.03  3.000
 SR3  OD1   CG   CB    126.85  3.000
 SR3  HAAB  CAA  HAAA  107.52  3.000
 SR3  HAAB  CAA  HAA   106.35  3.000
 SR3  HAAA  CAA  HAA   105.94  3.000
 SR3  HAAB  CAA  CB    112.96  3.000
 SR3  HAAA  CAA  CB    111.49  3.000
 SR3  HAA   CAA  CB    112.16  3.000
 SR3  HNAA  NAB  HNAB  117.37  3.000
 SR3  HNAA  NAB  CAP   121.88  3.000
 SR3  HNAB  NAB  CAP   120.74  3.000
 SR3  HAJ   CAJ  CAK   113.96  3.000
 SR3  HAJ   CAJ  OAC   119.74  3.000
 SR3  CAK   CAJ  OAC   126.30  3.000
 SR3  HAK   CAK  CAL   121.30  3.000
 SR3  HAK   CAK  CAJ   120.17  3.000
 SR3  CAL   CAK  CAJ   118.54  3.000
 SR3  HAL   CAL  CAK   118.98  3.000
 SR3  HAL   CAL  N     114.92  3.000
 SR3  CAK   CAL  N     126.09  3.000
 SR3  HAMA  CAM  HAM   107.70  3.000
 SR3  HAMA  CAM  OD2   112.66  3.000
 SR3  HAM   CAM  OD2   106.11  3.000
 SR3  HAMA  CAM  CAP   110.74  3.000
 SR3  HAM   CAM  CAP   108.22  3.000
 SR3  OD2   CAM  CAP   111.14  3.000
 SR3  CAM   CAP  OAD   121.85  3.000
 SR3  CAM   CAP  NAB   115.40  3.000
 SR3  OAD   CAP  NAB   122.70  3.000
 SR3  HSAT  SAT  OAH    86.31  3.000
 SR3  HSAT  SAT  OAG   101.05  3.000
 SR3  OAH   SAT  OAG    94.28  3.000
 SR3  HSAT  SAT  CB     79.74  3.000
 SR3  OAH   SAT  CB    165.55  3.000
 SR3  OAG   SAT  CB     92.09  3.000
 SR3  CAM   OD2  CG    115.79  3.000
 SR3  HOXT  OXT  C     110.55  3.000
 SR3  HOAG  OAG  SAT   111.67  3.000
 SR3  HOAH  OAH  SAT   107.10  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
 SR3  CONST_01  HNAB  NAB  CAP  OAD     0.00   0.0  0
 SR3  CONST_02  HNAA  NAB  CAP  OAD   180.00   0.0  0
 SR3  CONST_03  HNAB  NAB  CAP  CAM   180.00   0.0  0
 SR3  CONST_04  HNAA  NAB  CAP  CAM     0.00   0.0  0
 SR3  CONST_05  HOXT  OXT  C    O       0.00   0.0  0
 SR3  CONST_06  HOXT  OXT  C    CA    180.00   0.0  0
 SR3  Var_01    CAJ   CAK  CAL  N     179.44   0.0  2
 SR3  Var_02    CAK   CAL  N    CA    177.43  30.0  2
 SR3  Var_03    CAM   OD2  CG   CB    166.34  30.0  3
 SR3  Var_04    CAP   CAM  OD2  CG    -63.25  30.0  1
 SR3  Var_05    OD2   CAM  CAP  NAB   162.30  30.0  3
 SR3  Var_06    CAL   CAK  CAJ  OAC   179.60  30.0  2
 SR3  Var_07    OD2   CAM  CAP  OAD   -20.29  30.0  3
 SR3  Var_08    OD1   CG   OD2  CAM   -10.71  30.0  1
 SR3  Var_09    HAK   CAK  CAL  N      -1.02   0.0  2
 SR3  Var_10    HAL   CAL  CAK  CAJ     0.47   0.0  2
 SR3  Var_11    HAL   CAL  N    CA     -3.56  30.0  2
 SR3  Var_12    HAM   CAM  OD2  CG    179.32  30.0  1
 SR3  Var_13    HAMA  CAM  OD2  CG     61.70  30.0  1
 SR3  Var_14    HAM   CAM  CAP  NAB   -81.56  30.0  3
 SR3  Var_15    HAMA  CAM  CAP  NAB    36.27  30.0  3
 SR3  Var_16    HAK   CAK  CAJ  OAC     0.06  30.0  2
 SR3  Var_17    HAM   CAM  CAP  OAD    95.85  30.0  3
 SR3  Var_18    HAMA  CAM  CAP  OAD  -146.31  30.0  3
 SR3  Var_19    HN    N    CAL  CAK     3.18  30.0  1
 SR3  Var_20    HAJ   CAJ  CAK  CAL    -0.33  30.0  2
 SR3  Var_21    HAL   CAL  CAK  HAK  -179.99   0.0  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
 SR3  chir_01  CA  C    N   CB  positiv
 SR3  chir_02  CB  CAA  CG  CA  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
 SR3  plan-1  NAB   0.020
 SR3  plan-1  OAD   0.020
 SR3  plan-1  CAM   0.020
 SR3  plan-1  CAP   0.020
 SR3  plan-1  HNAB  0.020
 SR3  plan-1  HNAA  0.020
 SR3  plan-2  C     0.020
 SR3  plan-2  O     0.020
 SR3  plan-2  CA    0.020
 SR3  plan-2  OXT   0.020
 SR3  plan-2  HOXT  0.020
 SR3  plan-3  CB    0.020
 SR3  plan-3  CG    0.020
 SR3  plan-3  OD1   0.020
 SR3  plan-3  OD2   0.020
 SR3  plan-4  OAC   0.020
 SR3  plan-4  CAJ   0.020
 SR3  plan-4  CAK   0.020
 SR3  plan-4  HAJ   0.020
 SR3  plan-5  N     0.020
 SR3  plan-5  CAJ   0.020
 SR3  plan-5  CAK   0.020
 SR3  plan-5  CAL   0.020
 SR3  plan-5  HAK   0.020
 SR3  plan-5  HAL   0.020

