# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:42:13 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-[(4Z)-2-[(1R)-1-amino-2-hydroxy-ethyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)C1=N\\C(=C/c2c[nH]c3ccccc23)C(=O)N1CC(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
 SWG  SWG  '2-[(4Z)-2-[(1R)-1-amino-2-hydroxy-ethyl]-4-(1H-indol-3-ylmethylidene)-5-oxo-imidazol-1-yl]ethanoic acid'  L-peptide  39  24  .  2022-07-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_SWG
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
 SWG  CD2   C  CR56   0   0.051   3.8084  -0.3737  -0.0278
 SWG  CE3   C  CR16   0  -0.374   4.4786  -1.5301  -0.4350
 SWG  CZ3   C  CR16   0  -0.261   5.8584  -1.5612  -0.3618
 SWG  CH2   C  CR16   0  -0.283   6.5866  -0.4583   0.1111
 SWG  CZ2   C  CR16   0  -0.294   5.9488   0.6976   0.5199
 SWG  CE2   C  CR56   0   0.356   4.5594   0.7196   0.4429
 SWG  NE1   N  NR15   0  -0.673   3.6714   1.7121   0.7704
 SWG  CD1   C  CR15   0  -0.035   2.4086   1.3037   0.5310
 SWG  CG    C  CR5    0   0.021   2.4206   0.0123   0.0329
 SWG  CB2   C  C1     0  -0.415   1.3103  -0.7982  -0.3568
 SWG  CA2   C  CR5    0   0.071  -0.0005  -0.4770  -0.3171
 SWG  N2    N  N      0  -0.484  -0.5527   0.7257   0.1036
 SWG  C2    C  CR5    0   0.517  -1.0830  -1.3684  -0.7657
 SWG  O2    O  O      0  -0.468  -1.0531  -2.5203  -1.1610
 SWG  N3    N  NR5    0  -0.534  -2.2083  -0.5827  -0.6390
 SWG  CA3   C  CH2    0  -0.485  -3.5521  -1.0938  -0.7167
 SWG  C3    C  C      0   0.418  -4.1200  -1.5285   0.6553
 SWG  O3    O  O      0  -0.587  -3.4136  -1.3128   1.6531
 SWG  OXT   O  OC    -1  -0.610  -5.2506  -2.0447   0.6065
 SWG  C1    C  CR5    0   0.500  -1.8237   0.6166  -0.0808
 SWG  CA1   C  CH1    0  -0.239  -2.7994   1.7238   0.2151
 SWG  N1    N  NH2    0  -0.766  -2.3285   2.6577   1.2120
 SWG  CB1   C  CH2    0  -0.130  -3.1153   2.4417  -1.0964
 SWG  OG1   O  OH1    0  -0.663  -4.1808   3.3308  -0.8855
 SWG  HE3   H  HCR6   0   0.247   3.9346  -2.3904  -0.8050
 SWG  HZ3   H  HCR6   0   0.252   6.3894  -2.4501  -0.6762
 SWG  HH2   H  HCR6   0   0.254   7.6666  -0.5138   0.1553
 SWG  HZ2   H  HCR6   0   0.265   6.5067   1.5508   0.8838
 SWG  HE1   H  HNR5   0   0.420   3.9190   2.6181   1.1346
 SWG  HD1   H  HCR5   0   0.298   1.5663   1.9468   0.7240
 SWG  HB2   H  H      0   0.260   1.5441  -1.7899  -0.7311
 SWG  HA31  H  HCH2   0   0.267  -4.2082  -0.3455  -1.1674
 SWG  HA32  H  HCH2   0   0.274  -3.5491  -1.9426  -1.4011
 SWG  HA1   H  HCH1   0   0.267  -3.7249   1.2733   0.5848
 SWG  H11N  H  HNH2   0   0.350  -2.1961   2.1707   2.0897
 SWG  H12N  H  HNH2   0   0.344  -1.4108   2.9985   0.9489
 SWG  HB11  H  HCH2   0   0.203  -2.2064   2.9581  -1.4360
 SWG  HB12  H  HCH2   0   0.208  -3.3568   1.6974  -1.8667
 SWG  HG1   H  HOH1   0   0.456  -4.3454   3.7955  -1.7106

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
 SWG  CD2  CE3   aromatic  1.397  0.020  1.397
 SWG  CD2  CE2   aromatic  1.407  0.020  1.407
 SWG  CD2  CG    aromatic  1.442  0.020  1.442
 SWG  CE3  CZ3   aromatic  1.382  0.020  1.382
 SWG  CZ3  CH2   aromatic  1.404  0.020  1.404
 SWG  CH2  CZ2   aromatic  1.382  0.020  1.382
 SWG  CZ2  CE2   aromatic  1.392  0.020  1.392
 SWG  CE2  NE1   aromatic  1.371  0.020  1.371
 SWG  NE1  CD1   aromatic  1.349  0.020  1.349
 SWG  CD1  CG    aromatic  1.384  0.020  1.384
 SWG  CG   CB2   single    1.429  0.020  1.429
 SWG  CB2  CA2   double    1.350  0.020  1.350
 SWG  CA2  N2    single    1.389  0.020  1.389
 SWG  CA2  C2    single    1.472  0.020  1.472
 SWG  N2   C1    double    1.289  0.020  1.289
 SWG  C2   O2    double    1.218  0.020  1.218
 SWG  C2   N3    single    1.378  0.020  1.378
 SWG  N3   CA3   single    1.440  0.020  1.440
 SWG  N3   C1    single    1.378  0.020  1.378
 SWG  CA3  C3    single    1.547  0.020  1.547
 SWG  C3   O3    deloc     1.241  0.020  1.241
 SWG  C3   OXT   deloc     1.244  0.020  1.244
 SWG  C1   CA1   single    1.505  0.020  1.505
 SWG  CA1  N1    single    1.445  0.020  1.445
 SWG  CA1  CB1   single    1.528  0.020  1.528
 SWG  CB1  OG1   single    1.404  0.020  1.404
 SWG  CE3  HE3   single    0.930  0.020  1.080
 SWG  CZ3  HZ3   single    0.930  0.020  1.080
 SWG  CH2  HH2   single    0.930  0.020  1.080
 SWG  CZ2  HZ2   single    0.930  0.020  1.080
 SWG  NE1  HE1   single    0.860  0.020  1.020
 SWG  CD1  HD1   single    0.930  0.020  1.080
 SWG  CB2  HB2   single    0.930  0.020  1.080
 SWG  CA3  HA31  single    0.970  0.020  1.090
 SWG  CA3  HA32  single    0.970  0.020  1.090
 SWG  CA1  HA1   single    0.970  0.020  1.090
 SWG  N1   H11N  single    0.890  0.020  1.040
 SWG  N1   H12N  single    0.890  0.020  1.040
 SWG  CB1  HB11  single    0.970  0.020  1.090
 SWG  CB1  HB12  single    0.970  0.020  1.090
 SWG  OG1  HG1   single    0.850  0.020  0.980

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
 SWG  CG    CD2  CE2   106.95  3.000
 SWG  CG    CD2  CE3   134.07  3.000
 SWG  CE2   CD2  CE3   118.98  3.000
 SWG  HE3   CE3  CZ3   120.11  3.000
 SWG  HE3   CE3  CD2   121.07  3.000
 SWG  CZ3   CE3  CD2   118.82  3.000
 SWG  HZ3   CZ3  CH2   119.25  3.000
 SWG  HZ3   CZ3  CE3   119.54  3.000
 SWG  CH2   CZ3  CE3   121.21  3.000
 SWG  HH2   CH2  CZ2   119.43  3.000
 SWG  HH2   CH2  CZ3   119.42  3.000
 SWG  CZ2   CH2  CZ3   121.16  3.000
 SWG  HZ2   CZ2  CE2   121.38  3.000
 SWG  HZ2   CZ2  CH2   121.39  3.000
 SWG  CE2   CZ2  CH2   117.23  3.000
 SWG  NE1   CE2  CZ2   130.14  3.000
 SWG  NE1   CE2  CD2   107.25  3.000
 SWG  CZ2   CE2  CD2   122.61  3.000
 SWG  HE1   NE1  CD1   124.52  3.000
 SWG  HE1   NE1  CE2   125.31  3.000
 SWG  CD1   NE1  CE2   110.17  3.000
 SWG  HD1   CD1  CG    128.92  3.000
 SWG  HD1   CD1  NE1   121.31  3.000
 SWG  CG    CD1  NE1   109.77  3.000
 SWG  CB2   CG   CD1   128.36  3.000
 SWG  CB2   CG   CD2   125.78  3.000
 SWG  CD1   CG   CD2   105.86  3.000
 SWG  HB2   CB2  CA2   115.89  3.000
 SWG  HB2   CB2  CG    116.42  3.000
 SWG  CA2   CB2  CG    127.69  3.000
 SWG  C2    CA2  N2    108.93  3.000
 SWG  C2    CA2  CB2   124.11  3.000
 SWG  N2    CA2  CB2   126.94  3.000
 SWG  C1    N2   CA2   105.99  3.000
 SWG  N3    C2   O2    126.08  3.000
 SWG  N3    C2   CA2   103.13  3.000
 SWG  O2    C2   CA2   130.79  3.000
 SWG  C1    N3   CA3   126.26  3.000
 SWG  C1    N3   C2    107.79  3.000
 SWG  CA3   N3   C2    123.69  3.000
 SWG  HA32  CA3  HA31  106.02  3.000
 SWG  HA32  CA3  C3    109.81  3.000
 SWG  HA31  CA3  C3    109.75  3.000
 SWG  HA32  CA3  N3    107.92  3.000
 SWG  HA31  CA3  N3    109.85  3.000
 SWG  C3    CA3  N3    113.23  3.000
 SWG  OXT   C3   O3    128.38  3.000
 SWG  OXT   C3   CA3   114.54  3.000
 SWG  O3    C3   CA3   117.07  3.000
 SWG  CA1   C1   N3    122.62  3.000
 SWG  CA1   C1   N2    123.29  3.000
 SWG  N3    C1   N2    114.02  3.000
 SWG  HA1   CA1  CB1   107.98  3.000
 SWG  HA1   CA1  N1    107.98  3.000
 SWG  CB1   CA1  N1    110.84  3.000
 SWG  HA1   CA1  C1    108.18  3.000
 SWG  CB1   CA1  C1    108.12  3.000
 SWG  N1    CA1  C1    113.57  3.000
 SWG  H12N  N1   H11N  105.56  3.000
 SWG  H12N  N1   CA1   109.47  3.000
 SWG  H11N  N1   CA1   109.26  3.000
 SWG  HB12  CB1  HB11  106.48  3.000
 SWG  HB12  CB1  OG1   111.57  3.000
 SWG  HB11  CB1  OG1   112.12  3.000
 SWG  HB12  CB1  CA1   109.21  3.000
 SWG  HB11  CB1  CA1   108.36  3.000
 SWG  OG1   CB1  CA1   109.00  3.000
 SWG  HG1   OG1  CB1   107.90  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
 SWG  CONST_01  CH2  CZ3  CE3  CD2     0.00   0.0  0
 SWG  CONST_02  CH2  CZ2  CE2  CD2     0.00   0.0  0
 SWG  CONST_03  CD1  NE1  CE2  CD2     0.00   0.0  0
 SWG  CONST_04  NE1  CD1  CG   CD2     0.00   0.0  0
 SWG  CONST_05  CZ2  CE2  CD2  CE3     0.00   0.0  0
 SWG  CONST_06  NE1  CE2  CD2  CE3   180.00   0.0  0
 SWG  CONST_07  CD1  CG   CD2  CE3   180.00   0.0  0
 SWG  CONST_08  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 SWG  CONST_09  CE2  CD2  CE3  CZ3     0.00   0.0  0
 SWG  CONST_10  CG   CD2  CE3  CZ3   180.00   0.0  0
 SWG  CONST_11  CE2  CZ2  CH2  CZ3     0.00   0.0  0
 SWG  CONST_12  NE1  CE2  CZ2  CH2   180.00   0.0  0
 SWG  CONST_13  CG   CD2  CE2  CZ2   180.00   0.0  0
 SWG  CONST_14  CD1  NE1  CE2  CZ2   180.00   0.0  0
 SWG  CONST_15  CD1  CG   CD2  CE2     0.00   0.0  0
 SWG  CONST_16  CG   CD1  NE1  CE2     0.00   0.0  0
 SWG  CONST_17  CG   CD2  CE2  NE1     0.00   0.0  0
 SWG  CONST_18  N3   C1   N2   CA2     0.00   0.0  0
 SWG  CONST_19  C1   N3   C2   CA2     0.00   0.0  0
 SWG  CONST_20  N3   C2   CA2  N2      0.00   0.0  0
 SWG  CONST_21  C2   N3   C1   N2      0.00   0.0  0
 SWG  CONST_22  C1   N2   CA2  C2      0.00   0.0  0
 SWG  CONST_23  CB2  CG   CD2  CE3     0.00   0.0  0
 SWG  CONST_24  CB2  CG   CD2  CE2   180.00   0.0  0
 SWG  CONST_25  CB2  CG   CD1  NE1   180.00   0.0  0
 SWG  CONST_26  CA1  C1   N2   CA2   180.00   0.0  0
 SWG  CONST_27  CA3  N3   C2   CA2   180.00   0.0  0
 SWG  CONST_28  CA3  N3   C1   N2    180.00   0.0  0
 SWG  CONST_29  CA1  C1   N3   C2    180.00   0.0  0
 SWG  CONST_30  C1   N3   C2   O2    180.00   0.0  0
 SWG  CONST_31  HZ3  CZ3  CE3  CD2   180.00   0.0  0
 SWG  CONST_32  HZ2  CZ2  CE2  CD2   180.00   0.0  0
 SWG  CONST_33  HE1  NE1  CE2  CD2   180.00   0.0  0
 SWG  CONST_34  HD1  CD1  CG   CD2   180.00   0.0  0
 SWG  CONST_35  HH2  CH2  CZ3  CE3   180.00   0.0  0
 SWG  CONST_36  HE3  CE3  CZ3  CH2   180.00   0.0  0
 SWG  CONST_37  CA3  N3   C2   O2      0.00   0.0  0
 SWG  Var_01    CA2  CB2  CG   CD2  -179.97  30.0  2
 SWG  Var_02    N2   CA2  CB2  CG      0.64  30.0  2
 SWG  Var_03    C3   CA3  N3   C2     90.17  30.0  3
 SWG  Var_04    O3   C3   CA3  N3      4.59  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
 SWG  chir_01  CA1  C1  N1  CB1  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
 SWG  plan-1  CB2  0.020
 SWG  plan-1  CA2  0.020
 SWG  plan-1  N2   0.020
 SWG  plan-1  C2   0.020
 SWG  plan-1  O2   0.020
 SWG  plan-1  N3   0.020
 SWG  plan-1  CA3  0.020
 SWG  plan-1  C1   0.020
 SWG  plan-1  CA1  0.020
 SWG  plan-2  CD2  0.020
 SWG  plan-2  CE3  0.020
 SWG  plan-2  CZ3  0.020
 SWG  plan-2  CH2  0.020
 SWG  plan-2  CZ2  0.020
 SWG  plan-2  CE2  0.020
 SWG  plan-2  NE1  0.020
 SWG  plan-2  CD1  0.020
 SWG  plan-2  CG   0.020
 SWG  plan-2  CB2  0.020
 SWG  plan-2  HE3  0.020
 SWG  plan-2  HZ3  0.020
 SWG  plan-2  HH2  0.020
 SWG  plan-2  HZ2  0.020
 SWG  plan-2  HE1  0.020
 SWG  plan-2  HD1  0.020
 SWG  plan-3  CA3  0.020
 SWG  plan-3  C3   0.020
 SWG  plan-3  O3   0.020
 SWG  plan-3  OXT  0.020

