# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:08:44 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (6E)-4-[(2S)-2-amino-2-carboxyethyl]-6-[2-(4-hydroxybenzyl)hydraziniumylidene]-3-oxocyclohexa-1,4-dien-1-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CC(=[NH+]NCc2ccc(O)cc2)C(=CC1=O)[O-])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
 4HL  4HL  (6E)-4-[(2S)-2-amino-2-carboxyethyl]-6-[2-(4-hydroxybenzyl)hydraziniumylidene]-3-oxocyclohexa-1,4-dien-1-olate  L-peptide  40  24  .  2016-04-22  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_4HL
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
 4HL  C1   C  CH2    0  -0.413   3.7030  -1.4317  26.0549
 4HL  NX1  N  NC1    0  -0.437   2.7339  -1.4253  27.1623
 4HL  NX2  N  NC1    1  -0.437   1.4967  -1.8651  26.7317
 4HL  C4'  C  CR16   0  -0.282   2.6718  -0.4592  23.9697
 4HL  C5'  C  CR16   0  -0.325   2.4176   0.5991  23.1111
 4HL  C6'  C  CR6    0   0.342   2.9572   1.8549  23.3786
 4HL  C1'  C  CR16   0  -0.360   3.7475   2.0316  24.5128
 4HL  C2'  C  CR16   0  -0.273   3.9825   0.9664  25.3646
 4HL  C3'  C  CR6    0   0.106   3.4547  -0.2959  25.1088
 4HL  N    N  NH2    0  -0.805   0.6146   3.0294  25.6057
 4HL  CA   C  CH1    0  -0.218  -0.6803   3.2475  26.2155
 4HL  C    C  C      0   0.416  -0.8828   4.7386  26.6126
 4HL  O    O  O      0  -0.590  -0.0701   5.5591  26.1459
 4HL  CG   C  CR6    0   0.018  -0.7584   0.9080  27.0710
 4HL  CD1  C  CR6    0   0.392  -2.0187   0.2458  26.5459
 4HL  CD2  C  CR16   0  -0.341   0.4030   0.2267  27.1310
 4HL  CE1  C  CR16   0  -0.583  -1.9426  -1.0978  26.0948
 4HL  CE2  C  CR6    0   0.348   0.4390  -1.1290  26.6904
 4HL  CZ   C  CR6    0   0.332  -0.7793  -1.8504  26.1282
 4HL  OH   O  OC    -1  -0.508  -0.6014  -3.0251  25.7672
 4HL  OXT  O  OC    -1  -0.599  -1.8696   4.9823  27.3315
 4HL  H11  H  HCH2   0   0.255   3.6967  -2.3898  25.5214
 4HL  H12  H  HCH2   0   0.277   4.6802  -1.3318  26.5280
 4HL  H3   H  HNC1   0   0.404   3.0391  -2.0691  27.8856
 4HL  H4'  H  HCR6   0   0.255   2.2546  -1.4328  23.7384
 4HL  H5'  H  HCR6   0   0.261   1.8053   0.4527  22.2299
 4HL  H1'  H  HCR6   0   0.269   4.1747   3.0033  24.7339
 4HL  H2'  H  HCR6   0   0.254   4.5972   1.1232  26.2433
 4HL  H5   H  HOH1   0   0.473   3.1037   3.6738  22.8047
 4HL  HA   H  HCH1   0   0.215  -1.5116   3.0133  25.5325
 4HL  HD2  H  HCR6   0   0.287   1.3080   0.6825  27.5072
 4HL  HE1  H  HCR6   0   0.236  -2.8490  -1.5568  25.7187
 4HL  H4   H  HNC1   0   0.424   1.3863  -2.8169  26.3674
 4HL  OX1  O  O      0  -0.451  -3.0542   0.9115  26.5403
 4HL  CB   C  CH2    0  -0.486  -0.8369   2.3387  27.4552
 4HL  H    H  HNH2   0   0.340   0.5856   2.2534  24.9590
 4HL  HB2  H  HCH2   0   0.242  -0.0369   2.5755  28.1594
 4HL  HB3  H  HCH2   0   0.250  -1.7916   2.5544  27.9289
 4HL  OH'  O  OH1    0  -0.628   2.6846   2.8543  22.5171
 4HL  H2   H  HNH2   0   0.338   0.8676   3.8549  25.0800

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
 4HL  OH'  C6'  single    1.347  0.020  1.347
 4HL  C6'  C5'  aromatic  1.393  0.020  1.393
 4HL  C6'  C1'  aromatic  1.394  0.020  1.394
 4HL  C5'  C4'  aromatic  1.386  0.020  1.386
 4HL  C1'  C2'  aromatic  1.384  0.020  1.384
 4HL  C4'  C3'  aromatic  1.392  0.020  1.392
 4HL  C2'  C3'  aromatic  1.392  0.020  1.392
 4HL  C3'  C1   single    1.499  0.020  1.499
 4HL  OH   CZ   single    1.242  0.020  1.242
 4HL  N    CA   single    1.458  0.019  1.458
 4HL  C1   NX1  single    1.472  0.020  1.472
 4HL  CZ   CE1  double    1.386  0.020  1.386
 4HL  CZ   CE2  single    1.523  0.020  1.523
 4HL  CE1  CD1  single    1.419  0.020  1.419
 4HL  NX2  CE2  double    1.289  0.020  1.289
 4HL  NX2  NX1  single    1.382  0.020  1.382
 4HL  CE2  CD2  single    1.426  0.020  1.426
 4HL  CD1  OX1  double    1.231  0.020  1.231
 4HL  CD1  CG   single    1.517  0.020  1.517
 4HL  CA   C    single    1.525  0.021  1.525
 4HL  CA   CB   single    1.530  0.020  1.530
 4HL  CD2  CG   double    1.348  0.020  1.348
 4HL  CG   CB   single    1.483  0.020  1.483
 4HL  O    C    deloc     1.231  0.020  1.231
 4HL  C    OXT  deloc     1.245  0.020  1.245
 4HL  C1   H11  single    0.970  0.020  1.090
 4HL  C1   H12  single    0.970  0.020  1.090
 4HL  NX1  H3   single    0.890  0.020  1.040
 4HL  C4'  H4'  single    0.930  0.020  1.080
 4HL  C5'  H5'  single    0.930  0.020  1.080
 4HL  C1'  H1'  single    0.930  0.020  1.080
 4HL  C2'  H2'  single    0.930  0.020  1.080
 4HL  OH'  H5   single    0.850  0.020  0.980
 4HL  N    H    single    0.860  0.020  0.860
 4HL  N    H2   single    0.890  0.020  1.040
 4HL  CA   HA   single    0.970  0.020  0.970
 4HL  CB   HB2  single    0.970  0.020  1.090
 4HL  CB   HB3  single    0.970  0.020  1.090
 4HL  CD2  HD2  single    0.930  0.020  1.080
 4HL  CE1  HE1  single    0.930  0.020  1.080
 4HL  NX2  H4   single    0.860  0.020  1.020

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
 4HL  H12  C1   H11  107.23  3.000
 4HL  H12  C1   C3'  110.66  3.000
 4HL  H11  C1   C3'  110.73  3.000
 4HL  H12  C1   NX1  105.26  3.000
 4HL  H11  C1   NX1  111.48  3.000
 4HL  C3'  C1   NX1  111.26  3.000
 4HL  H3   NX1  NX2  106.82  3.000
 4HL  H3   NX1  C1   109.60  3.000
 4HL  NX2  NX1  C1   110.71  3.000
 4HL  H4   NX2  CE2  115.49  3.000
 4HL  H4   NX2  NX1  120.18  3.000
 4HL  CE2  NX2  NX1  124.25  3.000
 4HL  H4'  C4'  C3'  119.77  3.000
 4HL  H4'  C4'  C5'  118.87  3.000
 4HL  C3'  C4'  C5'  121.36  3.000
 4HL  H5'  C5'  C6'  119.82  3.000
 4HL  H5'  C5'  C4'  120.29  3.000
 4HL  C6'  C5'  C4'  119.89  3.000
 4HL  OH'  C6'  C1'  122.75  3.000
 4HL  C1'  C6'  C5'  119.36  3.000
 4HL  OH'  C6'  C5'  117.88  3.000
 4HL  H1'  C1'  C2'  119.83  3.000
 4HL  H1'  C1'  C6'  120.20  3.000
 4HL  C2'  C1'  C6'  119.97  3.000
 4HL  H2'  C2'  C3'  119.69  3.000
 4HL  H2'  C2'  C1'  118.94  3.000
 4HL  C3'  C2'  C1'  121.37  3.000
 4HL  C2'  C3'  C4'  118.04  3.000
 4HL  C2'  C3'  C1   120.56  3.000
 4HL  C4'  C3'  C1   121.38  3.000
 4HL  H2   N    H    107.54  3.000
 4HL  H2   N    CA   108.66  3.000
 4HL  H    N    CA   114.00  3.000
 4HL  HA   CA   CB   109.00  3.000
 4HL  HA   CA   C    109.00  3.000
 4HL  CB   CA   C    110.10  1.900
 4HL  HA   CA   N    110.00  3.000
 4HL  CB   CA   N    110.50  1.700
 4HL  C    CA   N    111.00  2.800
 4HL  OXT  C    O    127.20  3.000
 4HL  OXT  C    CA   115.98  3.000
 4HL  O    C    CA   120.80  1.700
 4HL  CD2  CG   CD1  120.70  3.000
 4HL  CD2  CG   CB   121.44  3.000
 4HL  CD1  CG   CB   117.81  3.000
 4HL  CE1  CD1  CG   118.59  3.000
 4HL  CG   CD1  OX1  117.66  3.000
 4HL  CE1  CD1  OX1  123.75  3.000
 4HL  HD2  CD2  CE2  119.16  3.000
 4HL  HD2  CD2  CG   121.59  3.000
 4HL  CE2  CD2  CG   119.25  3.000
 4HL  HE1  CE1  CZ   118.72  3.000
 4HL  HE1  CE1  CD1  117.81  3.000
 4HL  CZ   CE1  CD1  123.46  3.000
 4HL  CZ   CE2  CD2  122.95  3.000
 4HL  CD2  CE2  NX2  123.62  3.000
 4HL  CZ   CE2  NX2  113.42  3.000
 4HL  OH   CZ   CE2  116.15  3.000
 4HL  CE2  CZ   CE1  115.03  3.000
 4HL  OH   CZ   CE1  128.83  3.000
 4HL  HB3  CB   HB2  108.62  3.000
 4HL  HB3  CB   CG   110.53  3.000
 4HL  HB2  CB   CG   109.72  3.000
 4HL  HB3  CB   CA   108.77  3.000
 4HL  HB2  CB   CA   108.40  3.000
 4HL  CG   CB   CA   110.74  3.000
 4HL  H5   OH'  C6'  110.60  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
 4HL  CONST_01  C1'  C6'  C5'  C4'     0.00   0.0  0
 4HL  CONST_02  C1'  C2'  C3'  C4'     0.00   0.0  0
 4HL  CONST_03  C2'  C1'  C6'  C5'     0.00   0.0  0
 4HL  CONST_04  C2'  C3'  C4'  C5'     0.00   0.0  0
 4HL  CONST_05  C3'  C4'  C5'  C6'     0.00   0.0  0
 4HL  CONST_06  C3'  C2'  C1'  C6'     0.00   0.0  0
 4HL  CONST_07  C5'  C4'  C3'  C1    180.00   0.0  0
 4HL  CONST_08  C1'  C2'  C3'  C1    180.00   0.0  0
 4HL  CONST_09  OH'  C6'  C5'  C4'   180.00   0.0  0
 4HL  CONST_10  OH'  C6'  C1'  C2'   180.00   0.0  0
 4HL  CONST_11  H2'  C2'  C3'  C4'   180.00   0.0  0
 4HL  CONST_12  H1'  C1'  C6'  C5'   180.00   0.0  0
 4HL  CONST_13  H4'  C4'  C5'  C6'   180.00   0.0  0
 4HL  CONST_14  H5'  C5'  C6'  C1'   180.00   0.0  0
 4HL  Var_01    CZ   CE2  NX2  NX1   177.95   0.0  2
 4HL  Var_02    C4'  C3'  C1   NX1   -94.12  30.0  2
 4HL  Var_03    CD1  CG   CB   CA    -82.92  30.0  1
 4HL  Var_04    CE2  NX2  NX1  C1   -114.41  30.0  1
 4HL  Var_05    C3'  C1   NX1  NX2    74.56  30.0  1

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
 4HL  chir_01  CA  N  C  CB  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
 4HL  plan-1  C1   0.020
 4HL  plan-1  C4'  0.020
 4HL  plan-1  C5'  0.020
 4HL  plan-1  C6'  0.020
 4HL  plan-1  C1'  0.020
 4HL  plan-1  C2'  0.020
 4HL  plan-1  C3'  0.020
 4HL  plan-1  H4'  0.020
 4HL  plan-1  H5'  0.020
 4HL  plan-1  H1'  0.020
 4HL  plan-1  H2'  0.020
 4HL  plan-1  OH'  0.020
 4HL  plan-2  NX1  0.020
 4HL  plan-2  NX2  0.020
 4HL  plan-2  CG   0.020
 4HL  plan-2  CD1  0.020
 4HL  plan-2  CD2  0.020
 4HL  plan-2  CE1  0.020
 4HL  plan-2  CE2  0.020
 4HL  plan-2  CZ   0.020
 4HL  plan-2  OH   0.020
 4HL  plan-2  HD2  0.020
 4HL  plan-2  HE1  0.020
 4HL  plan-2  H4   0.020
 4HL  plan-2  OX1  0.020
 4HL  plan-2  CB   0.020
 4HL  plan-3  CA   0.020
 4HL  plan-3  C    0.020
 4HL  plan-3  O    0.020
 4HL  plan-3  OXT  0.020

