# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 21:38:35 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)C1=N\C(=C/c2ccc(O)c(c2)[N](=O)=O)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
 QCA  QCA  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  41  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QCA
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
 QCA  N1   N  NH2    0  -0.799  8.8068   6.4035   2.1333
 QCA  CA1  C  CH1    0  -0.216  7.5532   6.3418   2.8797
 QCA  CB1  C  CH1    0   0.050  7.7773   6.5438   4.3833
 QCA  CG1  C  CH3    0  -0.699  8.3989   5.3008   5.0124
 QCA  OG1  O  OH1    0  -0.658  8.5802   7.6808   4.5967
 QCA  C1   C  CR5    0   0.582  6.6128   7.3562   2.2959
 QCA  N2   N  N      0  -0.489  6.3969   8.5338   2.7738
 QCA  N3   N  NR5    0  -0.544  5.9320   7.0943   1.1242
 QCA  C2   C  CR5    0   0.529  5.1350   8.1823   0.8470
 QCA  O2   O  O      0  -0.438  4.3450   8.2840  -0.0683
 QCA  CA2  C  CR5    0   0.113  5.4911   9.1412   1.9206
 QCA  CA3  C  CH2    0  -0.486  5.7491   5.8076   0.4993
 QCA  C3   C  C      0   0.420  4.7226   4.9108   1.2384
 QCA  O3   O  O      0  -0.598  4.4569   3.8479   0.6531
 QCA  CB2  C  C1     0  -0.399  5.0025  10.3920   1.9953
 QCA  CG2  C  C      0   0.150  5.3066  11.4202   2.9713
 QCA  CD1  C  C1     0  -0.392  6.1829  11.2431   4.0340
 QCA  CD2  C  C1     0  -0.272  4.6915  12.6789   2.8375
 QCA  CE1  C  C      0   0.214  6.4383  12.2807   4.9236
 QCA  CE2  C  C1     0  -0.339  4.9421  13.7077   3.7103
 QCA  CZ   C  C      0   0.367  5.8263  13.5440   4.7825
 QCA  OH   O  OH1    0  -0.591  6.0186  14.5842   5.5744
 QCA  N4   N  N      1   0.365  7.3569  12.0250   6.0037
 QCA  O4   O  O     -1  -0.358  7.8608  10.9367   6.1039
 QCA  O5   O  O      0  -0.422  7.5927  12.9353   6.7863
 QCA  H1   H  HNH2   0   0.357  9.4352   5.6889   2.4800
 QCA  H2   H  HNH2   0   0.355  8.6471   6.1654   1.1619
 QCA  H4   H  HCH1   0   0.251  7.0518   5.3674   2.7974
 QCA  H5   H  HCH1   0   0.209  6.7814   6.6781   4.8281
 QCA  H6   H  HCH3   0   0.241  8.4935   5.4295   6.0921
 QCA  H7   H  HCH3   0   0.230  7.7759   4.4222   4.8416
 QCA  H8   H  HCH3   0   0.226  9.3959   5.0947   4.6188
 QCA  H9   H  HOH1   0   0.447  8.6485   7.8164   5.5467
 QCA  H10  H  HCH2   0   0.267  6.7069   5.2881   0.4306
 QCA  H11  H  HCH2   0   0.272  5.4257   5.9762  -0.5281
 QCA  H13  H  H      0   0.271  4.2997  10.6753   1.2182
 QCA  H14  H  H      0   0.317  6.6752  10.2898   4.1639
 QCA  H15  H  H      0   0.280  4.0004  12.8465   2.0205
 QCA  H16  H  H      0   0.289  4.4584  14.6672   3.5832
 QCA  H17  H  HOH1   0   0.483  6.6484  14.3398   6.2784
 QCA  OXT  O  OC    -1  -0.586  4.2906   5.3319   2.3242

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
 QCA  O3   C3   deloc     1.242  0.020  1.242
 QCA  O2   C2   double    1.213  0.020  1.213
 QCA  CA3  C3   single    1.551  0.020  1.551
 QCA  CA3  N3   single    1.442  0.020  1.442
 QCA  C2   N3   single    1.377  0.020  1.377
 QCA  C2   CA2  single    1.483  0.020  1.483
 QCA  N3   C1   single    1.380  0.020  1.380
 QCA  CA2  CB2  double    1.345  0.020  1.345
 QCA  CA2  N2   single    1.385  0.020  1.385
 QCA  N1   CA1  single    1.460  0.020  1.460
 QCA  CB2  CG2  single    1.450  0.020  1.450
 QCA  C1   N2   double    1.289  0.020  1.289
 QCA  C1   CA1  single    1.501  0.020  1.501
 QCA  CD2  CG2  aromatic  1.407  0.020  1.407
 QCA  CD2  CE2  aromatic  1.372  0.020  1.372
 QCA  CA1  CB1  single    1.534  0.020  1.534
 QCA  CG2  CD1  aromatic  1.389  0.020  1.389
 QCA  CE2  CZ   aromatic  1.399  0.020  1.399
 QCA  CD1  CE1  aromatic  1.390  0.020  1.390
 QCA  CB1  OG1  single    1.408  0.020  1.408
 QCA  CB1  CG1  single    1.526  0.020  1.526
 QCA  CZ   CE1  aromatic  1.411  0.020  1.411
 QCA  CZ   OH   single    1.321  0.020  1.321
 QCA  CE1  N4   single    1.441  0.020  1.441
 QCA  N4   O4   single    1.203  0.020  1.203
 QCA  N4   O5   double    1.223  0.020  1.223
 QCA  N1   H1   single    0.890  0.020  1.040
 QCA  N1   H2   single    0.890  0.020  1.040
 QCA  CA1  H4   single    0.970  0.020  1.090
 QCA  CB1  H5   single    0.970  0.020  1.090
 QCA  CG1  H6   single    0.970  0.020  1.090
 QCA  CG1  H7   single    0.970  0.020  1.090
 QCA  CG1  H8   single    0.970  0.020  1.090
 QCA  OG1  H9   single    0.850  0.020  0.980
 QCA  CA3  H10  single    0.970  0.020  1.090
 QCA  CA3  H11  single    0.970  0.020  1.090
 QCA  CB2  H13  single    0.930  0.020  1.080
 QCA  CD1  H14  single    0.930  0.020  1.080
 QCA  CD2  H15  single    0.930  0.020  1.080
 QCA  CE2  H16  single    0.930  0.020  1.080
 QCA  OH   H17  single    0.850  0.020  0.980
 QCA  C3   OXT  deloc     1.242  0.020  1.242

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
 QCA  H2   N1   H1   105.09  3.000
 QCA  H2   N1   CA1  110.17  3.000
 QCA  H1   N1   CA1  109.14  3.000
 QCA  H4   CA1  C1   106.51  3.000
 QCA  H4   CA1  CB1  104.88  3.000
 QCA  C1   CA1  CB1  112.56  3.000
 QCA  H4   CA1  N1   113.01  3.000
 QCA  CB1  CA1  N1   111.72  3.000
 QCA  C1   CA1  N1   108.09  3.000
 QCA  H5   CB1  OG1  110.90  3.000
 QCA  H5   CB1  CG1  107.57  3.000
 QCA  OG1  CB1  CG1  111.29  3.000
 QCA  H5   CB1  CA1  106.29  3.000
 QCA  CG1  CB1  CA1  110.89  3.000
 QCA  OG1  CB1  CA1  109.77  3.000
 QCA  H8   CG1  H7   108.25  3.000
 QCA  H8   CG1  H6   107.45  3.000
 QCA  H7   CG1  H6   107.42  3.000
 QCA  H8   CG1  CB1  112.18  3.000
 QCA  H7   CG1  CB1  111.05  3.000
 QCA  H6   CG1  CB1  110.32  3.000
 QCA  H9   OG1  CB1  107.70  3.000
 QCA  N3   C1   N2   113.92  3.000
 QCA  N2   C1   CA1  125.31  3.000
 QCA  N3   C1   CA1  120.72  3.000
 QCA  CA2  N2   C1   106.37  3.000
 QCA  CA3  N3   C2   122.98  3.000
 QCA  C2   N3   C1   107.85  3.000
 QCA  CA3  N3   C1   126.85  3.000
 QCA  CA2  C2   O2   130.41  3.000
 QCA  CA2  C2   N3   103.07  3.000
 QCA  O2   C2   N3   126.51  3.000
 QCA  CB2  CA2  C2   123.67  3.000
 QCA  CB2  CA2  N2   127.69  3.000
 QCA  C2   CA2  N2   108.63  3.000
 QCA  H11  CA3  H10  105.93  3.000
 QCA  H11  CA3  C3   110.01  3.000
 QCA  H10  CA3  C3   109.61  3.000
 QCA  H11  CA3  N3   107.94  3.000
 QCA  H10  CA3  N3   109.91  3.000
 QCA  C3   CA3  N3   113.17  3.000
 QCA  OXT  C3   O3   128.87  3.000
 QCA  OXT  C3   CA3  116.80  3.000
 QCA  O3   C3   CA3  114.32  3.000
 QCA  H13  CB2  CG2  115.64  3.000
 QCA  H13  CB2  CA2  115.99  3.000
 QCA  CG2  CB2  CA2  128.37  3.000
 QCA  CD2  CG2  CD1  117.56  3.000
 QCA  CD1  CG2  CB2  123.85  3.000
 QCA  CD2  CG2  CB2  118.59  3.000
 QCA  H14  CD1  CE1  119.85  3.000
 QCA  H14  CD1  CG2  119.47  3.000
 QCA  CE1  CD1  CG2  120.68  3.000
 QCA  H15  CD2  CE2  118.70  3.000
 QCA  H15  CD2  CG2  119.27  3.000
 QCA  CE2  CD2  CG2  122.02  3.000
 QCA  N4   CE1  CZ   120.70  3.000
 QCA  N4   CE1  CD1  117.67  3.000
 QCA  CZ   CE1  CD1  121.64  3.000
 QCA  H16  CE2  CZ   118.44  3.000
 QCA  H16  CE2  CD2  120.56  3.000
 QCA  CZ   CE2  CD2  121.00  3.000
 QCA  OH   CZ   CE2  117.33  3.000
 QCA  OH   CZ   CE1  125.58  3.000
 QCA  CE2  CZ   CE1  117.10  3.000
 QCA  H17  OH   CZ   109.22  3.000
 QCA  O5   N4   O4   122.61  3.000
 QCA  O5   N4   CE1  118.06  3.000
 QCA  O4   N4   CE1  119.33  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
 QCA  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 QCA  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 QCA  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 QCA  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 QCA  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 QCA  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 QCA  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 QCA  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 QCA  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 QCA  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 QCA  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 QCA  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 QCA  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 QCA  CONST_14  N4   CE1  CD1  CG2  180.00   0.0  0
 QCA  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 QCA  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 QCA  CONST_17  N4   CE1  CZ   CE2  180.00   0.0  0
 QCA  CONST_18  C2   N3   C1   CA1  180.00   0.0  0
 QCA  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 QCA  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 QCA  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 QCA  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 QCA  CONST_23  H16  CE2  CD2  CG2  180.00   0.0  0
 QCA  CONST_24  H15  CD2  CG2  CD1  180.00   0.0  0
 QCA  CONST_25  H14  CD1  CG2  CD2  180.00   0.0  0
 QCA  CONST_26  O4   N4   CE1  CD1    0.00   0.0  0
 QCA  CONST_27  O5   N4   CE1  CD1  180.00   0.0  0
 QCA  CONST_28  O4   N4   CE1  CZ   180.00   0.0  0
 QCA  CONST_29  O5   N4   CE1  CZ     0.00   0.0  0
 QCA  CONST_31  CA3  N3   C2   O2     0.00   0.0  0
 QCA  Var_01    CG2  CB2  CA2  N2     0.70   0.0  2
 QCA  Var_02    CD2  CG2  CB2  CA2  178.68  30.0  2
 QCA  Var_03    C3   CA3  N3   C1    73.87  30.0  1
 QCA  Var_04    O3   C3   CA3  N3   173.76  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
 QCA  chir_01  CA1  N1   C1   CB1  positiv
 QCA  chir_02  CB1  OG1  CA1  CG1  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
 QCA  plan-1  CA1  0.020
 QCA  plan-1  C1   0.020
 QCA  plan-1  N2   0.020
 QCA  plan-1  N3   0.020
 QCA  plan-1  C2   0.020
 QCA  plan-1  O2   0.020
 QCA  plan-1  CA2  0.020
 QCA  plan-1  CA3  0.020
 QCA  plan-1  CB2  0.020
 QCA  plan-1  CG2  0.020
 QCA  plan-1  H13  0.020
 QCA  plan-2  CB2  0.020
 QCA  plan-2  CG2  0.020
 QCA  plan-2  CD1  0.020
 QCA  plan-2  CD2  0.020
 QCA  plan-2  CE1  0.020
 QCA  plan-2  CE2  0.020
 QCA  plan-2  CZ   0.020
 QCA  plan-2  OH   0.020
 QCA  plan-2  N4   0.020
 QCA  plan-2  H14  0.020
 QCA  plan-2  H15  0.020
 QCA  plan-2  H16  0.020
 QCA  plan-3  CE1  0.020
 QCA  plan-3  N4   0.020
 QCA  plan-3  O4   0.020
 QCA  plan-3  O5   0.020
 QCA  plan-4  CA3  0.020
 QCA  plan-4  C3   0.020
 QCA  plan-4  O3   0.020
 QCA  plan-4  OXT  0.020

