# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 22:58:10 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-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](N)C1=N\C(=C/c2ccc(O)cc2)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
 PIA  PIA  '[(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  35  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PIA
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
 PIA  N1    N  NH2    0  -0.733  -1.1276  -3.2104  -1.1683
 PIA  CA1   C  CH1    0  -0.211  -2.0500  -2.2477  -0.5942
 PIA  CB1   C  CH3    0  -0.592  -2.5535  -2.6142   0.8077
 PIA  C1    C  CR5    0   0.606  -1.3882  -0.9052  -0.5466
 PIA  N2    N  N      0  -0.445  -0.1161  -0.7532  -0.3958
 PIA  N3    N  NR5    0  -0.543  -2.0898   0.2764  -0.6219
 PIA  C2    C  CR5    0   0.569  -1.1947   1.3096  -0.4687
 PIA  O2    O  O      0  -0.570  -1.4651   2.4949  -0.4736
 PIA  CA2   C  CR5    0   0.004   0.1060   0.6157  -0.3381
 PIA  CA3   C  CH2    0  -0.481  -3.5137   0.4890  -0.6492
 PIA  C3    C  C      0   0.292  -4.1105   0.8504   0.7319
 PIA  O3    O  O      0  -0.658  -3.3593   0.7694   1.7159
 PIA  CB2   C  C1     0  -0.303   1.2743   1.2716  -0.1938
 PIA  CG2   C  CR6    0   0.148   2.6163   0.7473  -0.0690
 PIA  CD1   C  CR16   0  -0.268   2.9367  -0.6199  -0.0974
 PIA  CD2   C  CR16   0  -0.253   3.6705   1.6561   0.0848
 PIA  CE1   C  CR16   0  -0.281   4.2416  -1.0500   0.0234
 PIA  CE2   C  CR16   0  -0.351   4.9815   1.2364   0.2071
 PIA  CZ    C  CR6    0   0.381   5.2777  -0.1252   0.1772
 PIA  OH    O  OH1    0  -0.584   6.5278  -0.5986   0.2888
 PIA  O31   O  OC    -1  -0.481  -5.3108   1.1766   0.7011
 PIA  HN11  H  HNH2   0   0.339  -0.3160  -3.2963  -0.5684
 PIA  HN12  H  HNH2   0   0.346  -1.5735  -4.1195  -1.1712
 PIA  HA1   H  HCH1   0   0.238  -2.9130  -2.1869  -1.2635
 PIA  HB11  H  HCH3   0   0.235  -1.7123  -2.7167   1.4953
 PIA  HB12  H  HCH3   0   0.177  -3.2306  -1.8670   1.2198
 PIA  HB13  H  HCH3   0   0.251  -3.0806  -3.5682   0.7691
 PIA  HA31  H  HCH2   0   0.230  -3.7341   1.2840  -1.3635
 PIA  HA32  H  HCH2   0   0.290  -4.0038  -0.4070  -1.0322
 PIA  HB2   H  H      0   0.199   1.1947   2.3544  -0.1693
 PIA  HD1   H  HCR6   0   0.284   2.1488  -1.3499  -0.2151
 PIA  HD2   H  HCR6   0   0.220   3.4594   2.7184   0.1087
 PIA  HE1   H  HCR6   0   0.259   4.4691  -2.1085  -0.0010
 PIA  HE2   H  HCR6   0   0.236   5.7737   1.9665   0.3240
 PIA  HH    H  HOH1   0   0.448   7.1575   0.1247   0.3896

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
 PIA  N1   CA1   single    1.452  0.020  1.452
 PIA  N1   HN11  single    0.890  0.020  1.040
 PIA  N1   HN12  single    0.890  0.020  1.040
 PIA  CA1  CB1   single    1.534  0.020  1.534
 PIA  CA1  C1    single    1.498  0.020  1.498
 PIA  CA1  HA1   single    0.970  0.020  1.090
 PIA  CB1  HB11  single    0.970  0.020  1.090
 PIA  CB1  HB12  single    0.970  0.020  1.090
 PIA  CB1  HB13  single    0.970  0.020  1.090
 PIA  C1   N2    double    1.290  0.020  1.290
 PIA  C1   N3    single    1.376  0.020  1.376
 PIA  N2   CA2   single    1.388  0.020  1.388
 PIA  N3   C2    single    1.376  0.020  1.376
 PIA  N3   CA3   single    1.440  0.020  1.440
 PIA  C2   O2    double    1.216  0.020  1.216
 PIA  C2   CA2   single    1.480  0.020  1.480
 PIA  CA2  CB2   double    1.348  0.020  1.348
 PIA  CA3  C3    single    1.547  0.020  1.547
 PIA  CA3  HA31  single    0.970  0.020  1.090
 PIA  CA3  HA32  single    0.970  0.020  1.090
 PIA  C3   O3    deloc     1.241  0.020  1.241
 PIA  C3   O31   deloc     1.244  0.020  1.244
 PIA  CB2  CG2   single    1.446  0.020  1.446
 PIA  CB2  HB2   single    0.930  0.020  1.080
 PIA  CG2  CD1   aromatic  1.404  0.020  1.404
 PIA  CG2  CD2   aromatic  1.400  0.020  1.400
 PIA  CD1  CE1   aromatic  1.379  0.020  1.379
 PIA  CD1  HD1   single    0.930  0.020  1.080
 PIA  CD2  CE2   aromatic  1.382  0.020  1.382
 PIA  CD2  HD2   single    0.930  0.020  1.080
 PIA  CE1  CZ    aromatic  1.397  0.020  1.397
 PIA  CE1  HE1   single    0.930  0.020  1.080
 PIA  CE2  CZ    aromatic  1.394  0.020  1.394
 PIA  CE2  HE2   single    0.930  0.020  1.080
 PIA  CZ   OH    single    1.341  0.020  1.341
 PIA  OH   HH    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
 PIA  HN12  N1   HN11  106.17  3.000
 PIA  HN12  N1   CA1   108.47  3.000
 PIA  HN11  N1   CA1   109.34  3.000
 PIA  HA1   CA1  C1    108.55  3.000
 PIA  HA1   CA1  CB1   108.27  3.000
 PIA  C1    CA1  CB1   109.28  3.000
 PIA  HA1   CA1  N1    107.23  3.000
 PIA  C1    CA1  N1    109.04  3.000
 PIA  CB1   CA1  N1    114.30  3.000
 PIA  HB13  CB1  HB12  108.25  3.000
 PIA  HB13  CB1  HB11  108.23  3.000
 PIA  HB12  CB1  HB11  107.77  3.000
 PIA  HB13  CB1  CA1   109.59  3.000
 PIA  HB12  CB1  CA1   112.70  3.000
 PIA  HB11  CB1  CA1   110.19  3.000
 PIA  N3    C1   N2    114.07  3.000
 PIA  N3    C1   CA1   122.87  3.000
 PIA  N2    C1   CA1   123.03  3.000
 PIA  CA2   N2   C1    106.19  3.000
 PIA  CA3   N3   C2    122.33  3.000
 PIA  CA3   N3   C1    129.18  3.000
 PIA  C2    N3   C1    107.88  3.000
 PIA  CA2   C2   O2    130.77  3.000
 PIA  CA2   C2   N3    103.27  3.000
 PIA  O2    C2   N3    125.95  3.000
 PIA  CB2   CA2  C2    122.90  3.000
 PIA  CB2   CA2  N2    128.55  3.000
 PIA  C2    CA2  N2    108.55  3.000
 PIA  HA32  CA3  HA31  106.13  3.000
 PIA  HA32  CA3  C3    109.39  3.000
 PIA  HA31  CA3  C3    109.64  3.000
 PIA  HA32  CA3  N3    109.25  3.000
 PIA  HA31  CA3  N3    108.64  3.000
 PIA  C3    CA3  N3    113.51  3.000
 PIA  O31   C3   O3    128.38  3.000
 PIA  O31   C3   CA3   114.28  3.000
 PIA  O3    C3   CA3   117.33  3.000
 PIA  HB2   CB2  CG2   115.31  3.000
 PIA  HB2   CB2  CA2   115.10  3.000
 PIA  CG2   CB2  CA2   129.59  3.000
 PIA  CD2   CG2  CD1   117.53  3.000
 PIA  CD2   CG2  CB2   118.22  3.000
 PIA  CD1   CG2  CB2   124.25  3.000
 PIA  HD1   CD1  CE1   119.26  3.000
 PIA  HD1   CD1  CG2   119.57  3.000
 PIA  CE1   CD1  CG2   121.17  3.000
 PIA  HD2   CD2  CE2   118.73  3.000
 PIA  HD2   CD2  CG2   119.48  3.000
 PIA  CE2   CD2  CG2   121.79  3.000
 PIA  HE1   CE1  CZ    119.58  3.000
 PIA  HE1   CE1  CD1   120.10  3.000
 PIA  CZ    CE1  CD1   120.32  3.000
 PIA  HE2   CE2  CZ    120.34  3.000
 PIA  HE2   CE2  CD2   119.90  3.000
 PIA  CZ    CE2  CD2   119.76  3.000
 PIA  OH    CZ   CE2   122.75  3.000
 PIA  OH    CZ   CE1   117.82  3.000
 PIA  CE2   CZ   CE1   119.43  3.000
 PIA  HH    OH   CZ    110.64  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
 PIA  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 PIA  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 PIA  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 PIA  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PIA  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 PIA  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PIA  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 PIA  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 PIA  CONST_09  C2   N3   C1   N2     0.00   0.0  0
 PIA  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 PIA  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 PIA  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 PIA  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 PIA  CONST_14  OH   CZ   CE1  CD1  180.00   0.0  0
 PIA  CONST_15  OH   CZ   CE2  CD2  180.00   0.0  0
 PIA  CONST_16  CA2  N2   C1   CA1  180.00   0.0  0
 PIA  CONST_17  C2   N3   C1   CA1  180.00   0.0  0
 PIA  CONST_18  O2   C2   N3   C1   180.00   0.0  0
 PIA  CONST_19  CA3  N3   C1   N2   180.00   0.0  0
 PIA  CONST_20  CA3  N3   C2   CA2  180.00   0.0  0
 PIA  CONST_21  HE1  CE1  CD1  CG2  180.00   0.0  0
 PIA  CONST_22  HE2  CE2  CD2  CG2  180.00   0.0  0
 PIA  CONST_23  HD2  CD2  CG2  CD1  180.00   0.0  0
 PIA  CONST_24  HD1  CD1  CG2  CD2  180.00   0.0  0
 PIA  CONST_25  CA3  N3   C1   CA1    0.00   0.0  0
 PIA  CONST_26  CA3  N3   C2   O2     0.00   0.0  0
 PIA  Var_01    CG2  CB2  CA2  N2     0.51  30.0  2
 PIA  Var_02    CD1  CG2  CB2  CA2    0.90  30.0  2
 PIA  Var_03    C3   CA3  N3   C1    97.78  30.0  3
 PIA  Var_04    O3   C3   CA3  N3    -8.02  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
 PIA  chir_01  CA1  N1  CB1  C1  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
 PIA  plan-1  CA1  0.020
 PIA  plan-1  C1   0.020
 PIA  plan-1  N2   0.020
 PIA  plan-1  N3   0.020
 PIA  plan-1  C2   0.020
 PIA  plan-1  O2   0.020
 PIA  plan-1  CA2  0.020
 PIA  plan-1  CA3  0.020
 PIA  plan-1  CB2  0.020
 PIA  plan-2  CB2  0.020
 PIA  plan-2  CG2  0.020
 PIA  plan-2  CD1  0.020
 PIA  plan-2  CD2  0.020
 PIA  plan-2  CE1  0.020
 PIA  plan-2  CE2  0.020
 PIA  plan-2  CZ   0.020
 PIA  plan-2  OH   0.020
 PIA  plan-2  HD1  0.020
 PIA  plan-2  HD2  0.020
 PIA  plan-2  HE1  0.020
 PIA  plan-2  HE2  0.020
 PIA  plan-3  CA3  0.020
 PIA  plan-3  C3   0.020
 PIA  plan-3  O3   0.020
 PIA  plan-3  O31  0.020

