# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 04:38:43 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: {(4Z)-2-[(1S)-1-aminoethyl]-4-[(3-chloro-4-hydroxyphenyl)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](N)C1=N\C(=C/c2ccc(O)c(Cl)c2)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
 OHD  OHD  '{(4Z)-2-[(1S)-1-aminoethyl]-4-[(3-chloro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  36  22  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OHD
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
 OHD  N1   N   NH2   0  -0.764  -1.0451   3.1307   1.1516
 OHD  CA1  C   CH1   0  -0.214  -2.1081   2.2669   0.6905
 OHD  CB1  C   CH3   0  -0.657  -2.6666   2.7969  -0.6307
 OHD  C1   C   CR5   0   0.535  -1.6775   0.8337   0.5227
 OHD  N2   N   N     0  -0.487  -0.4491   0.4718   0.3943
 OHD  N3   N   NR5   0  -0.563  -2.5667  -0.2237   0.4807
 OHD  C2   C   CR5   0   0.545  -1.8478  -1.3873   0.2888
 OHD  O2   O   O     0  -0.442  -2.3205  -2.5009   0.2032
 OHD  CA2  C   CR5   0   0.098  -0.4511  -0.9079   0.2406
 OHD  CA3  C   CH2   0  -0.464  -3.9950  -0.2136   0.5772
 OHD  C3   C   C     0   0.548  -4.6452  -0.4598  -0.7689
 OHD  O3   O   O     0  -0.426  -4.0529  -0.4857  -1.8140
 OHD  CB2  C   C1    0  -0.381   0.6057  -1.7277   0.0807
 OHD  CG2  C   CR6   0   0.125   2.0135  -1.3981   0.0285
 OHD  CD1  C   CR16  0  -0.279   2.9364  -2.4373  -0.1501
 OHD  CD2  C   CR16  0  -0.271   2.5087  -0.0939   0.1498
 OHD  CE1  C   CR16  0  -0.336   4.2934  -2.1977  -0.2065
 OHD  CE2  C   CR6   0  -0.139   3.8656   0.1387   0.0924
 OHD  CZ   C   CR6   0   0.424   4.7871  -0.9000  -0.0852
 OHD  OH   O   OH1   0  -0.600   6.1063  -0.7142  -0.1445
 OHD  CL   CL  CL    0  -0.107   4.4669   1.7596   0.2419
 OHD  O1   O   OH1   0  -0.584  -5.9491  -0.6287  -0.6334
 OHD  H1   H   HNH2  0   0.353  -0.6881   2.7981   2.0388
 OHD  H2   H   HNH2  0   0.347  -0.2653   3.0874   0.5058
 OHD  H4   H   HCH1  0   0.271  -2.9047   2.2968   1.4407
 OHD  H5   H   HCH3  0   0.238  -1.9011   2.7716  -1.4075
 OHD  H6   H   HCH3  0   0.234  -3.5186   2.2202  -0.9856
 OHD  H7   H   HCH3  0   0.253  -2.9916   3.8279  -0.4997
 OHD  H9   H   HCH2  0   0.323  -4.3265  -0.9729   1.2883
 OHD  H10  H   HCH2  0   0.329  -4.3426   0.7422   0.9718
 OHD  H11  H   H     0   0.272   0.3704  -2.7825  -0.0211
 OHD  H13  H   HCR6  0   0.270   2.5805  -3.4552  -0.2478
 OHD  H14  H   HCR6  0   0.301   1.8276   0.7340   0.2871
 OHD  H15  H   HCR6  0   0.283   4.9906  -3.0140  -0.3446
 OHD  H16  H   HOH1  0   0.474   6.3367   0.2194  -0.0460
 OHD  H17  H   HOH1  0   0.489  -6.3639  -0.7736  -1.4974

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
 OHD  O2   C2   double    1.213  0.020  1.213
 OHD  O3   C3   double    1.202  0.020  1.202
 OHD  C3   CA3  single    1.515  0.020  1.515
 OHD  C2   CA2  single    1.477  0.020  1.477
 OHD  C2   N3   single    1.381  0.020  1.381
 OHD  CL   CE2  single    1.735  0.020  1.735
 OHD  CB2  CA2  double    1.347  0.020  1.347
 OHD  CB2  CG2  single    1.447  0.020  1.447
 OHD  CD2  CE2  aromatic  1.378  0.020  1.378
 OHD  CD2  CG2  aromatic  1.400  0.020  1.400
 OHD  CA3  N3   single    1.432  0.020  1.432
 OHD  CA2  N2   single    1.388  0.020  1.388
 OHD  N3   C1   single    1.382  0.020  1.382
 OHD  CE2  CZ   aromatic  1.400  0.020  1.400
 OHD  CG2  CD1  aromatic  1.401  0.020  1.401
 OHD  N2   C1   double    1.287  0.020  1.287
 OHD  C1   CA1  single    1.506  0.020  1.506
 OHD  CZ   OH   single    1.334  0.020  1.334
 OHD  CZ   CE1  aromatic  1.394  0.020  1.394
 OHD  CD1  CE1  aromatic  1.379  0.020  1.379
 OHD  CA1  N1   single    1.445  0.020  1.445
 OHD  CA1  CB1  single    1.529  0.020  1.529
 OHD  C3   O1   single    1.322  0.020  1.322
 OHD  N1   H1   single    0.890  0.020  1.040
 OHD  N1   H2   single    0.890  0.020  1.040
 OHD  CA1  H4   single    0.970  0.020  1.090
 OHD  CB1  H5   single    0.970  0.020  1.090
 OHD  CB1  H6   single    0.970  0.020  1.090
 OHD  CB1  H7   single    0.970  0.020  1.090
 OHD  CA3  H9   single    0.970  0.020  1.090
 OHD  CA3  H10  single    0.970  0.020  1.090
 OHD  CB2  H11  single    0.930  0.020  1.080
 OHD  CD1  H13  single    0.930  0.020  1.080
 OHD  CD2  H14  single    0.930  0.020  1.080
 OHD  CE1  H15  single    0.930  0.020  1.080
 OHD  OH   H16  single    0.850  0.020  0.980
 OHD  O1   H17  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
 OHD  H2   N1   H1   105.85  3.000
 OHD  H2   N1   CA1  109.70  3.000
 OHD  H1   N1   CA1  110.04  3.000
 OHD  H4   CA1  C1   108.08  3.000
 OHD  H4   CA1  CB1  108.48  3.000
 OHD  C1   CA1  CB1  109.76  3.000
 OHD  H4   CA1  N1   107.48  3.000
 OHD  CB1  CA1  N1   109.70  3.000
 OHD  C1   CA1  N1   113.20  3.000
 OHD  H7   CB1  H6   107.89  3.000
 OHD  H7   CB1  H5   108.48  3.000
 OHD  H6   CB1  H5   107.75  3.000
 OHD  H7   CB1  CA1  109.47  3.000
 OHD  H6   CB1  CA1  112.58  3.000
 OHD  H5   CB1  CA1  110.55  3.000
 OHD  N3   C1   N2   113.32  3.000
 OHD  N2   C1   CA1  123.48  3.000
 OHD  N3   C1   CA1  123.20  3.000
 OHD  CA2  N2   C1   106.81  3.000
 OHD  CA3  N3   C2   122.32  3.000
 OHD  CA3  N3   C1   129.38  3.000
 OHD  C2   N3   C1   108.29  3.000
 OHD  CA2  C2   O2   131.61  3.000
 OHD  CA2  C2   N3   102.90  3.000
 OHD  O2   C2   N3   125.49  3.000
 OHD  CB2  CA2  C2   123.24  3.000
 OHD  CB2  CA2  N2   128.09  3.000
 OHD  C2   CA2  N2   108.67  3.000
 OHD  H10  CA3  H9   106.08  3.000
 OHD  H10  CA3  C3   109.09  3.000
 OHD  H9   CA3  C3   109.60  3.000
 OHD  H10  CA3  N3   110.39  3.000
 OHD  H9   CA3  N3   110.00  3.000
 OHD  C3   CA3  N3   111.54  3.000
 OHD  O1   C3   O3   124.94  3.000
 OHD  O1   C3   CA3  110.67  3.000
 OHD  O3   C3   CA3  124.39  3.000
 OHD  H11  CB2  CG2  115.40  3.000
 OHD  H11  CB2  CA2  115.63  3.000
 OHD  CG2  CB2  CA2  128.98  3.000
 OHD  CD2  CG2  CD1  117.95  3.000
 OHD  CD1  CG2  CB2  118.46  3.000
 OHD  CD2  CG2  CB2  123.59  3.000
 OHD  H13  CD1  CE1  118.89  3.000
 OHD  H13  CD1  CG2  119.48  3.000
 OHD  CE1  CD1  CG2  121.63  3.000
 OHD  H14  CD2  CE2  119.77  3.000
 OHD  H14  CD2  CG2  120.10  3.000
 OHD  CE2  CD2  CG2  120.13  3.000
 OHD  H15  CE1  CZ   119.03  3.000
 OHD  H15  CE1  CD1  120.53  3.000
 OHD  CZ   CE1  CD1  120.44  3.000
 OHD  CL   CE2  CZ   118.42  3.000
 OHD  CZ   CE2  CD2  121.89  3.000
 OHD  CL   CE2  CD2  119.69  3.000
 OHD  OH   CZ   CE2  123.60  3.000
 OHD  OH   CZ   CE1  118.44  3.000
 OHD  CE2  CZ   CE1  117.96  3.000
 OHD  H16  OH   CZ   111.46  3.000
 OHD  H17  O1   C3   110.48  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
 OHD  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 OHD  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 OHD  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 OHD  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 OHD  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 OHD  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 OHD  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 OHD  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 OHD  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 OHD  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 OHD  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 OHD  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 OHD  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 OHD  CONST_14  CL   CE2  CD2  CG2  180.00   0.0  0
 OHD  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 OHD  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 OHD  CONST_17  CL   CE2  CZ   CE1  180.00   0.0  0
 OHD  CONST_18  C2   N3   C1   CA1  180.00   0.0  0
 OHD  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 OHD  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 OHD  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 OHD  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 OHD  CONST_23  H15  CE1  CD1  CG2  180.00   0.0  0
 OHD  CONST_24  H14  CD2  CG2  CD1  180.00   0.0  0
 OHD  CONST_25  H13  CD1  CG2  CD2  180.00   0.0  0
 OHD  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 OHD  CONST_27  CA3  N3   C2   O2     0.00   0.0  0
 OHD  CONST_28  H17  O1   C3   CA3  180.00   0.0  0
 OHD  Var_01    CG2  CB2  CA2  N2     0.11  30.0  2
 OHD  Var_02    CD2  CG2  CB2  CA2    0.26  30.0  2
 OHD  Var_03    C3   CA3  N3   C1   105.70  30.0  3
 OHD  Var_04    O3   C3   CA3  N3    -9.11  30.0  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
 OHD  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
 OHD  plan-1  CA1  0.020
 OHD  plan-1  C1   0.020
 OHD  plan-1  N2   0.020
 OHD  plan-1  N3   0.020
 OHD  plan-1  C2   0.020
 OHD  plan-1  O2   0.020
 OHD  plan-1  CA2  0.020
 OHD  plan-1  CA3  0.020
 OHD  plan-1  CB2  0.020
 OHD  plan-2  CB2  0.020
 OHD  plan-2  CG2  0.020
 OHD  plan-2  CD1  0.020
 OHD  plan-2  CD2  0.020
 OHD  plan-2  CE1  0.020
 OHD  plan-2  CE2  0.020
 OHD  plan-2  CZ   0.020
 OHD  plan-2  OH   0.020
 OHD  plan-2  CL   0.020
 OHD  plan-2  H13  0.020
 OHD  plan-2  H14  0.020
 OHD  plan-2  H15  0.020
 OHD  plan-3  CA3  0.020
 OHD  plan-3  C3   0.020
 OHD  plan-3  O3   0.020
 OHD  plan-3  O1   0.020
 OHD  plan-3  H17  0.020

