# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 21:44:00 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-dichloro-4-oxocyclohexa-2,5-dien-1-yl)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/C2C=C(Cl)C(=O)C(=C2)Cl)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
 4NU  4NU  "{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-dichloro-4-oxocyclohexa-2,5-dien-1-yl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid"  L-peptide  39  25  .  2022-09-15  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_4NU
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
 4NU  N1   N   NH2    0  -0.787  -2.6943   3.0406   0.8279
 4NU  CA1  C   CH1    0  -0.248  -3.3515   1.7863   0.5298
 4NU  CB1  C   CH1    0   0.010  -4.0995   1.7294  -0.8319
 4NU  CG1  C   CH3    0  -0.698  -5.2656   2.7043  -0.8562
 4NU  OG1  O   OH1    0  -0.656  -3.2108   1.9373  -1.9045
 4NU  C1   C   CR5    0   0.586  -2.3373   0.6892   0.5727
 4NU  N2   N   N      0  -0.487  -1.0822   0.8780   0.3492
 4NU  N3   N   NR5    0  -0.540  -2.6771  -0.6225   0.8323
 4NU  C2   C   CR5    0   0.541  -1.5386  -1.3823   0.7355
 4NU  O2   O   O      0  -0.434  -1.4528  -2.5792   0.8964
 4NU  CA2  C   CR5    0   0.110  -0.4860  -0.3717   0.4352
 4NU  CA3  C   CH2    0  -0.479  -3.9765  -1.2041   1.0586
 4NU  C3   C   C      0   0.424  -4.5540  -1.9357  -0.1761
 4NU  O3   O   O      0  -0.585  -3.9574  -1.7894  -1.2538
 4NU  CB2  C   C1     0  -0.282   0.8125  -0.6463   0.3015
 4NU  CG2  C   CR16   0  -0.484   1.8565   0.4078   0.0384
 4NU  CD1  C   CR16   0  -0.116   2.5688   0.0869  -1.2279
 4NU  CD2  C   CR16   0  -0.117   2.7385   0.5081   1.2335
 4NU  CE1  C   CR6    0  -0.162   3.8763  -0.1661  -1.2645
 4NU  CE2  C   CR6    0  -0.161   4.0442   0.2496   1.1789
 4NU  CZ   C   CR6    0   0.502   4.7380  -0.1225  -0.0681
 4NU  O4   O   O      0  -0.363   5.9212  -0.3658  -0.1076
 4NU  CL1  CL  CL     0  -0.083   4.6845  -0.5563  -2.7345
 4NU  CL2  CL  CL     0  -0.082   5.0474   0.3467   2.5754
 4NU  H1   H   HNH2   0   0.348  -1.9550   3.2302   0.1642
 4NU  H2   H   HNH2   0   0.360  -3.3528   3.8064   0.7870
 4NU  H4   H   HCH1   0   0.270  -4.0947   1.6051   1.3139
 4NU  H5   H   HCH1   0   0.250  -4.4856   0.7177  -0.9710
 4NU  H6   H   HCH3   0   0.221  -4.9310   3.7412  -0.7736
 4NU  H7   H   HCH3   0   0.250  -5.8213   2.6123  -1.7893
 4NU  H8   H   HCH3   0   0.236  -5.9563   2.5104  -0.0350
 4NU  H9   H   HOH1   0   0.439  -2.9344   2.8599  -1.9012
 4NU  H10  H   HCH2   0   0.273  -3.9054  -1.8975   1.8982
 4NU  H11  H   HCH2   0   0.274  -4.6658  -0.4191   1.3721
 4NU  OXT  O   OC    -1  -0.608  -5.5868  -2.5895   0.0540
 4NU  H15  H   H      0   0.301   1.1546  -1.6705   0.3996
 4NU  H16  H   HCR6   0   0.341   1.3425   1.3692  -0.0887
 4NU  H17  H   HCR6   0   0.318   1.9700   0.0477  -2.1290
 4NU  H18  H   HCR6   0   0.318   2.2662   0.7851   2.1675

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
 4NU  O3   C3   deloc   1.240  0.020  1.240
 4NU  O2   C2   double  1.211  0.020  1.211
 4NU  CA3  C3   single  1.547  0.020  1.547
 4NU  CA3  N3   single  1.442  0.020  1.442
 4NU  C2   N3   single  1.372  0.020  1.372
 4NU  C2   CA2  single  1.490  0.020  1.490
 4NU  N3   C1   single  1.380  0.020  1.380
 4NU  N1   CA1  single  1.447  0.020  1.447
 4NU  CA2  CB2  double  1.334  0.020  1.334
 4NU  CA2  N2   single  1.387  0.020  1.387
 4NU  CB2  CG2  single  1.507  0.020  1.507
 4NU  C1   CA1  single  1.495  0.020  1.495
 4NU  C1   N2   double  1.289  0.020  1.289
 4NU  CA1  CB1  single  1.555  0.020  1.555
 4NU  CD2  CG2  single  1.489  0.020  1.489
 4NU  CD2  CE2  double  1.332  0.020  1.332
 4NU  CG2  CD1  single  1.488  0.020  1.488
 4NU  CL2  CE2  single  1.722  0.020  1.722
 4NU  CE2  CZ   single  1.475  0.020  1.475
 4NU  CD1  CE1  double  1.332  0.020  1.332
 4NU  CB1  OG1  single  1.408  0.020  1.408
 4NU  CB1  CG1  single  1.520  0.020  1.520
 4NU  CZ   CE1  single  1.475  0.020  1.475
 4NU  CZ   O4   double  1.209  0.020  1.209
 4NU  CE1  CL1  single  1.722  0.020  1.722
 4NU  N1   H1   single  0.890  0.020  1.040
 4NU  N1   H2   single  0.890  0.020  1.040
 4NU  CA1  H4   single  0.970  0.020  1.090
 4NU  CB1  H5   single  0.970  0.020  1.090
 4NU  CG1  H6   single  0.970  0.020  1.090
 4NU  CG1  H7   single  0.970  0.020  1.090
 4NU  CG1  H8   single  0.970  0.020  1.090
 4NU  OG1  H9   single  0.850  0.020  0.980
 4NU  CA3  H10  single  0.970  0.020  1.090
 4NU  CA3  H11  single  0.970  0.020  1.090
 4NU  C3   OXT  deloc   1.244  0.020  1.244
 4NU  CB2  H15  single  0.930  0.020  1.080
 4NU  CG2  H16  single  0.970  0.020  1.090
 4NU  CD1  H17  single  0.930  0.020  1.080
 4NU  CD2  H18  single  0.930  0.020  1.080

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
 4NU  H2   N1   H1   107.91  3.000
 4NU  H2   N1   CA1  110.64  3.000
 4NU  H1   N1   CA1  111.06  3.000
 4NU  H4   CA1  C1   108.57  3.000
 4NU  H4   CA1  CB1  107.13  3.000
 4NU  C1   CA1  CB1  108.95  3.000
 4NU  H4   CA1  N1   107.70  3.000
 4NU  CB1  CA1  N1   115.51  3.000
 4NU  C1   CA1  N1   108.79  3.000
 4NU  H5   CB1  OG1  105.24  3.000
 4NU  H5   CB1  CG1  108.72  3.000
 4NU  OG1  CB1  CG1  112.16  3.000
 4NU  H5   CB1  CA1  108.40  3.000
 4NU  CG1  CB1  CA1  111.08  3.000
 4NU  OG1  CB1  CA1  110.98  3.000
 4NU  H8   CG1  H7   107.87  3.000
 4NU  H8   CG1  H6   107.80  3.000
 4NU  H7   CG1  H6   107.51  3.000
 4NU  H8   CG1  CB1  111.09  3.000
 4NU  H7   CG1  CB1  110.53  3.000
 4NU  H6   CG1  CB1  111.86  3.000
 4NU  H9   OG1  CB1  108.66  3.000
 4NU  N3   C1   N2   114.32  3.000
 4NU  N2   C1   CA1  123.25  3.000
 4NU  N3   C1   CA1  122.42  3.000
 4NU  CA2  N2   C1   106.01  3.000
 4NU  CA3  N3   C2   122.38  3.000
 4NU  C2   N3   C1   107.99  3.000
 4NU  CA3  N3   C1   129.44  3.000
 4NU  CA2  C2   O2   130.34  3.000
 4NU  CA2  C2   N3   102.99  3.000
 4NU  O2   C2   N3   126.64  3.000
 4NU  CB2  CA2  C2   124.64  3.000
 4NU  CB2  CA2  N2   126.69  3.000
 4NU  C2   CA2  N2   108.66  3.000
 4NU  H11  CA3  H10  106.10  3.000
 4NU  H11  CA3  C3   109.51  3.000
 4NU  H10  CA3  C3   109.75  3.000
 4NU  H11  CA3  N3   108.92  3.000
 4NU  H10  CA3  N3   108.56  3.000
 4NU  C3   CA3  N3   113.71  3.000
 4NU  OXT  C3   O3   128.47  3.000
 4NU  OXT  C3   CA3  114.26  3.000
 4NU  O3   C3   CA3  117.26  3.000
 4NU  H15  CB2  CG2  117.26  3.000
 4NU  H15  CB2  CA2  119.50  3.000
 4NU  CG2  CB2  CA2  123.23  3.000
 4NU  H16  CG2  CD2  108.14  3.000
 4NU  H16  CG2  CD1  108.33  3.000
 4NU  CD2  CG2  CD1  114.46  3.000
 4NU  H16  CG2  CB2  107.97  3.000
 4NU  CD1  CG2  CB2  109.24  3.000
 4NU  CD2  CG2  CB2  108.51  3.000
 4NU  H17  CD1  CE1  120.87  3.000
 4NU  H17  CD1  CG2  116.83  3.000
 4NU  CE1  CD1  CG2  122.29  3.000
 4NU  H18  CD2  CE2  120.83  3.000
 4NU  H18  CD2  CG2  116.83  3.000
 4NU  CE2  CD2  CG2  122.32  3.000
 4NU  CL1  CE1  CZ   115.14  3.000
 4NU  CL1  CE1  CD1  121.80  3.000
 4NU  CZ   CE1  CD1  123.05  3.000
 4NU  CL2  CE2  CZ   115.21  3.000
 4NU  CZ   CE2  CD2  123.00  3.000
 4NU  CL2  CE2  CD2  121.79  3.000
 4NU  O4   CZ   CE2  122.61  3.000
 4NU  O4   CZ   CE1  122.64  3.000
 4NU  CE2  CZ   CE1  114.74  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
 4NU  CONST_01  CA2  C2   N3   C1      0.00   0.0  0
 4NU  CONST_02  C2   CA2  N2   C1      0.00   0.0  0
 4NU  CONST_03  N3   C2   CA2  N2      0.00   0.0  0
 4NU  CONST_04  C2   N3   C1   N2      0.00   0.0  0
 4NU  CONST_05  CA2  N2   C1   N3      0.00   0.0  0
 4NU  CONST_06  C2   N3   C1   CA1   180.00   0.0  0
 4NU  CONST_07  CA2  N2   C1   CA1   180.00   0.0  0
 4NU  CONST_08  O2   C2   N3   C1    180.00   0.0  0
 4NU  CONST_09  CA3  N3   C1   N2    180.00   0.0  0
 4NU  CONST_10  CA3  N3   C2   CA2   180.00   0.0  0
 4NU  CONST_11  CA3  N3   C1   CA1     0.00   0.0  0
 4NU  CONST_12  CA3  N3   C2   O2      0.00   0.0  0
 4NU  Var_01    CZ   CE2  CD2  CG2     1.65  30.0  1
 4NU  Var_02    CZ   CE1  CD1  CG2    -1.40  30.0  1
 4NU  Var_03    CE2  CZ   CE1  CD1    -1.10  30.0  1
 4NU  Var_04    CE1  CZ   CE2  CD2     0.96  30.0  1
 4NU  Var_05    CG2  CB2  CA2  N2      0.52   0.0  2
 4NU  Var_06    CG2  CB2  CA2  C2   -178.09   0.0  2
 4NU  Var_07    CL2  CE2  CD2  CG2  -179.05  30.0  1
 4NU  Var_08    CL1  CE1  CD1  CG2   179.19  30.0  1
 4NU  Var_09    O4   CZ   CE1  CD1   179.28  30.0  1
 4NU  Var_10    O4   CZ   CE2  CD2  -179.41  30.0  1
 4NU  Var_11    CL2  CE2  CZ   CE1  -178.38  30.0  1
 4NU  Var_12    CL1  CE1  CZ   CE2   178.35  30.0  1
 4NU  Var_13    H18  CD2  CE2  CZ   -179.57  30.0  1
 4NU  Var_14    H17  CD1  CE1  CZ    179.82  30.0  1
 4NU  Var_15    C3   CA3  N3   C1    101.08  30.0  2
 4NU  Var_16    C3   CA3  N3   C2    -73.18  30.0  2
 4NU  Var_17    CL2  CE2  CZ   O4      1.25  30.0  1
 4NU  Var_18    CL1  CE1  CZ   O4     -1.27  30.0  1
 4NU  Var_19    H15  CB2  CA2  N2    179.50   0.0  2
 4NU  Var_20    H15  CB2  CA2  C2      0.88   0.0  2
 4NU  Var_21    H10  CA3  N3   C1   -136.45  30.0  2
 4NU  Var_22    H11  CA3  N3   C1    -21.33  30.0  2
 4NU  Var_23    H10  CA3  N3   C2     49.29  30.0  2
 4NU  Var_24    H11  CA3  N3   C2    164.40  30.0  2
 4NU  Var_25    H17  CD1  CE1  CL1     0.41  30.0  1
 4NU  Var_26    H18  CD2  CE2  CL2    -0.27  30.0  1
 4NU  Var_27    O3   C3   CA3  N3     -9.95  30.0  3
 4NU  Var_28    OXT  C3   CA3  N3    170.98  30.0  3
 4NU  Var_29    H10  CA3  C3   O3   -131.76  30.0  3
 4NU  Var_30    H11  CA3  C3   O3    112.14  30.0  3
 4NU  Var_31    OXT  C3   CA3  H10    49.17  30.0  3
 4NU  Var_32    OXT  C3   CA3  H11   -66.93  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
 4NU  chir_01  CA1  N1   C1   CB1  positiv
 4NU  chir_02  CB1  OG1  CA1  CG1  negativ
 4NU  chir_03  CG2  CB2  CD2  CD1  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
 4NU  plan-1  CA1  0.020
 4NU  plan-1  C1   0.020
 4NU  plan-1  N2   0.020
 4NU  plan-1  N3   0.020
 4NU  plan-1  C2   0.020
 4NU  plan-1  O2   0.020
 4NU  plan-1  CA2  0.020
 4NU  plan-1  CA3  0.020
 4NU  plan-1  CB2  0.020
 4NU  plan-1  CG2  0.020
 4NU  plan-1  H15  0.020
 4NU  plan-2  CE1  0.020
 4NU  plan-2  CE2  0.020
 4NU  plan-2  CZ   0.020
 4NU  plan-2  O4   0.020
 4NU  plan-3  CA3  0.020
 4NU  plan-3  C3   0.020
 4NU  plan-3  O3   0.020
 4NU  plan-3  OXT  0.020

