# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 22:07:05 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[2-[(1~{S})-1-azanyl-2-(1~{H}-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]cn1)C2=NC(=C\c3ccc(O)cc3)/C(=O)N2CC(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
 5SQ  5SQ  "2-[2-[(1S)-1-azanyl-2-(1H-imidazol-4-yl)ethyl]-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid"  L-peptide  42  26  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5SQ
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
 5SQ  C1   C  CR5    0   0.531   0.5539   0.2644   0.6489
 5SQ  C2   C  CR5    0   0.531  -0.3523   2.2708   0.3211
 5SQ  O    O  O      0  -0.589   2.0236   2.2598  -1.7305
 5SQ  C    C  C      0   0.422   2.6110   2.7198  -0.7380
 5SQ  CA3  C  CH2    0  -0.473   2.0916   2.2909   0.6549
 5SQ  N3   N  NR5    0  -0.539   0.8213   1.6136   0.6089
 5SQ  O2   O  O      0  -0.458  -0.4848   3.4727   0.1961
 5SQ  CA1  C  CH1    0  -0.216   1.6133  -0.7781   0.8728
 5SQ  N    N  NH2    0  -0.765   1.1040  -1.9955   1.4613
 5SQ  CB1  C  CH2    0  -0.536   2.2976  -1.0894  -0.4708
 5SQ  CG1  C  CR5    0   0.171   3.5214  -1.9158  -0.2920
 5SQ  C2H  C  CR15   0  -0.139   3.7474  -3.2023  -0.6935
 5SQ  N2H  N  NR15   0  -0.563   5.0156  -3.4969  -0.2800
 5SQ  N1H  N  N      0  -0.461   4.6264  -1.4334   0.3558
 5SQ  C1H  C  CR15   0   0.081   5.5002  -2.4085   0.3450
 5SQ  N2   N  N      0  -0.494  -0.6881  -0.0297   0.4550
 5SQ  CA2  C  CR5    0   0.089  -1.3433   1.1744   0.2389
 5SQ  CB2  C  C1     0  -0.392  -2.6512   1.3850  -0.0084
 5SQ  CG2  C  CR6    0   0.133  -3.7330   0.4308  -0.1132
 5SQ  CD2  C  CR16   0  -0.301  -3.5812  -0.9542   0.0473
 5SQ  CE2  C  CR16   0  -0.361  -4.6614  -1.8068  -0.0672
 5SQ  CD1  C  CR16   0  -0.288  -5.0193   0.9147  -0.3916
 5SQ  CE1  C  CR16   0  -0.331  -6.1060   0.0716  -0.5077
 5SQ  CZ1  C  CR6    0   0.359  -5.9333  -1.3027  -0.3453
 5SQ  OH   O  OH1    0  -0.621  -7.0128  -2.0904  -0.4662
 5SQ  OXY  O  OC    -1  -0.608   3.5957   3.4788  -0.7087
 5SQ  H1   H  HCH2   0   0.273   2.8281   1.6397   1.1281
 5SQ  H2   H  HCH2   0   0.267   2.0015   3.1649   1.3021
 5SQ  H3   H  HCH1   0   0.272   2.3699  -0.3705   1.5489
 5SQ  H4   H  HNH2   0   0.350   0.7351  -1.8016   2.3839
 5SQ  H5   H  HNH2   0   0.344   0.3181  -2.3281   0.9147
 5SQ  H7   H  HCH2   0   0.251   1.5823  -1.6134  -1.1110
 5SQ  H8   H  HCH2   0   0.265   2.5433  -0.1564  -0.9833
 5SQ  H9   H  HCR5   0   0.280   3.1317  -3.9101  -1.2223
 5SQ  H10  H  HNR5   0   0.418   5.4997  -4.3693  -0.4176
 5SQ  H12  H  HCR5   0   0.274   6.4917  -2.3784   0.7700
 5SQ  H14  H  H      0   0.262  -2.9323   2.4237  -0.1530
 5SQ  H16  H  HCR6   0   0.279  -2.6051  -1.3635   0.2657
 5SQ  H17  H  HCR6   0   0.276  -4.5164  -2.8737   0.0596
 5SQ  H18  H  HCR6   0   0.261  -5.1684   1.9802  -0.5199
 5SQ  H19  H  HCR6   0   0.269  -7.0889   0.4699  -0.7248
 5SQ  H20  H  HOH1   0   0.479  -6.7753  -3.0155  -0.3336

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
 5SQ  OH   CZ1  single    1.342  0.020  1.342
 5SQ  N    CA1  single    1.445  0.020  1.445
 5SQ  CZ1  CE1  aromatic  1.395  0.020  1.395
 5SQ  CZ1  CE2  aromatic  1.396  0.020  1.396
 5SQ  CE1  CD1  aromatic  1.380  0.020  1.380
 5SQ  CE2  CD2  aromatic  1.381  0.020  1.381
 5SQ  CD1  CG2  aromatic  1.402  0.020  1.402
 5SQ  CD2  CG2  aromatic  1.402  0.020  1.402
 5SQ  CG2  CB2  single    1.446  0.020  1.446
 5SQ  CA3  N3   single    1.440  0.020  1.440
 5SQ  CA3  C    single    1.547  0.020  1.547
 5SQ  CB1  CA1  single    1.540  0.020  1.540
 5SQ  CB1  CG1  single    1.488  0.020  1.488
 5SQ  CA1  C1   single    1.503  0.020  1.503
 5SQ  N3   C1   single    1.376  0.020  1.376
 5SQ  N3   C2   single    1.376  0.020  1.376
 5SQ  C1   N2   double    1.291  0.020  1.291
 5SQ  C2   O2   double    1.216  0.020  1.216
 5SQ  C2   CA2  single    1.480  0.020  1.480
 5SQ  N2   CA2  single    1.388  0.020  1.388
 5SQ  CA2  CB2  double    1.348  0.020  1.348
 5SQ  CG1  N1H  aromatic  1.369  0.020  1.369
 5SQ  CG1  C2H  aromatic  1.366  0.020  1.366
 5SQ  N1H  C1H  aromatic  1.309  0.020  1.309
 5SQ  C2H  N2H  aromatic  1.366  0.020  1.366
 5SQ  C1H  N2H  aromatic  1.345  0.020  1.345
 5SQ  O    C    deloc     1.242  0.020  1.242
 5SQ  C    OXY  deloc     1.244  0.020  1.244
 5SQ  CA3  H1   single    0.970  0.020  1.090
 5SQ  CA3  H2   single    0.970  0.020  1.090
 5SQ  CA1  H3   single    0.970  0.020  1.090
 5SQ  N    H4   single    0.890  0.020  1.040
 5SQ  N    H5   single    0.890  0.020  1.040
 5SQ  CB1  H7   single    0.970  0.020  1.090
 5SQ  CB1  H8   single    0.970  0.020  1.090
 5SQ  C2H  H9   single    0.930  0.020  1.080
 5SQ  N2H  H10  single    0.860  0.020  1.020
 5SQ  C1H  H12  single    0.930  0.020  1.080
 5SQ  CB2  H14  single    0.930  0.020  1.080
 5SQ  CD2  H16  single    0.930  0.020  1.080
 5SQ  CE2  H17  single    0.930  0.020  1.080
 5SQ  CD1  H18  single    0.930  0.020  1.080
 5SQ  CE1  H19  single    0.930  0.020  1.080
 5SQ  OH   H20  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
 5SQ  N2   C1   CA1  122.85  3.000
 5SQ  N2   C1   N3   113.96  3.000
 5SQ  CA1  C1   N3   123.19  3.000
 5SQ  CA2  C2   O2   130.82  3.000
 5SQ  CA2  C2   N3   103.23  3.000
 5SQ  O2   C2   N3   125.94  3.000
 5SQ  OXY  C    CA3  114.44  3.000
 5SQ  OXY  C    O    128.28  3.000
 5SQ  CA3  C    O    117.26  3.000
 5SQ  H2   CA3  H1   106.05  3.000
 5SQ  H2   CA3  N3   108.83  3.000
 5SQ  H1   CA3  N3   109.18  3.000
 5SQ  H2   CA3  C    109.85  3.000
 5SQ  H1   CA3  C    109.23  3.000
 5SQ  N3   CA3  C    113.44  3.000
 5SQ  CA3  N3   C2   122.31  3.000
 5SQ  C2   N3   C1   107.98  3.000
 5SQ  CA3  N3   C1   129.17  3.000
 5SQ  H3   CA1  CB1  107.90  3.000
 5SQ  H3   CA1  N    107.82  3.000
 5SQ  CB1  CA1  N    109.98  3.000
 5SQ  H3   CA1  C1   108.74  3.000
 5SQ  CB1  CA1  C1   108.88  3.000
 5SQ  N    CA1  C1   113.37  3.000
 5SQ  H5   N    H4   105.77  3.000
 5SQ  H5   N    CA1  109.28  3.000
 5SQ  H4   N    CA1  109.77  3.000
 5SQ  H8   CB1  H7   106.37  3.000
 5SQ  H8   CB1  CG1  110.23  3.000
 5SQ  H7   CB1  CG1  110.01  3.000
 5SQ  H8   CB1  CA1  109.67  3.000
 5SQ  H7   CB1  CA1  108.48  3.000
 5SQ  CG1  CB1  CA1  111.91  3.000
 5SQ  N1H  CG1  C2H  109.71  3.000
 5SQ  C2H  CG1  CB1  128.60  3.000
 5SQ  N1H  CG1  CB1  121.69  3.000
 5SQ  H9   C2H  N2H  122.52  3.000
 5SQ  H9   C2H  CG1  131.95  3.000
 5SQ  N2H  C2H  CG1  105.53  3.000
 5SQ  H10  N2H  C1H  126.23  3.000
 5SQ  H10  N2H  C2H  126.28  3.000
 5SQ  C1H  N2H  C2H  107.49  3.000
 5SQ  C1H  N1H  CG1  105.81  3.000
 5SQ  H12  C1H  N1H  126.10  3.000
 5SQ  H12  C1H  N2H  122.44  3.000
 5SQ  N1H  C1H  N2H  111.46  3.000
 5SQ  CA2  N2   C1   106.26  3.000
 5SQ  CB2  CA2  N2   128.49  3.000
 5SQ  CB2  CA2  C2   122.97  3.000
 5SQ  N2   CA2  C2   108.54  3.000
 5SQ  H14  CB2  CG2  115.33  3.000
 5SQ  H14  CB2  CA2  115.16  3.000
 5SQ  CG2  CB2  CA2  129.50  3.000
 5SQ  CD1  CG2  CD2  117.57  3.000
 5SQ  CD2  CG2  CB2  124.21  3.000
 5SQ  CD1  CG2  CB2  118.22  3.000
 5SQ  H16  CD2  CE2  119.30  3.000
 5SQ  H16  CD2  CG2  119.66  3.000
 5SQ  CE2  CD2  CG2  121.04  3.000
 5SQ  H17  CE2  CZ1  120.03  3.000
 5SQ  H17  CE2  CD2  119.56  3.000
 5SQ  CZ1  CE2  CD2  120.41  3.000
 5SQ  H18  CD1  CE1  118.85  3.000
 5SQ  H18  CD1  CG2  119.28  3.000
 5SQ  CE1  CD1  CG2  121.88  3.000
 5SQ  H19  CE1  CZ1  119.89  3.000
 5SQ  H19  CE1  CD1  120.46  3.000
 5SQ  CZ1  CE1  CD1  119.65  3.000
 5SQ  OH   CZ1  CE1  117.93  3.000
 5SQ  CE1  CZ1  CE2  119.46  3.000
 5SQ  OH   CZ1  CE2  122.61  3.000
 5SQ  H20  OH   CZ1  110.65  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
 5SQ  CONST_01  N2H  C1H  N1H  CG1     0.00   0.0  0
 5SQ  CONST_02  C1H  N2H  C2H  CG1     0.00   0.0  0
 5SQ  CONST_03  C1H  N1H  CG1  C2H     0.00   0.0  0
 5SQ  CONST_04  N1H  C1H  N2H  C2H     0.00   0.0  0
 5SQ  CONST_05  N1H  CG1  C2H  N2H     0.00   0.0  0
 5SQ  CONST_06  CZ1  CE1  CD1  CG2     0.00   0.0  0
 5SQ  CONST_07  CZ1  CE2  CD2  CG2     0.00   0.0  0
 5SQ  CONST_08  CE1  CZ1  CE2  CD2     0.00   0.0  0
 5SQ  CONST_09  CE1  CD1  CG2  CD2     0.00   0.0  0
 5SQ  CONST_10  CD1  CE1  CZ1  CE2     0.00   0.0  0
 5SQ  CONST_11  CD1  CG2  CD2  CE2     0.00   0.0  0
 5SQ  CONST_12  CA2  C2   N3   C1      0.00   0.0  0
 5SQ  CONST_13  C2   CA2  N2   C1      0.00   0.0  0
 5SQ  CONST_14  N2   C1   N3   C2      0.00   0.0  0
 5SQ  CONST_15  CA2  N2   C1   N3      0.00   0.0  0
 5SQ  CONST_16  N2   CA2  C2   N3      0.00   0.0  0
 5SQ  CONST_17  C1H  N1H  CG1  CB1   180.00   0.0  0
 5SQ  CONST_18  N2H  C2H  CG1  CB1   180.00   0.0  0
 5SQ  CONST_19  CE1  CD1  CG2  CB2   180.00   0.0  0
 5SQ  CONST_20  CE2  CD2  CG2  CB2   180.00   0.0  0
 5SQ  CONST_21  OH   CZ1  CE2  CD2   180.00   0.0  0
 5SQ  CONST_22  OH   CZ1  CE1  CD1   180.00   0.0  0
 5SQ  CONST_23  O2   C2   N3   C1    180.00   0.0  0
 5SQ  CONST_24  CA1  C1   N3   C2    180.00   0.0  0
 5SQ  CONST_25  N2   C1   N3   CA3   180.00   0.0  0
 5SQ  CONST_26  CA2  C2   N3   CA3   180.00   0.0  0
 5SQ  CONST_27  CA2  N2   C1   CA1   180.00   0.0  0
 5SQ  CONST_28  H12  C1H  N1H  CG1   180.00   0.0  0
 5SQ  CONST_29  H10  N2H  C2H  CG1   180.00   0.0  0
 5SQ  CONST_30  H12  C1H  N2H  C2H   180.00   0.0  0
 5SQ  CONST_31  H9   C2H  CG1  N1H   180.00   0.0  0
 5SQ  CONST_32  H10  N2H  C1H  N1H   180.00   0.0  0
 5SQ  CONST_33  H9   C2H  N2H  C1H   180.00   0.0  0
 5SQ  CONST_34  H19  CE1  CD1  CG2   180.00   0.0  0
 5SQ  CONST_35  H17  CE2  CD2  CG2   180.00   0.0  0
 5SQ  CONST_36  H18  CD1  CG2  CD2   180.00   0.0  0
 5SQ  CONST_37  H19  CE1  CZ1  CE2   180.00   0.0  0
 5SQ  CONST_38  H16  CD2  CG2  CD1   180.00   0.0  0
 5SQ  CONST_39  H17  CE2  CZ1  CE1   180.00   0.0  0
 5SQ  CONST_40  H18  CD1  CE1  CZ1   180.00   0.0  0
 5SQ  CONST_41  H16  CD2  CE2  CZ1   180.00   0.0  0
 5SQ  CONST_42  CA1  C1   N3   CA3     0.00   0.0  0
 5SQ  CONST_43  O2   C2   N3   CA3     0.00   0.0  0
 5SQ  Var_01    CG2  CB2  CA2  C2   -179.73   0.0  2
 5SQ  Var_02    CG2  CB2  CA2  N2      0.26   0.0  2
 5SQ  Var_03    CD1  CG2  CB2  CA2  -179.51  30.0  2
 5SQ  Var_04    CD2  CG2  CB2  CA2     0.56  30.0  2
 5SQ  Var_05    C    CA3  N3   C1     99.06  30.0  2
 5SQ  Var_06    C    CA3  N3   C2    -71.43  30.0  2
 5SQ  Var_07    N1H  CG1  CB1  CA1   -65.97  30.0  2
 5SQ  Var_08    C2H  CG1  CB1  CA1   113.36  30.0  2
 5SQ  Var_09    H14  CB2  CA2  C2      0.47   0.0  2
 5SQ  Var_10    H14  CB2  CA2  N2   -179.54   0.0  2
 5SQ  Var_11    H1   CA3  N3   C1    -23.00  30.0  2
 5SQ  Var_12    H2   CA3  N3   C1   -138.34  30.0  2
 5SQ  Var_13    H1   CA3  N3   C2    166.51  30.0  2
 5SQ  Var_14    H2   CA3  N3   C2     51.18  30.0  2
 5SQ  Var_15    H7   CB1  CG1  C2H    -7.31  30.0  2
 5SQ  Var_16    H8   CB1  CG1  C2H  -124.30  30.0  2
 5SQ  Var_17    H7   CB1  CG1  N1H   173.36  30.0  2
 5SQ  Var_18    H8   CB1  CG1  N1H    56.37  30.0  2
 5SQ  Var_19    H14  CB2  CG2  CD2  -179.65  30.0  2
 5SQ  Var_20    H14  CB2  CG2  CD1     0.28  30.0  2
 5SQ  Var_21    N3   CA3  C    O     -11.52  30.0  2
 5SQ  Var_22    OXY  C    CA3  N3    169.59  30.0  3
 5SQ  Var_23    H1   CA3  C    O     110.51  30.0  2
 5SQ  Var_24    H2   CA3  C    O    -133.56  30.0  2
 5SQ  Var_25    H1   CA3  C    OXY   -68.38  30.0  2
 5SQ  Var_26    H2   CA3  C    OXY    47.55  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
 5SQ  chir_01  CA1  N  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
 5SQ  plan-1  C1   0.020
 5SQ  plan-1  C2   0.020
 5SQ  plan-1  CA3  0.020
 5SQ  plan-1  N3   0.020
 5SQ  plan-1  O2   0.020
 5SQ  plan-1  CA1  0.020
 5SQ  plan-1  N2   0.020
 5SQ  plan-1  CA2  0.020
 5SQ  plan-1  CB2  0.020
 5SQ  plan-1  CG2  0.020
 5SQ  plan-1  H14  0.020
 5SQ  plan-2  CB1  0.020
 5SQ  plan-2  CG1  0.020
 5SQ  plan-2  C2H  0.020
 5SQ  plan-2  N2H  0.020
 5SQ  plan-2  N1H  0.020
 5SQ  plan-2  C1H  0.020
 5SQ  plan-2  H9   0.020
 5SQ  plan-2  H10  0.020
 5SQ  plan-2  H12  0.020
 5SQ  plan-3  CB2  0.020
 5SQ  plan-3  CG2  0.020
 5SQ  plan-3  CD2  0.020
 5SQ  plan-3  CE2  0.020
 5SQ  plan-3  CD1  0.020
 5SQ  plan-3  CE1  0.020
 5SQ  plan-3  CZ1  0.020
 5SQ  plan-3  OH   0.020
 5SQ  plan-3  H16  0.020
 5SQ  plan-3  H17  0.020
 5SQ  plan-3  H18  0.020
 5SQ  plan-3  H19  0.020
 5SQ  plan-4  O    0.020
 5SQ  plan-4  C    0.020
 5SQ  plan-4  CA3  0.020
 5SQ  plan-4  OXY  0.020

