# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 04:25:50 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-amino-1H-indol-3-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[nH]c3cccc(N)c23)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
 5ZA  5ZA  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(4-amino-1H-indol-3-yl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  45  26  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_5ZA
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
 5ZA  C25   C  CH3   0  -0.703  -4.6790   2.9619  -0.4258
 5ZA  C23   C  CH1   0   0.047  -3.6128   1.8809  -0.4897
 5ZA  O24   O  OH1   0  -0.662  -2.6640   2.1260  -1.5014
 5ZA  C22   C  CH1   0  -0.244  -2.8330   1.7602   0.8381
 5ZA  N26   N  NH2   0  -0.782  -2.1460   2.9556   1.2731
 5ZA  C14   C  CR5   0   0.567  -1.8405   0.6424   0.7263
 5ZA  N13   N  N     0  -0.476  -0.5730   0.8129   0.5985
 5ZA  C12   C  CR5   0   0.066  -0.0112  -0.4506   0.4711
 5ZA  C11   C  C1    0  -0.424   1.2998  -0.7499   0.3151
 5ZA  C7    C  CR5   0   0.049   2.4044   0.1548   0.2890
 5ZA  C8    C  CR15  0  -0.034   2.3603   1.5072   0.5899
 5ZA  N9    N  NR15  0  -0.672   3.6030   2.0197   0.5576
 5ZA  C6    C  CR56  0   0.353   4.5145   1.0465   0.2359
 5ZA  C5    C  CR16  0  -0.327   5.9004   1.1448   0.1289
 5ZA  C4    C  CR16  0  -0.276   6.5702  -0.0168  -0.1971
 5ZA  C3    C  CR16  0  -0.352   5.8887  -1.2160  -0.4347
 5ZA  C2    C  CR6   0   0.182   4.5037  -1.3092  -0.3344
 5ZA  N10   N  NH2   0  -0.862   3.8461  -2.5108  -0.5519
 5ZA  C1    C  CR56  0  -0.006   3.7987  -0.1477   0.0415
 5ZA  C16   C  CR5   0   0.531  -1.0754  -1.4566   0.5403
 5ZA  O17   O  O     0  -0.463  -1.0520  -2.6724   0.4909
 5ZA  N15   N  NR5   0  -0.564  -2.2139  -0.6900   0.7137
 5ZA  C18   C  CH2   0  -0.468  -3.5088  -1.2765   0.8703
 5ZA  C19   C  C     0   0.549  -4.0528  -1.8032  -0.4418
 5ZA  O21   O  O     0  -0.424  -3.5248  -1.6496  -1.5098
 5ZA  H251  H  HCH3  0   0.245  -5.2625   2.9739  -1.3479
 5ZA  H252  H  HCH3  0   0.234  -5.3723   2.7809   0.3964
 5ZA  H253  H  HCH3  0   0.228  -4.2445   3.9541  -0.2970
 5ZA  H23   H  HCH1  0   0.205  -4.1247   0.9257  -0.6672
 5ZA  H24   H  HOH1  0   0.455  -3.1285   2.1938  -2.3413
 5ZA  H22   H  HCH1  0   0.274  -3.5679   1.5041   1.6101
 5ZA  H261  H  HNH2  0   0.349  -1.4941   3.2590   0.5612
 5ZA  H262  H  HNH2  0   0.359  -2.8141   3.7045   1.4007
 5ZA  H11   H  H     0   0.258   1.5222  -1.8068   0.2262
 5ZA  H8    H  HCR5  0   0.301   1.5072   2.1152   0.8410
 5ZA  HN9   H  HNR5  0   0.420   3.8299   2.9809   0.7572
 5ZA  H5    H  HCR6  0   0.258   6.4204   2.0782   0.2976
 5ZA  H4    H  HCR6  0   0.251   7.6485  -0.0035  -0.2893
 5ZA  H3    H  HCR6  0   0.251   6.4534  -2.0966  -0.7186
 5ZA  H101  H  HNH2  0   0.379   4.4367  -3.2237  -0.9537
 5ZA  H102  H  HNH2  0   0.379   2.9982  -2.4348  -1.0936
 5ZA  H181  H  HCH2  0   0.322  -3.4596  -2.0958   1.5914
 5ZA  H182  H  HCH2  0   0.321  -4.2076  -0.5500   1.2874
 5ZA  OXT   O  OH1   0  -0.586  -5.1916  -2.4484  -0.2480
 5ZA  HXT   H  HOH1  0   0.488  -5.5486  -2.7649  -1.0917

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
 5ZA  C25  C23   single    1.520  0.020  1.520
 5ZA  C25  H251  single    0.970  0.020  1.090
 5ZA  C25  H252  single    0.970  0.020  1.090
 5ZA  C25  H253  single    0.970  0.020  1.090
 5ZA  C23  O24   single    1.409  0.020  1.409
 5ZA  C23  C22   single    1.545  0.020  1.545
 5ZA  C23  H23   single    0.970  0.020  1.090
 5ZA  O24  H24   single    0.850  0.020  0.980
 5ZA  C22  N26   single    1.446  0.020  1.446
 5ZA  C22  C14   single    1.499  0.020  1.499
 5ZA  C22  H22   single    0.970  0.020  1.090
 5ZA  N26  H261  single    0.890  0.020  1.040
 5ZA  N26  H262  single    0.890  0.020  1.040
 5ZA  C14  N13   double    1.285  0.020  1.285
 5ZA  C14  N15   single    1.384  0.020  1.384
 5ZA  N13  C12   single    1.389  0.020  1.389
 5ZA  C12  C11   double    1.354  0.020  1.354
 5ZA  C12  C16   single    1.466  0.020  1.466
 5ZA  C11  C7    single    1.428  0.020  1.428
 5ZA  C11  H11   single    0.930  0.020  1.080
 5ZA  C7   C8    aromatic  1.386  0.020  1.386
 5ZA  C7   C1    aromatic  1.448  0.020  1.448
 5ZA  C8   N9    aromatic  1.345  0.020  1.345
 5ZA  C8   H8    single    0.930  0.020  1.080
 5ZA  N9   C6    aromatic  1.372  0.020  1.372
 5ZA  N9   HN9   single    0.860  0.020  1.020
 5ZA  C6   C5    aromatic  1.394  0.020  1.394
 5ZA  C6   C1    aromatic  1.406  0.020  1.406
 5ZA  C5   C4    aromatic  1.380  0.020  1.380
 5ZA  C5   H5    single    0.930  0.020  1.080
 5ZA  C4   C3    aromatic  1.400  0.020  1.400
 5ZA  C4   H4    single    0.930  0.020  1.080
 5ZA  C3   C2    aromatic  1.392  0.020  1.392
 5ZA  C3   H3    single    0.930  0.020  1.080
 5ZA  C2   N10   single    1.387  0.020  1.387
 5ZA  C2   C1    aromatic  1.410  0.020  1.410
 5ZA  N10  H101  single    0.890  0.020  1.040
 5ZA  N10  H102  single    0.890  0.020  1.040
 5ZA  C16  O17   double    1.217  0.020  1.217
 5ZA  C16  N15   single    1.383  0.020  1.383
 5ZA  N15  C18   single    1.430  0.020  1.430
 5ZA  C18  C19   single    1.515  0.020  1.515
 5ZA  C18  H181  single    0.970  0.020  1.090
 5ZA  C18  H182  single    0.970  0.020  1.090
 5ZA  C19  O21   double    1.201  0.020  1.201
 5ZA  C19  OXT   single    1.323  0.020  1.323
 5ZA  OXT  HXT   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
 5ZA  H253  C25  H252  108.37  3.000
 5ZA  H253  C25  H251  107.62  3.000
 5ZA  H252  C25  H251  107.39  3.000
 5ZA  H253  C25  C23   111.88  3.000
 5ZA  H252  C25  C23   111.08  3.000
 5ZA  H251  C25  C23   110.33  3.000
 5ZA  H23   C23  C22   107.84  3.000
 5ZA  H23   C23  O24   110.45  3.000
 5ZA  C22   C23  O24   106.91  3.000
 5ZA  H23   C23  C25   107.37  3.000
 5ZA  C22   C23  C25   111.94  3.000
 5ZA  O24   C23  C25   112.27  3.000
 5ZA  H24   O24  C23   108.30  3.000
 5ZA  H22   C22  C14   108.80  3.000
 5ZA  H22   C22  N26   107.45  3.000
 5ZA  C14   C22  N26   108.93  3.000
 5ZA  H22   C22  C23   106.57  3.000
 5ZA  C14   C22  C23   109.17  3.000
 5ZA  N26   C22  C23   115.72  3.000
 5ZA  H262  N26  H261  106.99  3.000
 5ZA  H262  N26  C22   109.64  3.000
 5ZA  H261  N26  C22   110.02  3.000
 5ZA  N15   C14  N13   113.13  3.000
 5ZA  N15   C14  C22   122.69  3.000
 5ZA  N13   C14  C22   124.16  3.000
 5ZA  C12   N13  C14   106.70  3.000
 5ZA  C16   C12  C11   123.83  3.000
 5ZA  C16   C12  N13   109.05  3.000
 5ZA  C11   C12  N13   127.12  3.000
 5ZA  H11   C11  C7    117.23  3.000
 5ZA  H11   C11  C12   115.08  3.000
 5ZA  C7    C11  C12   127.67  3.000
 5ZA  C1    C7   C8    105.76  3.000
 5ZA  C1    C7   C11   127.99  3.000
 5ZA  C8    C7   C11   126.12  3.000
 5ZA  H8    C8   N9    121.49  3.000
 5ZA  H8    C8   C7    128.79  3.000
 5ZA  N9    C8   C7    109.71  3.000
 5ZA  HN9   N9   C6    125.01  3.000
 5ZA  HN9   N9   C8    124.54  3.000
 5ZA  C6    N9   C8    110.45  3.000
 5ZA  C1    C6   C5    123.76  3.000
 5ZA  C1    C6   N9    107.27  3.000
 5ZA  C5    C6   N9    128.97  3.000
 5ZA  H5    C5   C4    122.00  3.000
 5ZA  H5    C5   C6    121.80  3.000
 5ZA  C4    C5   C6    116.20  3.000
 5ZA  H4    C4   C3    118.76  3.000
 5ZA  H4    C4   C5    119.56  3.000
 5ZA  C3    C4   C5    121.67  3.000
 5ZA  H3    C3   C2    118.88  3.000
 5ZA  H3    C3   C4    119.13  3.000
 5ZA  C2    C3   C4    121.98  3.000
 5ZA  C1    C2   N10   121.23  3.000
 5ZA  C1    C2   C3    117.50  3.000
 5ZA  N10   C2   C3    121.23  3.000
 5ZA  H102  N10  H101  109.34  3.000
 5ZA  H102  N10  C2    114.67  3.000
 5ZA  H101  N10  C2    113.38  3.000
 5ZA  C2    C1   C6    118.82  3.000
 5ZA  C2    C1   C7    134.37  3.000
 5ZA  C6    C1   C7    106.81  3.000
 5ZA  N15   C16  O17   125.06  3.000
 5ZA  N15   C16  C12   102.89  3.000
 5ZA  O17   C16  C12   132.03  3.000
 5ZA  C18   N15  C16   122.12  3.000
 5ZA  C18   N15  C14   129.65  3.000
 5ZA  C16   N15  C14   108.22  3.000
 5ZA  H182  C18  H181  106.02  3.000
 5ZA  H182  C18  C19   109.42  3.000
 5ZA  H181  C18  C19   109.09  3.000
 5ZA  H182  C18  N15   110.42  3.000
 5ZA  H181  C18  N15   109.82  3.000
 5ZA  C19   C18  N15   111.89  3.000
 5ZA  OXT   C19  O21   124.82  3.000
 5ZA  OXT   C19  C18   110.60  3.000
 5ZA  O21   C19  C18   124.59  3.000
 5ZA  HXT   OXT  C19   110.41  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
 5ZA  CONST_01  C6    N9   C8   C7     0.00   0.0  0
 5ZA  CONST_02  N9    C6   C1   C7     0.00   0.0  0
 5ZA  CONST_03  C5    C6   C1   C7   180.00   0.0  0
 5ZA  CONST_04  C3    C2   C1   C7   180.00   0.0  0
 5ZA  CONST_05  C6    C1   C7   C8     0.00   0.0  0
 5ZA  CONST_06  C2    C1   C7   C8   180.00   0.0  0
 5ZA  CONST_07  C5    C6   N9   C8   180.00   0.0  0
 5ZA  CONST_08  C1    C6   N9   C8     0.00   0.0  0
 5ZA  CONST_09  C1    C7   C8   N9     0.00   0.0  0
 5ZA  CONST_10  C4    C5   C6   N9   180.00   0.0  0
 5ZA  CONST_11  C2    C1   C6   N9   180.00   0.0  0
 5ZA  CONST_12  C3    C4   C5   C6     0.00   0.0  0
 5ZA  CONST_13  C3    C2   C1   C6     0.00   0.0  0
 5ZA  CONST_14  C2    C1   C6   C5     0.00   0.0  0
 5ZA  CONST_15  C2    C3   C4   C5     0.00   0.0  0
 5ZA  CONST_16  C1    C6   C5   C4     0.00   0.0  0
 5ZA  CONST_17  C1    C2   C3   C4     0.00   0.0  0
 5ZA  CONST_18  C16   C12  N13  C14    0.00   0.0  0
 5ZA  CONST_19  C12   C16  N15  C14    0.00   0.0  0
 5ZA  CONST_20  C16   N15  C14  N13    0.00   0.0  0
 5ZA  CONST_21  N15   C16  C12  N13    0.00   0.0  0
 5ZA  CONST_22  N15   C14  N13  C12    0.00   0.0  0
 5ZA  CONST_23  N9    C8   C7   C11  180.00   0.0  0
 5ZA  CONST_24  C6    C1   C7   C11  180.00   0.0  0
 5ZA  CONST_25  C2    C1   C7   C11    0.00   0.0  0
 5ZA  CONST_26  N10   C2   C1   C7     0.00   0.0  0
 5ZA  CONST_27  N10   C2   C1   C6   180.00   0.0  0
 5ZA  CONST_28  N10   C2   C3   C4   180.00   0.0  0
 5ZA  CONST_29  C12   N13  C14  C22  180.00   0.0  0
 5ZA  CONST_30  C16   N15  C14  C22  180.00   0.0  0
 5ZA  CONST_31  O17   C16  N15  C14  180.00   0.0  0
 5ZA  CONST_32  C18   N15  C14  N13  180.00   0.0  0
 5ZA  CONST_33  C18   N15  C16  C12  180.00   0.0  0
 5ZA  CONST_34  HN9   N9   C8   C7   180.00   0.0  0
 5ZA  CONST_35  H5    C5   C6   N9     0.00   0.0  0
 5ZA  CONST_36  H8    C8   N9   C6   180.00   0.0  0
 5ZA  CONST_37  H4    C4   C5   C6   180.00   0.0  0
 5ZA  CONST_38  H3    C3   C4   C5   180.00   0.0  0
 5ZA  CONST_39  C18   N15  C14  C22    0.00   0.0  0
 5ZA  CONST_40  C18   N15  C16  O17    0.00   0.0  0
 5ZA  CONST_41  H101  N10  C2   C3     0.00   0.0  0
 5ZA  CONST_43  HXT   OXT  C19  C18  180.00   0.0  0
 5ZA  Var_01    C7    C11  C12  N13    2.20  30.0  2
 5ZA  Var_02    C8    C7   C11  C12    8.83  30.0  2
 5ZA  Var_03    C19   C18  N15  C14  106.39  30.0  3
 5ZA  Var_04    O21   C19  C18  N15   -6.12  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
 5ZA  chir_01  C23  C25  O24  C22  negativ
 5ZA  chir_02  C22  N26  C23  C14  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
 5ZA  plan-1  C22   0.020
 5ZA  plan-1  C14   0.020
 5ZA  plan-1  N13   0.020
 5ZA  plan-1  C12   0.020
 5ZA  plan-1  C11   0.020
 5ZA  plan-1  C16   0.020
 5ZA  plan-1  O17   0.020
 5ZA  plan-1  N15   0.020
 5ZA  plan-1  C18   0.020
 5ZA  plan-2  C11   0.020
 5ZA  plan-2  C7    0.020
 5ZA  plan-2  C8    0.020
 5ZA  plan-2  N9    0.020
 5ZA  plan-2  C6    0.020
 5ZA  plan-2  C5    0.020
 5ZA  plan-2  C4    0.020
 5ZA  plan-2  C3    0.020
 5ZA  plan-2  C2    0.020
 5ZA  plan-2  N10   0.020
 5ZA  plan-2  C1    0.020
 5ZA  plan-2  H8    0.020
 5ZA  plan-2  HN9   0.020
 5ZA  plan-2  H5    0.020
 5ZA  plan-2  H4    0.020
 5ZA  plan-2  H3    0.020
 5ZA  plan-3  C2    0.020
 5ZA  plan-3  N10   0.020
 5ZA  plan-3  H101  0.020
 5ZA  plan-3  H102  0.020
 5ZA  plan-4  C18   0.020
 5ZA  plan-4  C19   0.020
 5ZA  plan-4  O21   0.020
 5ZA  plan-4  OXT   0.020
 5ZA  plan-4  HXT   0.020

