# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 13:47:34 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  44  26  .  2022-07-23  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_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  -0.701  -4.6453   2.9290  -0.2881
 5ZA  C23   C  CH1    0   0.035  -3.5156   1.9201  -0.4228
 5ZA  O24   O  OH1    0  -0.665  -2.5010   2.3778  -1.2896
 5ZA  C22   C  CH1    0  -0.241  -2.8494   1.6241   0.9397
 5ZA  N26   N  NH2    0  -0.785  -2.2021   2.7505   1.5785
 5ZA  C14   C  CR5    0   0.563  -1.8500   0.5217   0.7655
 5ZA  N13   N  N      0  -0.486  -0.5821   0.7236   0.6460
 5ZA  C12   C  CR5    0   0.065  -0.0118  -0.5223   0.4278
 5ZA  C11   C  C1     0  -0.432   1.2954  -0.8018   0.2226
 5ZA  C7    C  CR5    0   0.053   2.3905   0.1183   0.1872
 5ZA  C8    C  CR15   0  -0.042   2.2997   1.4961   0.2943
 5ZA  N9    N  NR15   0  -0.674   3.5217   2.0449   0.1582
 5ZA  C6    C  CR56   0   0.352   4.4629   1.0699  -0.0447
 5ZA  C5    C  CR16   0  -0.328   5.8317   1.2083  -0.2686
 5ZA  C4    C  CR16   0  -0.277   6.5383   0.0403  -0.4681
 5ZA  C3    C  CR16   0  -0.353   5.9142  -1.2117  -0.4221
 5ZA  C2    C  CR6    0   0.178   4.5487  -1.3477  -0.1902
 5ZA  N10   N  NH2    0  -0.862   3.9457  -2.5970  -0.1797
 5ZA  C1    C  CR56   0  -0.007   3.7950  -0.1680  -0.0196
 5ZA  C16   C  CR5    0   0.524  -1.0737  -1.5409   0.4370
 5ZA  O17   O  O      0  -0.472  -1.0236  -2.7512   0.3035
 5ZA  N15   N  NR5    0  -0.542  -2.2124  -0.8048   0.6769
 5ZA  C18   C  CH2    0  -0.473  -3.5192  -1.4057   0.7358
 5ZA  C19   C  C      0   0.420  -4.0934  -1.8088  -0.6416
 5ZA  O21   O  O      0  -0.586  -3.4842  -1.4254  -1.6515
 5ZA  H251  H  HCH3   0   0.242  -5.1296   3.0909  -1.2527
 5ZA  H252  H  HCH3   0   0.230  -5.4097   2.5705   0.4031
 5ZA  H253  H  HCH3   0   0.222  -4.2881   3.8968   0.0672
 5ZA  H23   H  HCH1   0   0.223  -3.9399   0.9826  -0.8001
 5ZA  H24   H  HOH1   0   0.452  -2.8855   2.4901  -2.1642
 5ZA  H22   H  HCH1   0   0.267  -3.6466   1.2778   1.6057
 5ZA  H261  H  HNH2   0   0.349  -1.4736   3.1129   0.9767
 5ZA  H262  H  HNH2   0   0.354  -2.8712   3.4973   1.7137
 5ZA  H11   H  H      0   0.246   1.5146  -1.8465   0.0404
 5ZA  H8    H  HCR5   0   0.301   1.4235   2.1031   0.4493
 5ZA  HN9   H  HNR5   0   0.418   3.7104   3.0340   0.1877
 5ZA  H5    H  HCR6   0   0.257   6.3093   2.1787  -0.2909
 5ZA  H4    H  HCR6   0   0.250   7.6048   0.0847  -0.6477
 5ZA  H3    H  HCR6   0   0.250   6.5128  -2.1048  -0.5595
 5ZA  H101  H  HNH2   0   0.378   4.6049  -3.3611  -0.1879
 5ZA  H102  H  HNH2   0   0.379   3.2778  -2.7401   0.5623
 5ZA  H181  H  HCH2   0   0.264  -3.4675  -2.2864   1.3790
 5ZA  H182  H  HCH2   0   0.268  -4.2080  -0.7169   1.2270
 5ZA  OXT   O  OC    -1  -0.614  -5.1422  -2.4771  -0.5811

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    1.521  0.020  1.521
 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    1.411  0.020  1.411
 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    1.448  0.020  1.448
 5ZA  C22  C14   single    1.498  0.020  1.498
 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    1.289  0.020  1.289
 5ZA  C14  N15   single    1.378  0.020  1.378
 5ZA  N13  C12   single    1.387  0.020  1.387
 5ZA  C12  C11   double    1.352  0.020  1.352
 5ZA  C12  C16   single    1.471  0.020  1.471
 5ZA  C11  C7    single    1.431  0.020  1.431
 5ZA  C11  H11   single    0.930  0.020  1.080
 5ZA  C7   C8    aromatic  1.385  0.020  1.385
 5ZA  C7   C1    aromatic  1.448  0.020  1.448
 5ZA  C8   N9    aromatic  1.346  0.020  1.346
 5ZA  C8   H8    single    0.930  0.020  1.080
 5ZA  N9   C6    aromatic  1.370  0.020  1.370
 5ZA  N9   HN9   single    0.860  0.020  1.020
 5ZA  C6   C5    aromatic  1.394  0.020  1.394
 5ZA  C6   C1    aromatic  1.407  0.020  1.407
 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    1.219  0.020  1.219
 5ZA  C16  N15   single    1.377  0.020  1.377
 5ZA  N15  C18   single    1.439  0.020  1.439
 5ZA  C18  C19   single    1.546  0.020  1.546
 5ZA  C18  H181  single    0.970  0.020  1.090
 5ZA  C18  H182  single    0.970  0.020  1.090
 5ZA  C19  O21   deloc     1.240  0.020  1.240
 5ZA  C19  OXT   deloc     1.245  0.020  1.245

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  108.33  3.000
 5ZA  H253  C25  H251  107.55  3.000
 5ZA  H252  C25  H251  107.32  3.000
 5ZA  H253  C25  C23   111.97  3.000
 5ZA  H252  C25  C23   111.02  3.000
 5ZA  H251  C25  C23   110.47  3.000
 5ZA  H23   C23  C22   107.85  3.000
 5ZA  H23   C23  O24   110.14  3.000
 5ZA  C22   C23  O24   107.09  3.000
 5ZA  H23   C23  C25   108.08  3.000
 5ZA  C22   C23  C25   111.67  3.000
 5ZA  O24   C23  C25   111.93  3.000
 5ZA  H24   O24  C23   108.00  3.000
 5ZA  H22   C22  C14   108.89  3.000
 5ZA  H22   C22  N26   107.65  3.000
 5ZA  C14   C22  N26   109.00  3.000
 5ZA  H22   C22  C23   106.44  3.000
 5ZA  C14   C22  C23   109.03  3.000
 5ZA  N26   C22  C23   115.64  3.000
 5ZA  H262  N26  H261  106.94  3.000
 5ZA  H262  N26  C22   109.73  3.000
 5ZA  H261  N26  C22   109.76  3.000
 5ZA  N15   C14  N13   113.79  3.000
 5ZA  N15   C14  C22   122.71  3.000
 5ZA  N13   C14  C22   123.47  3.000
 5ZA  C12   N13  C14   106.15  3.000
 5ZA  C16   C12  C11   123.74  3.000
 5ZA  C16   C12  N13   108.91  3.000
 5ZA  C11   C12  N13   127.35  3.000
 5ZA  H11   C11  C7    117.47  3.000
 5ZA  H11   C11  C12   114.87  3.000
 5ZA  C7    C11  C12   127.64  3.000
 5ZA  C1    C7   C8    105.74  3.000
 5ZA  C1    C7   C11   128.22  3.000
 5ZA  C8    C7   C11   125.99  3.000
 5ZA  H8    C8   N9    121.54  3.000
 5ZA  H8    C8   C7    128.69  3.000
 5ZA  N9    C8   C7    109.76  3.000
 5ZA  HN9   N9   C6    125.05  3.000
 5ZA  HN9   N9   C8    124.56  3.000
 5ZA  C6    N9   C8    110.39  3.000
 5ZA  C1    C6   C5    123.81  3.000
 5ZA  C1    C6   N9    107.30  3.000
 5ZA  C5    C6   N9    128.88  3.000
 5ZA  H5    C5   C4    122.03  3.000
 5ZA  H5    C5   C6    121.73  3.000
 5ZA  C4    C5   C6    116.24  3.000
 5ZA  H4    C4   C3    118.79  3.000
 5ZA  H4    C4   C5    119.60  3.000
 5ZA  C3    C4   C5    121.61  3.000
 5ZA  H3    C3   C2    118.85  3.000
 5ZA  H3    C3   C4    119.11  3.000
 5ZA  C2    C3   C4    122.03  3.000
 5ZA  C1    C2   N10   121.34  3.000
 5ZA  C1    C2   C3    117.56  3.000
 5ZA  N10   C2   C3    121.05  3.000
 5ZA  H102  N10  H101  109.34  3.000
 5ZA  H102  N10  C2    114.91  3.000
 5ZA  H101  N10  C2    113.44  3.000
 5ZA  C2    C1   C6    118.70  3.000
 5ZA  C2    C1   C7    134.50  3.000
 5ZA  C6    C1   C7    106.80  3.000
 5ZA  N15   C16  O17   125.73  3.000
 5ZA  N15   C16  C12   103.17  3.000
 5ZA  O17   C16  C12   131.09  3.000
 5ZA  C18   N15  C16   122.32  3.000
 5ZA  C18   N15  C14   129.65  3.000
 5ZA  C16   N15  C14   107.95  3.000
 5ZA  H182  C18  H181  105.90  3.000
 5ZA  H182  C18  C19   109.35  3.000
 5ZA  H181  C18  C19   109.40  3.000
 5ZA  H182  C18  N15   109.15  3.000
 5ZA  H181  C18  N15   108.54  3.000
 5ZA  C19   C18  N15   114.18  3.000
 5ZA  OXT   C19  O21   128.27  3.000
 5ZA  OXT   C19  C18   114.18  3.000
 5ZA  O21   C19  C18   117.55  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  Var_01    C7    C11  C12  N13    0.23  30.0  2
 5ZA  Var_02    C8    C7   C11  C12   -3.43  30.0  2
 5ZA  Var_03    C19   C18  N15  C14  101.89  30.0  3
 5ZA  Var_04    O21   C19  C18  N15   -9.49  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

