# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 08:07:48 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: {(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-difluoro-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](O)[C@H](N)C1=N\C(=C/c2cc(F)c(O)c(F)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
 MHY  MHY  '{(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  40  25  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MHY
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
 MHY  N1   N  NH2   0  -0.782  -1.6600  -2.5593  -1.2438
 MHY  CA1  C  CH1   0  -0.248  -2.4376  -1.7970  -0.2940
 MHY  CB1  C  CH1   0   0.022  -2.7711  -2.5224   1.0414
 MHY  CG1  C  CH3   0  -0.699  -3.5931  -3.7776   0.8008
 MHY  OG1  O  OH1   0  -0.653  -1.6040  -2.7787   1.7840
 MHY  C1   C  CR5   0   0.588  -1.7110  -0.5297   0.0228
 MHY  N2   N  N     0  -0.484  -0.4401  -0.3794  -0.0945
 MHY  N3   N  NR5   0  -0.563  -2.3542   0.5716   0.5589
 MHY  C2   C  CR5   0   0.544  -1.4089   1.5602   0.7610
 MHY  O2   O  O     0  -0.434  -1.6297   2.6808   1.1649
 MHY  CA2  C  CR5   0   0.102  -0.1483   0.9006   0.3550
 MHY  CA3  C  CH2   0  -0.476  -3.7620   0.8249   0.6094
 MHY  C3   C  C     0   0.553  -4.2778   1.3169  -0.7277
 MHY  O3   O  O     0  -0.423  -3.5948   1.4225  -1.7109
 MHY  CB2  C  C1    0  -0.387   1.0506   1.5077   0.4325
 MHY  CG2  C  CR6   0   0.165   2.3547   0.9979   0.0677
 MHY  CD1  C  CR16  0  -0.500   2.5666  -0.2836  -0.4595
 MHY  CD2  C  CR16  0  -0.481   3.4573   1.8397   0.2493
 MHY  CE1  C  CR6   0   0.527   3.8390  -0.6799  -0.7844
 MHY  CE2  C  CR6   0   0.482   4.7152   1.4028  -0.0897
 MHY  CZ   C  CR6   0   0.077   4.9558   0.1383  -0.6159
 MHY  OH   O  OH1   0  -0.602   6.1582  -0.3253  -0.9620
 MHY  F13  F  F     0  -0.307   4.0480  -1.9013  -1.2896
 MHY  F17  F  F     0  -0.314   5.7763   2.2082   0.0815
 MHY  O1   O  OH1   0  -0.582  -5.5653   1.6017  -0.6604
 MHY  H1   H  HNH2  0   0.348  -0.7593  -2.8128  -0.8589
 MHY  H2   H  HNH2  0   0.364  -2.1409  -3.4139  -1.4901
 MHY  H4   H  HCH1  0   0.270  -3.3912  -1.5471  -0.7722
 MHY  H5   H  HCH1  0   0.236  -3.3646  -1.8440   1.6625
 MHY  H6   H  HCH3  0   0.225  -3.0357  -4.5265   0.2344
 MHY  H7   H  HCH3  0   0.255  -3.8818  -4.2283   1.7499
 MHY  H8   H  HCH3  0   0.239  -4.5046  -3.5494   0.2477
 MHY  H9   H  HOH1  0   0.442  -1.1119  -3.4891   1.3589
 MHY  H11  H  HCH2  0   0.320  -4.3141  -0.0668   0.9089
 MHY  H12  H  HCH2  0   0.332  -3.9624   1.5739   1.3775
 MHY  H13  H  H     0   0.274   1.0370   2.5203   0.8216
 MHY  H15  H  HCR6  0   0.301   1.7391  -0.9620  -0.6125
 MHY  H16  H  HCR6  0   0.292   3.3340   2.8363   0.6541
 MHY  H17  H  HOH1  0   0.487   6.8473   0.3293  -0.7950
 MHY  H18  H  HOH1  0   0.491  -5.8942   1.9043  -1.5207

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
 MHY  O3   C3   double    1.202  0.020  1.202
 MHY  C3   CA3  single    1.515  0.020  1.515
 MHY  CA3  N3   single    1.431  0.020  1.431
 MHY  N1   CA1  single    1.445  0.020  1.445
 MHY  N3   C2   single    1.383  0.020  1.383
 MHY  N3   C1   single    1.383  0.020  1.383
 MHY  O2   C2   double    1.211  0.020  1.211
 MHY  CA1  C1   single    1.495  0.020  1.495
 MHY  CA1  CB1  single    1.556  0.020  1.556
 MHY  C2   CA2  single    1.479  0.020  1.479
 MHY  C1   N2   double    1.285  0.020  1.285
 MHY  CG1  CB1  single    1.520  0.020  1.520
 MHY  CB1  OG1  single    1.407  0.020  1.407
 MHY  CA2  N2   single    1.388  0.020  1.388
 MHY  CA2  CB2  double    1.346  0.020  1.346
 MHY  CB2  CG2  single    1.447  0.020  1.447
 MHY  CG2  CD2  aromatic  1.399  0.020  1.399
 MHY  CG2  CD1  aromatic  1.402  0.020  1.402
 MHY  CD2  CE2  aromatic  1.374  0.020  1.374
 MHY  CD1  CE1  aromatic  1.372  0.020  1.372
 MHY  CE2  F17  single    1.343  0.020  1.343
 MHY  CE2  CZ   aromatic  1.391  0.020  1.391
 MHY  CE1  CZ   aromatic  1.395  0.020  1.395
 MHY  CE1  F13  single    1.338  0.020  1.338
 MHY  CZ   OH   single    1.334  0.020  1.334
 MHY  C3   O1   single    1.320  0.020  1.320
 MHY  N1   H1   single    0.890  0.020  1.040
 MHY  N1   H2   single    0.890  0.020  1.040
 MHY  CA1  H4   single    0.970  0.020  1.090
 MHY  CB1  H5   single    0.970  0.020  1.090
 MHY  CG1  H6   single    0.970  0.020  1.090
 MHY  CG1  H7   single    0.970  0.020  1.090
 MHY  CG1  H8   single    0.970  0.020  1.090
 MHY  OG1  H9   single    0.850  0.020  0.980
 MHY  CA3  H11  single    0.970  0.020  1.090
 MHY  CA3  H12  single    0.970  0.020  1.090
 MHY  CB2  H13  single    0.930  0.020  1.080
 MHY  CD1  H15  single    0.930  0.020  1.080
 MHY  CD2  H16  single    0.930  0.020  1.080
 MHY  OH   H17  single    0.850  0.020  0.980
 MHY  O1   H18  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
 MHY  H2   N1   H1   107.71  3.000
 MHY  H2   N1   CA1  110.50  3.000
 MHY  H1   N1   CA1  111.17  3.000
 MHY  H4   CA1  C1   108.79  3.000
 MHY  H4   CA1  CB1  107.12  3.000
 MHY  C1   CA1  CB1  108.52  3.000
 MHY  H4   CA1  N1   107.57  3.000
 MHY  CB1  CA1  N1   115.70  3.000
 MHY  C1   CA1  N1   108.97  3.000
 MHY  H5   CB1  OG1  105.25  3.000
 MHY  H5   CB1  CG1  107.97  3.000
 MHY  OG1  CB1  CG1  112.45  3.000
 MHY  H5   CB1  CA1  108.32  3.000
 MHY  OG1  CB1  CA1  111.11  3.000
 MHY  CG1  CB1  CA1  111.42  3.000
 MHY  H8   CG1  H7   107.87  3.000
 MHY  H8   CG1  H6   107.89  3.000
 MHY  H7   CG1  H6   107.66  3.000
 MHY  H8   CG1  CB1  111.08  3.000
 MHY  H7   CG1  CB1  110.31  3.000
 MHY  H6   CG1  CB1  111.87  3.000
 MHY  H9   OG1  CB1  108.98  3.000
 MHY  N3   C1   N2   113.71  3.000
 MHY  N2   C1   CA1  124.09  3.000
 MHY  N3   C1   CA1  122.08  3.000
 MHY  CA2  N2   C1   106.63  3.000
 MHY  CA3  N3   C2   122.74  3.000
 MHY  C2   N3   C1   107.94  3.000
 MHY  CA3  N3   C1   127.72  3.000
 MHY  CA2  C2   O2   131.23  3.000
 MHY  CA2  C2   N3   102.93  3.000
 MHY  O2   C2   N3   125.84  3.000
 MHY  CB2  CA2  C2   122.82  3.000
 MHY  CB2  CA2  N2   128.45  3.000
 MHY  C2   CA2  N2   108.72  3.000
 MHY  H12  CA3  H11  105.95  3.000
 MHY  H12  CA3  C3   109.61  3.000
 MHY  H11  CA3  C3   109.60  3.000
 MHY  H12  CA3  N3   109.08  3.000
 MHY  H11  CA3  N3   111.28  3.000
 MHY  C3   CA3  N3   111.17  3.000
 MHY  O1   C3   O3   125.24  3.000
 MHY  O1   C3   CA3  110.91  3.000
 MHY  O3   C3   CA3  123.85  3.000
 MHY  H13  CB2  CG2  115.50  3.000
 MHY  H13  CB2  CA2  115.50  3.000
 MHY  CG2  CB2  CA2  129.00  3.000
 MHY  CD2  CG2  CD1  118.67  3.000
 MHY  CD1  CG2  CB2  123.58  3.000
 MHY  CD2  CG2  CB2  117.75  3.000
 MHY  H15  CD1  CE1  119.69  3.000
 MHY  H15  CD1  CG2  120.75  3.000
 MHY  CE1  CD1  CG2  119.56  3.000
 MHY  H16  CD2  CE2  119.28  3.000
 MHY  H16  CD2  CG2  120.84  3.000
 MHY  CE2  CD2  CG2  119.88  3.000
 MHY  F13  CE1  CZ   117.13  3.000
 MHY  F13  CE1  CD1  119.87  3.000
 MHY  CZ   CE1  CD1  123.00  3.000
 MHY  F17  CE2  CZ   117.18  3.000
 MHY  CZ   CE2  CD2  122.74  3.000
 MHY  F17  CE2  CD2  120.08  3.000
 MHY  OH   CZ   CE2  124.75  3.000
 MHY  OH   CZ   CE1  119.10  3.000
 MHY  CE2  CZ   CE1  116.14  3.000
 MHY  H17  OH   CZ   111.28  3.000
 MHY  H18  O1   C3   110.66  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
 MHY  CONST_01  CZ   CE2  CD2  CG2     0.00   0.0  0
 MHY  CONST_02  CZ   CE1  CD1  CG2     0.00   0.0  0
 MHY  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 MHY  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 MHY  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 MHY  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 MHY  CONST_07  CA2  C2   N3   C1      0.00   0.0  0
 MHY  CONST_08  C2   CA2  N2   C1      0.00   0.0  0
 MHY  CONST_09  C2   N3   C1   N2      0.00   0.0  0
 MHY  CONST_10  N3   C2   CA2  N2      0.00   0.0  0
 MHY  CONST_11  CA2  N2   C1   N3      0.00   0.0  0
 MHY  CONST_12  CE2  CD2  CG2  CB2   180.00   0.0  0
 MHY  CONST_13  CE1  CD1  CG2  CB2   180.00   0.0  0
 MHY  CONST_14  F17  CE2  CD2  CG2   180.00   0.0  0
 MHY  CONST_15  F13  CE1  CD1  CG2   180.00   0.0  0
 MHY  CONST_16  OH   CZ   CE1  CD1   180.00   0.0  0
 MHY  CONST_17  OH   CZ   CE2  CD2   180.00   0.0  0
 MHY  CONST_18  F17  CE2  CZ   CE1   180.00   0.0  0
 MHY  CONST_19  F13  CE1  CZ   CE2   180.00   0.0  0
 MHY  CONST_20  C2   N3   C1   CA1   180.00   0.0  0
 MHY  CONST_21  CA2  N2   C1   CA1   180.00   0.0  0
 MHY  CONST_22  O2   C2   N3   C1    180.00   0.0  0
 MHY  CONST_23  CA3  N3   C1   N2    180.00   0.0  0
 MHY  CONST_24  CA3  N3   C2   CA2   180.00   0.0  0
 MHY  CONST_25  H16  CD2  CG2  CD1   180.00   0.0  0
 MHY  CONST_26  H15  CD1  CG2  CD2   180.00   0.0  0
 MHY  CONST_28  CA3  N3   C2   O2      0.00   0.0  0
 MHY  CONST_29  H18  O1   C3   CA3   180.00   0.0  0
 MHY  Var_01    CG2  CB2  CA2  N2      0.19  30.0  2
 MHY  Var_02    CD2  CG2  CB2  CA2  -179.93  30.0  2
 MHY  Var_03    C3   CA3  N3   C1    -78.57  30.0  1
 MHY  Var_04    O3   C3   CA3  N3      2.92  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
 MHY  chir_01  CA1  N1   C1   CB1  positiv
 MHY  chir_02  CB1  OG1  CA1  CG1  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
 MHY  plan-1  CA1  0.020
 MHY  plan-1  C1   0.020
 MHY  plan-1  N2   0.020
 MHY  plan-1  N3   0.020
 MHY  plan-1  C2   0.020
 MHY  plan-1  O2   0.020
 MHY  plan-1  CA2  0.020
 MHY  plan-1  CA3  0.020
 MHY  plan-1  CB2  0.020
 MHY  plan-2  CB2  0.020
 MHY  plan-2  CG2  0.020
 MHY  plan-2  CD1  0.020
 MHY  plan-2  CD2  0.020
 MHY  plan-2  CE1  0.020
 MHY  plan-2  CE2  0.020
 MHY  plan-2  CZ   0.020
 MHY  plan-2  OH   0.020
 MHY  plan-2  F13  0.020
 MHY  plan-2  F17  0.020
 MHY  plan-2  H15  0.020
 MHY  plan-2  H16  0.020
 MHY  plan-3  CA3  0.020
 MHY  plan-3  C3   0.020
 MHY  plan-3  O3   0.020
 MHY  plan-3  O1   0.020
 MHY  plan-3  H18  0.020

