# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:07:57 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: [(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(3-chloro-4-hydroxybenzylidene)-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/c2ccc(O)c(Cl)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
 4NT  4NT  '[(4Z)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(3-chloro-4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  40  24  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4NT
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
 4NT  N1   N   NH2   0  -0.795   1.8472   2.8942  -1.4011
 4NT  CA1  C   CH1   0  -0.235   2.6468   1.8065  -0.8776
 4NT  CB1  C   CH1   0   0.034   3.3083   2.2443   0.4526
 4NT  CG1  C   CH3   0  -0.693   4.4033   3.2661   0.1993
 4NT  OG1  O   OH1   0  -0.660   2.3310   2.7119   1.3494
 4NT  C1   C   CR5   0   0.549   1.8480   0.5548  -0.6619
 4NT  N2   N   N     0  -0.493   0.5645   0.5332  -0.5760
 4NT  N3   N   NR5   0  -0.563   2.4280  -0.6909  -0.5103
 4NT  C2   C   CR5   0   0.545   1.4228  -1.6131  -0.2983
 4NT  O2   O   O     0  -0.442   1.5847  -2.8040  -0.1339
 4NT  CA2  C   CR5   0   0.103   0.1993  -0.7864  -0.3448
 4NT  CA3  C   CH2   0  -0.465   3.8096  -1.0650  -0.5559
 4NT  C3   C   C     0   0.552   4.3342  -1.4242   0.8193
 4NT  O3   O   O     0  -0.426   3.7374  -1.2307   1.8445
 4NT  CB2  C   C1    0  -0.386  -1.0359  -1.2995  -0.1847
 4NT  CG2  C   CR6   0   0.134  -2.3173  -0.6292  -0.1991
 4NT  CD1  C   CR16  0  -0.253  -3.4633  -1.4179  -0.0384
 4NT  CD2  C   CR16  0  -0.293  -2.4874   0.7529  -0.3592
 4NT  CE1  C   CR6   0  -0.134  -4.7203  -0.8520  -0.0398
 4NT  CE2  C   CR16  0  -0.364  -3.7473   1.3150  -0.3566
 4NT  CZ   C   CR6   0   0.419  -4.8870   0.5256  -0.1981
 4NT  OH   O   OH1   0  -0.597  -6.1263   1.0169  -0.1883
 4NT  CL1  CL  CL    0  -0.102  -6.1210  -1.8445   0.1599
 4NT  H1   H   HNH2  0   0.365   1.8074   2.8394  -2.4095
 4NT  H2   H   HNH2  0   0.360   0.8905   2.8036  -1.0799
 4NT  H4   H   HCH1  0   0.279   3.4477   1.5902  -1.5921
 4NT  H5   H   HCH1  0   0.236   3.7542   1.3728   0.9381
 4NT  H6   H   HCH3  0   0.231   4.0163   4.1340  -0.3369
 4NT  H7   H   HCH3  0   0.242   4.8357   3.6053   1.1409
 4NT  H8   H   HCH3  0   0.230   5.2052   2.8331  -0.4001
 4NT  H9   H   HOH1  0   0.444   1.9642   3.5248   0.9819
 4NT  H10  H   HCH2  0   0.325   3.9469  -1.9100  -1.2337
 4NT  H11  H   HCH2  0   0.326   4.4096  -0.2500  -0.9640
 4NT  H13  H   H     0   0.273  -1.0746  -2.3723  -0.0229
 4NT  H15  H   HCR6  0   0.283  -3.3652  -2.4887   0.0875
 4NT  H16  H   HCR6  0   0.287  -1.6258   1.3915  -0.4848
 4NT  H17  H   HCR6  0   0.288  -3.8561   2.3865  -0.4788
 4NT  O1   O   OH1   0  -0.583   5.5390  -1.9594   0.7342
 4NT  H3   H   HOH1  0   0.488  -6.1134   1.9760  -0.2938
 4NT  H12  H   HOH1  0   0.490   5.8846  -2.1597   1.6174

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
 4NT  O3   C3   double    1.202  0.020  1.202
 4NT  O2   C2   double    1.213  0.020  1.213
 4NT  CA3  C3   single    1.515  0.020  1.515
 4NT  CA3  N3   single    1.432  0.020  1.432
 4NT  C2   N3   single    1.381  0.020  1.381
 4NT  C2   CA2  single    1.477  0.020  1.477
 4NT  N3   C1   single    1.382  0.020  1.382
 4NT  CA2  CB2  double    1.347  0.020  1.347
 4NT  CA2  N2   single    1.389  0.020  1.389
 4NT  N1   CA1  single    1.448  0.020  1.448
 4NT  CB2  CG2  single    1.446  0.020  1.446
 4NT  C1   N2   double    1.286  0.020  1.286
 4NT  C1   CA1  single    1.500  0.020  1.500
 4NT  CD2  CG2  aromatic  1.402  0.020  1.402
 4NT  CD2  CE2  aromatic  1.380  0.020  1.380
 4NT  CA1  CB1  single    1.549  0.020  1.549
 4NT  CG2  CD1  aromatic  1.400  0.020  1.400
 4NT  CE2  CZ   aromatic  1.395  0.020  1.395
 4NT  CD1  CE1  aromatic  1.379  0.020  1.379
 4NT  CB1  OG1  single    1.406  0.020  1.406
 4NT  CB1  CG1  single    1.519  0.020  1.519
 4NT  CZ   CE1  aromatic  1.397  0.020  1.397
 4NT  CZ   OH   single    1.333  0.020  1.333
 4NT  CE1  CL1  single    1.728  0.020  1.728
 4NT  N1   H1   single    0.890  0.020  1.040
 4NT  N1   H2   single    0.890  0.020  1.040
 4NT  CA1  H4   single    0.970  0.020  1.090
 4NT  CB1  H5   single    0.970  0.020  1.090
 4NT  CG1  H6   single    0.970  0.020  1.090
 4NT  CG1  H7   single    0.970  0.020  1.090
 4NT  CG1  H8   single    0.970  0.020  1.090
 4NT  OG1  H9   single    0.850  0.020  0.980
 4NT  CA3  H10  single    0.970  0.020  1.090
 4NT  CA3  H11  single    0.970  0.020  1.090
 4NT  CB2  H13  single    0.930  0.020  1.080
 4NT  CD1  H15  single    0.930  0.020  1.080
 4NT  CD2  H16  single    0.930  0.020  1.080
 4NT  CE2  H17  single    0.930  0.020  1.080
 4NT  C3   O1   single    1.321  0.020  1.321
 4NT  OH   H3   single    0.850  0.020  0.980
 4NT  O1   H12  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
 4NT  H2   N1   H1   105.92  3.000
 4NT  H2   N1   CA1  109.85  3.000
 4NT  H1   N1   CA1  109.99  3.000
 4NT  H4   CA1  C1   108.57  3.000
 4NT  H4   CA1  CB1  107.69  3.000
 4NT  C1   CA1  CB1  109.86  3.000
 4NT  H4   CA1  N1   108.44  3.000
 4NT  CB1  CA1  N1   109.52  3.000
 4NT  C1   CA1  N1   112.62  3.000
 4NT  H5   CB1  OG1  105.39  3.000
 4NT  H5   CB1  CG1  108.45  3.000
 4NT  OG1  CB1  CG1  112.56  3.000
 4NT  H5   CB1  CA1  109.30  3.000
 4NT  CG1  CB1  CA1  110.78  3.000
 4NT  OG1  CB1  CA1  110.17  3.000
 4NT  H8   CG1  H7   107.85  3.000
 4NT  H8   CG1  H6   107.85  3.000
 4NT  H7   CG1  H6   108.52  3.000
 4NT  H8   CG1  CB1  110.76  3.000
 4NT  H7   CG1  CB1  110.55  3.000
 4NT  H6   CG1  CB1  111.18  3.000
 4NT  H9   OG1  CB1  107.55  3.000
 4NT  N3   C1   N2   113.34  3.000
 4NT  N2   C1   CA1  123.69  3.000
 4NT  N3   C1   CA1  122.96  3.000
 4NT  CA2  N2   C1   106.83  3.000
 4NT  CA3  N3   C2   122.20  3.000
 4NT  C2   N3   C1   108.25  3.000
 4NT  CA3  N3   C1   129.55  3.000
 4NT  CA2  C2   O2   131.62  3.000
 4NT  CA2  C2   N3   102.97  3.000
 4NT  O2   C2   N3   125.41  3.000
 4NT  CB2  CA2  C2   122.85  3.000
 4NT  CB2  CA2  N2   128.54  3.000
 4NT  C2   CA2  N2   108.61  3.000
 4NT  H11  CA3  H10  106.06  3.000
 4NT  H11  CA3  C3   109.03  3.000
 4NT  H10  CA3  C3   109.66  3.000
 4NT  H11  CA3  N3   110.32  3.000
 4NT  H10  CA3  N3   110.07  3.000
 4NT  C3   CA3  N3   111.54  3.000
 4NT  O1   C3   O3   124.96  3.000
 4NT  O1   C3   CA3  110.69  3.000
 4NT  O3   C3   CA3  124.34  3.000
 4NT  H13  CB2  CG2  115.34  3.000
 4NT  H13  CB2  CA2  115.27  3.000
 4NT  CG2  CB2  CA2  129.39  3.000
 4NT  CD2  CG2  CD1  117.97  3.000
 4NT  CD1  CG2  CB2  117.57  3.000
 4NT  CD2  CG2  CB2  124.46  3.000
 4NT  H15  CD1  CE1  119.26  3.000
 4NT  H15  CD1  CG2  119.75  3.000
 4NT  CE1  CD1  CG2  120.99  3.000
 4NT  H16  CD2  CE2  119.20  3.000
 4NT  H16  CD2  CG2  119.97  3.000
 4NT  CE2  CD2  CG2  120.83  3.000
 4NT  CL1  CE1  CZ   118.87  3.000
 4NT  CL1  CE1  CD1  120.21  3.000
 4NT  CZ   CE1  CD1  120.92  3.000
 4NT  H17  CE2  CZ   119.34  3.000
 4NT  H17  CE2  CD2  119.63  3.000
 4NT  CZ   CE2  CD2  121.03  3.000
 4NT  OH   CZ   CE2  123.47  3.000
 4NT  OH   CZ   CE1  118.27  3.000
 4NT  CE2  CZ   CE1  118.26  3.000
 4NT  H3   OH   CZ   110.67  3.000
 4NT  H12  O1   C3   110.50  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
 4NT  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 4NT  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 4NT  CONST_03  CE2  CD2  CG2  CD1    0.00   0.0  0
 4NT  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 4NT  CONST_05  CE1  CD1  CG2  CD2    0.00   0.0  0
 4NT  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 4NT  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 4NT  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 4NT  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 4NT  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 4NT  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 4NT  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 4NT  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 4NT  CONST_14  CL1  CE1  CD1  CG2  180.00   0.0  0
 4NT  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 4NT  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 4NT  CONST_17  CL1  CE1  CZ   CE2  180.00   0.0  0
 4NT  CONST_18  C2   N3   C1   CA1  180.00   0.0  0
 4NT  CONST_19  CA2  N2   C1   CA1  180.00   0.0  0
 4NT  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 4NT  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 4NT  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 4NT  CONST_23  H17  CE2  CD2  CG2  180.00   0.0  0
 4NT  CONST_24  H16  CD2  CG2  CD1  180.00   0.0  0
 4NT  CONST_25  H15  CD1  CG2  CD2  180.00   0.0  0
 4NT  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 4NT  CONST_27  CA3  N3   C2   O2     0.00   0.0  0
 4NT  CONST_28  H12  O1   C3   CA3  180.00   0.0  0
 4NT  Var_01    CG2  CB2  CA2  N2    -0.45  30.0  2
 4NT  Var_02    CD2  CG2  CB2  CA2   -1.76  30.0  2
 4NT  Var_03    C3   CA3  N3   C1   108.25  30.0  1
 4NT  Var_04    O3   C3   CA3  N3   -10.44  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
 4NT  chir_01  CA1  N1   C1   CB1  positiv
 4NT  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
 4NT  plan-1  CA1  0.020
 4NT  plan-1  C1   0.020
 4NT  plan-1  N2   0.020
 4NT  plan-1  N3   0.020
 4NT  plan-1  C2   0.020
 4NT  plan-1  O2   0.020
 4NT  plan-1  CA2  0.020
 4NT  plan-1  CA3  0.020
 4NT  plan-1  CB2  0.020
 4NT  plan-2  CB2  0.020
 4NT  plan-2  CG2  0.020
 4NT  plan-2  CD1  0.020
 4NT  plan-2  CD2  0.020
 4NT  plan-2  CE1  0.020
 4NT  plan-2  CE2  0.020
 4NT  plan-2  CZ   0.020
 4NT  plan-2  OH   0.020
 4NT  plan-2  CL1  0.020
 4NT  plan-2  H15  0.020
 4NT  plan-2  H16  0.020
 4NT  plan-2  H17  0.020
 4NT  plan-3  CA3  0.020
 4NT  plan-3  C3   0.020
 4NT  plan-3  O3   0.020
 4NT  plan-3  O1   0.020
 4NT  plan-3  H12  0.020

