# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:33:16 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: [(2S)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(1H-imidazol-5-ylmethyl)-5-oxo-2,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO)[C@H]1N=C(Cc2[nH]cnc2)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
 IIC  IIC  '[(2S)-2-[(1R)-1-amino-2-hydroxyethyl]-4-(1H-imidazol-5-ylmethyl)-5-oxo-2,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  34  20  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IIC
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
 IIC  C1    C  CR15   0   0.044   0.8275  -0.6682  -0.3333
 IIC  N2    N  N      0  -0.353  -0.5132  -0.1447  -0.3309
 IIC  CA2   C  CR5    0   0.127  -0.5342   0.8880   0.4038
 IIC  C2    C  CR5    0   0.502   0.8237   1.2261   0.9409
 IIC  O2    O  O      0  -0.482   1.1346   2.1913   1.6178
 IIC  N3    N  NR5    0  -0.461   1.5953   0.2206   0.5054
 IIC  CA1   C  CH1    0  -0.146   0.8436  -2.1226   0.1884
 IIC  N1    N  NH2    0  -0.780   0.4030  -2.2788   1.5543
 IIC  CB1   C  CH2    0  -0.127   0.0326  -3.0030  -0.7488
 IIC  OG1   O  OH1    0  -0.668   0.3057  -4.3534  -0.4592
 IIC  CA3   C  CH2    0  -0.471   3.0306   0.2349   0.5337
 IIC  C3    C  C      0   0.418   3.6637   0.9808  -0.6671
 IIC  O3    O  O      0  -0.589   2.8897   1.5261  -1.4697
 IIC  CB2   C  CH2    0  -0.607  -1.7264   1.7342   0.6934
 IIC  CG2   C  C      0   0.329  -3.0152   1.1579   0.2352
 IIC  ND1   N  NC1    0  -0.597  -3.3261   0.9119  -1.0716
 IIC  CE1   C  C1     0   0.079  -4.5697   0.3940  -1.1114
 IIC  NE2   N  N      0  -0.444  -5.0867   0.2950   0.0860
 IIC  CD2   C  C1     0  -0.269  -4.1243   0.7684   0.9334
 IIC  OXT   O  OC    -1  -0.614   4.9076   0.9563  -0.6917
 IIC  H1    H  HCR5   0   0.270   1.2168  -0.6497  -1.3574
 IIC  HA1   H  HCH1   0   0.246   1.8870  -2.4534   0.1297
 IIC  H11   H  HNH2   0   0.350   0.9638  -1.7145   2.1797
 IIC  H12   H  HNH2   0   0.341  -0.5559  -1.9694   1.6613
 IIC  HB21  H  HCH2   0   0.292  -1.7793   1.9074   1.7708
 IIC  HB11  H  HCH2   0   0.198  -1.0334  -2.7704  -0.6303
 IIC  HB12  H  HCH2   0   0.200   0.2965  -2.7536  -1.7849
 IIC  HG1   H  HOH1   0   0.454  -0.1939  -4.8944  -1.0771
 IIC  HA31  H  HCH2   0   0.266   3.3573   0.7060   1.4628
 IIC  HA32  H  HCH2   0   0.259   3.3993  -0.7929   0.5660
 IIC  HB2   H  HCH2   0   0.293  -1.5520   2.7229   0.2529
 IIC  HD1   H  HNC1   0   0.415  -2.7210   1.0532  -1.8649
 IIC  HE1   H  H      0   0.275  -5.0463   0.1094  -2.0369
 IIC  HD2   H  H      0   0.251  -4.2712   0.8113   2.0025

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
 IIC  CB1   OG1   single    1.408  0.020  1.408
 IIC  CB1   CA1   single    1.520  0.020  1.520
 IIC  N1    CA1   single    1.444  0.020  1.444
 IIC  CA1   C1    single    1.545  0.020  1.545
 IIC  CE1   ND1   aromatic  1.348  0.020  1.348
 IIC  CE1   NE2   aromatic  1.308  0.020  1.308
 IIC  ND1   CG2   aromatic  1.366  0.020  1.366
 IIC  C1    N2    single    1.439  0.020  1.439
 IIC  C1    N3    single    1.443  0.020  1.443
 IIC  N2    CA2   double    1.268  0.020  1.268
 IIC  NE2   CD2   aromatic  1.367  0.020  1.367
 IIC  CG2   CD2   aromatic  1.367  0.020  1.367
 IIC  CG2   CB2   single    1.484  0.020  1.484
 IIC  N3    CA3   single    1.436  0.020  1.436
 IIC  N3    C2    single    1.340  0.020  1.340
 IIC  CA2   CB2   single    1.490  0.020  1.490
 IIC  CA2   C2    single    1.499  0.020  1.499
 IIC  CA3   C3    single    1.549  0.020  1.549
 IIC  OXT   C3    deloc     1.244  0.020  1.244
 IIC  C3    O3    deloc     1.241  0.020  1.241
 IIC  C2    O2    double    1.219  0.020  1.219
 IIC  C1    H1    single    0.970  0.020  1.090
 IIC  HB21  CB2   single    0.970  0.020  1.090
 IIC  CA1   HA1   single    0.970  0.020  1.090
 IIC  N1    H11   single    0.890  0.020  1.040
 IIC  N1    H12   single    0.890  0.020  1.040
 IIC  CB1   HB11  single    0.970  0.020  1.090
 IIC  CB1   HB12  single    0.970  0.020  1.090
 IIC  OG1   HG1   single    0.850  0.020  0.980
 IIC  CA3   HA31  single    0.970  0.020  1.090
 IIC  CA3   HA32  single    0.970  0.020  1.090
 IIC  CB2   HB2   single    0.970  0.020  1.090
 IIC  ND1   HD1   single    0.860  0.020  1.020
 IIC  CE1   HE1   single    0.930  0.020  1.080
 IIC  CD2   HD2   single    0.930  0.020  1.080

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
 IIC  H1    C1   CA1   109.13  3.000
 IIC  H1    C1   N3    110.10  3.000
 IIC  CA1   C1   N3    112.20  3.000
 IIC  H1    C1   N2    109.05  3.000
 IIC  N3    C1   N2    105.70  3.000
 IIC  CA1   C1   N2    110.58  3.000
 IIC  CA2   N2   C1    108.23  3.000
 IIC  CB2   CA2  C2    121.80  3.000
 IIC  C2    CA2  N2    112.11  3.000
 IIC  CB2   CA2  N2    126.05  3.000
 IIC  N3    C2   O2    128.87  3.000
 IIC  O2    C2   CA2   127.48  3.000
 IIC  N3    C2   CA2   103.65  3.000
 IIC  CA3   N3   C2    124.18  3.000
 IIC  C2    N3   C1    110.16  3.000
 IIC  CA3   N3   C1    123.33  3.000
 IIC  HA1   CA1  CB1   107.46  3.000
 IIC  HA1   CA1  N1    107.97  3.000
 IIC  CB1   CA1  N1    110.96  3.000
 IIC  HA1   CA1  C1    106.02  3.000
 IIC  N1    CA1  C1    114.71  3.000
 IIC  CB1   CA1  C1    109.35  3.000
 IIC  H12   N1   H11   106.79  3.000
 IIC  H12   N1   CA1   110.83  3.000
 IIC  H11   N1   CA1   110.81  3.000
 IIC  HB12  CB1  HB11  106.69  3.000
 IIC  HB12  CB1  OG1   111.43  3.000
 IIC  HB11  CB1  OG1   111.68  3.000
 IIC  HB12  CB1  CA1   108.78  3.000
 IIC  HB11  CB1  CA1   109.20  3.000
 IIC  OG1   CB1  CA1   108.98  3.000
 IIC  HG1   OG1  CB1   107.87  3.000
 IIC  HA32  CA3  HA31  106.25  3.000
 IIC  HA32  CA3  C3    109.76  3.000
 IIC  HA31  CA3  C3    109.25  3.000
 IIC  HA32  CA3  N3    109.19  3.000
 IIC  HA31  CA3  N3    108.68  3.000
 IIC  C3    CA3  N3    113.46  3.000
 IIC  OXT   C3   O3    128.26  3.000
 IIC  O3    C3   CA3   117.25  3.000
 IIC  OXT   C3   CA3   114.48  3.000
 IIC  HB2   CB2  HB21  105.13  3.000
 IIC  HB2   CB2  CG2   111.36  3.000
 IIC  HB21  CB2  CG2   108.90  3.000
 IIC  HB2   CB2  CA2   107.86  3.000
 IIC  HB21  CB2  CA2   108.69  3.000
 IIC  CG2   CB2  CA2   114.46  3.000
 IIC  CD2   CG2  ND1   104.64  3.000
 IIC  CD2   CG2  CB2   131.09  3.000
 IIC  ND1   CG2  CB2   124.27  3.000
 IIC  HD1   ND1  CE1   125.78  3.000
 IIC  HD1   ND1  CG2   126.25  3.000
 IIC  CE1   ND1  CG2   107.91  3.000
 IIC  HE1   CE1  NE2   126.19  3.000
 IIC  HE1   CE1  ND1   122.29  3.000
 IIC  NE2   CE1  ND1   111.52  3.000
 IIC  CD2   NE2  CE1   105.24  3.000
 IIC  HD2   CD2  NE2   122.11  3.000
 IIC  HD2   CD2  CG2   127.20  3.000
 IIC  NE2   CD2  CG2   110.69  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
 IIC  CONST_01  NE2  CE1  ND1  CG2     0.00   0.0  0
 IIC  CONST_02  CE1  NE2  CD2  CG2     0.00   0.0  0
 IIC  CONST_03  CD2  NE2  CE1  ND1     0.00   0.0  0
 IIC  CONST_04  NE2  CD2  CG2  ND1     0.00   0.0  0
 IIC  CONST_05  CD2  CG2  ND1  CE1     0.00   0.0  0
 IIC  CONST_06  CA2  C2   N3   C1      0.00   0.0  0
 IIC  CONST_07  CE1  ND1  CG2  CB2   180.00   0.0  0
 IIC  CONST_08  NE2  CD2  CG2  CB2   180.00   0.0  0
 IIC  CONST_09  O2   C2   N3   C1    180.00   0.0  0
 IIC  CONST_10  CA3  N3   C2   CA2   180.00   0.0  0
 IIC  CONST_11  HE1  CE1  ND1  CG2   180.00   0.0  0
 IIC  CONST_12  HD2  CD2  CG2  ND1   180.00   0.0  0
 IIC  CONST_13  HD1  ND1  CE1  NE2   180.00   0.0  0
 IIC  CONST_14  CA3  N3   C2   O2      0.00   0.0  0
 IIC  Var_01    C2   CA2  N2   C1      2.72  30.0  1
 IIC  Var_02    N3   C2   CA2  N2     -4.12  30.0  1
 IIC  Var_03    CG2  CB2  CA2  N2     10.08  30.0  3
 IIC  Var_04    ND1  CG2  CB2  CA2   -63.19  30.0  2
 IIC  Var_05    C3   CA3  N3   C1     78.31  30.0  3
 IIC  Var_06    OXT  C3   CA3  N3   -177.11  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
 IIC  chir_01  C1   CA1  N2  N3   negativ
 IIC  chir_02  CA1  N1   C1  CB1  positiv

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
 IIC  plan-1  CB2  0.020
 IIC  plan-1  CG2  0.020
 IIC  plan-1  ND1  0.020
 IIC  plan-1  CE1  0.020
 IIC  plan-1  NE2  0.020
 IIC  plan-1  CD2  0.020
 IIC  plan-1  HD1  0.020
 IIC  plan-1  HE1  0.020
 IIC  plan-1  HD2  0.020
 IIC  plan-2  CA3  0.020
 IIC  plan-2  C3   0.020
 IIC  plan-2  O3   0.020
 IIC  plan-2  OXT  0.020
 IIC  plan-3  C1   0.020
 IIC  plan-3  CA2  0.020
 IIC  plan-3  C2   0.020
 IIC  plan-3  O2   0.020
 IIC  plan-3  N3   0.020
 IIC  plan-3  CA3  0.020

