# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 20:22:30 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: {(2S)-2-[(1S)-1-aminoethyl]-4-benzyl-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@H]1N=C(Cc2ccccc2)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
 X9Q  X9Q  '{(2S)-2-[(1S)-1-aminoethyl]-4-benzyl-5-oxo-2,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  37  20  .  2022-09-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_X9Q
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
 X9Q  CD1   C  CR16  0  -0.299  -3.2783   0.0145  -1.3420
 X9Q  CE1   C  CR16  0  -0.242  -4.4493   0.7540  -1.2441
 X9Q  CZ    C  CR16  0  -0.271  -5.2234   0.6827  -0.0933
 X9Q  CE2   C  CR16  0  -0.243  -4.8193  -0.1331   0.9558
 X9Q  CD2   C  CR16  0  -0.303  -3.6483  -0.8719   0.8523
 X9Q  CG2   C  CR6   0   0.153  -2.8675  -0.8073  -0.2972
 X9Q  CB2   C  CH2   0  -0.609  -1.5899  -1.5870  -0.4016
 X9Q  CA2   C  CR5   0   0.148  -0.4091  -0.8546   0.1350
 X9Q  C2    C  CR5   0   0.513   0.9806  -1.4034   0.0062
 X9Q  O2    O  O     0  -0.474   1.3319  -2.4538  -0.4986
 X9Q  N2    N  N     0  -0.346  -0.4314   0.2466   0.7622
 X9Q  C1    C  CR15  0   0.077   0.9202   0.6241   1.0699
 X9Q  CA1   C  CH1   0  -0.116   1.2676   1.9503   0.3653
 X9Q  CB1   C  CH3   0  -0.671   0.5802   3.1136   1.0727
 X9Q  N1    N  NH2   0  -0.771   0.9677   1.8398  -1.0465
 X9Q  N3    N  NR5   0  -0.467   1.7358  -0.4842   0.6254
 X9Q  CA3   C  CH2   0  -0.458   3.1384  -0.6048   0.8533
 X9Q  C3    C  C     0   0.544   3.9783  -0.3120  -0.3736
 X9Q  O3    O  O     0  -0.415   3.5515  -0.1495  -1.4830
 X9Q  OXT   O  OH1   0  -0.593   5.2652  -0.2843  -0.0511
 X9Q  HD1   H  HCR6  0   0.247  -2.6794   0.0720  -2.2435
 X9Q  HE1   H  HCR6  0   0.253  -4.7586   1.3841  -2.0682
 X9Q  HZ    H  HCR6  0   0.254  -6.1380   1.2563  -0.0162
 X9Q  HE2   H  HCR6  0   0.254  -5.4186  -0.1951   1.8553
 X9Q  HD2   H  HCR6  0   0.248  -3.3419  -1.5102   1.6730
 X9Q  HB21  H  HCH2  0   0.289  -1.6682  -2.5393   0.1331
 X9Q  HB22  H  HCH2  0   0.285  -1.3792  -1.8539  -1.4411
 X9Q  H1    H  HCR5  0   0.274   1.0293   0.7575   2.1524
 X9Q  HA1   H  HCH1  0   0.246   2.3489   2.0830   0.4695
 X9Q  HB11  H  HCH3  0   0.228  -0.5051   3.0327   0.9925
 X9Q  HB12  H  HCH3  0   0.226   0.8363   3.1528   2.1330
 X9Q  HB13  H  HCH3  0   0.237   0.8831   4.0589   0.6221
 X9Q  HN11  H  HNH2  0   0.340  -0.0017   2.0799  -1.2129
 X9Q  HN12  H  HNH2  0   0.353   1.5214   2.5049  -1.5682
 X9Q  HA31  H  HCH2  0   0.312   3.4331   0.0623   1.6657
 X9Q  HA32  H  HCH2  0   0.315   3.3785  -1.6178   1.1914
 X9Q  HXT   H  HOH1  0   0.485   5.8053  -0.1225  -0.8390

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
 X9Q  CD1  CE1   aromatic  1.388  0.020  1.388
 X9Q  CD1  CG2   aromatic  1.391  0.020  1.391
 X9Q  CD1  HD1   single    0.930  0.020  1.080
 X9Q  CE1  CZ    aromatic  1.389  0.020  1.389
 X9Q  CE1  HE1   single    0.930  0.020  1.080
 X9Q  CZ   CE2   aromatic  1.389  0.020  1.389
 X9Q  CZ   HZ    single    0.930  0.020  1.080
 X9Q  CE2  CD2   aromatic  1.388  0.020  1.388
 X9Q  CE2  HE2   single    0.930  0.020  1.080
 X9Q  CD2  CG2   aromatic  1.391  0.020  1.391
 X9Q  CD2  HD2   single    0.930  0.020  1.080
 X9Q  CG2  CB2   single    1.500  0.020  1.500
 X9Q  CB2  CA2   single    1.490  0.020  1.490
 X9Q  CB2  HB21  single    0.970  0.020  1.090
 X9Q  CB2  HB22  single    0.970  0.020  1.090
 X9Q  CA2  N2    double    1.267  0.020  1.267
 X9Q  CA2  C2    single    1.500  0.020  1.500
 X9Q  C2   N3    single    1.341  0.020  1.341
 X9Q  C2   O2    double    1.217  0.020  1.217
 X9Q  N2   C1    single    1.437  0.020  1.437
 X9Q  C1   CA1   single    1.541  0.020  1.541
 X9Q  C1   N3    single    1.446  0.020  1.446
 X9Q  C1   H1    single    0.970  0.020  1.090
 X9Q  CA1  CB1   single    1.525  0.020  1.525
 X9Q  CA1  N1    single    1.448  0.020  1.448
 X9Q  CA1  HA1   single    0.970  0.020  1.090
 X9Q  CB1  HB11  single    0.970  0.020  1.090
 X9Q  CB1  HB12  single    0.970  0.020  1.090
 X9Q  CB1  HB13  single    0.970  0.020  1.090
 X9Q  N1   HN11  single    0.890  0.020  1.040
 X9Q  N1   HN12  single    0.890  0.020  1.040
 X9Q  N3   CA3   single    1.426  0.020  1.426
 X9Q  CA3  C3    single    1.515  0.020  1.515
 X9Q  CA3  HA31  single    0.970  0.020  1.090
 X9Q  CA3  HA32  single    0.970  0.020  1.090
 X9Q  C3   OXT   single    1.327  0.020  1.327
 X9Q  C3   O3    double    1.200  0.020  1.200
 X9Q  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
 X9Q  HD1   CD1  CG2   119.53  3.000
 X9Q  HD1   CD1  CE1   119.77  3.000
 X9Q  CG2   CD1  CE1   120.71  3.000
 X9Q  HE1   CE1  CZ    120.10  3.000
 X9Q  HE1   CE1  CD1   119.82  3.000
 X9Q  CZ    CE1  CD1   120.08  3.000
 X9Q  HZ    CZ   CE2   120.22  3.000
 X9Q  HZ    CZ   CE1   120.19  3.000
 X9Q  CE2   CZ   CE1   119.60  3.000
 X9Q  HE2   CE2  CD2   119.89  3.000
 X9Q  HE2   CE2  CZ    120.01  3.000
 X9Q  CD2   CE2  CZ    120.10  3.000
 X9Q  HD2   CD2  CG2   119.63  3.000
 X9Q  HD2   CD2  CE2   119.69  3.000
 X9Q  CG2   CD2  CE2   120.68  3.000
 X9Q  CB2   CG2  CD2   120.75  3.000
 X9Q  CB2   CG2  CD1   120.40  3.000
 X9Q  CD2   CG2  CD1   118.83  3.000
 X9Q  HB22  CB2  HB21  105.41  3.000
 X9Q  HB22  CB2  CA2   108.04  3.000
 X9Q  HB21  CB2  CA2   107.97  3.000
 X9Q  HB22  CB2  CG2   110.92  3.000
 X9Q  HB21  CB2  CG2   110.92  3.000
 X9Q  CA2   CB2  CG2   113.23  3.000
 X9Q  N2    CA2  C2    112.13  3.000
 X9Q  C2    CA2  CB2   121.58  3.000
 X9Q  N2    CA2  CB2   126.26  3.000
 X9Q  N3    C2   O2    128.35  3.000
 X9Q  O2    C2   CA2   128.23  3.000
 X9Q  N3    C2   CA2   103.38  3.000
 X9Q  C1    N2   CA2   108.52  3.000
 X9Q  H1    C1   N3    109.92  3.000
 X9Q  H1    C1   CA1   108.92  3.000
 X9Q  N3    C1   CA1   113.07  3.000
 X9Q  H1    C1   N2    109.70  3.000
 X9Q  N3    C1   N2    105.27  3.000
 X9Q  CA1   C1   N2    109.89  3.000
 X9Q  HA1   CA1  N1    107.87  3.000
 X9Q  HA1   CA1  CB1   107.98  3.000
 X9Q  N1    CA1  CB1   114.66  3.000
 X9Q  HA1   CA1  C1    106.47  3.000
 X9Q  N1    CA1  C1    109.48  3.000
 X9Q  CB1   CA1  C1    110.04  3.000
 X9Q  HB13  CB1  HB12  107.77  3.000
 X9Q  HB13  CB1  HB11  108.08  3.000
 X9Q  HB12  CB1  HB11  107.90  3.000
 X9Q  HB13  CB1  CA1   110.15  3.000
 X9Q  HB12  CB1  CA1   111.85  3.000
 X9Q  HB11  CB1  CA1   110.95  3.000
 X9Q  HN12  N1   HN11  106.48  3.000
 X9Q  HN12  N1   CA1   109.86  3.000
 X9Q  HN11  N1   CA1   109.91  3.000
 X9Q  CA3   N3   C1    124.78  3.000
 X9Q  CA3   N3   C2    124.72  3.000
 X9Q  C1    N3   C2    110.47  3.000
 X9Q  HA32  CA3  HA31  106.05  3.000
 X9Q  HA32  CA3  C3    107.89  3.000
 X9Q  HA31  CA3  C3    109.56  3.000
 X9Q  HA32  CA3  N3    110.08  3.000
 X9Q  HA31  CA3  N3    109.44  3.000
 X9Q  C3    CA3  N3    113.54  3.000
 X9Q  OXT   C3   O3    124.53  3.000
 X9Q  O3    C3   CA3   125.29  3.000
 X9Q  OXT   C3   CA3   110.17  3.000
 X9Q  HXT   OXT  C3    110.27  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
 X9Q  CONST_01  CE2  CZ   CE1  CD1    0.00   0.0  0
 X9Q  CONST_02  CE2  CD2  CG2  CD1    0.00   0.0  0
 X9Q  CONST_03  CD2  CG2  CD1  CE1    0.00   0.0  0
 X9Q  CONST_04  CD2  CE2  CZ   CE1    0.00   0.0  0
 X9Q  CONST_05  CG2  CD1  CE1  CZ     0.00   0.0  0
 X9Q  CONST_06  CG2  CD2  CE2  CZ     0.00   0.0  0
 X9Q  CONST_07  C1   N3   C2   CA2    0.00   0.0  0
 X9Q  CONST_08  CB2  CG2  CD1  CE1  180.00   0.0  0
 X9Q  CONST_09  CB2  CG2  CD2  CE2  180.00   0.0  0
 X9Q  CONST_10  CA3  N3   C2   CA2  180.00   0.0  0
 X9Q  CONST_11  C1   N3   C2   O2   180.00   0.0  0
 X9Q  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 X9Q  CONST_13  HD2  CD2  CG2  CD1  180.00   0.0  0
 X9Q  CONST_14  HE2  CE2  CZ   CE1  180.00   0.0  0
 X9Q  CONST_15  HD1  CD1  CE1  CZ   180.00   0.0  0
 X9Q  CONST_16  HE1  CE1  CZ   CE2  180.00   0.0  0
 X9Q  CONST_17  CA3  N3   C2   O2     0.00   0.0  0
 X9Q  CONST_18  HXT  OXT  C3   CA3  180.00   0.0  0
 X9Q  Var_01    N3   C2   CA2  N2    -0.29  30.0  1
 X9Q  Var_02    CA2  CB2  CG2  CD1   91.05  30.0  2
 X9Q  Var_03    N2   CA2  CB2  CG2    7.70  30.0  3
 X9Q  Var_04    C3   CA3  N3   C2    77.99  30.0  3
 X9Q  Var_05    OXT  C3   CA3  N3   172.49  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
 X9Q  chir_01  C1   N2  CA1  N3   positiv
 X9Q  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
 X9Q  plan-1  CD1  0.020
 X9Q  plan-1  CE1  0.020
 X9Q  plan-1  CZ   0.020
 X9Q  plan-1  CE2  0.020
 X9Q  plan-1  CD2  0.020
 X9Q  plan-1  CG2  0.020
 X9Q  plan-1  CB2  0.020
 X9Q  plan-1  HD1  0.020
 X9Q  plan-1  HE1  0.020
 X9Q  plan-1  HZ   0.020
 X9Q  plan-1  HE2  0.020
 X9Q  plan-1  HD2  0.020
 X9Q  plan-2  CA3  0.020
 X9Q  plan-2  C3   0.020
 X9Q  plan-2  O3   0.020
 X9Q  plan-2  OXT  0.020
 X9Q  plan-2  HXT  0.020
 X9Q  plan-3  CA2  0.020
 X9Q  plan-3  C2   0.020
 X9Q  plan-3  O2   0.020
 X9Q  plan-3  C1   0.020
 X9Q  plan-3  N3   0.020
 X9Q  plan-3  CA3  0.020

