# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:37:17 2022
#   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  36  20  .  2022-09-22  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_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  -3.2938  -0.0259  -1.3619
 X9Q  CE1   C  CR16   0  -0.243  -4.4719   0.7028  -1.2680
 X9Q  CZ    C  CR16   0  -0.272  -5.2470   0.6275  -0.1181
 X9Q  CE2   C  CR16   0  -0.243  -4.8364  -0.1816   0.9337
 X9Q  CD2   C  CR16   0  -0.304  -3.6583  -0.9095   0.8337
 X9Q  CG2   C  CR6    0   0.156  -2.8760  -0.8411  -0.3147
 X9Q  CB2   C  CH2    0  -0.609  -1.5913  -1.6093  -0.4143
 X9Q  CA2   C  CR5    0   0.143  -0.4181  -0.8684   0.1294
 X9Q  C2    C  CR5    0   0.499   0.9740  -1.4203   0.0323
 X9Q  O2    O  O      0  -0.497   1.3167  -2.4903  -0.4476
 X9Q  N2    N  N      0  -0.353  -0.4530   0.2418   0.7402
 X9Q  C1    C  CR15   0   0.069   0.9011   0.6189   1.0450
 X9Q  CA1   C  CH1    0  -0.102   1.2540   1.9180   0.2898
 X9Q  CB1   C  CH3    0  -0.674   0.6127   3.1155   0.9839
 X9Q  N1    N  NH2    0  -0.769   0.9030   1.7810  -1.1076
 X9Q  N3    N  NR5    0  -0.441   1.7187  -0.5026   0.6515
 X9Q  CA3   C  CH2    0  -0.466   3.1260  -0.6129   0.9147
 X9Q  C3    C  C      0   0.409   4.0703  -0.3139  -0.2732
 X9Q  O3    O  O      0  -0.575   3.5663  -0.1096  -1.3849
 X9Q  OXT   O  OC    -1  -0.626   5.2802  -0.3288   0.0324
 X9Q  HD1   H  HCR6   0   0.246  -2.6937   0.0359  -2.2623
 X9Q  HE1   H  HCR6   0   0.253  -4.7857   1.3280  -2.0942
 X9Q  HZ    H  HCR6   0   0.253  -6.1672   1.1926  -0.0438
 X9Q  HE2   H  HCR6   0   0.253  -5.4361  -0.2465   1.8328
 X9Q  HD2   H  HCR6   0   0.247  -3.3472  -1.5427   1.6565
 X9Q  HB21  H  HCH2   0   0.284  -1.6655  -2.5642   0.1162
 X9Q  HB22  H  HCH2   0   0.281  -1.3743  -1.8708  -1.4540
 X9Q  H1    H  HCR5   0   0.259   1.0045   0.7953   2.1222
 X9Q  HA1   H  HCH1   0   0.243   2.3397   2.0258   0.3534
 X9Q  HB11  H  HCH3   0   0.225  -0.4764   3.0511   0.9466
 X9Q  HB12  H  HCH3   0   0.223   0.9079   3.1841   2.0325
 X9Q  HB13  H  HCH3   0   0.234   0.9134   4.0418   0.4933
 X9Q  HN11  H  HNH2   0   0.336  -0.0493   2.0885  -1.2594
 X9Q  HN12  H  HNH2   0   0.348   1.4965   2.3702  -1.6735
 X9Q  HA31  H  HCH2   0   0.255   3.3689   0.0534   1.7456
 X9Q  HA32  H  HCH2   0   0.258   3.3369  -1.6262   1.2699

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    1.268  0.020  1.268
 X9Q  CA2  C2    single    1.501  0.020  1.501
 X9Q  C2   N3    single    1.334  0.020  1.334
 X9Q  C2   O2    double    1.222  0.020  1.222
 X9Q  N2   C1    single    1.438  0.020  1.438
 X9Q  C1   CA1   single    1.544  0.020  1.544
 X9Q  C1   N3    single    1.443  0.020  1.443
 X9Q  C1   H1    single    0.970  0.020  1.090
 X9Q  CA1  CB1   single    1.525  0.020  1.525
 X9Q  CA1  N1    single    1.447  0.020  1.447
 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    1.436  0.020  1.436
 X9Q  CA3  C3    single    1.547  0.020  1.547
 X9Q  CA3  HA31  single    0.970  0.020  1.090
 X9Q  CA3  HA32  single    0.970  0.020  1.090
 X9Q  C3   OXT   deloc     1.248  0.020  1.248
 X9Q  C3   O3    deloc     1.238  0.020  1.238

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   119.50  3.000
 X9Q  HD1   CD1  CE1   119.74  3.000
 X9Q  CG2   CD1  CE1   120.76  3.000
 X9Q  HE1   CE1  CZ    120.10  3.000
 X9Q  HE1   CE1  CD1   119.83  3.000
 X9Q  CZ    CE1  CD1   120.07  3.000
 X9Q  HZ    CZ   CE2   120.23  3.000
 X9Q  HZ    CZ   CE1   120.20  3.000
 X9Q  CE2   CZ   CE1   119.58  3.000
 X9Q  HE2   CE2  CD2   119.89  3.000
 X9Q  HE2   CE2  CZ    120.00  3.000
 X9Q  CD2   CE2  CZ    120.11  3.000
 X9Q  HD2   CD2  CG2   119.60  3.000
 X9Q  HD2   CD2  CE2   119.68  3.000
 X9Q  CG2   CD2  CE2   120.72  3.000
 X9Q  CB2   CG2  CD2   120.74  3.000
 X9Q  CB2   CG2  CD1   120.48  3.000
 X9Q  CD2   CG2  CD1   118.77  3.000
 X9Q  HB22  CB2  HB21  105.39  3.000
 X9Q  HB22  CB2  CA2   108.03  3.000
 X9Q  HB21  CB2  CA2   108.07  3.000
 X9Q  HB22  CB2  CG2   110.82  3.000
 X9Q  HB21  CB2  CG2   110.88  3.000
 X9Q  CA2   CB2  CG2   113.29  3.000
 X9Q  N2    CA2  C2    112.26  3.000
 X9Q  C2    CA2  CB2   121.59  3.000
 X9Q  N2    CA2  CB2   126.13  3.000
 X9Q  N3    C2   O2    128.92  3.000
 X9Q  O2    C2   CA2   127.43  3.000
 X9Q  N3    C2   CA2   103.57  3.000
 X9Q  C1    N2   CA2   107.81  3.000
 X9Q  H1    C1   N3    109.85  3.000
 X9Q  H1    C1   CA1   108.89  3.000
 X9Q  N3    C1   CA1   113.03  3.000
 X9Q  H1    C1   N2    109.83  3.000
 X9Q  N3    C1   N2    105.78  3.000
 X9Q  CA1   C1   N2    109.41  3.000
 X9Q  HA1   CA1  N1    107.85  3.000
 X9Q  HA1   CA1  CB1   108.29  3.000
 X9Q  N1    CA1  CB1   114.31  3.000
 X9Q  HA1   CA1  C1    106.36  3.000
 X9Q  N1    CA1  C1    109.71  3.000
 X9Q  CB1   CA1  C1    110.00  3.000
 X9Q  HB13  CB1  HB12  107.71  3.000
 X9Q  HB13  CB1  HB11  108.05  3.000
 X9Q  HB12  CB1  HB11  107.84  3.000
 X9Q  HB13  CB1  CA1   110.26  3.000
 X9Q  HB12  CB1  CA1   111.88  3.000
 X9Q  HB11  CB1  CA1   110.95  3.000
 X9Q  HN12  N1   HN11  106.96  3.000
 X9Q  HN12  N1   CA1   110.08  3.000
 X9Q  HN11  N1   CA1   110.14  3.000
 X9Q  CA3   N3   C1    124.42  3.000
 X9Q  CA3   N3   C2    125.39  3.000
 X9Q  C1    N3   C2    110.18  3.000
 X9Q  HA32  CA3  HA31  105.97  3.000
 X9Q  HA32  CA3  C3    108.10  3.000
 X9Q  HA31  CA3  C3    109.30  3.000
 X9Q  HA32  CA3  N3    108.64  3.000
 X9Q  HA31  CA3  N3    108.09  3.000
 X9Q  C3    CA3  N3    116.28  3.000
 X9Q  OXT   C3   O3    128.08  3.000
 X9Q  O3    C3   CA3   118.24  3.000
 X9Q  OXT   C3   CA3   113.67  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  HD2   CD2  CE2  CZ    180.00   0.0  0
 X9Q  CONST_17  HE1   CE1  CZ   CE2   180.00   0.0  0
 X9Q  CONST_18  HZ    CZ   CE2  CD2   180.00   0.0  0
 X9Q  CONST_19  HD1   CD1  CG2  CD2   180.00   0.0  0
 X9Q  CONST_20  HE1   CE1  CD1  CG2   180.00   0.0  0
 X9Q  CONST_21  HE2   CE2  CD2  CG2   180.00   0.0  0
 X9Q  CONST_22  CA3   N3   C2   O2      0.00   0.0  0
 X9Q  Var_01    C1    N2   CA2  C2      3.91  30.0  1
 X9Q  Var_02    N3    C2   CA2  N2     -0.07  30.0  1
 X9Q  Var_03    CA2   CB2  CG2  CD1    91.39  30.0  2
 X9Q  Var_04    CA2   CB2  CG2  CD2   -87.37  30.0  2
 X9Q  Var_05    N2    CA2  CB2  CG2     6.51  30.0  3
 X9Q  Var_06    C2    CA2  CB2  CG2  -175.44  30.0  3
 X9Q  Var_07    C1    N2   CA2  CB2  -177.89  30.0  1
 X9Q  Var_08    N3    C2   CA2  CB2  -178.36  30.0  1
 X9Q  Var_09    N2    CA2  C2   O2    176.81  30.0  1
 X9Q  Var_10    O2    C2   CA2  CB2    -1.48  30.0  1
 X9Q  Var_11    C3    CA3  N3   C2     79.02  30.0  3
 X9Q  Var_12    C3    CA3  N3   C1   -102.09  30.0  3
 X9Q  Var_13    HB21  CB2  CG2  CD1  -146.90  30.0  2
 X9Q  Var_14    HB22  CB2  CG2  CD1   -30.22  30.0  2
 X9Q  Var_15    HB21  CB2  CG2  CD2    34.34  30.0  2
 X9Q  Var_16    HB22  CB2  CG2  CD2   151.01  30.0  2
 X9Q  Var_17    HB21  CB2  CA2  C2     61.29  30.0  2
 X9Q  Var_18    HB22  CB2  CA2  C2    -52.28  30.0  2
 X9Q  Var_19    HA31  CA3  N3   C2   -157.68  30.0  3
 X9Q  Var_20    HA32  CA3  N3   C2    -43.13  30.0  3
 X9Q  Var_21    HB21  CB2  CA2  N2   -116.75  30.0  2
 X9Q  Var_22    HB22  CB2  CA2  N2    129.68  30.0  2
 X9Q  Var_23    HA31  CA3  N3   C1     21.20  30.0  3
 X9Q  Var_24    HA32  CA3  N3   C1    135.76  30.0  3
 X9Q  Var_25    OXT   C3   CA3  N3    175.08  30.0  3
 X9Q  Var_26    O3    C3   CA3  N3     -5.76  30.0  3
 X9Q  Var_27    HA31  CA3  C3   O3   -128.42  30.0  2
 X9Q  Var_28    HA32  CA3  C3   O3    116.68  30.0  2
 X9Q  Var_29    HA31  CA3  C3   OXT    52.42  30.0  2
 X9Q  Var_30    HA32  CA3  C3   OXT   -62.48  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
 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-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

