# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 21:52:21 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: {(4Z)-4-(4-aminobenzylidene)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-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(N)cc2)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
 CQ2  CQ2  '{(4Z)-4-(4-aminobenzylidene)-2-[(1R,2R)-1-amino-2-hydroxypropyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  40  23  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CQ2
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
 CQ2  CG1  C  CH3    0  -0.698  -3.0548   3.9071  -0.5915
 CQ2  CB1  C  CH1    0   0.023  -2.2532   2.6526  -0.9019
 CQ2  OG1  O  OH1    0  -0.658  -1.0789   2.9384  -1.6259
 CQ2  CA1  C  CH1    0  -0.248  -1.9469   1.8395   0.3850
 CQ2  N1   N  NH2    0  -0.788  -1.1804   2.5366   1.3960
 CQ2  C1   C  CR5    0   0.578  -1.2267   0.5870   0.0033
 CQ2  N2   N  N      0  -0.490   0.0450   0.4282   0.1274
 CQ2  N3   N  NR5    0  -0.540  -1.8685  -0.4653  -0.6151
 CQ2  CA3  C  CH2    0  -0.488  -3.2858  -0.7210  -0.6154
 CQ2  C3   C  C      0   0.420  -3.8232  -1.1587   0.7675
 CQ2  O3   O  O      0  -0.587  -3.0160  -1.1572   1.7107
 CQ2  C2   C  CR5    0   0.517  -0.9291  -1.4438  -0.8544
 CQ2  O2   O  O      0  -0.467  -1.1473  -2.5447  -1.3274
 CQ2  CA2  C  CR5    0   0.073   0.3310  -0.8239  -0.4019
 CQ2  CB2  C  C1     0  -0.390   1.5323  -1.4286  -0.5258
 CQ2  CG2  C  CR6    0   0.123   2.8442  -0.9635  -0.1558
 CQ2  CD2  C  CR16   0  -0.309   3.1063   0.2774   0.4515
 CQ2  CE2  C  CR16   0  -0.307   4.3884   0.6589   0.7753
 CQ2  CZ   C  CR6    0   0.335   5.4863  -0.1800   0.5070
 CQ2  NH   N  NH2    0  -0.853   6.7553   0.2222   0.7829
 CQ2  CE1  C  CR16   0  -0.326   5.2334  -1.4236  -0.0953
 CQ2  CD1  C  CR16   0  -0.291   3.9457  -1.7949  -0.4136
 CQ2  H1   H  HCH3   0   0.249  -3.3397   4.4137  -1.5137
 CQ2  H2   H  HCH3   0   0.235  -3.9684   3.6628  -0.0483
 CQ2  H3   H  HCH3   0   0.223  -2.4843   4.6162   0.0124
 CQ2  H4   H  HCH1   0   0.237  -2.8540   2.0230  -1.5656
 CQ2  H5   H  HOH1   0   0.438  -0.5357   3.5418  -1.1077
 CQ2  H6   H  HCH1   0   0.267  -2.9095   1.5685   0.8290
 CQ2  H7   H  HNH2   0   0.346  -0.2526   2.7614   1.0605
 CQ2  H8   H  HNH2   0   0.359  -1.6357   3.4036   1.6475
 CQ2  H13  H  HCH2   0   0.267  -3.8267   0.1630  -0.9580
 CQ2  H14  H  HCH2   0   0.274  -3.4850  -1.4990  -1.3530
 CQ2  O1   O  OC    -1  -0.610  -5.0299  -1.4598   0.7825
 CQ2  H20  H  H      0   0.258   1.5018  -2.4143  -0.9813
 CQ2  H21  H  HCR6   0   0.271   2.2855   0.9465   0.6697
 CQ2  H22  H  HCR6   0   0.260   4.5590   1.6209   1.2444
 CQ2  H23  H  HNH2   0   0.392   6.8859   0.9897   1.4200
 CQ2  H24  H  HNH2   0   0.391   7.4824  -0.4721   0.8154
 CQ2  H25  H  HCR6   0   0.260   6.0576  -2.0928  -0.3110
 CQ2  H26  H  HCR6   0   0.255   3.7807  -2.7601  -0.8789

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
 CQ2  O3   C3   deloc     1.241  0.020  1.241
 CQ2  C3   CA3  single    1.547  0.020  1.547
 CQ2  CA3  N3   single    1.440  0.020  1.440
 CQ2  N1   CA1  single    1.448  0.020  1.448
 CQ2  N3   C2   single    1.377  0.020  1.377
 CQ2  N3   C1   single    1.379  0.020  1.379
 CQ2  O2   C2   double    1.218  0.020  1.218
 CQ2  CA1  C1   single    1.494  0.020  1.494
 CQ2  CA1  CB1  single    1.553  0.020  1.553
 CQ2  C2   CA2  single    1.475  0.020  1.475
 CQ2  C1   N2   double    1.288  0.020  1.288
 CQ2  CG1  CB1  single    1.521  0.020  1.521
 CQ2  CB1  OG1  single    1.409  0.020  1.409
 CQ2  CA2  N2   single    1.389  0.020  1.389
 CQ2  CA2  CB2  double    1.351  0.020  1.351
 CQ2  CB2  CG2  single    1.440  0.020  1.440
 CQ2  CG2  CD2  aromatic  1.406  0.020  1.406
 CQ2  CG2  CD1  aromatic  1.404  0.020  1.404
 CQ2  CD2  CE2  aromatic  1.376  0.020  1.376
 CQ2  CD1  CE1  aromatic  1.377  0.020  1.377
 CQ2  CE2  CZ   aromatic  1.407  0.020  1.407
 CQ2  CE1  CZ   aromatic  1.405  0.020  1.405
 CQ2  CZ   NH   single    1.360  0.020  1.360
 CQ2  CG1  H1   single    0.970  0.020  1.090
 CQ2  CG1  H2   single    0.970  0.020  1.090
 CQ2  CG1  H3   single    0.970  0.020  1.090
 CQ2  CB1  H4   single    0.970  0.020  1.090
 CQ2  OG1  H5   single    0.850  0.020  0.980
 CQ2  CA1  H6   single    0.970  0.020  1.090
 CQ2  N1   H7   single    0.890  0.020  1.040
 CQ2  N1   H8   single    0.890  0.020  1.040
 CQ2  CA3  H13  single    0.970  0.020  1.090
 CQ2  CA3  H14  single    0.970  0.020  1.090
 CQ2  C3   O1   deloc     1.244  0.020  1.244
 CQ2  CB2  H20  single    0.930  0.020  1.080
 CQ2  CD2  H21  single    0.930  0.020  1.080
 CQ2  CE2  H22  single    0.930  0.020  1.080
 CQ2  NH   H23  single    0.890  0.020  1.040
 CQ2  NH   H24  single    0.890  0.020  1.040
 CQ2  CE1  H25  single    0.930  0.020  1.080
 CQ2  CD1  H26  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
 CQ2  H3   CG1  H2   107.91  3.000
 CQ2  H3   CG1  H1   107.61  3.000
 CQ2  H2   CG1  H1   107.85  3.000
 CQ2  H3   CG1  CB1  111.90  3.000
 CQ2  H2   CG1  CB1  111.00  3.000
 CQ2  H1   CG1  CB1  110.39  3.000
 CQ2  H4   CB1  CA1  108.04  3.000
 CQ2  H4   CB1  OG1  105.23  3.000
 CQ2  CA1  CB1  OG1  111.58  3.000
 CQ2  H4   CB1  CG1  108.00  3.000
 CQ2  OG1  CB1  CG1  112.14  3.000
 CQ2  CA1  CB1  CG1  111.52  3.000
 CQ2  H5   OG1  CB1  108.71  3.000
 CQ2  H6   CA1  C1   108.67  3.000
 CQ2  H6   CA1  N1   107.56  3.000
 CQ2  C1   CA1  N1   109.07  3.000
 CQ2  H6   CA1  CB1  107.00  3.000
 CQ2  C1   CA1  CB1  108.80  3.000
 CQ2  N1   CA1  CB1  115.54  3.000
 CQ2  H8   N1   H7   107.74  3.000
 CQ2  H8   N1   CA1  110.38  3.000
 CQ2  H7   N1   CA1  111.16  3.000
 CQ2  N3   C1   N2   114.13  3.000
 CQ2  N2   C1   CA1  123.69  3.000
 CQ2  N3   C1   CA1  121.99  3.000
 CQ2  CA2  N2   C1   106.13  3.000
 CQ2  C2   N3   CA3  123.02  3.000
 CQ2  C2   N3   C1   107.61  3.000
 CQ2  CA3  N3   C1   126.42  3.000
 CQ2  H14  CA3  H13  105.96  3.000
 CQ2  H14  CA3  C3   109.84  3.000
 CQ2  H13  CA3  C3   109.73  3.000
 CQ2  H14  CA3  N3   107.86  3.000
 CQ2  H13  CA3  N3   110.12  3.000
 CQ2  C3   CA3  N3   113.07  3.000
 CQ2  O1   C3   O3   128.46  3.000
 CQ2  O1   C3   CA3  114.60  3.000
 CQ2  O3   C3   CA3  116.93  3.000
 CQ2  CA2  C2   O2   130.68  3.000
 CQ2  CA2  C2   N3   103.34  3.000
 CQ2  O2   C2   N3   125.98  3.000
 CQ2  CB2  CA2  C2   122.92  3.000
 CQ2  CB2  CA2  N2   128.43  3.000
 CQ2  C2   CA2  N2   108.64  3.000
 CQ2  H20  CB2  CG2  115.23  3.000
 CQ2  H20  CB2  CA2  114.82  3.000
 CQ2  CG2  CB2  CA2  129.95  3.000
 CQ2  CD1  CG2  CD2  117.11  3.000
 CQ2  CD1  CG2  CB2  118.44  3.000
 CQ2  CD2  CG2  CB2  124.45  3.000
 CQ2  H21  CD2  CE2  119.22  3.000
 CQ2  H21  CD2  CG2  119.46  3.000
 CQ2  CE2  CD2  CG2  121.32  3.000
 CQ2  H22  CE2  CZ   119.26  3.000
 CQ2  H22  CE2  CD2  119.64  3.000
 CQ2  CZ   CE2  CD2  121.10  3.000
 CQ2  CE1  CZ   NH   121.13  3.000
 CQ2  NH   CZ   CE2  120.87  3.000
 CQ2  CE1  CZ   CE2  117.97  3.000
 CQ2  H24  NH   H23  114.35  3.000
 CQ2  H24  NH   CZ   118.49  3.000
 CQ2  H23  NH   CZ   118.39  3.000
 CQ2  H25  CE1  CD1  119.92  3.000
 CQ2  H25  CE1  CZ   119.68  3.000
 CQ2  CD1  CE1  CZ   120.40  3.000
 CQ2  H26  CD1  CE1  118.78  3.000
 CQ2  H26  CD1  CG2  119.13  3.000
 CQ2  CE1  CD1  CG2  122.10  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
 CQ2  CONST_01  CZ   CE2  CD2  CG2    0.00   0.0  0
 CQ2  CONST_02  CZ   CE1  CD1  CG2    0.00   0.0  0
 CQ2  CONST_03  CE1  CD1  CG2  CD2    0.00   0.0  0
 CQ2  CONST_04  CE1  CZ   CE2  CD2    0.00   0.0  0
 CQ2  CONST_05  CD1  CG2  CD2  CE2    0.00   0.0  0
 CQ2  CONST_06  CD1  CE1  CZ   CE2    0.00   0.0  0
 CQ2  CONST_07  CA2  C2   N3   C1     0.00   0.0  0
 CQ2  CONST_08  C2   CA2  N2   C1     0.00   0.0  0
 CQ2  CONST_09  C2   N3   C1   N2     0.00   0.0  0
 CQ2  CONST_10  N3   C2   CA2  N2     0.00   0.0  0
 CQ2  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 CQ2  CONST_12  CE2  CD2  CG2  CB2  180.00   0.0  0
 CQ2  CONST_13  CE1  CD1  CG2  CB2  180.00   0.0  0
 CQ2  CONST_14  NH   CZ   CE2  CD2  180.00   0.0  0
 CQ2  CONST_15  CD1  CE1  CZ   NH   180.00   0.0  0
 CQ2  CONST_16  C2   N3   C1   CA1  180.00   0.0  0
 CQ2  CONST_17  CA2  N2   C1   CA1  180.00   0.0  0
 CQ2  CONST_18  O2   C2   N3   C1   180.00   0.0  0
 CQ2  CONST_20  CA2  C2   N3   CA3  180.00   0.0  0
 CQ2  CONST_21  H22  CE2  CD2  CG2  180.00   0.0  0
 CQ2  CONST_22  H25  CE1  CD1  CG2  180.00   0.0  0
 CQ2  CONST_23  H26  CD1  CG2  CD2  180.00   0.0  0
 CQ2  CONST_24  H21  CD2  CE2  CZ   180.00   0.0  0
 CQ2  CONST_26  O2   C2   N3   CA3    0.00   0.0  0
 CQ2  Var_01    CG2  CB2  CA2  N2    -0.11  30.0  2
 CQ2  Var_02    CD2  CG2  CB2  CA2    0.80  30.0  2
 CQ2  Var_03    C3   CA3  N3   C1   -69.78  30.0  1
 CQ2  Var_04    O3   C3   CA3  N3     4.37  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
 CQ2  chir_01  CB1  CA1  CG1  OG1  negativ
 CQ2  chir_02  CA1  N1   CB1  C1   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
 CQ2  plan-1  CA1  0.020
 CQ2  plan-1  C1   0.020
 CQ2  plan-1  N2   0.020
 CQ2  plan-1  N3   0.020
 CQ2  plan-1  CA3  0.020
 CQ2  plan-1  C2   0.020
 CQ2  plan-1  O2   0.020
 CQ2  plan-1  CA2  0.020
 CQ2  plan-1  CB2  0.020
 CQ2  plan-2  CB2  0.020
 CQ2  plan-2  CG2  0.020
 CQ2  plan-2  CD2  0.020
 CQ2  plan-2  CE2  0.020
 CQ2  plan-2  CZ   0.020
 CQ2  plan-2  NH   0.020
 CQ2  plan-2  CE1  0.020
 CQ2  plan-2  CD1  0.020
 CQ2  plan-2  H21  0.020
 CQ2  plan-2  H22  0.020
 CQ2  plan-2  H25  0.020
 CQ2  plan-2  H26  0.020
 CQ2  plan-3  CZ   0.020
 CQ2  plan-3  NH   0.020
 CQ2  plan-3  H23  0.020
 CQ2  plan-3  H24  0.020
 CQ2  plan-4  CA3  0.020
 CQ2  plan-4  C3   0.020
 CQ2  plan-4  O3   0.020
 CQ2  plan-4  O1   0.020

