# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:24:32 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: {(4S)-2-(aminomethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-yl)methyl]-4,5-dihydro-1H-imidazol-1-yl}acetaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1=N[C@@H](CC2C=CC(=O)C=C2)C(=O)N1CC=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
 PBI  PBI  {(4S)-2-(aminomethyl)-5-oxo-4-[(4-oxocyclohexa-2,5-dien-1-yl)methyl]-4,5-dihydro-1H-imidazol-1-yl}acetaldehyde  ligand  34  19  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PBI
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
 PBI  N1    N  NH2   0  -0.786   3.2038   0.0984   2.4172
 PBI  CA1   C  CH2   0  -0.368   1.8839   0.0549   2.9976
 PBI  C1    C  CR5   0   0.511   0.8363   0.3762   1.9861
 PBI  N2    N  N     0  -0.417   1.0299   0.5135   0.7390
 PBI  N3    N  NR5   0  -0.555  -0.4946   0.5115   2.3852
 PBI  C2    C  CR5   0   0.563  -1.2560   0.7645   1.2728
 PBI  O2    O  O     0  -0.436  -2.4523   0.9349   1.2497
 PBI  CA2   C  CR15  0  -0.318  -0.2583   0.7656   0.1294
 PBI  CA3   C  CH2   0  -0.442  -1.0053   0.4117   3.7244
 PBI  C3    C  C1    0   0.169  -1.1154  -1.0212   4.1951
 PBI  O3    O  O     0  -0.358  -1.2152  -1.3236   5.3531
 PBI  CB2   C  CH2   0  -0.423  -0.6223  -0.2890  -0.9143
 PBI  CG2   C  CR16  0  -0.367   0.4543  -0.4729  -2.0034
 PBI  CD1   C  CR16  0  -0.142   0.0416  -1.5743  -2.9136
 PBI  CD2   C  CR16  0  -0.155   0.7658   0.7925  -2.7191
 PBI  CE1   C  CR16  0  -0.367  -0.0828  -1.4358  -4.2358
 PBI  CE2   C  CR16  0  -0.362   0.6475   0.9396  -4.0410
 PBI  CZ    C  CR6   0   0.383   0.2007  -0.1607  -4.9036
 PBI  OH    O  O     0  -0.444   0.0773  -0.0227  -6.1117
 PBI  HN11  H  HNH2  0   0.351   3.2874  -0.6073   1.6973
 PBI  HN12  H  HNH2  0   0.362   3.8775  -0.1428   3.1315
 PBI  HA11  H  HCH2  0   0.244   1.6142  -0.9119   3.4532
 PBI  HA12  H  HCH2  0   0.268   1.8252   0.7883   3.8075
 PBI  HA2   H  HCR5  0   0.311  -0.2603   1.7603  -0.3310
 PBI  HA31  H  HCH2  0   0.311  -0.4074   0.9986   4.4240
 PBI  HA32  H  HCH2  0   0.325  -2.0110   0.8425   3.7366
 PBI  HC3   H  H     0   0.214  -1.1206  -1.7776   3.3889
 PBI  HB21  H  HCH2  0   0.265  -0.7686  -1.2526  -0.4193
 PBI  HB22  H  HCH2  0   0.268  -1.5726  -0.0137  -1.3755
 PBI  HG2   H  HCR6  0   0.300   1.3681  -0.7917  -1.4832
 PBI  HD1   H  HCR6  0   0.281  -0.1793  -2.5288  -2.4482
 PBI  HD2   H  HCR6  0   0.283   1.1206   1.6259  -2.1231
 PBI  HE1   H  HCR6  0   0.267  -0.3955  -2.2675  -4.8558
 PBI  HE2   H  HCR6  0   0.268   0.8912   1.8808  -4.5188

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
 PBI  N1   CA1   single  1.443  0.020  1.443
 PBI  N1   HN11  single  0.890  0.020  1.040
 PBI  N1   HN12  single  0.890  0.020  1.040
 PBI  CA1  C1    single  1.491  0.020  1.491
 PBI  CA1  HA11  single  0.970  0.020  1.090
 PBI  CA1  HA12  single  0.970  0.020  1.090
 PBI  C1   N2    double  1.269  0.020  1.269
 PBI  C1   N3    single  1.396  0.020  1.396
 PBI  N2   CA2   single  1.447  0.020  1.447
 PBI  N3   C2    single  1.372  0.020  1.372
 PBI  N3   CA3   single  1.437  0.020  1.437
 PBI  C2   O2    double  1.209  0.020  1.209
 PBI  C2   CA2   single  1.517  0.020  1.517
 PBI  CA2  CB2   single  1.528  0.020  1.528
 PBI  CA2  HA2   single  0.970  0.020  1.090
 PBI  CA3  C3    single  1.512  0.020  1.512
 PBI  CA3  HA31  single  0.970  0.020  1.090
 PBI  CA3  HA32  single  0.970  0.020  1.090
 PBI  C3   O3    double  1.201  0.020  1.201
 PBI  C3   HC3   single  0.930  0.020  1.080
 PBI  CB2  CG2   single  1.542  0.020  1.542
 PBI  CB2  HB21  single  0.970  0.020  1.090
 PBI  CB2  HB22  single  0.970  0.020  1.090
 PBI  CG2  CD1   single  1.487  0.020  1.487
 PBI  CG2  CD2   single  1.487  0.020  1.487
 PBI  CG2  HG2   single  0.970  0.020  1.090
 PBI  CD1  CE1   double  1.335  0.020  1.335
 PBI  CD1  HD1   single  0.930  0.020  1.080
 PBI  CD2  CE2   double  1.335  0.020  1.335
 PBI  CD2  HD2   single  0.930  0.020  1.080
 PBI  CE1  CZ    single  1.467  0.020  1.467
 PBI  CE1  HE1   single  0.930  0.020  1.080
 PBI  CE2  CZ    single  1.468  0.020  1.468
 PBI  CE2  HE2   single  0.930  0.020  1.080
 PBI  CZ   OH    double  1.222  0.020  1.222

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
 PBI  HN12  N1   HN11  106.34  3.000
 PBI  HN12  N1   CA1   108.56  3.000
 PBI  HN11  N1   CA1   109.93  3.000
 PBI  HA12  CA1  HA11  105.59  3.000
 PBI  HA12  CA1  C1    108.66  3.000
 PBI  HA11  CA1  C1    107.30  3.000
 PBI  HA12  CA1  N1    109.07  3.000
 PBI  HA11  CA1  N1    114.62  3.000
 PBI  C1    CA1  N1    111.31  3.000
 PBI  N3    C1   N2    114.57  3.000
 PBI  N3    C1   CA1   119.78  3.000
 PBI  N2    C1   CA1   125.63  3.000
 PBI  CA2   N2   C1    107.27  3.000
 PBI  CA3   N3   C2    124.85  3.000
 PBI  CA3   N3   C1    126.77  3.000
 PBI  C2    N3   C1    108.38  3.000
 PBI  CA2   C2   O2    129.52  3.000
 PBI  CA2   C2   N3    104.25  3.000
 PBI  O2    C2   N3    126.23  3.000
 PBI  HA2   CA2  CB2   109.81  3.000
 PBI  HA2   CA2  C2    108.42  3.000
 PBI  CB2   CA2  C2    110.95  3.000
 PBI  HA2   CA2  N2    109.67  3.000
 PBI  CB2   CA2  N2    112.31  3.000
 PBI  C2    CA2  N2    105.53  3.000
 PBI  HA32  CA3  HA31  106.54  3.000
 PBI  HA32  CA3  C3    107.62  3.000
 PBI  HA31  CA3  C3    110.48  3.000
 PBI  HA32  CA3  N3    108.05  3.000
 PBI  HA31  CA3  N3    111.43  3.000
 PBI  C3    CA3  N3    112.44  3.000
 PBI  HC3   C3   O3    122.04  3.000
 PBI  HC3   C3   CA3   114.94  3.000
 PBI  O3    C3   CA3   123.01  3.000
 PBI  HB22  CB2  HB21  107.28  3.000
 PBI  HB22  CB2  CG2   109.84  3.000
 PBI  HB21  CB2  CG2   107.94  3.000
 PBI  HB22  CB2  CA2   108.79  3.000
 PBI  HB21  CB2  CA2   109.33  3.000
 PBI  CG2   CB2  CA2   113.48  3.000
 PBI  HG2   CG2  CD2   107.49  3.000
 PBI  HG2   CG2  CD1   107.80  3.000
 PBI  CD2   CG2  CD1   113.20  3.000
 PBI  HG2   CG2  CB2   106.31  3.000
 PBI  CD2   CG2  CB2   112.62  3.000
 PBI  CD1   CG2  CB2   109.07  3.000
 PBI  HD1   CD1  CE1   119.81  3.000
 PBI  HD1   CD1  CG2   116.46  3.000
 PBI  CE1   CD1  CG2   123.72  3.000
 PBI  HD2   CD2  CE2   119.24  3.000
 PBI  HD2   CD2  CG2   117.27  3.000
 PBI  CE2   CD2  CG2   123.48  3.000
 PBI  HE1   CE1  CZ    117.55  3.000
 PBI  HE1   CE1  CD1   120.92  3.000
 PBI  CZ    CE1  CD1   121.53  3.000
 PBI  HE2   CE2  CZ    117.42  3.000
 PBI  HE2   CE2  CD2   120.82  3.000
 PBI  CZ    CE2  CD2   121.75  3.000
 PBI  OH    CZ   CE2   121.80  3.000
 PBI  OH    CZ   CE1   121.91  3.000
 PBI  CE2   CZ   CE1   116.28  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
 PBI  CONST_01  CA2   C2   N3   C1     0.00   0.0  0
 PBI  CONST_02  C2    N3   C1   N2     0.00   0.0  0
 PBI  CONST_03  CA2   N2   C1   N3     0.00   0.0  0
 PBI  CONST_04  CA2   N2   C1   CA1  180.00   0.0  0
 PBI  CONST_05  C2    N3   C1   CA1  180.00   0.0  0
 PBI  CONST_06  O2    C2   N3   C1   180.00   0.0  0
 PBI  CONST_07  CA3   N3   C1   N2   180.00   0.0  0
 PBI  CONST_08  CA3   N3   C2   CA2  180.00   0.0  0
 PBI  CONST_09  CA3   N3   C1   CA1    0.00   0.0  0
 PBI  CONST_10  CA3   N3   C2   O2     0.00   0.0  0
 PBI  Var_01    CZ    CE1  CD1  CG2    0.74  30.0  1
 PBI  Var_02    CZ    CE2  CD2  CG2   -0.40  30.0  1
 PBI  Var_03    CE2   CZ   CE1  CD1    0.98  30.0  1
 PBI  Var_04    CE1   CZ   CE2  CD2   -1.15  30.0  1
 PBI  Var_05    N2    C1   CA1  N1     8.09  30.0  3
 PBI  Var_06    C3    CA3  N3   C1   -77.36  30.0  3
 PBI  Var_07    O3    C3   CA3  N3   162.16  30.0  3
 PBI  Var_08    HN11  N1   CA1  C1   -62.95  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
 PBI  chir_01  CA2  N2   C2   CB2  positiv
 PBI  chir_02  CG2  CD2  CD1  CB2  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
 PBI  plan-1  CE1  0.020
 PBI  plan-1  CE2  0.020
 PBI  plan-1  CZ   0.020
 PBI  plan-1  OH   0.020
 PBI  plan-2  CA1  0.020
 PBI  plan-2  C1   0.020
 PBI  plan-2  N2   0.020
 PBI  plan-2  N3   0.020
 PBI  plan-2  C2   0.020
 PBI  plan-2  O2   0.020
 PBI  plan-2  CA2  0.020
 PBI  plan-2  CA3  0.020
 PBI  plan-3  CA3  0.020
 PBI  plan-3  C3   0.020
 PBI  plan-3  O3   0.020
 PBI  plan-3  HC3  0.020

