# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 08:50:27 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(4Z)-2-(aminomethyl)-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1=NC(=C/c2ccc(cc2)C(=O)c3ccccc3)\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
 BF6  BF6  '[(4Z)-2-(aminomethyl)-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid'  L-peptide  44  27  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BF6
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
 BF6  CB2  C  C1    0  -0.389  -1.0863  -1.6725   0.0437
 BF6  CA3  C  CH2   0  -0.467  -5.5812   0.1180  -0.5401
 BF6  C3   C  C     0   0.549  -6.0697   0.5956   0.8120
 BF6  CA1  C  CH2   0  -0.387  -3.5966   2.2865  -1.2456
 BF6  C01  C  CR16  0  -0.282   4.7710   1.0750   1.1136
 BF6  C02  C  CR16  0  -0.241   5.4565   2.2403   1.4250
 BF6  C03  C  CR16  0  -0.246   6.6608   2.5266   0.7973
 BF6  C04  C  CR16  0  -0.244   7.1891   1.6372  -0.1320
 BF6  C05  C  CR16  0  -0.269   6.5182   0.4624  -0.4271
 BF6  C06  C  CR6   0  -0.036   5.2959   0.1778   0.1837
 BF6  CZ   C  CR6   0  -0.047   3.1436  -1.2017  -0.0485
 BF6  CE2  C  CR16  0  -0.253   2.3247  -0.1285  -0.4018
 BF6  CD2  C  CR16  0  -0.300   0.9475  -0.2532  -0.3934
 BF6  CG2  C  CR6   0   0.161   0.3484  -1.4598  -0.0097
 BF6  CD1  C  CR16  0  -0.292   1.1783  -2.5331   0.3418
 BF6  CE1  C  CR16  0  -0.260   2.5532  -2.4133   0.3094
 BF6  CA2  C  CR5   0   0.109  -2.0815  -0.8115  -0.2337
 BF6  C1   C  CR5   0   0.544  -3.2053   0.9234  -0.7942
 BF6  C2   C  CR5   0   0.549  -3.5142  -1.1921  -0.1432
 BF6  N2   N  N     0  -0.480  -1.9960   0.5135  -0.6355
 BF6  N3   N  NR5   0  -0.560  -4.1603  -0.0450  -0.5527
 BF6  N1   N  NH2   0  -0.785  -2.4477   3.1498  -1.3733
 BF6  O08  O  O     0  -0.388   5.2823  -2.0959  -0.4085
 BF6  O2   O  O     0  -0.429  -4.0437  -2.2272   0.1931
 BF6  O3   O  O     0  -0.425  -5.3443   0.8634   1.7320
 BF6  OXT  O  OH1   0  -0.583  -7.3873   0.6828   0.8316
 BF6  H1   H  H     0   0.274  -1.4001  -2.6650   0.3503
 BF6  H3   H  HCH2  0   0.329  -6.0568  -0.8329  -0.7868
 BF6  H4   H  HCH2  0   0.328  -5.8916   0.8238  -1.3128
 BF6  H5   H  HCH2  0   0.253  -4.1913   2.1703  -2.1656
 BF6  H6   H  HCH2  0   0.268  -4.2815   2.7133  -0.5056
 BF6  H8   H  HCR6  0   0.266   5.0479   2.9232   2.1577
 BF6  H9   H  HCR6  0   0.267   7.1899   3.4407   1.0335
 BF6  H10  H  HCR6  0   0.265   8.1280   1.8597  -0.6214
 BF6  H11  H  HCR6  0   0.265   6.9379  -0.2296  -1.1456
 BF6  H12  H  HCR6  0   0.275   2.7619   0.8121  -0.7103
 BF6  H13  H  HCR6  0   0.283   0.3338   0.5876  -0.6823
 BF6  H14  H  HCR6  0   0.267   0.7338  -3.4737   0.6425
 BF6  H15  H  HCR6  0   0.268   3.1706  -3.2592   0.5813
 BF6  H17  H  HNH2  0   0.352  -1.8485   2.8171  -2.1170
 BF6  H18  H  HNH2  0   0.363  -2.7649   4.0687  -1.6512
 BF6  HXT  H  HOH1  0   0.491  -7.6968   0.9978   1.6947
 BF6  C07  C  C     0   0.364   4.6271  -1.1152  -0.1153
 BF6  H7   H  HCR6  0   0.273   3.8375   0.8583   1.6159

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
 BF6  O3   C3   double    1.202  0.020  1.202
 BF6  O2   C2   double    1.210  0.020  1.210
 BF6  C3   CA3  single    1.515  0.020  1.515
 BF6  C2   N3   single    1.379  0.020  1.379
 BF6  C2   CA2  single    1.485  0.020  1.485
 BF6  CA3  N3   single    1.430  0.020  1.430
 BF6  CB2  CA2  double    1.345  0.020  1.345
 BF6  CB2  CG2  single    1.451  0.020  1.451
 BF6  CD2  CE2  aromatic  1.383  0.020  1.383
 BF6  CD2  CG2  aromatic  1.401  0.020  1.401
 BF6  C02  C01  aromatic  1.387  0.020  1.387
 BF6  C02  C03  aromatic  1.388  0.020  1.388
 BF6  N3   C1   single    1.381  0.020  1.381
 BF6  CA2  N2   single    1.387  0.020  1.387
 BF6  C01  C06  aromatic  1.395  0.020  1.395
 BF6  CE2  CZ   aromatic  1.395  0.020  1.395
 BF6  CG2  CD1  aromatic  1.402  0.020  1.402
 BF6  C03  C04  aromatic  1.391  0.020  1.391
 BF6  C1   N2   double    1.287  0.020  1.287
 BF6  C1   CA1  single    1.488  0.020  1.488
 BF6  CZ   C07  single    1.487  0.020  1.487
 BF6  CZ   CE1  aromatic  1.395  0.020  1.395
 BF6  CD1  CE1  aromatic  1.381  0.020  1.381
 BF6  C06  C07  single    1.486  0.020  1.486
 BF6  C06  C05  aromatic  1.396  0.020  1.396
 BF6  C04  C05  aromatic  1.385  0.020  1.385
 BF6  C07  O08  double    1.215  0.020  1.215
 BF6  CA1  N1   single    1.443  0.020  1.443
 BF6  C3   OXT  single    1.321  0.020  1.321
 BF6  CB2  H1   single    0.930  0.020  1.080
 BF6  CA3  H3   single    0.970  0.020  1.090
 BF6  CA3  H4   single    0.970  0.020  1.090
 BF6  CA1  H5   single    0.970  0.020  1.090
 BF6  CA1  H6   single    0.970  0.020  1.090
 BF6  C01  H7   single    0.930  0.020  1.080
 BF6  C02  H8   single    0.930  0.020  1.080
 BF6  C03  H9   single    0.930  0.020  1.080
 BF6  C04  H10  single    0.930  0.020  1.080
 BF6  C05  H11  single    0.930  0.020  1.080
 BF6  CE2  H12  single    0.930  0.020  1.080
 BF6  CD2  H13  single    0.930  0.020  1.080
 BF6  CD1  H14  single    0.930  0.020  1.080
 BF6  CE1  H15  single    0.930  0.020  1.080
 BF6  N1   H17  single    0.890  0.020  1.040
 BF6  N1   H18  single    0.890  0.020  1.040
 BF6  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
 BF6  H1   CB2  CA2  115.45  3.000
 BF6  H1   CB2  CG2  115.49  3.000
 BF6  CA2  CB2  CG2  129.06  3.000
 BF6  H4   CA3  H3   106.23  3.000
 BF6  H4   CA3  N3   110.48  3.000
 BF6  H3   CA3  N3   109.36  3.000
 BF6  H4   CA3  C3   109.65  3.000
 BF6  H3   CA3  C3   109.63  3.000
 BF6  N3   CA3  C3   111.35  3.000
 BF6  OXT  C3   O3   125.18  3.000
 BF6  OXT  C3   CA3  110.84  3.000
 BF6  O3   C3   CA3  123.98  3.000
 BF6  H6   CA1  H5   105.54  3.000
 BF6  H6   CA1  N1   108.95  3.000
 BF6  H5   CA1  N1   114.77  3.000
 BF6  H6   CA1  C1   108.45  3.000
 BF6  H5   CA1  C1   107.38  3.000
 BF6  N1   CA1  C1   111.44  3.000
 BF6  H7   C01  C06  120.36  3.000
 BF6  H7   C01  C02  119.36  3.000
 BF6  C06  C01  C02  120.26  3.000
 BF6  H8   C02  C03  120.26  3.000
 BF6  H8   C02  C01  119.71  3.000
 BF6  C03  C02  C01  120.03  3.000
 BF6  H9   C03  C04  120.02  3.000
 BF6  H9   C03  C02  119.98  3.000
 BF6  C04  C03  C02  120.00  3.000
 BF6  H10  C04  C05  119.90  3.000
 BF6  H10  C04  C03  120.04  3.000
 BF6  C05  C04  C03  120.06  3.000
 BF6  H11  C05  C06  119.98  3.000
 BF6  H11  C05  C04  119.75  3.000
 BF6  C06  C05  C04  120.27  3.000
 BF6  C07  C06  C05  118.91  3.000
 BF6  C05  C06  C01  119.35  3.000
 BF6  C07  C06  C01  121.63  3.000
 BF6  CE1  CZ   CE2  118.99  3.000
 BF6  CE1  CZ   C07  118.96  3.000
 BF6  CE2  CZ   C07  121.95  3.000
 BF6  H12  CE2  CD2  118.85  3.000
 BF6  H12  CE2  CZ   120.24  3.000
 BF6  CD2  CE2  CZ   120.90  3.000
 BF6  H13  CD2  CG2  120.04  3.000
 BF6  H13  CD2  CE2  119.60  3.000
 BF6  CG2  CD2  CE2  120.35  3.000
 BF6  CD1  CG2  CD2  118.36  3.000
 BF6  CD1  CG2  CB2  117.64  3.000
 BF6  CD2  CG2  CB2  124.00  3.000
 BF6  H14  CD1  CE1  119.38  3.000
 BF6  H14  CD1  CG2  119.46  3.000
 BF6  CE1  CD1  CG2  121.16  3.000
 BF6  H15  CE1  CD1  119.64  3.000
 BF6  H15  CE1  CZ   120.15  3.000
 BF6  CD1  CE1  CZ   120.20  3.000
 BF6  N2   CA2  C2   108.77  3.000
 BF6  N2   CA2  CB2  128.73  3.000
 BF6  C2   CA2  CB2  122.50  3.000
 BF6  N3   C1   N2   113.88  3.000
 BF6  N2   C1   CA1  125.19  3.000
 BF6  N3   C1   CA1  120.89  3.000
 BF6  O2   C2   N3   126.09  3.000
 BF6  N3   C2   CA2  102.76  3.000
 BF6  O2   C2   CA2  131.15  3.000
 BF6  C1   N2   CA2  106.39  3.000
 BF6  C2   N3   C1   108.13  3.000
 BF6  C1   N3   CA3  127.47  3.000
 BF6  C2   N3   CA3  123.90  3.000
 BF6  H18  N1   H17  106.42  3.000
 BF6  H18  N1   CA1  108.56  3.000
 BF6  H17  N1   CA1  109.88  3.000
 BF6  HXT  OXT  C3   110.68  3.000
 BF6  O08  C07  CZ   120.11  3.000
 BF6  O08  C07  C06  120.53  3.000
 BF6  CZ   C07  C06  119.36  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
 BF6  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 BF6  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 BF6  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 BF6  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 BF6  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 BF6  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 BF6  CONST_07  CG2  CD2  CE2  CZ     0.00   0.0  0
 BF6  CONST_08  CG2  CD1  CE1  CZ     0.00   0.0  0
 BF6  CONST_09  CD1  CG2  CD2  CE2    0.00   0.0  0
 BF6  CONST_10  CD1  CE1  CZ   CE2    0.00   0.0  0
 BF6  CONST_11  CE1  CZ   CE2  CD2    0.00   0.0  0
 BF6  CONST_12  CE1  CD1  CG2  CD2    0.00   0.0  0
 BF6  CONST_13  C1   N3   C2   CA2    0.00   0.0  0
 BF6  CONST_14  N3   C1   N2   CA2    0.00   0.0  0
 BF6  CONST_15  C2   CA2  N2   C1     0.00   0.0  0
 BF6  CONST_16  N2   C1   N3   C2     0.00   0.0  0
 BF6  CONST_17  N3   C2   CA2  N2     0.00   0.0  0
 BF6  CONST_18  CE2  CD2  CG2  CB2  180.00   0.0  0
 BF6  CONST_19  CE1  CD1  CG2  CB2  180.00   0.0  0
 BF6  CONST_20  C07  C06  C01  C02  180.00   0.0  0
 BF6  CONST_21  C07  C06  C05  C04  180.00   0.0  0
 BF6  CONST_22  CD2  CE2  CZ   C07  180.00   0.0  0
 BF6  CONST_23  CD1  CE1  CZ   C07  180.00   0.0  0
 BF6  CONST_24  CA2  C2   N3   CA3  180.00   0.0  0
 BF6  CONST_25  N2   C1   N3   CA3  180.00   0.0  0
 BF6  CONST_26  C2   N3   C1   CA1  180.00   0.0  0
 BF6  CONST_27  CA2  N2   C1   CA1  180.00   0.0  0
 BF6  CONST_28  O2   C2   N3   C1   180.00   0.0  0
 BF6  CONST_29  H9   C03  C02  C01  180.00   0.0  0
 BF6  CONST_30  H11  C05  C06  C01  180.00   0.0  0
 BF6  CONST_31  H10  C04  C03  C02  180.00   0.0  0
 BF6  CONST_32  H7   C01  C02  C03  180.00   0.0  0
 BF6  CONST_33  H8   C02  C03  C04  180.00   0.0  0
 BF6  CONST_34  H13  CD2  CE2  CZ   180.00   0.0  0
 BF6  CONST_35  H14  CD1  CE1  CZ   180.00   0.0  0
 BF6  CONST_36  H15  CE1  CZ   CE2  180.00   0.0  0
 BF6  CONST_37  H12  CE2  CD2  CG2  180.00   0.0  0
 BF6  CONST_38  O2   C2   N3   CA3    0.00   0.0  0
 BF6  CONST_39  CA1  C1   N3   CA3    0.00   0.0  0
 BF6  CONST_40  HXT  OXT  C3   CA3  180.00   0.0  0
 BF6  Var_01    CZ   C07  C06  C01   32.61  30.0  2
 BF6  Var_02    CE2  CZ   C07  C06   33.93  30.0  2
 BF6  Var_03    CA2  CB2  CG2  CD2   -0.62  30.0  1
 BF6  Var_04    C2   CA2  CB2  CG2  179.34  30.0  2
 BF6  Var_05    C2   N3   CA3  C3    85.93  30.0  3
 BF6  Var_06    N1   CA1  C1   N2    -5.24  30.0  3
 BF6  Var_07    O3   C3   CA3  N3     3.35  30.0  1
 BF6  Var_08    H17  N1   CA1  C1    65.84  30.0  3

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
 BF6  plan-1  CB2  0.020
 BF6  plan-1  CA3  0.020
 BF6  plan-1  CA1  0.020
 BF6  plan-1  CA2  0.020
 BF6  plan-1  C1   0.020
 BF6  plan-1  C2   0.020
 BF6  plan-1  N2   0.020
 BF6  plan-1  N3   0.020
 BF6  plan-1  O2   0.020
 BF6  plan-2  C01  0.020
 BF6  plan-2  C02  0.020
 BF6  plan-2  C03  0.020
 BF6  plan-2  C04  0.020
 BF6  plan-2  C05  0.020
 BF6  plan-2  C06  0.020
 BF6  plan-2  H8   0.020
 BF6  plan-2  H9   0.020
 BF6  plan-2  H10  0.020
 BF6  plan-2  H11  0.020
 BF6  plan-2  C07  0.020
 BF6  plan-2  H7   0.020
 BF6  plan-3  CB2  0.020
 BF6  plan-3  CZ   0.020
 BF6  plan-3  CE2  0.020
 BF6  plan-3  CD2  0.020
 BF6  plan-3  CG2  0.020
 BF6  plan-3  CD1  0.020
 BF6  plan-3  CE1  0.020
 BF6  plan-3  H12  0.020
 BF6  plan-3  H13  0.020
 BF6  plan-3  H14  0.020
 BF6  plan-3  H15  0.020
 BF6  plan-3  C07  0.020
 BF6  plan-4  C06  0.020
 BF6  plan-4  CZ   0.020
 BF6  plan-4  O08  0.020
 BF6  plan-4  C07  0.020
 BF6  plan-5  CA3  0.020
 BF6  plan-5  C3   0.020
 BF6  plan-5  O3   0.020
 BF6  plan-5  OXT  0.020
 BF6  plan-5  HXT  0.020

