# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 08:37:32 2022
#   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  43  27  .  2022-09-16  2022-09-22
;
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  -0.400  -1.1120  -1.7399   0.0159
 BF6  CA3  C  CH2    0  -0.480  -5.6139   0.0382  -0.6126
 BF6  C3   C  C      0   0.420  -6.1329   0.5747   0.7424
 BF6  CA1  C  CH2    0  -0.388  -3.6339   2.2371  -1.1687
 BF6  C01  C  CR16   0  -0.290   4.7610   1.0615   1.1135
 BF6  C02  C  CR16   0  -0.248   5.4477   2.2356   1.3888
 BF6  C03  C  CR16   0  -0.248   6.6357   2.5165   0.7281
 BF6  C04  C  CR16   0  -0.245   7.1476   1.6134  -0.1969
 BF6  C05  C  CR16   0  -0.270   6.4761   0.4302  -0.4556
 BF6  C06  C  CR6    0  -0.037   5.2693   0.1512   0.1874
 BF6  CZ   C  CR6    0  -0.047   3.1185  -1.2390  -0.0123
 BF6  CE2  C  CR16   0  -0.254   2.2948  -0.1652  -0.3533
 BF6  CD2  C  CR16   0  -0.306   0.9180  -0.2971  -0.3559
 BF6  CG2  C  CR6    0   0.161   0.3219  -1.5141  -0.0004
 BF6  CD1  C  CR16   0  -0.296   1.1565  -2.5870   0.3423
 BF6  CE1  C  CR16   0  -0.260   2.5306  -2.4582   0.3252
 BF6  CA2  C  CR5    0   0.110  -2.1064  -0.8734  -0.2464
 BF6  C1   C  CR5    0   0.543  -3.2411   0.8594  -0.7700
 BF6  C2   C  CR5    0   0.538  -3.5400  -1.2766  -0.2398
 BF6  N2   N  N      0  -0.490  -2.0260   0.4696  -0.5743
 BF6  N3   N  NR5    0  -0.535  -4.1850  -0.1348  -0.6427
 BF6  N1   N  NH2    0  -0.796  -2.5061   3.1375  -1.1611
 BF6  O08  O  O      0  -0.391   5.2601  -2.1349  -0.3476
 BF6  O2   O  O      0  -0.444  -4.0549  -2.3403   0.0331
 BF6  O3   O  O      0  -0.586  -5.2791   0.9056   1.5795
 BF6  OXT  O  OC    -1  -0.610  -7.3720   0.6304   0.8354
 BF6  H1   H  H      0   0.266  -1.4253  -2.7485   0.2656
 BF6  H3   H  HCH2   0   0.275  -6.0765  -0.9231  -0.8380
 BF6  H4   H  HCH2   0   0.271  -5.9119   0.7160  -1.4153
 BF6  H5   H  HCH2   0   0.240  -4.1572   2.1579  -2.1355
 BF6  H6   H  HCH2   0   0.267  -4.3847   2.5923  -0.4571
 BF6  H9   H  HCR6   0   0.266   7.1650   3.4377   0.9350
 BF6  H10  H  HCR6   0   0.264   8.0741   1.8312  -0.7117
 BF6  H11  H  HCR6   0   0.263   6.8828  -0.2731  -1.1707
 BF6  H12  H  HCR6   0   0.273   2.7282   0.7818  -0.6469
 BF6  H13  H  HCR6   0   0.286   0.2996   0.5440  -0.6351
 BF6  H14  H  HCR6   0   0.263   0.7158  -3.5359   0.6224
 BF6  H15  H  HCR6   0   0.266   3.1508  -3.3050   0.5879
 BF6  H17  H  HNH2   0   0.356  -1.8248   2.8402  -1.8471
 BF6  H18  H  HNH2   0   0.367  -2.8238   4.0528  -1.4509
 BF6  H7   H  HCR6   0   0.283   3.8397   0.8490   1.6399
 BF6  C07  C  C      0   0.370   4.6008  -1.1501  -0.0776
 BF6  H8   H  HCR6   0   0.275   5.0522   2.9301   2.1179

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   deloc     1.241  0.020  1.241
 BF6  O2   C2   double    1.213  0.020  1.213
 BF6  C3   CA3  single    1.547  0.020  1.547
 BF6  C2   N3   single    1.372  0.020  1.372
 BF6  C2   CA2  single    1.489  0.020  1.489
 BF6  CA3  N3   single    1.440  0.020  1.440
 BF6  CB2  CA2  double    1.345  0.020  1.345
 BF6  CB2  CG2  single    1.452  0.020  1.452
 BF6  CD2  CE2  aromatic  1.383  0.020  1.383
 BF6  CD2  CG2  aromatic  1.401  0.020  1.401
 BF6  C02  C01  aromatic  1.388  0.020  1.388
 BF6  C02  C03  aromatic  1.388  0.020  1.388
 BF6  N3   C1   single    1.377  0.020  1.377
 BF6  CA2  N2   single    1.385  0.020  1.385
 BF6  C01  C06  aromatic  1.395  0.020  1.395
 BF6  CE2  CZ   aromatic  1.396  0.020  1.396
 BF6  CG2  CD1  aromatic  1.402  0.020  1.402
 BF6  C03  C04  aromatic  1.390  0.020  1.390
 BF6  C1   N2   double    1.291  0.020  1.291
 BF6  C1   CA1  single    1.487  0.020  1.487
 BF6  CZ   C07  single    1.486  0.020  1.486
 BF6  CZ   CE1  aromatic  1.395  0.020  1.395
 BF6  CD1  CE1  aromatic  1.380  0.020  1.380
 BF6  C06  C07  single    1.487  0.020  1.487
 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  deloc     1.244  0.020  1.244
 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

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  115.48  3.000
 BF6  H1   CB2  CG2  115.61  3.000
 BF6  CA2  CB2  CG2  128.91  3.000
 BF6  H4   CA3  H3   106.23  3.000
 BF6  H4   CA3  N3   109.27  3.000
 BF6  H3   CA3  N3   108.11  3.000
 BF6  H4   CA3  C3   109.69  3.000
 BF6  H3   CA3  C3   110.15  3.000
 BF6  N3   CA3  C3   113.14  3.000
 BF6  OXT  C3   O3   128.55  3.000
 BF6  OXT  C3   CA3  114.53  3.000
 BF6  O3   C3   CA3  116.91  3.000
 BF6  H6   CA1  H5   105.55  3.000
 BF6  H6   CA1  N1   109.30  3.000
 BF6  H5   CA1  N1   114.87  3.000
 BF6  H6   CA1  C1   107.92  3.000
 BF6  H5   CA1  C1   107.09  3.000
 BF6  N1   CA1  C1   111.73  3.000
 BF6  H7   C01  C06  120.34  3.000
 BF6  H7   C01  C02  119.40  3.000
 BF6  C06  C01  C02  120.24  3.000
 BF6  H8   C02  C03  120.25  3.000
 BF6  H8   C02  C01  119.73  3.000
 BF6  C03  C02  C01  120.02  3.000
 BF6  H9   C03  C04  119.99  3.000
 BF6  H9   C03  C02  119.99  3.000
 BF6  C04  C03  C02  120.02  3.000
 BF6  H10  C04  C05  119.88  3.000
 BF6  H10  C04  C03  120.07  3.000
 BF6  C05  C04  C03  120.05  3.000
 BF6  H11  C05  C06  119.96  3.000
 BF6  H11  C05  C04  119.76  3.000
 BF6  C06  C05  C04  120.27  3.000
 BF6  C07  C06  C05  118.79  3.000
 BF6  C05  C06  C01  119.39  3.000
 BF6  C07  C06  C01  121.72  3.000
 BF6  CE1  CZ   CE2  118.87  3.000
 BF6  CE1  CZ   C07  118.89  3.000
 BF6  CE2  CZ   C07  122.13  3.000
 BF6  H12  CE2  CD2  118.80  3.000
 BF6  H12  CE2  CZ   120.21  3.000
 BF6  CD2  CE2  CZ   120.97  3.000
 BF6  H13  CD2  CG2  119.88  3.000
 BF6  H13  CD2  CE2  119.73  3.000
 BF6  CG2  CD2  CE2  120.39  3.000
 BF6  CD1  CG2  CD2  118.27  3.000
 BF6  CD1  CG2  CB2  117.80  3.000
 BF6  CD2  CG2  CB2  123.93  3.000
 BF6  H14  CD1  CE1  119.35  3.000
 BF6  H14  CD1  CG2  119.44  3.000
 BF6  CE1  CD1  CG2  121.22  3.000
 BF6  H15  CE1  CD1  119.65  3.000
 BF6  H15  CE1  CZ   120.08  3.000
 BF6  CD1  CE1  CZ   120.27  3.000
 BF6  N2   CA2  C2   108.63  3.000
 BF6  N2   CA2  CB2  128.91  3.000
 BF6  C2   CA2  CB2  122.45  3.000
 BF6  N3   C1   N2   114.41  3.000
 BF6  N2   C1   CA1  124.68  3.000
 BF6  N3   C1   CA1  120.85  3.000
 BF6  O2   C2   N3   126.62  3.000
 BF6  N3   C2   CA2  103.06  3.000
 BF6  O2   C2   CA2  130.32  3.000
 BF6  C1   N2   CA2  105.90  3.000
 BF6  C2   N3   C1   107.81  3.000
 BF6  C1   N3   CA3  126.56  3.000
 BF6  C2   N3   CA3  124.09  3.000
 BF6  H18  N1   H17  106.45  3.000
 BF6  H18  N1   CA1  108.52  3.000
 BF6  H17  N1   CA1  109.84  3.000
 BF6  O08  C07  CZ   120.14  3.000
 BF6  O08  C07  C06  120.32  3.000
 BF6  CZ   C07  C06  119.53  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  H11  C05  C04  C03   180.00   0.0  0
 BF6  CONST_34  H8   C02  C03  C04   180.00   0.0  0
 BF6  CONST_35  H7   C01  C06  C05   180.00   0.0  0
 BF6  CONST_36  H9   C03  C04  C05   180.00   0.0  0
 BF6  CONST_37  H8   C02  C01  C06   180.00   0.0  0
 BF6  CONST_38  H10  C04  C05  C06   180.00   0.0  0
 BF6  CONST_39  H13  CD2  CE2  CZ    180.00   0.0  0
 BF6  CONST_40  H14  CD1  CE1  CZ    180.00   0.0  0
 BF6  CONST_41  H15  CE1  CZ   CE2   180.00   0.0  0
 BF6  CONST_42  H14  CD1  CG2  CD2   180.00   0.0  0
 BF6  CONST_43  H12  CE2  CD2  CG2   180.00   0.0  0
 BF6  CONST_44  H15  CE1  CD1  CG2   180.00   0.0  0
 BF6  CONST_45  H13  CD2  CG2  CD1   180.00   0.0  0
 BF6  CONST_46  H12  CE2  CZ   CE1   180.00   0.0  0
 BF6  CONST_47  O2   C2   N3   CA3     0.00   0.0  0
 BF6  CONST_48  CA1  C1   N3   CA3     0.00   0.0  0
 BF6  Var_01    C2   CA2  CB2  CG2   177.48   0.0  2
 BF6  Var_02    N2   CA2  CB2  CG2    -1.47   0.0  2
 BF6  Var_03    CZ   C07  C06  C01    34.10  30.0  2
 BF6  Var_04    CZ   C07  C06  C05  -149.52  30.0  2
 BF6  Var_05    CE2  CZ   C07  C06    31.74  30.0  2
 BF6  Var_06    CE1  CZ   C07  C06  -152.09  30.0  2
 BF6  Var_07    CA2  CB2  CG2  CD2    -2.30  30.0  1
 BF6  Var_08    CA2  CB2  CG2  CD1   178.65  30.0  1
 BF6  Var_09    C2   N3   CA3  C3     87.66  30.0  3
 BF6  Var_10    C1   N3   CA3  C3    -76.42  30.0  3
 BF6  Var_11    O08  C07  C06  C01  -145.99  30.0  2
 BF6  Var_12    O08  C07  C06  C05    30.38  30.0  2
 BF6  Var_13    O08  C07  CZ   CE2  -148.17  30.0  2
 BF6  Var_14    O08  C07  CZ   CE1    28.01  30.0  2
 BF6  Var_15    N1   CA1  C1   N2     -6.77  30.0  3
 BF6  Var_16    N1   CA1  C1   N3    176.41  30.0  3
 BF6  Var_17    H1   CB2  CA2  C2     -1.94   0.0  2
 BF6  Var_18    H1   CB2  CA2  N2    179.11   0.0  2
 BF6  Var_19    H1   CB2  CG2  CD2   177.12  30.0  1
 BF6  Var_20    H1   CB2  CG2  CD1    -1.93  30.0  1
 BF6  Var_21    H3   CA3  N3   C1    161.31  30.0  1
 BF6  Var_22    H4   CA3  N3   C1     46.11  30.0  1
 BF6  Var_23    H3   CA3  N3   C2    -34.61  30.0  1
 BF6  Var_24    H4   CA3  N3   C2   -149.82  30.0  1
 BF6  Var_25    H5   CA1  C1   N2    119.83  30.0  3
 BF6  Var_26    H6   CA1  C1   N2   -126.96  30.0  3
 BF6  Var_27    H5   CA1  C1   N3    -56.99  30.0  3
 BF6  Var_28    H6   CA1  C1   N3     56.22  30.0  3
 BF6  Var_29    O3   C3   CA3  N3      6.47  30.0  3
 BF6  Var_30    OXT  C3   CA3  N3   -174.40  30.0  3
 BF6  Var_31    H17  N1   CA1  C1     63.19  30.0  3
 BF6  Var_32    H18  N1   CA1  C1    179.20  30.0  3
 BF6  Var_33    H3   CA3  C3   O3    127.59  30.0  3
 BF6  Var_34    H4   CA3  C3   O3   -115.82  30.0  3
 BF6  Var_35    H3   CA3  C3   OXT   -53.27  30.0  3
 BF6  Var_36    H4   CA3  C3   OXT    63.31  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  CG2  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-1  H1   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  H9   0.020
 BF6  plan-2  H10  0.020
 BF6  plan-2  H11  0.020
 BF6  plan-2  H7   0.020
 BF6  plan-2  C07  0.020
 BF6  plan-2  H8   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

