# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 08:37:35 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: [(4Z)-2-[(1R,2S)-1-amino-2-hydroxypropyl]-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: C[C@H](O)[C@H](N)C1=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
 BF9  BF9  "[(4Z)-2-[(1R,2S)-1-amino-2-hydroxypropyl]-4-{[4-(benzenecarbonyl)phenyl]methylidene}-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid"  L-peptide  50  30  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BF9
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
 BF9  C01  C  CR16   0  -0.280  -6.0433   0.9237   0.8775
 BF9  C02  C  CR16   0  -0.241  -7.1810   1.6639   1.1653
 BF9  C03  C  CR16   0  -0.247  -8.4107   1.2758   0.6516
 BF9  C04  C  CR16   0  -0.244  -8.5067   0.1339  -0.1360
 BF9  C05  C  CR16   0  -0.270  -7.3767  -0.6206  -0.4036
 BF9  C06  C  CR6    0  -0.037  -6.1330  -0.2232   0.0893
 BF9  C07  C  C      0   0.364  -4.9469  -1.0788  -0.1772
 BF9  CZ   C  CR6    0  -0.050  -3.6088  -0.4448  -0.3065
 BF9  CE2  C  CR16   0  -0.244  -2.4736  -1.1733   0.0568
 BF9  CD2  C  CR16   0  -0.308  -1.2101  -0.6388  -0.0936
 BF9  CG2  C  CR6    0   0.160  -1.0403   0.6403  -0.6457
 BF9  CD1  C  CR16   0  -0.289  -2.1814   1.3543  -1.0289
 BF9  CE1  C  CR16   0  -0.269  -3.4479   0.8270  -0.8535
 BF9  CB2  C  C1     0  -0.403   0.2527   1.2666  -0.8541
 BF9  CA2  C  CR5    0   0.110   1.4774   0.7920  -0.5640
 BF9  C1   C  CR5    0   0.616   3.1190  -0.4277   0.0627
 BF9  C2   C  CR5    0   0.530   2.7233   1.5497  -0.8642
 BF9  C3   C  C      0   0.419   5.5495   1.4448   1.0298
 BF9  CA1  C  CH1    0  -0.256   3.8751  -1.6046   0.5993
 BF9  CB1  C  CH1    0   0.034   3.9425  -2.6754  -0.5167
 BF9  CG1  C  CH3    0  -0.707   4.7909  -3.8675  -0.1100
 BF9  N2   N  N      0  -0.493   1.8280  -0.4134   0.0170
 BF9  N3   N  NR5    0  -0.540   3.7174   0.6831  -0.4793
 BF9  N1   N  NH2    0  -0.779   3.2390  -2.0470   1.8232
 BF9  O08  O  O      0  -0.389  -5.0677  -2.2830  -0.2904
 BF9  O2   O  O      0  -0.442   2.8712   2.6573  -1.3362
 BF9  O3   O  O      0  -0.584   4.6785   1.4289   1.9132
 BF9  OG1  O  OH1    0  -0.663   4.3907  -2.1056  -1.7300
 BF9  H1   H  HCR6   0   0.273  -5.0911   1.2308   1.2903
 BF9  H2   H  HCR6   0   0.266  -7.1054   2.5441   1.7896
 BF9  H3   H  HCR6   0   0.267  -9.2959   1.8605   0.8658
 BF9  H4   H  HCR6   0   0.265  -9.4647  -0.1689  -0.5373
 BF9  H5   H  HCR6   0   0.264  -7.4560  -1.5127  -1.0114
 BF9  H6   H  HCR6   0   0.265  -2.5832  -2.1646   0.4770
 BF9  H7   H  HCR6   0   0.280  -0.3441  -1.2099   0.2085
 BF9  H8   H  HCR6   0   0.265  -2.0725   2.3369  -1.4712
 BF9  H9   H  HCR6   0   0.275  -4.3081   1.4020  -1.1702
 BF9  H10  H  H      0   0.268   0.2273   2.2498  -1.3124
 BF9  H13  H  HCH2   0   0.277   5.2810   1.8680  -1.0822
 BF9  H14  H  HCH2   0   0.262   5.7258   0.2146  -0.7605
 BF9  H17  H  HCH1   0   0.268   4.8961  -1.3015   0.8477
 BF9  H18  H  HCH1   0   0.234   2.9173  -3.0091  -0.7072
 BF9  H19  H  HCH3   0   0.232   4.4002  -4.3589   0.7806
 BF9  H20  H  HCH3   0   0.251   4.8108  -4.6103  -0.9077
 BF9  H21  H  HCH3   0   0.230   5.8201  -3.5643   0.1001
 BF9  H22  H  HNH2   0   0.349   2.3136  -2.4063   1.6219
 BF9  H23  H  HNH2   0   0.358   3.7688  -2.8082   2.2269
 BF9  H26  H  HOH1   0   0.448   5.3466  -1.9975  -1.6841
 BF9  OXT  O  OC    -1  -0.609   6.7514   1.7480   1.1310
 BF9  CA3  C  CH2    0  -0.487   5.1100   1.0378  -0.3958

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
 BF9  O08  C07  double    1.216  0.020  1.216
 BF9  C07  C06  single    1.487  0.020  1.487
 BF9  C07  CZ   single    1.486  0.020  1.486
 BF9  C01  C02  aromatic  1.387  0.020  1.387
 BF9  C01  C06  aromatic  1.394  0.020  1.394
 BF9  CE1  CZ   aromatic  1.394  0.020  1.394
 BF9  CE1  CD1  aromatic  1.383  0.020  1.383
 BF9  C02  C03  aromatic  1.388  0.020  1.388
 BF9  C06  C05  aromatic  1.396  0.020  1.396
 BF9  CZ   CE2  aromatic  1.397  0.020  1.397
 BF9  CD1  CG2  aromatic  1.400  0.020  1.400
 BF9  C03  C04  aromatic  1.390  0.020  1.390
 BF9  C05  C04  aromatic  1.385  0.020  1.385
 BF9  CE2  CD2  aromatic  1.380  0.020  1.380
 BF9  CG2  CD2  aromatic  1.403  0.020  1.403
 BF9  CG2  CB2  single    1.452  0.020  1.452
 BF9  CB2  CA2  double    1.345  0.020  1.345
 BF9  CA2  C2   single    1.489  0.020  1.489
 BF9  CA2  N2   single    1.383  0.020  1.383
 BF9  O2   C2   double    1.213  0.020  1.213
 BF9  C2   N3   single    1.374  0.020  1.374
 BF9  N2   C1   double    1.292  0.020  1.292
 BF9  N3   C1   single    1.373  0.020  1.373
 BF9  N3   CA3  single    1.440  0.020  1.440
 BF9  C1   CA1  single    1.498  0.020  1.498
 BF9  CG1  CB1  single    1.519  0.020  1.519
 BF9  CA3  C3   single    1.546  0.020  1.546
 BF9  CA1  CB1  single    1.548  0.020  1.548
 BF9  CA1  N1   single    1.449  0.020  1.449
 BF9  CB1  OG1  single    1.413  0.020  1.413
 BF9  C3   O3   deloc     1.241  0.020  1.241
 BF9  C01  H1   single    0.930  0.020  1.080
 BF9  C02  H2   single    0.930  0.020  1.080
 BF9  C03  H3   single    0.930  0.020  1.080
 BF9  C04  H4   single    0.930  0.020  1.080
 BF9  C05  H5   single    0.930  0.020  1.080
 BF9  CE2  H6   single    0.930  0.020  1.080
 BF9  CD2  H7   single    0.930  0.020  1.080
 BF9  CD1  H8   single    0.930  0.020  1.080
 BF9  CE1  H9   single    0.930  0.020  1.080
 BF9  CB2  H10  single    0.930  0.020  1.080
 BF9  CA3  H13  single    0.970  0.020  1.090
 BF9  CA3  H14  single    0.970  0.020  1.090
 BF9  CA1  H17  single    0.970  0.020  1.090
 BF9  CB1  H18  single    0.970  0.020  1.090
 BF9  CG1  H19  single    0.970  0.020  1.090
 BF9  CG1  H20  single    0.970  0.020  1.090
 BF9  CG1  H21  single    0.970  0.020  1.090
 BF9  N1   H22  single    0.890  0.020  1.040
 BF9  N1   H23  single    0.890  0.020  1.040
 BF9  OG1  H26  single    0.850  0.020  0.980
 BF9  C3   OXT  deloc     1.244  0.020  1.244

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
 BF9  H1   C01  C06  120.37  3.000
 BF9  H1   C01  C02  119.40  3.000
 BF9  C06  C01  C02  120.22  3.000
 BF9  H2   C02  C03  120.20  3.000
 BF9  H2   C02  C01  119.77  3.000
 BF9  C03  C02  C01  120.03  3.000
 BF9  H3   C03  C04  119.96  3.000
 BF9  H3   C03  C02  120.02  3.000
 BF9  C04  C03  C02  120.03  3.000
 BF9  H4   C04  C05  119.89  3.000
 BF9  H4   C04  C03  120.07  3.000
 BF9  C05  C04  C03  120.04  3.000
 BF9  H5   C05  C06  119.88  3.000
 BF9  H5   C05  C04  119.86  3.000
 BF9  C06  C05  C04  120.25  3.000
 BF9  C07  C06  C05  118.94  3.000
 BF9  C05  C06  C01  119.41  3.000
 BF9  C07  C06  C01  121.56  3.000
 BF9  O08  C07  CZ   120.26  3.000
 BF9  CZ   C07  C06  119.24  3.000
 BF9  O08  C07  C06  120.51  3.000
 BF9  CE1  CZ   CE2  118.95  3.000
 BF9  CE2  CZ   C07  119.12  3.000
 BF9  CE1  CZ   C07  121.82  3.000
 BF9  H6   CE2  CD2  119.32  3.000
 BF9  H6   CE2  CZ   119.76  3.000
 BF9  CD2  CE2  CZ   120.91  3.000
 BF9  H7   CD2  CG2  119.66  3.000
 BF9  H7   CD2  CE2  119.91  3.000
 BF9  CG2  CD2  CE2  120.43  3.000
 BF9  CB2  CG2  CD1  117.83  3.000
 BF9  CB2  CG2  CD2  123.87  3.000
 BF9  CD1  CG2  CD2  118.30  3.000
 BF9  H8   CD1  CE1  119.32  3.000
 BF9  H8   CD1  CG2  119.52  3.000
 BF9  CE1  CD1  CG2  121.15  3.000
 BF9  H9   CE1  CD1  119.22  3.000
 BF9  H9   CE1  CZ   120.53  3.000
 BF9  CD1  CE1  CZ   120.22  3.000
 BF9  H10  CB2  CA2  115.60  3.000
 BF9  H10  CB2  CG2  115.51  3.000
 BF9  CA2  CB2  CG2  128.89  3.000
 BF9  N2   CA2  C2   108.43  3.000
 BF9  N2   CA2  CB2  128.96  3.000
 BF9  C2   CA2  CB2  122.61  3.000
 BF9  N3   C1   N2   114.36  3.000
 BF9  N3   C1   CA1  123.84  3.000
 BF9  N2   C1   CA1  121.72  3.000
 BF9  O2   C2   N3   126.64  3.000
 BF9  N3   C2   CA2  103.18  3.000
 BF9  O2   C2   CA2  130.19  3.000
 BF9  OXT  C3   O3   128.58  3.000
 BF9  OXT  C3   CA3  114.45  3.000
 BF9  O3   C3   CA3  116.97  3.000
 BF9  H17  CA1  N1   107.62  3.000
 BF9  H17  CA1  CB1  108.35  3.000
 BF9  N1   CA1  CB1  114.65  3.000
 BF9  H17  CA1  C1   109.56  3.000
 BF9  N1   CA1  C1   108.72  3.000
 BF9  CB1  CA1  C1   107.89  3.000
 BF9  H18  CB1  OG1  105.69  3.000
 BF9  H18  CB1  CG1  109.29  3.000
 BF9  OG1  CB1  CG1  111.66  3.000
 BF9  H18  CB1  CA1  107.19  3.000
 BF9  OG1  CB1  CA1  110.72  3.000
 BF9  CG1  CB1  CA1  111.98  3.000
 BF9  H21  CG1  H20  108.21  3.000
 BF9  H21  CG1  H19  107.79  3.000
 BF9  H20  CG1  H19  107.30  3.000
 BF9  H21  CG1  CB1  111.08  3.000
 BF9  H20  CG1  CB1  110.43  3.000
 BF9  H19  CG1  CB1  111.87  3.000
 BF9  C1   N2   CA2  106.13  3.000
 BF9  CA3  N3   C2   124.11  3.000
 BF9  CA3  N3   C1   126.73  3.000
 BF9  C2   N3   C1   107.79  3.000
 BF9  H23  N1   H22  106.91  3.000
 BF9  H23  N1   CA1  109.70  3.000
 BF9  H22  N1   CA1  109.97  3.000
 BF9  H26  OG1  CB1  108.61  3.000
 BF9  H14  CA3  H13  105.99  3.000
 BF9  H14  CA3  N3   109.93  3.000
 BF9  H13  CA3  N3   107.62  3.000
 BF9  H14  CA3  C3   110.27  3.000
 BF9  H13  CA3  C3   109.59  3.000
 BF9  N3   CA3  C3   113.16  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
 BF9  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 BF9  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 BF9  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 BF9  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 BF9  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 BF9  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 BF9  CONST_07  CG2  CD1  CE1  CZ      0.00   0.0  0
 BF9  CONST_08  CG2  CD2  CE2  CZ      0.00   0.0  0
 BF9  CONST_09  CD1  CE1  CZ   CE2     0.00   0.0  0
 BF9  CONST_10  CD1  CG2  CD2  CE2     0.00   0.0  0
 BF9  CONST_11  CE1  CZ   CE2  CD2     0.00   0.0  0
 BF9  CONST_12  CE1  CD1  CG2  CD2     0.00   0.0  0
 BF9  CONST_13  C1   N3   C2   CA2     0.00   0.0  0
 BF9  CONST_14  N3   C1   N2   CA2     0.00   0.0  0
 BF9  CONST_15  C2   CA2  N2   C1      0.00   0.0  0
 BF9  CONST_16  N2   C1   N3   C2      0.00   0.0  0
 BF9  CONST_17  N3   C2   CA2  N2      0.00   0.0  0
 BF9  CONST_18  C07  C06  C01  C02   180.00   0.0  0
 BF9  CONST_19  C07  C06  C05  C04   180.00   0.0  0
 BF9  CONST_20  CD1  CE1  CZ   C07   180.00   0.0  0
 BF9  CONST_21  CD2  CE2  CZ   C07   180.00   0.0  0
 BF9  CONST_22  CB2  CG2  CD2  CE2   180.00   0.0  0
 BF9  CONST_23  CB2  CG2  CD1  CE1   180.00   0.0  0
 BF9  CONST_24  CA3  N3   C2   CA2   180.00   0.0  0
 BF9  CONST_25  CA1  C1   N2   CA2   180.00   0.0  0
 BF9  CONST_26  O2   C2   N3   C1    180.00   0.0  0
 BF9  CONST_27  CA1  C1   N3   C2    180.00   0.0  0
 BF9  CONST_28  N2   C1   N3   CA3   180.00   0.0  0
 BF9  CONST_29  H3   C03  C02  C01   180.00   0.0  0
 BF9  CONST_30  H5   C05  C06  C01   180.00   0.0  0
 BF9  CONST_31  H4   C04  C03  C02   180.00   0.0  0
 BF9  CONST_32  H1   C01  C02  C03   180.00   0.0  0
 BF9  CONST_33  H5   C05  C04  C03   180.00   0.0  0
 BF9  CONST_34  H2   C02  C03  C04   180.00   0.0  0
 BF9  CONST_35  H1   C01  C06  C05   180.00   0.0  0
 BF9  CONST_36  H3   C03  C04  C05   180.00   0.0  0
 BF9  CONST_37  H2   C02  C01  C06   180.00   0.0  0
 BF9  CONST_38  H4   C04  C05  C06   180.00   0.0  0
 BF9  CONST_39  H8   CD1  CE1  CZ    180.00   0.0  0
 BF9  CONST_40  H7   CD2  CE2  CZ    180.00   0.0  0
 BF9  CONST_41  H9   CE1  CZ   CE2   180.00   0.0  0
 BF9  CONST_42  H8   CD1  CG2  CD2   180.00   0.0  0
 BF9  CONST_43  H9   CE1  CD1  CG2   180.00   0.0  0
 BF9  CONST_44  H6   CE2  CD2  CG2   180.00   0.0  0
 BF9  CONST_45  H7   CD2  CG2  CD1   180.00   0.0  0
 BF9  CONST_46  H6   CE2  CZ   CE1   180.00   0.0  0
 BF9  CONST_47  O2   C2   N3   CA3     0.00   0.0  0
 BF9  CONST_48  CA1  C1   N3   CA3     0.00   0.0  0
 BF9  Var_01    C2   CA2  CB2  CG2   178.80   0.0  2
 BF9  Var_02    N2   CA2  CB2  CG2    -0.47   0.0  2
 BF9  Var_03    CZ   C07  C06  C01   -34.18  30.0  2
 BF9  Var_04    CZ   C07  C06  C05   149.31  30.0  2
 BF9  Var_05    CE1  CZ   C07  C06   -33.22  30.0  2
 BF9  Var_06    CE2  CZ   C07  C06   150.62  30.0  2
 BF9  Var_07    CA2  CB2  CG2  CD2    -0.96  30.0  2
 BF9  Var_08    CA2  CB2  CG2  CD1   179.53  30.0  2
 BF9  Var_09    O08  C07  C06  C01   145.92  30.0  2
 BF9  Var_10    O08  C07  C06  C05   -30.58  30.0  2
 BF9  Var_11    O08  C07  CZ   CE2   -29.49  30.0  2
 BF9  Var_12    O08  C07  CZ   CE1   146.67  30.0  2
 BF9  Var_13    C3   CA3  N3   C1    -69.15  30.0  3
 BF9  Var_14    C3   CA3  N3   C2     95.83  30.0  3
 BF9  Var_15    H10  CB2  CA2  C2     -0.78   0.0  2
 BF9  Var_16    H10  CB2  CA2  N2    179.95   0.0  2
 BF9  Var_17    H10  CB2  CG2  CD2   178.61  30.0  2
 BF9  Var_18    H10  CB2  CG2  CD1    -0.89  30.0  2
 BF9  Var_19    H13  CA3  N3   C1    169.62  30.0  3
 BF9  Var_20    H14  CA3  N3   C1     54.62  30.0  3
 BF9  Var_21    H13  CA3  N3   C2    -25.40  30.0  3
 BF9  Var_22    H14  CA3  N3   C2   -140.40  30.0  3
 BF9  Var_23    O3   C3   CA3  N3     -0.43  30.0  3
 BF9  Var_24    OXT  C3   CA3  N3    179.56  30.0  3
 BF9  Var_25    H13  CA3  C3   O3    119.68  30.0  2
 BF9  Var_26    H14  CA3  C3   O3   -124.01  30.0  2
 BF9  Var_27    OXT  C3   CA3  H13   -60.33  30.0  3
 BF9  Var_28    OXT  C3   CA3  H14    55.98  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
 BF9  chir_01  CA1  C1   CB1  N1   positiv
 BF9  chir_02  CB1  OG1  CA1  CG1  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
 BF9  plan-1  CG2  0.020
 BF9  plan-1  CB2  0.020
 BF9  plan-1  CA2  0.020
 BF9  plan-1  C1   0.020
 BF9  plan-1  C2   0.020
 BF9  plan-1  CA1  0.020
 BF9  plan-1  N2   0.020
 BF9  plan-1  N3   0.020
 BF9  plan-1  O2   0.020
 BF9  plan-1  H10  0.020
 BF9  plan-1  CA3  0.020
 BF9  plan-2  C01  0.020
 BF9  plan-2  C02  0.020
 BF9  plan-2  C03  0.020
 BF9  plan-2  C04  0.020
 BF9  plan-2  C05  0.020
 BF9  plan-2  C06  0.020
 BF9  plan-2  C07  0.020
 BF9  plan-2  H1   0.020
 BF9  plan-2  H2   0.020
 BF9  plan-2  H3   0.020
 BF9  plan-2  H4   0.020
 BF9  plan-2  H5   0.020
 BF9  plan-3  C07  0.020
 BF9  plan-3  CZ   0.020
 BF9  plan-3  CE2  0.020
 BF9  plan-3  CD2  0.020
 BF9  plan-3  CG2  0.020
 BF9  plan-3  CD1  0.020
 BF9  plan-3  CE1  0.020
 BF9  plan-3  CB2  0.020
 BF9  plan-3  H6   0.020
 BF9  plan-3  H7   0.020
 BF9  plan-3  H8   0.020
 BF9  plan-3  H9   0.020
 BF9  plan-4  C06  0.020
 BF9  plan-4  C07  0.020
 BF9  plan-4  CZ   0.020
 BF9  plan-4  O08  0.020
 BF9  plan-5  C3   0.020
 BF9  plan-5  O3   0.020
 BF9  plan-5  OXT  0.020
 BF9  plan-5  CA3  0.020

