# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 02:47:33 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-methoxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)\C=C2/N=C([C@@H](N)CS)N(CC(O)=O)C2=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
 KXV  KXV  '{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-methoxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid'  L-peptide  41  24  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KXV
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
 KXV  N     N  NH2   0  -0.758  -2.0857   2.6275   1.4195
 KXV  CB1   C  CH2   0  -0.552  -3.2740   1.8424  -0.5406
 KXV  CA1   C  CH1   0  -0.206  -2.6899   1.4637   0.8205
 KXV  C1    C  CR5   0   0.538  -1.7334   0.3148   0.6297
 KXV  N2    N  N     0  -0.476  -0.4644   0.4706   0.4916
 KXV  N3    N  NR5   0  -0.564  -2.1379  -1.0038   0.5568
 KXV  C2    C  CR5   0   0.540  -1.0205  -1.7846   0.3265
 KXV  O2    O  O     0  -0.445  -1.0214  -2.9917   0.2014
 KXV  CA2   C  CR5   0   0.089   0.0735  -0.7949   0.2961
 KXV  CA3   C  CH2   0  -0.462  -3.4548  -1.5541   0.6526
 KXV  CB2   C  C1    0  -0.384   1.3647  -1.1368   0.1067
 KXV  CG2   C  CR6   0   0.161   2.5426  -0.3029   0.0543
 KXV  CD1   C  CR16  0  -0.447   3.7784  -0.9451  -0.1513
 KXV  CD2   C  CR16  0  -0.325   2.5279   1.0860   0.1947
 KXV  CE1   C  CR6   0   0.342   4.9606  -0.2348  -0.2170
 KXV  CE2   C  CR16  0  -0.354   3.7101   1.8038   0.1263
 KXV  CZ    C  CR6   0   0.280   4.9263   1.1666  -0.0782
 KXV  OH    O  OH1   0  -0.610   6.0976   1.8123  -0.1561
 KXV  C     C  C     0   0.550  -4.0142  -1.9065  -0.7103
 KXV  O     O  O     0  -0.426  -3.4802  -1.6343  -1.7521
 KXV  O4    O  O2    0  -0.465   6.1803  -0.7693  -0.4084
 KXV  HN1   H  HNH2  0   0.361  -1.7872   2.4196   2.3637
 KXV  HN2   H  HNH2  0   0.354  -1.2504   2.8858   0.9071
 KXV  HG1   H  HSH1  0   0.215  -5.2014   2.9764  -1.3491
 KXV  HB11  H  HCH2  0   0.284  -3.8264   1.0156  -0.9825
 KXV  HB12  H  HCH2  0   0.278  -2.4670   2.1064  -1.2262
 KXV  HA1   H  HCH1  0   0.278  -3.5118   1.1438   1.4674
 KXV  HA31  H  HCH2  0   0.324  -3.4371  -2.4476   1.2799
 KXV  HA32  H  HCH2  0   0.326  -4.1262  -0.8515   1.1483
 KXV  HB2   H  H     0   0.269   1.5411  -2.1998  -0.0274
 KXV  HD1   H  HCR6  0   0.287   3.7852  -2.0224  -0.2572
 KXV  HD2   H  HCR6  0   0.277   1.5973   1.6091   0.3581
 KXV  HE2   H  HCR6  0   0.279   3.6878   2.8824   0.2323
 KXV  H1    H  HOH1  0   0.481   5.9630   2.7621  -0.0577
 KXV  OXT   O  OH1   0  -0.583  -5.1684  -2.5385  -0.5926
 KXV  H2    H  HCH3  0   0.230   5.9248  -2.7033   0.3276
 KXV  H3    H  HCH3  0   0.230   5.7134  -2.5262  -1.4288
 KXV  H4    H  HCH3  0   0.263   7.3287  -2.3946  -0.7101
 KXV  HXT   H  HOH1  0   0.490  -5.5360  -2.7395  -1.4668
 KXV  SG1   S  S2    0  -0.227  -4.3982   3.2587  -0.3172
 KXV  CF    C  CH3   0  -0.440   6.2755  -2.1713  -0.5608

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
 KXV  CF   O4    single    1.413  0.020  1.413
 KXV  O4   CE1   single    1.345  0.020  1.345
 KXV  OH   CZ    single    1.340  0.020  1.340
 KXV  CE1  CZ    aromatic  1.409  0.020  1.409
 KXV  CE1  CD1   aromatic  1.381  0.020  1.381
 KXV  CZ   CE2   aromatic  1.388  0.020  1.388
 KXV  CD1  CG2   aromatic  1.408  0.020  1.408
 KXV  CE2  CD2   aromatic  1.385  0.020  1.385
 KXV  CG2  CD2   aromatic  1.396  0.020  1.396
 KXV  CG2  CB2   single    1.444  0.020  1.444
 KXV  CB2  CA2   double    1.349  0.020  1.349
 KXV  CA2  N2    single    1.389  0.020  1.389
 KXV  CA2  C2    single    1.476  0.020  1.476
 KXV  O2   C2    double    1.214  0.020  1.214
 KXV  N2   C1    double    1.286  0.020  1.286
 KXV  C2   N3    single    1.382  0.020  1.382
 KXV  C1   N3    single    1.381  0.020  1.381
 KXV  C1   CA1   single    1.507  0.020  1.507
 KXV  N3   CA3   single    1.431  0.020  1.431
 KXV  CB1  CA1   single    1.529  0.020  1.529
 KXV  CB1  SG1   single    1.822  0.020  1.822
 KXV  CA1  N     single    1.442  0.020  1.442
 KXV  C    CA3   single    1.515  0.020  1.515
 KXV  C    O     double    1.231  0.020  1.231
 KXV  N    HN1   single    0.890  0.020  1.040
 KXV  N    HN2   single    0.890  0.020  1.040
 KXV  SG1  HG1   single    1.200  0.020  1.300
 KXV  CB1  HB11  single    0.970  0.020  1.090
 KXV  CB1  HB12  single    0.970  0.020  1.090
 KXV  CA1  HA1   single    0.970  0.020  1.090
 KXV  CA3  HA31  single    0.970  0.020  1.090
 KXV  CA3  HA32  single    0.970  0.020  1.090
 KXV  CB2  HB2   single    0.930  0.020  1.080
 KXV  CD1  HD1   single    0.930  0.020  1.080
 KXV  CD2  HD2   single    0.930  0.020  1.080
 KXV  CE2  HE2   single    0.930  0.020  1.080
 KXV  OH   H1    single    0.850  0.020  0.980
 KXV  C    OXT   single    1.321  0.020  1.321
 KXV  CF   H2    single    0.970  0.020  1.090
 KXV  CF   H3    single    0.970  0.020  1.090
 KXV  CF   H4    single    0.970  0.020  1.090
 KXV  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
 KXV  HN2   N    HN1   106.32  3.000
 KXV  HN2   N    CA1   109.95  3.000
 KXV  HN1   N    CA1   110.21  3.000
 KXV  HB12  CB1  HB11  107.71  3.000
 KXV  HB12  CB1  CA1   109.67  3.000
 KXV  HB11  CB1  CA1   111.55  3.000
 KXV  HB12  CB1  SG1   110.20  3.000
 KXV  HB11  CB1  SG1   109.10  3.000
 KXV  CA1   CB1  SG1   108.61  3.000
 KXV  HA1   CA1  C1    109.20  3.000
 KXV  HA1   CA1  CB1   108.17  3.000
 KXV  C1    CA1  CB1   108.58  3.000
 KXV  HA1   CA1  N     107.78  3.000
 KXV  CB1   CA1  N     109.27  3.000
 KXV  C1    CA1  N     113.71  3.000
 KXV  N3    C1   N2    113.52  3.000
 KXV  N3    C1   CA1   123.28  3.000
 KXV  N2    C1   CA1   123.19  3.000
 KXV  CA2   N2   C1    106.67  3.000
 KXV  CA3   N3   C2    122.54  3.000
 KXV  CA3   N3   C1    129.30  3.000
 KXV  C2    N3   C1    108.14  3.000
 KXV  CA2   C2   O2    131.72  3.000
 KXV  O2    C2   N3    125.34  3.000
 KXV  CA2   C2   N3    102.94  3.000
 KXV  CB2   CA2  C2    122.86  3.000
 KXV  C2    CA2  N2    108.73  3.000
 KXV  CB2   CA2  N2    128.42  3.000
 KXV  HA32  CA3  HA31  106.02  3.000
 KXV  HA32  CA3  C     109.36  3.000
 KXV  HA31  CA3  C     109.42  3.000
 KXV  HA32  CA3  N3    110.44  3.000
 KXV  HA31  CA3  N3    109.77  3.000
 KXV  C     CA3  N3    111.66  3.000
 KXV  HB2   CB2  CG2   115.36  3.000
 KXV  HB2   CB2  CA2   114.90  3.000
 KXV  CG2   CB2  CA2   129.75  3.000
 KXV  CD2   CG2  CD1   118.54  3.000
 KXV  CD2   CG2  CB2   124.21  3.000
 KXV  CD1   CG2  CB2   117.25  3.000
 KXV  HD1   CD1  CE1   120.13  3.000
 KXV  HD1   CD1  CG2   118.28  3.000
 KXV  CE1   CD1  CG2   121.59  3.000
 KXV  HD2   CD2  CE2   119.48  3.000
 KXV  HD2   CD2  CG2   120.41  3.000
 KXV  CE2   CD2  CG2   120.11  3.000
 KXV  O4    CE1  CZ    115.55  3.000
 KXV  CZ    CE1  CD1   119.09  3.000
 KXV  O4    CE1  CD1   125.35  3.000
 KXV  HE2   CE2  CZ    119.28  3.000
 KXV  HE2   CE2  CD2   119.56  3.000
 KXV  CZ    CE2  CD2   121.15  3.000
 KXV  OH    CZ   CE2   123.59  3.000
 KXV  CE2   CZ   CE1   119.50  3.000
 KXV  OH    CZ   CE1   116.90  3.000
 KXV  H1    OH   CZ    110.29  3.000
 KXV  OXT   C    O     125.01  3.000
 KXV  OXT   C    CA3   110.72  3.000
 KXV  O     C    CA3   124.27  3.000
 KXV  CF    O4   CE1   118.06  3.000
 KXV  HXT   OXT  C     110.49  3.000
 KXV  HG1   SG1  CB1    96.42  3.000
 KXV  H4    CF   H3    108.81  3.000
 KXV  H4    CF   H2    108.81  3.000
 KXV  H3    CF   H2    108.80  3.000
 KXV  H4    CF   O4    106.49  3.000
 KXV  H3    CF   O4    111.91  3.000
 KXV  H2    CF   O4    111.92  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
 KXV  CONST_01  CZ   CE1  CD1  CG2    0.00   0.0  0
 KXV  CONST_02  CZ   CE2  CD2  CG2    0.00   0.0  0
 KXV  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 KXV  CONST_04  CE2  CD2  CG2  CD1    0.00   0.0  0
 KXV  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 KXV  CONST_06  CE1  CD1  CG2  CD2    0.00   0.0  0
 KXV  CONST_07  C2   CA2  N2   C1     0.00   0.0  0
 KXV  CONST_08  CA2  C2   N3   C1     0.00   0.0  0
 KXV  CONST_09  N3   C2   CA2  N2     0.00   0.0  0
 KXV  CONST_10  C2   N3   C1   N2     0.00   0.0  0
 KXV  CONST_11  CA2  N2   C1   N3     0.00   0.0  0
 KXV  CONST_12  CE1  CD1  CG2  CB2  180.00   0.0  0
 KXV  CONST_13  CE2  CD2  CG2  CB2  180.00   0.0  0
 KXV  CONST_14  O4   CE1  CD1  CG2  180.00   0.0  0
 KXV  CONST_15  OH   CZ   CE1  CD1  180.00   0.0  0
 KXV  CONST_16  OH   CZ   CE2  CD2  180.00   0.0  0
 KXV  CONST_17  O4   CE1  CZ   CE2  180.00   0.0  0
 KXV  CONST_18  CA2  N2   C1   CA1  180.00   0.0  0
 KXV  CONST_19  C2   N3   C1   CA1  180.00   0.0  0
 KXV  CONST_20  O2   C2   N3   C1   180.00   0.0  0
 KXV  CONST_21  CA3  N3   C1   N2   180.00   0.0  0
 KXV  CONST_22  CA3  N3   C2   CA2  180.00   0.0  0
 KXV  CONST_23  HE2  CE2  CD2  CG2  180.00   0.0  0
 KXV  CONST_24  HD2  CD2  CG2  CD1  180.00   0.0  0
 KXV  CONST_25  HD1  CD1  CG2  CD2  180.00   0.0  0
 KXV  CONST_26  CA3  N3   C1   CA1    0.00   0.0  0
 KXV  CONST_27  CA3  N3   C2   O2     0.00   0.0  0
 KXV  CONST_28  HXT  OXT  C    CA3  180.00   0.0  0
 KXV  Var_01    CG2  CB2  CA2  N2     0.08  30.0  2
 KXV  Var_02    CD1  CG2  CB2  CA2  179.60  30.0  2
 KXV  Var_03    C    CA3  N3   C1   101.54  30.0  3
 KXV  Var_04    O    C    CA3  N3    -7.11  30.0  1
 KXV  Var_05    H2   CF   O4   CE1  -61.65  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
 KXV  chir_01  CA1  C1  CB1  N  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
 KXV  plan-1  CA1  0.020
 KXV  plan-1  C1   0.020
 KXV  plan-1  N2   0.020
 KXV  plan-1  N3   0.020
 KXV  plan-1  C2   0.020
 KXV  plan-1  O2   0.020
 KXV  plan-1  CA2  0.020
 KXV  plan-1  CA3  0.020
 KXV  plan-1  CB2  0.020
 KXV  plan-2  CB2  0.020
 KXV  plan-2  CG2  0.020
 KXV  plan-2  CD1  0.020
 KXV  plan-2  CD2  0.020
 KXV  plan-2  CE1  0.020
 KXV  plan-2  CE2  0.020
 KXV  plan-2  CZ   0.020
 KXV  plan-2  OH   0.020
 KXV  plan-2  O4   0.020
 KXV  plan-2  HD1  0.020
 KXV  plan-2  HD2  0.020
 KXV  plan-2  HE2  0.020
 KXV  plan-3  CA3  0.020
 KXV  plan-3  C    0.020
 KXV  plan-3  O    0.020
 KXV  plan-3  OXT  0.020
 KXV  plan-3  HXT  0.020

