# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 02:30:56 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: [(4Z)-2-{(2R,5R)-2-[(1S,2S)-1-amino-2-methylbutyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](N)[C@@]1(O)O[C@H](C)C(=N1)C2=N\C(=C/c3ccc(O)cc3)C(=O)N2CC(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
 OIM  OIM  "[(4Z)-2-{(2R,5R)-2-[(1S,2S)-1-amino-2-methylbutyl]-2-hydroxy-5-methyl-2,5-dihydro-1,3-oxazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid"  L-peptide  56  31  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OIM
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
 OIM  N0   N  NH2    0  -0.785  -4.1982   3.0012   0.0340
 OIM  CA0  C  CH1    0  -0.157  -3.6923   1.6656   0.3039
 OIM  C0   C  CT     0   0.600  -2.9155   1.0906  -0.9131
 OIM  O0   O  OH1    0  -0.640  -3.7416   0.6945  -1.9478
 OIM  CB0  C  CH1    0  -0.216  -4.8582   0.7972   0.8194
 OIM  CGX  C  CH2    0  -0.409  -5.3977   1.3995   2.1263
 OIM  CGY  C  CH3    0  -0.663  -4.5168  -0.6756   1.0266
 OIM  CDX  C  CH3    0  -0.672  -6.7346   0.8252   2.5779
 OIM  N1   N  N      0  -0.375  -2.1083  -0.0462  -0.5559
 OIM  CA1  C  C      0   0.174  -0.8963   0.2409  -0.7638
 OIM  CB1  C  CH1    0  -0.009  -0.6827   1.6225  -1.3113
 OIM  CG1  C  CH3    0  -0.676  -0.0118   1.6492  -2.6728
 OIM  OG1  O  O2     0  -0.530  -2.0113   2.0960  -1.3619
 OIM  C1   C  CR5    0   0.533   0.2130  -0.6483  -0.4424
 OIM  N2   N  N      0  -0.481   1.3890  -0.1783  -0.1933
 OIM  N3   N  NR5    0  -0.547   0.0911  -2.0088  -0.2914
 OIM  C2   C  CR5    0   0.523   1.3393  -2.4956   0.0319
 OIM  O2   O  O      0  -0.456   1.6388  -3.6643   0.1809
 OIM  CA2  C  CR5    0   0.095   2.1694  -1.2749   0.1329
 OIM  CA3  C  CH2    0  -0.476  -0.9885  -2.8167  -0.8047
 OIM  C3   C  C      0   0.432  -1.1781  -2.6342  -2.3280
 OIM  O3   O  O      0  -0.582  -0.4294  -1.8214  -2.8965
 OIM  CB2  C  C1     0  -0.398   3.4685  -1.2933   0.5002
 OIM  CG2  C  CR6    0   0.134   4.3968  -0.2007   0.6587
 OIM  CD1  C  CR16   0  -0.299   4.0823   1.1475   0.4169
 OIM  CD2  C  CR16   0  -0.282   5.6976  -0.4982   1.0866
 OIM  CE1  C  CR16   0  -0.314   5.0210   2.1398   0.5978
 OIM  CE2  C  CR16   0  -0.377   6.6459   0.4886   1.2724
 OIM  CZ   C  CR6    0   0.362   6.3123   1.8204   1.0287
 OIM  OH   O  OH1    0  -0.616   7.1808   2.8274   1.1877
 OIM  H1   H  HNH2   0   0.355  -3.4856   3.5882  -0.3771
 OIM  H2   H  HNH2   0   0.338  -4.9879   2.9843  -0.6001
 OIM  H4   H  HCH1   0   0.224  -2.9506   1.7504   1.1087
 OIM  H5   H  HOH1   0   0.449  -4.4670   1.3227  -2.0430
 OIM  H6   H  HCH1   0   0.203  -5.6634   0.8520   0.0722
 OIM  H7   H  HCH2   0   0.206  -4.6492   1.2508   2.9128
 OIM  H8   H  HCH2   0   0.231  -5.5043   2.4776   2.0060
 OIM  H9   H  HCH3   0   0.225  -5.3769  -1.2069   1.4353
 OIM  H10  H  HCH3   0   0.243  -4.2342  -1.1771   0.1054
 OIM  H11  H  HCH3   0   0.208  -3.6913  -0.7921   1.7318
 OIM  H12  H  HCH3   0   0.215  -7.4915   0.9346   1.7983
 OIM  H13  H  HCH3   0   0.219  -6.6741  -0.2334   2.8313
 OIM  H14  H  HCH3   0   0.228  -7.0983   1.3486   3.4629
 OIM  H18  H  HCH1   0   0.258  -0.0997   2.2253  -0.6046
 OIM  H19  H  HCH3   0   0.239  -0.5229   0.9976  -3.3800
 OIM  H20  H  HCH3   0   0.242  -0.0040   2.6651  -3.0673
 OIM  H21  H  HCH3   0   0.236   1.0212   1.3164  -2.5847
 OIM  H23  H  HCH2   0   0.267  -0.7533  -3.8574  -0.5793
 OIM  H24  H  HCH2   0   0.278  -1.9156  -2.5721  -0.2887
 OIM  H28  H  H      0   0.270   3.8706  -2.2789   0.7155
 OIM  H30  H  HCR6   0   0.280   3.0894   1.4159   0.0856
 OIM  H31  H  HCR6   0   0.267   5.9704  -1.5284   1.2798
 OIM  H32  H  HCR6   0   0.271   4.7625   3.1740   0.4089
 OIM  H33  H  HCR6   0   0.279   7.6426   0.2240   1.6054
 OIM  H34  H  HOH1   0   0.480   8.0312   2.5005   1.5040
 OIM  OXT  O  OC    -1  -0.609  -2.0739  -3.3360  -2.8274

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
 OIM  O3   C3   deloc     1.243  0.020  1.243
 OIM  O2   C2   double    1.216  0.020  1.216
 OIM  CA3  C3   single    1.546  0.020  1.546
 OIM  CA3  N3   single    1.443  0.020  1.443
 OIM  N0   CA0  single    1.454  0.020  1.454
 OIM  C2   N3   single    1.378  0.020  1.378
 OIM  C2   CA2  single    1.480  0.020  1.480
 OIM  CGX  CDX  single    1.524  0.020  1.524
 OIM  CGX  CB0  single    1.537  0.020  1.537
 OIM  N3   C1   single    1.374  0.020  1.374
 OIM  CA0  CB0  single    1.542  0.020  1.542
 OIM  CA0  C0   single    1.554  0.020  1.554
 OIM  N1   C0   single    1.439  0.020  1.439
 OIM  N1   CA1  double    1.263  0.020  1.263
 OIM  CB0  CGY  single    1.526  0.020  1.526
 OIM  CA2  CB2  double    1.350  0.020  1.350
 OIM  CA2  N2   single    1.385  0.020  1.385
 OIM  C0   O0   single    1.382  0.020  1.382
 OIM  C0   OG1  single    1.425  0.020  1.425
 OIM  CB2  CG2  single    1.442  0.020  1.442
 OIM  C1   CA1  single    1.458  0.020  1.458
 OIM  C1   N2   double    1.291  0.020  1.291
 OIM  CA1  CB1  single    1.501  0.020  1.501
 OIM  CD2  CG2  aromatic  1.401  0.020  1.401
 OIM  CD2  CE2  aromatic  1.381  0.020  1.381
 OIM  CG2  CD1  aromatic  1.405  0.020  1.405
 OIM  CE2  CZ   aromatic  1.394  0.020  1.394
 OIM  OG1  CB1  single    1.411  0.020  1.411
 OIM  CB1  CG1  single    1.518  0.020  1.518
 OIM  CD1  CE1  aromatic  1.378  0.020  1.378
 OIM  CZ   CE1  aromatic  1.398  0.020  1.398
 OIM  CZ   OH   single    1.339  0.020  1.339
 OIM  N0   H1   single    0.890  0.020  1.040
 OIM  N0   H2   single    0.890  0.020  1.040
 OIM  CA0  H4   single    0.970  0.020  1.090
 OIM  O0   H5   single    0.850  0.020  0.980
 OIM  CB0  H6   single    0.970  0.020  1.090
 OIM  CGX  H7   single    0.970  0.020  1.090
 OIM  CGX  H8   single    0.970  0.020  1.090
 OIM  CGY  H9   single    0.970  0.020  1.090
 OIM  CGY  H10  single    0.970  0.020  1.090
 OIM  CGY  H11  single    0.970  0.020  1.090
 OIM  CDX  H12  single    0.970  0.020  1.090
 OIM  CDX  H13  single    0.970  0.020  1.090
 OIM  CDX  H14  single    0.970  0.020  1.090
 OIM  CB1  H18  single    0.970  0.020  1.090
 OIM  CG1  H19  single    0.970  0.020  1.090
 OIM  CG1  H20  single    0.970  0.020  1.090
 OIM  CG1  H21  single    0.970  0.020  1.090
 OIM  CA3  H23  single    0.970  0.020  1.090
 OIM  CA3  H24  single    0.970  0.020  1.090
 OIM  CB2  H28  single    0.930  0.020  1.080
 OIM  CD1  H30  single    0.930  0.020  1.080
 OIM  CD2  H31  single    0.930  0.020  1.080
 OIM  CE1  H32  single    0.930  0.020  1.080
 OIM  CE2  H33  single    0.930  0.020  1.080
 OIM  OH   H34  single    0.850  0.020  0.980
 OIM  C3   OXT  deloc     1.243  0.020  1.243

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
 OIM  H2   N0   H1   107.74  3.000
 OIM  H2   N0   CA0  111.85  3.000
 OIM  H1   N0   CA0  111.34  3.000
 OIM  H4   CA0  CB0  108.01  3.000
 OIM  H4   CA0  C0   105.36  3.000
 OIM  CB0  CA0  C0   115.55  3.000
 OIM  H4   CA0  N0   107.47  3.000
 OIM  C0   CA0  N0   111.63  3.000
 OIM  CB0  CA0  N0   108.44  3.000
 OIM  OG1  C0   N1   106.24  3.000
 OIM  OG1  C0   O0   110.23  3.000
 OIM  N1   C0   O0   107.14  3.000
 OIM  OG1  C0   CA0  107.63  3.000
 OIM  O0   C0   CA0  113.18  3.000
 OIM  N1   C0   CA0  112.22  3.000
 OIM  H5   O0   C0   109.68  3.000
 OIM  H6   CB0  CGY  107.71  3.000
 OIM  H6   CB0  CGX  107.53  3.000
 OIM  CGY  CB0  CGX  109.95  3.000
 OIM  H6   CB0  CA0  107.36  3.000
 OIM  CGY  CB0  CA0  114.81  3.000
 OIM  CGX  CB0  CA0  109.20  3.000
 OIM  H8   CGX  H7   106.27  3.000
 OIM  H8   CGX  CDX  108.64  3.000
 OIM  H7   CGX  CDX  109.60  3.000
 OIM  H8   CGX  CB0  109.15  3.000
 OIM  H7   CGX  CB0  108.51  3.000
 OIM  CDX  CGX  CB0  114.35  3.000
 OIM  H11  CGY  H10  107.57  3.000
 OIM  H11  CGY  H9   107.60  3.000
 OIM  H10  CGY  H9   107.34  3.000
 OIM  H11  CGY  CB0  111.09  3.000
 OIM  H10  CGY  CB0  112.87  3.000
 OIM  H9   CGY  CB0  110.16  3.000
 OIM  H14  CDX  H13  107.21  3.000
 OIM  H14  CDX  H12  107.46  3.000
 OIM  H13  CDX  H12  107.56  3.000
 OIM  H14  CDX  CGX  110.62  3.000
 OIM  H13  CDX  CGX  112.72  3.000
 OIM  H12  CDX  CGX  111.03  3.000
 OIM  CA1  N1   C0   108.54  3.000
 OIM  C1   CA1  CB1  122.24  3.000
 OIM  CB1  CA1  N1   113.94  3.000
 OIM  C1   CA1  N1   123.74  3.000
 OIM  H18  CB1  OG1  109.83  3.000
 OIM  H18  CB1  CG1  109.47  3.000
 OIM  OG1  CB1  CG1  112.21  3.000
 OIM  H18  CB1  CA1  110.27  3.000
 OIM  CG1  CB1  CA1  113.96  3.000
 OIM  OG1  CB1  CA1  100.83  3.000
 OIM  H21  CG1  H20  107.90  3.000
 OIM  H21  CG1  H19  108.35  3.000
 OIM  H20  CG1  H19  109.03  3.000
 OIM  H21  CG1  CB1  109.96  3.000
 OIM  H20  CG1  CB1  110.13  3.000
 OIM  H19  CG1  CB1  111.38  3.000
 OIM  CB1  OG1  C0   110.45  3.000
 OIM  N3   C1   N2   114.84  3.000
 OIM  N2   C1   CA1  120.92  3.000
 OIM  N3   C1   CA1  124.10  3.000
 OIM  CA2  N2   C1   105.69  3.000
 OIM  CA3  N3   C2   124.29  3.000
 OIM  C2   N3   C1   107.16  3.000
 OIM  CA3  N3   C1   125.57  3.000
 OIM  CA2  C2   O2   130.28  3.000
 OIM  CA2  C2   N3   103.46  3.000
 OIM  O2   C2   N3   126.26  3.000
 OIM  CB2  CA2  C2   123.17  3.000
 OIM  CB2  CA2  N2   128.11  3.000
 OIM  C2   CA2  N2   108.72  3.000
 OIM  H24  CA3  H23  107.46  3.000
 OIM  H24  CA3  C3   109.63  3.000
 OIM  H23  CA3  C3   110.05  3.000
 OIM  H24  CA3  N3   110.05  3.000
 OIM  H23  CA3  N3   107.43  3.000
 OIM  C3   CA3  N3   112.10  3.000
 OIM  OXT  C3   O3   128.30  3.000
 OIM  OXT  C3   CA3  114.69  3.000
 OIM  O3   C3   CA3  117.00  3.000
 OIM  H28  CB2  CG2  115.30  3.000
 OIM  H28  CB2  CA2  115.00  3.000
 OIM  CG2  CB2  CA2  129.70  3.000
 OIM  CD2  CG2  CD1  117.64  3.000
 OIM  CD1  CG2  CB2  124.31  3.000
 OIM  CD2  CG2  CB2  118.05  3.000
 OIM  H30  CD1  CE1  119.17  3.000
 OIM  H30  CD1  CG2  119.78  3.000
 OIM  CE1  CD1  CG2  121.05  3.000
 OIM  H31  CD2  CE2  118.86  3.000
 OIM  H31  CD2  CG2  119.35  3.000
 OIM  CE2  CD2  CG2  121.79  3.000
 OIM  H32  CE1  CZ   119.50  3.000
 OIM  H32  CE1  CD1  120.16  3.000
 OIM  CZ   CE1  CD1  120.34  3.000
 OIM  H33  CE2  CZ   120.46  3.000
 OIM  H33  CE2  CD2  119.90  3.000
 OIM  CZ   CE2  CD2  119.64  3.000
 OIM  OH   CZ   CE2  122.84  3.000
 OIM  OH   CZ   CE1  117.63  3.000
 OIM  CE2  CZ   CE1  119.53  3.000
 OIM  H34  OH   CZ   110.85  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
 OIM  CONST_01  CZ   CE2  CD2  CG2     0.00   0.0  0
 OIM  CONST_02  CZ   CE1  CD1  CG2     0.00   0.0  0
 OIM  CONST_03  CE2  CD2  CG2  CD1     0.00   0.0  0
 OIM  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 OIM  CONST_05  CE1  CD1  CG2  CD2     0.00   0.0  0
 OIM  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 OIM  CONST_07  C2   N3   C1   CA1   180.00   0.0  0
 OIM  CONST_08  CA2  N2   C1   CA1   180.00   0.0  0
 OIM  CONST_09  CA2  C2   N3   C1      0.00   0.0  0
 OIM  CONST_10  C2   CA2  N2   C1      0.00   0.0  0
 OIM  CONST_11  N3   C2   CA2  N2      0.00   0.0  0
 OIM  CONST_12  C2   N3   C1   N2      0.00   0.0  0
 OIM  CONST_13  CA2  N2   C1   N3      0.00   0.0  0
 OIM  CONST_14  CE2  CD2  CG2  CB2   180.00   0.0  0
 OIM  CONST_15  CE1  CD1  CG2  CB2   180.00   0.0  0
 OIM  CONST_16  OH   CZ   CE1  CD1   180.00   0.0  0
 OIM  CONST_17  OH   CZ   CE2  CD2   180.00   0.0  0
 OIM  CONST_19  O2   C2   N3   C1    180.00   0.0  0
 OIM  CONST_22  H33  CE2  CD2  CG2   180.00   0.0  0
 OIM  CONST_23  H32  CE1  CD1  CG2   180.00   0.0  0
 OIM  CONST_24  H31  CD2  CG2  CD1   180.00   0.0  0
 OIM  CONST_25  H30  CD1  CG2  CD2   180.00   0.0  0
 OIM  CONST_26  H33  CE2  CZ   CE1   180.00   0.0  0
 OIM  CONST_27  H32  CE1  CZ   CE2   180.00   0.0  0
 OIM  CONST_28  H31  CD2  CE2  CZ    180.00   0.0  0
 OIM  CONST_29  H30  CD1  CE1  CZ    180.00   0.0  0
 OIM  CONST_30  CA3  N3   C2   O2      0.00   0.0  0
 OIM  Var_01    C1   CA1  N1   C0    176.39  30.0  1
 OIM  Var_02    CB1  CA1  N1   C0     -0.55  30.0  1
 OIM  Var_03    N3   C1   CA1  N1     21.71  30.0  1
 OIM  Var_04    N2   C1   CA1  N1   -153.80  30.0  1
 OIM  Var_05    N3   C1   CA1  CB1  -161.60  30.0  1
 OIM  Var_06    N2   C1   CA1  CB1    22.89  30.0  1
 OIM  Var_07    CG2  CB2  CA2  N2      0.17  30.0  2
 OIM  Var_08    CG2  CB2  CA2  C2   -179.21  30.0  2
 OIM  Var_09    CD2  CG2  CB2  CA2   178.50  30.0  2
 OIM  Var_10    CD1  CG2  CB2  CA2    -1.25  30.0  2
 OIM  Var_11    C3   CA3  N3   C1     54.93  30.0  1
 OIM  Var_12    C3   CA3  N3   C2   -102.99  30.0  1
 OIM  Var_13    H23  CA3  N3   C1    175.94  30.0  1
 OIM  Var_14    H24  CA3  N3   C1    -67.36  30.0  1
 OIM  Var_15    H28  CB2  CA2  N2    179.65  30.0  2
 OIM  Var_16    H23  CA3  N3   C2     18.03  30.0  1
 OIM  Var_17    H24  CA3  N3   C2    134.73  30.0  1
 OIM  Var_18    H28  CB2  CA2  C2      0.26  30.0  2
 OIM  Var_19    H28  CB2  CG2  CD1   179.28  30.0  2
 OIM  Var_20    H28  CB2  CG2  CD2    -0.98  30.0  2
 OIM  Var_21    O3   C3   CA3  N3     -1.67  30.0  3
 OIM  Var_22    OXT  C3   CA3  N3    178.17  30.0  3
 OIM  Var_23    H12  CDX  CGX  CB0   -56.24  30.0  3
 OIM  Var_24    H13  CDX  CGX  CB0    64.51  30.0  3
 OIM  Var_25    H14  CDX  CGX  CB0  -175.47  30.0  3
 OIM  Var_26    H23  CA3  C3   O3   -121.16  30.0  2
 OIM  Var_27    H24  CA3  C3   O3    120.85  30.0  2
 OIM  Var_28    OXT  C3   CA3  H23    58.68  30.0  3
 OIM  Var_29    OXT  C3   CA3  H24   -59.31  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
 OIM  chir_01  CA0  N0   CB0  C0   negativ
 OIM  chir_02  C0   OG1  N1   CA0  negativ
 OIM  chir_03  CB0  CGX  CA0  CGY  negativ
 OIM  chir_04  CB1  OG1  CG1  CA1  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
 OIM  plan-1  CA1  0.020
 OIM  plan-1  C1   0.020
 OIM  plan-1  N2   0.020
 OIM  plan-1  N3   0.020
 OIM  plan-1  C2   0.020
 OIM  plan-1  O2   0.020
 OIM  plan-1  CA2  0.020
 OIM  plan-1  CA3  0.020
 OIM  plan-1  CB2  0.020
 OIM  plan-2  CB2  0.020
 OIM  plan-2  CG2  0.020
 OIM  plan-2  CD1  0.020
 OIM  plan-2  CD2  0.020
 OIM  plan-2  CE1  0.020
 OIM  plan-2  CE2  0.020
 OIM  plan-2  CZ   0.020
 OIM  plan-2  OH   0.020
 OIM  plan-2  H30  0.020
 OIM  plan-2  H31  0.020
 OIM  plan-2  H32  0.020
 OIM  plan-2  H33  0.020
 OIM  plan-3  CA3  0.020
 OIM  plan-3  C3   0.020
 OIM  plan-3  O3   0.020
 OIM  plan-3  OXT  0.020

