# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:10:26 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (betaR)-beta-hydroxy-1-{2-[(2R)-oxiran-2-yl]propan-2-yl}-L-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)([C@@H]1CO1)n2cc([C@@H](O)[C@H](N)C(O)=O)c3ccccc23
#
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
 54C  54C  (betaR)-beta-hydroxy-1-{2-[(2R)-oxiran-2-yl]propan-2-yl}-L-tryptophan  L-peptide  41  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_54C
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
 54C  CA   C  CH1    0  -0.249  -2.9697   0.1303  -0.4221
 54C  CB   C  CH1    0  -0.067  -2.0088   0.3475   0.7680
 54C  CG   C  CR5    0  -0.015  -0.6155  -0.0938   0.4379
 54C  N    N  NH2    0  -0.807  -2.6031   0.8634  -1.6164
 54C  C    C  C      0   0.411  -4.4071   0.4772   0.0343
 54C  O    O  O      0  -0.596  -4.9699   1.4458  -0.5101
 54C  CD1  C  CR15   0  -0.080   0.4788   0.6987   0.2654
 54C  NE2  N  NR5    0  -0.573   1.5871  -0.0491  -0.0657
 54C  C1   C  CT     0   0.071   2.9461   0.4770  -0.2910
 54C  C2   C  CH3    0  -0.672   3.8780  -0.0451   0.8011
 54C  C3   C  CH3    0  -0.657   3.4387   0.0916  -1.6890
 54C  CE2  C  CR56   0   0.382   1.2093  -1.3722  -0.0922
 54C  CD2  C  CR56   0   0.025  -0.1708  -1.4337   0.2154
 54C  CE3  C  CR16   0  -0.379  -0.8199  -2.6720   0.2718
 54C  CZ3  C  CR16   0  -0.269  -0.0980  -3.8220   0.0262
 54C  C70  C  CR16   0  -0.282   1.2688  -3.7518  -0.2779
 54C  CH2  C  CR16   0  -0.309   1.9351  -2.5425  -0.3391
 54C  OB   O  OH1    0  -0.663  -2.0369   1.6903   1.2028
 54C  C4   C  CH1    0  -0.033   2.8746   1.9944  -0.3031
 54C  C5   C  CH2    0  -0.243   3.9792   2.8454   0.1210
 54C  O6   O  O2     0  -0.479   2.8154   2.6950   0.9225
 54C  H1   H  HCH1   0   0.222  -2.9505  -0.9431  -0.6457
 54C  H2   H  HCH1   0   0.230  -2.3821  -0.2527   1.6040
 54C  H3   H  HNH2   0   0.336  -2.9807   1.8005  -1.5834
 54C  H4   H  HNH2   0   0.338  -1.5991   0.9141  -1.7389
 54C  H9   H  HCR5   0   0.288   0.5364   1.7685   0.3727
 54C  H10  H  HCH3   0   0.255   3.8544  -1.1317   0.8515
 54C  H11  H  HCH3   0   0.241   4.9105   0.2384   0.6038
 54C  H12  H  HCH3   0   0.248   3.5913   0.3370   1.7804
 54C  H13  H  HCH3   0   0.250   3.5155  -0.9840  -1.8254
 54C  H14  H  HCH3   0   0.244   2.7673   0.4792  -2.4562
 54C  H15  H  HCH3   0   0.247   4.4286   0.5144  -1.8604
 54C  H16  H  HCR6   0   0.240  -1.8748  -2.7319   0.5109
 54C  H17  H  HCR6   0   0.246  -0.5856  -4.7872   0.0719
 54C  H18  H  HCR6   0   0.249   1.8204  -4.6635  -0.4668
 54C  H19  H  HCR6   0   0.257   2.9908  -2.5352  -0.5682
 54C  H20  H  HOH1   0   0.432  -1.9878   2.2560   0.4235
 54C  H21  H  HCH1   0   0.280   2.2236   2.3930  -1.0830
 54C  H22  H  HCH2   0   0.246   4.8899   2.4157   0.5252
 54C  H23  H  HCH2   0   0.253   4.1042   3.8140  -0.3541
 54C  OXT  O  OC    -1  -0.616  -4.8725  -0.2499   0.9334

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
 54C  O6   C5   single    1.421  0.020  1.421
 54C  O6   C4   single    1.413  0.020  1.413
 54C  C5   C4   single    1.457  0.020  1.457
 54C  C4   C1   single    1.519  0.020  1.519
 54C  C3   C1   single    1.531  0.020  1.531
 54C  C1   C2   single    1.528  0.020  1.528
 54C  C1   NE2  single    1.475  0.020  1.475
 54C  NE2  CE2  aromatic  1.376  0.020  1.376
 54C  NE2  CD1  aromatic  1.377  0.020  1.377
 54C  CH2  CE2  aromatic  1.399  0.020  1.399
 54C  CH2  C70  aromatic  1.382  0.020  1.382
 54C  CE2  CD2  aromatic  1.415  0.020  1.415
 54C  CD1  CG   aromatic  1.362  0.020  1.362
 54C  C70  CZ3  aromatic  1.402  0.020  1.402
 54C  CD2  CG   aromatic  1.429  0.020  1.429
 54C  CD2  CE3  aromatic  1.399  0.020  1.399
 54C  CG   CB   single    1.498  0.020  1.498
 54C  CZ3  CE3  aromatic  1.380  0.020  1.380
 54C  OB   CB   single    1.412  0.020  1.412
 54C  CB   CA   single    1.530  0.020  1.530
 54C  CA   C    single    1.525  0.021  1.525
 54C  CA   N    single    1.458  0.019  1.458
 54C  C    O    deloc     1.231  0.020  1.231
 54C  CA   H1   single    0.970  0.020  1.090
 54C  CB   H2   single    0.970  0.020  1.090
 54C  N    H3   single    0.890  0.020  1.040
 54C  N    H4   single    0.890  0.020  1.040
 54C  CD1  H9   single    0.930  0.020  1.080
 54C  C2   H10  single    0.970  0.020  1.090
 54C  C2   H11  single    0.970  0.020  1.090
 54C  C2   H12  single    0.970  0.020  1.090
 54C  C3   H13  single    0.970  0.020  1.090
 54C  C3   H14  single    0.970  0.020  1.090
 54C  C3   H15  single    0.970  0.020  1.090
 54C  CE3  H16  single    0.930  0.020  1.080
 54C  CZ3  H17  single    0.930  0.020  1.080
 54C  C70  H18  single    0.930  0.020  1.080
 54C  CH2  H19  single    0.930  0.020  1.080
 54C  OB   H20  single    0.850  0.020  0.980
 54C  C4   H21  single    0.970  0.020  1.090
 54C  C5   H22  single    0.970  0.020  1.090
 54C  C5   H23  single    0.970  0.020  1.090
 54C  C    OXT  deloc     1.246  0.020  1.246

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
 54C  H1   CA   C    107.21  3.000
 54C  H1   CA   N    108.84  3.000
 54C  C    CA   N    111.00  2.800
 54C  H1   CA   CB   106.48  3.000
 54C  N    CA   CB   110.50  1.700
 54C  C    CA   CB   110.10  1.900
 54C  H2   CB   OB   106.23  3.000
 54C  H2   CB   CG   108.90  3.000
 54C  OB   CB   CG   111.50  3.000
 54C  H2   CB   CA   107.40  3.000
 54C  OB   CB   CA   111.01  3.000
 54C  CG   CB   CA   111.55  3.000
 54C  CD2  CG   CD1  106.01  3.000
 54C  CD2  CG   CB   126.85  3.000
 54C  CD1  CG   CB   127.13  3.000
 54C  H4   N    H3   109.14  3.000
 54C  H4   N    CA   112.09  3.000
 54C  H3   N    CA   110.35  3.000
 54C  OXT  C    O    126.89  3.000
 54C  OXT  C    CA   115.39  3.000
 54C  O    C    CA   120.80  1.700
 54C  H9   CD1  NE2  121.35  3.000
 54C  H9   CD1  CG   127.48  3.000
 54C  NE2  CD1  CG   111.16  3.000
 54C  CE2  NE2  C1   126.37  3.000
 54C  CE2  NE2  CD1  107.80  3.000
 54C  C1   NE2  CD1  125.77  3.000
 54C  C4   C1   C3   105.02  3.000
 54C  C3   C1   C2   111.74  3.000
 54C  C4   C1   C2   112.08  3.000
 54C  C2   C1   NE2  109.33  3.000
 54C  C3   C1   NE2  110.25  3.000
 54C  C4   C1   NE2  108.31  3.000
 54C  H12  C2   H11  108.73  3.000
 54C  H12  C2   H10  107.63  3.000
 54C  H11  C2   H10  106.80  3.000
 54C  H12  C2   C1   111.23  3.000
 54C  H11  C2   C1   111.10  3.000
 54C  H10  C2   C1   111.18  3.000
 54C  H15  C3   H14  108.09  3.000
 54C  H15  C3   H13  107.45  3.000
 54C  H14  C3   H13  107.87  3.000
 54C  H15  C3   C1   109.76  3.000
 54C  H14  C3   C1   110.78  3.000
 54C  H13  C3   C1   112.72  3.000
 54C  CH2  CE2  CD2  120.53  3.000
 54C  CD2  CE2  NE2  107.77  3.000
 54C  CH2  CE2  NE2  131.69  3.000
 54C  CE3  CD2  CE2  119.97  3.000
 54C  CE3  CD2  CG   132.77  3.000
 54C  CE2  CD2  CG   107.25  3.000
 54C  H16  CE3  CZ3  120.17  3.000
 54C  H16  CE3  CD2  120.63  3.000
 54C  CZ3  CE3  CD2  119.19  3.000
 54C  H17  CZ3  C70  119.54  3.000
 54C  H17  CZ3  CE3  120.01  3.000
 54C  C70  CZ3  CE3  120.46  3.000
 54C  H18  C70  CH2  118.93  3.000
 54C  H18  C70  CZ3  119.51  3.000
 54C  CH2  C70  CZ3  121.56  3.000
 54C  H19  CH2  C70  119.10  3.000
 54C  H19  CH2  CE2  122.60  3.000
 54C  C70  CH2  CE2  118.29  3.000
 54C  H20  OB   CB   107.94  3.000
 54C  H21  C4   O6   114.45  3.000
 54C  H21  C4   C5   116.54  3.000
 54C  O6   C4   C5    59.33  3.000
 54C  H21  C4   C1   113.49  3.000
 54C  C5   C4   C1   123.04  3.000
 54C  O6   C4   C1   119.36  3.000
 54C  H23  C5   H22  114.81  3.000
 54C  H23  C5   O6   115.80  3.000
 54C  H22  C5   O6   115.81  3.000
 54C  H23  C5   C4   118.72  3.000
 54C  H22  C5   C4   120.88  3.000
 54C  O6   C5   C4    58.78  3.000
 54C  C5   O6   C4    61.89  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
 54C  CONST_01  CE2  NE2  CD1  CG      0.00   0.0  0
 54C  CONST_02  NE2  CE2  CD2  CG      0.00   0.0  0
 54C  CONST_03  CH2  CE2  CD2  CG    180.00   0.0  0
 54C  CONST_04  CZ3  CE3  CD2  CG    180.00   0.0  0
 54C  CONST_05  CH2  CE2  NE2  CD1   180.00   0.0  0
 54C  CONST_06  CD2  CE2  NE2  CD1     0.00   0.0  0
 54C  CONST_07  CE2  CD2  CG   CD1     0.00   0.0  0
 54C  CONST_08  CE3  CD2  CG   CD1   180.00   0.0  0
 54C  CONST_09  C70  CH2  CE2  NE2   180.00   0.0  0
 54C  CONST_10  CE3  CD2  CE2  NE2   180.00   0.0  0
 54C  CONST_11  CD2  CG   CD1  NE2     0.00   0.0  0
 54C  CONST_12  CZ3  C70  CH2  CE2     0.00   0.0  0
 54C  CONST_13  CZ3  CE3  CD2  CE2     0.00   0.0  0
 54C  CONST_14  C70  CH2  CE2  CD2     0.00   0.0  0
 54C  CONST_15  C70  CZ3  CE3  CD2     0.00   0.0  0
 54C  CONST_16  CH2  CE2  CD2  CE3     0.00   0.0  0
 54C  CONST_17  CH2  C70  CZ3  CE3     0.00   0.0  0
 54C  CONST_18  NE2  CD1  CG   CB    180.00   0.0  0
 54C  CONST_19  CE2  CD2  CG   CB    180.00   0.0  0
 54C  CONST_20  CE3  CD2  CG   CB      0.00   0.0  0
 54C  CONST_21  C1   NE2  CD1  CG    180.00   0.0  0
 54C  CONST_22  CH2  CE2  NE2  C1      0.00   0.0  0
 54C  CONST_23  CD2  CE2  NE2  C1    180.00   0.0  0
 54C  CONST_24  H16  CE3  CD2  CG      0.00   0.0  0
 54C  CONST_25  H19  CH2  CE2  NE2     0.00   0.0  0
 54C  CONST_26  H9   CD1  NE2  CE2   180.00   0.0  0
 54C  CONST_27  H18  C70  CH2  CE2   180.00   0.0  0
 54C  CONST_28  H17  CZ3  CE3  CD2   180.00   0.0  0
 54C  Var_01    C4   C1   NE2  CD1    -8.42  30.0  3
 54C  Var_02    O6   C4   C1   NE2    79.67  30.0  1
 54C  Var_03    H22  C5   O6   C4   -111.94  30.0  1
 54C  Var_04    H21  C4   O6   C5   -107.52  30.0  1
 54C  Var_05    H13  C3   C1   NE2   -62.29  30.0  3
 54C  Var_06    H10  C2   C1   NE2    55.14  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
 54C  chir_01  CA  CB  C   N   negativ
 54C  chir_02  CB  OB  CA  CG  negativ
 54C  chir_03  C4  O6  C5  C1  both

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
 54C  plan-1  CB   0.020
 54C  plan-1  CG   0.020
 54C  plan-1  CD1  0.020
 54C  plan-1  NE2  0.020
 54C  plan-1  C1   0.020
 54C  plan-1  CE2  0.020
 54C  plan-1  CD2  0.020
 54C  plan-1  CE3  0.020
 54C  plan-1  CZ3  0.020
 54C  plan-1  C70  0.020
 54C  plan-1  CH2  0.020
 54C  plan-1  H9   0.020
 54C  plan-1  H16  0.020
 54C  plan-1  H17  0.020
 54C  plan-1  H18  0.020
 54C  plan-1  H19  0.020
 54C  plan-2  CA   0.020
 54C  plan-2  C    0.020
 54C  plan-2  O    0.020
 54C  plan-2  OXT  0.020

