# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:01:14 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[(2R,3R)-3-amino-2-hydroxy-4-phenylbutanoyl]-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(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
 EBT  EBT  N-[(2R,3R)-3-amino-2-hydroxy-4-phenylbutanoyl]-L-leucine  ligand  45  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EBT
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
 EBT  C     C  C      0   0.420  -4.1579  -1.0131   0.5261
 EBT  N     N  NH1    0  -0.614  -1.8492  -0.3377  -0.1348
 EBT  O     O  O      0  -0.594  -3.9571  -2.0341  -0.1514
 EBT  CA    C  CH1    0  -0.206  -3.0682   0.0908   0.5116
 EBT  CB    C  CH2    0  -0.440  -3.5950   1.3535  -0.1705
 EBT  CG    C  CH1    0  -0.231  -2.6119   2.5248  -0.2424
 EBT  OAA   O  OH1    0  -0.660   0.5358  -2.9007  -0.1870
 EBT  OAB   O  O      0  -0.510  -1.0416  -1.5391   1.6028
 EBT  NAF   N  NH2    0  -0.783   1.1819   0.7885  -0.2008
 EBT  CAJ   C  CH1    0  -0.121   1.4417  -0.6269  -0.0337
 EBT  CAK   C  CH1    0  -0.070   0.2478  -1.5431  -0.3984
 EBT  CAM   C  C      0   0.505  -0.9645  -1.1508   0.4414
 EBT  CAP   C  CR6    0   0.160   3.9307  -0.3744  -0.3276
 EBT  CAR   C  CR16   0  -0.312   4.6399  -0.9738   0.7117
 EBT  CAS   C  CR16   0  -0.308   4.3999   0.8341  -0.8366
 EBT  CAT   C  CR16   0  -0.241   5.7858  -0.3850   1.2297
 EBT  CAU   C  CR16   0  -0.245   5.5482   1.4258  -0.3262
 EBT  CAV   C  CR16   0  -0.276   6.2447   0.8192   0.7114
 EBT  CD1   C  CH3    0  -0.649  -3.2589   3.6930  -0.9806
 EBT  CD2   C  CH3    0  -0.663  -2.1329   2.9633   1.1368
 EBT  OXT   O  OC    -1  -0.617  -5.1590  -0.7491   1.2215
 EBT  HN    H  HNH1   0   0.390  -1.7725  -0.1916  -1.1291
 EBT  HA    H  HCH1   0   0.240  -2.8255   0.3282   1.5502
 EBT  HB    H  HCH2   0   0.224  -3.9176   1.1013  -1.1879
 EBT  HBA   H  HCH2   0   0.231  -4.4930   1.6705   0.3655
 EBT  HG    H  HCH1   0   0.207  -1.7359   2.2095  -0.8211
 EBT  HOAA  H  HOH1   0   0.442   0.5199  -3.0531   0.7661
 EBT  HNAF  H  HNH2   0   0.339   0.8868   0.9886  -1.1495
 EBT  HNAA  H  HNH2   0   0.352   0.4419   1.1060   0.4110
 EBT  HAJ   H  HCH1   0   0.243   1.6652  -0.7959   1.0268
 EBT  HAK   H  HCH1   0   0.244   0.0326  -1.4252  -1.4670
 EBT  HAR   H  HCR6   0   0.242   4.2941  -1.9172   1.1199
 EBT  HAS   H  HCR6   0   0.239   3.8625   1.3152  -1.6446
 EBT  HAT   H  HCR6   0   0.250   6.3238  -0.8700   2.0346
 EBT  HAU   H  HCR6   0   0.250   5.8981   2.3639  -0.7384
 EBT  HAV   H  HCR6   0   0.251   7.1398   1.2796   1.1098
 EBT  HD1   H  HCH3   0   0.213  -4.1467   4.0419  -0.4477
 EBT  HD1A  H  HCH3   0   0.225  -2.5724   4.5366  -1.0706
 EBT  HD1B  H  HCH3   0   0.224  -3.5682   3.4070  -1.9877
 EBT  HD2   H  HCH3   0   0.226  -1.6265   2.1600   1.6741
 EBT  HD2A  H  HCH3   0   0.229  -1.4309   3.7949   1.0584
 EBT  HD2B  H  HCH3   0   0.217  -2.9721   3.2945   1.7541
 EBT  CAL   C  CH2    0  -0.521   2.6780  -1.0143  -0.8523
 EBT  HAL   H  HCH2   0   0.255   2.7909  -2.0992  -0.8390
 EBT  HALA  H  HCH2   0   0.241   2.5131  -0.7266  -1.8958

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
 EBT  C    O     deloc     1.242  0.020  1.242
 EBT  C    CA    single    1.551  0.020  1.551
 EBT  C    OXT   deloc     1.247  0.020  1.247
 EBT  N    CA    single    1.445  0.020  1.445
 EBT  N    CAM   single    1.333  0.020  1.333
 EBT  CA   CB    single    1.529  0.020  1.529
 EBT  CB   CG    single    1.531  0.020  1.531
 EBT  CG   CD1   single    1.526  0.020  1.526
 EBT  CG   CD2   single    1.524  0.020  1.524
 EBT  OAA  CAK   single    1.404  0.020  1.404
 EBT  OAB  CAM   double    1.227  0.020  1.227
 EBT  NAF  CAJ   single    1.449  0.020  1.449
 EBT  CAJ  CAK   single    1.549  0.020  1.549
 EBT  CAJ  CAL   single    1.532  0.020  1.532
 EBT  CAK  CAM   single    1.526  0.020  1.526
 EBT  CAL  CAP   single    1.501  0.020  1.501
 EBT  CAP  CAR   aromatic  1.394  0.020  1.394
 EBT  CAP  CAS   aromatic  1.393  0.020  1.393
 EBT  CAR  CAT   aromatic  1.389  0.020  1.389
 EBT  CAS  CAU   aromatic  1.389  0.020  1.389
 EBT  CAT  CAV   aromatic  1.389  0.020  1.389
 EBT  CAU  CAV   aromatic  1.389  0.020  1.389
 EBT  N    HN    single    0.860  0.020  1.020
 EBT  CA   HA    single    0.970  0.020  1.090
 EBT  CB   HB    single    0.970  0.020  1.090
 EBT  CB   HBA   single    0.970  0.020  1.090
 EBT  CG   HG    single    0.970  0.020  1.090
 EBT  OAA  HOAA  single    0.850  0.020  0.980
 EBT  NAF  HNAF  single    0.890  0.020  1.040
 EBT  NAF  HNAA  single    0.890  0.020  1.040
 EBT  CAJ  HAJ   single    0.970  0.020  1.090
 EBT  CAK  HAK   single    0.970  0.020  1.090
 EBT  CAL  HAL   single    0.970  0.020  1.090
 EBT  CAL  HALA  single    0.970  0.020  1.090
 EBT  CAR  HAR   single    0.930  0.020  1.080
 EBT  CAS  HAS   single    0.930  0.020  1.080
 EBT  CAT  HAT   single    0.930  0.020  1.080
 EBT  CAU  HAU   single    0.930  0.020  1.080
 EBT  CAV  HAV   single    0.930  0.020  1.080
 EBT  CD1  HD1   single    0.970  0.020  1.090
 EBT  CD1  HD1A  single    0.970  0.020  1.090
 EBT  CD1  HD1B  single    0.970  0.020  1.090
 EBT  CD2  HD2   single    0.970  0.020  1.090
 EBT  CD2  HD2A  single    0.970  0.020  1.090
 EBT  CD2  HD2B  single    0.970  0.020  1.090

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
 EBT  OXT   C    CA    114.74  3.000
 EBT  OXT   C    O     127.45  3.000
 EBT  CA    C    O     117.81  3.000
 EBT  HN    N    CAM   117.68  3.000
 EBT  HN    N    CA    117.55  3.000
 EBT  CAM   N    CA    123.20  3.000
 EBT  HA    CA   CB    108.73  3.000
 EBT  HA    CA   N     107.59  3.000
 EBT  CB    CA   N     109.64  3.000
 EBT  HA    CA   C     107.56  3.000
 EBT  CB    CA   C     110.49  3.000
 EBT  N     CA   C     112.69  3.000
 EBT  HBA   CB   HB    106.27  3.000
 EBT  HBA   CB   CG    109.20  3.000
 EBT  HB    CB   CG    108.74  3.000
 EBT  HBA   CB   CA    107.69  3.000
 EBT  HB    CB   CA    108.98  3.000
 EBT  CG    CB   CA    115.57  3.000
 EBT  HG    CG   CD2   108.02  3.000
 EBT  HG    CG   CD1   107.67  3.000
 EBT  CD2   CG   CD1   110.53  3.000
 EBT  HG    CG   CB    108.54  3.000
 EBT  CD2   CG   CB    112.30  3.000
 EBT  CD1   CG   CB    109.64  3.000
 EBT  HOAA  OAA  CAK   107.34  3.000
 EBT  HNAA  NAF  HNAF  106.93  3.000
 EBT  HNAA  NAF  CAJ   111.60  3.000
 EBT  HNAF  NAF  CAJ   110.67  3.000
 EBT  HAJ   CAJ  CAL   108.25  3.000
 EBT  HAJ   CAJ  CAK   107.07  3.000
 EBT  CAL   CAJ  CAK   110.28  3.000
 EBT  HAJ   CAJ  NAF   107.37  3.000
 EBT  CAL   CAJ  NAF   109.28  3.000
 EBT  CAK   CAJ  NAF   114.37  3.000
 EBT  HAK   CAK  CAM   110.66  3.000
 EBT  HAK   CAK  CAJ   108.50  3.000
 EBT  CAM   CAK  CAJ   109.32  3.000
 EBT  HAK   CAK  OAA   106.92  3.000
 EBT  CAM   CAK  OAA   109.19  3.000
 EBT  CAJ   CAK  OAA   112.25  3.000
 EBT  CAK   CAM  OAB   119.30  3.000
 EBT  CAK   CAM  N     116.50  3.000
 EBT  OAB   CAM  N     124.10  3.000
 EBT  CAS   CAP  CAR   118.32  3.000
 EBT  CAS   CAP  CAL   121.55  3.000
 EBT  CAR   CAP  CAL   120.12  3.000
 EBT  HAR   CAR  CAT   119.44  3.000
 EBT  HAR   CAR  CAP   119.51  3.000
 EBT  CAT   CAR  CAP   121.05  3.000
 EBT  HAS   CAS  CAU   119.68  3.000
 EBT  HAS   CAS  CAP   119.40  3.000
 EBT  CAU   CAS  CAP   120.92  3.000
 EBT  HAT   CAT  CAV   120.10  3.000
 EBT  HAT   CAT  CAR   119.83  3.000
 EBT  CAV   CAT  CAR   120.07  3.000
 EBT  HAU   CAU  CAV   120.04  3.000
 EBT  HAU   CAU  CAS   119.76  3.000
 EBT  CAV   CAU  CAS   120.20  3.000
 EBT  HAV   CAV  CAU   120.26  3.000
 EBT  HAV   CAV  CAT   120.30  3.000
 EBT  CAU   CAV  CAT   119.45  3.000
 EBT  HD1B  CD1  HD1A  107.74  3.000
 EBT  HD1B  CD1  HD1   107.66  3.000
 EBT  HD1A  CD1  HD1   107.73  3.000
 EBT  HD1B  CD1  CG    111.47  3.000
 EBT  HD1A  CD1  CG    111.41  3.000
 EBT  HD1   CD1  CG    110.67  3.000
 EBT  HD2B  CD2  HD2A  107.67  3.000
 EBT  HD2B  CD2  HD2   107.53  3.000
 EBT  HD2A  CD2  HD2   107.33  3.000
 EBT  HD2B  CD2  CG    110.90  3.000
 EBT  HD2A  CD2  CG    110.88  3.000
 EBT  HD2   CD2  CG    112.31  3.000
 EBT  HALA  CAL  HAL   106.77  3.000
 EBT  HALA  CAL  CAP   110.29  3.000
 EBT  HAL   CAL  CAP   109.47  3.000
 EBT  HALA  CAL  CAJ   108.73  3.000
 EBT  HAL   CAL  CAJ   109.18  3.000
 EBT  CAP   CAL  CAJ   112.25  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
 EBT  CONST_01  CAV  CAT  CAR  CAP    0.00   0.0  0
 EBT  CONST_02  CAV  CAU  CAS  CAP    0.00   0.0  0
 EBT  CONST_03  CAU  CAS  CAP  CAR    0.00   0.0  0
 EBT  CONST_04  CAU  CAV  CAT  CAR    0.00   0.0  0
 EBT  CONST_05  CAT  CAR  CAP  CAS    0.00   0.0  0
 EBT  CONST_06  CAT  CAV  CAU  CAS    0.00   0.0  0
 EBT  CONST_07  CAT  CAR  CAP  CAL  180.00   0.0  0
 EBT  CONST_08  CAU  CAS  CAP  CAL  180.00   0.0  0
 EBT  CONST_09  HAT  CAT  CAR  CAP  180.00   0.0  0
 EBT  CONST_10  HAU  CAU  CAS  CAP  180.00   0.0  0
 EBT  CONST_11  HAS  CAS  CAP  CAR  180.00   0.0  0
 EBT  CONST_12  HAV  CAV  CAT  CAR  180.00   0.0  0
 EBT  CONST_13  HAR  CAR  CAP  CAS  180.00   0.0  0
 EBT  CONST_14  OAB  CAM  N    CA     0.00   0.0  0
 EBT  CONST_15  CAK  CAM  N    CA   180.00   0.0  0
 EBT  CONST_16  HN   N    CAM  OAB  180.00   0.0  0
 EBT  Var_01    CAR  CAP  CAL  CAJ   85.05  30.0  2
 EBT  Var_02    CD1  CG   CB   CA   178.37  30.0  3
 EBT  Var_03    HD1  CD1  CG   CB    61.61  30.0  3
 EBT  Var_04    HD2  CD2  CG   CB    59.66  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
 EBT  chir_01  CA   C    N    CB   negativ
 EBT  chir_02  CAJ  NAF  CAK  CAL  negativ
 EBT  chir_03  CAK  OAA  CAJ  CAM  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
 EBT  plan-1  CAP  0.020
 EBT  plan-1  CAR  0.020
 EBT  plan-1  CAS  0.020
 EBT  plan-1  CAT  0.020
 EBT  plan-1  CAU  0.020
 EBT  plan-1  CAV  0.020
 EBT  plan-1  HAR  0.020
 EBT  plan-1  HAS  0.020
 EBT  plan-1  HAT  0.020
 EBT  plan-1  HAU  0.020
 EBT  plan-1  HAV  0.020
 EBT  plan-1  CAL  0.020
 EBT  plan-2  N    0.020
 EBT  plan-2  CA   0.020
 EBT  plan-2  OAB  0.020
 EBT  plan-2  CAK  0.020
 EBT  plan-2  CAM  0.020
 EBT  plan-2  HN   0.020
 EBT  plan-3  C    0.020
 EBT  plan-3  O    0.020
 EBT  plan-3  CA   0.020
 EBT  plan-3  OXT  0.020

