# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:02:11 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: O-benzyl-N-(carboxycarbonyl)-D-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccc(OCc2ccccc2)cc1)NC(=O)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
 Y28  Y28  O-benzyl-N-(carboxycarbonyl)-D-tyrosine  D-peptide  40  25  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y28
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
 Y28  CAD   C  C1     0  -0.294  -49.3691  -57.5402   7.2432
 Y28  CAF   C  C1     0  -0.239  -49.3641  -58.8822   7.6014
 Y28  CAH   C  C1     0  -0.264  -48.4012  -59.3637   8.4773
 Y28  CAG   C  C1     0  -0.239  -47.4479  -58.4944   8.9933
 Y28  CAE   C  C1     0  -0.277  -47.4602  -57.1525   8.6410
 Y28  CAB   C  C      0   0.040  -48.4217  -56.6633   7.7602
 Y28  CAC   C  CH2    0  -0.250  -48.4629  -55.2007   7.3956
 Y28  OH    O  O2     0  -0.483  -47.1820  -54.6302   7.2291
 Y28  CZ    C  CR6    0   0.371  -46.4105  -55.0379   6.1919
 Y28  CE2   C  CR16   0  -0.347  -46.8560  -55.8209   5.1328
 Y28  CD2   C  CR16   0  -0.303  -45.9736  -56.1695   4.1154
 Y28  CE1   C  CR16   0  -0.338  -45.0808  -54.6174   6.2135
 Y28  CD1   C  CR16   0  -0.290  -44.2195  -54.9802   5.1940
 Y28  CG    C  CR6    0   0.141  -44.6466  -55.7653   4.1222
 Y28  CB    C  CH2    0  -0.529  -43.6769  -56.1697   3.0502
 Y28  CA    C  CH1    0  -0.173  -43.2045  -55.0063   2.1460
 Y28  C     C  C      0   0.411  -44.2746  -54.6972   1.0706
 Y28  OXT   O  OC    -1  -0.591  -45.3042  -54.1332   1.4780
 Y28  O     O  O      0  -0.596  -44.0237  -55.0696  -0.0936
 Y28  N     N  NH1    0  -0.615  -41.9538  -55.3206   1.5070
 Y28  CAR   C  C      0   0.341  -40.7596  -55.2803   2.1023
 Y28  OAW   O  O      0  -0.513  -40.5963  -55.0019   3.2865
 Y28  CAS   C  C      0   0.329  -39.5695  -55.6147   1.1473
 Y28  OAY   O  OC    -1  -0.586  -39.8805  -55.9083  -0.0223
 Y28  OAX   O  O      0  -0.576  -38.4426  -55.5518   1.6548
 Y28  HAD   H  H      0   0.253  -50.1149  -57.1735   6.5469
 Y28  HAF   H  H      0   0.254  -50.1073  -59.5519   7.1879
 Y28  HAH   H  H      0   0.254  -48.3897  -60.4102   8.7533
 Y28  HAG   H  H      0   0.254  -46.6923  -58.8630   9.6753
 Y28  HAE   H  H      0   0.252  -46.7112  -56.4878   9.0536
 Y28  HAC1  H  HCH2   0   0.240  -49.0907  -55.0473   6.5108
 Y28  HAC2  H  HCH2   0   0.270  -48.9186  -54.6283   8.2058
 Y28  HE2   H  HCR6   0   0.271  -47.8774  -56.1709   5.0748
 Y28  HE1   H  HCR6   0   0.254  -44.7261  -54.0136   7.0401
 Y28  HD2   H  HCR6   0   0.242  -46.3395  -56.7817   3.2997
 Y28  HD1   H  HCR6   0   0.240  -43.1862  -54.6533   5.2365
 Y28  HB1C  H  HCH2   0   0.249  -42.7936  -56.5977   3.5290
 Y28  HB2C  H  HCH2   0   0.237  -44.1066  -56.9617   2.4312
 Y28  HA    H  HCH1   0   0.230  -43.0672  -54.1209   2.7745
 Y28  H     H  HNH1   0   0.372  -41.9891  -55.5359   0.5216

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
 Y28  CAD  CAF   aromatic  1.389  0.020  1.389
 Y28  CAD  CAB   aromatic  1.391  0.020  1.391
 Y28  CAF  CAH   aromatic  1.388  0.020  1.388
 Y28  CAH  CAG   aromatic  1.389  0.020  1.389
 Y28  CAG  CAE   aromatic  1.387  0.020  1.387
 Y28  CAE  CAB   aromatic  1.393  0.020  1.393
 Y28  CAB  CAC   single    1.508  0.020  1.508
 Y28  CAC  OH    single    1.412  0.020  1.412
 Y28  OH   CZ    single    1.355  0.020  1.355
 Y28  CZ   CE2   aromatic  1.390  0.020  1.390
 Y28  CZ   CE1   aromatic  1.395  0.020  1.395
 Y28  CE2  CD2   aromatic  1.391  0.020  1.391
 Y28  CD2  CG    aromatic  1.387  0.020  1.387
 Y28  CE1  CD1   aromatic  1.383  0.020  1.383
 Y28  CD1  CG    aromatic  1.396  0.020  1.396
 Y28  CG   CB    single    1.501  0.020  1.501
 Y28  CB   CA    single    1.521  0.033  1.521
 Y28  CA   C     single    1.525  0.021  1.525
 Y28  CA   N     single    1.458  0.019  1.458
 Y28  C    OXT   deloc     1.243  0.020  1.243
 Y28  C    O     deloc     1.231  0.020  1.231
 Y28  N    CAR   single    1.335  0.020  1.335
 Y28  CAR  OAW   double    1.227  0.020  1.227
 Y28  CAR  CAS   single    1.562  0.020  1.562
 Y28  CAS  OAY   deloc     1.245  0.020  1.245
 Y28  CAS  OAX   deloc     1.238  0.020  1.238
 Y28  CAD  HAD   single    0.930  0.020  1.080
 Y28  CAF  HAF   single    0.930  0.020  1.080
 Y28  CAH  HAH   single    0.930  0.020  1.080
 Y28  CAG  HAG   single    0.930  0.020  1.080
 Y28  CAE  HAE   single    0.930  0.020  1.080
 Y28  CAC  HAC1  single    0.970  0.020  1.090
 Y28  CAC  HAC2  single    0.970  0.020  1.090
 Y28  CE2  HE2   single    0.930  0.020  1.080
 Y28  CE1  HE1   single    0.930  0.020  1.080
 Y28  CD2  HD2   single    0.930  0.020  1.080
 Y28  CD1  HD1   single    0.930  0.020  1.080
 Y28  CB   HB1C  single    0.970  0.020  1.090
 Y28  CB   HB2C  single    0.970  0.020  1.090
 Y28  CA   HA    single    0.970  0.020  0.970
 Y28  N    H     single    0.860  0.020  0.860

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
 Y28  HAD   CAD  CAB   119.61  3.000
 Y28  HAD   CAD  CAF   119.67  3.000
 Y28  CAB   CAD  CAF   120.72  3.000
 Y28  HAF   CAF  CAH   120.19  3.000
 Y28  HAF   CAF  CAD   119.78  3.000
 Y28  CAH   CAF  CAD   120.03  3.000
 Y28  HAH   CAH  CAG   120.20  3.000
 Y28  HAH   CAH  CAF   120.24  3.000
 Y28  CAG   CAH  CAF   119.56  3.000
 Y28  HAG   CAG  CAE   119.70  3.000
 Y28  HAG   CAG  CAH   119.99  3.000
 Y28  CAE   CAG  CAH   120.31  3.000
 Y28  HAE   CAE  CAB   120.18  3.000
 Y28  HAE   CAE  CAG   119.39  3.000
 Y28  CAB   CAE  CAG   120.43  3.000
 Y28  CAC   CAB  CAE   120.83  3.000
 Y28  CAC   CAB  CAD   120.21  3.000
 Y28  CAE   CAB  CAD   118.95  3.000
 Y28  HAC2  CAC  HAC1  106.66  3.000
 Y28  HAC2  CAC  OH    104.73  3.000
 Y28  HAC1  CAC  OH    111.58  3.000
 Y28  HAC2  CAC  CAB   109.91  3.000
 Y28  HAC1  CAC  CAB   110.29  3.000
 Y28  OH    CAC  CAB   113.31  3.000
 Y28  CZ    OH   CAC   119.02  3.000
 Y28  CE1   CZ   CE2   119.15  3.000
 Y28  CE1   CZ   OH    116.11  3.000
 Y28  CE2   CZ   OH    124.75  3.000
 Y28  HE2   CE2  CD2   118.61  3.000
 Y28  HE2   CE2  CZ    121.72  3.000
 Y28  CD2   CE2  CZ    119.67  3.000
 Y28  HD2   CD2  CG    119.43  3.000
 Y28  HD2   CD2  CE2   118.55  3.000
 Y28  CG    CD2  CE2   122.02  3.000
 Y28  HE1   CE1  CD1   120.31  3.000
 Y28  HE1   CE1  CZ    119.48  3.000
 Y28  CD1   CE1  CZ    120.21  3.000
 Y28  HD1   CD1  CG    119.42  3.000
 Y28  HD1   CD1  CE1   119.04  3.000
 Y28  CG    CD1  CE1   121.54  3.000
 Y28  CB    CG   CD1   120.15  3.000
 Y28  CB    CG   CD2   122.41  3.000
 Y28  CD1   CG   CD2   117.42  3.000
 Y28  HB2C  CB   HB1C  106.39  3.000
 Y28  HB2C  CB   CA    109.51  3.000
 Y28  HB1C  CB   CA    107.69  3.000
 Y28  HB2C  CB   CG    110.22  3.000
 Y28  HB1C  CB   CG    108.36  3.000
 Y28  CA    CB   CG    114.33  3.000
 Y28  HA    CA   N     110.00  3.000
 Y28  HA    CA   C     110.00  3.000
 Y28  N     CA   C     111.00  2.800
 Y28  HA    CA   CB    109.00  3.000
 Y28  N     CA   CB    110.40  1.500
 Y28  C     CA   CB    110.50  1.500
 Y28  O     C    OXT   127.44  3.000
 Y28  O     C    CA    120.80  1.700
 Y28  OXT   C    CA    120.80  1.700
 Y28  H     N    CAR   118.24  3.000
 Y28  H     N    CA    114.00  3.000
 Y28  CAR   N    CA    124.94  3.000
 Y28  CAS   CAR  OAW   122.48  3.000
 Y28  CAS   CAR  N     113.73  3.000
 Y28  OAW   CAR  N     123.79  3.000
 Y28  OAX   CAS  OAY   128.65  3.000
 Y28  OAX   CAS  CAR   115.60  3.000
 Y28  OAY   CAS  CAR   115.75  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
 Y28  CONST_01  CAG  CAH  CAF  CAD     0.00   0.0  0
 Y28  CONST_02  CAG  CAE  CAB  CAD     0.00   0.0  0
 Y28  CONST_03  CAE  CAB  CAD  CAF     0.00   0.0  0
 Y28  CONST_04  CAE  CAG  CAH  CAF     0.00   0.0  0
 Y28  CONST_05  CAB  CAD  CAF  CAH     0.00   0.0  0
 Y28  CONST_06  CAB  CAE  CAG  CAH     0.00   0.0  0
 Y28  CONST_07  CG   CD2  CE2  CZ      0.00   0.0  0
 Y28  CONST_08  CG   CD1  CE1  CZ      0.00   0.0  0
 Y28  CONST_09  CD1  CE1  CZ   CE2     0.00   0.0  0
 Y28  CONST_10  CD1  CG   CD2  CE2     0.00   0.0  0
 Y28  CONST_11  CE1  CZ   CE2  CD2     0.00   0.0  0
 Y28  CONST_12  CE1  CD1  CG   CD2     0.00   0.0  0
 Y28  CONST_13  CAC  CAB  CAD  CAF   180.00   0.0  0
 Y28  CONST_14  CAC  CAB  CAE  CAG   180.00   0.0  0
 Y28  CONST_15  CD2  CE2  CZ   OH    180.00   0.0  0
 Y28  CONST_16  CD1  CE1  CZ   OH    180.00   0.0  0
 Y28  CONST_17  CB   CG   CD2  CE2   180.00   0.0  0
 Y28  CONST_18  CB   CG   CD1  CE1   180.00   0.0  0
 Y28  CONST_19  HAH  CAH  CAF  CAD   180.00   0.0  0
 Y28  CONST_20  HAE  CAE  CAB  CAD   180.00   0.0  0
 Y28  CONST_21  HAG  CAG  CAH  CAF   180.00   0.0  0
 Y28  CONST_22  HAD  CAD  CAF  CAH   180.00   0.0  0
 Y28  CONST_23  HAF  CAF  CAH  CAG   180.00   0.0  0
 Y28  CONST_24  HD2  CD2  CE2  CZ    180.00   0.0  0
 Y28  CONST_25  HD1  CD1  CE1  CZ    180.00   0.0  0
 Y28  CONST_26  HE1  CE1  CZ   CE2   180.00   0.0  0
 Y28  CONST_27  HE2  CE2  CZ   CE1   180.00   0.0  0
 Y28  CONST_28  OAW  CAR  N    CA      0.00   0.0  0
 Y28  CONST_29  CAS  CAR  N    CA    180.00   0.0  0
 Y28  CONST_30  H    N    CAR  OAW   180.00   0.0  0
 Y28  Var_01    OH   CAC  CAB  CAD  -142.52  30.0  2
 Y28  Var_02    CE2  CZ   OH   CAC    11.27  30.0  2
 Y28  Var_03    CA   CB   CG   CD2   111.94  30.0  2
 Y28  Var_04    OAY  CAS  CAR  N      -1.86  30.0  2

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
 Y28  chir_01  CA  CB  C  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
 Y28  plan-1  CAD  0.020
 Y28  plan-1  CAF  0.020
 Y28  plan-1  CAH  0.020
 Y28  plan-1  CAG  0.020
 Y28  plan-1  CAE  0.020
 Y28  plan-1  CAB  0.020
 Y28  plan-1  CAC  0.020
 Y28  plan-1  HAD  0.020
 Y28  plan-1  HAF  0.020
 Y28  plan-1  HAH  0.020
 Y28  plan-1  HAG  0.020
 Y28  plan-1  HAE  0.020
 Y28  plan-2  OH   0.020
 Y28  plan-2  CZ   0.020
 Y28  plan-2  CE2  0.020
 Y28  plan-2  CD2  0.020
 Y28  plan-2  CE1  0.020
 Y28  plan-2  CD1  0.020
 Y28  plan-2  CG   0.020
 Y28  plan-2  CB   0.020
 Y28  plan-2  HE2  0.020
 Y28  plan-2  HE1  0.020
 Y28  plan-2  HD2  0.020
 Y28  plan-2  HD1  0.020
 Y28  plan-3  CA   0.020
 Y28  plan-3  N    0.020
 Y28  plan-3  CAR  0.020
 Y28  plan-3  OAW  0.020
 Y28  plan-3  CAS  0.020
 Y28  plan-3  H    0.020
 Y28  plan-4  CA   0.020
 Y28  plan-4  C    0.020
 Y28  plan-4  OXT  0.020
 Y28  plan-4  O    0.020
 Y28  plan-5  CAR  0.020
 Y28  plan-5  CAS  0.020
 Y28  plan-5  OAY  0.020
 Y28  plan-5  OAX  0.020

