# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 14:21:33 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: Nalpha-[(benzyloxy)carbonyl]-N-[(2S)-4-fluoro-3-oxobutan-2-yl]-L-tyrosinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)OCc2ccccc2)C(=O)CF
#
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
 ZYA  ZYA  Nalpha-[(benzyloxy)carbonyl]-N-[(2S)-4-fluoro-3-oxobutan-2-yl]-L-tyrosinamide  peptide  52  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZYA
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
 ZYA  C1    C  C     0   0.764  -1.0896  -0.7189  -0.7004
 ZYA  O1    O  O     0  -0.516  -0.5268  -1.2540  -1.6339
 ZYA  O2    O  O2    0  -0.478  -2.3611  -0.9363  -0.3592
 ZYA  C2    C  CH2   0  -0.242  -3.1071  -1.8515  -1.1724
 ZYA  C3    C  CR6   0   0.076  -4.4505  -2.0087  -0.5288
 ZYA  C4    C  CR16  0  -0.290  -5.5093  -1.1828  -0.8935
 ZYA  C5    C  CR16  0  -0.242  -6.7475  -1.3096  -0.2784
 ZYA  C6    C  CR16  0  -0.261  -6.9364  -2.2651   0.7115
 ZYA  C7    C  CR16  0  -0.242  -5.8844  -3.0936   1.0817
 ZYA  C8    C  CR16  0  -0.289  -4.6483  -2.9642   0.4640
 ZYA  N1    N  NH1   0  -0.661  -0.5112   0.1823   0.1153
 ZYA  CA1   C  CH1   0  -0.179   0.8893   0.4728   0.0001
 ZYA  C     C  C     0   0.563   1.7292  -0.7699   0.3040
 ZYA  O     O  O     0  -0.484   1.3700  -1.6043   1.1167
 ZYA  CB1   C  CH2   0  -0.556   1.2729   1.5872   0.9843
 ZYA  CG    C  CR6   0   0.123   0.5124   2.8592   0.7328
 ZYA  CD1   C  CR16  0  -0.313  -0.5154   3.2644   1.5756
 ZYA  CD2   C  CR16  0  -0.287   0.7987   3.6575  -0.3738
 ZYA  CE1   C  CR16  0  -0.369  -1.2408   4.4228   1.3307
 ZYA  CE2   C  CR16  0  -0.321   0.0860   4.8149  -0.6348
 ZYA  CZ    C  CR6   0   0.341  -0.9450   5.2047   0.2195
 ZYA  OH    O  OH1   0  -0.633  -1.6126   6.3391  -0.0739
 ZYA  N2    N  NH1   0  -0.636   2.9036  -0.8128  -0.3437
 ZYA  CA2   C  CH1   0  -0.208   3.8597  -1.8730  -0.1583
 ZYA  CT    C  C     0   0.338   5.2620  -1.3324  -0.3615
 ZYA  OT    O  O     0  -0.373   5.4941  -0.3641  -1.0390
 ZYA  CB2   C  CH3   0  -0.651   3.6163  -3.0409  -1.1223
 ZYA  CM    C  CH2   0  -0.099   6.3477  -2.1026   0.3426
 ZYA  F1    F  F     0  -0.356   7.5866  -1.6586  -0.0528
 ZYA  H21   H  HCH2  0   0.250  -2.5895  -2.8109  -1.2311
 ZYA  H22   H  HCH2  0   0.249  -3.2056  -1.4548  -2.1851
 ZYA  H4    H  HCR6  0   0.256  -5.3678  -0.4391  -1.6689
 ZYA  H5    H  HCR6  0   0.259  -7.5645  -0.6638  -0.5732
 ZYA  H6    H  HCR6  0   0.259  -7.9017  -2.3670   1.1903
 ZYA  H7    H  HCR6  0   0.259  -6.0263  -3.8427   1.8498
 ZYA  H8    H  HCR6  0   0.255  -3.8326  -3.6173   0.7518
 ZYA  HN1   H  HNH1  0   0.403  -1.0205   0.5138   0.9195
 ZYA  HA1   H  HCH1  0   0.279   1.1077   0.8194  -1.0156
 ZYA  HB11  H  HCH2  0   0.272   1.0976   1.2398   2.0062
 ZYA  HB12  H  HCH2  0   0.279   2.3467   1.7627   0.8937
 ZYA  HD1   H  HCR6  0   0.256  -0.7592   2.6727   2.4508
 ZYA  HD2   H  HCR6  0   0.250   1.5972   3.3748  -1.0507
 ZYA  HE1   H  HCR6  0   0.271  -2.0334   4.7139   2.0108
 ZYA  HE2   H  HCR6  0   0.263   0.3284   5.4217  -1.4984
 ZYA  HO    H  HOH1  0   0.474  -2.3005   6.5015   0.5811
 ZYA  HN2   H  HNH1  0   0.402   3.0887  -0.1375  -1.0701
 ZYA  HA2   H  HCH1  0   0.288   3.7695  -2.2419   0.8663
 ZYA  HB21  H  HCH3  0   0.261   2.6161  -3.4384  -0.9597
 ZYA  HB22  H  HCH3  0   0.243   3.6950  -2.7114  -2.1582
 ZYA  HB23  H  HCH3  0   0.242   4.3260  -3.8522  -0.9625
 ZYA  HM1   H  HCH2  0   0.250   6.2602  -3.1731   0.1416
 ZYA  HM2   H  HCH2  0   0.263   6.2324  -1.9567   1.4212

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
 ZYA  C1   N1    single    1.346  0.020  1.346
 ZYA  C1   O1    double    1.214  0.020  1.214
 ZYA  C1   O2    single    1.334  0.020  1.334
 ZYA  C2   C3    single    1.498  0.020  1.498
 ZYA  C2   O2    single    1.434  0.020  1.434
 ZYA  C2   H21   single    0.970  0.020  1.090
 ZYA  C2   H22   single    0.970  0.020  1.090
 ZYA  C3   C4    aromatic  1.391  0.020  1.391
 ZYA  C3   C8    aromatic  1.392  0.020  1.392
 ZYA  C4   C5    aromatic  1.388  0.020  1.388
 ZYA  C4   H4    single    0.930  0.020  1.080
 ZYA  C5   C6    aromatic  1.389  0.020  1.389
 ZYA  C5   H5    single    0.930  0.020  1.080
 ZYA  C6   C7    aromatic  1.389  0.020  1.389
 ZYA  C6   H6    single    0.930  0.020  1.080
 ZYA  C7   C8    aromatic  1.388  0.020  1.388
 ZYA  C7   H7    single    0.930  0.020  1.080
 ZYA  C8   H8    single    0.930  0.020  1.080
 ZYA  CA1  CB1   single    1.535  0.020  1.535
 ZYA  CA1  C     single    1.530  0.020  1.530
 ZYA  CA1  N1    single    1.435  0.020  1.435
 ZYA  CA1  HA1   single    0.970  0.020  1.090
 ZYA  CB1  CG    single    1.503  0.020  1.503
 ZYA  CB1  HB11  single    0.970  0.020  1.090
 ZYA  CB1  HB12  single    0.970  0.020  1.090
 ZYA  CG   CD1   aromatic  1.390  0.020  1.390
 ZYA  CG   CD2   aromatic  1.394  0.020  1.394
 ZYA  CD1  CE1   aromatic  1.389  0.020  1.389
 ZYA  CD1  HD1   single    0.930  0.020  1.080
 ZYA  CD2  CE2   aromatic  1.384  0.020  1.384
 ZYA  CD2  HD2   single    0.930  0.020  1.080
 ZYA  CE1  CZ    aromatic  1.391  0.020  1.391
 ZYA  CE1  HE1   single    0.930  0.020  1.080
 ZYA  CE2  CZ    aromatic  1.394  0.020  1.394
 ZYA  CE2  HE2   single    0.930  0.020  1.080
 ZYA  CZ   OH    single    1.349  0.020  1.349
 ZYA  C    N2    single    1.342  0.020  1.342
 ZYA  C    O     double    1.231  0.020  1.231
 ZYA  CA2  CB2   single    1.534  0.020  1.534
 ZYA  CA2  CT    single    1.517  0.020  1.517
 ZYA  CA2  N2    single    1.440  0.020  1.440
 ZYA  CA2  HA2   single    0.970  0.020  1.090
 ZYA  CB2  HB21  single    0.970  0.020  1.090
 ZYA  CB2  HB22  single    0.970  0.020  1.090
 ZYA  CB2  HB23  single    0.970  0.020  1.090
 ZYA  CT   CM    single    1.506  0.020  1.506
 ZYA  CT   OT    double    1.204  0.020  1.204
 ZYA  CM   HM1   single    0.970  0.020  1.090
 ZYA  CM   F1    single    1.374  0.020  1.374
 ZYA  CM   HM2   single    0.970  0.020  1.090
 ZYA  N1   HN1   single    0.860  0.020  1.020
 ZYA  N2   HN2   single    0.860  0.020  1.020
 ZYA  OH   HO    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
 ZYA  N1    C1   O2    111.32  3.000
 ZYA  O2    C1   O1    124.50  3.000
 ZYA  N1    C1   O1    124.17  3.000
 ZYA  C2    O2   C1    117.05  3.000
 ZYA  H22   C2   H21   108.18  3.000
 ZYA  H22   C2   C3    110.84  3.000
 ZYA  H21   C2   C3    110.86  3.000
 ZYA  H22   C2   O2    109.94  3.000
 ZYA  H21   C2   O2    110.17  3.000
 ZYA  C3    C2   O2    106.86  3.000
 ZYA  C8    C3   C4    119.10  3.000
 ZYA  C8    C3   C2    120.39  3.000
 ZYA  C4    C3   C2    120.50  3.000
 ZYA  H4    C4   C5    119.75  3.000
 ZYA  H4    C4   C3    119.71  3.000
 ZYA  C5    C4   C3    120.54  3.000
 ZYA  H5    C5   C6    120.13  3.000
 ZYA  H5    C5   C4    119.87  3.000
 ZYA  C6    C5   C4    120.00  3.000
 ZYA  H6    C6   C7    120.09  3.000
 ZYA  H6    C6   C5    120.09  3.000
 ZYA  C7    C6   C5    119.82  3.000
 ZYA  H7    C7   C8    119.82  3.000
 ZYA  H7    C7   C6    120.17  3.000
 ZYA  C8    C7   C6    120.02  3.000
 ZYA  H8    C8   C7    119.73  3.000
 ZYA  H8    C8   C3    119.74  3.000
 ZYA  C7    C8   C3    120.53  3.000
 ZYA  HN1   N1   CA1   119.38  3.000
 ZYA  HN1   N1   C1    119.11  3.000
 ZYA  CA1   N1   C1    120.42  3.000
 ZYA  HA1   CA1  CB1   108.36  3.000
 ZYA  HA1   CA1  C     109.37  3.000
 ZYA  CB1   CA1  C     108.96  3.000
 ZYA  HA1   CA1  N1    109.46  3.000
 ZYA  C     CA1  N1    110.81  3.000
 ZYA  CB1   CA1  N1    109.84  3.000
 ZYA  N2    C    O     123.91  3.000
 ZYA  O     C    CA1   121.77  3.000
 ZYA  N2    C    CA1   114.23  3.000
 ZYA  HB12  CB1  HB11  106.64  3.000
 ZYA  HB12  CB1  CG    110.34  3.000
 ZYA  HB11  CB1  CG    110.12  3.000
 ZYA  HB12  CB1  CA1   108.01  3.000
 ZYA  HB11  CB1  CA1   109.17  3.000
 ZYA  CG    CB1  CA1   112.37  3.000
 ZYA  CD2   CG   CD1   117.80  3.000
 ZYA  CD2   CG   CB1   120.89  3.000
 ZYA  CD1   CG   CB1   121.30  3.000
 ZYA  HD1   CD1  CE1   118.69  3.000
 ZYA  HD1   CD1  CG    119.79  3.000
 ZYA  CE1   CD1  CG    121.52  3.000
 ZYA  HD2   CD2  CE2   118.66  3.000
 ZYA  HD2   CD2  CG    119.83  3.000
 ZYA  CE2   CD2  CG    121.52  3.000
 ZYA  HE1   CE1  CZ    120.38  3.000
 ZYA  HE1   CE1  CD1   119.69  3.000
 ZYA  CZ    CE1  CD1   119.93  3.000
 ZYA  HE2   CE2  CZ    119.82  3.000
 ZYA  HE2   CE2  CD2   120.24  3.000
 ZYA  CZ    CE2  CD2   119.93  3.000
 ZYA  OH    CZ   CE2   117.90  3.000
 ZYA  OH    CZ   CE1   122.79  3.000
 ZYA  CE2   CZ   CE1   119.31  3.000
 ZYA  HO    OH   CZ    110.32  3.000
 ZYA  HN2   N2   CA2   117.63  3.000
 ZYA  HN2   N2   C     119.12  3.000
 ZYA  CA2   N2   C     122.86  3.000
 ZYA  HA2   CA2  CB2   108.61  3.000
 ZYA  HA2   CA2  CT    108.80  3.000
 ZYA  CB2   CA2  CT    109.51  3.000
 ZYA  HA2   CA2  N2    108.33  3.000
 ZYA  CT    CA2  N2    109.53  3.000
 ZYA  CB2   CA2  N2    111.99  3.000
 ZYA  CM    CT   OT    122.36  3.000
 ZYA  OT    CT   CA2   122.70  3.000
 ZYA  CM    CT   CA2   114.94  3.000
 ZYA  HB23  CB2  HB22  108.51  3.000
 ZYA  HB23  CB2  HB21  107.74  3.000
 ZYA  HB22  CB2  HB21  108.59  3.000
 ZYA  HB23  CB2  CA2   111.80  3.000
 ZYA  HB22  CB2  CA2   110.83  3.000
 ZYA  HB21  CB2  CA2   109.27  3.000
 ZYA  HM2   CM   HM1   107.67  3.000
 ZYA  HM2   CM   F1    109.60  3.000
 ZYA  HM1   CM   F1    109.61  3.000
 ZYA  HM2   CM   CT    108.46  3.000
 ZYA  F1    CM   CT    110.50  3.000
 ZYA  HM1   CM   CT    110.94  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
 ZYA  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 ZYA  CONST_02  C6   C7   C8   C3     0.00   0.0  0
 ZYA  CONST_03  C7   C8   C3   C4     0.00   0.0  0
 ZYA  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 ZYA  CONST_05  C8   C3   C4   C5     0.00   0.0  0
 ZYA  CONST_06  C8   C7   C6   C5     0.00   0.0  0
 ZYA  CONST_07  CZ   CE1  CD1  CG     0.00   0.0  0
 ZYA  CONST_08  CZ   CE2  CD2  CG     0.00   0.0  0
 ZYA  CONST_09  CE2  CD2  CG   CD1    0.00   0.0  0
 ZYA  CONST_10  CE2  CZ   CE1  CD1    0.00   0.0  0
 ZYA  CONST_11  CE1  CD1  CG   CD2    0.00   0.0  0
 ZYA  CONST_12  CE1  CZ   CE2  CD2    0.00   0.0  0
 ZYA  CONST_13  C5   C4   C3   C2   180.00   0.0  0
 ZYA  CONST_14  C7   C8   C3   C2   180.00   0.0  0
 ZYA  CONST_15  CE1  CD1  CG   CB1  180.00   0.0  0
 ZYA  CONST_16  CE2  CD2  CG   CB1  180.00   0.0  0
 ZYA  CONST_17  OH   CZ   CE1  CD1  180.00   0.0  0
 ZYA  CONST_18  OH   CZ   CE2  CD2  180.00   0.0  0
 ZYA  CONST_19  H5   C5   C4   C3   180.00   0.0  0
 ZYA  CONST_20  H7   C7   C8   C3   180.00   0.0  0
 ZYA  CONST_21  H8   C8   C3   C4   180.00   0.0  0
 ZYA  CONST_22  H6   C6   C5   C4   180.00   0.0  0
 ZYA  CONST_23  H4   C4   C5   C6   180.00   0.0  0
 ZYA  CONST_24  HE1  CE1  CD1  CG   180.00   0.0  0
 ZYA  CONST_25  HE2  CE2  CD2  CG   180.00   0.0  0
 ZYA  CONST_26  HD2  CD2  CG   CD1  180.00   0.0  0
 ZYA  CONST_27  HD1  CD1  CG   CD2  180.00   0.0  0
 ZYA  CONST_28  CA2  N2   C    CA1  180.00   0.0  0
 ZYA  CONST_29  CA2  N2   C    O      0.00   0.0  0
 ZYA  CONST_30  HN2  N2   C    CA1    0.00   0.0  0
 ZYA  Var_01    C4   C3   C2   O2    91.29  30.0  2
 ZYA  Var_02    CD1  CG   CB1  CA1  106.01  30.0  2
 ZYA  Var_03    C3   C2   O2   C1   175.54  30.0  1
 ZYA  Var_04    CA1  N1   C1   O1    -6.26  30.0  2
 ZYA  Var_05    N1   C1   O2   C2   178.35  30.0  1
 ZYA  Var_06    F1   CM   CT   CA2  171.35  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
 ZYA  chir_01  CA1  CB1  C    N1  negativ
 ZYA  chir_02  CA2  N2   CB2  CT  negativ

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
 ZYA  plan-1  C2   0.020
 ZYA  plan-1  C3   0.020
 ZYA  plan-1  C4   0.020
 ZYA  plan-1  C5   0.020
 ZYA  plan-1  C6   0.020
 ZYA  plan-1  C7   0.020
 ZYA  plan-1  C8   0.020
 ZYA  plan-1  H4   0.020
 ZYA  plan-1  H5   0.020
 ZYA  plan-1  H6   0.020
 ZYA  plan-1  H7   0.020
 ZYA  plan-1  H8   0.020
 ZYA  plan-2  CB1  0.020
 ZYA  plan-2  CG   0.020
 ZYA  plan-2  CD1  0.020
 ZYA  plan-2  CD2  0.020
 ZYA  plan-2  CE1  0.020
 ZYA  plan-2  CE2  0.020
 ZYA  plan-2  CZ   0.020
 ZYA  plan-2  OH   0.020
 ZYA  plan-2  HD1  0.020
 ZYA  plan-2  HD2  0.020
 ZYA  plan-2  HE1  0.020
 ZYA  plan-2  HE2  0.020
 ZYA  plan-3  CA1  0.020
 ZYA  plan-3  C    0.020
 ZYA  plan-3  O    0.020
 ZYA  plan-3  N2   0.020
 ZYA  plan-3  CA2  0.020
 ZYA  plan-3  HN2  0.020
 ZYA  plan-4  CA2  0.020
 ZYA  plan-4  CT   0.020
 ZYA  plan-4  OT   0.020
 ZYA  plan-4  CM   0.020
 ZYA  plan-5  C1   0.020
 ZYA  plan-5  O1   0.020
 ZYA  plan-5  O2   0.020
 ZYA  plan-5  N1   0.020

