# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 04:57:58 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: O-(7-amino-1,3-dihydro-2,1,3-benzoxadiazol-4-yl)-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(Oc2ccc(N)c3NONc23)cc1)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
 TYN  TYN  O-(7-amino-1,3-dihydro-2,1,3-benzoxadiazol-4-yl)-L-tyrosine  L-peptide  38  23  .  2012-08-28  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_TYN
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
 TYN  N     N  NH2    0  -0.808  106.8076  93.1854  61.1869
 TYN  CA    C  CH1    0  -0.188  106.3283  91.8190  61.4089
 TYN  CB    C  CH2    0  -0.474  106.8750  90.9332  60.2958
 TYN  CG    C  CR6    0   0.110  106.5524  89.4682  60.4246
 TYN  CD1   C  CR16   0  -0.301  105.3464  89.0042  60.9423
 TYN  CE1   C  CR16   0  -0.340  105.0606  87.6466  61.0304
 TYN  CD2   C  CR16   0  -0.309  107.4737  88.5121  59.9976
 TYN  CE2   C  CR16   0  -0.315  107.2048  87.1551  60.0628
 TYN  CZ    C  CR6    0   0.331  105.9920  86.7193  60.5820
 TYN  OC    O  O2     0  -0.504  105.8041  85.3677  60.6564
 TYN  C     C  C      0   0.403  106.8040  91.3415  62.8052
 TYN  O     O  O      0  -0.602  108.0087  91.0404  62.9146
 TYN  OXT   O  OC    -1  -0.608  105.9417  91.3246  63.7066
 TYN  O1    O  O      0  -0.320  102.6144  85.5330  57.7966
 TYN  N1    N  NR15   0  -0.420  101.5778  85.0777  58.6983
 TYN  N2    N  NR15   0  -0.393  103.6975  85.9410  58.5825
 TYN  C1    C  CR56   0   0.212  102.3181  84.5959  59.8006
 TYN  C2    C  CR6    0   0.240  101.9058  83.7796  60.8484
 TYN  C3    C  CR16   0  -0.339  102.8698  83.5236  61.8337
 TYN  C4    C  CR16   0  -0.358  104.1439  84.0693  61.7840
 TYN  C5    C  CR6    0   0.275  104.5280  84.8824  60.7244
 TYN  C6    C  CR56   0   0.151  103.5926  85.1241  59.7367
 TYN  H     H  HNH2   0   0.337  106.4378  93.7903  61.9107
 TYN  H2    H  HNH2   0   0.335  106.4122  93.5351  60.3215
 TYN  HA    H  HCH1   0   0.182  105.2299  91.7761  61.3890
 TYN  HB2   H  HCH2   0   0.233  106.4978  91.2978  59.3322
 TYN  HB3   H  HCH2   0   0.226  107.9588  91.0577  60.2600
 TYN  HD1   H  HCR6   0   0.250  104.5984  89.7040  61.2914
 TYN  HE1   H  HCR6   0   0.281  104.1200  87.3301  61.4650
 TYN  HD2   H  HCR6   0   0.247  108.4271  88.8361  59.5972
 TYN  HE2   H  HCR6   0   0.261  107.9345  86.4325  59.7190
 TYN  HN31  H  HNH2   0   0.381  100.4996  82.5416  61.5991
 TYN  HN32  H  HNH2   0   0.379  100.1554  83.0823  60.0738
 TYN  H3    H  HCR6   0   0.264  102.6077  82.8761  62.6617
 TYN  H4    H  HCR6   0   0.266  104.8543  83.8513  62.5710
 TYN  HN1   H  HNR5   0   0.392  101.1382  84.3268  58.1707
 TYN  N3    N  NH2    0  -0.858  100.6102  83.3022  60.9463
 TYN  HN2   H  HNR5   0   0.381  103.5375  86.9200  58.8343

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
 TYN  N    CA    single    1.458  0.019  1.458
 TYN  N    H     single    0.860  0.020  0.860
 TYN  N    H2    single    0.890  0.020  1.040
 TYN  CA   CB    single    1.530  0.020  1.530
 TYN  CA   C     single    1.525  0.021  1.525
 TYN  CA   HA    single    0.970  0.020  0.970
 TYN  CB   CG    single    1.506  0.020  1.506
 TYN  CB   HB2   single    0.970  0.020  1.090
 TYN  CB   HB3   single    0.970  0.020  1.090
 TYN  CG   CD1   aromatic  1.392  0.020  1.392
 TYN  CG   CD2   aromatic  1.395  0.020  1.395
 TYN  CD1  CE1   aromatic  1.390  0.020  1.390
 TYN  CD1  HD1   single    0.930  0.020  1.080
 TYN  CE1  CZ    aromatic  1.389  0.020  1.389
 TYN  CE1  HE1   single    0.930  0.020  1.080
 TYN  CD2  CE2   aromatic  1.385  0.020  1.385
 TYN  CD2  HD2   single    0.930  0.020  1.080
 TYN  CE2  CZ    aromatic  1.389  0.020  1.389
 TYN  CE2  HE2   single    0.930  0.020  1.080
 TYN  CZ   OC    single    1.367  0.020  1.367
 TYN  OC   C5    single    1.367  0.020  1.367
 TYN  C    O     deloc     1.231  0.020  1.231
 TYN  C    OXT   deloc     1.248  0.020  1.248
 TYN  O1   N1    single    1.447  0.020  1.447
 TYN  O1   N2    single    1.399  0.020  1.399
 TYN  N1   C1    single    1.413  0.020  1.413
 TYN  N1   HN1   single    0.890  0.020  1.040
 TYN  N2   C6    single    1.418  0.020  1.418
 TYN  N2   HN2   single    0.890  0.020  1.040
 TYN  N3   C2    single    1.384  0.020  1.384
 TYN  N3   HN31  single    0.890  0.020  1.040
 TYN  N3   HN32  single    0.890  0.020  1.040
 TYN  C1   C2    aromatic  1.391  0.020  1.391
 TYN  C1   C6    aromatic  1.381  0.020  1.381
 TYN  C2   C3    aromatic  1.402  0.020  1.402
 TYN  C3   C4    aromatic  1.387  0.020  1.387
 TYN  C3   H3    single    0.930  0.020  1.080
 TYN  C4   C5    aromatic  1.390  0.020  1.390
 TYN  C4   H4    single    0.930  0.020  1.080
 TYN  C5   C6    aromatic  1.382  0.020  1.382

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
 TYN  H2    N    H     105.16  3.000
 TYN  H2    N    CA    108.87  3.000
 TYN  H     N    CA    114.00  3.000
 TYN  HA    CA   C     109.00  3.000
 TYN  HA    CA   CB    109.00  3.000
 TYN  C     CA   CB    110.10  1.900
 TYN  HA    CA   N     110.00  3.000
 TYN  C     CA   N     111.00  2.800
 TYN  CB    CA   N     110.50  1.700
 TYN  HB3   CB   HB2   105.94  3.000
 TYN  HB3   CB   CG    109.06  3.000
 TYN  HB2   CB   CG    108.95  3.000
 TYN  HB3   CB   CA    108.30  3.000
 TYN  HB2   CB   CA    108.97  3.000
 TYN  CG    CB   CA    115.23  3.000
 TYN  CD2   CG   CD1   117.23  3.000
 TYN  CD2   CG   CB    119.96  3.000
 TYN  CD1   CG   CB    122.81  3.000
 TYN  HD1   CD1  CE1   117.97  3.000
 TYN  HD1   CD1  CG    120.21  3.000
 TYN  CE1   CD1  CG    121.82  3.000
 TYN  HE1   CE1  CZ    121.12  3.000
 TYN  HE1   CE1  CD1   119.29  3.000
 TYN  CZ    CE1  CD1   119.59  3.000
 TYN  HD2   CD2  CE2   118.76  3.000
 TYN  HD2   CD2  CG    119.29  3.000
 TYN  CE2   CD2  CG    121.95  3.000
 TYN  HE2   CE2  CZ    119.84  3.000
 TYN  HE2   CE2  CD2   120.53  3.000
 TYN  CZ    CE2  CD2   119.63  3.000
 TYN  OC    CZ   CE2   116.78  3.000
 TYN  OC    CZ   CE1   123.41  3.000
 TYN  CE2   CZ   CE1   119.78  3.000
 TYN  C5    OC   CZ    118.83  3.000
 TYN  OXT   C    O     126.96  3.000
 TYN  OXT   C    CA    116.28  3.000
 TYN  O     C    CA    120.80  1.700
 TYN  N2    O1   N1    107.23  3.000
 TYN  HN1   N1   C1    112.29  3.000
 TYN  HN1   N1   O1    102.62  3.000
 TYN  C1    N1   O1    102.60  3.000
 TYN  HN2   N2   C6    109.84  3.000
 TYN  HN2   N2   O1    107.22  3.000
 TYN  C6    N2   O1    103.41  3.000
 TYN  C6    C1   C2    122.21  3.000
 TYN  C6    C1   N1    108.48  3.000
 TYN  C2    C1   N1    129.25  3.000
 TYN  C3    C2   C1    115.64  3.000
 TYN  C3    C2   N3    122.07  3.000
 TYN  C1    C2   N3    122.22  3.000
 TYN  H3    C3   C4    119.00  3.000
 TYN  H3    C3   C2    118.68  3.000
 TYN  C4    C3   C2    122.32  3.000
 TYN  H4    C4   C5    119.40  3.000
 TYN  H4    C4   C3    119.84  3.000
 TYN  C5    C4   C3    120.76  3.000
 TYN  C6    C5   C4    117.41  3.000
 TYN  C6    C5   OC    122.30  3.000
 TYN  C4    C5   OC    120.24  3.000
 TYN  C5    C6   C1    121.65  3.000
 TYN  C5    C6   N2    129.24  3.000
 TYN  C1    C6   N2    109.05  3.000
 TYN  HN32  N3   HN31  110.26  3.000
 TYN  HN32  N3   C2    115.86  3.000
 TYN  HN31  N3   C2    114.11  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
 TYN  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 TYN  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 TYN  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 TYN  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 TYN  CONST_05  CD2  CG   CD1  CE1     0.00   0.0  0
 TYN  CONST_06  CD2  CE2  CZ   CE1     0.00   0.0  0
 TYN  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 TYN  CONST_08  C4   C5   C6   C1      0.00   0.0  0
 TYN  CONST_09  C5   C6   C1   C2      0.00   0.0  0
 TYN  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 TYN  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 TYN  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 TYN  CONST_13  CE1  CD1  CG   CB    180.00   0.0  0
 TYN  CONST_14  CE2  CD2  CG   CB    180.00   0.0  0
 TYN  CONST_15  OC   CZ   CE1  CD1   180.00   0.0  0
 TYN  CONST_16  OC   CZ   CE2  CD2   180.00   0.0  0
 TYN  CONST_17  C3   C4   C5   OC    180.00   0.0  0
 TYN  CONST_18  N2   C6   C5   OC      0.00   0.0  0
 TYN  CONST_19  C1   C6   C5   OC    180.00   0.0  0
 TYN  CONST_20  N3   C2   C1   N1      0.00   0.0  0
 TYN  CONST_21  C6   C1   C2   N3    180.00   0.0  0
 TYN  CONST_22  C4   C3   C2   N3    180.00   0.0  0
 TYN  CONST_23  HE1  CE1  CD1  CG    180.00   0.0  0
 TYN  CONST_24  HE2  CE2  CD2  CG    180.00   0.0  0
 TYN  CONST_25  HD2  CD2  CG   CD1   180.00   0.0  0
 TYN  CONST_26  HD1  CD1  CG   CD2   180.00   0.0  0
 TYN  CONST_27  H3   C3   C2   C1    180.00   0.0  0
 TYN  CONST_28  H4   C4   C3   C2    180.00   0.0  0
 TYN  Var_01    C4   C5   OC   CZ   -123.27  30.0  2
 TYN  Var_02    CD1  CG   CB   CA     35.42  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
 TYN  chir_01  CA  N  CB  C  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
 TYN  plan-1  CB    0.020
 TYN  plan-1  CG    0.020
 TYN  plan-1  CD1   0.020
 TYN  plan-1  CE1   0.020
 TYN  plan-1  CD2   0.020
 TYN  plan-1  CE2   0.020
 TYN  plan-1  CZ    0.020
 TYN  plan-1  OC    0.020
 TYN  plan-1  HD1   0.020
 TYN  plan-1  HE1   0.020
 TYN  plan-1  HD2   0.020
 TYN  plan-1  HE2   0.020
 TYN  plan-2  OC    0.020
 TYN  plan-2  O1    0.020
 TYN  plan-2  N1    0.020
 TYN  plan-2  N2    0.020
 TYN  plan-2  C1    0.020
 TYN  plan-2  C2    0.020
 TYN  plan-2  C3    0.020
 TYN  plan-2  C4    0.020
 TYN  plan-2  C5    0.020
 TYN  plan-2  C6    0.020
 TYN  plan-2  H3    0.020
 TYN  plan-2  H4    0.020
 TYN  plan-2  HN1   0.020
 TYN  plan-2  N3    0.020
 TYN  plan-2  HN2   0.020
 TYN  plan-3  C2    0.020
 TYN  plan-3  HN31  0.020
 TYN  plan-3  HN32  0.020
 TYN  plan-3  N3    0.020
 TYN  plan-4  CA    0.020
 TYN  plan-4  C     0.020
 TYN  plan-4  O     0.020
 TYN  plan-4  OXT   0.020

