# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:30:40 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-{(5E)-4-hydroxy-2-oxo-5-[(2-phenylcyclopropyl)imino]cyclohex-3-en-1-yl}alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(CC1CC(=NC2CC2c3ccccc3)C(=CC1=O)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
 TYT  TYT  3-{(5E)-4-hydroxy-2-oxo-5-[(2-phenylcyclopropyl)imino]cyclohex-3-en-1-yl}alanine  L-peptide  43  24  .  2022-03-23  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TYT
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
 TYT  N1   N  NH2    0  -0.788   3.2190  -1.8877  -1.7080
 TYT  C1   C  CH1    0  -0.219   2.7852  -1.5133  -0.3699
 TYT  C2   C  C      0   0.392   2.3940  -2.6999   0.5488
 TYT  O1   O  OC    -1  -0.623   2.2461  -2.4280   1.7586
 TYT  O2   O  O      0  -0.605   2.2415  -3.8152   0.0141
 TYT  C3   C  CH2    0  -0.412   1.6002  -0.5475  -0.4570
 TYT  C4   C  CH1    0  -0.386   1.9028   0.7631  -1.2025
 TYT  C5   C  C      0   0.417   2.7843   1.6532  -0.3594
 TYT  O3   O  O      0  -0.442   4.0031   1.5969  -0.4076
 TYT  C6   C  C1     0  -0.503   2.1191   2.5750   0.5526
 TYT  C7   C  C      0   0.381   0.7771   2.7250   0.5971
 TYT  O4   O  OH1    0  -0.594   0.1559   3.5715   1.4112
 TYT  C8   C  C      0   0.165  -0.1017   1.9565  -0.3235
 TYT  N2   N  N      0  -0.310  -1.3173   1.6411  -0.1664
 TYT  C9   C  CH1    0  -0.127  -2.1209   1.8685   0.9572
 TYT  C10  C  CH2    0  -0.485  -3.5650   2.1673   0.6644
 TYT  C11  C  CH1    0  -0.361  -3.2103   0.8219   1.1941
 TYT  C12  C  CR6    0   0.215  -3.2868  -0.4326   0.4077
 TYT  C13  C  CR16   0  -0.320  -3.2084  -1.6463   1.0908
 TYT  C14  C  CR16   0  -0.241  -3.2652  -2.8582   0.4169
 TYT  C15  C  CR16   0  -0.276  -3.4054  -2.8794  -0.9637
 TYT  C16  C  CR16   0  -0.242  -3.4899  -1.6779  -1.6555
 TYT  C17  C  CR16   0  -0.312  -3.4325  -0.4681  -0.9788
 TYT  C18  C  CH2    0  -0.519   0.6143   1.5068  -1.5639
 TYT  H1   H  HNH2   0   0.336   4.1422  -2.2999  -1.6474
 TYT  H2   H  HNH2   0   0.324   2.6252  -2.6499  -2.0171
 TYT  H3   H  HCH1   0   0.220   3.6158  -0.9900   0.1134
 TYT  H4   H  HCH2   0   0.229   0.7765  -1.0461  -0.9808
 TYT  H5   H  HCH2   0   0.228   1.2340  -0.3381   0.5503
 TYT  H6   H  HCH1   0   0.266   2.4434   0.5093  -2.1162
 TYT  H7   H  H      0   0.276   2.7523   3.1642   1.2084
 TYT  H20  H  HOH1   0   0.487   0.7886   4.0251   1.9853
 TYT  H8   H  HCH1   0   0.270  -1.7072   2.2966   1.8615
 TYT  H9   H  HCH2   0   0.264  -3.8410   2.2576  -0.3784
 TYT  H10  H  HCH2   0   0.270  -4.0772   2.8545   1.3249
 TYT  H11  H  HCH1   0   0.272  -3.4154   0.6774   2.2495
 TYT  H12  H  HCR6   0   0.244  -3.1028  -1.6422   2.1698
 TYT  H13  H  HCR6   0   0.249  -3.2007  -3.7848   0.9734
 TYT  H14  H  HCR6   0   0.248  -3.4535  -3.8210  -1.4958
 TYT  H15  H  HCR6   0   0.248  -3.6029  -1.6811  -2.7324
 TYT  H16  H  HCR6   0   0.234  -3.5029   0.4507  -1.5447
 TYT  H17  H  HCH2   0   0.266   0.8575   2.3759  -2.1840
 TYT  H18  H  HCH2   0   0.262  -0.0485   0.8602  -2.1381

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
 TYT  N1   C1   single    1.456  0.020  1.456
 TYT  N1   H1   single    0.890  0.020  1.040
 TYT  N1   H2   single    0.890  0.020  1.040
 TYT  C1   C2   single    1.551  0.020  1.551
 TYT  C1   C3   single    1.531  0.020  1.531
 TYT  C1   H3   single    0.970  0.020  1.090
 TYT  C2   O1   deloc     1.249  0.020  1.249
 TYT  C2   O2   deloc     1.246  0.020  1.246
 TYT  C3   C4   single    1.538  0.020  1.538
 TYT  C3   H4   single    0.970  0.020  1.090
 TYT  C3   H5   single    0.970  0.020  1.090
 TYT  C4   C5   single    1.510  0.020  1.510
 TYT  C4   C18  single    1.531  0.020  1.531
 TYT  C4   H6   single    0.970  0.020  1.090
 TYT  C5   O3   double    1.221  0.020  1.221
 TYT  C5   C6   single    1.457  0.020  1.457
 TYT  C6   C7   double    1.351  0.020  1.351
 TYT  C6   H7   single    0.930  0.020  1.080
 TYT  C7   O4   single    1.329  0.020  1.329
 TYT  C7   C8   single    1.487  0.020  1.487
 TYT  O4   H20  single    0.850  0.020  0.980
 TYT  C8   N2   double    1.266  0.020  1.266
 TYT  C8   C18  single    1.501  0.020  1.501
 TYT  N2   C9   single    1.400  0.020  1.400
 TYT  C9   C10  single    1.503  0.020  1.503
 TYT  C9   C11  single    1.529  0.020  1.529
 TYT  C9   H8   single    0.970  0.020  1.090
 TYT  C10  C11  single    1.489  0.020  1.489
 TYT  C10  H9   single    0.970  0.020  1.090
 TYT  C10  H10  single    0.970  0.020  1.090
 TYT  C11  C12  single    1.483  0.020  1.483
 TYT  C11  H11  single    0.970  0.020  1.090
 TYT  C12  C13  aromatic  1.395  0.020  1.395
 TYT  C12  C17  aromatic  1.395  0.020  1.395
 TYT  C13  C14  aromatic  1.388  0.020  1.388
 TYT  C13  H12  single    0.930  0.020  1.080
 TYT  C14  C15  aromatic  1.388  0.020  1.388
 TYT  C14  H13  single    0.930  0.020  1.080
 TYT  C15  C16  aromatic  1.389  0.020  1.389
 TYT  C15  H14  single    0.930  0.020  1.080
 TYT  C16  C17  aromatic  1.387  0.020  1.387
 TYT  C16  H15  single    0.930  0.020  1.080
 TYT  C17  H16  single    0.930  0.020  1.080
 TYT  C18  H17  single    0.970  0.020  1.090
 TYT  C18  H18  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
 TYT  H2   N1   H1   104.24  3.000
 TYT  H2   N1   C1   107.39  3.000
 TYT  H1   N1   C1   108.74  3.000
 TYT  H3   C1   C3   108.11  3.000
 TYT  H3   C1   C2   107.20  3.000
 TYT  C3   C1   C2   108.73  3.000
 TYT  H3   C1   N1   107.63  3.000
 TYT  C3   C1   N1   109.91  3.000
 TYT  C2   C1   N1   115.02  3.000
 TYT  O2   C2   O1   126.59  3.000
 TYT  O2   C2   C1   117.48  3.000
 TYT  O1   C2   C1   115.92  3.000
 TYT  H5   C3   H4   106.02  3.000
 TYT  H5   C3   C4   110.47  3.000
 TYT  H4   C3   C4   107.69  3.000
 TYT  H5   C3   C1   109.14  3.000
 TYT  H4   C3   C1   108.77  3.000
 TYT  C4   C3   C1   114.39  3.000
 TYT  H6   C4   C18  109.40  3.000
 TYT  H6   C4   C5   108.38  3.000
 TYT  C18  C4   C5   109.68  3.000
 TYT  H6   C4   C3   107.76  3.000
 TYT  C18  C4   C3   111.28  3.000
 TYT  C5   C4   C3   110.27  3.000
 TYT  C6   C5   O3   120.63  3.000
 TYT  C6   C5   C4   117.11  3.000
 TYT  O3   C5   C4   122.24  3.000
 TYT  H7   C6   C7   119.95  3.000
 TYT  H7   C6   C5   117.07  3.000
 TYT  C7   C6   C5   122.97  3.000
 TYT  C8   C7   O4   115.62  3.000
 TYT  C8   C7   C6   120.62  3.000
 TYT  O4   C7   C6   123.74  3.000
 TYT  H20  O4   C7   110.89  3.000
 TYT  C18  C8   N2   119.08  3.000
 TYT  C18  C8   C7   112.62  3.000
 TYT  N2   C8   C7   128.29  3.000
 TYT  C9   N2   C8   127.62  3.000
 TYT  H8   C9   C11  114.43  3.000
 TYT  H8   C9   C10  116.82  3.000
 TYT  C11  C9   C10   58.80  3.000
 TYT  H8   C9   N2   121.01  3.000
 TYT  C11  C9   N2   114.97  3.000
 TYT  C10  C9   N2   115.30  3.000
 TYT  H10  C10  H9   114.48  3.000
 TYT  H10  C10  C11  118.00  3.000
 TYT  H9   C10  C11  118.61  3.000
 TYT  H10  C10  C9   117.52  3.000
 TYT  H9   C10  C9   116.68  3.000
 TYT  C11  C10  C9    61.46  3.000
 TYT  H11  C11  C12  113.18  3.000
 TYT  H11  C11  C10  114.93  3.000
 TYT  C12  C11  C10  124.31  3.000
 TYT  H11  C11  C9   112.12  3.000
 TYT  C12  C11  C9   122.26  3.000
 TYT  C10  C11  C9    59.74  3.000
 TYT  C17  C12  C13  118.07  3.000
 TYT  C17  C12  C11  123.66  3.000
 TYT  C13  C12  C11  118.26  3.000
 TYT  H12  C13  C14  119.37  3.000
 TYT  H12  C13  C12  119.31  3.000
 TYT  C14  C13  C12  121.31  3.000
 TYT  H13  C14  C15  120.28  3.000
 TYT  H13  C14  C13  119.69  3.000
 TYT  C15  C14  C13  120.03  3.000
 TYT  H14  C15  C16  120.32  3.000
 TYT  H14  C15  C14  120.45  3.000
 TYT  C16  C15  C14  119.24  3.000
 TYT  H15  C16  C17  119.47  3.000
 TYT  H15  C16  C15  119.94  3.000
 TYT  C17  C16  C15  120.58  3.000
 TYT  H16  C17  C16  118.87  3.000
 TYT  H16  C17  C12  120.36  3.000
 TYT  C16  C17  C12  120.76  3.000
 TYT  H18  C18  H17  107.92  3.000
 TYT  H18  C18  C8   108.86  3.000
 TYT  H17  C18  C8   109.64  3.000
 TYT  H18  C18  C4   110.36  3.000
 TYT  H17  C18  C4   109.40  3.000
 TYT  C8   C18  C4   110.60  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
 TYT  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 TYT  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 TYT  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 TYT  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 TYT  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 TYT  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 TYT  CONST_07  C14  C13  C12  C11   180.00   0.0  0
 TYT  CONST_08  C16  C17  C12  C11   180.00   0.0  0
 TYT  CONST_09  H12  C13  C12  C11     0.00   0.0  0
 TYT  CONST_10  H16  C17  C12  C11     0.00   0.0  0
 TYT  CONST_11  H13  C14  C13  C12   180.00   0.0  0
 TYT  CONST_12  H15  C16  C17  C12   180.00   0.0  0
 TYT  CONST_13  H14  C15  C14  C13   180.00   0.0  0
 TYT  Var_01    C7   C6   C5   C4     -4.87  30.0  1
 TYT  Var_02    C7   C8   C18  C4     52.35  30.0  1
 TYT  Var_03    C8   C7   C6   C5     -1.22  30.0  1
 TYT  Var_04    C18  C8   C7   C6    -23.21  30.0  1
 TYT  Var_05    C12  C11  C10  C9   -110.48  30.0  1
 TYT  Var_06    C13  C12  C11  C9    120.55  30.0  2
 TYT  Var_07    C10  C9   N2   C8    145.19  30.0  3
 TYT  Var_08    C11  C10  C9   N2    105.04  30.0  1

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
 TYT  chir_01  C1   N1   C2   C3   positiv
 TYT  chir_02  C4   C18  C5   C3   negativ
 TYT  chir_03  C9   N2   C10  C11  both
 TYT  chir_04  C11  C9   C10  C12  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
 TYT  plan-1  C4   0.020
 TYT  plan-1  C5   0.020
 TYT  plan-1  O3   0.020
 TYT  plan-1  C6   0.020
 TYT  plan-2  C11  0.020
 TYT  plan-2  C12  0.020
 TYT  plan-2  C13  0.020
 TYT  plan-2  C14  0.020
 TYT  plan-2  C15  0.020
 TYT  plan-2  C16  0.020
 TYT  plan-2  C17  0.020
 TYT  plan-2  H12  0.020
 TYT  plan-2  H13  0.020
 TYT  plan-2  H14  0.020
 TYT  plan-2  H15  0.020
 TYT  plan-2  H16  0.020
 TYT  plan-3  C1   0.020
 TYT  plan-3  C2   0.020
 TYT  plan-3  O1   0.020
 TYT  plan-3  O2   0.020

