# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 20:12:14 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2E,4S)-4-amino-5-(4-hydroxyphenyl)pent-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)\C=C\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
 VLT  VLT  '(2E,4S)-4-amino-5-(4-hydroxyphenyl)pent-2-enoic acid'  peptide  28  15  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VLT
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
 VLT  N    N  NH2   0  -0.777  -0.5714   1.3273  -0.8357
 VLT  CA   C  CH1   0  -0.126  -0.7963  -0.0642  -0.5240
 VLT  C2   C  C1    0  -0.140  -2.2173  -0.4768  -0.2675
 VLT  C3   C  CH2   0  -0.535   0.0570  -0.4839   0.6881
 VLT  C4   C  CR6   0   0.142   1.5313  -0.3341   0.4508
 VLT  C5   C  CR16  0  -0.295   2.2184   0.8125   0.8330
 VLT  C6   C  CR16  0  -0.297   2.2571  -1.3416  -0.1808
 VLT  C7   C  CR16  0  -0.374   3.5797   0.9535   0.6033
 VLT  C8   C  CR16  0  -0.325   3.6160  -1.2182  -0.4240
 VLT  C9   C  CR6   0   0.335   4.2881  -0.0640  -0.0296
 VLT  O1   O  OH1   0  -0.636   5.6132   0.0143  -0.2779
 VLT  C10  C  C1    0  -0.415  -3.2615   0.3471  -0.1971
 VLT  C    C  C     0   0.530  -4.6154  -0.1641   0.0749
 VLT  O    O  O     0  -0.452  -4.9070  -1.3246   0.2525
 VLT  OXT  O  OH1   0  -0.603  -5.5108   0.8194   0.1041
 VLT  H    H  HNH2  0   0.354  -1.1175   1.6041  -1.6419
 VLT  H1   H  HCH1  0   0.260  -0.4539  -0.6591  -1.3808
 VLT  H3   H  H     0   0.268  -2.3731  -1.5422  -0.1203
 VLT  H4   H  HCH2  0   0.252  -0.2522   0.1134   1.5516
 VLT  H5   H  HCH2  0   0.257  -0.1738  -1.5232   0.9350
 VLT  H6   H  HCR6  0   0.245   1.6867   1.6165   1.3271
 VLT  H7   H  HCR6  0   0.246   1.7523  -2.2497  -0.4905
 VLT  H8   H  HCR6  0   0.266   4.0884   1.8569   0.9216
 VLT  H9   H  HCR6  0   0.259   4.1588  -2.0181  -0.9127
 VLT  H10  H  HOH1  0   0.472   5.9657   0.8486   0.0506
 VLT  H11  H  H     0   0.267  -3.1493   1.4156  -0.3386
 VLT  HXT  H  HOH1  0   0.480  -6.3922   0.4595   0.2820
 VLT  H2   H  HNH2  0   0.344  -0.8695   1.9157  -0.0666

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
 VLT  N    CA   single    1.458  0.019  1.458
 VLT  N    H    single    0.860  0.020  0.860
 VLT  CA   C2   single    1.502  0.020  1.502
 VLT  CA   C3   single    1.541  0.020  1.541
 VLT  CA   H1   single    0.970  0.020  1.090
 VLT  C2   C10  double    1.332  0.020  1.332
 VLT  C2   H3   single    0.930  0.020  1.080
 VLT  C3   C4   single    1.501  0.020  1.501
 VLT  C3   H4   single    0.970  0.020  1.090
 VLT  C3   H5   single    0.970  0.020  1.090
 VLT  C4   C5   aromatic  1.390  0.020  1.390
 VLT  C4   C6   aromatic  1.393  0.020  1.393
 VLT  C5   C7   aromatic  1.388  0.020  1.388
 VLT  C5   H6   single    0.930  0.020  1.080
 VLT  C6   C8   aromatic  1.386  0.020  1.386
 VLT  C6   H7   single    0.930  0.020  1.080
 VLT  C7   C9   aromatic  1.392  0.020  1.392
 VLT  C7   H8   single    0.930  0.020  1.080
 VLT  C8   C9   aromatic  1.393  0.020  1.393
 VLT  C8   H9   single    0.930  0.020  1.080
 VLT  C9   O1   single    1.350  0.020  1.350
 VLT  O1   H10  single    0.850  0.020  0.980
 VLT  C10  C    single    1.473  0.020  1.473
 VLT  C10  H11  single    0.930  0.020  1.080
 VLT  C    O    double    1.231  0.020  1.231
 VLT  C    OXT  single    1.330  0.020  1.330
 VLT  OXT  HXT  single    0.850  0.020  0.980
 VLT  N    H2   single    0.890  0.020  1.040

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
 VLT  H2   N    H    106.68  3.000
 VLT  H2   N    CA   110.49  3.000
 VLT  H    N    CA   114.00  3.000
 VLT  H1   CA   C3   107.07  3.000
 VLT  H1   CA   C2   106.23  3.000
 VLT  C3   CA   C2   108.35  3.000
 VLT  H1   CA   N    107.78  3.000
 VLT  C3   CA   N    110.25  3.000
 VLT  C2   CA   N    116.69  3.000
 VLT  H3   C2   C10  119.13  3.000
 VLT  H3   C2   CA   115.35  3.000
 VLT  C10  C2   CA   125.51  3.000
 VLT  H5   C3   H4   106.32  3.000
 VLT  H5   C3   C4   109.76  3.000
 VLT  H4   C3   C4   110.36  3.000
 VLT  H5   C3   CA   108.66  3.000
 VLT  H4   C3   CA   108.39  3.000
 VLT  C4   C3   CA   113.11  3.000
 VLT  C6   C4   C5   117.62  3.000
 VLT  C6   C4   C3   120.75  3.000
 VLT  C5   C4   C3   121.63  3.000
 VLT  H6   C5   C7   118.79  3.000
 VLT  H6   C5   C4   119.67  3.000
 VLT  C7   C5   C4   121.54  3.000
 VLT  H7   C6   C8   118.74  3.000
 VLT  H7   C6   C4   119.52  3.000
 VLT  C8   C6   C4   121.74  3.000
 VLT  H8   C7   C9   120.24  3.000
 VLT  H8   C7   C5   119.75  3.000
 VLT  C9   C7   C5   120.01  3.000
 VLT  H9   C8   C9   119.87  3.000
 VLT  H9   C8   C6   120.32  3.000
 VLT  C9   C8   C6   119.82  3.000
 VLT  O1   C9   C8   118.00  3.000
 VLT  O1   C9   C7   122.73  3.000
 VLT  C8   C9   C7   119.27  3.000
 VLT  H10  O1   C9   110.27  3.000
 VLT  H11  C10  C    117.49  3.000
 VLT  H11  C10  C2   121.46  3.000
 VLT  C    C10  C2   121.05  3.000
 VLT  OXT  C    O    122.94  3.000
 VLT  OXT  C    C10  111.48  3.000
 VLT  O    C    C10  125.58  3.000
 VLT  HXT  OXT  C    109.98  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
 VLT  CONST_01  C9   C7   C5   C4      0.00   0.0  0
 VLT  CONST_02  C9   C8   C6   C4      0.00   0.0  0
 VLT  CONST_03  C8   C6   C4   C5      0.00   0.0  0
 VLT  CONST_04  C8   C9   C7   C5      0.00   0.0  0
 VLT  CONST_05  C7   C5   C4   C6      0.00   0.0  0
 VLT  CONST_06  C7   C9   C8   C6      0.00   0.0  0
 VLT  CONST_07  C7   C5   C4   C3    180.00   0.0  0
 VLT  CONST_08  C8   C6   C4   C3    180.00   0.0  0
 VLT  CONST_09  O1   C9   C7   C5    180.00   0.0  0
 VLT  CONST_10  O1   C9   C8   C6    180.00   0.0  0
 VLT  CONST_11  H8   C7   C5   C4    180.00   0.0  0
 VLT  CONST_12  H9   C8   C6   C4    180.00   0.0  0
 VLT  CONST_13  H7   C6   C4   C5    180.00   0.0  0
 VLT  CONST_14  H6   C5   C4   C6    180.00   0.0  0
 VLT  CONST_15  HXT  OXT  C    C10   180.00   0.0  0
 VLT  Var_01    C5   C4   C3   CA     94.35  30.0  2
 VLT  Var_02    C    C10  C2   CA   -179.32   0.0  2
 VLT  Var_03    O    C    C10  C2     -0.06  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
 VLT  chir_01  CA  N  C2  C3  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
 VLT  plan-1  C3   0.020
 VLT  plan-1  C4   0.020
 VLT  plan-1  C5   0.020
 VLT  plan-1  C6   0.020
 VLT  plan-1  C7   0.020
 VLT  plan-1  C8   0.020
 VLT  plan-1  C9   0.020
 VLT  plan-1  O1   0.020
 VLT  plan-1  H6   0.020
 VLT  plan-1  H7   0.020
 VLT  plan-1  H8   0.020
 VLT  plan-1  H9   0.020
 VLT  plan-2  C10  0.020
 VLT  plan-2  C    0.020
 VLT  plan-2  O    0.020
 VLT  plan-2  OXT  0.020
 VLT  plan-2  HXT  0.020
 VLT  plan-3  CA   0.020
 VLT  plan-3  C2   0.020
 VLT  plan-3  C10  0.020
 VLT  plan-3  C    0.020
 VLT  plan-3  H3   0.020
 VLT  plan-3  H11  0.020

