[phenixbb] Refining peptides with beta-amino acids
Nigel Moriarty
nwmoriarty at lbl.gov
Mon Jun 26 18:47:21 PDT 2023
Bram
The planarity of the link in based on linking not the restraints included.
I have added B3L (in 1.21) and updated the linking (1.21). I can take a
look if you send me the model but you will likely need to down a 1.21
version.
https://phenix-online.org/download/nightly_builds.cgi
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Mon, Jun 26, 2023 at 3:00 PM Bram Mylemans <bram.mylemans at bristol.ac.uk>
wrote:
> Dear experts,
>
>
>
> I’m trying to refine a crystal structure of a peptide that contains some
> beta-amino acids. I have tried generating restraints with elbow from a sdf
> file. I changed the naming of the atoms to conform with the protein naming
> and added the L-peptide linking tag. This seems to work for refining and
> also local refine in coot works.
>
>
>
> However, the peptide bond is not kept planar. Does anyone have an idea how
> to make sure the amide bond is correctly constrained?
>
>
>
> I have included the restrained file I made for L-beta-Leucine below for
> reference.
>
>
>
> Best wishes,
>
> ----------
>
> Dr. Bram Mylemans
>
>
>
> Post-doctoral Research Associate
>
> Woolfson group
>
>
>
> School of Chemistry
>
> University of Bristol
>
>
>
>
>
> # electronic Ligand Builder and Optimisation Workbench (eLBOW)
>
> # - a module of PHENIX version 1.20.1-4487-
>
> # - file written: Sun May 14 14:31:25 2023
>
> #
>
> # Inital geometry file: a 60 line input string
>
> # Ligand name: (3S)-3-amino-5-methylhexanoic acid
>
> # Quantum optimisation: True
>
> # Method: uhf
>
> # Random seed: 3628800
>
> # SMILES string: CC(C)C[C at H](N)CC(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
>
> B3L B3L '(3S)-3-amino-5-methylhexanoic acid' L-peptide 24 10 .
>
> #
>
> data_comp_B3L
>
> #
>
> 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
>
> B3L O O O 0 -0.621 -0.0468 -0.0672 0.0379
>
> B3L C C C 0 0.403 1.2030 -0.0409 -0.0524
>
> B3L CA C CH2 0 -0.215 2.0004 0.0099 1.2717
>
> B3L CB C CH1 0 0.109 1.5936 -1.1463 2.1941
>
> B3L N N NH2 0 -0.452 2.4198 -2.3233 1.9111
>
> B3L CG C CH2 0 -0.173 1.7636 -0.6462 3.6485
>
> B3L CD C CH1 0 -0.040 1.5804 -1.7407 4.6994
>
> B3L CE2 C CH3 0 -0.160 1.9937 -1.1916 6.0651
>
> B3L CE1 C CH3 0 -0.159 0.1402 -2.2497 4.7124
>
> B3L HA H HCH2 0 0.055 3.0941 0.0115 1.0876
>
> B3L HAA H HCH2 0 0.036 1.7870 0.9871 1.7352
>
> B3L HB H HCH1 0 0.088 0.5145 -1.4120 2.0199
>
> B3L HN H HNH2 0 0.153 1.9179 -3.1939 1.9355
>
> B3L HG H HCH2 0 0.049 2.7650 -0.1815 3.7540
>
> B3L HGA H HCH2 0 0.063 1.0542 0.1844 3.8432
>
> B3L HD H HCH1 0 0.048 2.2575 -2.6020 4.4708
>
> B3L H3E2 H HCH3 0 0.033 2.4606 -1.9617 6.6915
>
> B3L H2E2 H HCH3 0 0.049 2.7302 -0.3796 5.9910
>
> B3L H1E2 H HCH3 0 0.045 1.1543 -0.7788 6.6358
>
> B3L H3E1 H HCH3 0 0.045 0.0304 -3.1957 4.1675
>
> B3L H2E1 H HCH3 0 0.034 -0.2410 -2.4354 5.7240
>
> B3L H1E1 H HCH3 0 0.068 -0.5687 -1.5528 4.2450
>
> B3L OXT O OC -1 -0.606 1.8564 -0.0003 -1.1279
>
> B3L HNA H HNH2 0 0.147 3.2587 -2.3840 2.4671
>
> #
>
> 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
>
> B3L C O single 1.253 0.015
>
> B3L C OXT single 1.259 0.016
>
> B3L CA C single 1.546 0.037
>
> B3L CB CA single 1.534 0.036
>
> B3L CB HB single 1.125 0.040
>
> B3L N CB single 1.466 0.036
>
> B3L N HNA single 1.008 0.037
>
> B3L CG CB single 1.547 0.037
>
> B3L CG HG single 1.109 0.039
>
> B3L CD CG single 1.528 0.035
>
> B3L CD CE1 single 1.528 0.035
>
> B3L CE2 CD single 1.529 0.035
>
> B3L CE2 H1E2 single 1.096 0.038
>
> B3L CE1 H1E1 single 1.098 0.038
>
> B3L CE1 H3E1 single 1.097 0.038
>
> B3L HA CA single 1.109 0.037
>
> B3L HAA CA single 1.102 0.040
>
> B3L HN N single 1.005 0.037
>
> B3L HGA CG single 1.110 0.039
>
> B3L HD CD single 1.119 0.040
>
> B3L H3E2 CE2 single 1.097 0.038
>
> B3L H2E2 CE2 single 1.099 0.038
>
> B3L H2E1 CE1 single 1.097 0.038
>
> #
>
> 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
>
> B3L OXT C CA 117.56 2.401
>
> B3L CA C O 116.95 2.270
>
> B3L OXT C O 125.42 1.837
>
> B3L HAA CA HA 105.03 2.935
>
> B3L HAA CA CB 111.34 2.722
>
> B3L HA CA CB 111.25 2.583
>
> B3L HAA CA C 106.82 2.670
>
> B3L HA CA C 111.50 2.415
>
> B3L CB CA C 110.69 2.417
>
> B3L HB CB CG 109.11 2.657
>
> B3L CG CB N 112.27 2.657
>
> B3L HB CB N 108.74 2.657
>
> B3L CG CB CA 107.01 2.247
>
> B3L N CB CA 109.86 2.386
>
> B3L HB CB CA 109.83 2.388
>
> B3L HNA N HN 110.49 3.000
>
> B3L HN N CB 114.17 2.677
>
> B3L HNA N CB 114.27 2.682
>
> B3L HGA CG HG 104.29 2.953
>
> B3L HGA CG CD 109.80 2.649
>
> B3L HG CG CD 110.06 1.813
>
> B3L HGA CG CB 109.67 2.659
>
> B3L CD CG CB 113.69 2.657
>
> B3L HG CG CB 108.91 2.671
>
> B3L HD CD CE1 108.40 2.672
>
> B3L HD CD CE2 107.17 2.674
>
> B3L CE1 CD CE2 111.53 2.389
>
> B3L HD CD CG 109.76 2.723
>
> B3L CE2 CD CG 108.95 2.259
>
> B3L CE1 CD CG 110.95 2.656
>
> B3L H1E2 CE2 H2E2 105.67 2.934
>
> B3L H2E2 CE2 H3E2 105.78 2.934
>
> B3L H1E2 CE2 H3E2 107.05 2.933
>
> B3L H2E2 CE2 CD 112.73 2.662
>
> B3L H3E2 CE2 CD 111.91 2.665
>
> B3L H1E2 CE2 CD 113.17 2.686
>
> B3L H1E1 CE1 H2E1 106.00 2.935
>
> B3L H2E1 CE1 H3E1 106.10 2.936
>
> B3L H1E1 CE1 H3E1 105.73 2.935
>
> B3L H2E1 CE1 CD 113.07 2.437
>
> B3L H3E1 CE1 CD 112.17 2.708
>
> B3L H1E1 CE1 CD 113.17 2.649
>
> #
>
> 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
>
> B3L Var_01 CB CA C O 54.55 30.0 2
>
> B3L Var_02 CE1 CD CG CB -66.07 30.0 1
>
> B3L Var_03 H1E1 CE1 CD CG -19.34 30.0 3
>
> B3L Var_04 H1E2 CE2 CD CG 93.46 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
>
> B3L chir_01 CB CA N CG 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
>
> B3L plan-1 O 0.020
>
> B3L plan-1 C 0.020
>
> B3L plan-1 CA 0.020
>
> B3L plan-1 OXT 0.020
>
>
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