Refining peptides with beta-amino acids
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@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
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 : [email protected]
Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Mon, Jun 26, 2023 at 3:00 PM Bram Mylemans
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@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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participants (2)
-
Bram Mylemans -
Nigel Moriarty