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custom-interactions.yaml
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custom-interactions.yaml
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---
### User defined interactions YAML file
### For full documentation and description see:
### https://github.com/n-szulc/fingeRNAt/blob/master/README.md
### -> user-defined-interactions
### To use include a given interaction in the detection procedure,
### just umcomment the desired block.
### you can validate this yaml file for correct syntax at
### http://www.yamllint.com/
### ------------------------------------------------------------------- ###
#
# __ _ _ _
# / | | (_) | |
# `| | __| |_ ___| |_ __ _ _ __ ___ ___
# | | / _` | / __| __/ _` | '_ \ / __/ _ \
# _| |__ | (_| | \__ \ || (_| | | | | (_| __/
# \___(_) \__,_|_|___/\__\__,_|_| |_|\___\___|
#
#
### POINT-POINT INTERACTIONS, DISTANCE ONLY
### provide two SMARTS patterns defining two atoms
### and min and max distance between them
### any contact between NA and ligand (finds all atoms but hydrogens)
#
any_contact:
Receptor_SMARTS:
- '[!#1]'
Ligand_SMARTS:
- '[!#1]'
Distance:
min: 0.5
max: 3.5
### cation - anion interactions, with atoms having explicit charges
#
cation-anion_explicit:
Receptor_SMARTS:
- '[-]'
Ligand_SMARTS:
- '[+]'
Distance:
min: 0.5
max: 5.5
### Nucleic acid - amino-acid
### any contact between any nucleic acid atom and amino acid war-head moiety
### as a ligand
#
NA-AA:
Receptor_SMARTS:
- '[!#1]'
Ligand_SMARTS:
- '[NX3,NX4+][CX4H]([*])[CX3](=[OX1])[O,N]'
Distance:
min: 0.5
max: 3.5
### polar interactions, i.e., hydrogen bonds without angle restraints
### hydrogen not included
polar_Don-Lig__Acc-NA:
Receptor_SMARTS:
- '[!$([#1,#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]'
Ligand_SMARTS:
- '[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]'
Distance:
min: 0.5
max: 3.5
### polar interactions, i.e., hydrogen bonds without angle restraints
### hydrogen not included
polar_Don-NA__Acc:Lig:
Receptor_SMARTS:
- '[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]'
Ligand_SMARTS:
- '[!$([#1,#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]'
Distance:
min: 0.5
max: 3.5
### weak polar interactions, i.e., weak hydrogen bonds without angle restraints
### C–H···O interaction
### J. Am. Chem. Soc. 1999, 121, 9411-9422
### Fundamental Properties of the CH‚‚‚O Interaction: Is It a True
### Hydrogen Bond;
### and
### PROTEINS: Structure, Function, and Bioinformatics 67:128–141 (2007)
### SMARTS od fonor includes H, receptor should not
weak_polar_Don-Lig__Acc-NA:
Receptor_SMARTS:
- '[!$([#1,#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]'
Ligand_SMARTS:
- '[#1;$([#1]-[C])]' # hydrogen connected to carbon
Distance:
min: 0.5
max: 3.05
### weak polar interactions, i.e., weak hydrogen bonds without angle restraints
### C–H···O interaction
#
weak_polar_Don-NA__Acc-Lig:
Receptor_SMARTS:
- '[#1;$([#1]-[C])]' # hydrogen connected to carbon
Ligand_SMARTS:
- '[!$([#1,#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]'
Distance:
min: 0.5
max: 3.05
### carbonyl-carbonyl
### Acta Cryst. (1998). B54, 320-329 doi: 10.1107/S0108768198001463
### J Mol Biol. 2017 Feb 3; 429(3): 365–371. doi: 10.1016/j.jmb.2016.12.004
### n→π* Interactions Are Competitive with Hydrogen Bonds.
### DOI:10.1021/acs.orglett.6b01655Corpus ID: 45227553
#
carbonyl_interaction:
Receptor_SMARTS:
- '[$([OH0]=[CX3,c]);!$([OH0]=[CX3,c]-[OH,O-])]' # carbonyl oxygen
Ligand_SMARTS:
- '[$([CX3,c]=[OH0]);!$([CX3,c](=[OH0])-[OH,O-])]' # carbonyl carbon
Distance:
min: 0.5 # minimum distance cutoff, Å
max: 3.6 # maximum distance cutoff, Å
# ### ---------------------------------------------------------------------- ###
# _____ _ _ _ _
# / __ \ | (_) | | _ | |
# `' / /' __| |_ ___| |_ _| |_ __ _ _ __ __ _| | ___
# / / / _` | / __| __| |_ _| / _` | '_ \ / _` | |/ _ \
# ./ /____ | (_| | \__ \ |_ |_| | (_| | | | | (_| | | __/
# \_____(_) \__,_|_|___/\__| \__,_|_| |_|\__, |_|\___|
# __/ |
# |___/
### POINT-POINT INTERACTIONS, DISTANCE AND ANGLE
### weak hydrogen bonds (C–H···O interaction) with an angle term
### J. Am. Chem. Soc. 1999, 121, 9411-9422
### Fundamental Properties of the CH‚‚‚O Interaction: Is It a True
### Hydrogen Bond;
### and
### PROTEINS: Structure, Function, and Bioinformatics 67:128–141 (2007)
### SMARTS od donor includes H, receptor should not
### Nucleic acid as donor, ligand as acceptor
weak_hbond_Don-NA__Acc-Lig:
Receptor_SMARTS:
- '[#6!H0]' # C in hydrogen bond donor
- '[#1;$([#1]-[C])]' # hydrogen connected to C
Ligand_SMARTS:
- '[!$([#1,#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]' # HBA
Distance:
# H···O
min: 0.5
max: 3.05
Angle1:
# PROTEINS: Structure, Function, and Bioinformatics 67:128–141 (2007)
# C–H···O
min: 90
max: 180
### Nucleic acid as acceptor, ligand as donor
weak_hbond_Don-Lig__Acc-NA:
Receptor_SMARTS:
- '[!$([#1,#6,F,Cl,Br,I,o,s,nX3,#7v5,#15v5,#16v4,#16v6,*+1,*+2,*+3])]' # HBA
Ligand_SMARTS:
- '[#1;$([#1]-[C])]' # hydrogen connected to C
- '[#6!H0]' # C in hydrogen bond donor
Distance:
# H···O
min: 0.5
max: 3.05
Angle1:
# PROTEINS: Structure, Function, and Bioinformatics 67:128–141 (2007)
# C–H···O
min: 90
max: 180
# ### ---------------------------------------------------------------------- ###
# _____ _ _ _ _____ _
# |____ | | (_) | | _ / __ \ | |
# / / __| |_ ___| |_ _| |_ `' / /' __ _ _ __ __ _| | ___ ___
# \ \ / _` | / __| __| |_ _| / / / _` | '_ \ / _` | |/ _ \/ __|
# .___/ / | (_| | \__ \ |_ |_| ./ /___ | (_| | | | | (_| | | __/\__ \
# \____(_) \__,_|_|___/\__| \_____/ \__,_|_| |_|\__, |_|\___||___/
# __/ |
# |___/
### POINT-POINT INTERACTIONS, DISTANCE AND TWO ANGLES
### multipolar halogen interaction
### O=C⋯X-A
### "Related to, but distinct from halogen bonds are multipolar interactions
### between halogen atoms and carbonyl carbon or amide nitrogen"
### Medchemcomm. 2017 Oct 1; 8(10): 1970–1981. Published online
### 2017 Sep 26. doi: 10.1039/c7md00381a
multipolar_halogen_bond:
Receptor_SMARTS:
# carbonyl oxygen (non bodning)
- '[$([OH0]=[CX3,c]);!$([OH0]=[CX3,c]-[OH,O-])]'
# carbonyl carbon, forms the bond
- '[$([CX3,c]=[OH0]);!$([CX3,c](=[OH0])-[OH,O-])]'
Ligand_SMARTS:
- '[F,Cl,Br,I]' # halogen, forms the bond
- '[#6]' # any carbon atom connected to the halogen
Distance:
min: 0.5
max: 3.65
Angle1:
min: 70 # receptor, teta2 - O=C⋯X
max: 110 # receptor, teta2 - O=C⋯X
Angle2:
min: 90 # ligand, teta1 - C⋯X-#6
max: 180 # ligand, teta1 - C⋯X-#6
...