__  __    __   __  _____      _            _          _____ _          _ _ 
 |  \/  |   \ \ / / |  __ \    (_)          | |        / ____| |        | | |
 | \  / |_ __\ V /  | |__) | __ ___   ____ _| |_ ___  | (___ | |__   ___| | |
 | |\/| | '__|> <   |  ___/ '__| \ \ / / _` | __/ _ \  \___ \| '_ \ / _ \ | |
 | |  | | |_ / . \  | |   | |  | |\ V / (_| | ||  __/  ____) | | | |  __/ | |
 |_|  |_|_(_)_/ \_\ |_|   |_|  |_| \_/ \__,_|\__\___| |_____/|_| |_|\___V 2.1
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##############################################################################
#                                                                            #
#                   Open Babel file: phmodel.txt                             #
#                                                                            #
#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
#  Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison            #
#  Part of the Open Babel package, under the GNU General Public License (GPL)#
#                                                                            #
#  pH model data (used by phmodel.cpp:OBPhModel)                             #
#                                                                            #
# TRANSFORM: chemical transforms can be used to modify formal charges, bond  #
#            orders, and to delete atoms (i.e hydrogens). Changes are applied#
#        to vector bound atoms (use the [:#] SMARTS notation) and bonds      #
#            between vector bound atoms.                                     #
# SEEDCHARGE: used to seed partial charges.  Seed partial charges            #
#             are used as initial values in Gasteiger charge calculation     #
#                                                                            #
##############################################################################

#carboxylic acid							# pKa
#TRANSFORM O=CO[#1:1] >> O=CO						4.0 # pKa from acid (AH)
TRANSFORM O=C[OD1-0:1] >> O=C[O-:1]					4.0 # pKa from acid (AH)

#uncomment for vinylogous carboxylic acids (e.g. ascorbic acid)
TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O:1]=[C:2][C:3]=[C:4][O-:5]   4.0 # pKa from acid (AH)

#charged amine
TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]				10.0 # pKa from conjugated acid (BH+)

#imidazole: note pKa=7.0
#if you uncomment this, also uncomment the seedcharge statement below
TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1				7.0

#imine
TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6]				4.0 # pKa from conjugated acid (BH+)

#tetrazole
TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1	4.89 #pKa from acid (AH)
TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1	4.89 #pKa from acid (AH)
TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1		4.89 #pKa from acid (AH)

#azide (always apply these transformations)
TRANSFORM [ND1:1]~[ND2:2]~[ND1:3] >> [N-:1]=[N+:2]=[N-:3] 1E+10	    # azide ion
TRANSFORM [ND1:1]~[ND2:2]~[ND1:3]~* >> [N-:1]=[N+:2]=[N:3]-* 1E+10   # azide group
TRANSFORM [NH2:1]~[NH1:2]~[NH1:3]~* >> [N-:1]=[N+:2]=[N:3]-* 1E+10	# azide group
TRANSFORM [NH1:1]~[ND2:2]~[NH1:3]~* >> [N-:1]=[N+:2]=[N:3]-* 1E+10	# azide group

#nitro group (-NO2)
TRANSFORM [O:1]=[N:2]-[O:3] >> [O:1]=[N+:2]-[O-:3]  1E+10
TRANSFORM [O:1]-[N:2]-[O:3] >> [O:1]=[N+:2]-[O-:3]  1E+10

#hydroxamic acid
#TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1]				8.0
TRANSFORM O=CN[OD1-0:1]     >> O=CN[O-:1]				8.0

#sulfinic acid
TRANSFORM [SD3](=O)[OD1:1]   >> [SD3](=O)[O-:1]				2.0
TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1]			2.0

#sulfonic acid
TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]	-2.6
TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]	-2.6
#sulfuric acid (same as sulfonic acid...)
#TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]
#TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]

#guanidine or amidine
TRANSFORM [#6^2+0:1](=[N^2+0:2])(~[N^2:3])* >> [#6:1](=[N+1:2])(~[N:3])*		12.5

#phosphate ester
TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1]	2.0
#TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1]	2.0

# phosphonate
TRANSFORM [PD4](=O)([OD2])([!#8])[OD1:1] >> [PD4](=O)([OD2])([!#8])[O-:1]	2.2
# http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf

#phosphoric acid
#TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3]	2.12
TRANSFORM O=P([!D1])([O:1][#1:2])[OD1]       >> O=P([!D1])([O:1])O		2.12
TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2]	2.12
#phosphate

#
#	Amino acids
#									pKa sidechain
# aspartic acid
#TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O			3.8
TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1]		3.8 
TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1]     3.8 

# glutamic acid
#TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O		        4.3
TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1]		5.0
TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1]	5.0

# arginine
TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 	12.0
TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0

# lysine
TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 			10.5
TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 	        10.5

# histidine
TRANSFORM O=C(O)C(N)Cc1[nH0:1]c[nH]c1  >> O=C(O)C(N)Cc1[n+:1]c[nH]c1            6.08
TRANSFORM O=C(O)C(N)Cc1[nH]c[nH0:1]c1  >> O=C(O)C(N)Cc1[nH]c[n+:1]c1            6.08
TRANSFORM O=C(NCC=O)C(N)Cc1[nH0:1]c[nH]c1  >> O=C(NCC=O)C(N)Cc1[n+:1]c[nH]c1    6.08

# cysteine
TRANSFORM O=C(O)C(N)C[S:1]  >> O=C(O)C(N)C[S-:1]			 8.28
TRANSFORM O=C(NCC=O)C(N)C[S:1]  >> O=C(NCC=O)C(N)C[S-:1]		 8.28

# tyrosine
TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1  >> O=C(O)C(N)Cc1ccc([O-:1])cc1	        10.1
TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1  >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1    10.1

# old:
# histidine
#TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1
# uncomment for tryptophan
# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1
#, histidine pKa=6.0


#
#	Seeding partial charges for gasteiger calculation
#
#default charges
SEEDCHARGE [#6+]	1.0
SEEDCHARGE [#6-]	-1.0
SEEDCHARGE [#7+]	1.0
SEEDCHARGE [#7-]	-1.0
SEEDCHARGE [#8+]	1.0
SEEDCHARGE [#8-]	-1.0
SEEDCHARGE [#15+]	1.0
SEEDCHARGE [#15-]	-1.0
SEEDCHARGE [#16+]	1.0
SEEDCHARGE [#16-]	-1.0

#charges spread over multiple atoms
#carboxylic acid
SEEDCHARGE	C(=O)[O-]		0.0	-0.5	-0.5

#amines
SEEDCHARGE	[N+]		1.0
#tetrazole
SEEDCHARGE	[nD2]1[nD2][nD2][nD2]c1	-0.2	-0.2	-0.2   -0.2    -0.2

#sulfinic
SEEDCHARGE	[SD3](=O)[O-]		0.0	-0.5	-0.5
#sulfuric acid
SEEDCHARGE	[SD4](=O)(=O)([O-])[OH1]	0.0	-0.33	-0.33	-0.33	0.0
#sulfonic acid
SEEDCHARGE	[SD4]([D2])(~[OD1])(~[OD1])~[OD1]	0.0	0.0	-0.33	-0.33	-0.33

#guanidine
SEEDCHARGE	[#7^2]~[C^2](~[N^2])~[N^2]	0.33	0.0	0.33	0.33

#amidine
SEEDCHARGE	[#6]~[C^2](~[N^2])~[N^2]	0.0	0.0	0.5	0.5

#phosphoate ester
SEEDCHARGE	[PD4](=O)([OD2])([OD2])[OD1]	0.0	-0.5	0.0	0.0	-0.5
#phosphoric acid
SEEDCHARGE	O=P([!D1])([O-])[O-]	-0.66	0.0	0.0	-0.66	-0.66


#phosphuric acid
SEEDCHARGE	P(=O)(=O)([O-])[O-]	0.0	0.0	0.0     -0.5	-0.5
#phosphonic acid
SEEDCHARGE	[#6]P(~[OD1])(~[OD1])~[OD1]	0.0	0.0	-0.33  -0.33 -0.33

#hydroxamic acid
SEEDCHARGE	O=C[N;!$(N(C=O)C=O)][OD1]	-0.5	0.0	0.0	-0.5
SEEDCHARGE	O=CN([OD1])NC=O		-0.33	0.0	0.0	-0.33	0.0 0.0	-0.33

#imidazole: note pKa=7.0, histidine pKa=6.0
#if you uncomment this, also uncomment the transform statement above
SEEDCHARGE	[n+H]1c[nH]cc1		0.5	0.0	0.5	0.0	0.0

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DIR : / usr/ share/ openbabel/ 3.1.1/
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eqeqIonizations.txt File 4.76 KB 0644
gaff.dat File 330.66 KB 0644
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mmffs_tor.par File 54.54 KB 0644
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mmffvdw.par File 5.8 KB 0644
mpC.txt File 3.31 KB 0644
mr.txt File 4.03 KB 0644
patterns.txt File 3.67 KB 0644
phmodel.txt File 6.96 KB 0644
plugindefines.txt File 2.34 KB 0644
psa.txt File 2.36 KB 0644
qeq.txt File 3.02 KB 0644
resdata.txt File 14.35 KB 0644
rigid-fragments-index.txt File 154.25 KB 0644
rigid-fragments.txt File 1.85 MB 0644
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space-groups.txt File 103.4 KB 0644
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svgformat.script File 1.87 KB 0644
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