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;
; Shift model after Williamson & Asakura
; reimplements the model used in the TOTAL SHIFT program
;
; The next section describes all contributions considered in this model
; - the (linear) electric field effect
; - the ring current effect (using the Johnson-Bovey model)
; - the magnetic anisotropy of the peptide bond
; - the random coil shift of the amino acids
[ShiftModules]
key:type value:name
;
; module type identifier
;--------------------------------------------
HaighMallion ring_current
ElectricField electric_field_effect
Anisotropy anisotropy
RandomCoil random_coil_shift
[ElectricFieldEffect]
key:number value:first_atom value:second_atom value:epsilon1 value:epsilon2
@exclude_residue_field=true
;
; idx first atom expression 2nd atom expression epsilon1 epsilon2
;----------------------------------------------------------------------------------------------------------------------
0 "element(H) AND connectedTo((C))" "element(C)" 0.6 0.0
1 "element(H) AND connectedTo((N))" "element(N) AND connectedTo((-H)(-H)(-H)(-*))" 0.6 0.0
[HaighMallionRingCurrent]
@H_influenced_by_all_effectors=true
@HA_influenced_by_all_effectors=true
@use_cut_off=false
@cut_off=15.
@project_target_to_ring_plane=true
key:number value:residue_type value:intensity_factor value:ring_atoms
; number residue_type intensity_factor ring_atoms
;------------------------------------------------------------------
1 PHE 1.05 "CG CD2 CE2 CZ CE1 CD1"
2 TYR 0.92 "CG CD2 CE2 CZ CE1 CD1"
3 TRP1 1.04 "CD2 CE3 CZ3 CH2 CZ2 CE2"
4 TRP2 0.90 "CG CD2 CE2 NE1 CD1"
5 HIS 0.43 "CG ND1 CE1 NE2 CD2"
[RingCurrentTargets]
@all_hydrogens_are_targets=false
@correct_CA_shifts=true
@default_hydrogen_target_nucleus_factor=5.13
@negative_ringcurrent_factor=1.1
key:number value:name value:target_nucleus_factor
; number name target nucleus factor
;-------------------------------------------
1 CA 1.5
2 CB 1.0
3 C 1.0
4 N 1.0
5 H 7.058954
6 HA 5.13
7 1HA 5.13
8 2HA 5.13
9 3HA 5.13
10 HA1 5.13
11 HA2 5.13
12 HA3 5.13
13 1H 7.06
14 2H 7.06
15 3H 7.06
[Charges]
key:residue key:atom value:charge
@unit=ESU
@cut_off=6.0
;
; residue atom charge [ESU]
;--------------------------------
* C 1.6
* N -1.7
* O -2.3
* H 0.7
Ca Ca 9.6
[JB-Rings]
key:ring value:residue_name value:radius value:electrons value:name_list value:intensity
0 TRP 1.182e-10 3 CG,CD2,CE2,NE1,CD1 1.0
1 TRP 1.39e-10 3 CD2,CZ2,CZ3,CE3,CH2,CE2 1.0
2 PHE 1.39e-10 3 CG,CD2,CE2,CZ,CE1,CD1 1.0
3 TYR 1.39e-10 3 CG,CD2,CE2,CZ,CE1,CD1 1.0
4 HIS 1.182e-10 3 CB,CD2,NE2,CE1,ND1 1.0
[JB-ShiftAtoms]
key:number value:description
0 element(H)
[RandomCoilShifts]
key:residue key:atom value:shift
GLY H 8.35
GLY 1H 8.35
GLY 2H 8.35
GLY 3H 8.35
GLY 1HA 3.53
GLY 2HA 3.53
ALA H 8.04
ALA 1H 8.04
ALA 2H 8.04
ALA 3H 8.04
ALA HA 3.67
ALA 1HB 1.40
ALA 2HB 1.40
ALA 3HB 1.40
VAL H 7.83
VAL 1H 7.83
VAL 2H 7.83
VAL 3H 7.83
VAL HA 3.47
VAL HB 2.13
VAL 1HG1 0.96
VAL 2HG1 0.96
VAL 3HG1 0.96
VAL 1HG2 0.96
VAL 2HG2 0.96
VAL 3HG2 0.96
ILE H 7.80
ILE 1H 7.80
ILE 2H 7.80
ILE 3H 7.80
ILE HA 3.52
ILE HB 1.89
ILE 1HG2 0.94
ILE 2HG2 0.94
ILE 3HG2 0.94
ILE 1HG1 1.30
ILE 2HG1 1.30
ILE 1HD1 0.89
ILE 2HD1 0.89
ILE 3HD1 0.89
LEU H 7.94
LEU 1H 7.94
LEU 2H 7.94
LEU 3H 7.94
LEU HA 3.69
LEU 1HB 1.65
LEU 2HB 1.65
LEU HG 1.65
LEU 1HD1 0.92
LEU 2HD1 0.92
LEU 3HD1 0.92
LEU 1HD2 0.92
LEU 2HD2 0.92
LEU 3HD2 0.92
SER H 8.11
SER 3H 8.11
SER 2H 8.11
SER 1H 8.11
SER HA 3.82
SER 1HB 3.89
SER 2HB 3.89
SER HG 5.33
THR H 7.95
THR 1H 7.95
THR 2H 7.95
THR 3H 7.95
THR HA 3.70
THR HB 4.22
THR 1HG2 1.23
THR 2HG2 1.23
THR 3HG2 1.23
THR HG1 4.16
ASP H 8.14
ASP 1H 8.14
ASP 2H 8.14
ASP 3H 8.14
ASP HA 3.99
ASP 1HB 2.80
ASP 2HB 2.80
ASP HB1 2.80
ASP HB2 2.80
GLU H 8.22
GLU 1H 8.22
GLU 2H 8.22
GLU 3H 8.22
GLU HA 3.70
GLU 1HB 2.03
GLU 2HB 2.03
GLU 1HG 2.30
GLU 2HG 2.30
GLU HG1 2.30
GLU HG2 2.30
LYS H 8.09
LYS 1H 8.09
LYS 2H 8.09
LYS 3H 8.09
LYS HA 3.67
LYS 1HB 1.81
LYS 2HB 1.81
LYS 1HG 1.47
LYS 2HG 1.47
LYS 1HD 1.71
LYS 2HD 1.71
LYS 1HE 3.02
LYS 2HE 3.02
LYS 1HZ 7.52
LYS 2HZ 7.52
LYS 3HZ 7.52
ARG H 8.03
ARG 1H 8.03
ARG 2H 8.03
ARG 3H 8.03
ARG HA 3.69
ARG 1HB 1.85
ARG 2HB 1.85
ARG 1HG 1.72
ARG 2HG 1.72
ARG 1HD 3.31
ARG 2HD 3.31
ARG 1HH1 6.69
ARG 2HH1 6.69
ARG 1HH2 6.69
ARG 2HH2 6.69
ARG HE 7.32
ASN H 8.20
ASN 1H 8.20
ASN 2H 8.20
ASN 3H 8.20
ASN HA 4.09
ASN 1HB 2.80
ASN 2HB 2.80
ASN 1HD2 7.24
ASN 2HD2 7.24
GLN H 8.12
GLN 1H 8.12
GLN 2H 8.12
GLN 3H 8.12
GLN HA 3.69
GLN 1HB 2.08
GLN 2HB 2.08
GLN 1HG 2.38
GLN 2HG 2.38
GLN 1HE2 7.19
GLN 2HE2 7.06
MET H 8.08
MET 1H 8.08
MET 2H 8.08
MET 3H 8.08
MET HA 3.83
MET 1HB 2.08
MET 2HB 2.08
MET 1HG 2.63
MET 2HG 2.63
MET 1HE 2.13
MET 2HE 2.13
MET 3HE 2.13
CYS H 8.12
CYS 1H 8.12
CYS 2H 8.12
CYS 3H 8.12
CYS HA 3.90
CYS 1HB 3.16
CYS 2HB 3.16
TRP H 8.05
TRP 1H 8.05
TRP 2H 8.05
TRP 3H 8.05
TRP HA 4.01
TRP 1HB 3.26
TRP 2HB 3.26
TRP HE1 9.99
TRP HD1 7.24
TRP HE3 7.65
TRP HZ3 7.17
TRP HH2 7.24
TRP HZ2 7.50
PHE H 8.10
PHE 1H 8.10
PHE 2H 8.10
PHE 3H 8.10
PHE HA 3.97
PHE 1HB 3.11
PHE 2HB 3.11
PHE HD1 7.34
PHE HE1 7.34
PHE HD2 7.34
PHE HE2 7.34
PHE HZ 7.34
TYR H 7.92
TYR 1H 7.92
TYR 2H 7.92
TYR 3H 7.92
TYR HA 3.90
TYR 1HB 3.02
TYR 2HB 3.02
TYR HD1 7.15
TYR HE1 6.86
TYR HD2 7.15
TYR HE2 6.86
TYR HH 9.28
HIS H 8.22
HIS 1H 8.22
HIS 2H 8.22
HIS 3H 8.22
HIS HA 4.08
HIS 1HB 3.23
HIS 2HB 3.23
HIS HE1 8.12
HIS HD1 7.14
HIS HD2 7.11
PRO HA 3.77
PRO 1HB 2.16
PRO 2HB 2.16
PRO 1HG 2.03
PRO 2HG 2.03
PRO 1HD 3.65
PRO 2HD 3.65
[Anisotropy]
key:number value:description
0 "element(H) AND connectedTo(=O)"
|
