FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: N9GKQ

Calculation Name: 3E3P-A-Xray372

Preferred Name: Putative glycogen synthase kinase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3E3P

Chain ID: A

ChEMBL ID: CHEMBL2311227

UniProt ID: Q4QE15

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 337
LigandResidueName
LigandFragmentNumber 0
LigandCharge DLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5506244.348728
FMO2-HF: Nuclear repulsion 5368661.948352
FMO2-HF: Total energy -137582.400376
FMO2-MP2: Total energy -137979.227955


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:7:ALA)


Summations of interaction energy for fragment #1(A:7:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-0.9141.9040.154-1.151-1.8220.002
Interaction energy analysis for fragmet #1(A:7:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.011
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A9ALA0-0.023-0.0133.741-1.828-0.548-0.006-0.722-0.5530.001
4A10ASP-1-0.770-0.8616.4930.1960.1960.0000.0000.0000.000
5A11GLU-1-0.774-0.8368.8540.7560.7560.0000.0000.0000.000
6A12ARG10.8420.91411.0190.0680.0680.0000.0000.0000.000
7A13SER0-0.050-0.0718.238-0.021-0.0210.0000.0000.0000.000
8A14ARG10.8320.8926.989-0.967-0.9670.0000.0000.0000.000
9A15LYS10.8900.9287.945-0.309-0.3090.0000.0000.0000.000
10A16GLU-1-0.788-0.84310.7590.1360.1360.0000.0000.0000.000
11A17MET0-0.026-0.0122.761-0.507-0.1700.145-0.098-0.3840.000
12A18ASP-1-0.879-0.9388.5221.0241.0240.0000.0000.0000.000
13A19ARG10.7290.84110.467-0.232-0.2320.0000.0000.0000.000
14A20PHE0-0.026-0.02111.234-0.067-0.0670.0000.0000.0000.000
15A21GLN0-0.051-0.02711.3980.1200.1200.0000.0000.0000.000
16A22VAL00.0010.0068.630-0.049-0.0490.0000.0000.0000.000
17A23GLU-1-0.918-0.94012.0000.1610.1610.0000.0000.0000.000
18A34VAL0-0.001-0.00313.265-0.009-0.0090.0000.0000.0000.000
19A35GLN0-0.062-0.0308.6490.0080.0080.0000.0000.0000.000
20A36LEU00.0390.01413.0390.0010.0010.0000.0000.0000.000
21A37GLY00.0400.01114.2430.0200.0200.0000.0000.0000.000
22A38DLY10.8890.96214.946-0.141-0.1410.0000.0000.0000.000
23A39GLU-1-0.816-0.88815.2080.1790.1790.0000.0000.0000.000
24A40LYS10.8200.88611.857-0.508-0.5080.0000.0000.0000.000
25A41SER0-0.0260.00217.200-0.010-0.0100.0000.0000.0000.000
26A42THR00.0270.00319.739-0.014-0.0140.0000.0000.0000.000
27A43GLY0-0.0020.01620.639-0.014-0.0140.0000.0000.0000.000
28A44MET00.001-0.00120.563-0.009-0.0090.0000.0000.0000.000
29A45SER00.013-0.01719.0210.0150.0150.0000.0000.0000.000
30A46VAL00.0100.01815.290-0.006-0.0060.0000.0000.0000.000
31A47ALA0-0.015-0.00615.4290.0030.0030.0000.0000.0000.000
32A48ILE00.0000.0089.345-0.004-0.0040.0000.0000.0000.000
33A49LYS10.8280.87912.5840.0850.0850.0000.0000.0000.000
34A50LYS10.8700.9554.4571.1121.152-0.001-0.002-0.0380.000
35A51VAL0-0.008-0.01710.4260.0220.0220.0000.0000.0000.000
36A52ILE0-0.021-0.01111.935-0.050-0.0500.0000.0000.0000.000
37A53GLN0-0.012-0.02212.5930.0830.0830.0000.0000.0000.000
38A54ASP-1-0.779-0.85714.283-0.239-0.2390.0000.0000.0000.000
39A55PRO00.005-0.00616.1660.0200.0200.0000.0000.0000.000
40A56ARG10.8240.89218.2380.2010.2010.0000.0000.0000.000
41A57PHE0-0.048-0.01920.2710.0210.0210.0000.0000.0000.000
42A58ARG10.9840.98419.6620.0840.0840.0000.0000.0000.000
43A59ASN00.0330.02216.5780.0310.0310.0000.0000.0000.000
44A60ARG10.8670.88519.4960.0940.0940.0000.0000.0000.000
45A61GLU-1-0.774-0.85518.593-0.088-0.0880.0000.0000.0000.000
46A62LEU0-0.010-0.00816.2160.0090.0090.0000.0000.0000.000
47A63GLN0-0.055-0.03319.3260.0070.0070.0000.0000.0000.000
48A64ILE00.0090.01222.7340.0100.0100.0000.0000.0000.000
49A65MET00.0100.00020.1690.0070.0070.0000.0000.0000.000
50A66GLN0-0.041-0.03120.4510.0000.0000.0000.0000.0000.000
51A67ASP-1-0.803-0.88822.995-0.027-0.0270.0000.0000.0000.000
52A68LEU0-0.004-0.01125.7620.0050.0050.0000.0000.0000.000
53A69ALA0-0.029-0.00423.4260.0050.0050.0000.0000.0000.000
54A70VAL0-0.038-0.01425.5540.0070.0070.0000.0000.0000.000
55A71LEU0-0.041-0.01728.4960.0020.0020.0000.0000.0000.000
56A72HIS0-0.052-0.02827.0820.0050.0050.0000.0000.0000.000
57A73HIS00.0480.01829.6060.0020.0020.0000.0000.0000.000
58A74PRO00.0080.01330.2490.0010.0010.0000.0000.0000.000
59A75ASN0-0.047-0.03831.2980.0010.0010.0000.0000.0000.000
60A76ILE0-0.023-0.01426.289-0.005-0.0050.0000.0000.0000.000
61A77VAL0-0.054-0.01522.3880.0050.0050.0000.0000.0000.000
62A78GLN00.0550.02423.017-0.011-0.0110.0000.0000.0000.000
63A79LEU0-0.053-0.03017.3120.0010.0010.0000.0000.0000.000
64A80GLN0-0.010-0.01417.252-0.004-0.0040.0000.0000.0000.000
65A81SER0-0.054-0.04514.4980.0130.0130.0000.0000.0000.000
66A82TYR00.0470.02113.123-0.007-0.0070.0000.0000.0000.000
67A83PHE00.0030.0135.9930.0690.0690.0000.0000.0000.000
68A84TYR00.0250.0098.610-0.040-0.0400.0000.0000.0000.000
69A85THR00.0160.0143.575-0.0670.2870.010-0.121-0.2430.000
70A86LEU00.0100.0113.5630.3540.9340.008-0.200-0.3880.001
71A87GLY00.0400.0214.8720.0070.082-0.001-0.004-0.0690.000
72A88GLU-1-0.866-0.9434.962-1.290-1.138-0.001-0.004-0.1470.000
73A89ARG10.8530.8997.2740.5170.5170.0000.0000.0000.000
74A90ASP-1-0.815-0.9139.658-0.461-0.4610.0000.0000.0000.000
75A91ARG10.8910.9565.7830.7370.7370.0000.0000.0000.000
76A92ARG10.8210.8947.8080.3500.3500.0000.0000.0000.000
77A93ASP-1-0.841-0.8939.742-0.438-0.4380.0000.0000.0000.000
78A94ILE00.0370.0138.234-0.208-0.2080.0000.0000.0000.000
79A95TYR0-0.0160.0017.5480.1870.1870.0000.0000.0000.000
80A96LEU0-0.0070.0098.615-0.095-0.0950.0000.0000.0000.000
81A97ASN0-0.050-0.0376.6370.0210.0210.0000.0000.0000.000
82A98VAL00.0120.00110.3470.0430.0430.0000.0000.0000.000
83A99VAL00.0130.01112.185-0.001-0.0010.0000.0000.0000.000
84A100MET00.0250.02114.8330.0010.0010.0000.0000.0000.000
85A101GLU-1-0.738-0.84318.1740.0420.0420.0000.0000.0000.000
86A102TYR0-0.049-0.03219.431-0.011-0.0110.0000.0000.0000.000
87A103VAL00.0470.01721.4390.0100.0100.0000.0000.0000.000
88A104PRO00.0090.01223.467-0.006-0.0060.0000.0000.0000.000
89A105ASP-1-0.803-0.90324.4310.0000.0000.0000.0000.0000.000
90A106THR0-0.001-0.01625.783-0.002-0.0020.0000.0000.0000.000
91A107LEU00.0580.03028.6250.0010.0010.0000.0000.0000.000
92A108HIS0-0.018-0.00930.0090.0000.0000.0000.0000.0000.000
93A109ARG10.7660.88924.961-0.002-0.0020.0000.0000.0000.000
94A110CYS00.0240.02331.3670.0010.0010.0000.0000.0000.000
95A111CYS00.0420.01633.7970.0010.0010.0000.0000.0000.000
96A112ARG10.9040.95230.6120.0050.0050.0000.0000.0000.000
97A113ASN00.000-0.00532.318-0.001-0.0010.0000.0000.0000.000
98A114TYR0-0.085-0.04436.3960.0020.0020.0000.0000.0000.000
99A115TYR00.0970.03438.9930.0000.0000.0000.0000.0000.000
100A116ARG10.8790.93934.2240.0000.0000.0000.0000.0000.000
101A117ARG10.8220.90739.552-0.004-0.0040.0000.0000.0000.000
102A118GLN0-0.024-0.01242.6550.0010.0010.0000.0000.0000.000
103A119VAL0-0.0060.01243.1840.0000.0000.0000.0000.0000.000
104A120ALA00.0690.03543.044-0.001-0.0010.0000.0000.0000.000
105A121PRO0-0.035-0.01539.4800.0010.0010.0000.0000.0000.000
106A122PRO00.0200.00041.313-0.001-0.0010.0000.0000.0000.000
107A123PRO00.0510.01543.2500.0000.0000.0000.0000.0000.000
108A124ILE00.0280.02144.089-0.001-0.0010.0000.0000.0000.000
109A125LEU0-0.0030.00737.6890.0000.0000.0000.0000.0000.000
110A126ILE00.0180.00339.8230.0000.0000.0000.0000.0000.000
111A127LYS10.7660.87840.640-0.001-0.0010.0000.0000.0000.000
112A128VAL00.0550.02238.929-0.001-0.0010.0000.0000.0000.000
113A129PHE0-0.005-0.00435.0470.0000.0000.0000.0000.0000.000
114A130LEU00.0070.00536.998-0.001-0.0010.0000.0000.0000.000
115A131PHE00.0290.02238.966-0.002-0.0020.0000.0000.0000.000
116A132GLN0-0.013-0.04034.9680.0010.0010.0000.0000.0000.000
117A133LEU0-0.0120.00332.933-0.001-0.0010.0000.0000.0000.000
118A134ILE00.0120.01335.248-0.003-0.0030.0000.0000.0000.000
119A135ARG10.8040.88836.719-0.006-0.0060.0000.0000.0000.000
120A136SER0-0.085-0.04531.515-0.002-0.0020.0000.0000.0000.000
121A137ILE00.004-0.01133.050-0.002-0.0020.0000.0000.0000.000
122A138GLY00.0100.00234.533-0.002-0.0020.0000.0000.0000.000
123A139CYS0-0.0200.00033.3940.0000.0000.0000.0000.0000.000
124A140LEU0-0.021-0.01729.256-0.002-0.0020.0000.0000.0000.000
125A141HIS0-0.067-0.05232.967-0.001-0.0010.0000.0000.0000.000
126A142LEU00.0160.03635.8670.0000.0000.0000.0000.0000.000
127A143PRO00.019-0.00336.611-0.002-0.0020.0000.0000.0000.000
128A144SER0-0.039-0.01936.833-0.002-0.0020.0000.0000.0000.000
129A145VAL0-0.0370.00031.2230.0000.0000.0000.0000.0000.000
130A146ASN0-0.062-0.04432.264-0.004-0.0040.0000.0000.0000.000
131A147VAL0-0.011-0.00928.344-0.005-0.0050.0000.0000.0000.000
132A148CYS0-0.068-0.02430.8460.0030.0030.0000.0000.0000.000
133A149HIS0-0.007-0.01525.774-0.006-0.0060.0000.0000.0000.000
134A150ARG10.8250.87827.3560.0590.0590.0000.0000.0000.000
135A151ASP-1-0.718-0.80926.189-0.059-0.0590.0000.0000.0000.000
136A152ILE00.0180.02728.3500.0010.0010.0000.0000.0000.000
137A153LYS10.8500.90525.0850.0550.0550.0000.0000.0000.000
138A154PRO00.0380.01629.5600.0010.0010.0000.0000.0000.000
139A155HIS0-0.003-0.00426.1150.0020.0020.0000.0000.0000.000
140A156ASN0-0.031-0.00624.8720.0020.0020.0000.0000.0000.000
141A157VAL00.0160.00926.2660.0010.0010.0000.0000.0000.000
142A158LEU0-0.0060.00623.1260.0010.0010.0000.0000.0000.000
143A159VAL00.004-0.01027.5980.0000.0000.0000.0000.0000.000
144A160ASN0-0.035-0.01929.8800.0020.0020.0000.0000.0000.000
145A161GLU-1-0.847-0.91132.1380.0110.0110.0000.0000.0000.000
146A162ALA0-0.027-0.00835.027-0.001-0.0010.0000.0000.0000.000
147A163ASP-1-0.821-0.89633.7880.0290.0290.0000.0000.0000.000
148A164GLY00.0430.02236.577-0.001-0.0010.0000.0000.0000.000
149A165THR00.0130.01732.746-0.002-0.0020.0000.0000.0000.000
150A166LEU0-0.030-0.01131.537-0.001-0.0010.0000.0000.0000.000
151A167LYS10.8300.91126.892-0.022-0.0220.0000.0000.0000.000
152A168LEU0-0.0100.01627.831-0.002-0.0020.0000.0000.0000.000
153A169CYS0-0.058-0.04922.8140.0020.0020.0000.0000.0000.000
154A170ASP-1-0.807-0.89920.814-0.078-0.0780.0000.0000.0000.000
155A171PHE00.0720.03021.6640.0000.0000.0000.0000.0000.000
156A172GLY0-0.027-0.01220.776-0.006-0.0060.0000.0000.0000.000
157A173SER0-0.029-0.01221.519-0.011-0.0110.0000.0000.0000.000
158A174ALA0-0.0070.02424.6850.0030.0030.0000.0000.0000.000
159A175LYS10.7510.87025.9050.0560.0560.0000.0000.0000.000
160A176LYS10.8840.95028.3020.0440.0440.0000.0000.0000.000
161A177LEU0-0.0080.00230.968-0.004-0.0040.0000.0000.0000.000
162A178SER00.0500.01333.9970.0040.0040.0000.0000.0000.000
163A179PRO00.0410.01036.553-0.002-0.0020.0000.0000.0000.000
164A180SER0-0.0200.00137.712-0.001-0.0010.0000.0000.0000.000
165A181GLU-1-0.770-0.84930.658-0.073-0.0730.0000.0000.0000.000
166A182PRO00.0170.02434.5340.0010.0010.0000.0000.0000.000
167A183ASN0-0.076-0.05632.453-0.006-0.0060.0000.0000.0000.000
168A184VAL00.0410.03028.7540.0030.0030.0000.0000.0000.000
169A185ALA00.0780.03031.9900.0010.0010.0000.0000.0000.000
170A186TYR0-0.021-0.02126.6240.0040.0040.0000.0000.0000.000
171A187ILE0-0.049-0.02226.125-0.001-0.0010.0000.0000.0000.000
172A188CYS00.0310.05427.8020.0010.0010.0000.0000.0000.000
173A189SER0-0.031-0.05828.230-0.001-0.0010.0000.0000.0000.000
174A190ARG10.8530.92430.4230.0500.0500.0000.0000.0000.000
175A191TYR0-0.0070.00233.7710.0010.0010.0000.0000.0000.000
176A192TYR0-0.024-0.04332.0440.0010.0010.0000.0000.0000.000
177A193ARG10.8210.92231.8150.0530.0530.0000.0000.0000.000
178A194ALA00.0710.03836.0050.0020.0020.0000.0000.0000.000
179A195PRO00.0440.01438.904-0.003-0.0030.0000.0000.0000.000
180A196GLU-1-0.708-0.83139.120-0.032-0.0320.0000.0000.0000.000
181A197LEU0-0.049-0.02034.093-0.003-0.0030.0000.0000.0000.000
182A198ILE0-0.077-0.03537.200-0.004-0.0040.0000.0000.0000.000
183A199PHE0-0.029-0.01739.315-0.001-0.0010.0000.0000.0000.000
184A200GLY0-0.0020.00937.7480.0000.0000.0000.0000.0000.000
185A201ASN0-0.054-0.03738.7890.0000.0000.0000.0000.0000.000
186A202GLN0-0.028-0.01936.033-0.004-0.0040.0000.0000.0000.000
187A203HIS0-0.013-0.01536.934-0.002-0.0020.0000.0000.0000.000
188A204TYR00.0090.01032.9480.0010.0010.0000.0000.0000.000
189A205THR00.0290.00638.047-0.001-0.0010.0000.0000.0000.000
190A206THR00.0910.01635.066-0.002-0.0020.0000.0000.0000.000
191A207ALA00.0300.02636.9840.0010.0010.0000.0000.0000.000
192A208VAL0-0.004-0.00334.3810.0010.0010.0000.0000.0000.000
193A209ASP-1-0.696-0.82832.622-0.034-0.0340.0000.0000.0000.000
194A210ILE0-0.0020.00135.2630.0010.0010.0000.0000.0000.000
195A211TRP00.0330.03138.0900.0020.0020.0000.0000.0000.000
196A212SER0-0.026-0.01934.1390.0000.0000.0000.0000.0000.000
197A213VAL00.017-0.00235.1380.0010.0010.0000.0000.0000.000
198A214GLY00.0420.02637.0700.0020.0020.0000.0000.0000.000
199A215CYS0-0.066-0.03337.2520.0010.0010.0000.0000.0000.000
200A216ILE0-0.020-0.00732.8890.0010.0010.0000.0000.0000.000
201A217PHE0-0.011-0.00937.1200.0020.0020.0000.0000.0000.000
202A218ALA00.0320.01140.4230.0010.0010.0000.0000.0000.000
203A219GLU-1-0.778-0.87234.706-0.020-0.0200.0000.0000.0000.000
204A220MET0-0.038-0.02537.6090.0020.0020.0000.0000.0000.000
205A221MET0-0.0720.00239.7270.0020.0020.0000.0000.0000.000
206A222LEU0-0.0010.01041.9560.0000.0000.0000.0000.0000.000
207A223GLY0-0.004-0.01039.4900.0010.0010.0000.0000.0000.000
208A224GLU-1-1.003-1.00138.048-0.019-0.0190.0000.0000.0000.000
209A225PRO0-0.044-0.03535.3930.0000.0000.0000.0000.0000.000
210A226ILE00.0430.02938.178-0.001-0.0010.0000.0000.0000.000
211A227PHE00.0350.02239.7400.0000.0000.0000.0000.0000.000
212A228ARG10.9200.93736.6290.0280.0280.0000.0000.0000.000
213A229GLY00.0450.03039.2530.0000.0000.0000.0000.0000.000
214A230ASP-1-0.810-0.89437.108-0.038-0.0380.0000.0000.0000.000
215A231ASN0-0.040-0.02436.801-0.003-0.0030.0000.0000.0000.000
216A232SER00.0550.00937.7040.0010.0010.0000.0000.0000.000
217A233ALA00.0340.03039.0320.0010.0010.0000.0000.0000.000
218A234GLY00.0240.00441.8950.0020.0020.0000.0000.0000.000
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