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: 85VRY

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 OptHSide
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 -5494261.125851
FMO2-HF: Nuclear repulsion 5356679.477789
FMO2-HF: Total energy -137581.648063
FMO2-MP2: Total energy -137978.512308


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.
-1.0261.9890.952-1.509-2.4580.004
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 : 0.048 / q_NPA : 0.015
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].
3A9ALA0-0.014-0.0053.838-0.8210.251-0.005-0.650-0.4160.003
4A10ASP-1-0.774-0.8716.3930.1810.1810.0000.0000.0000.000
5A11GLU-1-0.780-0.8598.3530.6940.6940.0000.0000.0000.000
6A12ARG10.8370.90710.6970.0840.0840.0000.0000.0000.000
7A13SER0-0.050-0.0677.514-0.034-0.0340.0000.0000.0000.000
8A14ARG10.8520.9186.334-0.910-0.9100.0000.0000.0000.000
9A15LYS10.9190.9567.424-0.192-0.1920.0000.0000.0000.000
10A16GLU-1-0.818-0.89610.5490.1000.1000.0000.0000.0000.000
11A17MET0-0.016-0.0042.367-0.552-0.4760.906-0.243-0.7400.000
12A18ASP-1-0.890-0.9348.0800.8830.8830.0000.0000.0000.000
13A19ARG10.7480.86610.134-0.153-0.1530.0000.0000.0000.000
14A20PHE0-0.021-0.02810.992-0.053-0.0530.0000.0000.0000.000
15A21GLN0-0.082-0.03010.9170.1050.1050.0000.0000.0000.000
16A22VAL0-0.023-0.0108.749-0.043-0.0430.0000.0000.0000.000
17A23GLU-1-0.891-0.93511.8330.1150.1150.0000.0000.0000.000
18A34VAL0-0.008-0.00413.833-0.005-0.0050.0000.0000.0000.000
19A35GLN0-0.052-0.0218.4350.0090.0090.0000.0000.0000.000
20A36LEU00.0370.01512.8890.0050.0050.0000.0000.0000.000
21A37GLY00.0570.02413.8860.0130.0130.0000.0000.0000.000
22A38DLY10.8980.98514.833-0.084-0.0840.0000.0000.0000.000
23A39GLU-1-0.843-0.90714.9120.1130.1130.0000.0000.0000.000
24A40LYS10.8070.89311.651-0.380-0.3800.0000.0000.0000.000
25A41SER0-0.0260.00317.115-0.007-0.0070.0000.0000.0000.000
26A42THR00.0540.01919.716-0.008-0.0080.0000.0000.0000.000
27A43GLY00.0160.02020.513-0.010-0.0100.0000.0000.0000.000
28A44MET00.006-0.00520.454-0.008-0.0080.0000.0000.0000.000
29A45SER0-0.013-0.03418.3480.0140.0140.0000.0000.0000.000
30A46VAL00.0070.00014.692-0.006-0.0060.0000.0000.0000.000
31A47ALA0-0.014-0.00215.3480.0020.0020.0000.0000.0000.000
32A48ILE00.002-0.0089.235-0.002-0.0020.0000.0000.0000.000
33A49LYS10.8400.92312.3950.1300.1300.0000.0000.0000.000
34A50LYS10.9520.9925.1321.1491.1490.0000.0000.0000.000
35A51VAL0-0.016-0.01711.3890.0190.0190.0000.0000.0000.000
36A52ILE0-0.030-0.00911.806-0.045-0.0450.0000.0000.0000.000
37A53GLN0-0.002-0.00512.2590.0940.0940.0000.0000.0000.000
38A54ASP-1-0.770-0.85613.962-0.284-0.2840.0000.0000.0000.000
39A55PRO00.013-0.00116.1920.0190.0190.0000.0000.0000.000
40A56ARG10.8190.87918.2230.2310.2310.0000.0000.0000.000
41A57PHE0-0.047-0.02019.8940.0230.0230.0000.0000.0000.000
42A58ARG10.9981.00019.2230.1010.1010.0000.0000.0000.000
43A59ASN00.0230.00817.0860.0300.0300.0000.0000.0000.000
44A60ARG10.8960.92719.6000.1200.1200.0000.0000.0000.000
45A61GLU-1-0.787-0.86818.806-0.142-0.1420.0000.0000.0000.000
46A62LEU00.008-0.00116.1790.0110.0110.0000.0000.0000.000
47A63GLN0-0.029-0.01819.3650.0080.0080.0000.0000.0000.000
48A64ILE0-0.0030.00122.7440.0120.0120.0000.0000.0000.000
49A65MET00.000-0.00820.1310.0090.0090.0000.0000.0000.000
50A66GLN0-0.038-0.02819.8760.0030.0030.0000.0000.0000.000
51A67ASP-1-0.800-0.88022.966-0.050-0.0500.0000.0000.0000.000
52A68LEU0-0.020-0.01525.5000.0070.0070.0000.0000.0000.000
53A69ALA0-0.034-0.01223.2770.0060.0060.0000.0000.0000.000
54A70VAL0-0.027-0.01225.4170.0070.0070.0000.0000.0000.000
55A71LEU0-0.044-0.01928.2620.0040.0040.0000.0000.0000.000
56A72HIS0-0.068-0.02726.7130.0070.0070.0000.0000.0000.000
57A73HIS00.0510.02228.9990.0020.0020.0000.0000.0000.000
58A74PRO00.0220.01929.754-0.001-0.0010.0000.0000.0000.000
59A75ASN0-0.036-0.03831.0090.0010.0010.0000.0000.0000.000
60A76ILE0-0.045-0.01726.314-0.006-0.0060.0000.0000.0000.000
61A77VAL0-0.0410.00022.5680.0040.0040.0000.0000.0000.000
62A78GLN00.0500.02722.799-0.011-0.0110.0000.0000.0000.000
63A79LEU0-0.046-0.02317.113-0.001-0.0010.0000.0000.0000.000
64A80GLN0-0.004-0.00216.7700.0030.0030.0000.0000.0000.000
65A81SER0-0.052-0.05513.6150.0090.0090.0000.0000.0000.000
66A82TYR00.0400.02512.791-0.006-0.0060.0000.0000.0000.000
67A83PHE00.0140.0145.8100.0700.0700.0000.0000.0000.000
68A84TYR00.0390.0168.465-0.027-0.0270.0000.0000.0000.000
69A85THR0-0.008-0.0043.369-0.1600.2860.027-0.144-0.3300.000
70A86LEU00.008-0.0023.3070.1251.1440.026-0.431-0.6140.001
71A87GLY0-0.0060.0024.211-0.1760.036-0.001-0.035-0.1760.000
72A88GLU-1-0.903-0.9484.809-2.165-1.975-0.001-0.006-0.1820.000
73A89ARG10.8750.9127.5850.6940.6940.0000.0000.0000.000
74A90ASP-1-0.827-0.9259.692-0.473-0.4730.0000.0000.0000.000
75A91ARG10.8890.9515.7150.7910.7910.0000.0000.0000.000
76A92ARG10.8030.8957.6890.4380.4380.0000.0000.0000.000
77A93ASP-1-0.841-0.8999.752-0.539-0.5390.0000.0000.0000.000
78A94ILE00.0400.0168.079-0.268-0.2680.0000.0000.0000.000
79A95TYR0-0.022-0.0107.2650.1930.1930.0000.0000.0000.000
80A96LEU0-0.0040.0038.624-0.081-0.0810.0000.0000.0000.000
81A97ASN0-0.060-0.0446.7640.0330.0330.0000.0000.0000.000
82A98VAL00.009-0.00610.3750.0470.0470.0000.0000.0000.000
83A99VAL00.0180.02111.803-0.005-0.0050.0000.0000.0000.000
84A100MET00.0240.01714.4490.0080.0080.0000.0000.0000.000
85A101GLU-1-0.762-0.85718.0080.0000.0000.0000.0000.0000.000
86A102TYR0-0.016-0.01819.336-0.011-0.0110.0000.0000.0000.000
87A103VAL00.0340.01121.2150.0110.0110.0000.0000.0000.000
88A104PRO00.0140.01323.250-0.007-0.0070.0000.0000.0000.000
89A105ASP-1-0.811-0.90324.221-0.027-0.0270.0000.0000.0000.000
90A106THR00.0060.00025.918-0.002-0.0020.0000.0000.0000.000
91A107LEU00.0620.02328.4430.0030.0030.0000.0000.0000.000
92A108HIS00.0030.00529.9850.0010.0010.0000.0000.0000.000
93A109ARG10.7730.87825.2150.0340.0340.0000.0000.0000.000
94A110CYS00.0120.03031.4340.0020.0020.0000.0000.0000.000
95A111CYS00.0380.01033.8050.0020.0020.0000.0000.0000.000
96A112ARG10.9130.95730.4820.0330.0330.0000.0000.0000.000
97A113ASN0-0.010-0.01832.650-0.001-0.0010.0000.0000.0000.000
98A114TYR0-0.060-0.04336.6590.0020.0020.0000.0000.0000.000
99A115TYR00.0770.02439.3520.0010.0010.0000.0000.0000.000
100A116ARG10.8800.94634.0480.0220.0220.0000.0000.0000.000
101A117ARG10.8350.91739.9560.0130.0130.0000.0000.0000.000
102A118GLN0-0.020-0.00442.9130.0020.0020.0000.0000.0000.000
103A119VAL0-0.0090.00843.2850.0010.0010.0000.0000.0000.000
104A120ALA00.0580.02743.139-0.001-0.0010.0000.0000.0000.000
105A121PRO0-0.039-0.01639.5600.0020.0020.0000.0000.0000.000
106A122PRO00.0210.00341.4700.0000.0000.0000.0000.0000.000
107A123PRO00.0660.02143.366-0.001-0.0010.0000.0000.0000.000
108A124ILE00.0280.02243.937-0.001-0.0010.0000.0000.0000.000
109A125LEU00.0050.01337.6960.0000.0000.0000.0000.0000.000
110A126ILE00.0140.00340.040-0.001-0.0010.0000.0000.0000.000
111A127LYS10.7620.86841.0430.0110.0110.0000.0000.0000.000
112A128VAL00.0430.01338.766-0.001-0.0010.0000.0000.0000.000
113A129PHE0-0.006-0.01435.172-0.001-0.0010.0000.0000.0000.000
114A130LEU00.0070.00936.924-0.002-0.0020.0000.0000.0000.000
115A131PHE00.0330.02538.917-0.002-0.0020.0000.0000.0000.000
116A132GLN0-0.016-0.04234.9920.0000.0000.0000.0000.0000.000
117A133LEU0-0.020-0.00132.999-0.002-0.0020.0000.0000.0000.000
118A134ILE00.0090.00535.384-0.003-0.0030.0000.0000.0000.000
119A135ARG10.8230.91236.4880.0120.0120.0000.0000.0000.000
120A136SER0-0.092-0.04531.533-0.002-0.0020.0000.0000.0000.000
121A137ILE00.022-0.01033.259-0.002-0.0020.0000.0000.0000.000
122A138GLY00.0030.00434.823-0.001-0.0010.0000.0000.0000.000
123A139CYS0-0.0160.00833.7010.0000.0000.0000.0000.0000.000
124A140LEU0-0.003-0.00629.138-0.002-0.0020.0000.0000.0000.000
125A141HIS0-0.074-0.04732.9760.0000.0000.0000.0000.0000.000
126A142LEU00.0170.03235.9720.0010.0010.0000.0000.0000.000
127A143PRO00.0240.00336.318-0.003-0.0030.0000.0000.0000.000
128A144SER0-0.021-0.01536.267-0.002-0.0020.0000.0000.0000.000
129A145VAL0-0.039-0.00430.960-0.001-0.0010.0000.0000.0000.000
130A146ASN0-0.056-0.03332.098-0.004-0.0040.0000.0000.0000.000
131A147VAL0-0.028-0.02028.112-0.006-0.0060.0000.0000.0000.000
132A148CYS0-0.077-0.02330.9870.0040.0040.0000.0000.0000.000
133A149HIS0-0.008-0.02326.266-0.006-0.0060.0000.0000.0000.000
134A150ARG10.8180.88027.4180.0850.0850.0000.0000.0000.000
135A151ASP-1-0.715-0.81926.743-0.091-0.0910.0000.0000.0000.000
136A152ILE00.0260.03728.679-0.001-0.0010.0000.0000.0000.000
137A153LYS10.8510.89725.8180.0890.0890.0000.0000.0000.000
138A154PRO00.0370.02429.9660.0000.0000.0000.0000.0000.000
139A155HIS0-0.027-0.02926.3380.0010.0010.0000.0000.0000.000
140A156ASN0-0.060-0.01925.385-0.003-0.0030.0000.0000.0000.000
141A157VAL00.0360.02326.7060.0010.0010.0000.0000.0000.000
142A158LEU0-0.041-0.01823.2470.0000.0000.0000.0000.0000.000
143A159VAL00.0280.00227.8590.0010.0010.0000.0000.0000.000
144A160ASN0-0.0210.00229.9120.0000.0000.0000.0000.0000.000
145A161GLU-1-0.839-0.91831.902-0.009-0.0090.0000.0000.0000.000
146A162ALA0-0.025-0.00134.7450.0000.0000.0000.0000.0000.000
147A163ASP-1-0.846-0.93433.6230.0070.0070.0000.0000.0000.000
148A164GLY00.0430.03236.0160.0000.0000.0000.0000.0000.000
149A165THR00.0020.01232.344-0.002-0.0020.0000.0000.0000.000
150A166LEU0-0.022-0.01031.473-0.002-0.0020.0000.0000.0000.000
151A167LYS10.8310.91126.7090.0100.0100.0000.0000.0000.000
152A168LEU0-0.0120.00928.057-0.003-0.0030.0000.0000.0000.000
153A169CYS00.001-0.01422.9100.0010.0010.0000.0000.0000.000
154A170ASP-1-0.850-0.91721.255-0.123-0.1230.0000.0000.0000.000
155A171PHE00.0760.02722.0250.0010.0010.0000.0000.0000.000
156A172GLY0-0.044-0.03520.966-0.007-0.0070.0000.0000.0000.000
157A173SER0-0.0150.00221.618-0.014-0.0140.0000.0000.0000.000
158A174ALA00.0060.03024.8050.0070.0070.0000.0000.0000.000
159A175LYS10.7390.84525.9830.0770.0770.0000.0000.0000.000
160A176LYS10.8770.94728.0280.0690.0690.0000.0000.0000.000
161A177LEU0-0.033-0.01031.022-0.003-0.0030.0000.0000.0000.000
162A178SER00.0490.01433.9250.0050.0050.0000.0000.0000.000
163A179PRO00.0460.01136.335-0.002-0.0020.0000.0000.0000.000
164A180SER00.0020.00336.6000.0000.0000.0000.0000.0000.000
165A181GLU-1-0.834-0.88930.589-0.093-0.0930.0000.0000.0000.000
166A182PRO00.0150.02634.7050.0010.0010.0000.0000.0000.000
167A183ASN0-0.072-0.05332.368-0.010-0.0100.0000.0000.0000.000
168A184VAL00.0540.03729.0090.0030.0030.0000.0000.0000.000
169A185ALA00.0650.02932.3950.0020.0020.0000.0000.0000.000
170A186TYR0-0.030-0.03526.6000.0040.0040.0000.0000.0000.000
171A187ILE0-0.039-0.01426.214-0.003-0.0030.0000.0000.0000.000
172A188CYS00.0170.05028.183-0.001-0.0010.0000.0000.0000.000
173A189SER0-0.020-0.04728.873-0.001-0.0010.0000.0000.0000.000
174A190ARG10.8410.90530.9420.0730.0730.0000.0000.0000.000
175A191TYR0-0.018-0.01134.3440.0020.0020.0000.0000.0000.000
176A192TYR0-0.045-0.05332.5950.0010.0010.0000.0000.0000.000
177A193ARG10.8490.93232.0360.0760.0760.0000.0000.0000.000
178A194ALA00.0660.03136.5100.0020.0020.0000.0000.0000.000
179A195PRO00.0480.01539.374-0.003-0.0030.0000.0000.0000.000
180A196GLU-1-0.712-0.83639.712-0.048-0.0480.0000.0000.0000.000
181A197LEU0-0.049-0.01834.615-0.003-0.0030.0000.0000.0000.000
182A198ILE0-0.081-0.03737.851-0.004-0.0040.0000.0000.0000.000
183A199PHE0-0.023-0.01639.8240.0000.0000.0000.0000.0000.000
184A200GLY0-0.0200.01038.1370.0000.0000.0000.0000.0000.000
185A201ASN0-0.056-0.03139.1850.0010.0010.0000.0000.0000.000
186A202GLN0-0.005-0.00836.276-0.006-0.0060.0000.0000.0000.000
187A203HIS0-0.001-0.00236.734-0.003-0.0030.0000.0000.0000.000
188A204TYR00.006-0.00432.9730.0010.0010.0000.0000.0000.000
189A205THR00.0450.00938.298-0.001-0.0010.0000.0000.0000.000
190A206THR00.1100.02234.914-0.002-0.0020.0000.0000.0000.000
191A207ALA00.0300.02337.0300.0000.0000.0000.0000.0000.000
192A208VAL0-0.017-0.01434.6720.0010.0010.0000.0000.0000.000
193A209ASP-1-0.714-0.84932.901-0.059-0.0590.0000.0000.0000.000
194A210ILE0-0.0120.00035.6420.0010.0010.0000.0000.0000.000
195A211TRP00.0250.02738.3330.0020.0020.0000.0000.0000.000
196A212SER0-0.016-0.00934.3460.0000.0000.0000.0000.0000.000
197A213VAL00.0240.00835.3800.0010.0010.0000.0000.0000.000
198A214GLY00.0260.01837.3590.0020.0020.0000.0000.0000.000
199A215CYS0-0.057-0.03937.6790.0010.0010.0000.0000.0000.000
200A216ILE0-0.0110.00633.4190.0000.0000.0000.0000.0000.000
201A217PHE00.003-0.00337.4500.0020.0020.0000.0000.0000.000
202A218ALA00.0380.01340.6370.0020.0020.0000.0000.0000.000
203A219GLU-1-0.799-0.88235.549-0.043-0.0430.0000.0000.0000.000
204A220MET0-0.075-0.03337.7270.0010.0010.0000.0000.0000.000
205A221MET0-0.070-0.00939.9560.0020.0020.0000.0000.0000.000
206A222LEU00.0080.02642.3790.0010.0010.0000.0000.0000.000
207A223GLY0-0.013-0.00939.9940.0010.0010.0000.0000.0000.000
208A224GLU-1-0.999-1.00138.548-0.036-0.0360.0000.0000.0000.000
209A225PRO0-0.050-0.03036.1490.0010.0010.0000.0000.0000.000
210A226ILE00.0600.03838.8830.0010.0010.0000.0000.0000.000
211A227PHE00.0160.00940.5470.0000.0000.0000.0000.0000.000
212A228ARG10.9570.97036.7830.0470.0470.0000.0000.0000.000
213A229GLY00.0550.03639.4140.0010.0010.0000.0000.0000.000
214A230ASP-1-0.833-0.90537.912-0.057-0.0570.0000.0000.0000.000
215A231ASN0-0.057-0.04337.503-0.003-0.0030.0000.0000.0000.000
216A232SER00.0670.01838.0950.0010.0010.0000.0000.0000.000
217A233ALA00.0240.02539.4010.0020.0020.0000.0000.0000.000
218A234GLY00.0300.00142.2570.0020.0020.0000.0000.0000.000
219A235GLN0-0.041-0.03038.5640.0000.0000.0000.0000.0000.000
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