Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: JLKM9

Calculation Name: 1KGC-D-Xray372

Preferred Name: T-cell receptor

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 1KGC

Chain ID: D

ChEMBL ID: CHEMBL3580506

UniProt ID: P01848

Base Structure: X-ray

Registration Date: 2023-06-26

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1999960.38722
FMO2-HF: Nuclear repulsion 1920715.409079
FMO2-HF: Total energy -79244.978142
FMO2-MP2: Total energy -79473.207569


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(D:2:LYS)


Summations of interaction energy for fragment #1(D:2:LYS)
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.
-112.743-107.98910.277-7.576-7.454-0.069
Interaction energy analysis for fragmet #1(D:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.911 / q_NPA : 0.958
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].
3D4THR0-0.031-0.0191.791-46.482-43.35410.206-7.130-6.203-0.069
4D5GLN00.0460.0154.0303.9354.1980.000-0.090-0.1730.000
5D7PRO00.0450.0437.159-2.118-2.1180.0000.0000.0000.000
6D8ASN00.0500.0138.757-3.243-3.2430.0000.0000.0000.000
7D9SER0-0.009-0.00210.342-0.123-0.1230.0000.0000.0000.000
8D10MET0-0.048-0.01713.735-0.326-0.3260.0000.0000.0000.000
9D11GLU-1-0.793-0.87816.518-15.794-15.7940.0000.0000.0000.000
10D12SER0-0.026-0.00820.261-0.053-0.0530.0000.0000.0000.000
11D13ASN00.003-0.00522.6340.0600.0600.0000.0000.0000.000
12D14GLU-1-0.794-0.89226.090-10.520-10.5200.0000.0000.0000.000
13D15GLU-1-0.919-0.96227.721-9.432-9.4320.0000.0000.0000.000
14D16GLU-1-0.840-0.88925.328-12.190-12.1900.0000.0000.0000.000
15D17PRO0-0.052-0.01723.903-0.330-0.3300.0000.0000.0000.000
16D18VAL00.011-0.00918.055-0.259-0.2590.0000.0000.0000.000
17D19HIS00.0110.00318.020-0.660-0.6600.0000.0000.0000.000
18D20LEU00.0550.01913.098-0.588-0.5880.0000.0000.0000.000
19D21PRO0-0.0080.00611.947-0.656-0.6560.0000.0000.0000.000
20D22CYS0-0.057-0.0177.247-1.168-1.1680.0000.0000.0000.000
21D23ASN0-0.016-0.0026.7496.4456.4450.0000.0000.0000.000
22D24HIS00.0310.0114.885-7.571-7.5710.0000.0000.0000.000
23D25SER00.0110.0084.5322.7322.928-0.001-0.010-0.1840.000
24D26THR00.002-0.0036.3220.0090.0090.0000.0000.0000.000
25D27ILE0-0.0350.0086.480-0.084-0.0840.0000.0000.0000.000
26D28SER00.011-0.0248.9791.9931.9930.0000.0000.0000.000
27D29GLY00.002-0.00212.093-0.463-0.4630.0000.0000.0000.000
28D30THR0-0.013-0.01513.5500.8100.8100.0000.0000.0000.000
29D30ASP-1-0.863-0.8898.681-20.928-20.9280.0000.0000.0000.000
30D31TYR0-0.025-0.01910.0930.6850.6850.0000.0000.0000.000
31D32ILE00.0140.0117.125-1.999-1.9990.0000.0000.0000.000
32D33HIS0-0.014-0.0359.0012.5202.5200.0000.0000.0000.000
33D34TRP00.0360.01810.115-3.163-3.1630.0000.0000.0000.000
34D35TYR0-0.005-0.00212.4211.9271.9270.0000.0000.0000.000
35D36ARG10.7880.87513.29514.00914.0090.0000.0000.0000.000
36D37GLN00.006-0.00514.607-0.871-0.8710.0000.0000.0000.000
37D38LEU00.0380.03216.781-0.185-0.1850.0000.0000.0000.000
38D39PRO00.0520.00319.850-0.250-0.2500.0000.0000.0000.000
39D40SER0-0.026-0.01220.6480.3930.3930.0000.0000.0000.000
40D41GLN0-0.0050.02720.7380.9310.9310.0000.0000.0000.000
41D42GLY00.0030.00618.943-0.832-0.8320.0000.0000.0000.000
42D43PRO0-0.040-0.04115.0050.2480.2480.0000.0000.0000.000
43D44GLU-1-0.856-0.90117.149-13.923-13.9230.0000.0000.0000.000
44D45TYR0-0.043-0.05315.866-0.814-0.8140.0000.0000.0000.000
45D46VAL0-0.0280.00116.4380.7330.7330.0000.0000.0000.000
46D47ILE0-0.023-0.01715.6411.0381.0380.0000.0000.0000.000
47D48HIS00.0180.03213.077-1.459-1.4590.0000.0000.0000.000
48D49GLY00.0180.00513.3681.2781.2780.0000.0000.0000.000
49D50LEU00.0500.03213.089-1.276-1.2760.0000.0000.0000.000
50D51THR00.0080.01314.5250.0970.0970.0000.0000.0000.000
51D52SER00.0430.02817.035-0.712-0.7120.0000.0000.0000.000
52D54ASN0-0.031-0.02218.7530.5820.5820.0000.0000.0000.000
53D55VAL00.0180.04518.1150.5680.5680.0000.0000.0000.000
54D56ASN00.012-0.01720.148-0.605-0.6050.0000.0000.0000.000
55D57ASN0-0.039-0.02020.9090.6410.6410.0000.0000.0000.000
56D58ARG10.9420.96624.34511.28711.2870.0000.0000.0000.000
57D61MET00.0190.02222.013-0.086-0.0860.0000.0000.0000.000
58D62ALA00.0090.00519.873-0.142-0.1420.0000.0000.0000.000
59D63SER00.030-0.00620.5030.6740.6740.0000.0000.0000.000
60D64LEU0-0.042-0.00113.034-0.850-0.8500.0000.0000.0000.000
61D65ALA0-0.024-0.01616.1601.0291.0290.0000.0000.0000.000
62D66ILE0-0.029-0.02412.216-1.423-1.4230.0000.0000.0000.000
63D67ALA00.0050.01214.2071.3091.3090.0000.0000.0000.000
64D68GLU-1-0.895-0.95615.422-13.713-13.7130.0000.0000.0000.000
65D69ASP-1-0.830-0.90814.219-19.966-19.9660.0000.0000.0000.000
66D70ARG10.7820.86811.61717.66217.6620.0000.0000.0000.000
67D71LYS10.8580.9109.62118.71518.7150.0000.0000.0000.000
68D72SER0-0.0030.0019.909-1.903-1.9030.0000.0000.0000.000
69D73SER00.015-0.01410.1942.7222.7220.0000.0000.0000.000
70D74THR0-0.076-0.05512.334-0.845-0.8450.0000.0000.0000.000
71D75LEU00.0000.02714.5071.0181.0180.0000.0000.0000.000
72D76ILE00.010-0.01215.9440.0140.0140.0000.0000.0000.000
73D77LEU00.0130.01018.3390.4690.4690.0000.0000.0000.000
74D78HIS00.0090.01021.2950.0590.0590.0000.0000.0000.000
75D79ARG10.8260.89424.90510.55210.5520.0000.0000.0000.000
76D80ALA00.0080.03322.8100.0510.0510.0000.0000.0000.000
77D81THR0-0.012-0.01724.6030.6850.6850.0000.0000.0000.000
78D82LEU00.1210.04124.725-0.509-0.5090.0000.0000.0000.000
79D83ARG10.9210.95824.51911.97611.9760.0000.0000.0000.000
80D84ASP-1-0.833-0.87621.293-13.862-13.8620.0000.0000.0000.000
81D85ALA00.0410.05219.846-1.034-1.0340.0000.0000.0000.000
82D86ALA0-0.012-0.01917.4020.3830.3830.0000.0000.0000.000
83D87VAL0-0.0050.01811.485-0.579-0.5790.0000.0000.0000.000
84D88TYR00.002-0.02912.5350.6550.6550.0000.0000.0000.000
85D89TYR0-0.039-0.0308.309-3.217-3.2170.0000.0000.0000.000
86D91ILE0-0.041-0.0326.066-5.979-5.9790.0000.0000.0000.000
87D92LEU00.0300.0173.0511.7252.4140.075-0.242-0.5230.000
88D93PRO0-0.056-0.0124.014-1.875-1.636-0.001-0.066-0.1720.000
89D94LEU0-0.0040.0016.7480.2020.2020.0000.0000.0000.000
90D95ALA00.0460.0178.4000.8060.8060.0000.0000.0000.000
91D96GLY00.0340.02911.6870.3440.3440.0000.0000.0000.000
92D97GLY00.0120.00813.992-0.600-0.6000.0000.0000.0000.000
93D98THR0-0.007-0.00814.8820.4860.4860.0000.0000.0000.000
94D99SER0-0.072-0.04011.877-0.216-0.2160.0000.0000.0000.000
95D100TYR00.028-0.00413.5400.2230.2230.0000.0000.0000.000
96D102GLY00.0450.02212.8670.4900.4900.0000.0000.0000.000
97D103LYS10.9010.9669.60823.08823.0880.0000.0000.0000.000
98D104LEU00.0250.0208.695-1.056-1.0560.0000.0000.0000.000
99D105THR0-0.037-0.0325.2442.0892.0890.0000.0000.0000.000
100D106PHE00.0260.0216.112-3.450-3.4500.0000.0000.0000.000
101D107GLY0-0.013-0.0024.116-3.961-3.839-0.001-0.032-0.0890.000
102D108GLN0-0.017-0.0234.6295.9196.036-0.001-0.006-0.1100.000
103D109GLY00.0040.0036.0935.2815.2810.0000.0000.0000.000
104D110THR0-0.062-0.0268.057-1.352-1.3520.0000.0000.0000.000
105D111ILE0-0.005-0.01710.7611.1291.1290.0000.0000.0000.000
106D112LEU0-0.033-0.01014.2030.1520.1520.0000.0000.0000.000
107D113THR0-0.003-0.00116.9530.3420.3420.0000.0000.0000.000
108D114VAL0-0.070-0.04020.412-0.013-0.0130.0000.0000.0000.000
109D115HIS0-0.032-0.03522.7170.8290.8290.0000.0000.0000.000
110D116PRO00.0150.01226.5000.0410.0410.0000.0000.0000.000
111D117ASN0-0.008-0.00330.030-0.091-0.0910.0000.0000.0000.000
112D118ILE0-0.026-0.01332.4460.2580.2580.0000.0000.0000.000
113D119GLN0-0.007-0.00135.2440.2040.2040.0000.0000.0000.000
114D120ASN0-0.055-0.04238.3930.2060.2060.0000.0000.0000.000
115D121PRO0-0.033-0.01036.8270.0360.0360.0000.0000.0000.000
116D122ASP-1-0.913-0.94838.982-7.194-7.1940.0000.0000.0000.000
117D123PRO0-0.042-0.00337.793-0.044-0.0440.0000.0000.0000.000
118D124ALA00.0500.02539.4830.2420.2420.0000.0000.0000.000
119D125VAL0-0.029-0.01138.840-0.261-0.2610.0000.0000.0000.000
120D126TYR0-0.0010.00241.1610.3420.3420.0000.0000.0000.000
121D127GLN00.0310.00842.088-0.151-0.1510.0000.0000.0000.000
122D128LEU0-0.050-0.02141.0000.1500.1500.0000.0000.0000.000
123D129ARG10.8970.94144.7126.3406.3400.0000.0000.0000.000
124D130ASP-1-0.798-0.88746.168-6.938-6.9380.0000.0000.0000.000
125D131SER0-0.013-0.01045.2700.1460.1460.0000.0000.0000.000
126D132LYS10.9560.96047.1916.0656.0650.0000.0000.0000.000
127D133SER0-0.0050.00245.5070.0810.0810.0000.0000.0000.000
128D134SER0-0.050-0.02542.416-0.141-0.1410.0000.0000.0000.000
129D135ASP-1-0.799-0.87843.510-7.317-7.3170.0000.0000.0000.000
130D136LYS10.8320.90638.8697.8527.8520.0000.0000.0000.000
131D137SER00.0050.01142.3360.1080.1080.0000.0000.0000.000
132D138VAL0-0.018-0.02638.568-0.209-0.2090.0000.0000.0000.000
133D139CYS0-0.008-0.00839.0060.0940.0940.0000.0000.0000.000
134D140LEU00.000-0.01136.524-0.244-0.2440.0000.0000.0000.000
135D141PHE00.0070.02233.3600.1940.1940.0000.0000.0000.000
136D142THR0-0.021-0.07335.490-0.384-0.3840.0000.0000.0000.000
137D143ASP-1-0.746-0.82236.435-8.177-8.1770.0000.0000.0000.000
138D144PHE00.0040.02230.6050.0740.0740.0000.0000.0000.000
139D145ASP-1-0.794-0.90432.716-9.890-9.8900.0000.0000.0000.000
140D146SER00.026-0.02428.388-0.038-0.0380.0000.0000.0000.000
141D147GLN0-0.047-0.01727.615-0.492-0.4920.0000.0000.0000.000
142D148THR0-0.0190.01328.900-0.146-0.1460.0000.0000.0000.000
143D149ASN0-0.046-0.01925.827-0.484-0.4840.0000.0000.0000.000
144D150VAL00.0350.01527.7340.3900.3900.0000.0000.0000.000
145D151SER0-0.021-0.00827.342-0.569-0.5690.0000.0000.0000.000
146D152GLN0-0.009-0.01226.2550.5110.5110.0000.0000.0000.000
147D153SER00.0490.02629.0230.2010.2010.0000.0000.0000.000
148D154LYS10.8570.92731.3838.8728.8720.0000.0000.0000.000
149D155ASP-1-0.791-0.88933.494-8.206-8.2060.0000.0000.0000.000
150D156SER00.0060.00233.165-0.270-0.2700.0000.0000.0000.000
151D157ASP-1-0.851-0.91134.205-8.320-8.3200.0000.0000.0000.000
152D158VAL0-0.074-0.01035.2470.1940.1940.0000.0000.0000.000
153D159TYR0-0.045-0.00931.803-0.295-0.2950.0000.0000.0000.000
154D160ILE00.0330.00530.9500.2780.2780.0000.0000.0000.000
155D161THR0-0.0390.00028.745-0.262-0.2620.0000.0000.0000.000
156D162ASP-1-0.869-0.92623.597-12.836-12.8360.0000.0000.0000.000
157D163LYS10.8310.90325.71312.29412.2940.0000.0000.0000.000
158D164THR0-0.062-0.03126.473-0.414-0.4140.0000.0000.0000.000
159D165VAL00.0210.00927.6170.3120.3120.0000.0000.0000.000
160D166LEU0-0.036-0.00430.090-0.083-0.0830.0000.0000.0000.000
161D167ASP-1-0.776-0.87832.530-9.323-9.3230.0000.0000.0000.000
162D168MET0-0.0120.00534.4350.0990.0990.0000.0000.0000.000
163D169ARG10.7400.80034.8949.1689.1680.0000.0000.0000.000
164D170SER0-0.062-0.02938.0770.0640.0640.0000.0000.0000.000
165D171MET0-0.034-0.02541.1460.2090.2090.0000.0000.0000.000
166D172ASP-1-0.877-0.90737.438-8.624-8.6240.0000.0000.0000.000
167D173PHE00.0030.01138.481-0.028-0.0280.0000.0000.0000.000
168D174LYS10.8470.90732.0149.6929.6920.0000.0000.0000.000
169D175SER0-0.013-0.03834.3850.0390.0390.0000.0000.0000.000
170D176ASN0-0.029-0.01330.246-0.561-0.5610.0000.0000.0000.000
171D177SER0-0.022-0.01031.7140.3570.3570.0000.0000.0000.000
172D178ALA00.0290.01131.010-0.420-0.4200.0000.0000.0000.000
173D179VAL0-0.019-0.00832.5320.3830.3830.0000.0000.0000.000
174D180ALA00.0280.01933.421-0.278-0.2780.0000.0000.0000.000
175D181TRP0-0.027-0.01432.3320.2760.2760.0000.0000.0000.000
176D182SER0-0.012-0.03737.166-0.118-0.1180.0000.0000.0000.000
177D183ASN0-0.039-0.02939.6830.0290.0290.0000.0000.0000.000
178D184LYS10.7860.87239.6678.1538.1530.0000.0000.0000.000
179D185SER0-0.010-0.01243.6660.0190.0190.0000.0000.0000.000
180D186ASP-1-0.943-0.97144.460-6.810-6.8100.0000.0000.0000.000
181D187PHE0-0.033-0.00938.472-0.117-0.1170.0000.0000.0000.000
182D188ALA00.0550.02142.8730.1730.1730.0000.0000.0000.000
183D190ALA0-0.008-0.00141.571-0.127-0.1270.0000.0000.0000.000
184D191ASN0-0.028-0.01541.116-0.167-0.1670.0000.0000.0000.000
185D192ALA00.0020.01738.086-0.208-0.2080.0000.0000.0000.000
186D193PHE00.030-0.00233.637-0.227-0.2270.0000.0000.0000.000
187D194ASN00.0600.02435.782-0.114-0.1140.0000.0000.0000.000
188D195ASN0-0.127-0.05930.6150.2270.2270.0000.0000.0000.000
189D196SER00.0110.01731.666-0.490-0.4900.0000.0000.0000.000
190D197ILE0-0.0100.00130.9150.2690.2690.0000.0000.0000.000
191D198ILE0-0.0050.00033.151-0.233-0.2330.0000.0000.0000.000
192D199PRO00.0300.00935.2920.1310.1310.0000.0000.0000.000
193D200GLU-1-0.922-0.94637.999-7.564-7.5640.0000.0000.0000.000
194D201ASP-1-0.951-0.96741.233-7.254-7.2540.0000.0000.0000.000
195D202THR0-0.092-0.05539.459-0.026-0.0260.0000.0000.0000.000
196D203PHE00.016-0.00441.7530.2220.2220.0000.0000.0000.000
197D204PHE00.012-0.00740.647-0.130-0.1300.0000.0000.0000.000
198D205PRO0-0.042-0.01145.6100.1850.1850.0000.0000.0000.000
199D206SER0-0.037-0.01148.7110.0610.0610.0000.0000.0000.000