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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: N963Q

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 OptH
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 -1999967.267816
FMO2-HF: Nuclear repulsion 1920723.138737
FMO2-HF: Total energy -79244.129079
FMO2-MP2: Total energy -79472.434668


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.
-93.202-86.8393.867-4.298-5.932-0.038
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 : 0.913 / q_NPA : 0.956
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].
3D4THR0-0.038-0.0282.316-29.402-24.5003.826-3.937-4.791-0.039
4D5GLN00.0530.0214.1443.2943.5090.001-0.064-0.1520.000
5D7PRO00.0300.0367.728-2.218-2.2180.0000.0000.0000.000
6D8ASN00.0560.0168.895-3.123-3.1230.0000.0000.0000.000
7D9SER0-0.007-0.00410.622-0.228-0.2280.0000.0000.0000.000
8D10MET0-0.055-0.02114.050-0.205-0.2050.0000.0000.0000.000
9D11GLU-1-0.814-0.89716.933-15.583-15.5830.0000.0000.0000.000
10D12SER0-0.049-0.01720.6510.0190.0190.0000.0000.0000.000
11D13ASN00.0640.04023.080-0.066-0.0660.0000.0000.0000.000
12D14GLU-1-0.820-0.91326.535-10.295-10.2950.0000.0000.0000.000
13D15GLU-1-0.989-1.02328.097-9.260-9.2600.0000.0000.0000.000
14D16GLU-1-0.877-0.92125.838-11.892-11.8920.0000.0000.0000.000
15D17PRO0-0.055-0.01624.606-0.331-0.3310.0000.0000.0000.000
16D18VAL00.0290.00018.569-0.256-0.2560.0000.0000.0000.000
17D19HIS0-0.002-0.00418.334-0.580-0.5800.0000.0000.0000.000
18D20LEU00.0460.01213.711-0.582-0.5820.0000.0000.0000.000
19D21PRO0-0.0020.00512.177-0.568-0.5680.0000.0000.0000.000
20D22CYS0-0.050-0.0107.856-0.800-0.8000.0000.0000.0000.000
21D23ASN0-0.0080.0056.5115.8825.8820.0000.0000.0000.000
22D24HIS00.0250.0094.674-6.710-6.619-0.001-0.029-0.0610.000
23D25SER0-0.006-0.0014.4642.5102.693-0.001-0.009-0.1730.000
24D26THR00.006-0.0046.2900.2200.2200.0000.0000.0000.000
25D27ILE0-0.0310.0126.366-0.133-0.1330.0000.0000.0000.000
26D28SER00.002-0.0228.8251.7961.7960.0000.0000.0000.000
27D29GLY0-0.004-0.00411.960-0.327-0.3270.0000.0000.0000.000
28D30THR0-0.003-0.01113.3140.7230.7230.0000.0000.0000.000
29D30ASP-1-0.869-0.8968.860-20.250-20.2500.0000.0000.0000.000
30D31TYR0-0.027-0.02210.6200.6160.6160.0000.0000.0000.000
31D32ILE00.0240.0187.668-1.543-1.5430.0000.0000.0000.000
32D33HIS0-0.025-0.0419.9791.9831.9830.0000.0000.0000.000
33D34TRP00.0370.02110.651-2.679-2.6790.0000.0000.0000.000
34D35TYR0-0.010-0.00312.6551.7291.7290.0000.0000.0000.000
35D36ARG10.8110.89713.37513.59013.5900.0000.0000.0000.000
36D37GLN0-0.001-0.00514.431-0.868-0.8680.0000.0000.0000.000
37D38LEU00.0280.02516.588-0.174-0.1740.0000.0000.0000.000
38D39PRO00.0410.00119.623-0.266-0.2660.0000.0000.0000.000
39D40SER0-0.011-0.00720.5060.3800.3800.0000.0000.0000.000
40D41GLN0-0.0090.02720.5790.8480.8480.0000.0000.0000.000
41D42GLY00.0000.00218.862-0.826-0.8260.0000.0000.0000.000
42D43PRO0-0.039-0.04014.8470.2780.2780.0000.0000.0000.000
43D44GLU-1-0.855-0.89716.943-13.598-13.5980.0000.0000.0000.000
44D45TYR0-0.045-0.06616.379-0.675-0.6750.0000.0000.0000.000
45D46VAL0-0.0330.00316.6810.6760.6760.0000.0000.0000.000
46D47ILE0-0.018-0.01716.4580.9610.9610.0000.0000.0000.000
47D48HIS00.0200.04214.094-1.370-1.3700.0000.0000.0000.000
48D49GLY00.0190.00814.1131.1301.1300.0000.0000.0000.000
49D50LEU00.0540.03713.624-1.089-1.0890.0000.0000.0000.000
50D51THR0-0.003-0.00514.8660.1200.1200.0000.0000.0000.000
51D52SER00.0380.03017.217-0.634-0.6340.0000.0000.0000.000
52D54ASN0-0.0010.00118.9370.4850.4850.0000.0000.0000.000
53D55VAL00.0070.04218.4130.5000.5000.0000.0000.0000.000
54D56ASN00.038-0.01820.728-0.715-0.7150.0000.0000.0000.000
55D57ASN0-0.052-0.01921.3510.5020.5020.0000.0000.0000.000
56D58ARG10.9350.95825.17811.15911.1590.0000.0000.0000.000
57D61MET00.0090.00922.011-0.069-0.0690.0000.0000.0000.000
58D62ALA00.0140.01120.378-0.138-0.1380.0000.0000.0000.000
59D63SER00.0320.00421.0950.6220.6220.0000.0000.0000.000
60D64LEU0-0.0340.00513.549-0.816-0.8160.0000.0000.0000.000
61D65ALA0-0.026-0.01816.4910.9390.9390.0000.0000.0000.000
62D66ILE0-0.032-0.02212.341-1.287-1.2870.0000.0000.0000.000
63D67ALA00.0020.00714.0111.1691.1690.0000.0000.0000.000
64D68GLU-1-0.900-0.96115.206-13.299-13.2990.0000.0000.0000.000
65D69ASP-1-0.882-0.93213.816-19.057-19.0570.0000.0000.0000.000
66D70ARG10.7820.85811.47416.75916.7590.0000.0000.0000.000
67D71LYS10.9270.9559.48219.41819.4180.0000.0000.0000.000
68D72SER0-0.0120.0029.725-1.936-1.9360.0000.0000.0000.000
69D73SER00.028-0.01510.1252.5222.5220.0000.0000.0000.000
70D74THR0-0.072-0.05112.364-0.818-0.8180.0000.0000.0000.000
71D75LEU0-0.0080.02515.1180.9350.9350.0000.0000.0000.000
72D76ILE00.007-0.01416.570-0.015-0.0150.0000.0000.0000.000
73D77LEU00.0160.00818.9920.4290.4290.0000.0000.0000.000
74D78HIS00.0030.00221.8150.1360.1360.0000.0000.0000.000
75D79ARG10.9070.95725.46410.36510.3650.0000.0000.0000.000
76D80ALA00.0310.04523.2390.0650.0650.0000.0000.0000.000
77D81THR0-0.0050.00725.0000.6200.6200.0000.0000.0000.000
78D82LEU00.1250.04124.962-0.453-0.4530.0000.0000.0000.000
79D83ARG10.9040.94824.62911.58711.5870.0000.0000.0000.000
80D84ASP-1-0.834-0.90621.495-13.599-13.5990.0000.0000.0000.000
81D85ALA00.0280.04720.024-0.970-0.9700.0000.0000.0000.000
82D86ALA0-0.012-0.02417.3660.3670.3670.0000.0000.0000.000
83D87VAL0-0.0060.02511.489-0.502-0.5020.0000.0000.0000.000
84D88TYR0-0.011-0.04112.6890.6840.6840.0000.0000.0000.000
85D89TYR0-0.036-0.0348.059-3.015-3.0150.0000.0000.0000.000
86D91ILE0-0.029-0.0266.255-5.150-5.1500.0000.0000.0000.000
87D92LEU00.0320.0153.0401.3401.9110.045-0.209-0.4060.001
88D93PRO0-0.063-0.0164.945-0.290-0.141-0.001-0.003-0.1450.000
89D94LEU00.0020.0057.6360.1280.1280.0000.0000.0000.000
90D95ALA00.0430.0148.8550.7860.7860.0000.0000.0000.000
91D96GLY00.0290.02412.2140.2620.2620.0000.0000.0000.000
92D97GLY00.005-0.00714.090-0.624-0.6240.0000.0000.0000.000
93D98THR0-0.006-0.00714.6400.6460.6460.0000.0000.0000.000
94D99SER0-0.077-0.02612.297-0.260-0.2600.0000.0000.0000.000
95D100TYR00.0500.00413.7170.2820.2820.0000.0000.0000.000
96D102GLY00.0470.02213.6020.4780.4780.0000.0000.0000.000
97D103LYS10.9010.9619.76123.29323.2930.0000.0000.0000.000
98D104LEU00.0190.0199.323-0.803-0.8030.0000.0000.0000.000
99D105THR0-0.031-0.0215.1710.9500.9500.0000.0000.0000.000
100D106PHE00.0140.0146.127-2.535-2.5350.0000.0000.0000.000
101D107GLY0-0.016-0.0063.853-4.530-4.402-0.001-0.039-0.0890.000
102D108GLN00.001-0.0124.4134.4614.585-0.001-0.008-0.1150.000
103D109GLY0-0.0050.0006.0334.9684.9680.0000.0000.0000.000
104D110THR0-0.071-0.0328.089-1.249-1.2490.0000.0000.0000.000
105D111ILE00.001-0.01210.9871.1151.1150.0000.0000.0000.000
106D112LEU0-0.035-0.00914.3000.1670.1670.0000.0000.0000.000
107D113THR00.0140.01017.1870.3320.3320.0000.0000.0000.000
108D114VAL0-0.065-0.03820.602-0.005-0.0050.0000.0000.0000.000
109D115HIS0-0.048-0.04022.9330.8060.8060.0000.0000.0000.000
110D116PRO0-0.0070.00426.7650.0550.0550.0000.0000.0000.000
111D117ASN00.003-0.01130.294-0.166-0.1660.0000.0000.0000.000
112D118ILE0-0.034-0.01732.7940.2510.2510.0000.0000.0000.000
113D119GLN0-0.013-0.01135.5410.2650.2650.0000.0000.0000.000
114D120ASN0-0.046-0.03138.7400.1770.1770.0000.0000.0000.000
115D121PRO0-0.040-0.01337.2040.0300.0300.0000.0000.0000.000
116D122ASP-1-0.906-0.94739.283-7.154-7.1540.0000.0000.0000.000
117D123PRO0-0.042-0.00238.057-0.051-0.0510.0000.0000.0000.000
118D124ALA00.0610.02939.7190.2310.2310.0000.0000.0000.000
119D125VAL0-0.026-0.00638.995-0.263-0.2630.0000.0000.0000.000
120D126TYR00.0050.00041.3160.3200.3200.0000.0000.0000.000
121D127GLN00.0500.01442.203-0.167-0.1670.0000.0000.0000.000
122D128LEU0-0.057-0.02741.3120.1480.1480.0000.0000.0000.000
123D129ARG10.8900.93744.8026.3176.3170.0000.0000.0000.000
124D130ASP-1-0.841-0.91346.214-6.880-6.8800.0000.0000.0000.000
125D131SER0-0.028-0.02045.2970.1450.1450.0000.0000.0000.000
126D132LYS10.9540.95847.1976.0176.0170.0000.0000.0000.000
127D133SER0-0.025-0.00545.9470.0530.0530.0000.0000.0000.000
128D134SER0-0.019-0.01042.598-0.154-0.1540.0000.0000.0000.000
129D135ASP-1-0.872-0.92644.504-6.860-6.8600.0000.0000.0000.000
130D136LYS10.8410.92137.8748.1128.1120.0000.0000.0000.000
131D137SER00.0260.04242.3350.0870.0870.0000.0000.0000.000
132D138VAL00.001-0.02638.752-0.207-0.2070.0000.0000.0000.000
133D139CYS0-0.008-0.00439.1100.0940.0940.0000.0000.0000.000
134D140LEU0-0.001-0.01036.742-0.248-0.2480.0000.0000.0000.000
135D141PHE00.0050.02233.6770.1900.1900.0000.0000.0000.000
136D142THR0-0.009-0.05435.662-0.388-0.3880.0000.0000.0000.000
137D143ASP-1-0.819-0.89936.667-8.042-8.0420.0000.0000.0000.000
138D144PHE0-0.0140.01230.8780.0660.0660.0000.0000.0000.000
139D145ASP-1-0.798-0.91333.148-9.771-9.7710.0000.0000.0000.000
140D146SER00.015-0.03028.655-0.074-0.0740.0000.0000.0000.000
141D147GLN0-0.051-0.01527.689-0.495-0.4950.0000.0000.0000.000
142D148THR0-0.0080.01829.169-0.131-0.1310.0000.0000.0000.000
143D149ASN0-0.050-0.02026.071-0.541-0.5410.0000.0000.0000.000
144D150VAL00.0250.00827.8990.3840.3840.0000.0000.0000.000
145D151SER0-0.034-0.01827.464-0.533-0.5330.0000.0000.0000.000
146D152GLN0-0.006-0.00426.2300.4120.4120.0000.0000.0000.000
147D153SER00.0570.03529.0500.2050.2050.0000.0000.0000.000
148D154LYS10.9090.95631.3568.7308.7300.0000.0000.0000.000
149D155ASP-1-0.829-0.92233.462-8.233-8.2330.0000.0000.0000.000
150D156SER0-0.009-0.01233.067-0.276-0.2760.0000.0000.0000.000
151D157ASP-1-0.908-0.94834.101-8.344-8.3440.0000.0000.0000.000
152D158VAL0-0.096-0.03735.1030.2000.2000.0000.0000.0000.000
153D159TYR0-0.025-0.00431.644-0.229-0.2290.0000.0000.0000.000
154D160ILE00.028-0.00130.9350.2850.2850.0000.0000.0000.000
155D161THR0-0.034-0.00428.784-0.243-0.2430.0000.0000.0000.000
156D162ASP-1-0.873-0.92223.974-12.680-12.6800.0000.0000.0000.000
157D163LYS10.8470.91126.16612.04812.0480.0000.0000.0000.000
158D164THR0-0.069-0.03026.673-0.406-0.4060.0000.0000.0000.000
159D165VAL00.0290.00627.8570.3020.3020.0000.0000.0000.000
160D166LEU0-0.0320.00130.166-0.098-0.0980.0000.0000.0000.000
161D167ASP-1-0.786-0.88932.594-9.187-9.1870.0000.0000.0000.000
162D168MET0-0.0070.00734.4780.1000.1000.0000.0000.0000.000
163D169ARG10.7710.84135.0409.0029.0020.0000.0000.0000.000
164D170SER0-0.071-0.03538.1520.0720.0720.0000.0000.0000.000
165D171MET0-0.020-0.01641.2450.1950.1950.0000.0000.0000.000
166D172ASP-1-0.908-0.94337.940-8.403-8.4030.0000.0000.0000.000
167D173PHE00.0220.01838.681-0.032-0.0320.0000.0000.0000.000
168D174LYS10.8680.93731.6059.5299.5290.0000.0000.0000.000
169D175SER00.0300.02234.5430.0520.0520.0000.0000.0000.000
170D176ASN0-0.015-0.00330.338-0.533-0.5330.0000.0000.0000.000
171D177SER0-0.011-0.01031.9280.3330.3330.0000.0000.0000.000
172D178ALA00.0150.00931.178-0.413-0.4130.0000.0000.0000.000
173D179VAL0-0.013-0.00332.6670.3750.3750.0000.0000.0000.000
174D180ALA00.0180.01533.485-0.282-0.2820.0000.0000.0000.000
175D181TRP0-0.026-0.01832.3380.3030.3030.0000.0000.0000.000
176D182SER0-0.017-0.02637.149-0.113-0.1130.0000.0000.0000.000
177D183ASN00.0120.00439.6500.0530.0530.0000.0000.0000.000
178D184LYS10.9010.97040.1198.0348.0340.0000.0000.0000.000
179D185SER00.0320.00643.6060.0050.0050.0000.0000.0000.000
180D186ASP-1-0.973-0.98144.398-6.817-6.8170.0000.0000.0000.000
181D187PHE0-0.034-0.01738.360-0.123-0.1230.0000.0000.0000.000
182D188ALA00.0500.01842.8850.1760.1760.0000.0000.0000.000
183D190ALA0-0.0030.00141.669-0.124-0.1240.0000.0000.0000.000
184D191ASN0-0.019-0.02541.181-0.208-0.2080.0000.0000.0000.000
185D192ALA00.0050.02338.093-0.209-0.2090.0000.0000.0000.000
186D193PHE00.018-0.00733.663-0.241-0.2410.0000.0000.0000.000
187D194ASN00.0470.02535.890-0.101-0.1010.0000.0000.0000.000
188D195ASN0-0.179-0.10030.2120.1750.1750.0000.0000.0000.000
189D196SER00.0270.03331.798-0.485-0.4850.0000.0000.0000.000
190D197ILE00.0000.00931.0970.2660.2660.0000.0000.0000.000
191D198ILE0-0.016-0.00533.346-0.230-0.2300.0000.0000.0000.000
192D199PRO00.0170.00535.6010.1200.1200.0000.0000.0000.000
193D200GLU-1-0.913-0.94338.232-7.435-7.4350.0000.0000.0000.000
194D201ASP-1-0.941-0.96041.455-7.139-7.1390.0000.0000.0000.000
195D202THR0-0.093-0.05939.661-0.032-0.0320.0000.0000.0000.000
196D203PHE00.021-0.00241.9680.2100.2100.0000.0000.0000.000
197D204PHE00.006-0.01040.843-0.137-0.1370.0000.0000.0000.000
198D205PRO0-0.046-0.01145.7150.1790.1790.0000.0000.0000.000
199D206SER0-0.025-0.00848.8740.0070.0070.0000.0000.0000.000