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: 39GNL

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2002600.906382
FMO2-HF: Nuclear repulsion 1923355.610214
FMO2-HF: Total energy -79245.296167
FMO2-MP2: Total energy -79473.549703


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.
-116.446-112.56811.274-7.704-7.446-0.072
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 : 0.921 / q_NPA : 0.961
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].
3D4THR0-0.057-0.0281.770-47.750-45.62110.921-7.119-5.931-0.074
4D5GLN00.0440.0084.1443.3943.587-0.001-0.059-0.1330.000
5D7PRO00.0290.0407.282-1.941-1.9410.0000.0000.0000.000
6D8ASN00.0640.0189.251-2.285-2.2850.0000.0000.0000.000
7D9SER0-0.0110.00310.5760.0300.0300.0000.0000.0000.000
8D10MET0-0.037-0.01913.986-0.583-0.5830.0000.0000.0000.000
9D11GLU-1-0.799-0.86016.592-15.316-15.3160.0000.0000.0000.000
10D12SER0-0.044-0.02420.397-0.079-0.0790.0000.0000.0000.000
11D13ASN00.001-0.01422.8580.1530.1530.0000.0000.0000.000
12D14GLU-1-0.789-0.89325.912-10.546-10.5460.0000.0000.0000.000
13D15GLU-1-0.882-0.93027.749-9.398-9.3980.0000.0000.0000.000
14D16GLU-1-0.813-0.87925.241-12.322-12.3220.0000.0000.0000.000
15D17PRO0-0.051-0.01124.249-0.312-0.3120.0000.0000.0000.000
16D18VAL00.007-0.00618.313-0.249-0.2490.0000.0000.0000.000
17D19HIS0-0.005-0.00618.198-0.757-0.7570.0000.0000.0000.000
18D20LEU00.0670.02413.191-0.558-0.5580.0000.0000.0000.000
19D21PRO0-0.0110.00912.131-0.726-0.7260.0000.0000.0000.000
20D22CYS0-0.032-0.0177.265-1.275-1.2750.0000.0000.0000.000
21D23ASN0-0.008-0.0057.0726.7016.7010.0000.0000.0000.000
22D24HIS00.0000.0054.464-8.318-8.203-0.001-0.044-0.0700.000
23D25SER00.0240.0064.2462.8243.048-0.001-0.013-0.2100.000
24D26THR0-0.017-0.0116.064-0.045-0.0450.0000.0000.0000.000
25D27ILE0-0.0440.0036.1270.2370.2370.0000.0000.0000.000
26D28SER00.006-0.0328.6871.9661.9660.0000.0000.0000.000
27D29GLY00.014-0.00311.960-0.481-0.4810.0000.0000.0000.000
28D30THR0-0.008-0.01113.4170.6250.6250.0000.0000.0000.000
29D30ASP-1-0.858-0.8818.474-21.025-21.0250.0000.0000.0000.000
30D31TYR0-0.020-0.0209.5470.7830.7830.0000.0000.0000.000
31D32ILE00.0130.0076.820-2.191-2.1910.0000.0000.0000.000
32D33HIS0-0.012-0.0348.9932.7082.7080.0000.0000.0000.000
33D34TRP00.0330.01510.173-3.177-3.1770.0000.0000.0000.000
34D35TYR0-0.001-0.00212.4411.9801.9800.0000.0000.0000.000
35D36ARG10.7720.85913.30414.24314.2430.0000.0000.0000.000
36D37GLN0-0.006-0.00414.614-0.866-0.8660.0000.0000.0000.000
37D38LEU00.0370.03516.871-0.302-0.3020.0000.0000.0000.000
38D39PRO00.0540.01119.873-0.294-0.2940.0000.0000.0000.000
39D40SER0-0.023-0.01421.0410.3930.3930.0000.0000.0000.000
40D41GLN0-0.0180.02520.9010.7680.7680.0000.0000.0000.000
41D42GLY00.0130.01018.713-0.779-0.7790.0000.0000.0000.000
42D43PRO0-0.044-0.04314.8130.2250.2250.0000.0000.0000.000
43D44GLU-1-0.827-0.89017.060-13.853-13.8530.0000.0000.0000.000
44D45TYR0-0.043-0.05415.879-0.912-0.9120.0000.0000.0000.000
45D46VAL0-0.0220.00116.6710.7690.7690.0000.0000.0000.000
46D47ILE0-0.015-0.01215.4851.0191.0190.0000.0000.0000.000
47D48HIS00.0010.02912.993-1.518-1.5180.0000.0000.0000.000
48D49GLY00.0260.00713.1981.3251.3250.0000.0000.0000.000
49D50LEU00.0480.04112.688-1.352-1.3520.0000.0000.0000.000
50D51THR0-0.003-0.00114.053-0.025-0.0250.0000.0000.0000.000
51D52SER00.0590.02916.385-0.756-0.7560.0000.0000.0000.000
52D54ASN0-0.044-0.02418.1810.5960.5960.0000.0000.0000.000
53D55VAL00.0220.04917.8020.6250.6250.0000.0000.0000.000
54D56ASN00.006-0.01419.723-0.593-0.5930.0000.0000.0000.000
55D57ASN0-0.016-0.01420.7620.6840.6840.0000.0000.0000.000
56D58ARG10.9530.96324.09711.29711.2970.0000.0000.0000.000
57D61MET0-0.0130.02522.2140.0760.0760.0000.0000.0000.000
58D62ALA00.004-0.00119.932-0.182-0.1820.0000.0000.0000.000
59D63SER00.018-0.01220.5040.6470.6470.0000.0000.0000.000
60D64LEU0-0.0310.00212.915-0.857-0.8570.0000.0000.0000.000
61D65ALA0-0.010-0.01316.0051.1301.1300.0000.0000.0000.000
62D66ILE0-0.015-0.01911.591-1.487-1.4870.0000.0000.0000.000
63D67ALA0-0.0090.00713.6801.4251.4250.0000.0000.0000.000
64D68GLU-1-0.908-0.96214.706-13.916-13.9160.0000.0000.0000.000
65D69ASP-1-0.821-0.90813.635-20.455-20.4550.0000.0000.0000.000
66D70ARG10.7740.87310.94117.85417.8540.0000.0000.0000.000
67D71LYS10.8640.9268.92118.90718.9070.0000.0000.0000.000
68D72SER00.0000.0049.332-2.260-2.2600.0000.0000.0000.000
69D73SER00.027-0.0109.8242.5592.5590.0000.0000.0000.000
70D74THR0-0.073-0.04812.196-0.505-0.5050.0000.0000.0000.000
71D75LEU0-0.0090.02714.3161.0371.0370.0000.0000.0000.000
72D76ILE00.007-0.00915.8860.0100.0100.0000.0000.0000.000
73D77LEU00.0350.01618.4410.6010.6010.0000.0000.0000.000
74D78HIS00.0080.00321.2800.0650.0650.0000.0000.0000.000
75D79ARG10.8000.87524.94110.60010.6000.0000.0000.0000.000
76D80ALA00.0050.02922.8280.0680.0680.0000.0000.0000.000
77D81THR0-0.018-0.03524.6610.6980.6980.0000.0000.0000.000
78D82LEU00.1200.04824.786-0.530-0.5300.0000.0000.0000.000
79D83ARG10.8600.93423.45712.53312.5330.0000.0000.0000.000
80D84ASP-1-0.811-0.86921.454-13.716-13.7160.0000.0000.0000.000
81D85ALA00.0550.05420.079-1.002-1.0020.0000.0000.0000.000
82D86ALA0-0.026-0.02117.5700.3640.3640.0000.0000.0000.000
83D87VAL00.0070.02011.652-0.582-0.5820.0000.0000.0000.000
84D88TYR00.004-0.02212.5540.6880.6880.0000.0000.0000.000
85D89TYR0-0.041-0.0368.626-3.028-3.0280.0000.0000.0000.000
86D91ILE0-0.047-0.0236.179-6.571-6.5710.0000.0000.0000.000
87D92LEU00.0400.0222.6151.4842.3720.358-0.396-0.8490.002
88D93PRO0-0.057-0.0114.043-1.912-1.680-0.001-0.058-0.1730.000
89D94LEU00.0060.0026.7790.3640.3640.0000.0000.0000.000
90D95ALA00.0380.0128.0140.8330.8330.0000.0000.0000.000
91D96GLY00.0310.02511.2880.2380.2380.0000.0000.0000.000
92D97GLY00.0200.00513.837-0.602-0.6020.0000.0000.0000.000
93D98THR0-0.013-0.00814.3440.6790.6790.0000.0000.0000.000
94D99SER0-0.066-0.03111.501-0.324-0.3240.0000.0000.0000.000
95D100TYR00.017-0.00813.2450.2880.2880.0000.0000.0000.000
96D102GLY00.0460.02512.9380.3960.3960.0000.0000.0000.000
97D103LYS10.8990.9569.39224.43724.4370.0000.0000.0000.000
98D104LEU00.0320.0288.865-1.663-1.6630.0000.0000.0000.000
99D105THR0-0.045-0.0325.2841.9581.9580.0000.0000.0000.000
100D106PHE00.0360.0186.026-4.260-4.2600.0000.0000.0000.000
101D107GLY0-0.005-0.0084.193-5.730-5.633-0.001-0.015-0.0800.000
102D108GLN0-0.036-0.0264.9625.7185.7180.0000.0000.0000.000
103D109GLY00.0100.0136.2524.8844.8840.0000.0000.0000.000
104D110THR0-0.067-0.0298.149-1.400-1.4000.0000.0000.0000.000
105D111ILE00.012-0.00311.1541.0291.0290.0000.0000.0000.000
106D112LEU0-0.035-0.01014.5260.1010.1010.0000.0000.0000.000
107D113THR0-0.009-0.02917.0230.4080.4080.0000.0000.0000.000
108D114VAL0-0.072-0.02920.466-0.025-0.0250.0000.0000.0000.000
109D115HIS0-0.008-0.01023.3710.7320.7320.0000.0000.0000.000
110D116PRO00.0130.01126.7640.0390.0390.0000.0000.0000.000
111D117ASN0-0.009-0.01630.377-0.091-0.0910.0000.0000.0000.000
112D118ILE0-0.037-0.01532.7050.3090.3090.0000.0000.0000.000
113D119GLN0-0.024-0.00935.3210.2350.2350.0000.0000.0000.000
114D120ASN0-0.056-0.03438.2950.2170.2170.0000.0000.0000.000
115D121PRO0-0.026-0.01236.9280.0180.0180.0000.0000.0000.000
116D122ASP-1-0.927-0.95039.109-7.158-7.1580.0000.0000.0000.000
117D123PRO0-0.042-0.00238.154-0.052-0.0520.0000.0000.0000.000
118D124ALA00.0410.01739.7890.2230.2230.0000.0000.0000.000
119D125VAL0-0.028-0.01239.049-0.266-0.2660.0000.0000.0000.000
120D126TYR00.002-0.00241.4090.3450.3450.0000.0000.0000.000
121D127GLN00.006-0.01842.251-0.131-0.1310.0000.0000.0000.000
122D128LEU0-0.045-0.01840.9640.1380.1380.0000.0000.0000.000
123D129ARG10.9030.94244.7556.3416.3410.0000.0000.0000.000
124D130ASP-1-0.767-0.85546.186-6.924-6.9240.0000.0000.0000.000
125D131SER0-0.018-0.00345.5900.2060.2060.0000.0000.0000.000
126D132LYS10.9560.95447.3526.0726.0720.0000.0000.0000.000
127D133SER0-0.024-0.00645.3110.0900.0900.0000.0000.0000.000
128D134SER0-0.059-0.03243.564-0.200-0.2000.0000.0000.0000.000
129D135ASP-1-0.780-0.86743.578-7.354-7.3540.0000.0000.0000.000
130D136LYS10.8070.89439.3817.8117.8110.0000.0000.0000.000
131D137SER00.0230.00143.1350.0400.0400.0000.0000.0000.000
132D138VAL0-0.023-0.03238.899-0.206-0.2060.0000.0000.0000.000
133D139CYS0-0.0170.00139.2400.1100.1100.0000.0000.0000.000
134D140LEU0-0.006-0.00836.803-0.233-0.2330.0000.0000.0000.000
135D141PHE00.0260.03033.6300.2070.2070.0000.0000.0000.000
136D142THR0-0.012-0.06735.810-0.362-0.3620.0000.0000.0000.000
137D143ASP-1-0.761-0.82836.764-8.164-8.1640.0000.0000.0000.000
138D144PHE00.0070.01630.9410.0530.0530.0000.0000.0000.000
139D145ASP-1-0.767-0.85732.857-9.850-9.8500.0000.0000.0000.000
140D146SER00.032-0.01328.836-0.056-0.0560.0000.0000.0000.000
141D147GLN0-0.060-0.02427.923-0.435-0.4350.0000.0000.0000.000
142D148THR0-0.023-0.02728.874-0.234-0.2340.0000.0000.0000.000
143D149ASN0-0.041-0.01626.580-0.525-0.5250.0000.0000.0000.000
144D150VAL00.0260.00728.1190.3810.3810.0000.0000.0000.000
145D151SER0-0.031-0.01627.952-0.517-0.5170.0000.0000.0000.000
146D152GLN00.001-0.01626.6290.5690.5690.0000.0000.0000.000
147D153SER00.0560.03329.2990.2370.2370.0000.0000.0000.000
148D154LYS10.8400.92031.6018.8178.8170.0000.0000.0000.000
149D155ASP-1-0.818-0.89334.137-8.093-8.0930.0000.0000.0000.000
150D156SER00.012-0.00333.495-0.235-0.2350.0000.0000.0000.000
151D157ASP-1-0.841-0.88634.494-8.299-8.2990.0000.0000.0000.000
152D158VAL0-0.077-0.01335.9070.2150.2150.0000.0000.0000.000
153D159TYR0-0.050-0.02432.134-0.263-0.2630.0000.0000.0000.000
154D160ILE00.0360.00431.2220.2910.2910.0000.0000.0000.000
155D161THR0-0.058-0.01129.072-0.240-0.2400.0000.0000.0000.000
156D162ASP-1-0.830-0.91124.002-12.627-12.6270.0000.0000.0000.000
157D163LYS10.7970.89126.13912.19512.1950.0000.0000.0000.000
158D164THR0-0.075-0.03426.834-0.429-0.4290.0000.0000.0000.000
159D165VAL00.0320.01427.7180.3040.3040.0000.0000.0000.000
160D166LEU0-0.032-0.00230.280-0.038-0.0380.0000.0000.0000.000
161D167ASP-1-0.758-0.86132.806-9.348-9.3480.0000.0000.0000.000
162D168MET0-0.0090.00734.7690.0900.0900.0000.0000.0000.000
163D169ARG10.7440.80434.8149.2519.2510.0000.0000.0000.000
164D170SER0-0.068-0.03838.0540.0470.0470.0000.0000.0000.000
165D171MET0-0.055-0.03641.0410.2420.2420.0000.0000.0000.000
166D172ASP-1-0.859-0.90637.301-8.649-8.6490.0000.0000.0000.000
167D173PHE00.0130.02637.901-0.175-0.1750.0000.0000.0000.000
168D174LYS10.8280.90132.5539.5629.5620.0000.0000.0000.000
169D175SER0-0.017-0.04334.6840.0340.0340.0000.0000.0000.000
170D176ASN0-0.029-0.01030.516-0.589-0.5890.0000.0000.0000.000
171D177SER0-0.026-0.01532.0440.3580.3580.0000.0000.0000.000
172D178ALA00.0300.01031.305-0.422-0.4220.0000.0000.0000.000
173D179VAL0-0.009-0.00332.8470.3790.3790.0000.0000.0000.000
174D180ALA00.0260.01433.686-0.283-0.2830.0000.0000.0000.000
175D181TRP0-0.034-0.02132.4630.2640.2640.0000.0000.0000.000
176D182SER00.015-0.01437.518-0.113-0.1130.0000.0000.0000.000
177D183ASN0-0.052-0.03440.1540.0550.0550.0000.0000.0000.000
178D184LYS10.7780.86840.1198.0638.0630.0000.0000.0000.000
179D185SER0-0.020-0.04044.4210.0000.0000.0000.0000.0000.000
180D186ASP-1-0.894-0.92144.507-6.796-6.7960.0000.0000.0000.000
181D187PHE0-0.0320.00438.577-0.118-0.1180.0000.0000.0000.000
182D188ALA00.0560.01743.1640.1620.1620.0000.0000.0000.000
183D190ALA00.0170.01041.667-0.134-0.1340.0000.0000.0000.000
184D191ASN0-0.064-0.04741.571-0.103-0.1030.0000.0000.0000.000
185D192ALA0-0.0020.00938.423-0.197-0.1970.0000.0000.0000.000
186D193PHE00.0750.03434.279-0.232-0.2320.0000.0000.0000.000
187D194ASN00.0500.03835.765-0.235-0.2350.0000.0000.0000.000
188D195ASN0-0.126-0.09430.8450.2590.2590.0000.0000.0000.000
189D196SER0-0.0010.02431.778-0.452-0.4520.0000.0000.0000.000
190D197ILE0-0.023-0.00531.0150.2750.2750.0000.0000.0000.000
191D198ILE00.0060.00533.068-0.262-0.2620.0000.0000.0000.000
192D199PRO00.0300.01035.6660.1210.1210.0000.0000.0000.000
193D200GLU-1-0.933-0.94838.396-7.548-7.5480.0000.0000.0000.000
194D201ASP-1-0.944-0.97041.687-7.292-7.2920.0000.0000.0000.000
195D202THR0-0.095-0.05939.712-0.011-0.0110.0000.0000.0000.000
196D203PHE00.0160.00342.0490.2000.2000.0000.0000.0000.000
197D204PHE00.0240.00041.107-0.153-0.1530.0000.0000.0000.000
198D205PRO0-0.036-0.01045.9150.1870.1870.0000.0000.0000.000
199D206SER0-0.050-0.01349.0000.0710.0710.0000.0000.0000.000