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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: MVZ8Z

Calculation Name: 2CDG-A-Xray372

Preferred Name: T-cell receptor

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 2CDG

Chain ID: A

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1714713.119291
FMO2-HF: Nuclear repulsion 1641355.919581
FMO2-HF: Total energy -73357.19971
FMO2-MP2: Total energy -73567.606414


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:10:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-19.616-14.5916.855-4.769-7.111-0.016
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.031
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].
3A12LEU0-0.002-0.0063.833-1.645-0.4630.000-0.497-0.6840.002
4A13SER00.0310.0166.4860.5010.5010.0000.0000.0000.000
5A14ILE0-0.044-0.0109.731-0.022-0.0220.0000.0000.0000.000
6A15GLN00.0590.03312.7540.0390.0390.0000.0000.0000.000
7A16GLU-1-0.890-0.97816.583-0.777-0.7770.0000.0000.0000.000
8A17GLY0-0.024-0.01218.5910.0720.0720.0000.0000.0000.000
9A18GLU-1-0.874-0.93115.218-0.994-0.9940.0000.0000.0000.000
10A19ASN00.000-0.00615.434-0.025-0.0250.0000.0000.0000.000
11A20ALA00.0240.01310.879-0.121-0.1210.0000.0000.0000.000
12A21THR0-0.009-0.00510.4200.2290.2290.0000.0000.0000.000
13A22MET00.0050.0226.725-0.673-0.6730.0000.0000.0000.000
14A23ASN00.0010.0077.0070.8910.8910.0000.0000.0000.000
15A24CYS0-0.034-0.0197.181-0.102-0.1020.0000.0000.0000.000
16A25SER00.0130.0188.9660.3070.3070.0000.0000.0000.000
17A26TYR00.0140.00410.2900.0410.0410.0000.0000.0000.000
18A27LYS10.9930.98713.013-0.414-0.4140.0000.0000.0000.000
19A28THR00.0160.00415.732-0.010-0.0100.0000.0000.0000.000
20A29SER0-0.0010.00318.458-0.043-0.0430.0000.0000.0000.000
21A30ILE00.0110.02017.6720.0190.0190.0000.0000.0000.000
22A31ASN00.006-0.01020.8840.0580.0580.0000.0000.0000.000
23A32ASN0-0.057-0.04220.308-0.030-0.0300.0000.0000.0000.000
24A33LEU00.0350.03313.2820.0120.0120.0000.0000.0000.000
25A34GLN00.0060.00415.670-0.024-0.0240.0000.0000.0000.000
26A35TRP00.0290.0167.826-0.206-0.2060.0000.0000.0000.000
27A36TYR0-0.013-0.01611.7520.2490.2490.0000.0000.0000.000
28A37ARG10.8930.94211.0910.8860.8860.0000.0000.0000.000
29A38GLN0-0.006-0.00810.7080.1280.1280.0000.0000.0000.000
30A39ASN00.0560.02912.147-0.261-0.2610.0000.0000.0000.000
31A40SER00.0420.01214.5260.0790.0790.0000.0000.0000.000
32A41GLY00.0300.01712.4350.1610.1610.0000.0000.0000.000
33A42ARG10.9160.95913.4210.4350.4350.0000.0000.0000.000
34A43GLY00.0210.01815.450-0.046-0.0460.0000.0000.0000.000
35A44LEU0-0.002-0.01212.264-0.110-0.1100.0000.0000.0000.000
36A45VAL0-0.0120.00015.3460.1330.1330.0000.0000.0000.000
37A46HIS0-0.041-0.02515.813-0.108-0.1080.0000.0000.0000.000
38A47LEU0-0.0270.00113.2360.0360.0360.0000.0000.0000.000
39A48ILE00.0250.00916.1810.1010.1010.0000.0000.0000.000
40A49LEU0-0.008-0.00917.513-0.046-0.0460.0000.0000.0000.000
41A50ILE0-0.048-0.01117.8510.0440.0440.0000.0000.0000.000
42A51ARG10.8820.91820.5710.4100.4100.0000.0000.0000.000
43A52SER00.0420.02522.556-0.026-0.0260.0000.0000.0000.000
44A53ASN00.0020.01323.724-0.006-0.0060.0000.0000.0000.000
45A54GLU-1-0.900-0.95223.489-0.509-0.5090.0000.0000.0000.000
46A55ARG11.0141.01522.5850.4280.4280.0000.0000.0000.000
47A56GLU-1-0.918-0.97120.838-0.693-0.6930.0000.0000.0000.000
48A57LYS10.9300.97021.1730.6700.6700.0000.0000.0000.000
49A58HIS00.016-0.00220.974-0.081-0.0810.0000.0000.0000.000
50A59SER0-0.009-0.01020.8120.0600.0600.0000.0000.0000.000
51A60GLY00.0060.01621.831-0.044-0.0440.0000.0000.0000.000
52A61ARG10.8180.89318.2810.9930.9930.0000.0000.0000.000
53A62LEU0-0.0030.01616.225-0.098-0.0980.0000.0000.0000.000
54A63ARG10.9500.97617.4820.8580.8580.0000.0000.0000.000
55A64VAL0-0.0230.00315.152-0.123-0.1230.0000.0000.0000.000
56A65THR00.0270.01315.6060.1450.1450.0000.0000.0000.000
57A66LEU00.0180.00416.233-0.126-0.1260.0000.0000.0000.000
58A67ASP-1-0.806-0.90717.456-0.464-0.4640.0000.0000.0000.000
59A68THR0-0.033-0.02718.818-0.004-0.0040.0000.0000.0000.000
60A69SER0-0.042-0.02121.1380.0620.0620.0000.0000.0000.000
61A70LYS10.9870.99216.8880.3910.3910.0000.0000.0000.000
62A71LYS10.8560.95816.1480.1350.1350.0000.0000.0000.000
63A72SER0-0.016-0.00212.740-0.006-0.0060.0000.0000.0000.000
64A73SER0-0.042-0.04212.5450.0040.0040.0000.0000.0000.000
65A74SER00.007-0.00411.611-0.233-0.2330.0000.0000.0000.000
66A75LEU00.0050.00611.6370.2600.2600.0000.0000.0000.000
67A76LEU00.005-0.00712.278-0.234-0.2340.0000.0000.0000.000
68A77ILE0-0.0070.00213.0720.1500.1500.0000.0000.0000.000
69A78THR0-0.006-0.01715.9910.0170.0170.0000.0000.0000.000
70A79ALA00.0080.00818.9110.0280.0280.0000.0000.0000.000
71A80SER0-0.050-0.03316.117-0.017-0.0170.0000.0000.0000.000
72A81ARG10.9460.97317.8970.7590.7590.0000.0000.0000.000
73A82ALA00.1190.06217.113-0.123-0.1230.0000.0000.0000.000
74A83ALA0-0.034-0.02116.871-0.068-0.0680.0000.0000.0000.000
75A84ASP-1-0.784-0.87614.551-1.211-1.2110.0000.0000.0000.000
76A85THR00.0060.02412.162-0.315-0.3150.0000.0000.0000.000
77A86ALA0-0.046-0.02310.9750.2480.2480.0000.0000.0000.000
78A87SER0-0.0130.0166.783-1.018-1.0180.0000.0000.0000.000
79A88TYR00.007-0.0156.7940.8110.8110.0000.0000.0000.000
80A89PHE0-0.011-0.0056.241-1.555-1.5550.0000.0000.0000.000
81A91ALA00.0390.0049.9200.0950.0950.0000.0000.0000.000
82A92PRO00.0020.01612.6240.0760.0760.0000.0000.0000.000
83A93PHE00.0530.02315.6610.0600.0600.0000.0000.0000.000
84A94ASP-1-0.871-0.94519.235-0.205-0.2050.0000.0000.0000.000
85A95ARG10.9020.94321.7450.2580.2580.0000.0000.0000.000
86A96GLY00.0360.02825.046-0.002-0.0020.0000.0000.0000.000
87A97SER0-0.090-0.05228.5740.0160.0160.0000.0000.0000.000
88A98THR00.0320.02530.075-0.017-0.0170.0000.0000.0000.000
89A99LEU0-0.0190.00224.114-0.015-0.0150.0000.0000.0000.000
90A100GLY00.061-0.01923.912-0.012-0.0120.0000.0000.0000.000
91A101ARG10.9060.96919.5400.0800.0800.0000.0000.0000.000
92A102LEU00.0150.02016.1240.0000.0000.0000.0000.0000.000
93A103TYR0-0.036-0.00813.9190.0620.0620.0000.0000.0000.000
94A104PHE00.025-0.00310.433-0.135-0.1350.0000.0000.0000.000
95A105GLY0-0.018-0.0077.6340.2910.2910.0000.0000.0000.000
96A106ARG10.8990.9442.217-7.539-4.5410.957-1.609-2.3470.015
97A107GLY00.0500.0354.0570.9181.3120.002-0.112-0.2840.000
98A108THR0-0.032-0.0262.102-14.616-14.5355.888-2.516-3.453-0.032
99A109GLN00.0170.0093.4823.1763.5460.008-0.035-0.343-0.001
100A110LEU00.0180.0205.637-0.593-0.5930.0000.0000.0000.000
101A111THR0-0.023-0.0208.3620.5450.5450.0000.0000.0000.000
102A112VAL0-0.024-0.00211.257-0.106-0.1060.0000.0000.0000.000
103A113TRP00.009-0.00212.2300.1800.1800.0000.0000.0000.000
104A114PRO00.0230.00617.107-0.030-0.0300.0000.0000.0000.000
105A115ASP-1-0.860-0.93120.245-0.544-0.5440.0000.0000.0000.000
106A116ILE0-0.087-0.03222.2460.0200.0200.0000.0000.0000.000
107A117GLN00.0280.03624.730-0.013-0.0130.0000.0000.0000.000
108A118ASN0-0.052-0.04728.2800.0020.0020.0000.0000.0000.000
109A119PRO0-0.030-0.00925.7470.0080.0080.0000.0000.0000.000
110A120ASP-1-0.911-0.95127.683-0.116-0.1160.0000.0000.0000.000
111A121PRO0-0.058-0.01525.6940.0100.0100.0000.0000.0000.000
112A122ALA00.0370.02027.4100.0160.0160.0000.0000.0000.000
113A123VAL00.007-0.00726.637-0.002-0.0020.0000.0000.0000.000
114A124TYR0-0.010-0.00229.1900.0100.0100.0000.0000.0000.000
115A125GLN00.0340.01630.7350.0030.0030.0000.0000.0000.000
116A126LEU0-0.026-0.01731.288-0.010-0.0100.0000.0000.0000.000
117A127ARG10.9520.95734.309-0.007-0.0070.0000.0000.0000.000
118A128ASP-1-0.852-0.92036.3910.0280.0280.0000.0000.0000.000
119A129SER00.0290.01537.417-0.001-0.0010.0000.0000.0000.000
120A130LYS10.8720.94939.275-0.048-0.0480.0000.0000.0000.000
121A131SER00.013-0.00740.7390.0050.0050.0000.0000.0000.000
122A132SER0-0.093-0.04538.6320.0090.0090.0000.0000.0000.000
123A133ASP-1-0.801-0.90139.6740.0570.0570.0000.0000.0000.000
124A134LYS10.8520.93834.263-0.074-0.0740.0000.0000.0000.000
125A135SER0-0.034-0.01933.701-0.015-0.0150.0000.0000.0000.000
126A136VAL00.0080.00928.7780.0160.0160.0000.0000.0000.000
127A137CYS0-0.032-0.02327.3160.0050.0050.0000.0000.0000.000
128A138LEU0-0.006-0.01326.0860.0050.0050.0000.0000.0000.000
129A139PHE00.0040.02821.352-0.004-0.0040.0000.0000.0000.000
130A140THR0-0.009-0.06324.285-0.017-0.0170.0000.0000.0000.000
131A141ASP-1-0.834-0.89725.656-0.161-0.1610.0000.0000.0000.000
132A142PHE0-0.022-0.00519.058-0.007-0.0070.0000.0000.0000.000
133A143ASP-1-0.803-0.90620.824-0.330-0.3300.0000.0000.0000.000
134A144SER0-0.014-0.03918.0240.0230.0230.0000.0000.0000.000
135A145GLN0-0.112-0.03416.465-0.043-0.0430.0000.0000.0000.000
136A146THR00.0230.02717.5360.0640.0640.0000.0000.0000.000
137A147ASN0-0.052-0.03314.623-0.097-0.0970.0000.0000.0000.000
138A148VAL00.0330.01715.5860.0250.0250.0000.0000.0000.000
139A149SER0-0.0300.00015.4820.0520.0520.0000.0000.0000.000
140A150GLN00.0320.01712.162-0.057-0.0570.0000.0000.0000.000
141A151SER00.0270.01216.912-0.020-0.0200.0000.0000.0000.000
142A152LYS10.9170.95219.772-0.380-0.3800.0000.0000.0000.000
143A153ASP-1-0.861-0.95821.3590.2650.2650.0000.0000.0000.000
144A154SER0-0.0150.00023.3580.0010.0010.0000.0000.0000.000
145A155ASP-1-0.903-0.93724.3660.2880.2880.0000.0000.0000.000
146A156VAL0-0.076-0.03323.830-0.035-0.0350.0000.0000.0000.000
147A157TYR0-0.033-0.00622.2670.0550.0550.0000.0000.0000.000
148A158ILE0-0.007-0.01919.166-0.045-0.0450.0000.0000.0000.000
149A159THR0-0.064-0.02318.8010.0530.0530.0000.0000.0000.000
150A160ASP-1-0.878-0.93413.0880.2820.2820.0000.0000.0000.000
151A161LYS10.8850.95514.5960.4740.4740.0000.0000.0000.000
152A162CYS0-0.046-0.03417.261-0.053-0.0530.0000.0000.0000.000
153A163VAL00.0230.02819.1000.0150.0150.0000.0000.0000.000
154A164LEU0-0.0010.01021.267-0.019-0.0190.0000.0000.0000.000
155A165ASP-1-0.833-0.93224.538-0.375-0.3750.0000.0000.0000.000
156A166MET00.0090.01526.6650.0200.0200.0000.0000.0000.000
157A167ARG10.8420.90028.0820.3390.3390.0000.0000.0000.000
158A168SER0-0.057-0.03031.298-0.002-0.0020.0000.0000.0000.000
159A169MET0-0.005-0.01233.7210.0120.0120.0000.0000.0000.000
160A170ASP-1-0.936-0.95831.370-0.311-0.3110.0000.0000.0000.000
161A171PHE00.0290.00329.616-0.007-0.0070.0000.0000.0000.000
162A172LYS10.8790.94723.7300.4230.4230.0000.0000.0000.000
163A173SER00.0520.03325.2280.0060.0060.0000.0000.0000.000
164A174ASN0-0.020-0.00819.954-0.042-0.0420.0000.0000.0000.000
165A175SER00.0080.00321.7080.0350.0350.0000.0000.0000.000
166A176ALA0-0.012-0.00219.816-0.018-0.0180.0000.0000.0000.000
167A177VAL00.0020.00021.7430.0020.0020.0000.0000.0000.000
168A178ALA00.0170.01222.7630.0320.0320.0000.0000.0000.000
169A179TRP0-0.021-0.01122.948-0.025-0.0250.0000.0000.0000.000
170A180SER00.0260.01326.6910.0230.0230.0000.0000.0000.000
171A181ASN0-0.005-0.01029.231-0.014-0.0140.0000.0000.0000.000
172A182LYS10.8840.95031.092-0.220-0.2200.0000.0000.0000.000
173A183SER00.0170.00033.646-0.007-0.0070.0000.0000.0000.000
174A184ASP-1-0.907-0.95036.5020.0980.0980.0000.0000.0000.000
175A185PHE0-0.049-0.02727.831-0.002-0.0020.0000.0000.0000.000
176A186ALA00.0310.01533.633-0.011-0.0110.0000.0000.0000.000
177A188ALA0-0.049-0.02229.634-0.003-0.0030.0000.0000.0000.000
178A189ASN00.0210.00328.664-0.010-0.0100.0000.0000.0000.000
179A190ALA00.0120.02325.8840.0140.0140.0000.0000.0000.000
180A191PHE00.008-0.01321.486-0.022-0.0220.0000.0000.0000.000
181A192ASN0-0.045-0.00822.042-0.021-0.0210.0000.0000.0000.000
182A193ASN0-0.015-0.01119.4110.0510.0510.0000.0000.0000.000