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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: 2JGRR

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1722423.297448
FMO2-HF: Nuclear repulsion 1649064.439634
FMO2-HF: Total energy -73358.857814
FMO2-MP2: Total energy -73569.348546


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.
-24-19.3357.654-5.004-7.316-0.004
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 : -0.022 / q_NPA : -0.034
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].
3A12LEU0-0.006-0.0033.855-1.399-0.222-0.006-0.525-0.6460.001
4A13SER00.0350.0066.5710.5600.5600.0000.0000.0000.000
5A14ILE0-0.046-0.0099.8150.0080.0080.0000.0000.0000.000
6A15GLN00.030-0.01613.0500.0200.0200.0000.0000.0000.000
7A16GLU-1-0.908-0.97116.885-0.749-0.7490.0000.0000.0000.000
8A17GLY0-0.0070.00219.2600.0750.0750.0000.0000.0000.000
9A18GLU-1-0.834-0.90215.477-1.042-1.0420.0000.0000.0000.000
10A19ASN0-0.028-0.00915.6790.0220.0220.0000.0000.0000.000
11A20ALA00.0550.03810.978-0.124-0.1240.0000.0000.0000.000
12A21THR0-0.033-0.03410.1470.3120.3120.0000.0000.0000.000
13A22MET00.0050.0317.080-0.514-0.5140.0000.0000.0000.000
14A23ASN00.0310.0256.8060.6340.6340.0000.0000.0000.000
15A24CYS0-0.059-0.0186.9550.0900.0900.0000.0000.0000.000
16A25SER0-0.015-0.0108.6590.2770.2770.0000.0000.0000.000
17A26TYR0-0.028-0.0309.8270.0530.0530.0000.0000.0000.000
18A27LYS10.9940.99812.019-0.894-0.8940.0000.0000.0000.000
19A28THR00.0200.00015.1420.0030.0030.0000.0000.0000.000
20A29SER0-0.003-0.00117.487-0.037-0.0370.0000.0000.0000.000
21A30ILE0-0.0200.00816.9890.0120.0120.0000.0000.0000.000
22A31ASN00.0370.01120.0000.0270.0270.0000.0000.0000.000
23A32ASN0-0.074-0.05420.204-0.013-0.0130.0000.0000.0000.000
24A33LEU00.0290.02713.0150.0380.0380.0000.0000.0000.000
25A34GLN00.0130.00715.200-0.021-0.0210.0000.0000.0000.000
26A35TRP00.0300.0117.672-0.153-0.1530.0000.0000.0000.000
27A36TYR00.004-0.01111.7510.2090.2090.0000.0000.0000.000
28A37ARG10.8480.91811.0740.7990.7990.0000.0000.0000.000
29A38GLN0-0.026-0.01010.5820.1240.1240.0000.0000.0000.000
30A39ASN00.0460.02412.064-0.215-0.2150.0000.0000.0000.000
31A40SER00.0590.01114.8830.0600.0600.0000.0000.0000.000
32A41GLY00.0250.02812.3410.1370.1370.0000.0000.0000.000
33A42ARG10.9110.95113.3910.3960.3960.0000.0000.0000.000
34A43GLY00.0620.03515.455-0.003-0.0030.0000.0000.0000.000
35A44LEU0-0.022-0.01211.750-0.105-0.1050.0000.0000.0000.000
36A45VAL0-0.0080.00315.1250.1170.1170.0000.0000.0000.000
37A46HIS0-0.002-0.00815.507-0.137-0.1370.0000.0000.0000.000
38A47LEU0-0.031-0.00213.1710.0050.0050.0000.0000.0000.000
39A48ILE00.004-0.00115.8540.0680.0680.0000.0000.0000.000
40A49LEU00.0040.01917.181-0.039-0.0390.0000.0000.0000.000
41A50ILE0-0.0210.00217.6210.0360.0360.0000.0000.0000.000
42A51ARG10.8840.92520.2410.3060.3060.0000.0000.0000.000
43A52SER00.0240.01122.011-0.021-0.0210.0000.0000.0000.000
44A53ASN00.0220.01322.9340.0030.0030.0000.0000.0000.000
45A54GLU-1-0.812-0.88023.037-0.377-0.3770.0000.0000.0000.000
46A55ARG10.9840.98722.0980.3480.3480.0000.0000.0000.000
47A56GLU-1-0.814-0.89020.698-0.592-0.5920.0000.0000.0000.000
48A57LYS10.7790.87920.5730.5090.5090.0000.0000.0000.000
49A58HIS00.0590.02320.787-0.068-0.0680.0000.0000.0000.000
50A59SER0-0.005-0.00120.1950.0570.0570.0000.0000.0000.000
51A60GLY00.0420.02321.298-0.049-0.0490.0000.0000.0000.000
52A61ARG10.8070.88318.6080.9220.9220.0000.0000.0000.000
53A62LEU0-0.0080.01816.127-0.089-0.0890.0000.0000.0000.000
54A63ARG10.8490.88917.5330.7340.7340.0000.0000.0000.000
55A64VAL0-0.031-0.00514.532-0.123-0.1230.0000.0000.0000.000
56A65THR00.0150.00715.5220.1400.1400.0000.0000.0000.000
57A66LEU0-0.014-0.00916.056-0.086-0.0860.0000.0000.0000.000
58A67ASP-1-0.740-0.84917.187-0.175-0.1750.0000.0000.0000.000
59A68THR0-0.004-0.00417.6610.0060.0060.0000.0000.0000.000
60A69SER0-0.033-0.00820.0330.0450.0450.0000.0000.0000.000
61A70LYS10.9340.95816.9220.2470.2470.0000.0000.0000.000
62A71LYS10.8510.94315.556-0.095-0.0950.0000.0000.0000.000
63A72SER0-0.019-0.01612.9350.0160.0160.0000.0000.0000.000
64A73SER0-0.016-0.03512.366-0.033-0.0330.0000.0000.0000.000
65A74SER00.000-0.01311.272-0.159-0.1590.0000.0000.0000.000
66A75LEU00.0050.00511.2110.2590.2590.0000.0000.0000.000
67A76LEU00.0100.01011.982-0.260-0.2600.0000.0000.0000.000
68A77ILE0-0.007-0.00513.0000.1280.1280.0000.0000.0000.000
69A78THR0-0.002-0.01815.766-0.006-0.0060.0000.0000.0000.000
70A79ALA00.0250.01018.7440.0120.0120.0000.0000.0000.000
71A80SER0-0.055-0.04216.046-0.011-0.0110.0000.0000.0000.000
72A81ARG10.9500.96618.1880.7010.7010.0000.0000.0000.000
73A82ALA00.0960.05017.475-0.113-0.1130.0000.0000.0000.000
74A83ALA0-0.014-0.00317.038-0.069-0.0690.0000.0000.0000.000
75A84ASP-1-0.793-0.86014.854-1.098-1.0980.0000.0000.0000.000
76A85THR00.0160.02412.467-0.323-0.3230.0000.0000.0000.000
77A86ALA0-0.034-0.01011.2620.2540.2540.0000.0000.0000.000
78A87SER0-0.0030.0096.708-0.910-0.9100.0000.0000.0000.000
79A88TYR0-0.014-0.0327.1850.7460.7460.0000.0000.0000.000
80A89PHE0-0.018-0.0156.289-1.322-1.3220.0000.0000.0000.000
81A91ALA00.0330.0049.8400.0860.0860.0000.0000.0000.000
82A92PRO00.0150.01011.7060.0560.0560.0000.0000.0000.000
83A93PHE00.0250.01514.7730.0540.0540.0000.0000.0000.000
84A94ASP-1-0.820-0.90218.3900.0170.0170.0000.0000.0000.000
85A95ARG10.9290.95120.9650.1160.1160.0000.0000.0000.000
86A96GLY00.0430.03924.379-0.005-0.0050.0000.0000.0000.000
87A97SER0-0.088-0.05127.8530.0040.0040.0000.0000.0000.000
88A98THR00.0470.01629.566-0.014-0.0140.0000.0000.0000.000
89A99LEU0-0.0100.00923.927-0.002-0.0020.0000.0000.0000.000
90A100GLY00.032-0.02123.456-0.012-0.0120.0000.0000.0000.000
91A101ARG10.9210.97618.608-0.064-0.0640.0000.0000.0000.000
92A102LEU0-0.0040.00915.7070.0080.0080.0000.0000.0000.000
93A103TYR0-0.056-0.02813.5690.0580.0580.0000.0000.0000.000
94A104PHE00.013-0.01010.143-0.128-0.1280.0000.0000.0000.000
95A105GLY0-0.0070.0016.9550.3380.3380.0000.0000.0000.000
96A106ARG10.9110.9422.239-11.618-9.1732.760-2.009-3.1960.027
97A107GLY00.0350.0344.2570.9351.2100.001-0.080-0.1960.000
98A108THR0-0.038-0.0332.074-13.288-12.8434.897-2.339-3.003-0.032
99A109GLN00.0010.0103.6992.5552.8780.002-0.051-0.2750.000
100A110LEU00.0340.0215.926-0.919-0.9190.0000.0000.0000.000
101A111THR0-0.032-0.0328.6960.4960.4960.0000.0000.0000.000
102A112VAL0-0.0270.00311.741-0.112-0.1120.0000.0000.0000.000
103A113TRP00.0480.01712.3910.1790.1790.0000.0000.0000.000
104A114PRO00.0340.00717.154-0.008-0.0080.0000.0000.0000.000
105A115ASP-1-0.847-0.88520.431-0.597-0.5970.0000.0000.0000.000
106A116ILE0-0.067-0.02522.4590.0180.0180.0000.0000.0000.000
107A117GLN00.0110.00725.001-0.006-0.0060.0000.0000.0000.000
108A118ASN0-0.049-0.04128.5610.0110.0110.0000.0000.0000.000
109A119PRO0-0.019-0.00225.5650.0070.0070.0000.0000.0000.000
110A120ASP-1-0.927-0.95227.593-0.165-0.1650.0000.0000.0000.000
111A121PRO0-0.059-0.02025.5770.0030.0030.0000.0000.0000.000
112A122ALA00.0400.02927.3720.0200.0200.0000.0000.0000.000
113A123VAL0-0.016-0.01726.646-0.008-0.0080.0000.0000.0000.000
114A124TYR00.0000.00929.2050.0160.0160.0000.0000.0000.000
115A125GLN0-0.017-0.02730.5280.0010.0010.0000.0000.0000.000
116A126LEU0-0.038-0.00831.0100.0000.0000.0000.0000.0000.000
117A127ARG10.9960.97134.1040.0480.0480.0000.0000.0000.000
118A128ASP-1-0.791-0.87636.562-0.023-0.0230.0000.0000.0000.000
119A129SER00.0240.01037.4250.0000.0000.0000.0000.0000.000
120A130LYS10.8260.91139.1360.0040.0040.0000.0000.0000.000
121A131SER00.0080.00041.0610.0050.0050.0000.0000.0000.000
122A132SER0-0.028-0.01439.3070.0070.0070.0000.0000.0000.000
123A133ASP-1-0.847-0.92139.5220.0070.0070.0000.0000.0000.000
124A134LYS10.8010.90434.574-0.004-0.0040.0000.0000.0000.000
125A135SER0-0.017-0.00933.898-0.010-0.0100.0000.0000.0000.000
126A136VAL0-0.007-0.00128.7360.0110.0110.0000.0000.0000.000
127A137CYS0-0.031-0.02626.9210.0020.0020.0000.0000.0000.000
128A138LEU00.005-0.00425.7390.0000.0000.0000.0000.0000.000
129A139PHE00.0170.02521.1690.0040.0040.0000.0000.0000.000
130A140THR00.009-0.05724.450-0.019-0.0190.0000.0000.0000.000
131A141ASP-1-0.805-0.87725.644-0.233-0.2330.0000.0000.0000.000
132A142PHE00.0170.02419.028-0.005-0.0050.0000.0000.0000.000
133A143ASP-1-0.767-0.86220.718-0.424-0.4240.0000.0000.0000.000
134A144SER0-0.024-0.04117.8440.0140.0140.0000.0000.0000.000
135A145GLN0-0.017-0.01616.339-0.066-0.0660.0000.0000.0000.000
136A146THR0-0.057-0.02817.0760.0220.0220.0000.0000.0000.000
137A147ASN0-0.051-0.02213.892-0.085-0.0850.0000.0000.0000.000
138A148VAL00.023-0.00115.5750.0410.0410.0000.0000.0000.000
139A149SER0-0.046-0.01215.6880.0120.0120.0000.0000.0000.000
140A150GLN00.0450.02512.948-0.059-0.0590.0000.0000.0000.000
141A151SER00.0150.00916.927-0.011-0.0110.0000.0000.0000.000
142A152LYS10.9170.94119.154-0.164-0.1640.0000.0000.0000.000
143A153ASP-1-0.841-0.91921.4990.1470.1470.0000.0000.0000.000
144A154SER00.0360.01723.593-0.001-0.0010.0000.0000.0000.000
145A155ASP-1-0.816-0.85524.6320.1530.1530.0000.0000.0000.000
146A156VAL0-0.0440.00224.109-0.026-0.0260.0000.0000.0000.000
147A157TYR0-0.046-0.02122.1550.0310.0310.0000.0000.0000.000
148A158ILE0-0.014-0.02719.308-0.027-0.0270.0000.0000.0000.000
149A159THR0-0.067-0.02918.5660.0410.0410.0000.0000.0000.000
150A160ASP-1-0.894-0.94313.059-0.103-0.1030.0000.0000.0000.000
151A161LYS10.8380.94715.1860.6840.6840.0000.0000.0000.000
152A162CYS0-0.024-0.02116.518-0.061-0.0610.0000.0000.0000.000
153A163VAL0-0.0060.00819.0770.0170.0170.0000.0000.0000.000
154A164LEU0-0.027-0.00221.103-0.004-0.0040.0000.0000.0000.000
155A165ASP-1-0.807-0.90624.686-0.406-0.4060.0000.0000.0000.000
156A166MET00.002-0.00127.1450.0220.0220.0000.0000.0000.000
157A167ARG10.8140.88228.8870.3590.3590.0000.0000.0000.000
158A168SER0-0.042-0.01531.8640.0010.0010.0000.0000.0000.000
159A169MET0-0.032-0.02034.2530.0140.0140.0000.0000.0000.000
160A170ASP-1-0.873-0.92332.134-0.325-0.3250.0000.0000.0000.000
161A171PHE00.0300.02429.633-0.026-0.0260.0000.0000.0000.000
162A172LYS10.8520.90523.9000.4530.4530.0000.0000.0000.000
163A173SER0-0.022-0.00325.0690.0050.0050.0000.0000.0000.000
164A174ASN0-0.027-0.02319.659-0.066-0.0660.0000.0000.0000.000
165A175SER0-0.004-0.00321.3330.0450.0450.0000.0000.0000.000
166A176ALA00.0280.00919.776-0.033-0.0330.0000.0000.0000.000
167A177VAL0-0.002-0.00121.5060.0160.0160.0000.0000.0000.000
168A178ALA00.0180.01022.4250.0160.0160.0000.0000.0000.000
169A179TRP0-0.019-0.01122.632-0.014-0.0140.0000.0000.0000.000
170A180SER0-0.001-0.02026.5470.0160.0160.0000.0000.0000.000
171A181ASN0-0.036-0.02529.009-0.005-0.0050.0000.0000.0000.000
172A182LYS10.7670.86429.346-0.122-0.1220.0000.0000.0000.000
173A183SER00.0200.00133.092-0.007-0.0070.0000.0000.0000.000
174A184ASP-1-0.923-0.96035.7270.0330.0330.0000.0000.0000.000
175A185PHE00.001-0.00127.396-0.004-0.0040.0000.0000.0000.000
176A186ALA00.0300.02233.279-0.010-0.0100.0000.0000.0000.000
177A188ALA00.0040.00629.570-0.008-0.0080.0000.0000.0000.000
178A189ASN0-0.023-0.01628.7850.0030.0030.0000.0000.0000.000
179A190ALA00.0160.02625.8220.0100.0100.0000.0000.0000.000
180A191PHE0-0.002-0.02021.327-0.013-0.0130.0000.0000.0000.000
181A192ASN0-0.0310.00222.217-0.034-0.0340.0000.0000.0000.000
182A193ASN0-0.037-0.02019.1250.0320.0320.0000.0000.0000.000