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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: 724NK

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1715606.600032
FMO2-HF: Nuclear repulsion 1642248.336177
FMO2-HF: Total energy -73358.263855
FMO2-MP2: Total energy -73568.632937


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.
-21.165-14.5144.136-4.033-6.7550.006
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 : -0.013 / q_NPA : -0.027
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].
3A12LEU00.003-0.0023.833-2.014-0.797-0.003-0.544-0.6710.001
4A13SER00.0370.0206.4860.7070.7070.0000.0000.0000.000
5A14ILE0-0.043-0.0159.655-0.055-0.0550.0000.0000.0000.000
6A15GLN00.037-0.00112.7270.0460.0460.0000.0000.0000.000
7A16GLU-1-0.885-0.97316.538-0.776-0.7760.0000.0000.0000.000
8A17GLY0-0.026-0.01318.5730.0700.0700.0000.0000.0000.000
9A18GLU-1-0.855-0.91315.120-1.193-1.1930.0000.0000.0000.000
10A19ASN0-0.026-0.02615.4300.0170.0170.0000.0000.0000.000
11A20ALA00.0260.01810.933-0.156-0.1560.0000.0000.0000.000
12A21THR00.0070.00510.4890.2080.2080.0000.0000.0000.000
13A22MET00.0060.0236.608-0.698-0.6980.0000.0000.0000.000
14A23ASN00.0150.0206.9780.8930.8930.0000.0000.0000.000
15A24CYS0-0.028-0.0086.759-0.217-0.2170.0000.0000.0000.000
16A25SER0-0.0210.0048.3420.2860.2860.0000.0000.0000.000
17A26TYR00.0320.0109.7870.1550.1550.0000.0000.0000.000
18A27LYS11.0040.99312.535-0.896-0.8960.0000.0000.0000.000
19A28THR00.0390.02015.355-0.034-0.0340.0000.0000.0000.000
20A29SER00.0060.00618.052-0.026-0.0260.0000.0000.0000.000
21A30ILE00.0070.01417.2020.0170.0170.0000.0000.0000.000
22A31ASN00.008-0.01120.4090.0280.0280.0000.0000.0000.000
23A32ASN0-0.041-0.03120.126-0.026-0.0260.0000.0000.0000.000
24A33LEU00.0300.03313.1620.0400.0400.0000.0000.0000.000
25A34GLN00.0100.00515.366-0.034-0.0340.0000.0000.0000.000
26A35TRP00.0180.0127.557-0.101-0.1010.0000.0000.0000.000
27A36TYR0-0.007-0.02511.8550.1850.1850.0000.0000.0000.000
28A37ARG10.8780.93711.2180.7250.7250.0000.0000.0000.000
29A38GLN0-0.037-0.02711.0120.1840.1840.0000.0000.0000.000
30A39ASN00.0410.01912.492-0.232-0.2320.0000.0000.0000.000
31A40SER00.0550.01714.7510.0780.0780.0000.0000.0000.000
32A41GLY00.0160.01512.9730.1270.1270.0000.0000.0000.000
33A42ARG10.9280.96013.9210.2010.2010.0000.0000.0000.000
34A43GLY00.0480.03515.935-0.002-0.0020.0000.0000.0000.000
35A44LEU0-0.009-0.01212.163-0.100-0.1000.0000.0000.0000.000
36A45VAL0-0.018-0.00615.6300.0870.0870.0000.0000.0000.000
37A46HIS0-0.022-0.01816.007-0.124-0.1240.0000.0000.0000.000
38A47LEU0-0.0400.00013.1970.0070.0070.0000.0000.0000.000
39A48ILE00.0190.00616.0250.0580.0580.0000.0000.0000.000
40A49LEU00.0120.01017.478-0.015-0.0150.0000.0000.0000.000
41A50ILE0-0.031-0.00417.6370.0280.0280.0000.0000.0000.000
42A51ARG10.8540.90920.3210.3160.3160.0000.0000.0000.000
43A52SER00.0590.02822.246-0.027-0.0270.0000.0000.0000.000
44A53ASN00.0030.01323.248-0.010-0.0100.0000.0000.0000.000
45A54GLU-1-0.810-0.89423.215-0.389-0.3890.0000.0000.0000.000
46A55ARG10.9801.00122.2250.3840.3840.0000.0000.0000.000
47A56GLU-1-0.823-0.90520.718-0.679-0.6790.0000.0000.0000.000
48A57LYS10.8120.89520.6960.5170.5170.0000.0000.0000.000
49A58HIS00.0510.01420.674-0.081-0.0810.0000.0000.0000.000
50A59SER00.0140.01520.6350.0730.0730.0000.0000.0000.000
51A60GLY00.0010.00321.666-0.037-0.0370.0000.0000.0000.000
52A61ARG10.7940.86918.6380.9240.9240.0000.0000.0000.000
53A62LEU0-0.0020.01416.024-0.099-0.0990.0000.0000.0000.000
54A63ARG10.8660.90517.1540.8050.8050.0000.0000.0000.000
55A64VAL0-0.0210.00114.802-0.119-0.1190.0000.0000.0000.000
56A65THR00.0100.00515.8840.1040.1040.0000.0000.0000.000
57A66LEU00.0080.00115.870-0.085-0.0850.0000.0000.0000.000
58A67ASP-1-0.767-0.88917.424-0.342-0.3420.0000.0000.0000.000
59A68THR0-0.011-0.01818.1880.0100.0100.0000.0000.0000.000
60A69SER0-0.038-0.01420.4930.0500.0500.0000.0000.0000.000
61A70LYS10.9360.96916.9090.3920.3920.0000.0000.0000.000
62A71LYS10.8290.93415.809-0.042-0.0420.0000.0000.0000.000
63A72SER0-0.005-0.00612.8430.0480.0480.0000.0000.0000.000
64A73SER0-0.059-0.05012.0970.0060.0060.0000.0000.0000.000
65A74SER00.023-0.01011.368-0.203-0.2030.0000.0000.0000.000
66A75LEU0-0.023-0.00611.2550.2800.2800.0000.0000.0000.000
67A76LEU0-0.002-0.00912.169-0.262-0.2620.0000.0000.0000.000
68A77ILE0-0.0030.00412.8770.1700.1700.0000.0000.0000.000
69A78THR0-0.010-0.01515.831-0.014-0.0140.0000.0000.0000.000
70A79ALA00.0180.00718.9050.0400.0400.0000.0000.0000.000
71A80SER0-0.047-0.02616.0820.0080.0080.0000.0000.0000.000
72A81ARG10.9610.97518.2970.7130.7130.0000.0000.0000.000
73A82ALA00.1000.05017.525-0.113-0.1130.0000.0000.0000.000
74A83ALA0-0.027-0.01717.221-0.053-0.0530.0000.0000.0000.000
75A84ASP-1-0.767-0.84514.843-1.073-1.0730.0000.0000.0000.000
76A85THR00.0160.03512.534-0.288-0.2880.0000.0000.0000.000
77A86ALA0-0.041-0.01611.3410.2620.2620.0000.0000.0000.000
78A87SER0-0.0080.0157.116-0.867-0.8670.0000.0000.0000.000
79A88TYR0-0.010-0.0266.9100.7480.7480.0000.0000.0000.000
80A89PHE0-0.006-0.0026.365-1.121-1.1210.0000.0000.0000.000
81A91ALA00.0440.0099.6990.2050.2050.0000.0000.0000.000
82A92PRO0-0.0030.01112.2510.0050.0050.0000.0000.0000.000
83A93PHE00.0410.01315.2490.0610.0610.0000.0000.0000.000
84A94ASP-1-0.905-0.95218.8690.0270.0270.0000.0000.0000.000
85A95ARG10.9170.95621.3920.1040.1040.0000.0000.0000.000
86A96GLY00.0310.02624.746-0.011-0.0110.0000.0000.0000.000
87A97SER0-0.093-0.05328.2800.0060.0060.0000.0000.0000.000
88A98THR00.0340.02329.790-0.010-0.0100.0000.0000.0000.000
89A99LEU0-0.0100.00024.072-0.008-0.0080.0000.0000.0000.000
90A100GLY00.063-0.01223.669-0.018-0.0180.0000.0000.0000.000
91A101ARG10.9100.97119.185-0.145-0.1450.0000.0000.0000.000
92A102LEU00.0170.02415.917-0.002-0.0020.0000.0000.0000.000
93A103TYR0-0.036-0.01413.8340.0780.0780.0000.0000.0000.000
94A104PHE00.022-0.00310.405-0.139-0.1390.0000.0000.0000.000
95A105GLY0-0.020-0.0087.3280.2930.2930.0000.0000.0000.000
96A106ARG10.9190.9572.524-12.573-9.8161.894-1.793-2.8580.023
97A107GLY00.0270.0213.7810.8841.1680.002-0.100-0.1860.000
98A108THR0-0.044-0.0312.628-8.486-6.4192.235-1.564-2.738-0.018
99A109GLN00.0100.0033.5432.2962.6220.008-0.032-0.3020.000
100A110LEU00.0260.0195.937-0.944-0.9440.0000.0000.0000.000
101A111THR0-0.017-0.0188.7470.4990.4990.0000.0000.0000.000
102A112VAL0-0.019-0.00211.530-0.152-0.1520.0000.0000.0000.000
103A113TRP00.0170.00212.3260.2230.2230.0000.0000.0000.000
104A114PRO00.0240.00717.022-0.024-0.0240.0000.0000.0000.000
105A115ASP-1-0.849-0.90620.168-0.665-0.6650.0000.0000.0000.000
106A116ILE0-0.078-0.02522.1930.0320.0320.0000.0000.0000.000
107A117GLN00.0270.02324.654-0.014-0.0140.0000.0000.0000.000
108A118ASN0-0.053-0.04528.2080.0060.0060.0000.0000.0000.000
109A119PRO0-0.034-0.01425.5820.0110.0110.0000.0000.0000.000
110A120ASP-1-0.924-0.95427.612-0.172-0.1720.0000.0000.0000.000
111A121PRO0-0.049-0.01325.4900.0090.0090.0000.0000.0000.000
112A122ALA00.0330.02327.3370.0190.0190.0000.0000.0000.000
113A123VAL0-0.004-0.01326.572-0.006-0.0060.0000.0000.0000.000
114A124TYR0-0.012-0.00129.1110.0160.0160.0000.0000.0000.000
115A125GLN0-0.006-0.01330.6490.0000.0000.0000.0000.0000.000
116A126LEU0-0.024-0.00530.922-0.005-0.0050.0000.0000.0000.000
117A127ARG10.9810.96534.2170.0300.0300.0000.0000.0000.000
118A128ASP-1-0.810-0.87136.6150.0120.0120.0000.0000.0000.000
119A129SER00.0200.01037.509-0.002-0.0020.0000.0000.0000.000
120A130LYS10.8850.95039.529-0.032-0.0320.0000.0000.0000.000
121A131SER00.0540.01141.0090.0010.0010.0000.0000.0000.000
122A132SER0-0.135-0.08238.7120.0090.0090.0000.0000.0000.000
123A133ASP-1-0.815-0.90539.5880.0280.0280.0000.0000.0000.000
124A134LYS10.8010.90734.343-0.041-0.0410.0000.0000.0000.000
125A135SER0-0.032-0.01833.859-0.012-0.0120.0000.0000.0000.000
126A136VAL00.0020.00528.7260.0130.0130.0000.0000.0000.000
127A137CYS0-0.026-0.01827.2160.0030.0030.0000.0000.0000.000
128A138LEU0-0.001-0.01025.9100.0030.0030.0000.0000.0000.000
129A139PHE00.0110.03220.8690.0000.0000.0000.0000.0000.000
130A140THR00.003-0.06324.196-0.017-0.0170.0000.0000.0000.000
131A141ASP-1-0.804-0.87325.547-0.227-0.2270.0000.0000.0000.000
132A142PHE00.0060.01118.835-0.007-0.0070.0000.0000.0000.000
133A143ASP-1-0.813-0.90120.805-0.453-0.4530.0000.0000.0000.000
134A144SER0-0.011-0.03917.8080.0220.0220.0000.0000.0000.000
135A145GLN0-0.086-0.03016.407-0.078-0.0780.0000.0000.0000.000
136A146THR00.0160.01617.4790.0630.0630.0000.0000.0000.000
137A147ASN0-0.062-0.03414.130-0.111-0.1110.0000.0000.0000.000
138A148VAL00.0300.00915.5290.0510.0510.0000.0000.0000.000
139A149SER0-0.0160.00615.4110.0170.0170.0000.0000.0000.000
140A150GLN00.0240.01312.302-0.048-0.0480.0000.0000.0000.000
141A151SER00.0200.01316.849-0.021-0.0210.0000.0000.0000.000
142A152LYS10.9290.95619.722-0.191-0.1910.0000.0000.0000.000
143A153ASP-1-0.804-0.93521.3190.1680.1680.0000.0000.0000.000
144A154SER0-0.0110.00723.3030.0000.0000.0000.0000.0000.000
145A155ASP-1-0.820-0.88424.3140.1900.1900.0000.0000.0000.000
146A156VAL0-0.095-0.02623.996-0.027-0.0270.0000.0000.0000.000
147A157TYR0-0.0320.00022.1930.0390.0390.0000.0000.0000.000
148A158ILE0-0.020-0.02319.442-0.035-0.0350.0000.0000.0000.000
149A159THR0-0.054-0.01718.7170.0440.0440.0000.0000.0000.000
150A160ASP-1-0.890-0.93813.5200.0170.0170.0000.0000.0000.000
151A161LYS10.8940.96215.0470.7120.7120.0000.0000.0000.000
152A162CYS0-0.050-0.03217.157-0.035-0.0350.0000.0000.0000.000
153A163VAL00.0230.01819.0240.0140.0140.0000.0000.0000.000
154A164LEU0-0.0080.01221.273-0.004-0.0040.0000.0000.0000.000
155A165ASP-1-0.794-0.90224.665-0.392-0.3920.0000.0000.0000.000
156A166MET00.0120.01326.8590.0240.0240.0000.0000.0000.000
157A167ARG10.8450.89328.3480.3460.3460.0000.0000.0000.000
158A168SER0-0.054-0.02731.552-0.004-0.0040.0000.0000.0000.000
159A169MET0-0.016-0.01833.9420.0110.0110.0000.0000.0000.000
160A170ASP-1-0.916-0.92831.795-0.331-0.3310.0000.0000.0000.000
161A171PHE00.0200.01029.876-0.010-0.0100.0000.0000.0000.000
162A172LYS10.8260.90223.6510.4610.4610.0000.0000.0000.000
163A173SER0-0.011-0.00725.0850.0040.0040.0000.0000.0000.000
164A174ASN0-0.030-0.01520.158-0.045-0.0450.0000.0000.0000.000
165A175SER00.0010.00321.5910.0430.0430.0000.0000.0000.000
166A176ALA00.0090.00119.768-0.026-0.0260.0000.0000.0000.000
167A177VAL0-0.002-0.00221.6490.0110.0110.0000.0000.0000.000
168A178ALA00.0160.01322.6740.0210.0210.0000.0000.0000.000
169A179TRP0-0.019-0.00923.053-0.017-0.0170.0000.0000.0000.000
170A180SER00.007-0.02326.6120.0190.0190.0000.0000.0000.000
171A181ASN0-0.042-0.03229.155-0.004-0.0040.0000.0000.0000.000
172A182LYS10.8040.90329.686-0.152-0.1520.0000.0000.0000.000
173A183SER00.0240.00333.579-0.006-0.0060.0000.0000.0000.000
174A184ASP-1-0.916-0.95636.4380.0490.0490.0000.0000.0000.000
175A185PHE0-0.043-0.02227.646-0.005-0.0050.0000.0000.0000.000
176A186ALA00.0480.02633.564-0.009-0.0090.0000.0000.0000.000
177A188ALA0-0.041-0.01829.565-0.008-0.0080.0000.0000.0000.000
178A189ASN00.019-0.00228.615-0.011-0.0110.0000.0000.0000.000
179A190ALA00.0230.02925.8180.0040.0040.0000.0000.0000.000
180A191PHE00.023-0.00921.288-0.017-0.0170.0000.0000.0000.000
181A192ASN0-0.056-0.01021.984-0.033-0.0330.0000.0000.0000.000
182A193ASN0-0.026-0.01219.0130.0230.0230.0000.0000.0000.000