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: J3789

Calculation Name: 2IFT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IFT

Chain ID: A

ChEMBL ID:

UniProt ID: P44869

Base Structure: X-ray

Registration Date: 2023-06-19

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1965566.981582
FMO2-HF: Nuclear repulsion 1895466.113268
FMO2-HF: Total energy -70100.868314
FMO2-MP2: Total energy -70308.285429


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:11:GLY)


Summations of interaction energy for fragment #1(A:11:GLY)
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.
0.6624.6221.748-2.695-3.014-0.008
Interaction energy analysis for fragmet #1(A:11:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.072 / q_NPA : 0.040
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].
3A13VAL00.0280.0133.8040.4342.411-0.018-1.140-0.8190.004
4A14ARG10.8620.9207.1390.6140.6140.0000.0000.0000.000
5A15ILE00.0170.03010.0280.1490.1490.0000.0000.0000.000
6A16ILE00.0140.02213.2780.0280.0280.0000.0000.0000.000
7A17ALA0-0.033-0.03615.8100.0450.0450.0000.0000.0000.000
8A18GLY00.0640.07718.659-0.040-0.0400.0000.0000.0000.000
9A19LEU0-0.006-0.01220.899-0.012-0.0120.0000.0000.0000.000
10A20TRP0-0.019-0.01616.351-0.039-0.0390.0000.0000.0000.000
11A21ARG10.8990.98116.0040.2180.2180.0000.0000.0000.000
12A22GLY0-0.030-0.02514.8370.0300.0300.0000.0000.0000.000
13A23ARG10.9580.98812.2370.7560.7560.0000.0000.0000.000
14A24LYS10.8210.8957.7771.5311.5310.0000.0000.0000.000
15A25LEU0-0.033-0.0138.1140.1490.1490.0000.0000.0000.000
16A26PRO00.0120.0215.213-0.886-0.8860.0000.0000.0000.000
17A27VAL00.0050.0182.3182.0031.7891.278-0.226-0.8380.002
18A28LEU00.0420.0292.802-4.943-2.7460.488-1.329-1.357-0.014
19A38ASP-1-0.755-0.87016.7900.0490.0490.0000.0000.0000.000
20A39ARG10.8610.90018.374-0.077-0.0770.0000.0000.0000.000
21A40VAL0-0.006-0.01221.996-0.017-0.0170.0000.0000.0000.000
22A41LYS11.0251.00514.4430.0710.0710.0000.0000.0000.000
23A42GLU-1-0.839-0.91219.542-0.180-0.1800.0000.0000.0000.000
24A43THR0-0.065-0.02822.3150.0000.0000.0000.0000.0000.000
25A44LEU00.0180.03221.6210.0020.0020.0000.0000.0000.000
26A45PHE00.051-0.00118.590-0.006-0.0060.0000.0000.0000.000
27A46ASN0-0.062-0.02824.208-0.011-0.0110.0000.0000.0000.000
28A47TRP0-0.014-0.02327.1380.0030.0030.0000.0000.0000.000
29A48LEU00.0630.04324.3360.0010.0010.0000.0000.0000.000
30A49MET0-0.063-0.01026.103-0.006-0.0060.0000.0000.0000.000
31A50PRO0-0.043-0.01228.462-0.004-0.0040.0000.0000.0000.000
32A51TYR00.0390.00330.6300.0030.0030.0000.0000.0000.000
33A52ILE0-0.029-0.00523.717-0.002-0.0020.0000.0000.0000.000
34A53HIS00.0680.03727.431-0.012-0.0120.0000.0000.0000.000
35A54GLN0-0.094-0.05629.1520.0020.0020.0000.0000.0000.000
36A55SER0-0.062-0.01826.7040.0060.0060.0000.0000.0000.000
37A56GLU-1-0.943-0.98526.204-0.162-0.1620.0000.0000.0000.000
38A57CYS0-0.046-0.03721.8750.0120.0120.0000.0000.0000.000
39A58LEU00.0240.02421.408-0.013-0.0130.0000.0000.0000.000
40A59ASP-1-0.885-0.94815.245-0.258-0.2580.0000.0000.0000.000
41A60GLY00.011-0.00918.263-0.012-0.0120.0000.0000.0000.000
42A61PHE00.0150.00116.1020.0180.0180.0000.0000.0000.000
43A62ALA00.0370.03713.6400.0040.0040.0000.0000.0000.000
44A63GLY00.0740.04710.723-0.007-0.0070.0000.0000.0000.000
45A64SER0-0.061-0.0526.876-0.138-0.1380.0000.0000.0000.000
46A65GLY00.0540.0318.252-0.229-0.2290.0000.0000.0000.000
47A66SER0-0.026-0.0229.934-0.019-0.0190.0000.0000.0000.000
48A67LEU00.0140.01811.3660.0050.0050.0000.0000.0000.000
49A68GLY00.0890.04414.9580.0120.0120.0000.0000.0000.000
50A69PHE00.002-0.02710.6080.0000.0000.0000.0000.0000.000
51A70GLU-1-0.840-0.90614.934-0.418-0.4180.0000.0000.0000.000
52A71ALA00.0330.00216.4710.0310.0310.0000.0000.0000.000
53A72LEU0-0.020-0.00517.0110.0110.0110.0000.0000.0000.000
54A73SER0-0.066-0.07117.4750.0210.0210.0000.0000.0000.000
55A74ARG10.8050.89018.6850.2680.2680.0000.0000.0000.000
56A75GLN0-0.028-0.01922.4120.0320.0320.0000.0000.0000.000
57A76ALA00.0160.01922.9230.0220.0220.0000.0000.0000.000
58A77LYS10.9100.98424.6470.1300.1300.0000.0000.0000.000
59A78LYS10.9460.95924.2950.1840.1840.0000.0000.0000.000
60A79VAL0-0.0180.02118.3730.0130.0130.0000.0000.0000.000
61A80THR00.0050.00521.258-0.017-0.0170.0000.0000.0000.000
62A81PHE0-0.039-0.04214.689-0.002-0.0020.0000.0000.0000.000
63A82LEU0-0.0020.01218.204-0.003-0.0030.0000.0000.0000.000
64A83GLU-1-0.859-0.94413.562-0.131-0.1310.0000.0000.0000.000
65A84LEU00.0010.00716.745-0.006-0.0060.0000.0000.0000.000
66A85ASP-1-0.813-0.90013.630-0.010-0.0100.0000.0000.0000.000
67A86LYS10.9550.96614.8090.1290.1290.0000.0000.0000.000
68A87THR0-0.028-0.02410.739-0.083-0.0830.0000.0000.0000.000
69A88VAL00.0140.0189.551-0.163-0.1630.0000.0000.0000.000
70A89ALA00.0310.01711.329-0.146-0.1460.0000.0000.0000.000
71A90ASN0-0.047-0.03613.609-0.015-0.0150.0000.0000.0000.000
72A91GLN0-0.033-0.0087.7340.1860.1860.0000.0000.0000.000
73A92LEU00.0200.01511.099-0.114-0.1140.0000.0000.0000.000
74A93LYS10.9880.99012.6620.3170.3170.0000.0000.0000.000
75A94LYS10.9690.99010.0021.3131.3130.0000.0000.0000.000
76A95ASN00.019-0.0078.621-0.033-0.0330.0000.0000.0000.000
77A96LEU00.0180.01013.0470.0380.0380.0000.0000.0000.000
78A97GLN0-0.078-0.01916.2550.0150.0150.0000.0000.0000.000
79A98THR0-0.074-0.03013.109-0.021-0.0210.0000.0000.0000.000
80A99LEU0-0.063-0.03813.8240.0390.0390.0000.0000.0000.000
81A100LYS10.9080.94717.4700.4130.4130.0000.0000.0000.000
82A101CYS00.0150.02319.2420.0160.0160.0000.0000.0000.000
83A102SER0-0.026-0.00221.783-0.009-0.0090.0000.0000.0000.000
84A103SER00.0380.00023.698-0.017-0.0170.0000.0000.0000.000
85A104GLU-1-0.879-0.94025.102-0.201-0.2010.0000.0000.0000.000
86A105GLN0-0.045-0.00422.7030.0040.0040.0000.0000.0000.000
87A106ALA0-0.015-0.02119.307-0.007-0.0070.0000.0000.0000.000
88A107GLU-1-0.920-0.95421.082-0.191-0.1910.0000.0000.0000.000
89A108VAL0-0.046-0.01516.776-0.011-0.0110.0000.0000.0000.000
90A109ILE0-0.0030.00619.4810.0130.0130.0000.0000.0000.000
91A110ASN0-0.042-0.03518.744-0.007-0.0070.0000.0000.0000.000
92A111GLN00.0280.00420.2310.0300.0300.0000.0000.0000.000
93A112SER00.0670.05120.326-0.011-0.0110.0000.0000.0000.000
94A113SER00.034-0.02620.753-0.007-0.0070.0000.0000.0000.000
95A114LEU0-0.027-0.00822.8760.0010.0010.0000.0000.0000.000
96A115ASP-1-0.902-0.96025.0320.0000.0000.0000.0000.0000.000
97A116PHE0-0.005-0.00824.600-0.004-0.0040.0000.0000.0000.000
98A117LEU0-0.015-0.01724.889-0.004-0.0040.0000.0000.0000.000
99A118LYS10.9180.97828.0870.0050.0050.0000.0000.0000.000
100A119GLN0-0.0010.02230.710-0.003-0.0030.0000.0000.0000.000
101A120PRO00.0210.01732.616-0.006-0.0060.0000.0000.0000.000
102A121GLN0-0.080-0.04531.711-0.009-0.0090.0000.0000.0000.000
103A122ASN00.0180.00735.0140.0060.0060.0000.0000.0000.000
104A123GLN0-0.031-0.01235.9800.0050.0050.0000.0000.0000.000
105A124PRO00.0470.04433.415-0.005-0.0050.0000.0000.0000.000
106A125HIS10.7870.87028.9650.0910.0910.0000.0000.0000.000
107A126PHE0-0.005-0.00425.280-0.010-0.0100.0000.0000.0000.000
108A127ASP-1-0.810-0.89827.947-0.104-0.1040.0000.0000.0000.000
109A128VAL0-0.001-0.01923.0560.0090.0090.0000.0000.0000.000
110A129VAL00.0160.01923.075-0.012-0.0120.0000.0000.0000.000
111A130PHE0-0.041-0.01918.2720.0110.0110.0000.0000.0000.000
112A131LEU0-0.007-0.01419.627-0.009-0.0090.0000.0000.0000.000
113A132ASP-1-0.899-0.96014.285-0.019-0.0190.0000.0000.0000.000
114A133PRO0-0.0110.02015.8740.0180.0180.0000.0000.0000.000
115A134PRO00.012-0.00815.4120.0220.0220.0000.0000.0000.000
116A135PHE00.0160.00517.556-0.027-0.0270.0000.0000.0000.000
117A136HIS0-0.051-0.04320.3970.0060.0060.0000.0000.0000.000
118A137PHE00.0290.02421.920-0.009-0.0090.0000.0000.0000.000
119A138ASN00.004-0.00324.712-0.007-0.0070.0000.0000.0000.000
120A139LEU00.0310.01820.632-0.014-0.0140.0000.0000.0000.000
121A140ALA00.0370.01422.321-0.015-0.0150.0000.0000.0000.000
122A141GLU-1-0.873-0.94123.8290.0260.0260.0000.0000.0000.000
123A142GLN0-0.039-0.02526.458-0.016-0.0160.0000.0000.0000.000
124A143ALA0-0.003-0.00324.176-0.009-0.0090.0000.0000.0000.000
125A144ILE0-0.0060.00425.972-0.012-0.0120.0000.0000.0000.000
126A145SER00.0110.01128.375-0.006-0.0060.0000.0000.0000.000
127A146LEU00.0230.01427.713-0.005-0.0050.0000.0000.0000.000
128A147LEU0-0.060-0.02525.832-0.008-0.0080.0000.0000.0000.000
129A148CYS0-0.039-0.02129.954-0.005-0.0050.0000.0000.0000.000
130A149GLU-1-0.940-0.97333.382-0.006-0.0060.0000.0000.0000.000
131A150ASN0-0.068-0.03531.9650.0000.0000.0000.0000.0000.000
132A151ASN0-0.014-0.00833.893-0.006-0.0060.0000.0000.0000.000
133A152TRP00.0330.01228.752-0.014-0.0140.0000.0000.0000.000
134A153LEU0-0.028-0.00828.197-0.012-0.0120.0000.0000.0000.000
135A154LYS10.9370.98831.1460.1080.1080.0000.0000.0000.000
136A155PRO00.0300.00933.1990.0020.0020.0000.0000.0000.000
137A156ASN0-0.020-0.02134.169-0.001-0.0010.0000.0000.0000.000
138A157ALA00.0020.02829.205-0.004-0.0040.0000.0000.0000.000
139A158LEU0-0.024-0.01326.8830.0100.0100.0000.0000.0000.000
140A159ILE00.002-0.00925.247-0.010-0.0100.0000.0000.0000.000
141A160TYR0-0.122-0.12118.0480.0080.0080.0000.0000.0000.000
142A161VAL00.0220.00621.822-0.003-0.0030.0000.0000.0000.000
143A162GLU-1-0.823-0.85416.3910.0600.0600.0000.0000.0000.000
144A163THR0-0.007-0.02020.3840.0060.0060.0000.0000.0000.000
145A164GLU-1-0.816-0.87721.8770.2300.2300.0000.0000.0000.000
146A165LYS10.7730.87122.913-0.196-0.1960.0000.0000.0000.000
147A166ASP-1-0.851-0.91624.7470.1270.1270.0000.0000.0000.000
148A167LYS10.8600.89628.223-0.125-0.1250.0000.0000.0000.000
149A168PRO0-0.0570.00526.981-0.004-0.0040.0000.0000.0000.000
150A169LEU00.0130.01126.384-0.003-0.0030.0000.0000.0000.000
151A170ILE00.0320.03130.2160.0000.0000.0000.0000.0000.000
152A171THR0-0.062-0.03232.556-0.001-0.0010.0000.0000.0000.000
153A172PRO00.0450.04631.8580.0010.0010.0000.0000.0000.000
154A173GLU-1-0.913-0.98234.856-0.005-0.0050.0000.0000.0000.000
155A174ASN00.0000.02535.7230.0040.0040.0000.0000.0000.000
156A175TRP0-0.002-0.01428.568-0.005-0.0050.0000.0000.0000.000
157A176THR00.001-0.00234.0860.0030.0030.0000.0000.0000.000
158A177LEU0-0.012-0.00329.412-0.005-0.0050.0000.0000.0000.000
159A178LEU0-0.0080.00330.3260.0010.0010.0000.0000.0000.000
160A179LYS10.8330.89327.3500.0170.0170.0000.0000.0000.000
161A180GLU-1-0.793-0.90227.2620.0410.0410.0000.0000.0000.000
162A181LYS10.8470.94824.518-0.001-0.0010.0000.0000.0000.000
163A182THR00.0950.04824.3230.0010.0010.0000.0000.0000.000
164A183THR0-0.055-0.02620.335-0.009-0.0090.0000.0000.0000.000
165A184GLY00.0090.00320.9150.0180.0180.0000.0000.0000.000
166A185ILE00.040-0.02217.573-0.009-0.0090.0000.0000.0000.000
167A186VAL00.0250.03117.489-0.001-0.0010.0000.0000.0000.000
168A187SER0-0.018-0.01220.931-0.010-0.0100.0000.0000.0000.000
169A188TYR0-0.038-0.02217.736-0.001-0.0010.0000.0000.0000.000
170A189ARG10.8760.93222.900-0.054-0.0540.0000.0000.0000.000
171A190LEU0-0.019-0.00424.522-0.010-0.0100.0000.0000.0000.000
172A191TYR00.0400.00926.7990.0080.0080.0000.0000.0000.000
173A192GLN0-0.022-0.01329.222-0.014-0.0140.0000.0000.0000.000
174A193ASN0-0.059-0.04531.9170.0120.0120.0000.0000.0000.000
175A194LEU0-0.037-0.01533.641-0.005-0.0050.0000.0000.0000.000
176A195GLU-1-0.846-0.91436.281-0.037-0.0370.0000.0000.0000.000