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: JQ6R9

Calculation Name: 2IAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IAI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9XA31

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2145651.015149
FMO2-HF: Nuclear repulsion 2065250.708819
FMO2-HF: Total energy -80400.30633
FMO2-MP2: Total energy -80636.545314


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:-8:GLY)


Summations of interaction energy for fragment #1(A:-8: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.
-9.389-4.9532.081-2.581-3.9360.005
Interaction energy analysis for fragmet #1(A:-8:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.005
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].
3A-6GLU-1-0.745-0.8053.436-6.370-4.8880.014-0.768-0.728-0.002
4A-5ASN00.0170.0025.6660.5650.5650.0000.0000.0000.000
5A-4LEU00.0170.0029.122-0.005-0.0050.0000.0000.0000.000
6A-3TYR0-0.060-0.02911.1620.1440.1440.0000.0000.0000.000
7A-2PHE00.0510.02214.5960.0820.0820.0000.0000.0000.000
8A-1GLN0-0.018-0.01716.049-0.018-0.0180.0000.0000.0000.000
9A0GLY00.0120.01614.5230.0290.0290.0000.0000.0000.000
10A1MET0-0.0330.00113.046-0.028-0.0280.0000.0000.0000.000
11A2THR0-0.003-0.0197.4100.0000.0000.0000.0000.0000.000
12A3THR0-0.021-0.0315.4370.1120.1120.0000.0000.0000.000
13A4ALA00.0100.0096.929-0.147-0.1470.0000.0000.0000.000
14A5LYS10.8080.8942.785-6.166-5.0621.230-0.903-1.4310.011
15A6ARG10.7870.8522.708-1.4820.1890.838-0.904-1.605-0.004
16A7ASP-1-0.792-0.8814.8724.2214.400-0.001-0.006-0.1720.000
17A8THR0-0.011-0.0077.542-0.325-0.3250.0000.0000.0000.000
18A9TYR0-0.030-0.0129.0200.1000.1000.0000.0000.0000.000
19A10THR0-0.019-0.02813.1330.0110.0110.0000.0000.0000.000
20A11PRO0-0.0110.00314.803-0.017-0.0170.0000.0000.0000.000
21A12GLU-1-0.887-0.93016.7890.1510.1510.0000.0000.0000.000
22A13THR00.004-0.00819.9700.0100.0100.0000.0000.0000.000
23A14LEU00.0560.00822.739-0.007-0.0070.0000.0000.0000.000
24A15LEU0-0.0090.00523.770-0.008-0.0080.0000.0000.0000.000
25A16SER00.0450.03422.543-0.008-0.0080.0000.0000.0000.000
26A17VAL00.0420.01919.098-0.012-0.0120.0000.0000.0000.000
27A18ALA0-0.021-0.02921.605-0.012-0.0120.0000.0000.0000.000
28A19VAL00.000-0.00124.615-0.011-0.0110.0000.0000.0000.000
29A20GLN00.0240.01118.420-0.003-0.0030.0000.0000.0000.000
30A21VAL00.0140.00420.661-0.012-0.0120.0000.0000.0000.000
31A22PHE0-0.036-0.02823.055-0.007-0.0070.0000.0000.0000.000
32A23ILE0-0.026-0.00325.026-0.007-0.0070.0000.0000.0000.000
33A24GLU-1-0.874-0.91619.610-0.003-0.0030.0000.0000.0000.000
34A25ARG10.8020.89819.140-0.013-0.0130.0000.0000.0000.000
35A26GLY00.0470.03626.2590.0000.0000.0000.0000.0000.000
36A27TYR00.0460.01428.6720.0080.0080.0000.0000.0000.000
37A28ASP-1-0.905-0.94930.5730.0190.0190.0000.0000.0000.000
38A29GLY00.0300.01128.9960.0040.0040.0000.0000.0000.000
39A30THR0-0.0020.00825.2710.0040.0040.0000.0000.0000.000
40A31SER00.005-0.00424.8250.0050.0050.0000.0000.0000.000
41A32MET00.0480.00824.9580.0030.0030.0000.0000.0000.000
42A33GLU-1-0.811-0.87321.4120.1400.1400.0000.0000.0000.000
43A34HIS00.0240.01420.5960.0170.0170.0000.0000.0000.000
44A35LEU00.0380.02920.1330.0120.0120.0000.0000.0000.000
45A36SER0-0.054-0.03820.2960.0150.0150.0000.0000.0000.000
46A37LYS10.7950.86615.386-0.140-0.1400.0000.0000.0000.000
47A38ALA00.0200.02015.6680.0280.0280.0000.0000.0000.000
48A39ALA00.0160.01416.8000.0150.0150.0000.0000.0000.000
49A40GLY00.0230.03415.5720.0310.0310.0000.0000.0000.000
50A41ILE00.0020.01016.1990.0270.0270.0000.0000.0000.000
51A42SER00.0300.01819.464-0.027-0.0270.0000.0000.0000.000
52A43LYS10.9280.92421.869-0.116-0.1160.0000.0000.0000.000
53A44SER0-0.0070.01224.931-0.007-0.0070.0000.0000.0000.000
54A45SER00.0270.00923.139-0.013-0.0130.0000.0000.0000.000
55A46ILE00.0330.00623.303-0.005-0.0050.0000.0000.0000.000
56A47TYR0-0.020-0.01726.435-0.008-0.0080.0000.0000.0000.000
57A48HIS0-0.0390.00426.721-0.014-0.0140.0000.0000.0000.000
58A49HIS0-0.0240.00525.464-0.011-0.0110.0000.0000.0000.000
59A50VAL0-0.029-0.02628.796-0.010-0.0100.0000.0000.0000.000
60A51THR00.0550.02631.3230.0040.0040.0000.0000.0000.000
61A52GLY00.0380.00730.7920.0000.0000.0000.0000.0000.000
62A53LYS10.8350.89429.248-0.034-0.0340.0000.0000.0000.000
63A54GLU-1-0.782-0.86230.6640.0330.0330.0000.0000.0000.000
64A55GLU-1-0.761-0.83733.1750.0540.0540.0000.0000.0000.000
65A56LEU0-0.034-0.01626.9800.0000.0000.0000.0000.0000.000
66A57LEU00.0340.01530.716-0.002-0.0020.0000.0000.0000.000
67A58ARG10.8820.90932.480-0.049-0.0490.0000.0000.0000.000
68A59ARG10.8010.87730.999-0.076-0.0760.0000.0000.0000.000
69A60ALA00.0180.01630.363-0.002-0.0020.0000.0000.0000.000
70A61VAL0-0.013-0.02232.231-0.004-0.0040.0000.0000.0000.000
71A62SER0-0.065-0.04535.539-0.003-0.0030.0000.0000.0000.000
72A63ARG10.7540.85531.983-0.030-0.0300.0000.0000.0000.000
73A64ALA00.0160.00234.709-0.003-0.0030.0000.0000.0000.000
74A65LEU0-0.034-0.02036.364-0.003-0.0030.0000.0000.0000.000
75A66ASP-1-0.861-0.91838.9480.0270.0270.0000.0000.0000.000
76A67GLU-1-0.836-0.90536.2320.0210.0210.0000.0000.0000.000
77A68LEU0-0.021-0.01039.347-0.002-0.0020.0000.0000.0000.000
78A69PHE0-0.052-0.05441.652-0.002-0.0020.0000.0000.0000.000
79A70GLY00.0140.02043.394-0.001-0.0010.0000.0000.0000.000
80A71ILE00.0180.02041.749-0.001-0.0010.0000.0000.0000.000
81A72LEU0-0.060-0.03345.623-0.001-0.0010.0000.0000.0000.000
82A73ASP-1-0.842-0.89548.4250.0100.0100.0000.0000.0000.000
83A74GLU-1-0.758-0.81444.4370.0080.0080.0000.0000.0000.000
84A75GLU-1-0.899-0.94949.1200.0050.0050.0000.0000.0000.000
85A76HIS0-0.010-0.02350.399-0.001-0.0010.0000.0000.0000.000
86A77ALA00.0130.02149.696-0.001-0.0010.0000.0000.0000.000
87A78ARG10.7620.86751.786-0.008-0.0080.0000.0000.0000.000
88A79VAL0-0.032-0.00654.9260.0000.0000.0000.0000.0000.000
89A80GLY00.0630.04056.3930.0000.0000.0000.0000.0000.000
90A81THR0-0.022-0.03058.6980.0010.0010.0000.0000.0000.000
91A82ALA0-0.020-0.02157.4170.0000.0000.0000.0000.0000.000
92A83ALA0-0.003-0.00555.8890.0000.0000.0000.0000.0000.000
93A84GLU-1-0.874-0.91654.454-0.003-0.0030.0000.0000.0000.000
94A85ARG10.7870.89852.938-0.001-0.0010.0000.0000.0000.000
95A86LEU0-0.026-0.01051.2960.0000.0000.0000.0000.0000.000
96A87GLU-1-0.821-0.90349.616-0.010-0.0100.0000.0000.0000.000
97A88TYR0-0.040-0.04146.522-0.001-0.0010.0000.0000.0000.000
98A89VAL00.019-0.00446.8930.0000.0000.0000.0000.0000.000
99A90VAL0-0.014-0.01345.5910.0000.0000.0000.0000.0000.000
100A91ARG10.7630.85044.1720.0100.0100.0000.0000.0000.000
101A92ARG10.8540.88040.326-0.005-0.0050.0000.0000.0000.000
102A93MET0-0.060-0.02041.1870.0010.0010.0000.0000.0000.000
103A94VAL0-0.0020.00539.0270.0000.0000.0000.0000.0000.000
104A95GLU-1-0.869-0.92737.805-0.004-0.0040.0000.0000.0000.000
105A96VAL0-0.004-0.00236.5010.0010.0010.0000.0000.0000.000
106A97LEU0-0.072-0.02034.9930.0020.0020.0000.0000.0000.000
107A98MET0-0.056-0.01633.368-0.003-0.0030.0000.0000.0000.000
108A99ALA0-0.0250.00031.794-0.001-0.0010.0000.0000.0000.000
109A100GLU-1-0.806-0.89031.0150.0260.0260.0000.0000.0000.000
110A101LEU00.0430.04928.3130.0030.0030.0000.0000.0000.000
111A102PRO0-0.010-0.00226.736-0.001-0.0010.0000.0000.0000.000
112A103TYR00.027-0.00228.1670.0040.0040.0000.0000.0000.000
113A104VAL00.0520.01731.4760.0010.0010.0000.0000.0000.000
114A105THR00.001-0.00930.083-0.003-0.0030.0000.0000.0000.000
115A106LEU0-0.064-0.03228.525-0.001-0.0010.0000.0000.0000.000
116A107LEU0-0.0050.00132.5400.0000.0000.0000.0000.0000.000
117A108LEU0-0.027-0.01435.7510.0000.0000.0000.0000.0000.000
118A109ARG10.8760.93128.2960.0140.0140.0000.0000.0000.000
119A110VAL0-0.055-0.00535.5590.0000.0000.0000.0000.0000.000
120A111ARG10.8760.93637.294-0.002-0.0020.0000.0000.0000.000
121A112GLY00.0600.04638.285-0.001-0.0010.0000.0000.0000.000
122A113ASN0-0.008-0.00939.4180.0000.0000.0000.0000.0000.000
123A114THR0-0.035-0.02737.1270.0020.0020.0000.0000.0000.000
124A115GLY0-0.020-0.01240.504-0.002-0.0020.0000.0000.0000.000
125A116THR0-0.007-0.02636.564-0.001-0.0010.0000.0000.0000.000
126A117GLU-1-0.784-0.87737.2250.0160.0160.0000.0000.0000.000
127A118ARG10.8880.94840.013-0.022-0.0220.0000.0000.0000.000
128A119TRP00.0550.03639.392-0.002-0.0020.0000.0000.0000.000
129A120ALA00.0400.01139.435-0.001-0.0010.0000.0000.0000.000
130A121LEU0-0.020-0.02141.428-0.003-0.0030.0000.0000.0000.000
131A122GLU-1-0.963-0.99643.6810.0140.0140.0000.0000.0000.000
132A123ARG10.9130.96743.287-0.017-0.0170.0000.0000.0000.000
133A124ARG10.9080.95039.619-0.004-0.0040.0000.0000.0000.000
134A125ARG10.8870.95544.654-0.010-0.0100.0000.0000.0000.000
135A126GLU-1-0.912-0.95448.3120.0080.0080.0000.0000.0000.000
136A127PHE00.0160.00344.836-0.001-0.0010.0000.0000.0000.000
137A128ASP-1-0.845-0.90447.609-0.003-0.0030.0000.0000.0000.000
138A129HIS00.0190.01749.133-0.002-0.0020.0000.0000.0000.000
139A130ARG10.8460.90850.345-0.010-0.0100.0000.0000.0000.000
140A131VAL00.0380.02347.747-0.001-0.0010.0000.0000.0000.000
141A132ALA0-0.010-0.00551.165-0.001-0.0010.0000.0000.0000.000
142A133ALA0-0.056-0.02353.786-0.001-0.0010.0000.0000.0000.000
143A134LEU00.0460.02751.6920.0000.0000.0000.0000.0000.000
144A135LEU00.0120.01152.852-0.001-0.0010.0000.0000.0000.000
145A136LYS10.8590.91355.750-0.001-0.0010.0000.0000.0000.000
146A137ASP-1-0.885-0.93958.7390.0010.0010.0000.0000.0000.000
147A138ALA00.0180.00957.2190.0000.0000.0000.0000.0000.000
148A139ALA0-0.035-0.01359.303-0.001-0.0010.0000.0000.0000.000
149A140ALA0-0.088-0.04561.4840.0000.0000.0000.0000.0000.000
150A141GLU-1-0.830-0.91661.702-0.001-0.0010.0000.0000.0000.000
151A142GLY0-0.0260.00063.7170.0000.0000.0000.0000.0000.000
152A143ASP-1-0.848-0.90859.640-0.005-0.0050.0000.0000.0000.000
153A144VAL0-0.064-0.03356.857-0.001-0.0010.0000.0000.0000.000
154A145ARG10.7860.85357.4000.0120.0120.0000.0000.0000.000
155A146ALA00.0640.01860.4190.0000.0000.0000.0000.0000.000
156A147ASP-1-0.841-0.87361.444-0.010-0.0100.0000.0000.0000.000
157A148VAL0-0.044-0.02756.190-0.001-0.0010.0000.0000.0000.000
158A149GLU-1-0.846-0.92458.015-0.004-0.0040.0000.0000.0000.000
159A150VAL00.0840.05256.637-0.001-0.0010.0000.0000.0000.000
160A151ARG10.9110.94253.5540.0000.0000.0000.0000.0000.000
161A152LEU0-0.0210.00452.7460.0000.0000.0000.0000.0000.000
162A153ALA00.0310.01052.324-0.001-0.0010.0000.0000.0000.000
163A154THR00.022-0.00650.038-0.001-0.0010.0000.0000.0000.000
164A155ARG10.7840.87247.4550.0040.0040.0000.0000.0000.000
165A156LEU0-0.004-0.00747.503-0.001-0.0010.0000.0000.0000.000
166A157VAL00.0330.02847.053-0.002-0.0020.0000.0000.0000.000
167A158PHE00.010-0.01044.9000.0000.0000.0000.0000.0000.000
168A159GLY0-0.0200.00043.2200.0000.0000.0000.0000.0000.000
169A160MET0-0.026-0.01242.256-0.002-0.0020.0000.0000.0000.000
170A161ILE00.0380.01940.950-0.002-0.0020.0000.0000.0000.000
171A162ASN0-0.021-0.04338.9660.0000.0000.0000.0000.0000.000
172A163SER0-0.015-0.00437.476-0.001-0.0010.0000.0000.0000.000
173A164ILE00.0240.01735.353-0.003-0.0030.0000.0000.0000.000
174A165VAL0-0.036-0.02732.590-0.003-0.0030.0000.0000.0000.000
175A166GLU-1-0.996-0.99731.561-0.033-0.0330.0000.0000.0000.000
176A167TRP0-0.069-0.03231.792-0.006-0.0060.0000.0000.0000.000
177A168TYR0-0.051-0.04331.225-0.003-0.0030.0000.0000.0000.000
178A169ARG10.8110.86724.3930.0880.0880.0000.0000.0000.000
179A170PRO0-0.0050.02226.4710.0000.0000.0000.0000.0000.000
180A171GLU-1-0.863-0.90126.283-0.085-0.0850.0000.0000.0000.000
181A183SER00.010-0.00540.0880.0000.0000.0000.0000.0000.000
182A184GLY0-0.0020.00439.6150.0010.0010.0000.0000.0000.000
183A185VAL0-0.001-0.01835.210-0.002-0.0020.0000.0000.0000.000
184A186SER00.0270.02233.507-0.002-0.0020.0000.0000.0000.000
185A187GLY00.0640.03633.9000.0020.0020.0000.0000.0000.000
186A188ALA0-0.016-0.00735.5430.0010.0010.0000.0000.0000.000
187A189GLY00.0930.04735.2020.0010.0010.0000.0000.0000.000
188A190GLU-1-0.805-0.89532.681-0.029-0.0290.0000.0000.0000.000
189A191ARG10.8730.92236.6630.0210.0210.0000.0000.0000.000
190A192GLU-1-0.961-0.96638.544-0.037-0.0370.0000.0000.0000.000
191A193VAL00.0260.00536.6510.0010.0010.0000.0000.0000.000
192A194VAL00.0080.00739.7070.0010.0010.0000.0000.0000.000
193A195ASP-1-0.762-0.85541.988-0.016-0.0160.0000.0000.0000.000
194A196ALA0-0.054-0.02042.7420.0000.0000.0000.0000.0000.000
195A197VAL00.005-0.00641.7220.0010.0010.0000.0000.0000.000
196A198ALA00.0190.02144.8270.0010.0010.0000.0000.0000.000
197A199ARG10.8350.89646.9270.0200.0200.0000.0000.0000.000
198A200LEU0-0.031-0.02244.9920.0000.0000.0000.0000.0000.000
199A201VAL0-0.039-0.02347.3050.0000.0000.0000.0000.0000.000
200A202PHE00.0240.01150.0020.0010.0010.0000.0000.0000.000
201A203GLY0-0.0220.00352.6020.0010.0010.0000.0000.0000.000
202A204GLY0-0.059-0.01351.1660.0000.0000.0000.0000.0000.000
203A205LEU00.002-0.01948.003-0.001-0.0010.0000.0000.0000.000
204A206ARG10.8830.95052.0140.0180.0180.0000.0000.0000.000
205A207LYS11.0381.02754.2740.0260.0260.0000.0000.0000.000