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: VQ681

Calculation Name: 1I49-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I49

Chain ID: A

ChEMBL ID:

UniProt ID: P53365

Base Structure: X-ray

Registration Date: 2023-09-23

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1894197.994888
FMO2-HF: Nuclear repulsion 1814393.647244
FMO2-HF: Total energy -79804.347644
FMO2-MP2: Total energy -80039.948881


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:23:SER)


Summations of interaction energy for fragment #1(A:23:SER)
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.
-2.703-0.993-0.024-0.791-0.8960.002
Interaction energy analysis for fragmet #1(A:23:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.019
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].
3A25THR0-0.046-0.0353.822-0.7260.773-0.023-0.729-0.7470.002
4A26VAL0-0.073-0.0365.4650.4420.4420.0000.0000.0000.000
5A27ASP-1-0.779-0.8918.184-0.271-0.2710.0000.0000.0000.000
6A28LEU00.026-0.00610.3050.0370.0370.0000.0000.0000.000
7A29GLU-1-0.874-0.92612.8620.0450.0450.0000.0000.0000.000
8A30LEU00.003-0.00115.6320.0200.0200.0000.0000.0000.000
9A31GLU-1-0.816-0.90910.4180.5360.5360.0000.0000.0000.000
10A32LEU00.0490.03315.0010.0200.0200.0000.0000.0000.000
11A33GLN0-0.011-0.00417.304-0.001-0.0010.0000.0000.0000.000
12A34ILE0-0.054-0.04416.560-0.011-0.0110.0000.0000.0000.000
13A35GLU-1-0.954-0.98017.4950.3640.3640.0000.0000.0000.000
14A36LEU00.0290.01219.361-0.013-0.0130.0000.0000.0000.000
15A37LEU0-0.0200.00422.639-0.012-0.0120.0000.0000.0000.000
16A38ARG10.8580.88917.062-0.302-0.3020.0000.0000.0000.000
17A39GLU-1-0.953-0.97623.3780.2240.2240.0000.0000.0000.000
18A40THR0-0.037-0.01725.042-0.018-0.0180.0000.0000.0000.000
19A41LYS10.9140.95426.746-0.150-0.1500.0000.0000.0000.000
20A42ARG10.9670.99522.511-0.266-0.2660.0000.0000.0000.000
21A43LYS10.9240.96328.112-0.178-0.1780.0000.0000.0000.000
22A44TYR00.040-0.01131.028-0.012-0.0120.0000.0000.0000.000
23A45GLU-1-0.872-0.92929.9730.1370.1370.0000.0000.0000.000
24A46SER0-0.068-0.03033.103-0.006-0.0060.0000.0000.0000.000
25A47VAL00.0380.01634.921-0.006-0.0060.0000.0000.0000.000
26A48LEU0-0.022-0.00236.367-0.007-0.0070.0000.0000.0000.000
27A49GLN0-0.043-0.02236.262-0.009-0.0090.0000.0000.0000.000
28A50LEU00.0180.00238.519-0.005-0.0050.0000.0000.0000.000
29A51GLY00.0400.02840.868-0.005-0.0050.0000.0000.0000.000
30A52ARG10.9380.96338.042-0.090-0.0900.0000.0000.0000.000
31A53ALA0-0.0100.02043.299-0.003-0.0030.0000.0000.0000.000
32A54LEU00.005-0.00444.937-0.003-0.0030.0000.0000.0000.000
33A55THR0-0.027-0.01946.409-0.004-0.0040.0000.0000.0000.000
34A56ALA0-0.017-0.01047.623-0.003-0.0030.0000.0000.0000.000
35A57HIS00.017-0.00847.168-0.004-0.0040.0000.0000.0000.000
36A58LEU00.0160.01950.946-0.002-0.0020.0000.0000.0000.000
37A59TYR00.0270.01752.449-0.003-0.0030.0000.0000.0000.000
38A60SER00.0070.00153.437-0.002-0.0020.0000.0000.0000.000
39A61LEU0-0.043-0.02155.172-0.002-0.0020.0000.0000.0000.000
40A62LEU00.011-0.00455.987-0.002-0.0020.0000.0000.0000.000
41A63GLN0-0.013-0.00157.809-0.001-0.0010.0000.0000.0000.000
42A64THR0-0.022-0.00259.282-0.001-0.0010.0000.0000.0000.000
43A65GLN0-0.033-0.02360.425-0.001-0.0010.0000.0000.0000.000
44A66HIS00.0470.03161.689-0.002-0.0020.0000.0000.0000.000
45A67ALA0-0.0110.01564.387-0.001-0.0010.0000.0000.0000.000
46A68LEU0-0.042-0.01964.827-0.001-0.0010.0000.0000.0000.000
47A69GLY00.0420.01666.928-0.001-0.0010.0000.0000.0000.000
48A70ASP-1-0.910-0.96368.7630.0300.0300.0000.0000.0000.000
49A71ALA0-0.035-0.01470.168-0.001-0.0010.0000.0000.0000.000
50A72PHE0-0.009-0.01868.777-0.001-0.0010.0000.0000.0000.000
51A73ALA00.0040.00572.924-0.001-0.0010.0000.0000.0000.000
52A74ASP-1-0.856-0.92274.8160.0260.0260.0000.0000.0000.000
53A75LEU0-0.005-0.00774.446-0.001-0.0010.0000.0000.0000.000
54A76SER0-0.059-0.04877.221-0.001-0.0010.0000.0000.0000.000
55A77GLN0-0.074-0.04578.9790.0000.0000.0000.0000.0000.000
56A78LYS10.7940.87279.058-0.026-0.0260.0000.0000.0000.000
57A79SER00.0040.01680.6580.0000.0000.0000.0000.0000.000
58A80PRO00.0000.00982.6720.0000.0000.0000.0000.0000.000
59A81GLU-1-0.920-0.96583.3940.0240.0240.0000.0000.0000.000
60A82LEU0-0.028-0.02479.2450.0000.0000.0000.0000.0000.000
61A83GLN0-0.0360.00479.6580.0000.0000.0000.0000.0000.000
62A84GLU-1-0.912-0.92079.3200.0240.0240.0000.0000.0000.000
63A85GLU-1-0.818-0.92076.3210.0270.0270.0000.0000.0000.000
64A86PHE0-0.0230.00374.4330.0010.0010.0000.0000.0000.000
65A87GLY00.0680.01874.2570.0010.0010.0000.0000.0000.000
66A88TYR0-0.044-0.01073.8590.0010.0010.0000.0000.0000.000
67A89ASN0-0.055-0.05570.5240.0010.0010.0000.0000.0000.000
68A90ALA0-0.038-0.01969.7890.0010.0010.0000.0000.0000.000
69A91GLU-1-0.888-0.92770.5200.0280.0280.0000.0000.0000.000
70A92THR0-0.017-0.01765.8820.0000.0000.0000.0000.0000.000
71A93GLN00.0070.00463.9560.0000.0000.0000.0000.0000.000
72A94LYS11.0020.99865.075-0.028-0.0280.0000.0000.0000.000
73A95LEU0-0.058-0.01365.0150.0000.0000.0000.0000.0000.000
74A96LEU0-0.022-0.03961.4360.0010.0010.0000.0000.0000.000
75A97CYS0-0.0300.00860.9400.0020.0020.0000.0000.0000.000
76A98LYS10.9440.98860.842-0.028-0.0280.0000.0000.0000.000
77A99ASN0-0.076-0.04160.4040.0000.0000.0000.0000.0000.000
78A100GLY00.0580.01957.3210.0010.0010.0000.0000.0000.000
79A101GLU-1-0.877-0.96156.2220.0390.0390.0000.0000.0000.000
80A102THR0-0.0300.00056.1870.0000.0000.0000.0000.0000.000
81A103LEU0-0.008-0.00451.6350.0010.0010.0000.0000.0000.000
82A104LEU0-0.0110.00251.5590.0030.0030.0000.0000.0000.000
83A105GLY00.0500.02751.0960.0020.0020.0000.0000.0000.000
84A106ALA0-0.034-0.01450.6540.0000.0000.0000.0000.0000.000
85A107VAL00.0100.00946.4540.0020.0020.0000.0000.0000.000
86A108ASN00.007-0.01246.3930.0020.0020.0000.0000.0000.000
87A109PHE0-0.029-0.00346.6330.0010.0010.0000.0000.0000.000
88A110PHE00.010-0.00341.0120.0020.0020.0000.0000.0000.000
89A111VAL00.0120.00041.8260.0030.0030.0000.0000.0000.000
90A112SER0-0.009-0.00841.3010.0040.0040.0000.0000.0000.000
91A113SER0-0.052-0.03141.601-0.001-0.0010.0000.0000.0000.000
92A114ILE00.019-0.00336.6260.0010.0010.0000.0000.0000.000
93A115ASN00.0520.02036.6550.0110.0110.0000.0000.0000.000
94A116THR0-0.034-0.00136.4730.0030.0030.0000.0000.0000.000
95A117LEU0-0.004-0.00133.7610.0000.0000.0000.0000.0000.000
96A118VAL00.0550.01531.9150.0030.0030.0000.0000.0000.000
97A119THR0-0.023-0.02331.9020.0040.0040.0000.0000.0000.000
98A120LYS10.9150.95633.435-0.055-0.0550.0000.0000.0000.000
99A121THR0-0.034-0.00532.226-0.001-0.0010.0000.0000.0000.000
100A122MET0-0.010-0.01128.8820.0020.0020.0000.0000.0000.000
101A123GLU-1-0.922-0.95327.7590.1270.1270.0000.0000.0000.000
102A124ASP-1-0.833-0.88827.9000.0460.0460.0000.0000.0000.000
103A125THR00.0340.01524.693-0.006-0.0060.0000.0000.0000.000
104A126LEU0-0.025-0.02522.5590.0050.0050.0000.0000.0000.000
105A127MET0-0.0230.00223.2010.0120.0120.0000.0000.0000.000
106A128THR00.018-0.00622.1220.0000.0000.0000.0000.0000.000
107A129VAL0-0.0240.01018.450-0.010-0.0100.0000.0000.0000.000
108A130LYS10.9830.99618.612-0.158-0.1580.0000.0000.0000.000
109A131GLN0-0.0080.00218.963-0.007-0.0070.0000.0000.0000.000
110A132TYR0-0.028-0.02413.3280.0150.0150.0000.0000.0000.000
111A133GLU-1-0.832-0.90314.5690.2860.2860.0000.0000.0000.000
112A134ALA00.0020.01114.0990.0160.0160.0000.0000.0000.000
113A135ALA0-0.012-0.01515.255-0.020-0.0200.0000.0000.0000.000
114A136ARG10.9270.97210.230-0.283-0.2830.0000.0000.0000.000
115A137LEU0-0.038-0.00710.137-0.076-0.0760.0000.0000.0000.000
116A138GLU-1-0.911-0.97011.301-0.085-0.0850.0000.0000.0000.000
117A139TYR0-0.046-0.0068.807-0.093-0.0930.0000.0000.0000.000
118A140ASP-1-0.748-0.8757.128-1.091-1.0910.0000.0000.0000.000
119A141ALA0-0.0170.0028.425-0.065-0.0650.0000.0000.0000.000
120A142TYR00.043-0.01010.707-0.023-0.0230.0000.0000.0000.000
121A143ARG10.8940.9474.0121.4881.699-0.001-0.062-0.1490.000
122A144THR0-0.005-0.0036.349-0.239-0.2390.0000.0000.0000.000
123A145ASP-1-0.883-0.9208.251-0.267-0.2670.0000.0000.0000.000
124A146LEU0-0.083-0.04411.6850.0290.0290.0000.0000.0000.000
125A147GLU-1-0.947-0.9795.756-2.755-2.7550.0000.0000.0000.000
126A148GLU-1-0.910-0.96210.007-0.305-0.3050.0000.0000.0000.000
127A149LEU0-0.062-0.03711.4820.0720.0720.0000.0000.0000.000
128A150SER0-0.084-0.04212.3690.0560.0560.0000.0000.0000.000
129A151LEU0-0.059-0.02111.1530.0180.0180.0000.0000.0000.000
130A152GLY0-0.0460.00314.7380.0580.0580.0000.0000.0000.000
131A153PRO0-0.030-0.00318.107-0.016-0.0160.0000.0000.0000.000
132A154ARG10.9700.95919.4360.3440.3440.0000.0000.0000.000
133A155ASP-1-0.824-0.92222.606-0.206-0.2060.0000.0000.0000.000
134A156ALA0-0.013-0.00524.622-0.014-0.0140.0000.0000.0000.000
135A157GLY00.0610.02325.6220.0130.0130.0000.0000.0000.000
136A158THR0-0.013-0.00319.5300.0010.0010.0000.0000.0000.000
137A159ARG10.9370.95820.9250.2320.2320.0000.0000.0000.000
138A160GLY00.0420.03422.523-0.005-0.0050.0000.0000.0000.000
139A161ARG10.9580.96719.5560.2070.2070.0000.0000.0000.000
140A162LEU00.0360.01715.9560.0000.0000.0000.0000.0000.000
141A163GLU-1-0.928-0.95618.891-0.236-0.2360.0000.0000.0000.000
142A164SER0-0.057-0.02621.1180.0060.0060.0000.0000.0000.000
143A165ALA00.019-0.00116.0540.0070.0070.0000.0000.0000.000
144A166GLN00.0350.02716.035-0.038-0.0380.0000.0000.0000.000
145A167ALA0-0.021-0.00218.092-0.005-0.0050.0000.0000.0000.000
146A168THR0-0.027-0.01418.043-0.014-0.0140.0000.0000.0000.000
147A169PHE00.0290.03111.2820.0070.0070.0000.0000.0000.000
148A170GLN00.0530.02915.710-0.059-0.0590.0000.0000.0000.000
149A171ALA00.0430.02517.7390.0120.0120.0000.0000.0000.000
150A172HIS10.8300.90915.5330.1910.1910.0000.0000.0000.000
151A173ARG10.9280.96413.6020.4550.4550.0000.0000.0000.000
152A174ASP-1-0.907-0.93915.553-0.209-0.2090.0000.0000.0000.000
153A175LYS10.8720.93518.8800.0810.0810.0000.0000.0000.000
154A176TYR00.0190.00211.9640.0090.0090.0000.0000.0000.000
155A177GLU-1-0.890-0.95615.286-0.308-0.3080.0000.0000.0000.000
156A178LYS10.9030.96917.3790.0840.0840.0000.0000.0000.000
157A179LEU0-0.0230.00419.1070.0200.0200.0000.0000.0000.000
158A180ARG10.9020.94613.2150.2550.2550.0000.0000.0000.000
159A181GLY0-0.010-0.00818.3840.0130.0130.0000.0000.0000.000
160A182ASP-1-0.874-0.96321.582-0.026-0.0260.0000.0000.0000.000
161A183VAL00.001-0.00219.5240.0170.0170.0000.0000.0000.000
162A184ALA00.0410.02820.7710.0140.0140.0000.0000.0000.000
163A185ILE0-0.059-0.02222.4210.0050.0050.0000.0000.0000.000
164A186LYS10.8730.91125.396-0.027-0.0270.0000.0000.0000.000
165A187LEU0-0.036-0.01120.8210.0070.0070.0000.0000.0000.000
166A188LYS10.9560.97625.477-0.001-0.0010.0000.0000.0000.000
167A189PHE00.0230.01127.8860.0000.0000.0000.0000.0000.000
168A190LEU0-0.033-0.00927.1350.0030.0030.0000.0000.0000.000
169A191GLU-1-0.837-0.94328.2910.0900.0900.0000.0000.0000.000
170A192GLU-1-0.960-0.96030.2320.0230.0230.0000.0000.0000.000
171A193ASN0-0.013-0.02533.507-0.002-0.0020.0000.0000.0000.000
172A194LYS10.8740.95129.292-0.103-0.1030.0000.0000.0000.000
173A195ILE00.0250.01733.0130.0020.0020.0000.0000.0000.000
174A196LYS10.9780.99535.851-0.031-0.0310.0000.0000.0000.000
175A197VAL0-0.041-0.03537.279-0.002-0.0020.0000.0000.0000.000
176A198MET0-0.035-0.01635.379-0.001-0.0010.0000.0000.0000.000
177A199HIS00.0570.05038.6080.0030.0030.0000.0000.0000.000
178A200LYS10.9460.95341.418-0.038-0.0380.0000.0000.0000.000
179A201GLN0-0.014-0.00241.1800.0000.0000.0000.0000.0000.000
180A202LEU00.0340.01438.5530.0000.0000.0000.0000.0000.000
181A203LEU0-0.0050.01442.7770.0000.0000.0000.0000.0000.000
182A204LEU0-0.003-0.00746.1210.0000.0000.0000.0000.0000.000
183A205PHE0-0.0040.02145.256-0.001-0.0010.0000.0000.0000.000
184A206HIS00.0740.02646.6490.0000.0000.0000.0000.0000.000
185A207ASN0-0.032-0.02448.297-0.001-0.0010.0000.0000.0000.000
186A208ALA00.0130.00350.862-0.002-0.0020.0000.0000.0000.000
187A209VAL00.005-0.00249.139-0.001-0.0010.0000.0000.0000.000
188A210SER0-0.022-0.00352.229-0.002-0.0020.0000.0000.0000.000
189A211ALA0-0.004-0.00854.449-0.002-0.0020.0000.0000.0000.000
190A212TYR00.0130.01255.489-0.001-0.0010.0000.0000.0000.000
191A213PHE00.0060.01153.870-0.001-0.0010.0000.0000.0000.000
192A214ALA0-0.0150.00658.368-0.001-0.0010.0000.0000.0000.000
193A215GLY0-0.036-0.02560.287-0.001-0.0010.0000.0000.0000.000
194A216ASN00.012-0.02359.793-0.002-0.0020.0000.0000.0000.000
195A217GLN00.0190.00362.686-0.001-0.0010.0000.0000.0000.000
196A218LYS10.9340.98064.626-0.028-0.0280.0000.0000.0000.000
197A219GLN0-0.030-0.00866.541-0.001-0.0010.0000.0000.0000.000
198A220LEU00.0140.01165.4990.0000.0000.0000.0000.0000.000
199A221GLU-1-0.934-0.95966.7700.0300.0300.0000.0000.0000.000
200A222GLN0-0.114-0.05270.4060.0000.0000.0000.0000.0000.000
201A223THR0-0.017-0.01071.700-0.001-0.0010.0000.0000.0000.000