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: ZNNYN

Calculation Name: 3IWZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IWZ

Chain ID: A

ChEMBL ID:

UniProt ID: P22260

Base Structure: X-ray

Registration Date: 2023-09-27

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2314637.672497
FMO2-HF: Nuclear repulsion 2233343.385321
FMO2-HF: Total energy -81294.287175
FMO2-MP2: Total energy -81533.501599


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:22:LEU)


Summations of interaction energy for fragment #1(A:22:LEU)
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.
-11.216-5.42112.846-4.992-13.649-0.024
Interaction energy analysis for fragmet #1(A:22:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.021
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].
3A24ALA00.0850.0123.262-2.834-0.6000.043-1.147-1.130-0.001
4A25GLY00.0160.0145.8720.1430.1430.0000.0000.0000.000
5A26THR0-0.047-0.0372.1700.785-0.7024.674-0.696-2.491-0.001
6A27ILE0-0.006-0.0021.950-0.611-1.2285.280-1.145-3.518-0.011
7A28GLU-1-0.903-0.9604.066-0.950-0.7050.004-0.073-0.1750.000
8A29ARG10.7700.8506.655-0.148-0.1480.0000.0000.0000.000
9A30PHE0-0.004-0.0094.9380.0840.0840.0000.0000.0000.000
10A31LEU0-0.015-0.0116.5020.1040.1040.0000.0000.0000.000
11A32ALA0-0.0130.0278.7010.0760.0760.0000.0000.0000.000
12A33HIS0-0.041-0.02510.8800.0640.0640.0000.0000.0000.000
13A34SER0-0.093-0.0419.8650.0030.0030.0000.0000.0000.000
14A35HIS0-0.003-0.00412.0060.0090.0090.0000.0000.0000.000
15A36ARG10.9350.97910.6120.6100.6100.0000.0000.0000.000
16A37ARG10.9360.98515.0360.3170.3170.0000.0000.0000.000
17A38ARG10.9550.97016.9450.2740.2740.0000.0000.0000.000
18A39TYR00.003-0.00316.7420.0250.0250.0000.0000.0000.000
19A40PRO00.0190.01820.618-0.016-0.0160.0000.0000.0000.000
20A41THR00.0290.01722.361-0.012-0.0120.0000.0000.0000.000
21A42ARG10.8800.92723.5200.1980.1980.0000.0000.0000.000
22A43THR00.0150.00422.3810.0190.0190.0000.0000.0000.000
23A44ASP-1-0.759-0.84721.904-0.207-0.2070.0000.0000.0000.000
24A45VAL0-0.068-0.04217.3510.0060.0060.0000.0000.0000.000
25A46PHE0-0.008-0.00816.388-0.005-0.0050.0000.0000.0000.000
26A47ARG10.7850.87021.9470.1300.1300.0000.0000.0000.000
27A48PRO00.0380.01524.270-0.002-0.0020.0000.0000.0000.000
28A49GLY00.0360.02125.2920.0050.0050.0000.0000.0000.000
29A50ASP-1-0.867-0.91423.401-0.147-0.1470.0000.0000.0000.000
30A51PRO00.0320.00023.311-0.001-0.0010.0000.0000.0000.000
31A52ALA0-0.049-0.00819.454-0.022-0.0220.0000.0000.0000.000
32A53GLY00.0620.02518.8420.0130.0130.0000.0000.0000.000
33A54THR0-0.080-0.04615.2380.0040.0040.0000.0000.0000.000
34A55LEU00.0020.0298.0050.0020.0020.0000.0000.0000.000
35A56TYR00.004-0.01211.3880.0010.0010.0000.0000.0000.000
36A57TYR00.0130.0163.396-0.691-0.3190.013-0.076-0.3090.000
37A58VAL00.010-0.0038.5350.0950.0950.0000.0000.0000.000
38A59ILE00.0050.0188.627-0.201-0.2010.0000.0000.0000.000
39A60SER0-0.027-0.01910.202-0.014-0.0140.0000.0000.0000.000
40A61GLY00.0160.00213.2050.0420.0420.0000.0000.0000.000
41A62SER00.011-0.00414.063-0.062-0.0620.0000.0000.0000.000
42A63VAL00.0370.00514.2020.0520.0520.0000.0000.0000.000
43A64SER0-0.012-0.00716.659-0.003-0.0030.0000.0000.0000.000
44A65ILE00.0240.02715.538-0.001-0.0010.0000.0000.0000.000
45A66ILE0-0.070-0.05219.0030.0100.0100.0000.0000.0000.000
46A67ALA00.0470.03722.6780.0000.0000.0000.0000.0000.000
47A68GLU-1-0.827-0.92724.804-0.121-0.1210.0000.0000.0000.000
48A69GLU-1-0.874-0.93527.979-0.073-0.0730.0000.0000.0000.000
49A70ASP-1-0.889-0.94131.420-0.072-0.0720.0000.0000.0000.000
50A71ASP-1-0.980-0.99234.509-0.074-0.0740.0000.0000.0000.000
51A72ASP-1-0.897-0.95432.560-0.097-0.0970.0000.0000.0000.000
52A73ARG10.9701.09532.5930.0700.0700.0000.0000.0000.000
53A74GLU-1-0.827-0.92127.360-0.156-0.1560.0000.0000.0000.000
54A75LEU0-0.040-0.01425.5250.0040.0040.0000.0000.0000.000
55A76VAL0-0.059-0.04422.187-0.009-0.0090.0000.0000.0000.000
56A77LEU00.011-0.01619.7950.0100.0100.0000.0000.0000.000
57A78GLY0-0.017-0.00518.0900.0030.0030.0000.0000.0000.000
58A79TYR0-0.078-0.08817.1440.0190.0190.0000.0000.0000.000
59A80PHE00.0580.01611.868-0.008-0.0080.0000.0000.0000.000
60A81GLY00.0560.02811.9040.0550.0550.0000.0000.0000.000
61A82SER0-0.012-0.0369.182-0.003-0.0030.0000.0000.0000.000
62A83GLY0-0.0070.0034.980-0.127-0.1270.0000.0000.0000.000
63A84GLU-1-0.959-0.9724.888-1.274-1.172-0.001-0.001-0.1000.000
64A85PHE0-0.016-0.0062.590-0.671-0.0070.360-0.148-0.8760.000
65A86VAL00.0010.0007.9560.0890.0890.0000.0000.0000.000
66A87GLY00.0500.01911.6990.0030.0030.0000.0000.0000.000
67A88GLU-1-0.834-0.95210.401-0.322-0.3220.0000.0000.0000.000
68A89MET00.0320.03512.3350.0370.0370.0000.0000.0000.000
69A90GLY00.0730.03815.3940.0290.0290.0000.0000.0000.000
70A91LEU0-0.100-0.03910.4140.0090.0090.0000.0000.0000.000
71A92PHE0-0.099-0.07310.1430.0350.0350.0000.0000.0000.000
72A93ILE0-0.037-0.02015.9610.0240.0240.0000.0000.0000.000
73A94GLU-1-0.957-0.97419.390-0.034-0.0340.0000.0000.0000.000
74A95SER00.017-0.00221.4710.0030.0030.0000.0000.0000.000
75A96ASP-1-0.859-0.91622.160-0.076-0.0760.0000.0000.0000.000
76A97THR0-0.045-0.02423.993-0.006-0.0060.0000.0000.0000.000
77A98ARG10.7670.90816.1370.2200.2200.0000.0000.0000.000
78A99GLU-1-0.839-0.93220.991-0.089-0.0890.0000.0000.0000.000
79A100VAL0-0.068-0.03218.734-0.001-0.0010.0000.0000.0000.000
80A101ILE00.0090.01021.707-0.007-0.0070.0000.0000.0000.000
81A102LEU0-0.0290.00715.477-0.018-0.0180.0000.0000.0000.000
82A103ARG10.7310.83419.3670.1910.1910.0000.0000.0000.000
83A104THR00.0030.00618.202-0.016-0.0160.0000.0000.0000.000
84A105ARG10.7810.87419.3600.2750.2750.0000.0000.0000.000
85A106THR0-0.016-0.01218.5110.0130.0130.0000.0000.0000.000
86A107GLN0-0.042-0.01520.396-0.005-0.0050.0000.0000.0000.000
87A108CYS0-0.033-0.01715.905-0.030-0.0300.0000.0000.0000.000
88A109GLU-1-0.856-0.93314.069-0.472-0.4720.0000.0000.0000.000
89A110LEU0-0.026-0.00512.369-0.077-0.0770.0000.0000.0000.000
90A111ALA00.0470.0309.6480.0570.0570.0000.0000.0000.000
91A112GLU-1-0.892-0.95111.120-0.328-0.3280.0000.0000.0000.000
92A113ILE00.016-0.0039.8220.0220.0220.0000.0000.0000.000
93A114SER00.0410.02212.993-0.005-0.0050.0000.0000.0000.000
94A115TYR00.0510.01313.6140.0000.0000.0000.0000.0000.000
95A116GLU-1-0.904-0.94414.976-0.046-0.0460.0000.0000.0000.000
96A117ARG10.9440.98214.4400.1590.1590.0000.0000.0000.000
97A118LEU00.0180.0098.4400.0090.0090.0000.0000.0000.000
98A119GLN00.0590.01411.9190.0690.0690.0000.0000.0000.000
99A120GLN00.0080.01613.8760.0310.0310.0000.0000.0000.000
100A121LEU0-0.054-0.04211.4390.0290.0290.0000.0000.0000.000
101A122PHE0-0.004-0.0087.4220.0620.0620.0000.0000.0000.000
102A123GLN0-0.016-0.00111.7660.0450.0450.0000.0000.0000.000
103A124THR0-0.044-0.01014.214-0.005-0.0050.0000.0000.0000.000
104A125SER0-0.013-0.01913.0420.0280.0280.0000.0000.0000.000
105A126LEU0-0.026-0.0127.5550.0170.0170.0000.0000.0000.000
106A127SER00.0120.0308.9770.1150.1150.0000.0000.0000.000
107A128PRO0-0.017-0.0319.5730.0860.0860.0000.0000.0000.000
108A129ASP-1-0.768-0.8564.6340.7860.826-0.001-0.004-0.0350.000
109A130ALA00.0320.0405.2240.2340.2340.0000.0000.0000.000
110A131PRO00.009-0.0036.9720.0090.0090.0000.0000.0000.000
111A132ARG10.8740.9232.527-3.290-2.3720.831-0.369-1.3810.001
112A133ILE00.0310.0132.711-2.807-0.6690.824-0.968-1.994-0.010
113A134LEU00.0110.0063.702-0.458-0.4370.0120.103-0.1350.000
114A135TYR0-0.0030.0064.601-0.340-0.241-0.001-0.004-0.0940.000
115A136ALA0-0.011-0.0122.593-1.366-0.4300.809-0.444-1.302-0.002
116A137ILE00.0370.0204.595-0.221-0.091-0.001-0.020-0.1090.000
117A138GLY00.0480.0276.6870.0210.0210.0000.0000.0000.000
118A139VAL0-0.047-0.0165.5480.0210.0210.0000.0000.0000.000
119A140GLN00.0260.0045.8130.1880.1880.0000.0000.0000.000
120A141LEU00.0240.0289.5060.0550.0550.0000.0000.0000.000
121A142SER0-0.003-0.00211.8660.0510.0510.0000.0000.0000.000
122A143LYS10.9120.9569.4060.3820.3820.0000.0000.0000.000
123A144ARG10.8990.9589.7770.5410.5410.0000.0000.0000.000
124A145LEU00.0360.04315.3920.0200.0200.0000.0000.0000.000
125A146LEU0-0.031-0.00316.8050.0200.0200.0000.0000.0000.000
126A147ASP-1-0.881-0.95117.405-0.193-0.1930.0000.0000.0000.000
127A148THR0-0.030-0.03618.7920.0070.0070.0000.0000.0000.000
128A149THR0-0.0100.00621.1620.0170.0170.0000.0000.0000.000
129A150ARG10.9260.94419.7830.0700.0700.0000.0000.0000.000
130A151LYS10.8390.92722.9740.1540.1540.0000.0000.0000.000
131A152ALA00.0590.02525.2800.0050.0050.0000.0000.0000.000
132A153SER0-0.017-0.01327.0800.0090.0090.0000.0000.0000.000
133A154ARG10.8120.89723.8830.1050.1050.0000.0000.0000.000
134A155LEU0-0.023-0.01328.0060.0010.0010.0000.0000.0000.000
135A156ALA0-0.0020.02031.3350.0020.0020.0000.0000.0000.000
136A157PHE0-0.032-0.01832.4290.0040.0040.0000.0000.0000.000
137A158LEU0-0.035-0.00831.1010.0010.0010.0000.0000.0000.000
138A159ASP-1-0.775-0.85534.929-0.055-0.0550.0000.0000.0000.000
139A160VAL00.028-0.02234.712-0.004-0.0040.0000.0000.0000.000
140A161THR0-0.015-0.01634.720-0.008-0.0080.0000.0000.0000.000
141A162ASP-1-0.846-0.94333.949-0.055-0.0550.0000.0000.0000.000
142A163ARG10.7710.87930.6680.0680.0680.0000.0000.0000.000
143A164ILE00.0030.00330.106-0.011-0.0110.0000.0000.0000.000
144A165VAL00.0100.01930.852-0.009-0.0090.0000.0000.0000.000
145A166ARG10.9520.97027.8320.0480.0480.0000.0000.0000.000
146A167THR00.0120.01825.752-0.009-0.0090.0000.0000.0000.000
147A168LEU0-0.059-0.04026.101-0.015-0.0150.0000.0000.0000.000
148A169HIS00.013-0.00726.713-0.006-0.0060.0000.0000.0000.000
149A170ASP-1-0.864-0.91322.090-0.134-0.1340.0000.0000.0000.000
150A171LEU0-0.002-0.01121.894-0.019-0.0190.0000.0000.0000.000
151A172SER0-0.079-0.04022.702-0.012-0.0120.0000.0000.0000.000
152A173LYS10.9290.96218.3020.1590.1590.0000.0000.0000.000
153A174GLU-1-0.902-0.94516.669-0.411-0.4110.0000.0000.0000.000
154A175PRO00.002-0.00614.8590.0250.0250.0000.0000.0000.000
155A176GLU-1-0.979-0.98318.147-0.283-0.2830.0000.0000.0000.000
156A177ALA0-0.073-0.03420.2730.0260.0260.0000.0000.0000.000
157A178MET0-0.0100.00823.2680.0110.0110.0000.0000.0000.000
158A179SER00.0640.01925.5580.0160.0160.0000.0000.0000.000
159A180HIS00.0070.00927.718-0.001-0.0010.0000.0000.0000.000
160A181PRO00.020-0.00131.4910.0030.0030.0000.0000.0000.000
161A182GLN0-0.038-0.02734.1580.0020.0020.0000.0000.0000.000
162A183GLY00.0360.02431.2830.0050.0050.0000.0000.0000.000
163A184THR0-0.0350.00025.596-0.008-0.0080.0000.0000.0000.000
164A185GLN0-0.050-0.04928.2650.0130.0130.0000.0000.0000.000
165A186LEU00.0170.03426.281-0.016-0.0160.0000.0000.0000.000
166A187ARG10.8890.93725.1820.1940.1940.0000.0000.0000.000
167A188VAL00.0890.05925.875-0.011-0.0110.0000.0000.0000.000
168A189SER0-0.082-0.04628.1550.0110.0110.0000.0000.0000.000
169A190ARG11.0060.98030.8080.1110.1110.0000.0000.0000.000
170A191GLN0-0.045-0.03031.1040.0000.0000.0000.0000.0000.000
171A192GLU-1-0.702-0.76824.674-0.190-0.1900.0000.0000.0000.000
172A193LEU00.0420.03428.087-0.001-0.0010.0000.0000.0000.000
173A194ALA0-0.023-0.03029.7970.0030.0030.0000.0000.0000.000
174A195ARG10.8810.92227.2020.1570.1570.0000.0000.0000.000
175A196LEU0-0.0140.01723.5010.0020.0020.0000.0000.0000.000
176A197VAL0-0.020-0.00826.9780.0040.0040.0000.0000.0000.000
177A198GLY00.0980.06829.7730.0100.0100.0000.0000.0000.000
178A199CYS0-0.050-0.01631.4850.0080.0080.0000.0000.0000.000
179A200SER00.0810.04534.268-0.006-0.0060.0000.0000.0000.000
180A201ARG10.8740.82435.2940.0880.0880.0000.0000.0000.000
181A202GLU-1-0.966-0.99036.365-0.065-0.0650.0000.0000.0000.000
182A203MET00.0780.05937.9830.0010.0010.0000.0000.0000.000
183A204ALA00.0590.02234.2110.0010.0010.0000.0000.0000.000
184A205GLY0-0.081-0.04536.178-0.001-0.0010.0000.0000.0000.000
185A206ARG10.9090.94338.4510.0580.0580.0000.0000.0000.000
186A207VAL00.0500.02136.2930.0030.0030.0000.0000.0000.000
187A208LEU00.0000.00433.6680.0010.0010.0000.0000.0000.000
188A209LYS10.9030.95637.6780.0690.0690.0000.0000.0000.000
189A210LYS10.8520.95140.9620.0510.0510.0000.0000.0000.000
190A211LEU00.0770.02535.2780.0020.0020.0000.0000.0000.000
191A212GLN00.0160.01939.327-0.004-0.0040.0000.0000.0000.000
192A213ALA0-0.084-0.03040.4790.0020.0020.0000.0000.0000.000
193A214ASP-1-0.828-0.92240.807-0.047-0.0470.0000.0000.0000.000
194A215GLY0-0.038-0.01741.2470.0020.0020.0000.0000.0000.000
195A216LEU0-0.011-0.01336.064-0.001-0.0010.0000.0000.0000.000
196A217LEU0-0.009-0.00333.890-0.006-0.0060.0000.0000.0000.000
197A218HIS00.0380.08036.2290.0080.0080.0000.0000.0000.000
198A219ALA0-0.004-0.00435.613-0.008-0.0080.0000.0000.0000.000
199A220ARG10.9890.98235.3950.1020.1020.0000.0000.0000.000
200A221GLY0-0.0100.00334.842-0.007-0.0070.0000.0000.0000.000
201A222LYS10.8870.93228.6080.1640.1640.0000.0000.0000.000
202A223THR00.0100.00230.215-0.014-0.0140.0000.0000.0000.000
203A224VAL00.0210.02630.7310.0100.0100.0000.0000.0000.000
204A225VAL0-0.028-0.01631.004-0.010-0.0100.0000.0000.0000.000
205A226LEU00.0170.01028.5400.0070.0070.0000.0000.0000.000
206A227TYR0-0.022-0.06031.561-0.002-0.0020.0000.0000.0000.000
207A228GLY00.0050.01331.0450.0000.0000.0000.0000.0000.000