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: QNN1Y

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2320923.440817
FMO2-HF: Nuclear repulsion 2239627.258605
FMO2-HF: Total energy -81296.182213
FMO2-MP2: Total energy -81535.168961


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.
-7.809-0.22210.019-4.689-12.917-0.017
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 : 0.022 / q_NPA : 0.015
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].
3A24ALA00.0670.0083.362-1.5150.8730.028-1.243-1.1740.002
4A25GLY00.0010.0105.7060.4300.4300.0000.0000.0000.000
5A26THR0-0.019-0.0542.2980.307-0.0522.878-0.457-2.062-0.001
6A27ILE0-0.0220.0042.269-1.166-0.0591.771-0.512-2.366-0.004
7A28GLU-1-0.813-0.9144.420-0.604-0.4470.000-0.030-0.1270.000
8A29ARG10.7460.8596.1100.5230.5230.0000.0000.0000.000
9A30PHE00.0220.0005.3640.1370.1370.0000.0000.0000.000
10A31LEU0-0.020-0.0096.7510.1100.1100.0000.0000.0000.000
11A32ALA0-0.0290.0058.9930.0650.0650.0000.0000.0000.000
12A33HIS0-0.0040.00910.8120.0650.0650.0000.0000.0000.000
13A34SER0-0.076-0.03710.4860.0250.0250.0000.0000.0000.000
14A35HIS00.0190.00612.584-0.029-0.0290.0000.0000.0000.000
15A36ARG10.8950.94110.9950.4860.4860.0000.0000.0000.000
16A37ARG10.8930.96014.9410.1270.1270.0000.0000.0000.000
17A38ARG10.9070.95016.6270.1860.1860.0000.0000.0000.000
18A39TYR00.015-0.01016.8410.0260.0260.0000.0000.0000.000
19A40PRO00.0190.01120.516-0.015-0.0150.0000.0000.0000.000
20A41THR0-0.0030.01722.0330.0040.0040.0000.0000.0000.000
21A42ARG10.8970.92823.5340.0600.0600.0000.0000.0000.000
22A43THR00.0150.02022.3590.0070.0070.0000.0000.0000.000
23A44ASP-1-0.725-0.84922.041-0.016-0.0160.0000.0000.0000.000
24A45VAL0-0.066-0.03817.041-0.003-0.0030.0000.0000.0000.000
25A46PHE00.0020.01116.1340.0040.0040.0000.0000.0000.000
26A47ARG10.7430.82621.657-0.014-0.0140.0000.0000.0000.000
27A48PRO00.0130.00623.9110.0050.0050.0000.0000.0000.000
28A49GLY00.0300.02125.247-0.007-0.0070.0000.0000.0000.000
29A50ASP-1-0.843-0.91123.2380.0130.0130.0000.0000.0000.000
30A51PRO00.030-0.00523.0760.0100.0100.0000.0000.0000.000
31A52ALA0-0.034-0.00719.626-0.008-0.0080.0000.0000.0000.000
32A53GLY00.0580.02819.1950.0100.0100.0000.0000.0000.000
33A54THR0-0.050-0.02715.3800.0050.0050.0000.0000.0000.000
34A55LEU0-0.0020.0337.9760.0170.0170.0000.0000.0000.000
35A56TYR0-0.027-0.03211.350-0.038-0.0380.0000.0000.0000.000
36A57TYR00.0170.0053.624-0.416-0.1280.006-0.046-0.2490.000
37A58VAL0-0.0130.0058.536-0.023-0.0230.0000.0000.0000.000
38A59ILE00.0170.0218.518-0.127-0.1270.0000.0000.0000.000
39A60SER0-0.014-0.00410.366-0.041-0.0410.0000.0000.0000.000
40A61GLY00.0200.00713.3440.0430.0430.0000.0000.0000.000
41A62SER0-0.008-0.00614.213-0.017-0.0170.0000.0000.0000.000
42A63VAL00.0450.00414.1850.0130.0130.0000.0000.0000.000
43A64SER00.0030.00416.7870.0020.0020.0000.0000.0000.000
44A65ILE00.0430.04215.231-0.005-0.0050.0000.0000.0000.000
45A66ILE0-0.080-0.05118.496-0.002-0.0020.0000.0000.0000.000
46A67ALA00.0420.03822.2600.0040.0040.0000.0000.0000.000
47A68GLU-1-0.804-0.90224.5830.0160.0160.0000.0000.0000.000
48A69GLU-1-0.903-0.94727.9270.0640.0640.0000.0000.0000.000
49A70ASP-1-0.899-0.94531.4490.0420.0420.0000.0000.0000.000
50A71ASP-1-0.889-0.93434.6270.0270.0270.0000.0000.0000.000
51A72ASP-1-0.927-0.95532.5990.0130.0130.0000.0000.0000.000
52A73ARG10.7540.87132.277-0.030-0.0300.0000.0000.0000.000
53A74GLU-1-0.717-0.82827.2930.0050.0050.0000.0000.0000.000
54A75LEU0-0.059-0.02925.581-0.002-0.0020.0000.0000.0000.000
55A76VAL0-0.025-0.01521.3870.0060.0060.0000.0000.0000.000
56A77LEU00.012-0.00919.4210.0020.0020.0000.0000.0000.000
57A78GLY0-0.013-0.00817.8470.0140.0140.0000.0000.0000.000
58A79TYR0-0.065-0.05717.178-0.005-0.0050.0000.0000.0000.000
59A80PHE00.0550.02212.0740.0210.0210.0000.0000.0000.000
60A81GLY00.0590.01711.4110.0000.0000.0000.0000.0000.000
61A82SER0-0.059-0.0559.2850.0460.0460.0000.0000.0000.000
62A83GLY00.0120.0195.028-0.124-0.1240.0000.0000.0000.000
63A84GLU-1-0.899-0.9365.0360.1930.302-0.001-0.001-0.1060.000
64A85PHE00.0200.0062.489-0.792-0.1940.569-0.190-0.9770.000
65A86VAL0-0.030-0.0117.6650.0680.0680.0000.0000.0000.000
66A87GLY00.0700.02811.500-0.022-0.0220.0000.0000.0000.000
67A88GLU-1-0.823-0.92110.6420.2230.2230.0000.0000.0000.000
68A89MET0-0.0040.00712.5840.0270.0270.0000.0000.0000.000
69A90GLY00.0960.04315.7560.0190.0190.0000.0000.0000.000
70A91LEU0-0.097-0.03110.416-0.009-0.0090.0000.0000.0000.000
71A92PHE0-0.083-0.0589.8670.0550.0550.0000.0000.0000.000
72A93ILE0-0.037-0.01416.0710.0040.0040.0000.0000.0000.000
73A94GLU-1-0.942-0.96819.6190.1310.1310.0000.0000.0000.000
74A95SER00.0090.00121.988-0.008-0.0080.0000.0000.0000.000
75A96ASP-1-0.879-0.92722.4470.0840.0840.0000.0000.0000.000
76A97THR0-0.086-0.04624.010-0.012-0.0120.0000.0000.0000.000
77A98ARG10.7380.86516.247-0.040-0.0400.0000.0000.0000.000
78A99GLU-1-0.786-0.88721.1050.0920.0920.0000.0000.0000.000
79A100VAL0-0.070-0.04318.5870.0010.0010.0000.0000.0000.000
80A101ILE0-0.0010.00821.468-0.007-0.0070.0000.0000.0000.000
81A102LEU0-0.0200.00315.4010.0050.0050.0000.0000.0000.000
82A103ARG10.7550.83919.237-0.001-0.0010.0000.0000.0000.000
83A104THR0-0.019-0.03118.3550.0000.0000.0000.0000.0000.000
84A105ARG10.7440.85219.5600.0520.0520.0000.0000.0000.000
85A106THR0-0.012-0.01218.6270.0030.0030.0000.0000.0000.000
86A107GLN00.0350.01920.632-0.004-0.0040.0000.0000.0000.000
87A108CYS0-0.041-0.00316.033-0.014-0.0140.0000.0000.0000.000
88A109GLU-1-0.910-0.96514.325-0.321-0.3210.0000.0000.0000.000
89A110LEU0-0.0030.01112.251-0.039-0.0390.0000.0000.0000.000
90A111ALA00.0580.0339.4340.0050.0050.0000.0000.0000.000
91A112GLU-1-0.825-0.89911.414-0.053-0.0530.0000.0000.0000.000
92A113ILE0-0.007-0.00810.272-0.015-0.0150.0000.0000.0000.000
93A114SER00.0640.03013.4810.0220.0220.0000.0000.0000.000
94A115TYR00.021-0.01213.7020.0080.0080.0000.0000.0000.000
95A116GLU-1-0.905-0.94414.7390.1030.1030.0000.0000.0000.000
96A117ARG10.9000.94814.1500.0360.0360.0000.0000.0000.000
97A118LEU00.000-0.0018.085-0.008-0.0080.0000.0000.0000.000
98A119GLN00.0740.03111.7400.0580.0580.0000.0000.0000.000
99A120GLN00.0180.01313.9420.0100.0100.0000.0000.0000.000
100A121LEU0-0.050-0.01011.325-0.009-0.0090.0000.0000.0000.000
101A122PHE00.007-0.0107.2090.0420.0420.0000.0000.0000.000
102A123GLN00.0000.00511.7520.0130.0130.0000.0000.0000.000
103A124THR0-0.031-0.03214.178-0.032-0.0320.0000.0000.0000.000
104A125SER0-0.031-0.01613.4950.0150.0150.0000.0000.0000.000
105A126LEU0-0.030-0.0057.681-0.044-0.0440.0000.0000.0000.000
106A127SER00.0130.0188.9760.1390.1390.0000.0000.0000.000
107A128PRO0-0.002-0.0209.8950.1050.1050.0000.0000.0000.000
108A129ASP-1-0.774-0.8575.2630.2460.2460.0000.0000.0000.000
109A130ALA00.0110.0275.2920.5100.5100.0000.0000.0000.000
110A131PRO00.0050.0006.8530.1970.1970.0000.0000.0000.000
111A132ARG10.8180.9032.312-1.628-0.8941.106-0.424-1.4160.001
112A133ILE00.0230.0072.685-1.6710.3181.414-1.114-2.288-0.013
113A134LEU00.0180.0123.627-0.090-0.1690.0090.209-0.1390.000
114A135TYR0-0.0010.0074.884-0.464-0.4640.0000.0000.0000.000
115A136ALA0-0.011-0.0092.335-0.962-0.5072.239-0.821-1.873-0.002
116A137ILE00.0340.0164.356-0.733-0.5330.000-0.060-0.1400.000
117A138GLY00.0540.0366.644-0.186-0.1860.0000.0000.0000.000
118A139VAL0-0.015-0.0016.610-0.306-0.3060.0000.0000.0000.000
119A140GLN0-0.046-0.0265.250-0.222-0.2220.0000.0000.0000.000
120A141LEU00.0300.0148.980-0.139-0.1390.0000.0000.0000.000
121A142SER0-0.022-0.02011.627-0.111-0.1110.0000.0000.0000.000
122A143LYS10.9070.9559.687-0.436-0.4360.0000.0000.0000.000
123A144ARG10.8210.8809.654-0.291-0.2910.0000.0000.0000.000
124A145LEU00.0400.04615.026-0.047-0.0470.0000.0000.0000.000
125A146LEU0-0.0010.01516.776-0.045-0.0450.0000.0000.0000.000
126A147ASP-1-0.831-0.91817.2930.1350.1350.0000.0000.0000.000
127A148THR0-0.012-0.01018.543-0.037-0.0370.0000.0000.0000.000
128A149THR0-0.015-0.01720.887-0.020-0.0200.0000.0000.0000.000
129A150ARG10.8340.90618.742-0.187-0.1870.0000.0000.0000.000
130A151LYS10.8290.92022.632-0.078-0.0780.0000.0000.0000.000
131A152ALA00.0440.01724.909-0.012-0.0120.0000.0000.0000.000
132A153SER0-0.004-0.01426.582-0.007-0.0070.0000.0000.0000.000
133A154ARG10.7690.85424.088-0.077-0.0770.0000.0000.0000.000
134A155LEU0-0.051-0.04027.559-0.008-0.0080.0000.0000.0000.000
135A156ALA0-0.0060.01830.929-0.005-0.0050.0000.0000.0000.000
136A157PHE0-0.020-0.00631.654-0.002-0.0020.0000.0000.0000.000
137A158LEU0-0.0250.00231.082-0.003-0.0030.0000.0000.0000.000
138A159ASP-1-0.738-0.85034.7320.0260.0260.0000.0000.0000.000
139A160VAL00.004-0.00434.4250.0010.0010.0000.0000.0000.000
140A161THR0-0.048-0.05734.382-0.004-0.0040.0000.0000.0000.000
141A162ASP-1-0.754-0.85133.5870.0390.0390.0000.0000.0000.000
142A163ARG10.8100.90830.503-0.044-0.0440.0000.0000.0000.000
143A164ILE0-0.0110.01029.804-0.001-0.0010.0000.0000.0000.000
144A165VAL00.0280.01430.369-0.004-0.0040.0000.0000.0000.000
145A166ARG10.8290.88428.088-0.057-0.0570.0000.0000.0000.000
146A167THR00.000-0.01325.2610.0020.0020.0000.0000.0000.000
147A168LEU0-0.055-0.03425.755-0.008-0.0080.0000.0000.0000.000
148A169HIS00.004-0.00926.644-0.012-0.0120.0000.0000.0000.000
149A170ASP-1-0.790-0.85521.9530.0450.0450.0000.0000.0000.000
150A171LEU0-0.005-0.01721.875-0.014-0.0140.0000.0000.0000.000
151A172SER0-0.111-0.05823.096-0.017-0.0170.0000.0000.0000.000
152A173LYS10.8990.93518.2370.0590.0590.0000.0000.0000.000
153A174GLU-1-0.854-0.92116.342-0.091-0.0910.0000.0000.0000.000
154A175PRO0-0.020-0.02014.716-0.006-0.0060.0000.0000.0000.000
155A176GLU-1-0.962-0.97318.041-0.130-0.1300.0000.0000.0000.000
156A177ALA0-0.026-0.00120.3290.0100.0100.0000.0000.0000.000
157A178MET0-0.042-0.02623.2430.0000.0000.0000.0000.0000.000
158A179SER00.0120.01525.5570.0130.0130.0000.0000.0000.000
159A180HIS00.005-0.01227.856-0.002-0.0020.0000.0000.0000.000
160A181PRO00.019-0.00131.6680.0030.0030.0000.0000.0000.000
161A182GLN00.0000.00934.5200.0010.0010.0000.0000.0000.000
162A183GLY00.0520.03431.2360.0070.0070.0000.0000.0000.000
163A184THR0-0.036-0.00525.914-0.010-0.0100.0000.0000.0000.000
164A185GLN00.0040.02427.4730.0110.0110.0000.0000.0000.000
165A186LEU00.0500.04626.168-0.010-0.0100.0000.0000.0000.000
166A187ARG10.8840.92524.8180.0980.0980.0000.0000.0000.000
167A188VAL00.0820.03426.413-0.001-0.0010.0000.0000.0000.000
168A189SER0-0.051-0.03227.817-0.001-0.0010.0000.0000.0000.000
169A190ARG10.8960.92330.4570.0300.0300.0000.0000.0000.000
170A191GLN00.0490.02531.2320.0030.0030.0000.0000.0000.000
171A192GLU-1-0.748-0.82924.683-0.020-0.0200.0000.0000.0000.000
172A193LEU00.0290.01127.5130.0050.0050.0000.0000.0000.000
173A194ALA0-0.009-0.02329.4680.0060.0060.0000.0000.0000.000
174A195ARG10.8210.89026.5740.0110.0110.0000.0000.0000.000
175A196LEU0-0.0260.01222.8890.0080.0080.0000.0000.0000.000
176A197VAL0-0.0040.00426.3650.0100.0100.0000.0000.0000.000
177A198GLY00.1190.07529.3300.0040.0040.0000.0000.0000.000
178A199CYS0-0.085-0.03631.2620.0000.0000.0000.0000.0000.000
179A200SER00.0530.02034.187-0.002-0.0020.0000.0000.0000.000
180A201ARG11.0210.99235.2860.0100.0100.0000.0000.0000.000
181A202GLU-1-0.825-0.88936.2570.0040.0040.0000.0000.0000.000
182A203MET00.0450.04037.447-0.002-0.0020.0000.0000.0000.000
183A204ALA00.0610.03133.808-0.001-0.0010.0000.0000.0000.000
184A205GLY0-0.048-0.03135.671-0.003-0.0030.0000.0000.0000.000
185A206ARG10.8370.89337.981-0.010-0.0100.0000.0000.0000.000
186A207VAL00.0570.02936.033-0.001-0.0010.0000.0000.0000.000
187A208LEU0-0.0090.00333.033-0.002-0.0020.0000.0000.0000.000
188A209LYS10.9290.95737.1480.0080.0080.0000.0000.0000.000
189A210LYS10.8430.91240.757-0.006-0.0060.0000.0000.0000.000
190A211LEU00.0380.01035.1510.0000.0000.0000.0000.0000.000
191A212GLN0-0.009-0.00239.148-0.003-0.0030.0000.0000.0000.000
192A213ALA0-0.060-0.02840.304-0.001-0.0010.0000.0000.0000.000
193A214ASP-1-0.833-0.88840.7570.0030.0030.0000.0000.0000.000
194A215GLY00.0010.01041.3590.0000.0000.0000.0000.0000.000
195A216LEU00.004-0.00635.955-0.002-0.0020.0000.0000.0000.000
196A217LEU0-0.030-0.00833.724-0.003-0.0030.0000.0000.0000.000
197A218HIS00.0200.03935.7730.0040.0040.0000.0000.0000.000
198A219ALA0-0.0020.00235.122-0.004-0.0040.0000.0000.0000.000
199A220ARG10.9690.97335.0400.0470.0470.0000.0000.0000.000
200A221GLY00.0300.02634.770-0.004-0.0040.0000.0000.0000.000
201A222LYS10.7840.88327.3290.0680.0680.0000.0000.0000.000
202A223THR00.0530.03129.854-0.007-0.0070.0000.0000.0000.000
203A224VAL0-0.011-0.01230.4780.0050.0050.0000.0000.0000.000
204A225VAL0-0.0140.00530.624-0.005-0.0050.0000.0000.0000.000
205A226LEU00.0280.01628.9350.0050.0050.0000.0000.0000.000
206A227TYR0-0.033-0.04431.840-0.006-0.0060.0000.0000.0000.000
207A228GLY00.0090.00831.4590.0020.0020.0000.0000.0000.000