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: RYY58

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 OptHSide
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 -2315357.626502
FMO2-HF: Nuclear repulsion 2234061.951867
FMO2-HF: Total energy -81295.674635
FMO2-MP2: Total energy -81534.689437


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.
-8.844-1.64111.907-4.868-14.241-0.018
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 : 0.001 / q_NPA : 0.007
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].
3A24ALA00.0760.0113.450-1.9500.6460.007-1.373-1.2300.004
4A25GLY00.0090.0176.1040.3830.3830.0000.0000.0000.000
5A26THR0-0.043-0.0652.3470.211-0.0672.698-0.412-2.008-0.001
6A27ILE0-0.0160.0002.110-1.004-0.3612.986-0.724-2.905-0.007
7A28GLU-1-0.877-0.9554.205-0.737-0.5490.002-0.045-0.1440.000
8A29ARG10.7750.8636.4830.2830.2830.0000.0000.0000.000
9A30PHE0-0.004-0.0114.9700.1160.1160.0000.0000.0000.000
10A31LEU0-0.017-0.0116.6440.0980.0980.0000.0000.0000.000
11A32ALA0-0.0250.0198.8140.0510.0510.0000.0000.0000.000
12A33HIS00.0010.00310.9980.0510.0510.0000.0000.0000.000
13A34SER0-0.090-0.0399.9230.0190.0190.0000.0000.0000.000
14A35HIS0-0.011-0.00612.064-0.023-0.0230.0000.0000.0000.000
15A36ARG10.9290.97011.0620.4680.4680.0000.0000.0000.000
16A37ARG10.9310.98915.1500.1240.1240.0000.0000.0000.000
17A38ARG10.9330.95116.9830.1820.1820.0000.0000.0000.000
18A39TYR00.017-0.00117.0960.0190.0190.0000.0000.0000.000
19A40PRO00.0300.02420.675-0.016-0.0160.0000.0000.0000.000
20A41THR00.0100.00922.4330.0030.0030.0000.0000.0000.000
21A42ARG10.8950.93623.6010.0660.0660.0000.0000.0000.000
22A43THR00.0080.00722.4870.0080.0080.0000.0000.0000.000
23A44ASP-1-0.744-0.85121.971-0.023-0.0230.0000.0000.0000.000
24A45VAL0-0.078-0.04617.271-0.003-0.0030.0000.0000.0000.000
25A46PHE00.0100.00216.2960.0050.0050.0000.0000.0000.000
26A47ARG10.7680.84021.920-0.010-0.0100.0000.0000.0000.000
27A48PRO00.0180.00824.1980.0030.0030.0000.0000.0000.000
28A49GLY00.0320.02225.212-0.007-0.0070.0000.0000.0000.000
29A50ASP-1-0.860-0.91323.3240.0130.0130.0000.0000.0000.000
30A51PRO00.0390.00423.1760.0090.0090.0000.0000.0000.000
31A52ALA0-0.049-0.01419.401-0.007-0.0070.0000.0000.0000.000
32A53GLY00.0640.02718.7430.0120.0120.0000.0000.0000.000
33A54THR0-0.073-0.03815.1660.0050.0050.0000.0000.0000.000
34A55LEU00.0040.0327.8060.0180.0180.0000.0000.0000.000
35A56TYR0-0.034-0.04411.385-0.034-0.0340.0000.0000.0000.000
36A57TYR00.0170.0103.346-0.460-0.1410.012-0.054-0.2780.000
37A58VAL0-0.002-0.0068.582-0.015-0.0150.0000.0000.0000.000
38A59ILE00.0170.0238.708-0.138-0.1380.0000.0000.0000.000
39A60SER0-0.013-0.00210.267-0.052-0.0520.0000.0000.0000.000
40A61GLY00.0080.00513.2880.0450.0450.0000.0000.0000.000
41A62SER00.001-0.00814.163-0.021-0.0210.0000.0000.0000.000
42A63VAL00.0340.00214.1110.0170.0170.0000.0000.0000.000
43A64SER0-0.003-0.00316.7550.0040.0040.0000.0000.0000.000
44A65ILE00.0210.02415.453-0.004-0.0040.0000.0000.0000.000
45A66ILE0-0.078-0.05718.8950.0010.0010.0000.0000.0000.000
46A67ALA00.0500.04022.5680.0030.0030.0000.0000.0000.000
47A68GLU-1-0.793-0.89324.6920.0140.0140.0000.0000.0000.000
48A69GLU-1-0.883-0.94627.8730.0600.0600.0000.0000.0000.000
49A70ASP-1-0.892-0.94031.3110.0400.0400.0000.0000.0000.000
50A71ASP-1-0.913-0.94334.4060.0240.0240.0000.0000.0000.000
51A72ASP-1-0.932-0.96032.4470.0100.0100.0000.0000.0000.000
52A73ARG10.7690.88532.483-0.027-0.0270.0000.0000.0000.000
53A74GLU-1-0.757-0.85927.4020.0000.0000.0000.0000.0000.000
54A75LEU0-0.031-0.01425.715-0.003-0.0030.0000.0000.0000.000
55A76VAL0-0.057-0.03521.9310.0050.0050.0000.0000.0000.000
56A77LEU00.018-0.01219.7500.0030.0030.0000.0000.0000.000
57A78GLY0-0.022-0.00617.9660.0150.0150.0000.0000.0000.000
58A79TYR0-0.067-0.05717.246-0.005-0.0050.0000.0000.0000.000
59A80PHE00.0580.02211.9970.0210.0210.0000.0000.0000.000
60A81GLY00.0580.02912.022-0.003-0.0030.0000.0000.0000.000
61A82SER0-0.018-0.0499.1370.0580.0580.0000.0000.0000.000
62A83GLY0-0.0170.0055.062-0.113-0.1130.0000.0000.0000.000
63A84GLU-1-0.902-0.9474.9860.1860.298-0.001-0.001-0.1100.000
64A85PHE0-0.0040.0022.411-0.818-0.2080.722-0.200-1.1320.000
65A86VAL0-0.003-0.0067.8730.0620.0620.0000.0000.0000.000
66A87GLY00.0590.02611.614-0.016-0.0160.0000.0000.0000.000
67A88GLU-1-0.795-0.91510.3450.2240.2240.0000.0000.0000.000
68A89MET00.0160.02412.2650.0280.0280.0000.0000.0000.000
69A90GLY00.0840.05015.3140.0170.0170.0000.0000.0000.000
70A91LEU0-0.100-0.03610.411-0.009-0.0090.0000.0000.0000.000
71A92PHE0-0.099-0.0759.9030.0580.0580.0000.0000.0000.000
72A93ILE0-0.045-0.02415.9050.0000.0000.0000.0000.0000.000
73A94GLU-1-0.941-0.96519.3270.1300.1300.0000.0000.0000.000
74A95SER00.010-0.00421.424-0.009-0.0090.0000.0000.0000.000
75A96ASP-1-0.879-0.92622.1140.0840.0840.0000.0000.0000.000
76A97THR0-0.055-0.02423.985-0.012-0.0120.0000.0000.0000.000
77A98ARG10.7460.89016.000-0.044-0.0440.0000.0000.0000.000
78A99GLU-1-0.810-0.92020.9040.0930.0930.0000.0000.0000.000
79A100VAL0-0.077-0.04118.664-0.002-0.0020.0000.0000.0000.000
80A101ILE0-0.0010.00721.620-0.007-0.0070.0000.0000.0000.000
81A102LEU0-0.0240.01315.5700.0010.0010.0000.0000.0000.000
82A103ARG10.7370.82919.2990.0060.0060.0000.0000.0000.000
83A104THR0-0.002-0.00518.321-0.003-0.0030.0000.0000.0000.000
84A105ARG10.7770.86619.4530.0580.0580.0000.0000.0000.000
85A106THR0-0.017-0.02018.687-0.001-0.0010.0000.0000.0000.000
86A107GLN0-0.0040.01020.481-0.003-0.0030.0000.0000.0000.000
87A108CYS0-0.040-0.02415.934-0.016-0.0160.0000.0000.0000.000
88A109GLU-1-0.859-0.92614.344-0.327-0.3270.0000.0000.0000.000
89A110LEU0-0.029-0.00712.416-0.038-0.0380.0000.0000.0000.000
90A111ALA00.0450.0289.7160.0130.0130.0000.0000.0000.000
91A112GLU-1-0.852-0.91811.166-0.049-0.0490.0000.0000.0000.000
92A113ILE00.014-0.0039.770-0.014-0.0140.0000.0000.0000.000
93A114SER00.0520.02812.9730.0240.0240.0000.0000.0000.000
94A115TYR00.042-0.00613.4460.0090.0090.0000.0000.0000.000
95A116GLU-1-0.900-0.93914.8540.1080.1080.0000.0000.0000.000
96A117ARG10.9110.95514.2150.0170.0170.0000.0000.0000.000
97A118LEU00.0030.0038.272-0.001-0.0010.0000.0000.0000.000
98A119GLN00.0720.02211.7940.0650.0650.0000.0000.0000.000
99A120GLN00.0030.01313.7060.0100.0100.0000.0000.0000.000
100A121LEU0-0.056-0.03911.4800.0010.0010.0000.0000.0000.000
101A122PHE0-0.011-0.0107.1780.0390.0390.0000.0000.0000.000
102A123GLN0-0.0070.00311.6220.0200.0200.0000.0000.0000.000
103A124THR0-0.044-0.03014.130-0.032-0.0320.0000.0000.0000.000
104A125SER0-0.0100.00013.2040.0070.0070.0000.0000.0000.000
105A126LEU0-0.027-0.0117.579-0.016-0.0160.0000.0000.0000.000
106A127SER00.0110.0268.9000.1260.1260.0000.0000.0000.000
107A128PRO0-0.002-0.0229.5630.0950.0950.0000.0000.0000.000
108A129ASP-1-0.771-0.8474.7260.4760.506-0.001-0.003-0.0260.000
109A130ALA00.0290.0445.0460.3500.438-0.0010.000-0.0860.000
110A131PRO00.0250.0016.6940.1900.1900.0000.0000.0000.000
111A132ARG10.8490.9112.170-1.708-1.3881.774-0.543-1.5510.002
112A133ILE00.0310.0082.629-1.7990.1632.171-1.293-2.840-0.014
113A134LEU00.0100.0063.3880.145-0.1620.0280.465-0.1860.000
114A135TYR0-0.0020.0055.224-0.396-0.3960.0000.0000.0000.000
115A136ALA0-0.010-0.0112.422-1.076-0.3251.510-0.643-1.618-0.002
116A137ILE00.0300.0124.396-0.757-0.5880.000-0.042-0.1270.000
117A138GLY00.0550.0356.584-0.221-0.2210.0000.0000.0000.000
118A139VAL0-0.028-0.0066.537-0.320-0.3200.0000.0000.0000.000
119A140GLN0-0.021-0.0075.446-0.231-0.2310.0000.0000.0000.000
120A141LEU00.0380.0319.373-0.145-0.1450.0000.0000.0000.000
121A142SER0-0.012-0.01411.827-0.123-0.1230.0000.0000.0000.000
122A143LYS10.9090.9589.457-0.468-0.4680.0000.0000.0000.000
123A144ARG10.8280.9019.871-0.298-0.2980.0000.0000.0000.000
124A145LEU00.0430.04915.259-0.049-0.0490.0000.0000.0000.000
125A146LEU0-0.0210.01017.014-0.046-0.0460.0000.0000.0000.000
126A147ASP-1-0.829-0.92217.2590.1220.1220.0000.0000.0000.000
127A148THR0-0.028-0.02918.663-0.034-0.0340.0000.0000.0000.000
128A149THR0-0.013-0.01621.030-0.018-0.0180.0000.0000.0000.000
129A150ARG10.8600.91519.045-0.173-0.1730.0000.0000.0000.000
130A151LYS10.8290.91822.962-0.071-0.0710.0000.0000.0000.000
131A152ALA00.0470.01825.148-0.012-0.0120.0000.0000.0000.000
132A153SER0-0.015-0.01227.098-0.007-0.0070.0000.0000.0000.000
133A154ARG10.7990.88123.888-0.072-0.0720.0000.0000.0000.000
134A155LEU0-0.039-0.02227.858-0.009-0.0090.0000.0000.0000.000
135A156ALA0-0.0110.01831.202-0.005-0.0050.0000.0000.0000.000
136A157PHE0-0.026-0.01532.237-0.003-0.0030.0000.0000.0000.000
137A158LEU0-0.0350.00231.324-0.003-0.0030.0000.0000.0000.000
138A159ASP-1-0.757-0.86034.8750.0220.0220.0000.0000.0000.000
139A160VAL00.018-0.01334.6180.0000.0000.0000.0000.0000.000
140A161THR0-0.051-0.05334.591-0.004-0.0040.0000.0000.0000.000
141A162ASP-1-0.755-0.86533.5070.0320.0320.0000.0000.0000.000
142A163ARG10.8340.93030.544-0.037-0.0370.0000.0000.0000.000
143A164ILE0-0.0050.00229.977-0.002-0.0020.0000.0000.0000.000
144A165VAL00.0190.01930.798-0.006-0.0060.0000.0000.0000.000
145A166ARG10.8490.88927.796-0.050-0.0500.0000.0000.0000.000
146A167THR0-0.005-0.00625.6640.0020.0020.0000.0000.0000.000
147A168LEU0-0.056-0.03526.022-0.009-0.0090.0000.0000.0000.000
148A169HIS00.005-0.01626.576-0.013-0.0130.0000.0000.0000.000
149A170ASP-1-0.829-0.88122.0050.0360.0360.0000.0000.0000.000
150A171LEU00.009-0.00721.741-0.014-0.0140.0000.0000.0000.000
151A172SER0-0.085-0.03822.643-0.018-0.0180.0000.0000.0000.000
152A173LYS10.8990.93817.8380.0670.0670.0000.0000.0000.000
153A174GLU-1-0.872-0.93016.658-0.125-0.1250.0000.0000.0000.000
154A175PRO0-0.011-0.00814.762-0.003-0.0030.0000.0000.0000.000
155A176GLU-1-0.987-0.98718.062-0.143-0.1430.0000.0000.0000.000
156A177ALA0-0.077-0.03520.3210.0120.0120.0000.0000.0000.000
157A178MET0-0.0130.00823.249-0.002-0.0020.0000.0000.0000.000
158A179SER00.0240.00825.6060.0150.0150.0000.0000.0000.000
159A180HIS00.013-0.00427.6690.0000.0000.0000.0000.0000.000
160A181PRO00.0270.00431.4370.0020.0020.0000.0000.0000.000
161A182GLN0-0.016-0.01034.3550.0010.0010.0000.0000.0000.000
162A183GLY00.0440.02931.2230.0070.0070.0000.0000.0000.000
163A184THR0-0.030-0.00625.452-0.010-0.0100.0000.0000.0000.000
164A185GLN00.0110.01128.0960.0120.0120.0000.0000.0000.000
165A186LEU00.0130.02526.542-0.011-0.0110.0000.0000.0000.000
166A187ARG10.8580.91325.2910.1020.1020.0000.0000.0000.000
167A188VAL00.0790.04825.9890.0000.0000.0000.0000.0000.000
168A189SER0-0.075-0.03528.2670.0020.0020.0000.0000.0000.000
169A190ARG10.9680.95730.9150.0360.0360.0000.0000.0000.000
170A191GLN00.0050.00731.6120.0010.0010.0000.0000.0000.000
171A192GLU-1-0.745-0.82524.925-0.028-0.0280.0000.0000.0000.000
172A193LEU00.0470.03328.1780.0050.0050.0000.0000.0000.000
173A194ALA0-0.011-0.02529.9010.0060.0060.0000.0000.0000.000
174A195ARG10.8230.89626.9500.0180.0180.0000.0000.0000.000
175A196LEU0-0.0330.00523.3610.0080.0080.0000.0000.0000.000
176A197VAL0-0.027-0.00726.8550.0100.0100.0000.0000.0000.000
177A198GLY00.1040.07029.6460.0040.0040.0000.0000.0000.000
178A199CYS0-0.055-0.01631.3590.0000.0000.0000.0000.0000.000
179A200SER00.0710.04534.147-0.003-0.0030.0000.0000.0000.000
180A201ARG11.0420.99335.4920.0140.0140.0000.0000.0000.000
181A202GLU-1-0.877-0.93636.4460.0000.0000.0000.0000.0000.000
182A203MET00.0620.05737.857-0.002-0.0020.0000.0000.0000.000
183A204ALA00.0610.02334.278-0.001-0.0010.0000.0000.0000.000
184A205GLY0-0.077-0.04236.252-0.003-0.0030.0000.0000.0000.000
185A206ARG10.8360.88938.558-0.006-0.0060.0000.0000.0000.000
186A207VAL00.0540.02436.272-0.001-0.0010.0000.0000.0000.000
187A208LEU0-0.0050.00333.722-0.001-0.0010.0000.0000.0000.000
188A209LYS10.9130.95337.7890.0120.0120.0000.0000.0000.000
189A210LYS10.8460.91741.118-0.001-0.0010.0000.0000.0000.000
190A211LEU00.0710.02635.1440.0000.0000.0000.0000.0000.000
191A212GLN00.0140.00839.170-0.003-0.0030.0000.0000.0000.000
192A213ALA0-0.077-0.02340.374-0.001-0.0010.0000.0000.0000.000
193A214ASP-1-0.829-0.89240.613-0.002-0.0020.0000.0000.0000.000
194A215GLY0-0.027-0.01241.1280.0000.0000.0000.0000.0000.000
195A216LEU0-0.011-0.01235.758-0.002-0.0020.0000.0000.0000.000
196A217LEU0-0.0120.00133.721-0.003-0.0030.0000.0000.0000.000
197A218HIS00.0210.04636.1570.0050.0050.0000.0000.0000.000
198A219ALA00.0010.00035.725-0.003-0.0030.0000.0000.0000.000
199A220ARG10.9860.98235.5110.0530.0530.0000.0000.0000.000
200A221GLY00.0020.00734.956-0.004-0.0040.0000.0000.0000.000
201A222LYS10.8930.93227.8390.0730.0730.0000.0000.0000.000
202A223THR00.003-0.01130.328-0.006-0.0060.0000.0000.0000.000
203A224VAL00.0180.01930.9520.0050.0050.0000.0000.0000.000
204A225VAL0-0.018-0.00931.042-0.006-0.0060.0000.0000.0000.000
205A226LEU00.0070.00728.4940.0050.0050.0000.0000.0000.000
206A227TYR0-0.007-0.03231.465-0.005-0.0050.0000.0000.0000.000
207A228GLY00.0100.01930.9360.0020.0020.0000.0000.0000.000