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: QV58Y

Calculation Name: 3RV1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RV1

Chain ID: A

ChEMBL ID:

UniProt ID: A7TR32

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2346712.68286
FMO2-HF: Nuclear repulsion 2258926.794354
FMO2-HF: Total energy -87785.888506
FMO2-MP2: Total energy -88043.079141


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:15:SER)


Summations of interaction energy for fragment #1(A:15: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.
-24.54-20.9115.789-3.809-5.6080.027
Interaction energy analysis for fragmet #1(A:15:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.022
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].
3A17GLU-1-0.792-0.8763.486-3.171-1.1690.006-0.900-1.1080.002
4A18LEU00.0440.0222.215-1.794-0.3490.925-0.700-1.669-0.004
5A19LYS10.8680.9312.008-18.441-18.2594.858-2.209-2.8310.029
6A20VAL00.0050.0106.4240.0780.0780.0000.0000.0000.000
7A21ARG10.7430.8526.3930.6090.6090.0000.0000.0000.000
8A22GLU-1-0.782-0.8708.634-0.288-0.2880.0000.0000.0000.000
9A23PHE0-0.0190.00710.2170.0740.0740.0000.0000.0000.000
10A24TYR00.001-0.04312.2110.0020.0020.0000.0000.0000.000
11A25ARG10.7910.87411.8230.2920.2920.0000.0000.0000.000
12A26LEU0-0.001-0.00314.4860.0070.0070.0000.0000.0000.000
13A27HIS0-0.003-0.00316.1170.0060.0060.0000.0000.0000.000
14A28ASN00.0240.00517.921-0.027-0.0270.0000.0000.0000.000
15A29ALA00.0390.02819.293-0.007-0.0070.0000.0000.0000.000
16A30CYS0-0.055-0.02819.5140.0040.0040.0000.0000.0000.000
17A31VAL0-0.0040.00522.196-0.003-0.0030.0000.0000.0000.000
18A32LYS10.8590.91324.063-0.022-0.0220.0000.0000.0000.000
19A33LEU0-0.0250.02324.889-0.006-0.0060.0000.0000.0000.000
20A34LYS10.8310.90226.406-0.116-0.1160.0000.0000.0000.000
21A35GLU-1-0.882-0.93128.3010.0280.0280.0000.0000.0000.000
22A36SER0-0.027-0.04328.834-0.003-0.0030.0000.0000.0000.000
23A37ILE00.001-0.00330.390-0.004-0.0040.0000.0000.0000.000
24A38LYS10.8370.90532.420-0.056-0.0560.0000.0000.0000.000
25A39LEU0-0.015-0.01233.592-0.003-0.0030.0000.0000.0000.000
26A40ILE0-0.027-0.00533.433-0.005-0.0050.0000.0000.0000.000
27A41TYR0-0.015-0.02733.9360.0000.0000.0000.0000.0000.000
28A42GLU-1-0.815-0.88738.1850.0500.0500.0000.0000.0000.000
29A43ASN00.0000.01239.802-0.003-0.0030.0000.0000.0000.000
30A44PRO00.0320.00241.8330.0000.0000.0000.0000.0000.000
31A45LEU0-0.0210.00443.789-0.001-0.0010.0000.0000.0000.000
32A46VAL0-0.038-0.02740.462-0.001-0.0010.0000.0000.0000.000
33A47THR0-0.0020.00143.0060.0000.0000.0000.0000.0000.000
34A48ASP-1-0.907-0.95945.1760.0270.0270.0000.0000.0000.000
35A49GLN0-0.024-0.00946.616-0.002-0.0020.0000.0000.0000.000
36A50ASN0-0.002-0.00149.570-0.001-0.0010.0000.0000.0000.000
37A51VAL00.0340.01549.548-0.001-0.0010.0000.0000.0000.000
38A52LEU0-0.032-0.02047.871-0.001-0.0010.0000.0000.0000.000
39A53ASN0-0.052-0.02652.051-0.002-0.0020.0000.0000.0000.000
40A54LEU00.0300.03247.677-0.001-0.0010.0000.0000.0000.000
41A55GLY0-0.014-0.01252.0690.0010.0010.0000.0000.0000.000
42A56THR0-0.041-0.02654.281-0.001-0.0010.0000.0000.0000.000
43A57ALA0-0.0130.00156.1020.0000.0000.0000.0000.0000.000
44A58GLU-1-0.900-0.91157.8300.0040.0040.0000.0000.0000.000
45A59ASN0-0.032-0.03155.712-0.002-0.0020.0000.0000.0000.000
46A60THR00.0450.00655.5080.0000.0000.0000.0000.0000.000
47A61ILE00.0150.02751.673-0.001-0.0010.0000.0000.0000.000
48A62ASP-1-0.764-0.86350.9880.0060.0060.0000.0000.0000.000
49A63TYR0-0.052-0.05651.1230.0000.0000.0000.0000.0000.000
50A64THR0-0.036-0.02348.133-0.001-0.0010.0000.0000.0000.000
51A65ILE0-0.013-0.01346.1570.0000.0000.0000.0000.0000.000
52A66LEU00.000-0.00246.2480.0010.0010.0000.0000.0000.000
53A67ASN0-0.052-0.02947.1560.0010.0010.0000.0000.0000.000
54A68THR0-0.035-0.00842.727-0.001-0.0010.0000.0000.0000.000
55A69PRO00.0360.00739.5670.0020.0020.0000.0000.0000.000
56A70THR00.0080.00438.0850.0020.0020.0000.0000.0000.000
57A71LEU00.0420.02939.5380.0030.0030.0000.0000.0000.000
58A72ASN0-0.015-0.00941.9320.0040.0040.0000.0000.0000.000
59A73VAL0-0.0010.01135.1010.0030.0030.0000.0000.0000.000
60A74ALA00.0120.01037.7360.0040.0040.0000.0000.0000.000
61A75LYS10.9230.93938.788-0.016-0.0160.0000.0000.0000.000
62A76THR0-0.042-0.01537.5260.0020.0020.0000.0000.0000.000
63A77LEU0-0.047-0.02732.9900.0040.0040.0000.0000.0000.000
64A78LEU0-0.027-0.01036.6960.0050.0050.0000.0000.0000.000
65A79GLY00.0150.00539.4070.0030.0030.0000.0000.0000.000
66A80ASN0-0.041-0.02434.456-0.001-0.0010.0000.0000.0000.000
67A81ARG10.8330.91136.638-0.047-0.0470.0000.0000.0000.000
68A82TYR0-0.029-0.00937.4780.0050.0050.0000.0000.0000.000
69A83SER0-0.063-0.02035.8250.0010.0010.0000.0000.0000.000
70A84LEU0-0.025-0.03229.3560.0060.0060.0000.0000.0000.000
71A85ASP-1-0.714-0.81934.0120.0610.0610.0000.0000.0000.000
72A86LEU00.032-0.01328.4150.0080.0080.0000.0000.0000.000
73A87ILE0-0.024-0.00329.7920.0090.0090.0000.0000.0000.000
74A88ASP-1-0.870-0.93031.5570.0880.0880.0000.0000.0000.000
75A89LEU0-0.0370.01126.3450.0100.0100.0000.0000.0000.000
76A90PHE00.009-0.00823.7400.0140.0140.0000.0000.0000.000
77A91GLN0-0.033-0.01327.6890.0070.0070.0000.0000.0000.000
78A92SER0-0.055-0.05329.9980.0090.0090.0000.0000.0000.000
79A93HIS0-0.079-0.04024.0000.0180.0180.0000.0000.0000.000
80A94ASP-1-0.874-0.91925.1790.1850.1850.0000.0000.0000.000
81A95PHE00.0060.01220.8600.0130.0130.0000.0000.0000.000
82A96LYS10.8250.89024.014-0.212-0.2120.0000.0000.0000.000
83A97ASP-1-0.793-0.89523.1620.1240.1240.0000.0000.0000.000
84A98SER0-0.049-0.03322.768-0.006-0.0060.0000.0000.0000.000
85A99ASN0-0.042-0.02022.0220.0020.0020.0000.0000.0000.000
86A100THR0-0.009-0.02617.3230.0170.0170.0000.0000.0000.000
87A101ASP-1-0.870-0.93716.9240.3740.3740.0000.0000.0000.000
88A102VAL0-0.046-0.01911.9080.0810.0810.0000.0000.0000.000
89A103ASP-1-0.765-0.84114.1850.2850.2850.0000.0000.0000.000
90A104MET0-0.050-0.01714.083-0.034-0.0340.0000.0000.0000.000
91A105PHE0-0.064-0.0349.4630.0960.0960.0000.0000.0000.000
92A106ILE0-0.059-0.00811.977-0.003-0.0030.0000.0000.0000.000
93A107LYS10.9090.94014.195-0.332-0.3320.0000.0000.0000.000
94A108TYR00.0060.01315.381-0.017-0.0170.0000.0000.0000.000
95A109PRO00.0450.02316.3110.0120.0120.0000.0000.0000.000
96A110VAL00.0560.05111.298-0.012-0.0120.0000.0000.0000.000
97A111VAL00.0250.02313.4810.0080.0080.0000.0000.0000.000
98A112TYR0-0.074-0.05211.436-0.033-0.0330.0000.0000.0000.000
99A113ASP-1-0.767-0.89110.133-0.735-0.7350.0000.0000.0000.000
100A114GLU-1-0.901-0.9576.429-1.878-1.8780.0000.0000.0000.000
101A115ASN0-0.088-0.0519.9170.1120.1120.0000.0000.0000.000
102A116LEU0-0.018-0.00812.8510.0750.0750.0000.0000.0000.000
103A117GLU-1-0.775-0.85911.642-0.115-0.1150.0000.0000.0000.000
104A118ASN0-0.042-0.04110.6180.1290.1290.0000.0000.0000.000
105A119LEU0-0.021-0.00114.5510.0420.0420.0000.0000.0000.000
106A120ALA00.016-0.00117.4820.0300.0300.0000.0000.0000.000
107A121PHE0-0.016-0.02716.1980.0350.0350.0000.0000.0000.000
108A122MET0-0.037-0.00318.7910.0080.0080.0000.0000.0000.000
109A123HIS00.006-0.00621.2030.0100.0100.0000.0000.0000.000
110A124LYS10.8560.93024.7150.0790.0790.0000.0000.0000.000
111A125SER0-0.0040.00327.8510.0080.0080.0000.0000.0000.000
112A140GLN00.0030.00024.648-0.001-0.0010.0000.0000.0000.000
113A141LEU0-0.041-0.02620.0840.0090.0090.0000.0000.0000.000
114A142SER0-0.031-0.04423.6090.0010.0010.0000.0000.0000.000
115A143ASN00.0530.02822.073-0.007-0.0070.0000.0000.0000.000
116A144GLU-1-0.759-0.84623.328-0.090-0.0900.0000.0000.0000.000
117A145ARG10.9460.96325.2490.1300.1300.0000.0000.0000.000
118A146LEU00.0070.01819.7730.0050.0050.0000.0000.0000.000
119A147GLU-1-0.871-0.92824.028-0.051-0.0510.0000.0000.0000.000
120A148PHE00.001-0.00226.3960.0090.0090.0000.0000.0000.000
121A149LEU00.0110.01624.1070.0060.0060.0000.0000.0000.000
122A150GLY00.0530.01725.3060.0080.0080.0000.0000.0000.000
123A151ASP-1-0.893-0.92726.139-0.020-0.0200.0000.0000.0000.000
124A152SER0-0.035-0.02029.5070.0070.0070.0000.0000.0000.000
125A153TRP00.0280.00127.0780.0070.0070.0000.0000.0000.000
126A154LEU0-0.0080.00927.9660.0080.0080.0000.0000.0000.000
127A155GLY00.0260.01029.2750.0070.0070.0000.0000.0000.000
128A156ALA0-0.0150.01231.3490.0050.0050.0000.0000.0000.000
129A157LEU00.0310.00926.5790.0060.0060.0000.0000.0000.000
130A158VAL00.0040.00430.8770.0060.0060.0000.0000.0000.000
131A159SER0-0.033-0.03932.9640.0030.0030.0000.0000.0000.000
132A160TYR00.0400.02332.5940.0010.0010.0000.0000.0000.000
133A161ILE00.0040.01629.7670.0040.0040.0000.0000.0000.000
134A162VAL0-0.048-0.02934.3730.0040.0040.0000.0000.0000.000
135A163TYR0-0.010-0.00737.7570.0010.0010.0000.0000.0000.000
136A164THR0-0.027-0.03335.9170.0020.0020.0000.0000.0000.000
137A165ARG10.9090.97334.573-0.042-0.0420.0000.0000.0000.000
138A166PHE0-0.026-0.01938.7570.0020.0020.0000.0000.0000.000
139A167PRO00.0990.05341.847-0.003-0.0030.0000.0000.0000.000
140A168SER0-0.082-0.05144.0460.0000.0000.0000.0000.0000.000
141A169ALA0-0.0380.00144.571-0.001-0.0010.0000.0000.0000.000
142A170ASN00.007-0.00146.494-0.002-0.0020.0000.0000.0000.000
143A171GLU-1-0.808-0.89945.0930.0020.0020.0000.0000.0000.000
144A172GLY00.0850.05644.9480.0000.0000.0000.0000.0000.000
145A173MET0-0.056-0.03445.5700.0010.0010.0000.0000.0000.000
146A174LEU0-0.0060.00941.1250.0010.0010.0000.0000.0000.000
147A175SER0-0.015-0.04640.7010.0000.0000.0000.0000.0000.000
148A176GLN0-0.016-0.00141.115-0.002-0.0020.0000.0000.0000.000
149A177MET0-0.025-0.00738.3720.0010.0010.0000.0000.0000.000
150A178LYS10.9390.97436.0680.0060.0060.0000.0000.0000.000
151A179GLU-1-0.860-0.92836.438-0.003-0.0030.0000.0000.0000.000
152A180SER0-0.099-0.05937.4820.0010.0010.0000.0000.0000.000
153A181ILE0-0.035-0.01532.2060.0030.0030.0000.0000.0000.000
154A182VAL0-0.006-0.00832.4890.0000.0000.0000.0000.0000.000
155A183ASN0-0.0080.01733.375-0.004-0.0040.0000.0000.0000.000
156A184ASN00.029-0.01832.716-0.001-0.0010.0000.0000.0000.000
157A185ASN0-0.032-0.00532.477-0.002-0.0020.0000.0000.0000.000
158A186ASN00.0540.01231.3590.0070.0070.0000.0000.0000.000
159A187LEU00.0370.02228.1290.0040.0040.0000.0000.0000.000
160A188PHE0-0.023-0.00428.0570.0000.0000.0000.0000.0000.000
161A189ASP-1-0.876-0.93728.5610.0310.0310.0000.0000.0000.000
162A190TRP0-0.056-0.03026.3060.0100.0100.0000.0000.0000.000
163A191SER0-0.008-0.02324.1360.0110.0110.0000.0000.0000.000
164A192THR0-0.053-0.03223.8340.0060.0060.0000.0000.0000.000
165A193LYS10.9260.96424.939-0.065-0.0650.0000.0000.0000.000
166A194LEU0-0.014-0.00220.7750.0190.0190.0000.0000.0000.000
167A195ASN0-0.049-0.03520.0500.0130.0130.0000.0000.0000.000
168A196PHE00.0610.03018.7040.0020.0020.0000.0000.0000.000
169A197THR00.0060.00620.704-0.013-0.0130.0000.0000.0000.000
170A198LYS10.8920.92719.505-0.117-0.1170.0000.0000.0000.000
171A199ARG10.8270.90913.2160.0690.0690.0000.0000.0000.000
172A200LEU0-0.037-0.00517.890-0.027-0.0270.0000.0000.0000.000
173A201GLN0-0.0100.03220.815-0.020-0.0200.0000.0000.0000.000
174A202GLY00.0310.00021.2730.0120.0120.0000.0000.0000.000
175A203ASN0-0.032-0.00822.8450.0070.0070.0000.0000.0000.000
176A204ILE0-0.0130.00125.201-0.002-0.0020.0000.0000.0000.000
177A205ALA00.0190.01927.3340.0030.0030.0000.0000.0000.000
178A217LYS10.8010.86930.7400.0440.0440.0000.0000.0000.000
179A218ARG10.9560.96526.2350.0470.0470.0000.0000.0000.000
180A219TYR0-0.011-0.02524.631-0.006-0.0060.0000.0000.0000.000
181A220ALA00.0380.04625.4630.0040.0040.0000.0000.0000.000
182A221ASP-1-0.717-0.85026.385-0.045-0.0450.0000.0000.0000.000
183A222CYS0-0.048-0.01121.526-0.011-0.0110.0000.0000.0000.000
184A223VAL0-0.0100.00421.750-0.005-0.0050.0000.0000.0000.000
185A224GLN0-0.044-0.03723.337-0.003-0.0030.0000.0000.0000.000
186A225ALA00.0180.00721.922-0.006-0.0060.0000.0000.0000.000
187A226TYR0-0.050-0.05015.159-0.021-0.0210.0000.0000.0000.000
188A227ILE0-0.0050.00019.820-0.004-0.0040.0000.0000.0000.000
189A228GLY00.0420.01622.423-0.001-0.0010.0000.0000.0000.000
190A229ALA0-0.023-0.01417.096-0.007-0.0070.0000.0000.0000.000
191A230LEU0-0.059-0.03517.109-0.010-0.0100.0000.0000.0000.000
192A231VAL00.0220.01919.1870.0060.0060.0000.0000.0000.000
193A232ILE0-0.023-0.01419.1850.0010.0010.0000.0000.0000.000
194A233ASP-1-0.757-0.88314.841-0.276-0.2760.0000.0000.0000.000
195A234ARG10.7570.88216.3050.0470.0470.0000.0000.0000.000
196A235PHE0-0.0470.00020.9520.0150.0150.0000.0000.0000.000
197A236GLY00.0560.01423.816-0.011-0.0110.0000.0000.0000.000
198A237THR0-0.025-0.03225.8730.0020.0020.0000.0000.0000.000
199A238GLU-1-0.912-0.93327.4210.0070.0070.0000.0000.0000.000
200A239PHE00.0260.01228.8320.0030.0030.0000.0000.0000.000
201A240LEU0-0.0120.00629.505-0.003-0.0030.0000.0000.0000.000
202A241ASP-1-0.812-0.90631.955-0.019-0.0190.0000.0000.0000.000
203A242ILE0-0.019-0.01035.023-0.002-0.0020.0000.0000.0000.000
204A243LYS10.8070.89830.6360.0610.0610.0000.0000.0000.000
205A244GLU-1-0.912-0.97132.912-0.049-0.0490.0000.0000.0000.000
206A245TRP00.0180.01935.9420.0000.0000.0000.0000.0000.000
207A246LEU0-0.013-0.01436.5060.0000.0000.0000.0000.0000.000
208A247GLU-1-0.870-0.90933.603-0.063-0.0630.0000.0000.0000.000
209A248GLU-1-0.922-0.97037.541-0.031-0.0310.0000.0000.0000.000
210A249LEU0-0.045-0.02540.7260.0000.0000.0000.0000.0000.000
211A250SER0-0.066-0.04238.9100.0010.0010.0000.0000.0000.000
212A251GLU-1-0.856-0.91240.084-0.053-0.0530.0000.0000.0000.000
213A252LYS10.8970.93541.4350.0380.0380.0000.0000.0000.000
214A253LYS10.8640.92541.0830.0340.0340.0000.0000.0000.000
215A254LEU00.0370.01336.000-0.002-0.0020.0000.0000.0000.000
216A255ALA00.0220.03239.053-0.004-0.0040.0000.0000.0000.000
217A256LYS10.8270.92740.9950.0380.0380.0000.0000.0000.000