FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JQMV9

Calculation Name: 3MVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DWD0

Base Structure: X-ray

Registration Date: 2023-09-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2282170.810741
FMO2-HF: Nuclear repulsion 2201006.504253
FMO2-HF: Total energy -81164.306487
FMO2-MP2: Total energy -81406.942579


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:14:LYS)


Summations of interaction energy for fragment #1(A:14:LYS)
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.
77.10679.5980.028-1.031-1.4890.001
Interaction energy analysis for fragmet #1(A:14:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.979 / q_NPA : 0.972
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].
3A16ILE00.0660.0423.2199.82412.3070.029-1.025-1.4870.001
4A17ARG10.9630.9765.37618.80518.814-0.001-0.006-0.0020.000
5A18LYS10.8630.9425.36846.58446.5840.0000.0000.0000.000
6A19PRO00.0400.0118.149-1.809-1.8090.0000.0000.0000.000
7A20LYS10.9920.9797.18827.29127.2910.0000.0000.0000.000
8A21GLN00.0310.0388.200-0.234-0.2340.0000.0000.0000.000
9A22GLU-1-0.754-0.8895.613-46.534-46.5340.0000.0000.0000.000
10A23ARG10.9010.9449.36824.04424.0440.0000.0000.0000.000
11A24SER00.0200.01211.3511.7461.7460.0000.0000.0000.000
12A25ILE00.0430.02311.8561.8771.8770.0000.0000.0000.000
13A26GLU-1-0.847-0.90713.141-21.997-21.9970.0000.0000.0000.000
14A27LYS10.9500.97415.61218.33218.3320.0000.0000.0000.000
15A28ARG10.9591.00217.05215.93715.9370.0000.0000.0000.000
16A29ASN00.0400.01317.0241.7441.7440.0000.0000.0000.000
17A30LYS10.8700.97019.69613.79313.7930.0000.0000.0000.000
18A31ILE0-0.011-0.01520.8810.6740.6740.0000.0000.0000.000
19A32LEU0-0.037-0.01021.4360.5400.5400.0000.0000.0000.000
20A33GLN0-0.030-0.02424.1260.1780.1780.0000.0000.0000.000
21A34VAL0-0.011-0.01225.7690.4840.4840.0000.0000.0000.000
22A35ALA00.000-0.00327.3630.4430.4430.0000.0000.0000.000
23A36LYS10.8610.91828.59110.69910.6990.0000.0000.0000.000
24A37ASP-1-0.825-0.89029.814-10.390-10.3900.0000.0000.0000.000
25A38LEU0-0.041-0.02830.8520.3150.3150.0000.0000.0000.000
26A39PHE0-0.033-0.03531.0130.2610.2610.0000.0000.0000.000
27A40SER0-0.012-0.02433.8050.2830.2830.0000.0000.0000.000
28A41ASP-1-0.970-0.96236.104-8.296-8.2960.0000.0000.0000.000
29A42LYS10.8420.89836.9908.7218.7210.0000.0000.0000.000
30A43THR0-0.0110.00238.7820.2820.2820.0000.0000.0000.000
31A44TYR0-0.025-0.05833.267-0.187-0.1870.0000.0000.0000.000
32A45PHE00.008-0.00137.058-0.194-0.1940.0000.0000.0000.000
33A46ASN0-0.0330.01039.7620.0730.0730.0000.0000.0000.000
34A47VAL00.0200.02133.389-0.122-0.1220.0000.0000.0000.000
35A48THR00.0130.01134.979-0.090-0.0900.0000.0000.0000.000
36A49THR00.0470.00129.272-0.148-0.1480.0000.0000.0000.000
37A50ASN00.009-0.00229.999-0.630-0.6300.0000.0000.0000.000
38A51GLU-1-0.822-0.88530.921-9.176-9.1760.0000.0000.0000.000
39A52ILE00.0280.01427.184-0.256-0.2560.0000.0000.0000.000
40A53ALA0-0.013-0.00926.327-0.422-0.4220.0000.0000.0000.000
41A54LYS10.8920.94226.31210.78310.7830.0000.0000.0000.000
42A55LYS10.9800.99427.8039.8199.8190.0000.0000.0000.000
43A56ALA0-0.026-0.02223.637-0.259-0.2590.0000.0000.0000.000
44A57ASP-1-0.874-0.92923.058-12.787-12.7870.0000.0000.0000.000
45A58VAL0-0.096-0.04220.780-0.975-0.9750.0000.0000.0000.000
46A59SER00.0370.00923.2270.7060.7060.0000.0000.0000.000
47A60VAL00.0880.01824.991-0.300-0.3000.0000.0000.0000.000
48A61GLY00.0440.02825.821-0.005-0.0050.0000.0000.0000.000
49A62THR0-0.046-0.02119.728-0.272-0.2720.0000.0000.0000.000
50A63LEU00.0020.00821.672-0.558-0.5580.0000.0000.0000.000
51A64TYR00.0310.00623.859-0.128-0.1280.0000.0000.0000.000
52A65ALA0-0.043-0.00320.3240.0170.0170.0000.0000.0000.000
53A66TYR0-0.134-0.08116.041-0.751-0.7510.0000.0000.0000.000
54A67PHE0-0.027-0.03321.521-0.189-0.1890.0000.0000.0000.000
55A68ALA00.0660.04225.2540.1420.1420.0000.0000.0000.000
56A69SER0-0.037-0.03228.0000.4280.4280.0000.0000.0000.000
57A70LYS10.8690.91229.3088.5148.5140.0000.0000.0000.000
58A71GLU-1-0.728-0.85830.908-9.362-9.3620.0000.0000.0000.000
59A72ASP-1-0.875-0.88827.007-10.941-10.9410.0000.0000.0000.000
60A73ILE0-0.045-0.02826.094-0.377-0.3770.0000.0000.0000.000
61A74LEU00.0390.02127.765-0.229-0.2290.0000.0000.0000.000
62A75THR0-0.015-0.01228.5060.0540.0540.0000.0000.0000.000
63A76ALA0-0.077-0.03924.673-0.156-0.1560.0000.0000.0000.000
64A77LEU0-0.043-0.02126.656-0.204-0.2040.0000.0000.0000.000
65A78LEU00.0380.02528.5890.0810.0810.0000.0000.0000.000
66A79LYS10.9320.97527.27411.32111.3210.0000.0000.0000.000
67A80ARG10.8920.93620.26714.17714.1770.0000.0000.0000.000
68A81TYR00.026-0.00527.769-0.107-0.1070.0000.0000.0000.000
69A82ASN0-0.024-0.01030.8600.6210.6210.0000.0000.0000.000
70A83ASP-1-0.861-0.92727.031-11.231-11.2310.0000.0000.0000.000
71A84PHE0-0.0090.02129.315-0.055-0.0550.0000.0000.0000.000
72A85PHE00.0500.03830.3410.1840.1840.0000.0000.0000.000
73A86LEU0-0.022-0.01931.8830.2160.2160.0000.0000.0000.000
74A87THR0-0.079-0.06928.2420.1020.1020.0000.0000.0000.000
75A88THR0-0.080-0.04430.7000.0500.0500.0000.0000.0000.000
76A89ILE00.0190.02433.3940.2220.2220.0000.0000.0000.000
77A90PHE0-0.038-0.02436.3700.2360.2360.0000.0000.0000.000
78A91ALA0-0.0050.00234.3160.2010.2010.0000.0000.0000.000
79A92ASP-1-0.875-0.94036.482-8.383-8.3830.0000.0000.0000.000
80A93ILE00.0090.01139.1440.2270.2270.0000.0000.0000.000
81A94ASN00.008-0.00238.4600.4440.4440.0000.0000.0000.000
82A95SER00.0080.01340.4360.0850.0850.0000.0000.0000.000
83A96GLN0-0.008-0.02341.8360.0900.0900.0000.0000.0000.000
84A97ASP-1-0.838-0.88943.213-7.067-7.0670.0000.0000.0000.000
85A98SER0-0.028-0.02944.2160.1790.1790.0000.0000.0000.000
86A99LEU0-0.0060.00346.2330.1610.1610.0000.0000.0000.000
87A100ASP-1-0.795-0.87548.522-6.367-6.3670.0000.0000.0000.000
88A101ARG10.7830.87945.2787.1007.1000.0000.0000.0000.000
89A102PHE00.000-0.01450.6580.1430.1430.0000.0000.0000.000
90A103LYS10.7810.88452.5765.9955.9950.0000.0000.0000.000
91A104LYS10.8300.91853.1176.0586.0580.0000.0000.0000.000
92A105ASN00.017-0.01454.9060.1850.1850.0000.0000.0000.000
93A106PRO00.0510.04454.588-0.103-0.1030.0000.0000.0000.000
94A107LYS10.8720.93053.9845.3065.3060.0000.0000.0000.000
95A108GLU-1-0.889-0.91051.451-6.112-6.1120.0000.0000.0000.000
96A109TRP0-0.001-0.01047.605-0.086-0.0860.0000.0000.0000.000
97A110LEU00.0150.01749.276-0.137-0.1370.0000.0000.0000.000
98A111ASN0-0.028-0.02550.113-0.109-0.1090.0000.0000.0000.000
99A112VAL0-0.036-0.01245.099-0.104-0.1040.0000.0000.0000.000
100A113LEU00.0430.03144.721-0.172-0.1720.0000.0000.0000.000
101A114ILE00.0280.00545.315-0.144-0.1440.0000.0000.0000.000
102A115ASN00.0060.00445.527-0.024-0.0240.0000.0000.0000.000
103A116GLN00.007-0.00641.102-0.019-0.0190.0000.0000.0000.000
104A117LEU0-0.018-0.01841.191-0.208-0.2080.0000.0000.0000.000
105A118LEU0-0.0040.01342.729-0.060-0.0600.0000.0000.0000.000
106A119ALA0-0.033-0.02139.849-0.103-0.1030.0000.0000.0000.000
107A120ALA0-0.0010.01637.802-0.277-0.2770.0000.0000.0000.000
108A121GLU-1-0.822-0.90434.543-8.573-8.5730.0000.0000.0000.000
109A122ASP-1-0.861-0.92932.171-10.014-10.0140.0000.0000.0000.000
110A123LYS10.8800.93135.0048.0748.0740.0000.0000.0000.000
111A124ILE00.0380.02835.9990.1170.1170.0000.0000.0000.000
112A125PHE0-0.017-0.01531.695-0.026-0.0260.0000.0000.0000.000
113A126HIS00.0000.00836.029-0.226-0.2260.0000.0000.0000.000
114A127ALA00.0940.05137.9940.0940.0940.0000.0000.0000.000
115A128GLN0-0.018-0.00736.9490.1280.1280.0000.0000.0000.000
116A129ILE0-0.042-0.03134.1590.0090.0090.0000.0000.0000.000
117A130GLU-1-0.799-0.91038.304-7.375-7.3750.0000.0000.0000.000
118A131MET0-0.044-0.00841.0670.1650.1650.0000.0000.0000.000
119A132LEU0-0.035-0.02636.5320.0740.0740.0000.0000.0000.000
120A133ALA00.0130.01440.660-0.003-0.0030.0000.0000.0000.000
121A134TYR0-0.034-0.01242.3990.1630.1630.0000.0000.0000.000
122A135ALA0-0.035-0.01742.1160.1110.1110.0000.0000.0000.000
123A136ILE0-0.046-0.01636.435-0.102-0.1020.0000.0000.0000.000
124A137PRO00.0270.00039.402-0.053-0.0530.0000.0000.0000.000
125A138GLN0-0.013-0.02232.429-0.157-0.1570.0000.0000.0000.000
126A139ALA00.0290.01636.896-0.079-0.0790.0000.0000.0000.000
127A140LYS10.8460.90737.9037.1527.1520.0000.0000.0000.000
128A141ALA00.0150.00938.6230.0590.0590.0000.0000.0000.000
129A142LEU0-0.038-0.01334.226-0.018-0.0180.0000.0000.0000.000
130A143LEU00.0140.01337.684-0.020-0.0200.0000.0000.0000.000
131A144GLU-1-0.796-0.87940.590-7.052-7.0520.0000.0000.0000.000
132A145GLU-1-0.845-0.90838.407-7.814-7.8140.0000.0000.0000.000
133A146HIS10.8560.92735.1538.8248.8240.0000.0000.0000.000
134A147ASN00.0370.02940.4010.1460.1460.0000.0000.0000.000
135A148ASN0-0.005-0.01343.1260.2970.2970.0000.0000.0000.000
136A149ASN0-0.096-0.06138.929-0.045-0.0450.0000.0000.0000.000
137A150LEU00.0330.02141.6830.0610.0610.0000.0000.0000.000
138A151LYS10.8020.90844.3286.6936.6930.0000.0000.0000.000
139A152ASN0-0.005-0.01844.7170.3050.3050.0000.0000.0000.000
140A153LEU0-0.0210.00343.8870.0780.0780.0000.0000.0000.000
141A154THR00.0560.02246.0440.1320.1320.0000.0000.0000.000
142A155TYR0-0.024-0.01349.4450.1700.1700.0000.0000.0000.000
143A156LYS10.8780.94343.0417.4657.4650.0000.0000.0000.000
144A157CYS0-0.045-0.01148.4850.0440.0440.0000.0000.0000.000
145A158LEU00.009-0.00151.1040.1110.1110.0000.0000.0000.000
146A159LEU0-0.055-0.01551.6160.1160.1160.0000.0000.0000.000
147A160TYR00.009-0.02651.3630.1340.1340.0000.0000.0000.000
148A161TYR0-0.014-0.01153.5720.0540.0540.0000.0000.0000.000
149A162SER0-0.062-0.03756.3390.1250.1250.0000.0000.0000.000
150A163ASP-1-0.846-0.90855.129-5.747-5.7470.0000.0000.0000.000
151A164GLN00.0070.02556.616-0.009-0.0090.0000.0000.0000.000
152A165ALA00.0250.00554.322-0.105-0.1050.0000.0000.0000.000
153A166ALA0-0.023-0.02853.661-0.130-0.1300.0000.0000.0000.000
154A167ASN00.0620.04655.6860.1360.1360.0000.0000.0000.000
155A168PRO00.0480.01256.987-0.075-0.0750.0000.0000.0000.000
156A169SER0-0.013-0.00158.089-0.028-0.0280.0000.0000.0000.000
157A170PHE00.0640.02155.931-0.048-0.0480.0000.0000.0000.000
158A171LYS10.8930.96349.0626.3876.3870.0000.0000.0000.000
159A172THR0-0.009-0.00654.089-0.092-0.0920.0000.0000.0000.000
160A173LEU00.0140.01156.147-0.041-0.0410.0000.0000.0000.000
161A174SER0-0.058-0.04851.270-0.090-0.0900.0000.0000.0000.000
162A175LEU0-0.032-0.02051.258-0.124-0.1240.0000.0000.0000.000
163A176VAL00.0430.02652.538-0.062-0.0620.0000.0000.0000.000
164A177VAL00.0120.00252.516-0.022-0.0220.0000.0000.0000.000
165A178PHE00.0250.00245.276-0.057-0.0570.0000.0000.0000.000
166A179ASP-1-0.769-0.87049.891-6.525-6.5250.0000.0000.0000.000
167A180PHE0-0.036-0.02351.4190.0280.0280.0000.0000.0000.000
168A181ILE0-0.027-0.00948.2350.0100.0100.0000.0000.0000.000
169A182SER0-0.070-0.04047.329-0.106-0.1060.0000.0000.0000.000
170A183ALA00.0220.01448.797-0.026-0.0260.0000.0000.0000.000
171A184LEU0-0.036-0.00551.7350.0360.0360.0000.0000.0000.000
172A185VAL0-0.001-0.01745.207-0.010-0.0100.0000.0000.0000.000
173A186ASP-1-0.822-0.92346.380-6.985-6.9850.0000.0000.0000.000
174A187GLU-1-0.932-0.95848.355-5.992-5.9920.0000.0000.0000.000
175A188LEU0-0.045-0.03249.3430.0150.0150.0000.0000.0000.000
176A189LEU0-0.076-0.02143.037-0.133-0.1330.0000.0000.0000.000
177A190TYR0-0.086-0.04042.493-0.227-0.2270.0000.0000.0000.000
178A191HIS0-0.0230.00347.4890.0980.0980.0000.0000.0000.000
179A192GLU-1-0.965-0.97450.523-6.431-6.4310.0000.0000.0000.000
180A193HIS0-0.006-0.01752.0700.2050.2050.0000.0000.0000.000
181A194THR0-0.0090.00152.665-0.074-0.0740.0000.0000.0000.000
182A195GLN00.0320.00349.475-0.038-0.0380.0000.0000.0000.000
183A196GLU-1-0.871-0.93153.611-5.531-5.5310.0000.0000.0000.000
184A197GLU-1-0.913-0.95456.499-5.392-5.3920.0000.0000.0000.000
185A198ALA00.0640.02851.7150.0000.0000.0000.0000.0000.000
186A199HIS0-0.064-0.02253.862-0.114-0.1140.0000.0000.0000.000
187A200GLN00.015-0.00755.0750.0550.0550.0000.0000.0000.000
188A201ILE00.0500.04654.6290.0670.0670.0000.0000.0000.000
189A202LYS10.9150.96249.6886.4506.4500.0000.0000.0000.000
190A203LYS10.8350.91954.3115.3175.3170.0000.0000.0000.000
191A204THR00.019-0.01457.1450.0810.0810.0000.0000.0000.000
192A205GLY00.0390.03156.1220.0700.0700.0000.0000.0000.000
193A206ILE0-0.015-0.01652.1310.0160.0160.0000.0000.0000.000
194A207ASP-1-0.864-0.93856.166-5.330-5.3300.0000.0000.0000.000
195A208SER0-0.031-0.02359.2950.0910.0910.0000.0000.0000.000
196A209LEU00.0060.00053.5450.0380.0380.0000.0000.0000.000
197A210ASP-1-0.792-0.89557.620-5.483-5.4830.0000.0000.0000.000
198A211LEU0-0.0090.00458.7480.0490.0490.0000.0000.0000.000
199A212ILE00.0140.00559.1820.0500.0500.0000.0000.0000.000
200A213ILE00.0000.00654.7940.0270.0270.0000.0000.0000.000
201A214LYS10.8040.86459.1095.4465.4460.0000.0000.0000.000
202A215SER0-0.101-0.04061.9710.0840.0840.0000.0000.0000.000
203A216TYR0-0.022-0.01261.0400.0720.0720.0000.0000.0000.000
204A217LEU0-0.065-0.01457.4830.0300.0300.0000.0000.0000.000