Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 53KVZ

Calculation Name: 5BVL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BVL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2196861.947109
FMO2-HF: Nuclear repulsion 2121870.929762
FMO2-HF: Total energy -74991.017347
FMO2-MP2: Total energy -75213.888644


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
158.321167.1441.024-4.566-5.28-0.002
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.878 / q_NPA : -0.935
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].
3A3ASP-1-0.939-0.9802.53427.75134.8530.953-4.056-3.998-0.003
4A4GLU-1-0.948-0.9752.82323.12024.1990.068-0.398-0.7490.001
5A5ALA00.0170.0074.434-4.321-4.142-0.001-0.028-0.1510.000
6A6TRP0-0.035-0.0226.661-3.634-3.6340.0000.0000.0000.000
7A7LYS10.8180.9037.594-22.340-22.3400.0000.0000.0000.000
8A8CYS00.0010.0028.535-2.807-2.8070.0000.0000.0000.000
9A9VAL00.0760.03411.147-1.881-1.8810.0000.0000.0000.000
10A10GLU-1-0.846-0.88212.48416.69616.6960.0000.0000.0000.000
11A11GLN0-0.028-0.01813.580-2.145-2.1450.0000.0000.0000.000
12A12LEU00.022-0.00314.999-1.074-1.0740.0000.0000.0000.000
13A13ARG10.8490.94416.942-15.819-15.8190.0000.0000.0000.000
14A14ARG10.7610.87217.902-15.010-15.0100.0000.0000.0000.000
15A15GLU-1-0.842-0.90019.24012.33912.3390.0000.0000.0000.000
16A16GLY0-0.0080.01121.507-0.467-0.4670.0000.0000.0000.000
17A17ALA0-0.030-0.02120.1790.0530.0530.0000.0000.0000.000
18A18THR0-0.025-0.00321.645-0.349-0.3490.0000.0000.0000.000
19A19GLN0-0.039-0.01822.201-0.458-0.4580.0000.0000.0000.000
20A20ILE0-0.026-0.00515.8250.3140.3140.0000.0000.0000.000
21A21ALA00.0030.00016.337-0.273-0.2730.0000.0000.0000.000
22A22TYR0-0.089-0.0616.7070.8870.8870.0000.0000.0000.000
23A23ARG10.9000.94710.896-24.444-24.4440.0000.0000.0000.000
24A24SER0-0.035-0.0537.9253.5893.5890.0000.0000.0000.000
25A25ASP-1-0.860-0.9248.06927.76527.7650.0000.0000.0000.000
26A26ASP-1-0.774-0.8708.69725.19625.1960.0000.0000.0000.000
27A27TRP00.0490.01210.354-0.849-0.8490.0000.0000.0000.000
28A28ARG10.8870.93612.424-20.077-20.0770.0000.0000.0000.000
29A29ASP-1-0.770-0.8367.44337.42537.4250.0000.0000.0000.000
30A30LEU00.0510.03610.522-1.045-1.0450.0000.0000.0000.000
31A31LYS10.8490.91512.857-16.951-16.9510.0000.0000.0000.000
32A32GLU-1-0.865-0.94112.47317.72217.7220.0000.0000.0000.000
33A33ALA00.0560.03411.737-0.831-0.8310.0000.0000.0000.000
34A34TRP00.0310.05313.788-1.017-1.0170.0000.0000.0000.000
35A35LYS10.8740.92517.197-17.477-17.4770.0000.0000.0000.000
36A36LYS10.6890.80413.885-20.634-20.6340.0000.0000.0000.000
37A37GLY0-0.108-0.05817.403-0.449-0.4490.0000.0000.0000.000
38A38ALA00.0570.04914.595-0.030-0.0300.0000.0000.0000.000
39A39ASP-1-0.803-0.90616.75414.53714.5370.0000.0000.0000.000
40A40ILE0-0.043-0.01818.448-0.422-0.4220.0000.0000.0000.000
41A41LEU0-0.0100.00015.1611.2711.2710.0000.0000.0000.000
42A42ILE0-0.037-0.01814.175-1.142-1.1420.0000.0000.0000.000
43A43VAL00.0350.01813.4381.8351.8350.0000.0000.0000.000
44A44ASP-1-0.803-0.88611.73323.80523.8050.0000.0000.0000.000
45A45ALA0-0.030-0.00613.689-0.249-0.2490.0000.0000.0000.000
46A46THR00.011-0.00712.4760.7290.7290.0000.0000.0000.000
47A47ASP-1-0.876-0.92115.34916.32716.3270.0000.0000.0000.000
48A48LYS10.8100.88418.308-13.764-13.7640.0000.0000.0000.000
49A49ASP-1-0.862-0.90720.54313.70213.7020.0000.0000.0000.000
50A50GLU-1-0.890-0.95115.63117.87517.8750.0000.0000.0000.000
51A51ALA00.0290.01316.9210.1070.1070.0000.0000.0000.000
52A52TRP0-0.024-0.03417.837-0.435-0.4350.0000.0000.0000.000
53A53LYS10.8980.94019.867-14.989-14.9890.0000.0000.0000.000
54A54GLN0-0.034-0.02913.129-0.152-0.1520.0000.0000.0000.000
55A55VAL0-0.0120.00618.204-0.209-0.2090.0000.0000.0000.000
56A56GLU-1-0.864-0.92220.50311.99911.9990.0000.0000.0000.000
57A57GLN0-0.030-0.00819.390-0.973-0.9730.0000.0000.0000.000
58A58LEU0-0.004-0.01516.305-0.338-0.3380.0000.0000.0000.000
59A59ARG10.9960.99320.615-11.735-11.7350.0000.0000.0000.000
60A60ARG10.7490.86423.292-13.469-13.4690.0000.0000.0000.000
61A61GLU-1-0.872-0.93020.46414.49514.4950.0000.0000.0000.000
62A62GLY0-0.0190.00623.471-0.119-0.1190.0000.0000.0000.000
63A63ALA0-0.037-0.02120.340-0.122-0.1220.0000.0000.0000.000
64A64THR0-0.018-0.02122.272-0.064-0.0640.0000.0000.0000.000
65A65GLN00.0000.00721.905-0.281-0.2810.0000.0000.0000.000
66A66ILE0-0.0150.00619.3010.9920.9920.0000.0000.0000.000
67A67ALA00.006-0.00218.376-0.720-0.7200.0000.0000.0000.000
68A68TYR0-0.005-0.00917.9970.8020.8020.0000.0000.0000.000
69A69ARG10.7710.85513.702-22.235-22.2350.0000.0000.0000.000
70A70SER0-0.011-0.01918.7700.6790.6790.0000.0000.0000.000
71A71ASP-1-0.859-0.91720.76814.35714.3570.0000.0000.0000.000
72A72ASP-1-0.787-0.85122.88311.05211.0520.0000.0000.0000.000
73A73TRP00.041-0.00725.4570.1170.1170.0000.0000.0000.000
74A74ARG10.7810.86227.818-11.198-11.1980.0000.0000.0000.000
75A75ASP-1-0.779-0.88123.16213.47813.4780.0000.0000.0000.000
76A76LEU0-0.0160.00222.4180.1440.1440.0000.0000.0000.000
77A77LYS10.8750.92125.183-9.681-9.6810.0000.0000.0000.000
78A78GLU-1-0.839-0.91526.22910.90710.9070.0000.0000.0000.000
79A79ALA00.0150.01222.5710.0090.0090.0000.0000.0000.000
80A80TRP0-0.029-0.00424.453-0.076-0.0760.0000.0000.0000.000
81A81LYS10.7930.88327.061-10.522-10.5220.0000.0000.0000.000
82A82LYS10.8180.92324.914-12.244-12.2440.0000.0000.0000.000
83A83GLY0-0.057-0.04425.4910.2420.2420.0000.0000.0000.000
84A84ALA0-0.0120.02022.5580.1740.1740.0000.0000.0000.000
85A85ASP-1-0.850-0.93123.85212.08112.0810.0000.0000.0000.000
86A86ILE0-0.037-0.02622.241-0.333-0.3330.0000.0000.0000.000
87A87LEU0-0.049-0.02622.3780.6910.6910.0000.0000.0000.000
88A88ILE0-0.007-0.01418.319-0.324-0.3240.0000.0000.0000.000
89A89VAL00.0300.01921.6990.4210.4210.0000.0000.0000.000
90A90ASP-1-0.821-0.90417.76718.11518.1150.0000.0000.0000.000
91A91ALA0-0.017-0.00421.381-0.314-0.3140.0000.0000.0000.000
92A92THR0-0.003-0.00320.0190.3220.3220.0000.0000.0000.000
93A93ASP-1-0.859-0.93523.23910.66710.6670.0000.0000.0000.000
94A94LYS10.8050.88226.752-10.947-10.9470.0000.0000.0000.000
95A95ASP-1-0.871-0.95528.9849.3119.3110.0000.0000.0000.000
96A96GLU-1-0.860-0.91328.8179.9309.9300.0000.0000.0000.000
97A97ALA00.0380.03126.5300.1140.1140.0000.0000.0000.000
98A98TRP0-0.033-0.02928.127-0.129-0.1290.0000.0000.0000.000
99A99LYS10.9100.95131.194-9.740-9.7400.0000.0000.0000.000
100A100GLN0-0.021-0.00226.643-0.154-0.1540.0000.0000.0000.000
101A101VAL00.0110.01028.600-0.023-0.0230.0000.0000.0000.000
102A102GLU-1-0.856-0.91630.5778.8108.8100.0000.0000.0000.000
103A103GLN0-0.029-0.01432.114-0.363-0.3630.0000.0000.0000.000
104A104LEU00.019-0.00327.181-0.217-0.2170.0000.0000.0000.000
105A105ARG11.0031.01331.898-9.066-9.0660.0000.0000.0000.000
106A106ARG10.7460.87334.438-9.231-9.2310.0000.0000.0000.000
107A107GLU-1-0.855-0.90133.2179.0019.0010.0000.0000.0000.000
108A108GLY0-0.014-0.00735.260-0.022-0.0220.0000.0000.0000.000
109A109ALA0-0.040-0.02329.8380.0550.0550.0000.0000.0000.000
110A110THR0-0.015-0.01330.296-0.062-0.0620.0000.0000.0000.000
111A111GLN00.0250.01327.0990.0110.0110.0000.0000.0000.000
112A112ILE0-0.0100.02126.5150.5400.5400.0000.0000.0000.000
113A113ALA00.0150.00423.124-0.159-0.1590.0000.0000.0000.000
114A114TYR00.034-0.00824.491-0.088-0.0880.0000.0000.0000.000
115A115ARG10.7640.85915.158-19.026-19.0260.0000.0000.0000.000
116A116SER00.023-0.00621.904-0.380-0.3800.0000.0000.0000.000
117A117ASP-1-0.856-0.91721.12113.63813.6380.0000.0000.0000.000
118A118ASP-1-0.716-0.81222.58710.34310.3430.0000.0000.0000.000
119A119TRP00.029-0.00226.369-0.244-0.2440.0000.0000.0000.000
120A120ARG10.7960.86128.197-10.435-10.4350.0000.0000.0000.000
121A121ASP-1-0.765-0.85927.77010.79310.7930.0000.0000.0000.000
122A122LEU0-0.0030.00624.158-0.210-0.2100.0000.0000.0000.000
123A123LYS10.8300.89528.456-8.943-8.9430.0000.0000.0000.000
124A124GLU-1-0.849-0.90332.0048.6008.6000.0000.0000.0000.000
125A125ALA00.0320.00529.294-0.209-0.2090.0000.0000.0000.000
126A126TRP0-0.031-0.00431.121-0.168-0.1680.0000.0000.0000.000
127A127LYS10.7510.85832.263-8.928-8.9280.0000.0000.0000.000
128A128LYS10.7910.89833.534-9.304-9.3040.0000.0000.0000.000
129A129GLY0-0.062-0.03633.752-0.091-0.0910.0000.0000.0000.000
130A130ALA0-0.0260.00628.2970.1500.1500.0000.0000.0000.000
131A131ASP-1-0.879-0.95029.3819.8549.8540.0000.0000.0000.000
132A132ILE0-0.075-0.03523.3260.1490.1490.0000.0000.0000.000
133A133LEU0-0.038-0.01725.5880.2150.2150.0000.0000.0000.000
134A134ILE0-0.014-0.02318.7990.2400.2400.0000.0000.0000.000
135A135VAL00.0040.00521.019-0.046-0.0460.0000.0000.0000.000
136A136ASP-1-0.796-0.88816.14220.13420.1340.0000.0000.0000.000
137A137ALA00.0090.01716.694-0.622-0.6220.0000.0000.0000.000
138A138THR0-0.028-0.02313.6091.2331.2330.0000.0000.0000.000
139A139ASP-1-0.934-0.96115.76414.92714.9270.0000.0000.0000.000
140A140LYS10.8280.87912.300-21.491-21.4910.0000.0000.0000.000
141A141ASP-1-0.928-0.95217.60812.26012.2600.0000.0000.0000.000
142A142GLU-1-0.793-0.87620.60911.35811.3580.0000.0000.0000.000
143A143ALA00.0630.02820.075-0.479-0.4790.0000.0000.0000.000
144A144TRP0-0.034-0.02319.777-0.599-0.5990.0000.0000.0000.000
145A145LYS10.8420.91123.867-11.548-11.5480.0000.0000.0000.000
146A146GLN0-0.046-0.02423.408-0.511-0.5110.0000.0000.0000.000
147A147VAL00.0150.01223.235-0.228-0.2280.0000.0000.0000.000
148A148GLU-1-0.834-0.91126.27910.22910.2290.0000.0000.0000.000
149A149GLN0-0.049-0.02329.467-0.649-0.6490.0000.0000.0000.000
150A150LEU00.0230.01126.714-0.365-0.3650.0000.0000.0000.000
151A151ARG10.8740.93928.982-10.711-10.7110.0000.0000.0000.000
152A152ARG10.8550.93431.600-8.821-8.8210.0000.0000.0000.000
153A153GLU-1-0.875-0.92533.5818.4818.4810.0000.0000.0000.000
154A154GLY00.0070.01334.404-0.230-0.2300.0000.0000.0000.000
155A155ALA0-0.029-0.00430.331-0.025-0.0250.0000.0000.0000.000
156A156THR0-0.018-0.02531.4510.1440.1440.0000.0000.0000.000
157A157GLN00.0060.00826.9430.0070.0070.0000.0000.0000.000
158A158ILE00.0040.01824.3890.1880.1880.0000.0000.0000.000
159A159ALA00.003-0.00520.4760.1580.1580.0000.0000.0000.000
160A160TYR00.0520.00517.271-0.070-0.0700.0000.0000.0000.000
161A161ARG10.7820.88210.963-23.491-23.4910.0000.0000.0000.000
162A162SER00.0180.00113.537-0.140-0.1400.0000.0000.0000.000
163A163ASP-1-0.853-0.9048.49524.62524.6250.0000.0000.0000.000
164A164ASP-1-0.820-0.9069.59919.27619.2760.0000.0000.0000.000
165A165TRP00.020-0.00411.708-1.672-1.6720.0000.0000.0000.000
166A166ARG10.8660.92512.787-18.501-18.5010.0000.0000.0000.000
167A167ASP-1-0.773-0.90215.74716.25516.2550.0000.0000.0000.000
168A168LEU0-0.033-0.01313.530-0.861-0.8610.0000.0000.0000.000
169A169LYS10.8580.91617.553-13.679-13.6790.0000.0000.0000.000
170A170GLU-1-0.832-0.90619.86811.26011.2600.0000.0000.0000.000
171A171ALA00.0260.01720.636-0.653-0.6530.0000.0000.0000.000
172A172TRP0-0.016-0.00121.681-0.593-0.5930.0000.0000.0000.000
173A173LYS10.7860.87823.297-12.146-12.1460.0000.0000.0000.000
174A174LYS10.7660.88625.375-11.772-11.7720.0000.0000.0000.000
175A175GLY0-0.003-0.00326.431-0.356-0.3560.0000.0000.0000.000
176A176ALA0-0.034-0.00322.512-0.114-0.1140.0000.0000.0000.000
177A177ASP-1-0.863-0.94924.55911.22411.2240.0000.0000.0000.000
178A178ILE0-0.032-0.01219.8680.2480.2480.0000.0000.0000.000
179A179LEU0-0.017-0.00817.6660.1340.1340.0000.0000.0000.000
180A180ILE0-0.012-0.01713.8620.6110.6110.0000.0000.0000.000
181A181CYS0-0.025-0.01810.912-0.230-0.2300.0000.0000.0000.000
182A182ASP-1-0.801-0.8869.71830.24330.2430.0000.0000.0000.000
183A183ALA00.017-0.0015.548-1.657-1.6570.0000.0000.0000.000
184A184THR00.0130.0273.8529.67410.1370.004-0.084-0.3820.000