FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 977N2

Calculation Name: 3VX8-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VX8

Chain ID: B

ChEMBL ID:

UniProt ID: Q0WWQ1

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2028200.809371
FMO2-HF: Nuclear repulsion 1954817.73607
FMO2-HF: Total energy -73383.073301
FMO2-MP2: Total energy -73593.90613


3D Structure Molmil
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:23:PRO)


Summations of interaction energy for fragment #1(A:23:PRO)
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.
-45.549-42.31715.827-9.094-9.965-0.095
Interaction energy analysis for fragmet #1(A:23:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.889
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].
3A25MET00.0410.0343.5164.0325.9090.003-0.792-1.088-0.002
4A26ALA0-0.017-0.0092.3884.1015.2530.948-0.611-1.490-0.004
5A27PHE00.0190.0074.0486.4756.9870.000-0.153-0.3600.000
10A32VAL0-0.058-0.0224.4291.5481.648-0.001-0.008-0.0900.000
11A33LEU00.0010.0094.464-8.350-8.343-0.001-0.0140.0090.000
12A34SER0-0.060-0.0372.52710.17310.9690.296-0.303-0.788-0.001
13A35VAL00.0450.0074.6033.2513.284-0.001-0.013-0.0190.000
15A37GLU-1-0.753-0.8621.919-128.829-130.30414.583-7.151-5.957-0.088
155A280VAL0-0.041-0.0273.6302.0302.2600.000-0.049-0.1820.000
6A28LYS10.9160.9485.43934.03634.0360.0000.0000.0000.000
7A29GLU-1-0.896-0.9427.348-27.126-27.1260.0000.0000.0000.000
8A30LYS10.8810.9245.79940.43040.4300.0000.0000.0000.000
9A31GLY00.0390.0488.4532.1552.1550.0000.0000.0000.000
14A36SER0-0.0040.0045.1472.0162.0160.0000.0000.0000.000
16A38PHE00.0140.0066.1533.5593.5590.0000.0000.0000.000
17A39VAL00.0020.0059.2522.6102.6100.0000.0000.0000.000
18A40LEU00.0240.0118.5271.7331.7330.0000.0000.0000.000
19A41ALA00.0190.0009.5262.2722.2720.0000.0000.0000.000
20A42GLY00.0010.00311.3581.9421.9420.0000.0000.0000.000
21A43ASP-1-0.810-0.87313.819-18.270-18.2700.0000.0000.0000.000
22A44ASN0-0.028-0.02913.5172.9332.9330.0000.0000.0000.000
23A45LEU0-0.009-0.00415.4111.0111.0110.0000.0000.0000.000
24A46VAL00.0090.00217.2220.9630.9630.0000.0000.0000.000
25A47SER0-0.059-0.01718.3790.6830.6830.0000.0000.0000.000
26A48LYS10.8430.92118.20617.45417.4540.0000.0000.0000.000
27A49CYS0-0.0300.01021.0650.5100.5100.0000.0000.0000.000
28A50PRO00.0420.00922.730-0.168-0.1680.0000.0000.0000.000
29A51THR00.003-0.00324.5500.2200.2200.0000.0000.0000.000
30A52TRP0-0.059-0.02220.656-0.134-0.1340.0000.0000.0000.000
31A53SER0-0.020-0.01422.1730.2610.2610.0000.0000.0000.000
32A54TRP0-0.050-0.03513.680-0.570-0.5700.0000.0000.0000.000
33A55GLU-1-0.831-0.89620.635-11.490-11.4900.0000.0000.0000.000
34A56SER00.004-0.03021.015-0.625-0.6250.0000.0000.0000.000
35A57GLY0-0.053-0.01722.826-0.306-0.3060.0000.0000.0000.000
36A58ASP-1-0.845-0.93424.800-10.762-10.7620.0000.0000.0000.000
37A59ALA0-0.013-0.01725.213-0.439-0.4390.0000.0000.0000.000
38A60SER0-0.023-0.01725.658-0.328-0.3280.0000.0000.0000.000
39A61LYS10.8470.92223.39511.83111.8310.0000.0000.0000.000
40A62ARG10.8970.96919.43113.88313.8830.0000.0000.0000.000
41A63LYS10.9380.97215.97316.78716.7870.0000.0000.0000.000
42A64PRO0-0.003-0.00617.123-0.412-0.4120.0000.0000.0000.000
43A65TYR0-0.023-0.02111.9520.2230.2230.0000.0000.0000.000
44A66LEU00.0020.00211.932-2.344-2.3440.0000.0000.0000.000
45A67PRO00.0420.03114.0471.1351.1350.0000.0000.0000.000
46A68SER0-0.0090.00017.2820.1150.1150.0000.0000.0000.000
47A69ASP-1-0.871-0.93019.703-15.471-15.4710.0000.0000.0000.000
48A70LYS10.8270.90415.92618.53118.5310.0000.0000.0000.000
49A71GLN0-0.030-0.00816.385-1.026-1.0260.0000.0000.0000.000
50A72PHE0-0.038-0.04417.070-0.843-0.8430.0000.0000.0000.000
51A73LEU00.0270.02715.2180.3190.3190.0000.0000.0000.000
52A74ILE0-0.035-0.02819.3330.1580.1580.0000.0000.0000.000
53A75THR00.0120.00122.7830.0680.0680.0000.0000.0000.000
54A76ARG10.8850.90825.08911.47511.4750.0000.0000.0000.000
55A77ASN0-0.015-0.01828.8500.1820.1820.0000.0000.0000.000
56A78VAL00.0250.03826.9550.1790.1790.0000.0000.0000.000
57A79PRO00.0260.00830.4050.1530.1530.0000.0000.0000.000
58A80CYS0-0.0460.00531.779-0.288-0.2880.0000.0000.0000.000
59A81LEU00.0080.00333.7730.3290.3290.0000.0000.0000.000
60A82ARG10.9090.97035.2679.0179.0170.0000.0000.0000.000
61A83ARG10.8690.88935.4628.4768.4760.0000.0000.0000.000
62A84ALA00.0080.00231.9170.0330.0330.0000.0000.0000.000
63A85ALA0-0.058-0.02433.772-0.066-0.0660.0000.0000.0000.000
64A86SER-1-0.959-0.96636.120-7.985-7.9850.0000.0000.0000.000
65A190LEU00.009-0.00540.990-0.068-0.0680.0000.0000.0000.000
66A191ARG10.8870.94340.9647.5137.5130.0000.0000.0000.000
67A192THR00.0050.01138.635-0.131-0.1310.0000.0000.0000.000
68A193ARG10.8300.90834.7778.9888.9880.0000.0000.0000.000
69A194THR0-0.009-0.00333.678-0.135-0.1350.0000.0000.0000.000
70A195TYR0-0.021-0.05228.849-0.059-0.0590.0000.0000.0000.000
71A196ASP-1-0.825-0.86828.259-10.406-10.4060.0000.0000.0000.000
72A197LEU0-0.047-0.02223.438-0.018-0.0180.0000.0000.0000.000
73A198SER0-0.0040.00321.762-0.254-0.2540.0000.0000.0000.000
74A199ILE00.0070.00115.355-0.255-0.2550.0000.0000.0000.000
75A200THR00.0350.03116.9750.0580.0580.0000.0000.0000.000
76A201TYR0-0.048-0.0586.9580.5240.5240.0000.0000.0000.000
77A202ASP-1-0.804-0.90913.277-18.070-18.0700.0000.0000.0000.000
78A203LYS10.9170.9438.97724.05924.0590.0000.0000.0000.000
79A204TYR0-0.0360.00011.256-1.196-1.1960.0000.0000.0000.000
80A205TYR00.0620.02412.122-0.730-0.7300.0000.0000.0000.000
81A206GLN0-0.086-0.0255.205-1.022-1.0220.0000.0000.0000.000
82A207THR00.0400.0158.330-3.577-3.5770.0000.0000.0000.000
83A208PRO0-0.0100.00510.6430.9260.9260.0000.0000.0000.000
84A209ARG10.8870.94713.20316.08916.0890.0000.0000.0000.000
85A210VAL00.0430.02816.8310.0260.0260.0000.0000.0000.000
86A211TRP0-0.032-0.01919.4820.7050.7050.0000.0000.0000.000
87A212LEU00.0250.00323.284-0.107-0.1070.0000.0000.0000.000
88A213THR0-0.016-0.00726.5500.1640.1640.0000.0000.0000.000
89A214GLY00.0730.03729.912-0.073-0.0730.0000.0000.0000.000
90A215TYR0-0.104-0.07531.8370.2160.2160.0000.0000.0000.000
91A216ASP-1-0.833-0.92936.085-7.845-7.8450.0000.0000.0000.000
92A217GLU-1-0.835-0.91139.218-7.568-7.5680.0000.0000.0000.000
93A218SER0-0.078-0.04141.3570.0230.0230.0000.0000.0000.000
94A219ARG10.8180.90232.3969.4099.4090.0000.0000.0000.000
95A220MET00.0280.03339.063-0.107-0.1070.0000.0000.0000.000
96A221LEU0-0.029-0.01733.961-0.171-0.1710.0000.0000.0000.000
97A222LEU0-0.0140.00734.8630.1790.1790.0000.0000.0000.000
98A223GLN00.0100.00335.627-0.318-0.3180.0000.0000.0000.000
99A224PRO00.018-0.00731.713-0.090-0.0900.0000.0000.0000.000
100A225GLU-1-0.903-0.95632.769-8.951-8.9510.0000.0000.0000.000
101A226LEU00.0230.01134.845-0.016-0.0160.0000.0000.0000.000
102A227VAL0-0.013-0.00629.437-0.047-0.0470.0000.0000.0000.000
103A228MET0-0.031-0.01929.904-0.361-0.3610.0000.0000.0000.000
104A229GLU-1-0.855-0.91332.399-8.395-8.3950.0000.0000.0000.000
105A230ASP-1-0.730-0.82831.367-9.256-9.2560.0000.0000.0000.000
106A231VAL0-0.029-0.01627.511-0.442-0.4420.0000.0000.0000.000
107A232SER0-0.012-0.02328.4590.4790.4790.0000.0000.0000.000
108A233GLN0-0.054-0.03829.774-0.175-0.1750.0000.0000.0000.000
109A234ASP-1-0.863-0.91731.999-9.162-9.1620.0000.0000.0000.000
110A235HIS0-0.048-0.02027.254-0.356-0.3560.0000.0000.0000.000
111A236ALA00.0150.02725.538-0.648-0.6480.0000.0000.0000.000
112A237ARG10.8630.94819.92114.63514.6350.0000.0000.0000.000
113A238LYS0-0.049-0.05818.166-0.942-0.9420.0000.0000.0000.000
114A239THR00.0230.02723.2850.3190.3190.0000.0000.0000.000
115A240VAL00.001-0.00724.027-0.611-0.6110.0000.0000.0000.000
116A241THR0-0.054-0.04724.6760.6080.6080.0000.0000.0000.000
117A242ILE00.0300.01526.862-0.287-0.2870.0000.0000.0000.000
118A243GLU-1-0.834-0.90024.739-11.645-11.6450.0000.0000.0000.000
119A244ASP-1-0.878-0.93926.651-10.384-10.3840.0000.0000.0000.000
120A245HIS00.0330.02422.238-0.399-0.3990.0000.0000.0000.000
121A246PRO0-0.059-0.03819.6820.2090.2090.0000.0000.0000.000
122A247HIS0-0.025-0.02417.606-0.069-0.0690.0000.0000.0000.000
123A248LEU00.0460.04123.1610.3360.3360.0000.0000.0000.000
124A249PRO00.0580.03126.703-0.052-0.0520.0000.0000.0000.000
125A250GLY00.0320.02929.773-0.115-0.1150.0000.0000.0000.000
126A251LYS10.8470.92329.36710.08310.0830.0000.0000.0000.000
127A252HIS10.8190.89426.73811.35511.3550.0000.0000.0000.000
128A253ALA00.0780.05927.788-0.131-0.1310.0000.0000.0000.000
129A254SER0-0.050-0.04521.974-0.527-0.5270.0000.0000.0000.000
130A255VAL00.0350.02320.9360.2810.2810.0000.0000.0000.000
131A256HIS0-0.087-0.10819.998-0.775-0.7750.0000.0000.0000.000
132A257PRO00.000-0.02715.252-0.106-0.1060.0000.0000.0000.000
133A258CYS-1-0.808-0.82115.530-17.149-17.1490.0000.0000.0000.000
134A259ARG0-0.032-0.01915.964-1.132-1.1320.0000.0000.0000.000
135A260HIS00.0510.03213.977-0.521-0.5210.0000.0000.0000.000
136A261GLY00.0350.02711.268-0.776-0.7760.0000.0000.0000.000
137A262ALA0-0.002-0.00612.051-0.461-0.4610.0000.0000.0000.000
138A263VAL0-0.075-0.03714.8970.8050.8050.0000.0000.0000.000
139A264MET0-0.026-0.00810.8320.0150.0150.0000.0000.0000.000
140A265LYS10.9790.99111.64721.98421.9840.0000.0000.0000.000
141A266LYS10.9460.98412.64016.97016.9700.0000.0000.0000.000
142A267ILE0-0.009-0.00414.7071.0441.0440.0000.0000.0000.000
143A268ILE00.000-0.0039.9430.3900.3900.0000.0000.0000.000
144A269ASP-1-0.886-0.93813.398-20.052-20.0520.0000.0000.0000.000
145A270VAL0-0.030-0.01216.0830.9700.9700.0000.0000.0000.000
146A271LEU0-0.070-0.03014.8850.9030.9030.0000.0000.0000.000
147A272MET00.0420.01212.599-0.228-0.2280.0000.0000.0000.000
148A273SER0-0.041-0.01816.5420.9340.9340.0000.0000.0000.000
149A274ARG10.8760.94519.97715.38015.3800.0000.0000.0000.000
150A275GLY00.0330.02119.6130.4980.4980.0000.0000.0000.000
151A276VAL0-0.055-0.02216.519-0.111-0.1110.0000.0000.0000.000
152A277GLU-1-0.873-0.95012.918-22.723-22.7230.0000.0000.0000.000
153A278PRO0-0.039-0.00311.293-0.262-0.2620.0000.0000.0000.000
154A279GLU-1-0.865-0.9458.639-28.982-28.9820.0000.0000.0000.000
156A281ASP-1-0.806-0.8936.980-24.736-24.7360.0000.0000.0000.000
157A282LYS10.8920.93110.05926.17726.1770.0000.0000.0000.000
158A283TYR0-0.034-0.0317.2022.8312.8310.0000.0000.0000.000
159A284LEU00.013-0.01110.5291.5031.5030.0000.0000.0000.000
160A285PHE00.0460.04213.4821.0981.0980.0000.0000.0000.000
161A286LEU0-0.006-0.00211.7431.1781.1780.0000.0000.0000.000
162A287PHE0-0.008-0.02313.3150.8350.8350.0000.0000.0000.000
163A288LEU00.0040.01315.2780.9760.9760.0000.0000.0000.000
164A289LYS10.9961.01517.66217.76417.7640.0000.0000.0000.000
165A290PHE0-0.040-0.01317.4470.5560.5560.0000.0000.0000.000
166A291MET00.0110.00718.5710.6110.6110.0000.0000.0000.000
167A292ALA00.0360.03121.0610.6220.6220.0000.0000.0000.000
168A293SER0-0.070-0.04522.7230.5570.5570.0000.0000.0000.000
169A294VAL0-0.020-0.01722.0020.3930.3930.0000.0000.0000.000
170A295ILE0-0.008-0.01023.7410.3940.3940.0000.0000.0000.000
171A296PRO00.0240.02226.959-0.032-0.0320.0000.0000.0000.000
172A297THR0-0.036-0.01328.7710.0390.0390.0000.0000.0000.000
173A298ILE0-0.029-0.01127.5090.2280.2280.0000.0000.0000.000
174A299GLU-1-0.932-0.96727.559-10.056-10.0560.0000.0000.0000.000
175A300TYR0-0.039-0.04521.6990.0830.0830.0000.0000.0000.000
176A301ASP-1-0.833-0.89624.228-12.088-12.0880.0000.0000.0000.000
177A302TYR0-0.008-0.03519.922-0.991-0.9910.0000.0000.0000.000
178A303THR0-0.003-0.00820.2840.4200.4200.0000.0000.0000.000
179A304MET-1-0.949-0.96516.446-15.999-15.9990.0000.0000.0000.000