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: VZQL1

Calculation Name: 4V6W-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V6W

Chain ID: A

ChEMBL ID:

UniProt ID: P13060

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1824493.598303
FMO2-HF: Nuclear repulsion 1751642.421106
FMO2-HF: Total energy -72851.177197
FMO2-MP2: Total energy -73064.070044


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
166.283168.720.144-1.351-1.23-0.013
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.911
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].
3A3ALA00.016-0.0152.818-13.719-11.3310.145-1.350-1.184-0.013
4A4VAL00.0430.0385.3113.1383.187-0.001-0.001-0.0460.000
5A5THR0-0.017-0.0127.4213.2383.2380.0000.0000.0000.000
6A6LYS10.9791.0039.32920.41520.4150.0000.0000.0000.000
7A7LYS10.9570.96712.68520.54820.5480.0000.0000.0000.000
8A8ILE00.0460.01314.3230.9370.9370.0000.0000.0000.000
9A9LYS10.9600.98417.34713.01113.0110.0000.0000.0000.000
10A10ARG10.9300.95318.40815.81215.8120.0000.0000.0000.000
11A11ASP-1-0.792-0.89422.183-11.474-11.4740.0000.0000.0000.000
12A12PRO0-0.0120.01021.638-0.742-0.7420.0000.0000.0000.000
13A13ALA0-0.137-0.07519.128-0.414-0.4140.0000.0000.0000.000
14A14LYS11.0151.00820.80011.05811.0580.0000.0000.0000.000
15A15ASN00.0140.01521.068-1.117-1.1170.0000.0000.0000.000
16A16PRO0-0.055-0.02622.6790.4740.4740.0000.0000.0000.000
17A17MET00.1050.06625.6240.3250.3250.0000.0000.0000.000
18A18ARG10.8730.92419.16515.07115.0710.0000.0000.0000.000
19A19ASP-1-0.858-0.95123.829-11.921-11.9210.0000.0000.0000.000
20A20LEU0-0.0300.01824.038-0.028-0.0280.0000.0000.0000.000
21A21HIS00.024-0.00526.5300.4710.4710.0000.0000.0000.000
22A22ILE00.0530.03628.539-0.422-0.4220.0000.0000.0000.000
23A23ARG10.7580.89026.59610.62810.6280.0000.0000.0000.000
24A24LYS10.9070.94428.90010.41010.4100.0000.0000.0000.000
25A25LEU00.0630.06931.959-0.338-0.3380.0000.0000.0000.000
26A26CYS0-0.099-0.05933.8400.2350.2350.0000.0000.0000.000
27A27LEU00.0640.05035.463-0.105-0.1050.0000.0000.0000.000
28A28ASN0-0.066-0.06737.5080.0850.0850.0000.0000.0000.000
29A29ILE00.0570.05039.3670.0180.0180.0000.0000.0000.000
30A30CYS0-0.051-0.03039.1820.0730.0730.0000.0000.0000.000
31A31VAL00.0380.02041.6670.0750.0750.0000.0000.0000.000
32A32GLY0-0.018-0.01244.612-0.033-0.0330.0000.0000.0000.000
33A33GLU-1-0.857-0.91445.517-5.907-5.9070.0000.0000.0000.000
34A34SER0-0.012-0.01847.861-0.013-0.0130.0000.0000.0000.000
35A35GLY00.0340.01149.1910.0280.0280.0000.0000.0000.000
36A36ASP-1-0.823-0.92852.219-5.575-5.5750.0000.0000.0000.000
37A37ARG10.8610.95149.9746.1196.1190.0000.0000.0000.000
38A38LEU0-0.0080.01545.329-0.083-0.0830.0000.0000.0000.000
39A39THR0-0.013-0.01848.744-0.084-0.0840.0000.0000.0000.000
40A40ARG10.8650.93351.2745.6825.6820.0000.0000.0000.000
41A41ALA00.0330.02246.409-0.028-0.0280.0000.0000.0000.000
42A42ALA0-0.028-0.02246.886-0.099-0.0990.0000.0000.0000.000
43A43LYS11.0251.01247.9565.5705.5700.0000.0000.0000.000
44A44VAL00.0090.02146.3440.0310.0310.0000.0000.0000.000
45A45LEU0-0.042-0.01942.226-0.101-0.1010.0000.0000.0000.000
46A46GLU-1-0.913-0.96545.472-6.209-6.2090.0000.0000.0000.000
47A47GLN0-0.040-0.03147.7760.0290.0290.0000.0000.0000.000
48A48LEU0-0.0040.02143.4220.0030.0030.0000.0000.0000.000
49A49THR0-0.004-0.01642.283-0.082-0.0820.0000.0000.0000.000
50A50GLY00.0250.01945.168-0.022-0.0220.0000.0000.0000.000
51A51GLN0-0.066-0.03340.5060.0660.0660.0000.0000.0000.000
52A52GLN00.0850.03845.263-0.106-0.1060.0000.0000.0000.000
53A53PRO0-0.0170.00743.048-0.168-0.1680.0000.0000.0000.000
54A54VAL0-0.0080.00239.8380.1320.1320.0000.0000.0000.000
55A55PHE00.0710.03241.816-0.096-0.0960.0000.0000.0000.000
56A56SER0-0.054-0.04438.470-0.239-0.2390.0000.0000.0000.000
57A57LYS10.9550.98440.5526.8016.8010.0000.0000.0000.000
58A58ALA00.0220.02839.424-0.226-0.2260.0000.0000.0000.000
59A59ARG10.9640.97634.0748.4938.4930.0000.0000.0000.000
60A60TYR00.026-0.00834.048-0.006-0.0060.0000.0000.0000.000
61A61THR00.0070.00639.7360.0350.0350.0000.0000.0000.000
62A62VAL00.0320.03238.907-0.031-0.0310.0000.0000.0000.000
63A63ARG10.9731.00041.5246.4286.4280.0000.0000.0000.000
64A64SER00.0010.00141.9300.1640.1640.0000.0000.0000.000
65A65PHE00.0280.00337.3070.0440.0440.0000.0000.0000.000
66A66GLY00.0700.04443.2980.0110.0110.0000.0000.0000.000
67A67ILE0-0.0170.01340.4710.0990.0990.0000.0000.0000.000
68A68ARG10.8410.88044.6386.2906.2900.0000.0000.0000.000
69A69ARG10.9420.97339.5507.2317.2310.0000.0000.0000.000
70A70ASN0-0.052-0.05742.5930.0460.0460.0000.0000.0000.000
71A71GLU-1-0.762-0.86344.223-6.434-6.4340.0000.0000.0000.000
72A72LYS10.8290.90843.7106.4786.4780.0000.0000.0000.000
73A73ILE00.0520.02540.8960.0800.0800.0000.0000.0000.000
74A74ALA00.0530.03940.2820.0530.0530.0000.0000.0000.000
75A75VAL0-0.023-0.01542.311-0.011-0.0110.0000.0000.0000.000
76A76HIS0-0.0080.00237.284-0.127-0.1270.0000.0000.0000.000
77A77CYS00.004-0.00139.5910.0730.0730.0000.0000.0000.000
78A78THR0-0.067-0.02034.870-0.215-0.2150.0000.0000.0000.000
79A79VAL00.0460.01837.1000.1170.1170.0000.0000.0000.000
80A80ARG10.8900.91231.2498.9078.9070.0000.0000.0000.000
81A81GLY00.0300.02436.2690.1400.1400.0000.0000.0000.000
82A82ALA00.0470.02237.9440.1580.1580.0000.0000.0000.000
83A83LYS10.9700.98040.5196.9636.9630.0000.0000.0000.000
84A84ALA0-0.058-0.03036.1590.0010.0010.0000.0000.0000.000
85A85GLU-1-0.897-0.96135.220-8.941-8.9410.0000.0000.0000.000
86A86GLU-1-0.897-0.94538.082-7.001-7.0010.0000.0000.0000.000
87A87ILE0-0.043-0.01340.3430.0910.0910.0000.0000.0000.000
88A88LEU0-0.031-0.01433.129-0.052-0.0520.0000.0000.0000.000
89A89GLU-1-0.828-0.90137.833-7.865-7.8650.0000.0000.0000.000
90A90ARG10.9220.95739.5926.9686.9680.0000.0000.0000.000
91A91GLY00.003-0.00539.6060.0920.0920.0000.0000.0000.000
92A92LEU0-0.042-0.02034.501-0.062-0.0620.0000.0000.0000.000
93A93LYS10.9780.99238.5866.6606.6600.0000.0000.0000.000
94A94VAL0-0.018-0.00742.0430.0580.0580.0000.0000.0000.000
95A95ARG10.8240.92034.2088.4558.4550.0000.0000.0000.000
96A96GLU-1-0.844-0.90239.007-7.363-7.3630.0000.0000.0000.000
97A97TYR0-0.093-0.08736.528-0.172-0.1720.0000.0000.0000.000
98A98GLU-1-0.892-0.93934.933-8.347-8.3470.0000.0000.0000.000
99A99LEU0-0.082-0.03930.347-0.045-0.0450.0000.0000.0000.000
100A100ARG10.9460.97429.7729.6689.6680.0000.0000.0000.000
101A101ARG10.9000.92422.59911.51011.5100.0000.0000.0000.000
102A102GLU-1-0.936-0.97224.064-12.438-12.4380.0000.0000.0000.000
103A103ASN0-0.0050.01626.6780.3760.3760.0000.0000.0000.000
104A104PHE00.0670.04723.563-0.205-0.2050.0000.0000.0000.000
105A105SER0-0.007-0.01521.992-0.437-0.4370.0000.0000.0000.000
106A106SER00.029-0.00516.4540.1130.1130.0000.0000.0000.000
107A107THR0-0.081-0.04317.452-1.158-1.1580.0000.0000.0000.000
108A108GLY00.0230.02819.9550.2680.2680.0000.0000.0000.000
109A109ASN0-0.016-0.00622.2150.5520.5520.0000.0000.0000.000
110A110PHE00.0780.04625.347-0.355-0.3550.0000.0000.0000.000
111A111GLY00.017-0.00128.1710.1490.1490.0000.0000.0000.000
112A112PHE00.0080.00631.580-0.144-0.1440.0000.0000.0000.000
113A113GLY00.0220.02434.856-0.012-0.0120.0000.0000.0000.000
114A114ILE0-0.001-0.00137.336-0.059-0.0590.0000.0000.0000.000
115A115GLN00.013-0.00940.9160.1080.1080.0000.0000.0000.000
116A116GLU-1-0.857-0.93244.453-6.326-6.3260.0000.0000.0000.000
117A117HIS0-0.017-0.01945.9310.0140.0140.0000.0000.0000.000
118A118ILE0-0.021-0.01446.8980.0060.0060.0000.0000.0000.000
119A119ASP-1-0.819-0.89346.645-6.403-6.4030.0000.0000.0000.000
120A120LEU0-0.099-0.05243.054-0.055-0.0550.0000.0000.0000.000
121A121GLY0-0.036-0.01646.686-0.028-0.0280.0000.0000.0000.000
122A122ILE0-0.052-0.01647.5150.1310.1310.0000.0000.0000.000
123A123LYS11.0000.99651.3065.3825.3820.0000.0000.0000.000
124A124TYR00.024-0.01354.4870.0080.0080.0000.0000.0000.000
125A125ASP-1-0.842-0.90155.649-5.373-5.3730.0000.0000.0000.000
126A126PRO00.0390.01756.588-0.072-0.0720.0000.0000.0000.000
127A127SER0-0.082-0.03958.372-0.009-0.0090.0000.0000.0000.000
128A128ILE0-0.067-0.04152.157-0.045-0.0450.0000.0000.0000.000
129A129GLY00.0300.00853.440-0.055-0.0550.0000.0000.0000.000
130A130ILE00.0200.00649.344-0.102-0.1020.0000.0000.0000.000
131A131TYR0-0.032-0.00946.203-0.081-0.0810.0000.0000.0000.000
132A132GLY00.0310.01443.668-0.011-0.0110.0000.0000.0000.000
133A133LEU0-0.051-0.02841.0970.0130.0130.0000.0000.0000.000
134A134ASP-1-0.859-0.91136.107-8.202-8.2020.0000.0000.0000.000
135A135PHE00.017-0.00335.3550.0210.0210.0000.0000.0000.000
136A136TYR0-0.019-0.02426.187-0.421-0.4210.0000.0000.0000.000
137A137VAL00.0340.02829.9470.1340.1340.0000.0000.0000.000
138A138VAL0-0.075-0.03826.039-0.387-0.3870.0000.0000.0000.000
139A139LEU00.0740.04625.3100.2910.2910.0000.0000.0000.000
140A140GLY0-0.006-0.03724.091-0.331-0.3310.0000.0000.0000.000
141A141ARG10.8970.96319.30514.39314.3930.0000.0000.0000.000
142A142PRO00.0250.02225.1040.0630.0630.0000.0000.0000.000
143A143GLY00.0510.01726.341-0.314-0.3140.0000.0000.0000.000
144A144TYR0-0.031-0.03022.392-0.149-0.1490.0000.0000.0000.000
145A145ASN00.0190.00125.239-0.186-0.1860.0000.0000.0000.000
146A146VAL0-0.0030.00021.4620.1570.1570.0000.0000.0000.000
147A147ASN00.0270.02120.591-0.388-0.3880.0000.0000.0000.000
148A148HIS0-0.034-0.01423.0580.1980.1980.0000.0000.0000.000
149A149ARG10.8480.93924.62612.34612.3460.0000.0000.0000.000
150A150LYS11.0150.99327.4378.8598.8590.0000.0000.0000.000
151A151ARG11.0241.01728.7619.4829.4820.0000.0000.0000.000
152A152LYS10.9800.97925.69411.59511.5950.0000.0000.0000.000
153A153SER00.0110.03023.699-0.372-0.3720.0000.0000.0000.000
154A154GLY00.0440.01620.139-0.259-0.2590.0000.0000.0000.000
155A155THR00.0190.00315.3240.3390.3390.0000.0000.0000.000
156A156VAL0-0.027-0.02016.083-0.928-0.9280.0000.0000.0000.000
157A157GLY00.0090.00214.4530.1520.1520.0000.0000.0000.000
158A158PHE00.0220.01310.284-0.233-0.2330.0000.0000.0000.000
159A159GLN00.0570.03013.0541.1701.1700.0000.0000.0000.000
160A160HIS0-0.011-0.04415.7840.3930.3930.0000.0000.0000.000
161A161ARG10.8400.93914.34417.90717.9070.0000.0000.0000.000
162A162LEU0-0.0120.02516.587-0.284-0.2840.0000.0000.0000.000
163A163THR0-0.012-0.03514.944-0.203-0.2030.0000.0000.0000.000
164A164LYS10.9340.95818.15513.68813.6880.0000.0000.0000.000
165A165GLU-1-0.876-0.91918.085-14.827-14.8270.0000.0000.0000.000
166A166ASP-1-0.840-0.91018.233-15.102-15.1020.0000.0000.0000.000
167A167ALA0-0.037-0.01821.1860.5620.5620.0000.0000.0000.000
168A168MET00.0070.01822.2850.5820.5820.0000.0000.0000.000
169A169LYS10.9540.98322.60312.09112.0910.0000.0000.0000.000
170A170TRP0-0.031-0.03325.1870.2940.2940.0000.0000.0000.000
171A171PHE0-0.020-0.00827.2490.2430.2430.0000.0000.0000.000
172A172GLN00.0500.04127.742-0.051-0.0510.0000.0000.0000.000
173A173GLN0-0.049-0.01028.297-0.196-0.1960.0000.0000.0000.000
174A174LYS10.8880.94330.9579.3599.3590.0000.0000.0000.000
175A175TYR0-0.018-0.04233.051-0.319-0.3190.0000.0000.0000.000
176A176ASP-1-0.921-0.93234.301-8.320-8.3200.0000.0000.0000.000
177A177GLY00.0200.01332.6850.0900.0900.0000.0000.0000.000
178A178ILE00.0270.02031.652-0.395-0.3950.0000.0000.0000.000
179A179ILE0-0.064-0.05927.302-0.031-0.0310.0000.0000.0000.000
180A180LEU00.0430.01529.801-0.329-0.3290.0000.0000.0000.000
181A181ASN0-0.083-0.05228.574-0.468-0.4680.0000.0000.0000.000
182A182THR-1-0.876-0.92130.716-8.956-8.9560.0000.0000.0000.000