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: GV4V1

Calculation Name: 3EIY-A-Xray547

Preferred Name:

Target Type:

Ligand Name: pyrophosphate 2- | tetraethylene glycol | di(hydroxyethyl)ether | potassium ion

Ligand 3-letter code: POP | PG4 | PEG | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3EIY

Chain ID: A

ChEMBL ID:

UniProt ID: Q3JUV5

Base Structure: X-ray

Registration Date: 2025-10-05

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1775510.364902
FMO2-HF: Nuclear repulsion 1709166.843649
FMO2-HF: Total energy -66343.521252
FMO2-MP2: Total energy -66538.191025


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-110.921-104.111.104-3.657-4.257-0.032
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.920
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].
3A4SER00.0540.0373.1880.2862.7370.043-1.146-1.348-0.006
4A5ASN0-0.053-0.0203.400-1.701-0.5260.007-0.579-0.603-0.003
5A6VAL0-0.0060.0154.6104.2594.428-0.001-0.023-0.1450.000
35A36ALA0-0.034-0.0095.077-6.403-6.425-0.001-0.0020.0260.000
37A38GLY0-0.098-0.0362.693-7.893-7.3790.566-0.524-0.556-0.003
38A39LEU0-0.008-0.0132.759-8.580-6.0560.490-1.383-1.631-0.020
6A7PRO00.0180.0036.8991.6231.6230.0000.0000.0000.000
7A8ALA00.0860.06710.6800.1740.1740.0000.0000.0000.000
8A9GLY00.020-0.01413.2230.9490.9490.0000.0000.0000.000
9A10LYS10.8020.91914.01319.57019.5700.0000.0000.0000.000
10A11ASP-1-0.879-0.94317.144-13.075-13.0750.0000.0000.0000.000
11A12LEU0-0.0250.01716.4000.0120.0120.0000.0000.0000.000
12A13PRO00.0260.01120.6930.4230.4230.0000.0000.0000.000
13A14GLN00.0170.00321.371-0.365-0.3650.0000.0000.0000.000
14A15ASP-1-0.836-0.87619.178-16.060-16.0600.0000.0000.0000.000
15A16PHE00.0720.01716.035-0.678-0.6780.0000.0000.0000.000
16A17ASN0-0.111-0.07111.3551.1411.1410.0000.0000.0000.000
17A18VAL00.0250.00712.324-0.161-0.1610.0000.0000.0000.000
18A19ILE0-0.023-0.0095.669-1.452-1.4520.0000.0000.0000.000
19A20ILE0-0.025-0.0099.3761.5891.5890.0000.0000.0000.000
20A21GLU-1-0.822-0.92210.270-26.699-26.6990.0000.0000.0000.000
21A22ILE0-0.013-0.00311.9970.3770.3770.0000.0000.0000.000
22A23PRO0-0.0100.00314.9170.4960.4960.0000.0000.0000.000
23A24ALA00.0250.02117.1720.5460.5460.0000.0000.0000.000
24A25GLN0-0.017-0.01820.7990.1150.1150.0000.0000.0000.000
25A26SER0-0.045-0.01318.9740.3190.3190.0000.0000.0000.000
26A27GLU-1-0.861-0.93621.006-11.752-11.7520.0000.0000.0000.000
27A28PRO0-0.0170.01321.090-0.621-0.6210.0000.0000.0000.000
28A29VAL0-0.033-0.01917.7050.3200.3200.0000.0000.0000.000
29A30LYS10.8280.90115.82817.69317.6930.0000.0000.0000.000
30A31TYR0-0.006-0.01212.624-0.277-0.2770.0000.0000.0000.000
31A32GLU-1-0.780-0.86812.112-18.737-18.7370.0000.0000.0000.000
32A33ALA0-0.055-0.0356.668-1.480-1.4800.0000.0000.0000.000
33A34ASP-1-0.775-0.8847.599-32.177-32.1770.0000.0000.0000.000
34A35LYS10.8850.9265.58223.44023.4400.0000.0000.0000.000
36A37LEU0-0.031-0.0176.196-1.754-1.7540.0000.0000.0000.000
39A40LEU0-0.006-0.0105.5471.1781.1780.0000.0000.0000.000
40A41VAL00.0020.0028.6250.6880.6880.0000.0000.0000.000
41A42VAL0-0.022-0.01311.7190.3610.3610.0000.0000.0000.000
42A43ASP-1-0.820-0.88015.385-15.784-15.7840.0000.0000.0000.000
43A44ARG10.8000.87217.14115.02915.0290.0000.0000.0000.000
44A45PHE0-0.008-0.00620.011-0.393-0.3930.0000.0000.0000.000
45A46ILE0-0.019-0.00621.0760.2360.2360.0000.0000.0000.000
46A47GLY00.0180.00824.1780.3660.3660.0000.0000.0000.000
47A48THR0-0.055-0.04627.7160.3280.3280.0000.0000.0000.000
48A49GLY0-0.027-0.00927.0980.2840.2840.0000.0000.0000.000
49A50MET0-0.054-0.01827.112-0.004-0.0040.0000.0000.0000.000
50A51ARG10.8500.90723.97911.51411.5140.0000.0000.0000.000
51A52TYR00.0730.04119.8790.3060.3060.0000.0000.0000.000
52A53PRO0-0.019-0.00422.763-0.082-0.0820.0000.0000.0000.000
53A54VAL0-0.020-0.02121.5000.2740.2740.0000.0000.0000.000
54A55ASN0-0.016-0.01316.583-0.444-0.4440.0000.0000.0000.000
55A56TYR0-0.009-0.02516.6810.6410.6410.0000.0000.0000.000
56A57GLY00.0570.03213.046-1.099-1.0990.0000.0000.0000.000
57A58PHE00.0430.0367.556-0.240-0.2400.0000.0000.0000.000
58A59ILE00.0080.01911.726-1.693-1.6930.0000.0000.0000.000
59A60PRO0-0.046-0.0078.397-0.331-0.3310.0000.0000.0000.000
60A61GLN0-0.044-0.0577.9054.7064.7060.0000.0000.0000.000
61A62THR0-0.027-0.02211.5872.3172.3170.0000.0000.0000.000
62A63LEU0-0.062-0.02114.167-1.431-1.4310.0000.0000.0000.000
63A64SER00.042-0.00516.8571.1951.1950.0000.0000.0000.000
64A65GLY0-0.047-0.03220.002-0.110-0.1100.0000.0000.0000.000
65A66ASP-1-0.855-0.92719.661-15.547-15.5470.0000.0000.0000.000
66A67GLY0-0.047-0.01718.5240.1760.1760.0000.0000.0000.000
67A68ASP-1-0.899-0.93415.340-20.877-20.8770.0000.0000.0000.000
68A69PRO0-0.110-0.07711.4950.1390.1390.0000.0000.0000.000
69A70VAL00.0280.01514.7060.7350.7350.0000.0000.0000.000
70A71ASP-1-0.735-0.83515.913-18.636-18.6360.0000.0000.0000.000
71A72VAL0-0.083-0.05616.2521.0571.0570.0000.0000.0000.000
72A73LEU0-0.0050.00517.289-0.499-0.4990.0000.0000.0000.000
73A74VAL0-0.021-0.01716.1750.3890.3890.0000.0000.0000.000
74A75ILE00.0170.01019.4070.1200.1200.0000.0000.0000.000
75A76THR0-0.002-0.04319.135-0.244-0.2440.0000.0000.0000.000
76A77PRO0-0.037-0.01322.3990.2190.2190.0000.0000.0000.000
77A78PHE00.0180.00521.7570.4120.4120.0000.0000.0000.000
78A79PRO00.0030.02319.445-0.429-0.4290.0000.0000.0000.000
79A80LEU0-0.0080.00414.587-0.129-0.1290.0000.0000.0000.000
80A81LEU00.0090.00311.7150.0700.0700.0000.0000.0000.000
81A82ALA00.0550.03911.656-1.193-1.1930.0000.0000.0000.000
82A83GLY00.0080.0057.430-0.598-0.5980.0000.0000.0000.000
83A84SER0-0.111-0.0616.346-3.573-3.5730.0000.0000.0000.000
84A85VAL00.007-0.0076.847-0.566-0.5660.0000.0000.0000.000
85A86VAL0-0.011-0.0019.4281.6301.6300.0000.0000.0000.000
86A87ARG10.7810.85313.20515.48915.4890.0000.0000.0000.000
87A88ALA0-0.031-0.02515.4990.9050.9050.0000.0000.0000.000
88A89ARG10.8260.91618.09511.96311.9630.0000.0000.0000.000
89A90ALA00.0370.00921.408-0.046-0.0460.0000.0000.0000.000
90A91LEU0-0.088-0.03123.2890.4180.4180.0000.0000.0000.000
91A92GLY00.007-0.00725.3680.5970.5970.0000.0000.0000.000
92A93MET0-0.038-0.00224.885-0.570-0.5700.0000.0000.0000.000
93A94LEU0-0.018-0.00925.7140.6300.6300.0000.0000.0000.000
94A95LYS10.8810.93726.4239.5449.5440.0000.0000.0000.000
95A96MET0-0.027-0.02024.6890.5620.5620.0000.0000.0000.000
96A97THR0-0.016-0.01628.759-0.045-0.0450.0000.0000.0000.000
97A98ASP-1-0.788-0.90724.773-12.430-12.4300.0000.0000.0000.000
98A99GLU-1-0.843-0.90725.520-11.840-11.8400.0000.0000.0000.000
99A100SER0-0.025-0.01024.4560.0910.0910.0000.0000.0000.000
100A101GLY0-0.0170.00226.396-0.063-0.0630.0000.0000.0000.000
101A102VAL0-0.053-0.03726.7040.1720.1720.0000.0000.0000.000
102A103ASP-1-0.775-0.86722.964-14.199-14.1990.0000.0000.0000.000
103A104ALA0-0.007-0.01323.6030.5780.5780.0000.0000.0000.000
104A105LYS10.8130.89120.10714.14814.1480.0000.0000.0000.000
105A106LEU0-0.005-0.01219.9630.7860.7860.0000.0000.0000.000
106A107VAL0-0.018-0.00721.664-0.201-0.2010.0000.0000.0000.000
107A108ALA00.0290.01019.6890.2320.2320.0000.0000.0000.000
108A109VAL00.0070.01121.3660.1970.1970.0000.0000.0000.000
109A110PRO00.0280.00118.586-0.511-0.5110.0000.0000.0000.000
110A111HIS00.0390.02519.2110.7550.7550.0000.0000.0000.000
111A112ASP-1-0.744-0.86821.145-11.616-11.6160.0000.0000.0000.000
112A113LYS10.8800.92323.25811.78011.7800.0000.0000.0000.000
113A114VAL0-0.046-0.01217.410-0.122-0.1220.0000.0000.0000.000
114A115CYS0-0.013-0.00120.7390.1270.1270.0000.0000.0000.000
115A116PRO00.0680.04122.9690.2920.2920.0000.0000.0000.000
116A117MET0-0.032-0.01825.8580.1740.1740.0000.0000.0000.000
117A118THR0-0.006-0.01623.8760.0750.0750.0000.0000.0000.000
118A119ALA00.0220.02426.5800.0600.0600.0000.0000.0000.000
119A120ASN0-0.043-0.02428.1180.1930.1930.0000.0000.0000.000
120A121LEU0-0.0130.01926.8550.2540.2540.0000.0000.0000.000
121A122LYS10.8810.93128.3269.5169.5160.0000.0000.0000.000
122A123SER00.007-0.00829.152-0.244-0.2440.0000.0000.0000.000
123A124ILE00.0340.01127.846-0.043-0.0430.0000.0000.0000.000
124A125ASP-1-0.898-0.94830.070-9.021-9.0210.0000.0000.0000.000
125A126ASP-1-0.847-0.91431.429-9.314-9.3140.0000.0000.0000.000
126A127VAL0-0.033-0.00428.082-0.038-0.0380.0000.0000.0000.000
127A128PRO00.002-0.00830.4900.2740.2740.0000.0000.0000.000
128A129ALA00.0360.01632.505-0.210-0.2100.0000.0000.0000.000
129A130TYR00.0700.02431.160-0.198-0.1980.0000.0000.0000.000
130A131LEU0-0.0090.00826.810-0.119-0.1190.0000.0000.0000.000
131A132LYS10.8700.93929.3379.1409.1400.0000.0000.0000.000
132A133ASP-1-0.890-0.94930.799-9.009-9.0090.0000.0000.0000.000
133A134GLN0-0.047-0.03129.411-0.301-0.3010.0000.0000.0000.000
134A135ILE0-0.017-0.00525.390-0.224-0.2240.0000.0000.0000.000
135A136LYS10.8570.91627.7518.9098.9090.0000.0000.0000.000
136A137HIS00.006-0.00230.397-0.231-0.2310.0000.0000.0000.000
137A138PHE0-0.002-0.00823.0540.0500.0500.0000.0000.0000.000
138A139PHE00.020-0.00221.879-0.166-0.1660.0000.0000.0000.000
139A140GLU-1-0.839-0.90827.417-9.212-9.2120.0000.0000.0000.000
140A141GLN0-0.059-0.02429.9500.3970.3970.0000.0000.0000.000
141A142TYR00.0300.00922.133-0.154-0.1540.0000.0000.0000.000
142A143LYS10.8500.92224.15812.34712.3470.0000.0000.0000.000
143A144ALA00.0000.00527.9130.1370.1370.0000.0000.0000.000
144A145LEU0-0.039-0.01830.4340.3410.3410.0000.0000.0000.000
145A146GLU-1-0.806-0.88825.120-12.507-12.5070.0000.0000.0000.000
146A147LYS10.9390.95029.3999.2859.2850.0000.0000.0000.000
147A148GLY00.000-0.00229.851-0.252-0.2520.0000.0000.0000.000
148A149LYS10.8620.94723.26212.76212.7620.0000.0000.0000.000
149A150TRP0-0.053-0.01829.0050.3960.3960.0000.0000.0000.000
150A151VAL00.0410.00827.178-0.387-0.3870.0000.0000.0000.000
151A152LYS10.7880.89230.1599.6209.6200.0000.0000.0000.000
152A153VAL00.0170.00730.147-0.247-0.2470.0000.0000.0000.000
153A154GLU-1-0.837-0.88031.593-9.173-9.1730.0000.0000.0000.000
154A155GLY0-0.018-0.01532.1010.3510.3510.0000.0000.0000.000
155A156TRP0-0.017-0.01127.639-0.425-0.4250.0000.0000.0000.000
156A157ASP-1-0.825-0.90429.694-9.741-9.7410.0000.0000.0000.000
157A158GLY00.0490.02429.575-0.248-0.2480.0000.0000.0000.000
158A159ILE00.003-0.01226.758-0.316-0.3160.0000.0000.0000.000
159A160ASP-1-0.902-0.94527.174-10.633-10.6330.0000.0000.0000.000
160A161ALA0-0.0020.00728.369-0.255-0.2550.0000.0000.0000.000
161A162ALA00.0340.01423.748-0.385-0.3850.0000.0000.0000.000
162A163HIS00.015-0.01223.454-0.918-0.9180.0000.0000.0000.000
163A164LYS10.8180.90324.32811.36211.3620.0000.0000.0000.000
164A165GLU-1-0.831-0.88621.512-14.586-14.5860.0000.0000.0000.000
165A166ILE0-0.023-0.00818.793-0.679-0.6790.0000.0000.0000.000
166A167THR0-0.059-0.04520.060-0.682-0.6820.0000.0000.0000.000
167A168ASP-1-0.816-0.89421.983-12.669-12.6690.0000.0000.0000.000
168A169GLY00.0610.03819.173-0.300-0.3000.0000.0000.0000.000
169A170VAL0-0.032-0.03316.580-1.159-1.1590.0000.0000.0000.000
170A171ALA0-0.075-0.03417.975-0.430-0.4300.0000.0000.0000.000
171A172ASN00.0170.00219.5710.2300.2300.0000.0000.0000.000
172A173PHE0-0.0120.01110.177-1.071-1.0710.0000.0000.0000.000
173A174LYS10.8370.92215.53316.25316.2530.0000.0000.0000.000
174A175LYS00.0040.02217.4420.9420.9420.0000.0000.0000.000