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: VN5L1

Calculation Name: 3FB4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: bis(adenosine)-5'-pentaphosphate

Ligand 3-letter code: AP5

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FB4

Chain ID: A

ChEMBL ID:

UniProt ID: Q6B341

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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2537963.115554
FMO2-HF: Nuclear repulsion 2453302.351726
FMO2-HF: Total energy -84660.763828
FMO2-MP2: Total energy -84904.458562


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.
-205.419-194.94117.344-9.499-18.321-0.062
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 : 0.846 / q_NPA : 0.940
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].
3A3ILE00.0310.0122.3505.8956.6714.338-1.285-3.8280.006
20A20ILE0-0.002-0.0053.502-1.062-0.7710.019-0.052-0.2580.000
21A21ILE0-0.050-0.0344.993-2.550-2.483-0.001-0.001-0.0650.000
24A24TYR00.000-0.0102.159-2.462-2.2484.142-1.284-3.072-0.014
25A25GLU-1-0.940-0.9573.748-34.619-34.2240.006-0.197-0.204-0.001
26A26ILE0-0.0310.0022.519-3.376-2.3041.432-0.496-2.008-0.002
27A27PRO0-0.013-0.0055.3094.4564.554-0.001-0.005-0.0910.000
80A80GLY00.0020.0082.636-21.016-19.5010.292-0.912-0.894-0.006
81A81PHE00.007-0.0103.46613.00213.5470.017-0.105-0.4580.000
82A82LEU00.0100.0244.297-5.042-4.937-0.001-0.046-0.0580.000
108A108ASP-1-0.880-0.9372.190-75.798-73.1914.288-3.773-3.123-0.039
212A212LEU0-0.037-0.0432.848-3.593-2.5151.259-0.369-1.9680.003
213A213GLY00.0110.0214.300-4.114-3.3290.024-0.290-0.519-0.002
215A215LEU-1-1.001-0.9882.279-47.257-46.3271.530-0.684-1.775-0.007
4A4VAL00.0160.0125.4872.2752.2750.0000.0000.0000.000
5A5LEU0-0.0100.0167.8260.7470.7470.0000.0000.0000.000
6A6MET0-0.013-0.01610.6540.9500.9500.0000.0000.0000.000
7A7GLY00.0950.04614.360-0.010-0.0100.0000.0000.0000.000
8A8LEU00.0010.00617.230-0.062-0.0620.0000.0000.0000.000
9A9PRO0-0.026-0.02819.387-0.507-0.5070.0000.0000.0000.000
10A10GLY00.0300.01320.2820.3770.3770.0000.0000.0000.000
11A11ALA0-0.021-0.01517.6560.0640.0640.0000.0000.0000.000
12A12GLY00.0650.02516.057-0.065-0.0650.0000.0000.0000.000
13A13LYS10.8210.92712.55116.63016.6300.0000.0000.0000.000
14A14GLY00.0790.04111.800-0.911-0.9110.0000.0000.0000.000
15A15THR00.0080.00412.650-0.530-0.5300.0000.0000.0000.000
16A16GLN00.031-0.00410.070-0.850-0.8500.0000.0000.0000.000
17A17ALA0-0.004-0.0038.140-1.534-1.5340.0000.0000.0000.000
18A18GLU-1-0.906-0.9688.705-16.982-16.9820.0000.0000.0000.000
19A19GLN0-0.048-0.0179.3830.5180.5180.0000.0000.0000.000
22A22GLU-1-0.956-0.9746.919-19.436-19.4360.0000.0000.0000.000
23A23LYS10.8270.9235.84426.53726.5370.0000.0000.0000.000
28A28HIS0-0.024-0.0307.687-1.987-1.9870.0000.0000.0000.000
29A29ILE0-0.044-0.0279.1952.2232.2230.0000.0000.0000.000
30A30SER00.021-0.00211.6780.5210.5210.0000.0000.0000.000
31A31THR00.0470.01414.2220.8970.8970.0000.0000.0000.000
32A32GLY0-0.030-0.01117.4270.9390.9390.0000.0000.0000.000
33A33ASP-1-0.774-0.86516.290-15.239-15.2390.0000.0000.0000.000
34A34MET00.0200.02515.9640.5140.5140.0000.0000.0000.000
35A35PHE00.0500.01319.6370.7710.7710.0000.0000.0000.000
36A36ARG10.8710.91018.66514.86414.8640.0000.0000.0000.000
37A37ALA0-0.0430.00121.2410.5360.5360.0000.0000.0000.000
38A38ALA00.0210.01523.2190.5060.5060.0000.0000.0000.000
39A39ILE0-0.037-0.02825.6700.4990.4990.0000.0000.0000.000
40A40LYS10.8730.92922.59113.00213.0020.0000.0000.0000.000
41A41ASN0-0.0190.00125.2820.4390.4390.0000.0000.0000.000
42A42GLY00.0080.01228.8590.2100.2100.0000.0000.0000.000
43A43THR00.0130.00227.7330.2860.2860.0000.0000.0000.000
44A44GLU-1-0.831-0.90630.869-9.453-9.4530.0000.0000.0000.000
45A45LEU00.0130.00824.6920.1120.1120.0000.0000.0000.000
46A46GLY00.0580.01727.262-0.164-0.1640.0000.0000.0000.000
47A47LEU0-0.019-0.02128.2180.0520.0520.0000.0000.0000.000
48A48LYS10.8500.92031.0029.5349.5340.0000.0000.0000.000
49A49ALA00.0390.02326.2040.0920.0920.0000.0000.0000.000
50A50LYS10.8590.90428.3559.6729.6720.0000.0000.0000.000
51A51SER0-0.046-0.00929.4330.0970.0970.0000.0000.0000.000
52A52PHE00.0350.01328.2870.1490.1490.0000.0000.0000.000
53A53MET0-0.010-0.00223.385-0.060-0.0600.0000.0000.0000.000
54A54ASP-1-0.832-0.91327.472-9.783-9.7830.0000.0000.0000.000
55A55GLN0-0.009-0.00130.4490.0790.0790.0000.0000.0000.000
56A56GLY0-0.022-0.01627.4910.1150.1150.0000.0000.0000.000
57A57ASN0-0.012-0.00327.690-0.222-0.2220.0000.0000.0000.000
58A58LEU0-0.007-0.00823.011-0.319-0.3190.0000.0000.0000.000
59A59VAL0-0.0150.00024.2990.4830.4830.0000.0000.0000.000
60A60PRO00.0190.00225.061-0.380-0.3800.0000.0000.0000.000
61A61ASP-1-0.787-0.88823.728-13.293-13.2930.0000.0000.0000.000
62A62GLU-1-0.925-0.95723.432-11.914-11.9140.0000.0000.0000.000
63A63VAL0-0.025-0.01124.397-0.366-0.3660.0000.0000.0000.000
64A64THR0-0.032-0.02619.470-0.407-0.4070.0000.0000.0000.000
65A65ILE00.0210.00519.528-0.897-0.8970.0000.0000.0000.000
66A66GLY00.0010.01319.522-0.713-0.7130.0000.0000.0000.000
67A67ILE0-0.006-0.01119.319-0.421-0.4210.0000.0000.0000.000
68A68VAL0-0.0050.00114.341-0.826-0.8260.0000.0000.0000.000
69A69HIS00.0620.02915.343-2.049-2.0490.0000.0000.0000.000
70A70GLU-1-0.916-0.95316.295-16.853-16.8530.0000.0000.0000.000
71A71ARG10.7290.82313.04222.75822.7580.0000.0000.0000.000
72A72LEU00.0510.0009.946-1.001-1.0010.0000.0000.0000.000
73A73SER0-0.022-0.01511.669-1.699-1.6990.0000.0000.0000.000
74A74LYS10.8510.94613.49418.61818.6180.0000.0000.0000.000
75A75ASP-1-0.854-0.93611.704-22.817-22.8170.0000.0000.0000.000
76A76ASP-1-0.809-0.87110.438-27.346-27.3460.0000.0000.0000.000
77A77CYS0-0.040-0.0058.044-2.914-2.9140.0000.0000.0000.000
78A78GLN0-0.020-0.0046.635-7.484-7.4840.0000.0000.0000.000
79A79LYS10.9390.9564.90830.84830.8480.0000.0000.0000.000
83A83LEU00.0100.0126.3133.8073.8070.0000.0000.0000.000
84A84ASP-1-0.834-0.9189.747-19.573-19.5730.0000.0000.0000.000
85A85GLY0-0.031-0.02212.0721.2451.2450.0000.0000.0000.000
86A86PHE00.0110.00914.1301.5461.5460.0000.0000.0000.000
87A87PRO00.0740.04013.203-1.525-1.5250.0000.0000.0000.000
88A88ARG10.8110.88116.51715.01915.0190.0000.0000.0000.000
89A89THR00.0160.01219.5160.7110.7110.0000.0000.0000.000
90A90VAL00.0590.02720.342-0.664-0.6640.0000.0000.0000.000
91A91ALA00.0590.03120.708-0.511-0.5110.0000.0000.0000.000
92A92GLN0-0.049-0.04518.675-0.958-0.9580.0000.0000.0000.000
93A93ALA00.0010.00816.362-0.986-0.9860.0000.0000.0000.000
94A94ASP-1-0.882-0.94816.424-15.526-15.5260.0000.0000.0000.000
95A95ALA0-0.031-0.00118.196-0.403-0.4030.0000.0000.0000.000
96A96LEU0-0.012-0.00711.435-0.461-0.4610.0000.0000.0000.000
97A97ASP-1-0.831-0.92413.455-22.369-22.3690.0000.0000.0000.000
98A98SER0-0.031-0.00714.509-0.312-0.3120.0000.0000.0000.000
99A99LEU0-0.0160.00612.828-0.327-0.3270.0000.0000.0000.000
100A100LEU0-0.030-0.0268.824-1.205-1.2050.0000.0000.0000.000
101A101THR0-0.009-0.01011.943-0.851-0.8510.0000.0000.0000.000
102A102ASP-1-0.941-0.96314.291-16.876-16.8760.0000.0000.0000.000
103A103LEU0-0.090-0.03511.0540.1790.1790.0000.0000.0000.000
104A104GLY0-0.026-0.00611.242-1.483-1.4830.0000.0000.0000.000
105A105LYS10.7630.8736.25236.28636.2860.0000.0000.0000.000
106A106LYS10.9620.9936.28839.83739.8370.0000.0000.0000.000
107A107LEU00.0040.0006.213-5.861-5.8610.0000.0000.0000.000
109A109TYR00.014-0.0115.0705.6685.6680.0000.0000.0000.000
110A110VAL0-0.025-0.0127.034-1.571-1.5710.0000.0000.0000.000
111A111LEU00.0280.0106.6961.8041.8040.0000.0000.0000.000
112A112ASN0-0.012-0.03511.0010.6060.6060.0000.0000.0000.000
113A113ILE0-0.0110.00611.4080.7390.7390.0000.0000.0000.000
114A114LYS10.8250.90415.36014.46114.4610.0000.0000.0000.000
115A115VAL0-0.010-0.00219.125-0.016-0.0160.0000.0000.0000.000
116A116GLU-1-0.836-0.89621.832-10.195-10.1950.0000.0000.0000.000
117A117GLN00.017-0.02925.672-0.326-0.3260.0000.0000.0000.000
118A118GLU-1-0.898-0.95327.682-8.983-8.9830.0000.0000.0000.000
119A119GLU-1-0.773-0.87323.727-11.015-11.0150.0000.0000.0000.000
120A120LEU0-0.021-0.00221.528-0.190-0.1900.0000.0000.0000.000
121A121MET0-0.028-0.01824.8570.0900.0900.0000.0000.0000.000
122A122LYS10.9320.98627.6089.5049.5040.0000.0000.0000.000
123A123ARG10.7750.88819.16912.91712.9170.0000.0000.0000.000
124A124LEU0-0.065-0.03422.867-0.112-0.1120.0000.0000.0000.000
125A125THR0-0.031-0.03525.9610.1840.1840.0000.0000.0000.000
126A126GLY00.0120.01528.1330.2550.2550.0000.0000.0000.000
127A127ARG10.8190.91619.80912.50012.5000.0000.0000.0000.000
128A128TRP00.0080.00524.9610.3310.3310.0000.0000.0000.000
129A129ILE0-0.034-0.01521.333-0.510-0.5100.0000.0000.0000.000
130A130CYS0-0.0090.02522.1350.5660.5660.0000.0000.0000.000
131A131LYS10.7830.86623.2559.1439.1430.0000.0000.0000.000
132A132THR0-0.018-0.01423.718-0.046-0.0460.0000.0000.0000.000
133A133CYS0-0.044-0.04619.301-0.415-0.4150.0000.0000.0000.000
134A134GLY0-0.0250.00118.480-0.713-0.7130.0000.0000.0000.000
135A135ALA00.0150.00717.748-0.210-0.2100.0000.0000.0000.000
136A136THR0-0.090-0.04417.6920.7450.7450.0000.0000.0000.000
137A137TYR00.0670.02019.967-0.259-0.2590.0000.0000.0000.000
138A138HIS0-0.068-0.04022.8110.0870.0870.0000.0000.0000.000
139A139THR0-0.010-0.03225.1040.0820.0820.0000.0000.0000.000
140A140ILE0-0.060-0.02527.9040.2690.2690.0000.0000.0000.000
141A141PHE0-0.002-0.02223.7360.0990.0990.0000.0000.0000.000
142A142ASN0-0.031-0.01219.675-0.263-0.2630.0000.0000.0000.000
143A143PRO00.0230.03023.308-0.205-0.2050.0000.0000.0000.000
144A144PRO0-0.0040.00725.130-0.242-0.2420.0000.0000.0000.000
145A145ALA0-0.024-0.02326.1300.3240.3240.0000.0000.0000.000
146A146VAL0-0.047-0.02928.1080.3880.3880.0000.0000.0000.000
147A147GLU-1-0.915-0.95729.835-8.541-8.5410.0000.0000.0000.000
148A148GLY00.0140.00130.6330.1480.1480.0000.0000.0000.000
149A149ILE0-0.045-0.01728.408-0.056-0.0560.0000.0000.0000.000
150A150CYS0-0.112-0.02922.955-0.410-0.4100.0000.0000.0000.000
151A151ASP-1-0.758-0.88922.781-10.837-10.8370.0000.0000.0000.000
152A152LYS10.9050.93616.59715.14315.1430.0000.0000.0000.000
153A153ASP-1-0.736-0.86222.147-12.179-12.1790.0000.0000.0000.000
154A154GLY00.0120.01624.7990.2860.2860.0000.0000.0000.000
155A155GLY0-0.044-0.01526.4940.3380.3380.0000.0000.0000.000
156A156GLU-1-0.825-0.89727.689-9.127-9.1270.0000.0000.0000.000
157A157LEU0-0.0140.00325.020-0.402-0.4020.0000.0000.0000.000
158A158TYR0-0.066-0.04223.8700.4590.4590.0000.0000.0000.000
159A159GLN00.0460.03027.149-0.101-0.1010.0000.0000.0000.000
160A160ARG10.8230.86920.54012.60212.6020.0000.0000.0000.000
161A161ILE0-0.005-0.00927.3930.2050.2050.0000.0000.0000.000
162A162ASP-1-0.724-0.83324.941-11.462-11.4620.0000.0000.0000.000
163A163ASP-1-0.763-0.86525.123-11.599-11.5990.0000.0000.0000.000
164A164LYS10.9670.99928.0209.0069.0060.0000.0000.0000.000
165A165PRO00.0790.01531.548-0.099-0.0990.0000.0000.0000.000
166A166GLU-1-0.882-0.91332.868-8.236-8.2360.0000.0000.0000.000
167A167THR00.0090.01329.101-0.005-0.0050.0000.0000.0000.000
168A168VAL0-0.036-0.00827.618-0.349-0.3490.0000.0000.0000.000
169A169LYS10.8790.93328.6498.2468.2460.0000.0000.0000.000
170A170ASN0-0.030-0.01930.616-0.065-0.0650.0000.0000.0000.000
171A171ARG10.7970.89723.88711.05011.0500.0000.0000.0000.000
172A172LEU0-0.025-0.00325.135-0.462-0.4620.0000.0000.0000.000
173A173ASP-1-0.825-0.88927.027-9.841-9.8410.0000.0000.0000.000
174A174VAL00.0340.00626.157-0.233-0.2330.0000.0000.0000.000
175A175ASN0-0.057-0.04122.157-0.916-0.9160.0000.0000.0000.000
176A176MET0-0.0190.01023.896-0.281-0.2810.0000.0000.0000.000
177A177LYS10.8290.89725.8809.5519.5510.0000.0000.0000.000
178A178GLN00.0230.01922.985-0.144-0.1440.0000.0000.0000.000
179A179THR0-0.043-0.02421.069-0.522-0.5220.0000.0000.0000.000
180A180GLN0-0.029-0.02221.407-0.437-0.4370.0000.0000.0000.000
181A181PRO00.0410.01022.508-0.343-0.3430.0000.0000.0000.000
182A182LEU0-0.0220.00017.487-0.387-0.3870.0000.0000.0000.000
183A183LEU0-0.001-0.00617.922-0.924-0.9240.0000.0000.0000.000
184A184ASP-1-0.859-0.92518.638-13.084-13.0840.0000.0000.0000.000
185A185PHE0-0.023-0.00815.663-0.183-0.1830.0000.0000.0000.000
186A186TYR00.051-0.00513.132-0.573-0.5730.0000.0000.0000.000
187A187SER0-0.053-0.01515.014-0.896-0.8960.0000.0000.0000.000
188A188GLN0-0.022-0.01517.455-0.354-0.3540.0000.0000.0000.000
189A189LYS10.8540.93013.39118.22018.2200.0000.0000.0000.000
190A190GLY0-0.0150.00813.368-1.236-1.2360.0000.0000.0000.000
191A191VAL0-0.0050.0049.267-0.577-0.5770.0000.0000.0000.000
192A192LEU0-0.027-0.00110.252-1.287-1.2870.0000.0000.0000.000
193A193LYS10.9250.96710.34921.64821.6480.0000.0000.0000.000
194A194ASP-1-0.809-0.88113.041-15.538-15.5380.0000.0000.0000.000
195A195ILE0-0.007-0.00611.504-0.260-0.2600.0000.0000.0000.000
196A196ASP-1-0.838-0.90815.197-12.713-12.7130.0000.0000.0000.000
197A197GLY00.0690.01416.797-0.456-0.4560.0000.0000.0000.000
198A198GLN0-0.095-0.06617.6550.0460.0460.0000.0000.0000.000
199A199GLN0-0.025-0.02316.7500.8540.8540.0000.0000.0000.000
200A200ASP-1-0.813-0.89719.390-11.994-11.9940.0000.0000.0000.000
201A201ILE00.0170.00815.095-0.558-0.5580.0000.0000.0000.000
202A202LYS10.9850.97914.24513.13013.1300.0000.0000.0000.000
203A203LYS10.8300.91814.37411.58611.5860.0000.0000.0000.000
204A204VAL00.0230.02213.091-0.491-0.4910.0000.0000.0000.000
205A205PHE00.010-0.0076.697-0.929-0.9290.0000.0000.0000.000
206A206VAL0-0.0210.00210.117-1.132-1.1320.0000.0000.0000.000
207A207ASP-1-0.820-0.90111.188-17.230-17.2300.0000.0000.0000.000
208A208ILE0-0.045-0.0276.864-1.219-1.2190.0000.0000.0000.000
209A209ASN00.0110.0116.578-4.071-4.0710.0000.0000.0000.000
210A210ASP-1-0.902-0.9527.580-20.257-20.2570.0000.0000.0000.000
211A211LEU0-0.089-0.0438.233-0.669-0.6690.0000.0000.0000.000
214A214GLY0-0.066-0.0277.0351.6141.6140.0000.0000.0000.000