FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: VN6G1

Calculation Name: 4X9L-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphomethylphosphonic acid adenylate ester | tetraethylene glycol

Ligand 3-letter code: ACP | PG4

Ligand of Interest (LOI):

PDB ID: 4X9L

Chain ID: A

ChEMBL ID:

UniProt ID: Q07078

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2492855.848114
FMO2-HF: Nuclear repulsion 2410085.534525
FMO2-HF: Total energy -82770.313588
FMO2-MP2: Total energy -83015.15313


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-168.197-163.4952.349-3.232-3.819-0.03
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / 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].
3A4GLU-1-0.805-0.9042.542-60.595-55.9962.350-3.224-3.725-0.030
4A5THR0-0.035-0.0134.8534.3464.449-0.001-0.008-0.0940.000
5A6GLU-1-0.862-0.9138.145-23.176-23.1760.0000.0000.0000.000
6A7THR0-0.023-0.02411.1071.2981.2980.0000.0000.0000.000
7A8PHE00.0070.00714.0920.6270.6270.0000.0000.0000.000
8A9ALA00.012-0.00517.6970.1150.1150.0000.0000.0000.000
9A10PHE0-0.012-0.00221.3120.0150.0150.0000.0000.0000.000
10A11GLN00.0290.02623.8220.0680.0680.0000.0000.0000.000
11A12ALA0-0.007-0.01326.8200.1140.1140.0000.0000.0000.000
12A13GLU-1-0.847-0.94829.937-9.268-9.2680.0000.0000.0000.000
13A14ILE00.0000.01525.9390.2450.2450.0000.0000.0000.000
14A15ASN00.017-0.00326.365-0.124-0.1240.0000.0000.0000.000
15A16GLN0-0.013-0.00529.3280.3680.3680.0000.0000.0000.000
16A17LEU00.0190.00830.1270.1920.1920.0000.0000.0000.000
17A18LEU00.0090.00725.8590.1530.1530.0000.0000.0000.000
18A19SER0-0.026-0.00730.4220.2020.2020.0000.0000.0000.000
19A20LEU00.004-0.00833.1620.1810.1810.0000.0000.0000.000
20A21ILE0-0.016-0.01031.3880.2470.2470.0000.0000.0000.000
21A22ILE0-0.025-0.01828.7630.1210.1210.0000.0000.0000.000
22A23ASN0-0.051-0.02733.3600.0360.0360.0000.0000.0000.000
23A24THR0-0.0060.00536.3260.3290.3290.0000.0000.0000.000
24A25PHE0-0.030-0.02038.316-0.117-0.1170.0000.0000.0000.000
25A26TYR0-0.0040.00236.8170.3270.3270.0000.0000.0000.000
26A27SER0-0.015-0.01140.362-0.122-0.1220.0000.0000.0000.000
27A28ASN0-0.020-0.01240.853-0.155-0.1550.0000.0000.0000.000
28A29LYS10.9560.97135.4848.7918.7910.0000.0000.0000.000
29A30GLU-1-0.811-0.90735.960-7.861-7.8610.0000.0000.0000.000
30A31ILE0-0.0070.00435.861-0.104-0.1040.0000.0000.0000.000
31A32PHE00.0500.02430.414-0.050-0.0500.0000.0000.0000.000
32A33LEU00.0080.02031.887-0.213-0.2130.0000.0000.0000.000
33A34ARG10.8090.89033.0718.1518.1510.0000.0000.0000.000
34A35GLU-1-0.739-0.85832.319-8.842-8.8420.0000.0000.0000.000
35A36LEU0-0.051-0.02327.177-0.248-0.2480.0000.0000.0000.000
36A37ILE00.0210.00830.023-0.171-0.1710.0000.0000.0000.000
37A38SER0-0.0180.00232.4400.1520.1520.0000.0000.0000.000
38A39ASN0-0.030-0.01628.2170.1610.1610.0000.0000.0000.000
39A40SER0-0.012-0.02327.076-0.199-0.1990.0000.0000.0000.000
40A41SER0-0.0020.00029.1430.0550.0550.0000.0000.0000.000
41A42ASP-1-0.890-0.94330.822-9.335-9.3350.0000.0000.0000.000
42A43ALA0-0.026-0.00826.534-0.034-0.0340.0000.0000.0000.000
43A44LEU0-0.0160.00128.603-0.131-0.1310.0000.0000.0000.000
44A45ASP-1-0.818-0.89430.647-8.595-8.5950.0000.0000.0000.000
45A46LYS0-0.086-0.04129.0060.2910.2910.0000.0000.0000.000
46A47ILE00.0440.01526.6450.1090.1090.0000.0000.0000.000
47A48ARG10.9430.98429.8038.4948.4940.0000.0000.0000.000
48A49PHE0-0.049-0.00533.3260.3040.3040.0000.0000.0000.000
49A50GLU-1-0.826-0.91727.855-10.777-10.7770.0000.0000.0000.000
50A51SER0-0.062-0.02931.9920.1470.1470.0000.0000.0000.000
51A52LEU0-0.063-0.03033.0190.2880.2880.0000.0000.0000.000
52A53THR0-0.047-0.02832.6870.1980.1980.0000.0000.0000.000
53A54ASP-1-0.852-0.93629.004-10.266-10.2660.0000.0000.0000.000
54A55LYS10.8410.91331.7478.4388.4380.0000.0000.0000.000
55A56SER00.0100.01126.762-0.159-0.1590.0000.0000.0000.000
56A57LYS10.8630.95625.13111.15511.1550.0000.0000.0000.000
57A58LEU00.0240.00126.893-0.286-0.2860.0000.0000.0000.000
58A59ASP-1-0.887-0.95428.027-10.188-10.1880.0000.0000.0000.000
59A60ALA0-0.054-0.01223.224-0.102-0.1020.0000.0000.0000.000
60A61GLN0-0.005-0.01423.4800.0830.0830.0000.0000.0000.000
61A62PRO0-0.0220.00726.9330.1900.1900.0000.0000.0000.000
62A63GLU-1-0.952-0.97530.106-9.328-9.3280.0000.0000.0000.000
63A64LEU0-0.030-0.00430.066-0.308-0.3080.0000.0000.0000.000
64A65PHE00.0060.00326.3250.3510.3510.0000.0000.0000.000
65A66ILE00.0390.01329.720-0.329-0.3290.0000.0000.0000.000
66A67HIS00.0140.01427.9010.5010.5010.0000.0000.0000.000
67A68ILE00.006-0.00628.553-0.326-0.3260.0000.0000.0000.000
68A69VAL00.012-0.01126.9270.2910.2910.0000.0000.0000.000
69A70PRO0-0.0210.00527.711-0.361-0.3610.0000.0000.0000.000
70A71ASP-1-0.762-0.85225.439-11.963-11.9630.0000.0000.0000.000
71A72LYS10.8210.88528.2088.8998.8990.0000.0000.0000.000
72A73ALA0-0.0270.00526.2580.1150.1150.0000.0000.0000.000
73A74SER0-0.084-0.07723.022-0.206-0.2060.0000.0000.0000.000
74A75ASN00.0180.00224.874-0.054-0.0540.0000.0000.0000.000
75A76THR0-0.030-0.01422.5500.0340.0340.0000.0000.0000.000
76A77LEU0-0.011-0.00425.9810.4330.4330.0000.0000.0000.000
77A78SER0-0.027-0.01224.007-0.618-0.6180.0000.0000.0000.000
78A79ILE0-0.016-0.01425.2150.5780.5780.0000.0000.0000.000
79A80ILE0-0.022-0.01523.346-0.597-0.5970.0000.0000.0000.000
80A81ASP-1-0.759-0.85824.853-11.487-11.4870.0000.0000.0000.000
81A82SER00.005-0.00224.549-0.483-0.4830.0000.0000.0000.000
82A83GLY00.0430.00325.9760.2720.2720.0000.0000.0000.000
83A84VAL0-0.009-0.01723.992-0.301-0.3010.0000.0000.0000.000
84A85GLY00.0020.01621.261-0.435-0.4350.0000.0000.0000.000
85A86MET0-0.046-0.03219.5690.5520.5520.0000.0000.0000.000
86A87THR0-0.038-0.04417.537-0.946-0.9460.0000.0000.0000.000
87A88LYS10.8830.93210.43824.77324.7730.0000.0000.0000.000
88A89SER00.013-0.00115.392-0.153-0.1530.0000.0000.0000.000
89A90ASP-1-0.810-0.87618.450-13.677-13.6770.0000.0000.0000.000
90A91LEU00.0060.00115.0330.3750.3750.0000.0000.0000.000
91A92VAL0-0.040-0.02215.8710.3700.3700.0000.0000.0000.000
92A93ASN0-0.068-0.03418.6960.4880.4880.0000.0000.0000.000
93A94ASN00.0700.02522.2450.4630.4630.0000.0000.0000.000
94A95LEU00.0100.03219.8970.6530.6530.0000.0000.0000.000
95A96GLY00.0240.03921.6420.5420.5420.0000.0000.0000.000
96A97THR0-0.030-0.02822.4240.2170.2170.0000.0000.0000.000
97A98ILE00.0200.02125.1060.3900.3900.0000.0000.0000.000
98A99ALA00.0440.03327.939-0.031-0.0310.0000.0000.0000.000
99A100ARG10.8200.89225.97411.30611.3060.0000.0000.0000.000
100A101SER0-0.0090.00232.3830.3040.3040.0000.0000.0000.000
101A102GLY0-0.0020.00235.1770.1980.1980.0000.0000.0000.000
102A103THR00.013-0.00135.828-0.187-0.1870.0000.0000.0000.000
103A104LYS10.8900.93235.3178.4988.4980.0000.0000.0000.000
104A105GLU0-0.090-0.08736.9590.0480.0480.0000.0000.0000.000
105A106PHE0-0.049-0.01338.6160.2200.2200.0000.0000.0000.000
106A107MET0-0.047-0.01638.4810.0600.0600.0000.0000.0000.000
107A108GLU-1-0.798-0.83439.799-7.969-7.9690.0000.0000.0000.000
108A109ALA00.0030.00141.7330.1900.1900.0000.0000.0000.000
109A110LEU0-0.043-0.02943.769-0.034-0.0340.0000.0000.0000.000
110A111ALA00.0480.03144.4900.0310.0310.0000.0000.0000.000
111A112ALA0-0.061-0.02146.6320.1050.1050.0000.0000.0000.000
112A113GLY00.0250.01544.8540.0310.0310.0000.0000.0000.000
113A114ALA0-0.024-0.01441.218-0.003-0.0030.0000.0000.0000.000
114A115ASP-1-0.891-0.94542.489-7.233-7.2330.0000.0000.0000.000
115A116VAL0-0.051-0.02841.8020.1790.1790.0000.0000.0000.000
116A117SER0-0.034-0.02345.0290.1060.1060.0000.0000.0000.000
117A118MET0-0.058-0.01046.7800.1680.1680.0000.0000.0000.000
118A119ILE00.038-0.00240.761-0.149-0.1490.0000.0000.0000.000
119A120GLY00.0340.02743.8640.1620.1620.0000.0000.0000.000
120A121GLN0-0.041-0.03241.474-0.131-0.1310.0000.0000.0000.000
121A122PHE0-0.020-0.00939.585-0.075-0.0750.0000.0000.0000.000
122A123GLY00.0490.02436.969-0.053-0.0530.0000.0000.0000.000
123A124VAL0-0.077-0.03332.7860.0800.0800.0000.0000.0000.000
124A125GLY00.0270.00831.311-0.272-0.2720.0000.0000.0000.000
125A126PHE00.0040.00022.4610.1560.1560.0000.0000.0000.000
126A127TYR00.010-0.02624.334-0.174-0.1740.0000.0000.0000.000
127A128SER00.005-0.00528.5330.0250.0250.0000.0000.0000.000
128A129ALA00.0400.01526.8640.1860.1860.0000.0000.0000.000
129A130TYR00.015-0.01622.2260.0630.0630.0000.0000.0000.000
130A131LEU0-0.0220.00828.8560.1580.1580.0000.0000.0000.000
131A132VAL0-0.036-0.01929.9680.2220.2220.0000.0000.0000.000
132A133ALA00.0290.02526.1590.0240.0240.0000.0000.0000.000
133A134GLU-1-0.923-0.96924.612-12.341-12.3410.0000.0000.0000.000
134A135ARG10.8140.89816.99016.43316.4330.0000.0000.0000.000
135A136VAL0-0.017-0.00821.7580.3340.3340.0000.0000.0000.000
136A137VAL00.0240.00715.955-0.633-0.6330.0000.0000.0000.000
137A138VAL0-0.023-0.01117.6640.8180.8180.0000.0000.0000.000
138A139THR00.0050.01314.566-1.257-1.2570.0000.0000.0000.000
139A140THR0-0.021-0.01715.8901.1641.1640.0000.0000.0000.000
140A141LYS10.8770.94515.77115.09115.0910.0000.0000.0000.000
141A142HIS00.0220.04217.7781.1681.1680.0000.0000.0000.000
142A143ASN00.023-0.01419.490-0.109-0.1090.0000.0000.0000.000
143A144ASP-1-0.915-0.96320.144-13.125-13.1250.0000.0000.0000.000
144A145ASP-1-0.816-0.89314.257-19.689-19.6890.0000.0000.0000.000
145A146GLU-1-0.839-0.91810.138-26.526-26.5260.0000.0000.0000.000
146A147GLN0-0.003-0.00812.7282.2682.2680.0000.0000.0000.000
147A148TYR0-0.001-0.00210.246-3.237-3.2370.0000.0000.0000.000
148A149VAL00.0220.00911.5421.6021.6020.0000.0000.0000.000
149A150TRP0-0.0030.00412.742-1.096-1.0960.0000.0000.0000.000
150A151GLU-1-0.823-0.90214.822-19.156-19.1560.0000.0000.0000.000
151A152SER0-0.014-0.03116.7120.0140.0140.0000.0000.0000.000
152A153GLN0-0.0030.00819.6420.7580.7580.0000.0000.0000.000
153A154ALA00.0510.02922.5980.5500.5500.0000.0000.0000.000
154A155GLY00.0110.01923.5640.4590.4590.0000.0000.0000.000
155A156GLY0-0.017-0.01123.641-0.321-0.3210.0000.0000.0000.000
156A157SER0-0.056-0.02818.883-0.311-0.3110.0000.0000.0000.000
157A158PHE0-0.0010.02317.0620.4690.4690.0000.0000.0000.000
158A159THR0-0.031-0.00512.496-1.055-1.0550.0000.0000.0000.000
159A160VAL00.0290.00212.4451.1141.1140.0000.0000.0000.000
160A161THR0-0.0080.0046.882-2.593-2.5930.0000.0000.0000.000
161A162ARG10.7850.8874.85038.91338.9130.0000.0000.0000.000
162A163ASP-1-0.877-0.9506.637-30.259-30.2590.0000.0000.0000.000
163A164THR0-0.020-0.0027.0111.4241.4240.0000.0000.0000.000
164A165SER0-0.057-0.0397.841-1.087-1.0870.0000.0000.0000.000
165A166GLY00.0190.0169.8390.7080.7080.0000.0000.0000.000
166A167GLU-1-0.953-0.97413.111-15.333-15.3330.0000.0000.0000.000
167A168GLN0-0.046-0.04312.023-0.594-0.5940.0000.0000.0000.000
168A169LEU00.0150.01416.5630.7650.7650.0000.0000.0000.000
169A170GLY0-0.0130.00918.5010.7460.7460.0000.0000.0000.000
170A171ARG10.6870.80920.09211.35411.3540.0000.0000.0000.000
171A172GLY00.0340.05021.6770.3050.3050.0000.0000.0000.000
172A173THR0-0.016-0.02520.530-1.127-1.1270.0000.0000.0000.000
173A174LYS10.9751.00018.63816.12116.1210.0000.0000.0000.000
174A175ILE00.0000.00620.114-0.779-0.7790.0000.0000.0000.000
175A176THR0-0.012-0.01020.2800.4520.4520.0000.0000.0000.000
176A177LEU0-0.011-0.00821.739-0.459-0.4590.0000.0000.0000.000
177A178TYR00.0140.00319.354-0.079-0.0790.0000.0000.0000.000
178A179LEU0-0.039-0.02125.0560.1610.1610.0000.0000.0000.000
179A180LYS10.8920.94728.73910.20810.2080.0000.0000.0000.000
180A181ASP-1-0.869-0.94130.464-10.139-10.1390.0000.0000.0000.000
181A182ASP-1-0.923-0.95432.640-8.948-8.9480.0000.0000.0000.000
182A183GLN0-0.060-0.04732.7010.3100.3100.0000.0000.0000.000
183A184LEU00.0430.01930.671-0.050-0.0500.0000.0000.0000.000
184A185GLU-1-0.813-0.88933.960-8.134-8.1340.0000.0000.0000.000
185A186TYR0-0.057-0.03633.0380.2050.2050.0000.0000.0000.000
186A187LEU00.0460.02329.608-0.214-0.2140.0000.0000.0000.000
187A188GLU-1-0.858-0.90933.440-8.546-8.5460.0000.0000.0000.000
188A189GLU-1-0.876-0.94037.036-7.860-7.8600.0000.0000.0000.000
189A190ARG10.8210.90738.2667.3197.3190.0000.0000.0000.000
190A191ARG10.8100.89138.1278.0308.0300.0000.0000.0000.000
191A192LEU00.0670.02733.1870.0510.0510.0000.0000.0000.000
192A193LYS10.9290.96737.4047.4227.4220.0000.0000.0000.000
193A194ASP-1-0.883-0.94339.914-7.118-7.1180.0000.0000.0000.000
194A195LEU0-0.045-0.03737.7220.1340.1340.0000.0000.0000.000
195A196VAL00.0130.01736.379-0.002-0.0020.0000.0000.0000.000
196A197LYS10.9370.97538.7696.7876.7870.0000.0000.0000.000
197A198LYS10.8730.94041.3957.6457.6450.0000.0000.0000.000
198A199HIS00.008-0.01740.7000.0870.0870.0000.0000.0000.000
199A200SER0-0.039-0.03037.434-0.299-0.2990.0000.0000.0000.000
200A201GLU-1-0.884-0.91038.443-7.479-7.4790.0000.0000.0000.000
201A202PHE0-0.080-0.05040.8290.0240.0240.0000.0000.0000.000
202A203ILE0-0.0090.00835.801-0.033-0.0330.0000.0000.0000.000
203A204SER0-0.009-0.00136.8860.1410.1410.0000.0000.0000.000
204A205TYR0-0.073-0.07234.3320.0560.0560.0000.0000.0000.000
205A206PRO0-0.0120.00134.8210.1080.1080.0000.0000.0000.000
206A207ILE00.0300.01533.913-0.304-0.3040.0000.0000.0000.000
207A208SER0-0.026-0.01832.8240.3660.3660.0000.0000.0000.000
208A209LEU0-0.065-0.01732.731-0.274-0.2740.0000.0000.0000.000
209A210TRP0-0.023-0.00730.7770.3010.3010.0000.0000.0000.000
210A211THR00.025-0.01431.915-0.073-0.0730.0000.0000.0000.000
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