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: LG7Q9

Calculation Name: 3N2N-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion

Ligand 3-letter code: ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3N2N

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H6X2

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2164234.270235
FMO2-HF: Nuclear repulsion 2089559.191703
FMO2-HF: Total energy -74675.078532
FMO2-MP2: Total energy -74893.42207


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:36:SER)


Summations of interaction energy for fragment #1(A:36: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.
-38.536-34.0591.659-2.586-3.5520.006
Interaction energy analysis for fragmet #1(A:36:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.889 / q_NPA : 0.930
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].
3A38ALA00.0110.0262.3490.3233.8591.639-2.204-2.9720.008
4A220CYS-1-0.901-0.9274.144-27.225-27.0610.004-0.053-0.1150.000
105A140ARG10.8260.9023.78846.39146.9230.017-0.219-0.331-0.002
183A218LYS10.8320.9474.07555.46255.707-0.001-0.110-0.1340.000
5A40TYR0-0.017-0.0125.885-6.738-6.7380.0000.0000.0000.000
6A41GLY00.0260.0078.9621.8391.8390.0000.0000.0000.000
7A42GLY00.0420.02711.7901.7871.7870.0000.0000.0000.000
8A43PHE0-0.017-0.01112.187-2.374-2.3740.0000.0000.0000.000
9A44ASP-1-0.780-0.86514.268-17.170-17.1700.0000.0000.0000.000
10A45LEU0-0.006-0.00716.349-0.690-0.6900.0000.0000.0000.000
11A46TYR00.025-0.00716.9951.4531.4530.0000.0000.0000.000
12A47PHE00.0370.01120.688-0.318-0.3180.0000.0000.0000.000
13A48ILE0-0.013-0.00222.1210.4750.4750.0000.0000.0000.000
14A49LEU0-0.030-0.02025.146-0.040-0.0400.0000.0000.0000.000
15A50ASP-1-0.748-0.83428.419-9.644-9.6440.0000.0000.0000.000
16A51LYS10.9530.97131.0739.0029.0020.0000.0000.0000.000
17A52SER00.017-0.02134.4910.3860.3860.0000.0000.0000.000
18A53GLY0-0.049-0.02936.4390.0780.0780.0000.0000.0000.000
19A54SER0-0.035-0.01735.5970.1830.1830.0000.0000.0000.000
20A55VAL00.0220.00933.0580.0850.0850.0000.0000.0000.000
21A56LEU0-0.0200.00136.491-0.009-0.0090.0000.0000.0000.000
22A57HIS0-0.019-0.02239.6390.0130.0130.0000.0000.0000.000
23A58HIS0-0.034-0.03634.8450.2000.2000.0000.0000.0000.000
24A59TRP00.0230.01631.676-0.393-0.3930.0000.0000.0000.000
25A60ASN00.016-0.00234.245-0.259-0.2590.0000.0000.0000.000
26A61GLU-1-0.892-0.93532.262-9.547-9.5470.0000.0000.0000.000
27A62ILE0-0.014-0.01129.360-0.386-0.3860.0000.0000.0000.000
28A63TYR0-0.069-0.05629.584-0.394-0.3940.0000.0000.0000.000
29A64TYR00.0110.00530.586-0.311-0.3110.0000.0000.0000.000
30A65PHE00.0150.01023.083-0.351-0.3510.0000.0000.0000.000
31A66VAL0-0.009-0.00725.967-0.530-0.5300.0000.0000.0000.000
32A67GLU-1-0.855-0.90326.877-9.735-9.7350.0000.0000.0000.000
33A68GLN0-0.017-0.01027.770-0.260-0.2600.0000.0000.0000.000
34A69LEU0-0.039-0.02221.718-0.323-0.3230.0000.0000.0000.000
35A70ALA00.009-0.00124.216-0.371-0.3710.0000.0000.0000.000
36A71HIS0-0.031-0.01525.8930.0160.0160.0000.0000.0000.000
37A72LYS10.8500.93023.08713.33513.3350.0000.0000.0000.000
38A73PHE0-0.076-0.03720.407-0.441-0.4410.0000.0000.0000.000
39A74ILE00.0610.02723.267-0.213-0.2130.0000.0000.0000.000
40A75SER0-0.038-0.01920.0270.3430.3430.0000.0000.0000.000
41A76PRO00.0590.01721.360-0.498-0.4980.0000.0000.0000.000
42A77GLN00.0070.01216.6080.2030.2030.0000.0000.0000.000
43A78LEU0-0.076-0.01816.719-1.133-1.1330.0000.0000.0000.000
44A79ARG10.8060.86617.01317.30717.3070.0000.0000.0000.000
45A80MET0-0.003-0.00419.359-0.530-0.5300.0000.0000.0000.000
46A81SER0-0.036-0.02521.8210.4370.4370.0000.0000.0000.000
47A82PHE00.0090.00223.945-0.301-0.3010.0000.0000.0000.000
48A83ILE0-0.030-0.01023.9260.3440.3440.0000.0000.0000.000
49A84VAL00.0190.01527.703-0.051-0.0510.0000.0000.0000.000
50A85PHE00.001-0.00927.9800.0190.0190.0000.0000.0000.000
51A86SER00.005-0.00631.9640.0410.0410.0000.0000.0000.000
52A87THR0-0.023-0.02934.822-0.126-0.1260.0000.0000.0000.000
53A88ARG10.9060.96534.5898.7968.7960.0000.0000.0000.000
54A89GLY00.0550.02130.641-0.033-0.0330.0000.0000.0000.000
55A90THR0-0.069-0.04931.2210.1570.1570.0000.0000.0000.000
56A91THR00.003-0.00326.798-0.037-0.0370.0000.0000.0000.000
57A92LEU0-0.0260.01229.3270.1590.1590.0000.0000.0000.000
58A93MET00.0150.03025.8570.3240.3240.0000.0000.0000.000
59A94LYS10.9500.97626.32611.10311.1030.0000.0000.0000.000
60A95LEU0-0.031-0.00118.7210.1010.1010.0000.0000.0000.000
61A96THR0-0.013-0.00123.1910.1100.1100.0000.0000.0000.000
62A97GLU-1-0.897-0.95121.720-13.030-13.0300.0000.0000.0000.000
63A98ASP-1-0.790-0.89023.405-10.270-10.2700.0000.0000.0000.000
64A99ARG10.8190.86722.00613.29113.2910.0000.0000.0000.000
65A100GLU-1-0.808-0.84628.745-8.849-8.8490.0000.0000.0000.000
66A101GLN0-0.043-0.02829.0870.1990.1990.0000.0000.0000.000
67A102ILE0-0.008-0.00924.6940.0500.0500.0000.0000.0000.000
68A103ARG10.7520.83529.1168.8548.8540.0000.0000.0000.000
69A104GLN00.000-0.00332.5700.1200.1200.0000.0000.0000.000
70A105GLY00.0550.01830.9050.1510.1510.0000.0000.0000.000
71A106LEU0-0.014-0.00629.258-0.014-0.0140.0000.0000.0000.000
72A107GLU-1-0.833-0.90832.603-8.326-8.3260.0000.0000.0000.000
73A108GLU-1-1.037-1.02634.593-8.658-8.6580.0000.0000.0000.000
74A109LEU0-0.010-0.00929.2520.1390.1390.0000.0000.0000.000
75A110GLN0-0.007-0.00533.9950.2400.2400.0000.0000.0000.000
76A111LYS10.8770.94736.5388.3738.3730.0000.0000.0000.000
77A112VAL0-0.054-0.01234.4950.1820.1820.0000.0000.0000.000
78A113LEU0-0.0030.00137.7540.0810.0810.0000.0000.0000.000
79A114PRO0-0.034-0.01537.247-0.051-0.0510.0000.0000.0000.000
80A115GLY00.0040.00338.6090.2900.2900.0000.0000.0000.000
81A116GLY0-0.0270.00739.120-0.149-0.1490.0000.0000.0000.000
82A117ASP-1-0.883-0.92537.590-8.123-8.1230.0000.0000.0000.000
83A118THR00.0500.01332.085-0.018-0.0180.0000.0000.0000.000
84A119TYR00.005-0.00332.582-0.214-0.2140.0000.0000.0000.000
85A120MET0-0.0070.00825.914-0.247-0.2470.0000.0000.0000.000
86A121HIS0-0.027-0.02326.887-0.155-0.1550.0000.0000.0000.000
87A122GLU-1-0.804-0.88627.074-9.930-9.9300.0000.0000.0000.000
88A123GLY0-0.006-0.01127.185-0.095-0.0950.0000.0000.0000.000
89A124PHE00.0350.00320.045-0.446-0.4460.0000.0000.0000.000
90A125GLU-1-0.830-0.89423.192-11.459-11.4590.0000.0000.0000.000
91A126ARG10.7610.85524.87810.60210.6020.0000.0000.0000.000
92A127ALA00.0120.01820.775-0.149-0.1490.0000.0000.0000.000
93A128SER00.000-0.01320.383-0.700-0.7000.0000.0000.0000.000
94A129GLU-1-0.859-0.91821.189-11.795-11.7950.0000.0000.0000.000
95A130GLN0-0.087-0.04621.7590.3080.3080.0000.0000.0000.000
96A131ILE00.0570.03115.682-0.193-0.1930.0000.0000.0000.000
97A132TYR0-0.015-0.00617.550-0.414-0.4140.0000.0000.0000.000
98A133TYR0-0.054-0.02619.6490.1570.1570.0000.0000.0000.000
99A134GLU-1-0.776-0.89316.756-15.441-15.4410.0000.0000.0000.000
100A135ASN0-0.016-0.01414.171-1.027-1.0270.0000.0000.0000.000
101A136ARG10.8610.93715.78913.30113.3010.0000.0000.0000.000
102A137GLN0-0.056-0.01617.2410.8080.8080.0000.0000.0000.000
103A138GLY0-0.029-0.00814.5330.0510.0510.0000.0000.0000.000
104A139TYR0-0.0060.00212.664-1.468-1.4680.0000.0000.0000.000
106A141THR00.0260.0129.286-1.183-1.1830.0000.0000.0000.000
107A142ALA0-0.031-0.0169.454-2.732-2.7320.0000.0000.0000.000
108A143SER00.0280.02210.6642.7542.7540.0000.0000.0000.000
109A144VAL0-0.033-0.01612.395-1.261-1.2610.0000.0000.0000.000
110A145ILE00.0210.01514.7881.2021.2020.0000.0000.0000.000
111A146ILE0-0.026-0.01117.872-0.523-0.5230.0000.0000.0000.000
112A147ALA00.0090.00720.4630.5820.5820.0000.0000.0000.000
113A148LEU0-0.025-0.00123.478-0.001-0.0010.0000.0000.0000.000
114A149THR00.013-0.03926.5940.2940.2940.0000.0000.0000.000
115A150ASP-1-0.726-0.83829.202-9.532-9.5320.0000.0000.0000.000
116A151GLY0-0.024-0.01529.849-0.054-0.0540.0000.0000.0000.000
117A152GLU-1-0.901-0.94230.534-8.570-8.5700.0000.0000.0000.000
118A153LEU0-0.067-0.03429.3760.1390.1390.0000.0000.0000.000
119A154HIS00.0320.00633.394-0.043-0.0430.0000.0000.0000.000
120A155GLU-1-0.908-0.95633.996-9.115-9.1150.0000.0000.0000.000
121A156ASP-1-0.890-0.94832.887-9.167-9.1670.0000.0000.0000.000
122A157LEU0-0.023-0.00932.350-0.302-0.3020.0000.0000.0000.000
123A158PHE0-0.0010.01726.593-0.479-0.4790.0000.0000.0000.000
124A159PHE00.0120.01528.163-0.540-0.5400.0000.0000.0000.000
125A160TYR0-0.011-0.01627.870-0.458-0.4580.0000.0000.0000.000
126A161SER00.001-0.02926.400-0.397-0.3970.0000.0000.0000.000
127A162GLU-1-0.908-0.95423.389-13.373-13.3730.0000.0000.0000.000
128A163ARG10.8840.95522.84110.50110.5010.0000.0000.0000.000
129A164GLU-1-0.871-0.95622.906-13.210-13.2100.0000.0000.0000.000
130A165ALA00.0050.01520.274-0.644-0.6440.0000.0000.0000.000
131A166ASN00.0190.01418.666-1.746-1.7460.0000.0000.0000.000
132A167ARG10.9210.96718.35114.90414.9040.0000.0000.0000.000
133A168SER00.018-0.00217.935-0.430-0.4300.0000.0000.0000.000
134A169ARG10.8020.88914.34916.83916.8390.0000.0000.0000.000
135A170ASP-1-0.946-0.96813.850-19.470-19.4700.0000.0000.0000.000
136A171LEU0-0.157-0.07015.676-0.026-0.0260.0000.0000.0000.000
137A172GLY0-0.0010.00511.609-0.421-0.4210.0000.0000.0000.000
138A173ALA0-0.054-0.02711.227-1.750-1.7500.0000.0000.0000.000
139A174ILE0-0.040-0.0138.317-0.423-0.4230.0000.0000.0000.000
140A175VAL00.0070.00012.6641.2051.2050.0000.0000.0000.000
141A176TYR0-0.026-0.01813.006-0.926-0.9260.0000.0000.0000.000
142A177ALA0-0.0170.00418.2400.5300.5300.0000.0000.0000.000
143A178VAL0-0.033-0.02222.021-0.202-0.2020.0000.0000.0000.000
144A179GLY00.0680.03224.6130.3290.3290.0000.0000.0000.000
145A180VAL0-0.026-0.01627.9340.0860.0860.0000.0000.0000.000
146A181LYS10.7580.85531.3258.7448.7440.0000.0000.0000.000
147A182ASP-1-0.939-0.96133.210-9.146-9.1460.0000.0000.0000.000
148A183PHE00.0130.03526.787-0.051-0.0510.0000.0000.0000.000
149A184ASN00.028-0.00329.872-0.411-0.4110.0000.0000.0000.000
150A185GLU-1-0.884-0.95424.673-12.959-12.9590.0000.0000.0000.000
151A186THR0-0.035-0.03125.256-0.501-0.5010.0000.0000.0000.000
152A187GLN0-0.0260.00026.103-0.393-0.3930.0000.0000.0000.000
153A188LEU00.0510.01724.342-0.343-0.3430.0000.0000.0000.000
154A189ALA0-0.049-0.02521.470-0.643-0.6430.0000.0000.0000.000
155A190ARG10.9100.97821.11011.64511.6450.0000.0000.0000.000
156A191ILE0-0.0150.00821.691-0.321-0.3210.0000.0000.0000.000
157A192ALA00.0210.00318.548-0.756-0.7560.0000.0000.0000.000
158A193ASP-1-0.806-0.91513.089-22.384-22.3840.0000.0000.0000.000
159A194SER0-0.081-0.06015.864-0.542-0.5420.0000.0000.0000.000
160A195LYS11.0441.01617.60015.07515.0750.0000.0000.0000.000
161A196ASP-1-0.865-0.91016.108-17.683-17.6830.0000.0000.0000.000
162A197HIS10.7650.88912.35521.27821.2780.0000.0000.0000.000
163A198VAL00.0220.01617.5680.2510.2510.0000.0000.0000.000
164A199PHE00.0260.01617.730-0.181-0.1810.0000.0000.0000.000
165A200PRO00.0610.03923.5630.2790.2790.0000.0000.0000.000
166A201VAL00.0420.00526.550-0.339-0.3390.0000.0000.0000.000
167A202ASN0-0.046-0.03527.750-0.078-0.0780.0000.0000.0000.000
168A203ASP-1-0.943-0.95924.324-12.884-12.8840.0000.0000.0000.000
169A204GLY00.019-0.00822.687-0.547-0.5470.0000.0000.0000.000
170A205PHE00.0320.02122.209-0.652-0.6520.0000.0000.0000.000
171A206GLN00.0190.00322.731-0.345-0.3450.0000.0000.0000.000
172A207ALA00.0070.01019.379-0.634-0.6340.0000.0000.0000.000
173A208LEU00.021-0.00217.032-1.141-1.1410.0000.0000.0000.000
174A209GLN00.0430.04518.282-0.762-0.7620.0000.0000.0000.000
175A210GLY0-0.015-0.00418.119-0.339-0.3390.0000.0000.0000.000
176A211ILE0-0.020-0.01312.902-1.179-1.1790.0000.0000.0000.000
177A212ILE00.0280.01214.006-1.492-1.4920.0000.0000.0000.000
178A213HIS00.0410.02215.979-0.003-0.0030.0000.0000.0000.000
179A214SER0-0.062-0.02711.984-0.746-0.7460.0000.0000.0000.000
180A215ILE00.004-0.00610.178-1.697-1.6970.0000.0000.0000.000
181A216LEU00.0120.01312.032-0.463-0.4630.0000.0000.0000.000
182A217LYS10.8400.92914.27517.45417.4540.0000.0000.0000.000
184A219SER0-0.003-0.0209.750-2.051-2.0510.0000.0000.0000.000