FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 3N5NL

Calculation Name: 2AXO-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AXO

Chain ID: A

ChEMBL ID:

UniProt ID: A9CHH7

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2561166.972845
FMO2-HF: Nuclear repulsion 2476031.400891
FMO2-HF: Total energy -85135.571954
FMO2-MP2: Total energy -85382.676747


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:37:ACE )


Summations of interaction energy for fragment #1(A:37:ACE )
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.
0.4721.271-0.005-0.359-0.434-0.001
Interaction energy analysis for fragmet #1(A:37:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.010
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].
3A39GLN 00.007-0.0013.8421.0141.813-0.005-0.359-0.434-0.001
4A40GLU -1-0.952-0.9606.825-0.171-0.1710.0000.0000.0000.000
5A41ALA 0-0.021-0.0059.948-0.072-0.0720.0000.0000.0000.000
6A42VAL 00.0150.00811.0170.0740.0740.0000.0000.0000.000
7A43LYS 10.9040.94214.3890.2480.2480.0000.0000.0000.000
8A44GLY 0-0.015-0.00917.2870.0290.0290.0000.0000.0000.000
9A45VAL 00.0000.00619.800-0.019-0.0190.0000.0000.0000.000
10A46VAL 00.000-0.00222.4820.0190.0190.0000.0000.0000.000
11A47GLU -1-0.750-0.83525.487-0.119-0.1190.0000.0000.0000.000
12A48LEU 00.0010.00028.4290.0090.0090.0000.0000.0000.000
13A49PHE 0-0.0010.01931.2760.0000.0000.0000.0000.0000.000
14A50THR 00.008-0.03834.3290.0060.0060.0000.0000.0000.000
15A51SER 00.0670.02836.7600.0020.0020.0000.0000.0000.000
16A52GLN 00.0220.02139.403-0.001-0.0010.0000.0000.0000.000
17A53GLY 0-0.015-0.00540.9280.0020.0020.0000.0000.0000.000
18A57CYS 0-0.0480.01037.6550.0010.0010.0000.0000.0000.000
19A55ALA 00.0410.00041.740-0.002-0.0020.0000.0000.0000.000
20A56SER 0-0.032-0.01941.684-0.001-0.0010.0000.0000.0000.000
21A58PRO 00.0550.04636.561-0.005-0.0050.0000.0000.0000.000
22A59PRO 0-0.014-0.01635.571-0.005-0.0050.0000.0000.0000.000
23A60ALA 00.011-0.00533.301-0.004-0.0040.0000.0000.0000.000
24A61ASP -1-0.784-0.88631.800-0.089-0.0890.0000.0000.0000.000
25A62GLU -1-0.965-0.97931.084-0.088-0.0880.0000.0000.0000.000
26A63ALA 0-0.015-0.02029.689-0.008-0.0080.0000.0000.0000.000
27A64LEU 00.0480.01926.090-0.010-0.0100.0000.0000.0000.000
28A65ARG 10.9540.98926.0240.0860.0860.0000.0000.0000.000
29A66LYS 10.8520.92625.6540.0830.0830.0000.0000.0000.000
30A67MET 0-0.0080.01522.973-0.010-0.0100.0000.0000.0000.000
31A68ILE 0-0.013-0.00221.410-0.024-0.0240.0000.0000.0000.000
32A69GLN 0-0.081-0.03921.051-0.014-0.0140.0000.0000.0000.000
33A70LYS 10.8950.94718.6040.1570.1570.0000.0000.0000.000
34A71GLY 00.0260.02117.292-0.030-0.0300.0000.0000.0000.000
35A72ASP -1-0.820-0.88915.856-0.271-0.2710.0000.0000.0000.000
36A73VAL 0-0.027-0.01216.9190.0090.0090.0000.0000.0000.000
37A74VAL 00.0130.01618.289-0.011-0.0110.0000.0000.0000.000
38A75GLY 0-0.005-0.00820.4690.0220.0220.0000.0000.0000.000
39A76LEU 0-0.016-0.00823.874-0.004-0.0040.0000.0000.0000.000
40A77SER 00.0110.01026.9290.0090.0090.0000.0000.0000.000
41A78TYR 0-0.011-0.02628.5460.0000.0000.0000.0000.0000.000
42A79HIS 0-0.023-0.00733.359-0.001-0.0010.0000.0000.0000.000
43A80VAL 00.012-0.00336.7080.0010.0010.0000.0000.0000.000
44A81ASP -1-0.807-0.90339.520-0.052-0.0520.0000.0000.0000.000
45A82TYR 0-0.061-0.03840.3330.0030.0030.0000.0000.0000.000
46A83TRP 0-0.033-0.02742.1610.0030.0030.0000.0000.0000.000
47A84ASN 0-0.053-0.02243.6090.0000.0000.0000.0000.0000.000
48A85TYR 00.0360.00447.1550.0020.0020.0000.0000.0000.000
49A86LEU 0-0.016-0.01850.5770.0010.0010.0000.0000.0000.000
50A87GLY 0-0.0080.01950.8820.0000.0000.0000.0000.0000.000
51A88TRP 0-0.047-0.01144.411-0.002-0.0020.0000.0000.0000.000
52A89THR 0-0.029-0.03645.337-0.001-0.0010.0000.0000.0000.000
53A90ASP -1-0.736-0.88440.024-0.064-0.0640.0000.0000.0000.000
54A91SER 0-0.046-0.02541.0500.0010.0010.0000.0000.0000.000
55A92LEU 0-0.072-0.04435.202-0.002-0.0020.0000.0000.0000.000
56A93ALA 0-0.0090.01537.179-0.004-0.0040.0000.0000.0000.000
57A94SER 00.0080.00137.4340.0010.0010.0000.0000.0000.000
58A95LYS 10.9620.99740.0150.0490.0490.0000.0000.0000.000
59A96GLU -1-0.846-0.93737.164-0.060-0.0600.0000.0000.0000.000
60A97ASN 0-0.029-0.01434.876-0.005-0.0050.0000.0000.0000.000
61A98THR 0-0.045-0.04936.724-0.002-0.0020.0000.0000.0000.000
62A99GLU -1-0.914-0.97139.204-0.053-0.0530.0000.0000.0000.000
63A100ARG 10.8410.92428.6800.1020.1020.0000.0000.0000.000
64A101GLN 00.0140.00535.6570.0010.0010.0000.0000.0000.000
65A102TYR 0-0.039-0.02136.8110.0030.0030.0000.0000.0000.000
66A103GLY 00.0290.01336.7680.0030.0030.0000.0000.0000.000
67A104TYR 0-0.002-0.02828.9280.0020.0020.0000.0000.0000.000
68A105MET 0-0.080-0.01535.5030.0030.0030.0000.0000.0000.000
69A106ARG 10.8460.92038.8390.0530.0530.0000.0000.0000.000
70A107ALA 00.0020.01334.7480.0030.0030.0000.0000.0000.000
71A108LEU 0-0.072-0.04332.8350.0020.0020.0000.0000.0000.000
72A109GLY 0-0.0010.01336.7030.0020.0020.0000.0000.0000.000
73A110ARG 10.8710.94737.7870.0520.0520.0000.0000.0000.000
74A111ASN 00.015-0.00441.5810.0000.0000.0000.0000.0000.000
75A112GLY 00.022-0.00443.0370.0020.0020.0000.0000.0000.000
76A113VAL 0-0.031-0.01040.067-0.002-0.0020.0000.0000.0000.000
77A114TYR 0-0.091-0.05736.8850.0020.0020.0000.0000.0000.000
78A115THR 00.0390.05538.489-0.003-0.0030.0000.0000.0000.000
79A116PRO 0-0.009-0.02035.5470.0030.0030.0000.0000.0000.000
80A117GLN 0-0.009-0.00534.5300.0010.0010.0000.0000.0000.000
81A118ALA 00.0150.01029.704-0.004-0.0040.0000.0000.0000.000
82A119ILE 0-0.022-0.00429.2910.0060.0060.0000.0000.0000.000
83A120LEU 00.012-0.00526.024-0.010-0.0100.0000.0000.0000.000
84A121ASN 00.0640.02821.630-0.005-0.0050.0000.0000.0000.000
85A122GLY 00.0420.02024.8140.0050.0050.0000.0000.0000.000
86A123ARG 10.8710.93824.1700.0940.0940.0000.0000.0000.000
87A124ASP -1-0.803-0.89629.210-0.055-0.0550.0000.0000.0000.000
88A125HIS 0-0.0100.00830.740-0.008-0.0080.0000.0000.0000.000
89A126VAL 00.0260.01830.3050.0040.0040.0000.0000.0000.000
90A127LYS 10.9640.97333.4640.0500.0500.0000.0000.0000.000
91A128GLY 00.0510.02132.526-0.003-0.0030.0000.0000.0000.000
92A129ALA 00.004-0.00731.968-0.005-0.0050.0000.0000.0000.000
93A130ASP -1-0.925-0.93732.422-0.066-0.0660.0000.0000.0000.000
94A131VAL 00.018-0.03127.199-0.003-0.0030.0000.0000.0000.000
95A132ARG 10.9280.95627.6480.0650.0650.0000.0000.0000.000
96A133GLY 00.1030.06428.127-0.002-0.0020.0000.0000.0000.000
97A134ILE 0-0.046-0.01226.546-0.002-0.0020.0000.0000.0000.000
98A135TYR 0-0.058-0.05820.5550.0040.0040.0000.0000.0000.000
99A136ASP -1-0.882-0.93423.707-0.078-0.0780.0000.0000.0000.000
100A137ARG 10.8330.92125.8460.0720.0720.0000.0000.0000.000
101A138LEU 0-0.035-0.02221.4420.0020.0020.0000.0000.0000.000
102A139ASP -1-0.904-0.94720.823-0.093-0.0930.0000.0000.0000.000
103A140ALA 0-0.019-0.01722.1200.0070.0070.0000.0000.0000.000
104A141PHE 0-0.029-0.01922.9610.0070.0070.0000.0000.0000.000
105A142LYS 10.9831.00015.2090.1160.1160.0000.0000.0000.000
106A143ARG 10.8530.93220.0630.0540.0540.0000.0000.0000.000
107A144GLU -1-0.906-0.94221.875-0.025-0.0250.0000.0000.0000.000
108A145GLY 0-0.029-0.00220.1840.0040.0040.0000.0000.0000.000
109A146GLN 0-0.075-0.04721.265-0.005-0.0050.0000.0000.0000.000
110A147GLY 00.0190.00019.109-0.005-0.0050.0000.0000.0000.000
111A148LEU 0-0.054-0.01916.3250.0110.0110.0000.0000.0000.000
112A149ASN 0-0.022-0.02315.698-0.039-0.0390.0000.0000.0000.000
113A150VAL 0-0.0310.00215.9600.0090.0090.0000.0000.0000.000
114A151PRO 0-0.0170.00312.153-0.028-0.0280.0000.0000.0000.000
115A152VAL 00.0380.00414.0640.0440.0440.0000.0000.0000.000
116A153SER 0-0.0070.00212.301-0.106-0.1060.0000.0000.0000.000
117A154SER 00.0140.00614.4350.0620.0620.0000.0000.0000.000
118A155LYS 10.9840.99614.5710.2150.2150.0000.0000.0000.000
119A156PHE 00.0240.00817.4340.0330.0330.0000.0000.0000.000
120A157ALA 0-0.054-0.03119.472-0.012-0.0120.0000.0000.0000.000
121A158GLY 00.0080.00321.2640.0160.0160.0000.0000.0000.000
122A159ASP -1-0.928-0.96123.800-0.093-0.0930.0000.0000.0000.000
123A160GLU -1-0.946-0.98324.491-0.088-0.0880.0000.0000.0000.000
124A161VAL 0-0.069-0.02821.495-0.016-0.0160.0000.0000.0000.000
125A162GLU -1-0.912-0.95517.705-0.149-0.1490.0000.0000.0000.000
126A163ILE 0-0.017-0.01818.651-0.033-0.0330.0000.0000.0000.000
127A164ASP -1-0.834-0.92015.180-0.170-0.1700.0000.0000.0000.000
128A165ILE 0-0.035-0.01916.353-0.037-0.0370.0000.0000.0000.000
129A166GLY 00.0210.00615.8140.0210.0210.0000.0000.0000.000
130A167ALA 0-0.016-0.01616.6690.0110.0110.0000.0000.0000.000
131A168GLY 0-0.014-0.03518.209-0.012-0.0120.0000.0000.0000.000
132A169ASN 0-0.025-0.00720.8800.0140.0140.0000.0000.0000.000
133A170GLY 0-0.0040.00224.522-0.006-0.0060.0000.0000.0000.000
134A171LYS 10.9350.96026.9450.0430.0430.0000.0000.0000.000
135A172ALA 0-0.019-0.00925.162-0.001-0.0010.0000.0000.0000.000
136A173ASP -1-0.864-0.91327.243-0.074-0.0740.0000.0000.0000.000
137A174VAL 0-0.019-0.01723.268-0.011-0.0110.0000.0000.0000.000
138A175VAL 0-0.011-0.00425.6320.0060.0060.0000.0000.0000.000
139A176VAL 00.0080.00524.433-0.017-0.0170.0000.0000.0000.000
140A177ALA 00.0040.01025.8520.0130.0130.0000.0000.0000.000
141A178TYR 0-0.034-0.03826.359-0.017-0.0170.0000.0000.0000.000
142A179PHE 00.0270.01122.9440.0090.0090.0000.0000.0000.000
143A180THR 00.0090.01928.328-0.007-0.0070.0000.0000.0000.000
144A181ARG 10.9450.96422.0250.1900.1900.0000.0000.0000.000
145A182GLU -1-0.906-0.97827.576-0.101-0.1010.0000.0000.0000.000
146A183GLN 00.0370.02530.4370.0000.0000.0000.0000.0000.000
147A184THR 0-0.019-0.01134.1180.0040.0040.0000.0000.0000.000
148A185VAL 00.0040.00537.1160.0020.0020.0000.0000.0000.000
149A186ASP -1-0.886-0.94940.371-0.054-0.0540.0000.0000.0000.000
150A187VAL 0-0.077-0.03742.5400.0000.0000.0000.0000.0000.000
151A188NME 00.0180.01444.8250.0010.0010.0000.0000.0000.000
152A194ACE 00.0400.01248.6290.0000.0000.0000.0000.0000.000
153A195LYS 10.9090.94344.0300.0480.0480.0000.0000.0000.000
154A196LYS 10.9560.97740.1750.0610.0610.0000.0000.0000.000
155A197MET 0-0.0140.01338.2820.0010.0010.0000.0000.0000.000
156A198SER 0-0.034-0.01333.049-0.002-0.0020.0000.0000.0000.000
157A199TYR 00.0160.01833.0120.0010.0010.0000.0000.0000.000
158A200TRP 00.013-0.01126.178-0.007-0.0070.0000.0000.0000.000
159A201HIS 0-0.010-0.01722.173-0.003-0.0030.0000.0000.0000.000
160A202SER 00.0060.01227.8500.0000.0000.0000.0000.0000.000
161A203VAL 0-0.016-0.02328.779-0.001-0.0010.0000.0000.0000.000
162A204TYR 0-0.039-0.01830.3770.0100.0100.0000.0000.0000.000
163A205ASP -1-0.871-0.95132.215-0.080-0.0800.0000.0000.0000.000
164A206VAL 00.0030.01429.980-0.010-0.0100.0000.0000.0000.000
165A207GLN 00.0210.01829.9130.0030.0030.0000.0000.0000.000
166A208THR 00.0270.01229.328-0.010-0.0100.0000.0000.0000.000
167A209VAL 0-0.038-0.01926.7570.0050.0050.0000.0000.0000.000
168A210GLY 00.0340.01927.8260.0030.0030.0000.0000.0000.000
169A211MET 0-0.032-0.01128.442-0.001-0.0010.0000.0000.0000.000
170A212TRP 00.0370.02620.6550.0030.0030.0000.0000.0000.000
171A213ASP -1-0.882-0.94925.761-0.048-0.0480.0000.0000.0000.000
172A214GLY 00.0120.01423.3130.0080.0080.0000.0000.0000.000
173A215SER 0-0.019-0.02522.1360.0040.0040.0000.0000.0000.000
174A216PRO 0-0.078-0.03718.095-0.010-0.0100.0000.0000.0000.000
175A217MET 0-0.0340.00119.7650.0120.0120.0000.0000.0000.000
176A218THR 00.0260.01418.572-0.011-0.0110.0000.0000.0000.000
177A219VAL 0-0.059-0.02520.9620.0160.0160.0000.0000.0000.000
178A220LYS 10.9380.96821.6580.0900.0900.0000.0000.0000.000
179A221LEU 0-0.009-0.00424.7090.0100.0100.0000.0000.0000.000
180A222PRO 00.0820.03326.569-0.003-0.0030.0000.0000.0000.000
181A223ALA 00.1270.05528.658-0.006-0.0060.0000.0000.0000.000
182A224SER 0-0.053-0.02830.073-0.005-0.0050.0000.0000.0000.000
183A225VAL 00.0300.00526.394-0.001-0.0010.0000.0000.0000.000
184A226VAL 00.0210.03525.313-0.008-0.0080.0000.0000.0000.000
185A227ALA 0-0.014-0.01427.168-0.005-0.0050.0000.0000.0000.000
186A228LYS 10.8540.93929.5390.0960.0960.0000.0000.0000.000
187A229VAL 00.0240.01523.050-0.001-0.0010.0000.0000.0000.000
188A230LYS 10.8710.92423.6730.1520.1520.0000.0000.0000.000
189A231LYS 10.8510.95427.3540.0930.0930.0000.0000.0000.000
190A232GLY 0-0.041-0.04327.3930.0070.0070.0000.0000.0000.000
191A233GLY 00.0090.02423.953-0.016-0.0160.0000.0000.0000.000
192A234CYS 0-0.044-0.00822.9760.0130.0130.0000.0000.0000.000
193A235ALA 00.0220.01621.561-0.025-0.0250.0000.0000.0000.000
194A236VAL 00.0030.00219.9470.0210.0210.0000.0000.0000.000
195A237LEU 0-0.023-0.03120.947-0.019-0.0190.0000.0000.0000.000
196A238LEU 00.0130.01820.4610.0120.0120.0000.0000.0000.000
197A239GLN 0-0.048-0.03723.034-0.001-0.0010.0000.0000.0000.000
198A240THR 0-0.012-0.00426.0980.0090.0090.0000.0000.0000.000
199A241ALA 00.0540.01928.462-0.002-0.0020.0000.0000.0000.000
200A242ASN 00.0270.01832.1940.0030.0030.0000.0000.0000.000
201A243ALA 00.013-0.01434.9590.0000.0000.0000.0000.0000.000
202A244SER 0-0.051-0.02438.1830.0020.0020.0000.0000.0000.000
203A245GLY 00.0100.02036.1710.0000.0000.0000.0000.0000.000
204A246ASP -1-0.864-0.91835.910-0.055-0.0550.0000.0000.0000.000
205A247PRO 0-0.048-0.01931.493-0.001-0.0010.0000.0000.0000.000
206A248ALA 00.0310.01030.5310.0030.0030.0000.0000.0000.000
207A249ALA 0-0.011-0.00625.920-0.007-0.0070.0000.0000.0000.000
208A250ILE 00.0100.01921.9710.0010.0010.0000.0000.0000.000
209A251VAL 0-0.014-0.01521.202-0.004-0.0040.0000.0000.0000.000
210A252GLY 00.0460.02218.055-0.009-0.0090.0000.0000.0000.000
211A253ALA 0-0.029-0.02117.3360.0220.0220.0000.0000.0000.000
212A254SER 0-0.0010.01416.063-0.064-0.0640.0000.0000.0000.000
213A255ILE 0-0.0060.00416.8880.0490.0490.0000.0000.0000.000
214A256LEU 0-0.0210.02017.247-0.040-0.0400.0000.0000.0000.000
215A257LEU 0-0.003-0.02119.1680.0370.0370.0000.0000.0000.000
216A258GLY 00.0650.02521.014-0.002-0.0020.0000.0000.0000.000
217A259ASN 0-0.0540.00422.3200.0120.0120.0000.0000.0000.000
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