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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LNKZ9

Calculation Name: 4RAX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RAX

Chain ID: A

ChEMBL ID:

UniProt ID: E2JF22

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2774333.84057
FMO2-HF: Nuclear repulsion 2684417.394529
FMO2-HF: Total energy -89916.446041
FMO2-MP2: Total energy -90180.271506


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:2218:GLY)


Summations of interaction energy for fragment #1(A:2218:GLY)
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.
-2.490.8341.891-2.408-2.806-0.008
Interaction energy analysis for fragmet #1(A:2218:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.007
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].
3A2220VAL00.0400.0253.8030.3621.854-0.012-0.766-0.7140.004
4A2221ASN0-0.023-0.0146.7070.1520.1520.0000.0000.0000.000
5A2222GLN00.0220.0158.7610.1600.1600.0000.0000.0000.000
6A2223PRO0-0.009-0.00712.1010.0240.0240.0000.0000.0000.000
7A2224ILE0-0.032-0.02315.321-0.036-0.0360.0000.0000.0000.000
8A2225ASP-1-0.813-0.88817.786-0.167-0.1670.0000.0000.0000.000
9A2226VAL0-0.0110.00719.2990.0020.0020.0000.0000.0000.000
10A2227THR0-0.0010.00721.6260.0120.0120.0000.0000.0000.000
11A2228VAL0-0.020-0.00824.7330.0120.0120.0000.0000.0000.000
12A2229THR0-0.088-0.06727.0260.0030.0030.0000.0000.0000.000
13A2230LEU00.0500.03230.5200.0040.0040.0000.0000.0000.000
14A2231LYS10.8670.93533.3950.0270.0270.0000.0000.0000.000
15A2232LEU00.0650.03935.8680.0030.0030.0000.0000.0000.000
16A2233GLY00.0550.01839.0760.0000.0000.0000.0000.0000.000
17A2234GLY0-0.045-0.03638.562-0.001-0.0010.0000.0000.0000.000
18A2235TYR0-0.059-0.04240.515-0.002-0.0020.0000.0000.0000.000
19A2236GLU-1-0.868-0.94339.422-0.044-0.0440.0000.0000.0000.000
20A2237PRO0-0.038-0.02034.8980.0000.0000.0000.0000.0000.000
21A2238LEU00.0210.02037.079-0.002-0.0020.0000.0000.0000.000
22A2239PHE00.0180.00430.2930.0000.0000.0000.0000.0000.000
23A2240THR0-0.017-0.01431.4360.0050.0050.0000.0000.0000.000
24A2241MET0-0.0260.01128.125-0.005-0.0050.0000.0000.0000.000
25A2242SER00.007-0.01625.8580.0070.0070.0000.0000.0000.000
26A2243ALA0-0.0150.00723.480-0.002-0.0020.0000.0000.0000.000
27A2244GLN00.023-0.01522.100-0.025-0.0250.0000.0000.0000.000
28A2245GLN0-0.0200.01221.164-0.021-0.0210.0000.0000.0000.000
29A2246PRO0-0.017-0.02222.5170.0190.0190.0000.0000.0000.000
30A2247SER00.0350.00023.4460.0030.0030.0000.0000.0000.000
31A2248ILE0-0.059-0.00817.5490.0180.0180.0000.0000.0000.000
32A2249VAL0-0.016-0.01219.388-0.043-0.0430.0000.0000.0000.000
33A2250PRO00.000-0.00214.9690.0190.0190.0000.0000.0000.000
34A2251PHE00.0160.00415.7290.0600.0600.0000.0000.0000.000
35A2252THR00.0130.01816.515-0.059-0.0590.0000.0000.0000.000
36A2253PRO00.017-0.02517.0200.0170.0170.0000.0000.0000.000
37A2254GLN00.0230.02418.7670.0200.0200.0000.0000.0000.000
38A2255ALA00.0530.03419.7070.0220.0220.0000.0000.0000.000
39A2256TYR0-0.028-0.02114.3550.0220.0220.0000.0000.0000.000
40A2257GLU-1-0.951-0.96518.995-0.119-0.1190.0000.0000.0000.000
41A2258GLU-1-0.910-0.96021.842-0.141-0.1410.0000.0000.0000.000
42A2259LEU0-0.038-0.01418.2690.0200.0200.0000.0000.0000.000
43A2260SER0-0.031-0.04319.8290.0310.0310.0000.0000.0000.000
44A2261GLN0-0.005-0.01121.9980.0190.0190.0000.0000.0000.000
45A2262GLN0-0.064-0.01224.7890.0030.0030.0000.0000.0000.000
46A2263PHE0-0.037-0.03922.6760.0130.0130.0000.0000.0000.000
47A2264ASP-1-0.895-0.94624.7600.0040.0040.0000.0000.0000.000
48A2265PRO0-0.053-0.01825.7150.0130.0130.0000.0000.0000.000
49A2266TYR0-0.012-0.00225.2390.0140.0140.0000.0000.0000.000
50A2267PRO00.0210.00223.7680.0030.0030.0000.0000.0000.000
51A2268LEU00.0030.00821.9040.0130.0130.0000.0000.0000.000
52A2269ALA00.0640.02920.5100.0150.0150.0000.0000.0000.000
53A2270MET00.0200.01919.388-0.008-0.0080.0000.0000.0000.000
54A2271GLN0-0.052-0.03117.8980.0130.0130.0000.0000.0000.000
55A2272PHE00.0000.01115.0810.0350.0350.0000.0000.0000.000
56A2273ILE00.0570.01414.475-0.004-0.0040.0000.0000.0000.000
57A2274SER0-0.083-0.03014.263-0.034-0.0340.0000.0000.0000.000
58A2275GLN0-0.079-0.03910.788-0.027-0.0270.0000.0000.0000.000
59A2276TYR0-0.087-0.0559.4240.0320.0320.0000.0000.0000.000
60A2277SER0-0.009-0.0128.924-0.006-0.0060.0000.0000.0000.000
61A2278PRO00.018-0.01010.958-0.027-0.0270.0000.0000.0000.000
62A2279GLU-1-0.883-0.9477.454-2.289-2.2890.0000.0000.0000.000
63A2280ASP-1-0.791-0.8707.331-1.658-1.6580.0000.0000.0000.000
64A2281ILE0-0.032-0.00610.1420.1480.1480.0000.0000.0000.000
65A2282VAL0-0.0110.00213.822-0.046-0.0460.0000.0000.0000.000
66A2283THR00.000-0.00716.6430.0640.0640.0000.0000.0000.000
67A2284ALA0-0.018-0.00520.346-0.019-0.0190.0000.0000.0000.000
68A2285GLN00.032-0.00421.8480.0410.0410.0000.0000.0000.000
69A2286ILE0-0.031-0.01024.3280.0010.0010.0000.0000.0000.000
70A2287GLU-1-0.817-0.91427.165-0.132-0.1320.0000.0000.0000.000
71A2288GLY00.0640.01730.7270.0050.0050.0000.0000.0000.000
72A2289SER0-0.067-0.03033.1980.0120.0120.0000.0000.0000.000
73A2290SER0-0.005-0.00834.332-0.007-0.0070.0000.0000.0000.000
74A2291GLY00.0110.00933.351-0.001-0.0010.0000.0000.0000.000
75A2292ALA0-0.042-0.01834.3150.0000.0000.0000.0000.0000.000
76A2293LEU0-0.002-0.00337.0960.0030.0030.0000.0000.0000.000
77A2294TRP0-0.048-0.05140.0300.0010.0010.0000.0000.0000.000
78A2295ARG10.8620.91437.7900.0580.0580.0000.0000.0000.000
79A2296ILE0-0.0720.00142.5070.0030.0030.0000.0000.0000.000
80A2297SER00.0700.03544.7460.0000.0000.0000.0000.0000.000
81A2298PRO00.0630.00648.2230.0010.0010.0000.0000.0000.000
82A2299PRO00.0030.00251.0650.0010.0010.0000.0000.0000.000
83A2300SER00.0460.02146.4560.0010.0010.0000.0000.0000.000
84A2301ARG10.8050.89047.5210.0350.0350.0000.0000.0000.000
85A2302ALA0-0.035-0.02148.5970.0010.0010.0000.0000.0000.000
86A2303GLN0-0.009-0.00348.5030.0000.0000.0000.0000.0000.000
87A2304MET00.0330.03143.3370.0010.0010.0000.0000.0000.000
88A2305LYS10.9470.97947.6230.0240.0240.0000.0000.0000.000
89A2306GLN00.0200.00849.9610.0000.0000.0000.0000.0000.000
90A2307GLU-1-0.866-0.91045.765-0.009-0.0090.0000.0000.0000.000
91A2308LEU0-0.0110.00344.1980.0020.0020.0000.0000.0000.000
92A2309TYR0-0.050-0.03548.1410.0010.0010.0000.0000.0000.000
93A2310ASN0-0.097-0.06451.6550.0010.0010.0000.0000.0000.000
94A2311GLY00.0010.02249.9520.0010.0010.0000.0000.0000.000
95A2312THR0-0.023-0.02950.8790.0000.0000.0000.0000.0000.000
96A2313ALA00.0150.02046.7150.0020.0020.0000.0000.0000.000
97A2314ASP-1-0.825-0.91842.5130.0040.0040.0000.0000.0000.000
98A2315ILE0-0.066-0.02841.801-0.001-0.0010.0000.0000.0000.000
99A2316THR0-0.015-0.01436.133-0.001-0.0010.0000.0000.0000.000
100A2317LEU0-0.037-0.01435.749-0.004-0.0040.0000.0000.0000.000
101A2318ARG10.9560.97731.0000.0300.0300.0000.0000.0000.000
102A2319PHE00.0460.01726.559-0.006-0.0060.0000.0000.0000.000
103A2320THR0-0.0160.00227.0710.0080.0080.0000.0000.0000.000
104A2321TRP00.0200.00120.895-0.016-0.0160.0000.0000.0000.000
105A2322ASN00.006-0.00821.4820.0190.0190.0000.0000.0000.000
106A2323PHE00.0060.00116.769-0.022-0.0220.0000.0000.0000.000
107A2324GLN0-0.001-0.00917.7050.0130.0130.0000.0000.0000.000
108A2325ARG10.8090.91212.2060.1420.1420.0000.0000.0000.000
109A2326ASP-1-0.824-0.92313.368-0.501-0.5010.0000.0000.0000.000
110A2327LEU00.0260.00312.034-0.107-0.1070.0000.0000.0000.000
111A2328ALA0-0.051-0.01012.0150.0030.0030.0000.0000.0000.000
112A2329LYS10.8950.9428.8970.9410.9410.0000.0000.0000.000
113A2330GLY00.0230.0087.305-0.362-0.3620.0000.0000.0000.000
114A2331GLY00.0010.0077.9310.0300.0300.0000.0000.0000.000
115A2332THR0-0.034-0.0319.2570.0010.0010.0000.0000.0000.000
116A2333VAL00.0010.00612.724-0.004-0.0040.0000.0000.0000.000
117A2334GLU-1-0.859-0.91614.270-0.214-0.2140.0000.0000.0000.000
118A2335TYR0-0.007-0.01116.184-0.039-0.0390.0000.0000.0000.000
119A2336THR0-0.045-0.02214.9580.0340.0340.0000.0000.0000.000
120A2337ASN0-0.065-0.04017.774-0.017-0.0170.0000.0000.0000.000
121A2338GLU-1-0.829-0.89420.9700.0510.0510.0000.0000.0000.000
122A2339LYS10.8320.90623.616-0.032-0.0320.0000.0000.0000.000
123A2340HIS00.0040.01926.9060.0120.0120.0000.0000.0000.000
124A2341THR0-0.070-0.05129.196-0.006-0.0060.0000.0000.0000.000
125A2342LEU00.0400.04132.8750.0030.0030.0000.0000.0000.000
126A2343GLU-1-0.825-0.89636.0410.0010.0010.0000.0000.0000.000
127A2344LEU0-0.040-0.02239.4220.0000.0000.0000.0000.0000.000
128A2345ALA00.0990.04842.0990.0000.0000.0000.0000.0000.000
129A2346PRO00.0300.01245.254-0.003-0.0030.0000.0000.0000.000
130A2347ASN0-0.064-0.03748.559-0.001-0.0010.0000.0000.0000.000
131A2348SER00.0070.01945.697-0.001-0.0010.0000.0000.0000.000
132A2349THR00.026-0.01547.040-0.001-0.0010.0000.0000.0000.000
133A2350ALA00.0790.04442.632-0.002-0.0020.0000.0000.0000.000
134A2351ARG10.7970.90744.7530.0050.0050.0000.0000.0000.000
135A2352ARG10.9250.94445.7510.0090.0090.0000.0000.0000.000
136A2353GLN0-0.008-0.00946.236-0.002-0.0020.0000.0000.0000.000
137A2354LEU00.0380.02441.732-0.002-0.0020.0000.0000.0000.000
138A2355ALA0-0.012-0.01145.372-0.002-0.0020.0000.0000.0000.000
139A2356GLN0-0.035-0.01448.351-0.002-0.0020.0000.0000.0000.000
140A2357LEU00.0340.03343.826-0.001-0.0010.0000.0000.0000.000
141A2358LEU0-0.034-0.01046.147-0.002-0.0020.0000.0000.0000.000
142A2359GLU-1-0.957-0.98249.119-0.023-0.0230.0000.0000.0000.000
143A2360GLY0-0.055-0.02650.0060.0000.0000.0000.0000.0000.000
144A2361ARG10.8770.95351.0720.0270.0270.0000.0000.0000.000
145A2362PRO00.0150.00648.5730.0000.0000.0000.0000.0000.000
146A2363ASP-1-0.922-0.96147.564-0.039-0.0390.0000.0000.0000.000
147A2364GLN0-0.020-0.00548.0470.0000.0000.0000.0000.0000.000
148A2365SER0-0.004-0.01442.929-0.003-0.0030.0000.0000.0000.000
149A2366VAL0-0.030-0.01041.5130.0030.0030.0000.0000.0000.000
150A2367VAL00.0110.00738.799-0.004-0.0040.0000.0000.0000.000
151A2368ILE0-0.060-0.02536.7830.0050.0050.0000.0000.0000.000
152A2369PRO00.012-0.00736.530-0.004-0.0040.0000.0000.0000.000
153A2370HIS00.0150.02032.9710.0020.0020.0000.0000.0000.000
154A2371LEU00.0140.00332.2630.0040.0040.0000.0000.0000.000
155A2372PHE00.007-0.00925.985-0.001-0.0010.0000.0000.0000.000
156A2373PRO00.0250.02324.4710.0000.0000.0000.0000.0000.000
157A2374LYS10.9050.96723.7430.1120.1120.0000.0000.0000.000
158A2375TYR00.0140.01020.307-0.022-0.0220.0000.0000.0000.000
159A2376ILE00.0280.01218.4970.0280.0280.0000.0000.0000.000
160A2377ARG10.8950.95511.937-0.286-0.2860.0000.0000.0000.000
161A2378ALA0-0.002-0.00813.4010.0240.0240.0000.0000.0000.000
162A2379PRO0-0.0130.01411.278-0.044-0.0440.0000.0000.0000.000
163A2380ASN00.041-0.0066.998-0.273-0.2730.0000.0000.0000.000
164A2381GLY0-0.026-0.00710.934-0.035-0.0350.0000.0000.0000.000
165A2382PRO00.0290.00314.633-0.043-0.0430.0000.0000.0000.000
166A2383GLU-1-0.866-0.90217.6310.0820.0820.0000.0000.0000.000
167A2384ALA0-0.021-0.00817.4440.0220.0220.0000.0000.0000.000
168A2385ASN0-0.022-0.02718.413-0.029-0.0290.0000.0000.0000.000
169A2386PRO00.0400.01419.339-0.010-0.0100.0000.0000.0000.000
170A2387VAL0-0.046-0.02017.6640.0250.0250.0000.0000.0000.000
171A2388LYS10.9990.99720.263-0.101-0.1010.0000.0000.0000.000
172A2389GLN0-0.066-0.03318.1420.0040.0040.0000.0000.0000.000
173A2390LEU0-0.027-0.01219.554-0.004-0.0040.0000.0000.0000.000
174A2391GLN0-0.077-0.03022.722-0.027-0.0270.0000.0000.0000.000
175A2392PRO0-0.014-0.00425.6860.0080.0080.0000.0000.0000.000
176A2393ASP-1-0.896-0.93227.1510.0380.0380.0000.0000.0000.000
177A2394GLU-1-0.989-1.02227.1160.0580.0580.0000.0000.0000.000
178A2395GLU-1-0.904-0.96428.637-0.002-0.0020.0000.0000.0000.000
179A2396GLU-1-0.948-0.97131.0280.0020.0020.0000.0000.0000.000
180A2397ASP-1-0.842-0.92628.4240.0020.0020.0000.0000.0000.000
181A2398TYR0-0.081-0.04026.240-0.010-0.0100.0000.0000.0000.000
182A2399LEU00.012-0.00428.6040.0000.0000.0000.0000.0000.000
183A2400GLY00.0250.01731.5430.0010.0010.0000.0000.0000.000
184A2401VAL0-0.030-0.00832.629-0.007-0.0070.0000.0000.0000.000
185A2402ARG10.7960.90035.4030.0590.0590.0000.0000.0000.000
186A2403ILE0-0.003-0.00237.499-0.005-0.0050.0000.0000.0000.000
187A2404GLN00.028-0.00839.6520.0030.0030.0000.0000.0000.000
188A2405LEU0-0.032-0.00241.323-0.003-0.0030.0000.0000.0000.000
189A2406ARG10.9300.97442.2060.0660.0660.0000.0000.0000.000
190A2407ARG10.8850.91544.5530.0400.0400.0000.0000.0000.000
191A2408GLU-1-0.916-0.95446.090-0.065-0.0650.0000.0000.0000.000
192A2409GLN0-0.048-0.00648.9860.0000.0000.0000.0000.0000.000
193A2410VAL0-0.019-0.00650.514-0.001-0.0010.0000.0000.0000.000
194A2424SER0-0.014-0.03051.8210.0000.0000.0000.0000.0000.000
195A2425ASP-1-0.907-0.94552.827-0.035-0.0350.0000.0000.0000.000
196A2426PHE0-0.036-0.02449.901-0.001-0.0010.0000.0000.0000.000
197A2427LEU00.0030.01345.7400.0010.0010.0000.0000.0000.000
198A2428GLU-1-0.730-0.85045.051-0.040-0.0400.0000.0000.0000.000
199A2429TRP00.0120.00539.2270.0000.0000.0000.0000.0000.000
200A2430TRP00.0300.01638.4160.0030.0030.0000.0000.0000.000
201A2431VAL0-0.011-0.01737.253-0.006-0.0060.0000.0000.0000.000
202A2432ILE0-0.030-0.01131.6860.0070.0070.0000.0000.0000.000
203A2433GLU-1-0.755-0.86234.150-0.075-0.0750.0000.0000.0000.000
204A2434LEU00.0210.00629.1850.0070.0070.0000.0000.0000.000
205A2435GLN00.001-0.01333.7320.0000.0000.0000.0000.0000.000
206A2436ASP-1-0.922-0.96734.669-0.046-0.0460.0000.0000.0000.000
207A2437CYS0-0.110-0.04632.876-0.004-0.0040.0000.0000.0000.000
208A2438LYS10.9100.94134.5490.0650.0650.0000.0000.0000.000
209A2439ALA0-0.005-0.00633.4830.0030.0030.0000.0000.0000.000
210A2440ASP-1-0.873-0.93031.698-0.133-0.1330.0000.0000.0000.000
211A2442ASN0-0.0170.00232.7530.0070.0070.0000.0000.0000.000
212A2443LEU00.0000.00828.497-0.005-0.0050.0000.0000.0000.000
213A2444LEU0-0.059-0.02428.8290.0100.0100.0000.0000.0000.000
214A2445PRO0-0.019-0.00725.018-0.007-0.0070.0000.0000.0000.000
215A2446MET00.0210.02321.0880.0110.0110.0000.0000.0000.000
216A2447VAL0-0.049-0.01718.359-0.029-0.0290.0000.0000.0000.000
217A2448ILE0-0.017-0.00714.8850.0310.0310.0000.0000.0000.000
218A2449PHE00.0150.00813.139-0.070-0.0700.0000.0000.0000.000
219A2450SER00.0280.00210.1950.1090.1090.0000.0000.0000.000
220A2451ASP-1-0.813-0.8687.6050.1150.1150.0000.0000.0000.000
221A2452LYS10.7850.8762.4972.8742.8691.376-0.402-0.968-0.002
222A2453VAL0-0.0160.0034.3561.0711.2450.000-0.043-0.1320.000
223A2454SER0-0.035-0.0252.880-2.455-0.9400.515-1.143-0.887-0.010
224A2455PRO00.021-0.0033.340-0.521-0.3730.012-0.054-0.1050.000
225A2456PRO00.0260.0296.3250.3860.3860.0000.0000.0000.000
226A2457SER0-0.044-0.0089.9670.0340.0340.0000.0000.0000.000