Manual

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: MNQVZ

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 OptAll
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 -2778756.066587
FMO2-HF: Nuclear repulsion 2688838.735612
FMO2-HF: Total energy -89917.330975
FMO2-MP2: Total energy -90181.221916


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.
-3.370.2862.446-3.015-3.087-0.014
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 : 0.017 / q_NPA : 0.009
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].
3A2220VAL00.0290.0183.872-0.1171.127-0.005-0.661-0.5780.003
4A2221ASN0-0.039-0.0166.7150.3530.3530.0000.0000.0000.000
5A2222GLN00.017-0.0048.4710.2170.2170.0000.0000.0000.000
6A2223PRO0-0.004-0.00111.8380.0570.0570.0000.0000.0000.000
7A2224ILE0-0.048-0.01815.146-0.039-0.0390.0000.0000.0000.000
8A2225ASP-1-0.800-0.87517.620-0.189-0.1890.0000.0000.0000.000
9A2226VAL0-0.002-0.00119.103-0.012-0.0120.0000.0000.0000.000
10A2227THR0-0.012-0.00721.4700.0210.0210.0000.0000.0000.000
11A2228VAL0-0.013-0.00724.2580.0050.0050.0000.0000.0000.000
12A2229THR0-0.085-0.05026.8570.0090.0090.0000.0000.0000.000
13A2230LEU00.0440.03330.3410.0020.0020.0000.0000.0000.000
14A2231LYS10.8280.91533.2060.0420.0420.0000.0000.0000.000
15A2232LEU00.0630.03635.7860.0010.0010.0000.0000.0000.000
16A2233GLY00.0560.02038.7630.0020.0020.0000.0000.0000.000
17A2234GLY0-0.022-0.01638.567-0.002-0.0020.0000.0000.0000.000
18A2235TYR0-0.058-0.06040.550-0.002-0.0020.0000.0000.0000.000
19A2236GLU-1-0.801-0.90638.899-0.059-0.0590.0000.0000.0000.000
20A2237PRO0-0.040-0.01234.5160.0000.0000.0000.0000.0000.000
21A2238LEU00.0150.02236.695-0.002-0.0020.0000.0000.0000.000
22A2239PHE00.0310.00430.2510.0010.0010.0000.0000.0000.000
23A2240THR0-0.022-0.01731.4480.0050.0050.0000.0000.0000.000
24A2241MET0-0.0200.01528.116-0.003-0.0030.0000.0000.0000.000
25A2242SER00.014-0.01525.8200.0060.0060.0000.0000.0000.000
26A2243ALA0-0.0020.02223.593-0.002-0.0020.0000.0000.0000.000
27A2244GLN00.014-0.02221.874-0.021-0.0210.0000.0000.0000.000
28A2245GLN0-0.0050.01120.786-0.026-0.0260.0000.0000.0000.000
29A2246PRO0-0.024-0.02922.3890.0240.0240.0000.0000.0000.000
30A2247SER00.0280.00823.095-0.013-0.0130.0000.0000.0000.000
31A2248ILE0-0.060-0.00417.4930.0120.0120.0000.0000.0000.000
32A2249VAL00.0060.00519.706-0.037-0.0370.0000.0000.0000.000
33A2250PRO0-0.009-0.00715.1900.0150.0150.0000.0000.0000.000
34A2251PHE00.0020.00316.1120.0710.0710.0000.0000.0000.000
35A2252THR00.0280.01816.675-0.058-0.0580.0000.0000.0000.000
36A2253PRO00.015-0.02017.4010.0100.0100.0000.0000.0000.000
37A2254GLN0-0.061-0.02718.9550.0140.0140.0000.0000.0000.000
38A2255ALA00.0690.04220.2740.0200.0200.0000.0000.0000.000
39A2256TYR0-0.038-0.02813.7940.0330.0330.0000.0000.0000.000
40A2257GLU-1-0.892-0.92818.987-0.168-0.1680.0000.0000.0000.000
41A2258GLU-1-0.852-0.92621.773-0.199-0.1990.0000.0000.0000.000
42A2259LEU0-0.030-0.01118.1950.0220.0220.0000.0000.0000.000
43A2260SER0-0.025-0.03219.9200.0250.0250.0000.0000.0000.000
44A2261GLN0-0.065-0.05022.0900.0330.0330.0000.0000.0000.000
45A2262GLN0-0.0300.01924.7660.0000.0000.0000.0000.0000.000
46A2263PHE0-0.013-0.02922.8090.0150.0150.0000.0000.0000.000
47A2264ASP-1-0.908-0.95224.686-0.059-0.0590.0000.0000.0000.000
48A2265PRO0-0.041-0.02125.6130.0140.0140.0000.0000.0000.000
49A2266TYR0-0.019-0.00225.6910.0160.0160.0000.0000.0000.000
50A2267PRO00.0220.00023.797-0.004-0.0040.0000.0000.0000.000
51A2268LEU00.0170.01321.7600.0020.0020.0000.0000.0000.000
52A2269ALA00.0620.03320.7520.0060.0060.0000.0000.0000.000
53A2270MET00.0060.01919.537-0.024-0.0240.0000.0000.0000.000
54A2271GLN0-0.045-0.02417.981-0.013-0.0130.0000.0000.0000.000
55A2272PHE00.0150.02415.0610.0060.0060.0000.0000.0000.000
56A2273ILE00.0300.00314.650-0.033-0.0330.0000.0000.0000.000
57A2274SER0-0.070-0.04314.288-0.053-0.0530.0000.0000.0000.000
58A2275GLN0-0.083-0.03910.912-0.016-0.0160.0000.0000.0000.000
59A2276TYR0-0.069-0.0399.443-0.047-0.0470.0000.0000.0000.000
60A2277SER00.0130.0078.4970.1090.1090.0000.0000.0000.000
61A2278PRO0-0.006-0.01910.853-0.016-0.0160.0000.0000.0000.000
62A2279GLU-1-0.865-0.9227.599-2.419-2.4190.0000.0000.0000.000
63A2280ASP-1-0.777-0.8727.407-2.353-2.3530.0000.0000.0000.000
64A2281ILE0-0.019-0.00410.2400.1620.1620.0000.0000.0000.000
65A2282VAL0-0.0130.00113.936-0.030-0.0300.0000.0000.0000.000
66A2283THR00.0130.00416.7840.0610.0610.0000.0000.0000.000
67A2284ALA0-0.013-0.00420.516-0.013-0.0130.0000.0000.0000.000
68A2285GLN00.0290.00521.9150.0370.0370.0000.0000.0000.000
69A2286ILE0-0.044-0.02924.2160.0050.0050.0000.0000.0000.000
70A2287GLU-1-0.810-0.90027.137-0.147-0.1470.0000.0000.0000.000
71A2288GLY00.0830.03230.7700.0040.0040.0000.0000.0000.000
72A2289SER0-0.052-0.03033.3370.0130.0130.0000.0000.0000.000
73A2290SER0-0.023-0.02334.178-0.008-0.0080.0000.0000.0000.000
74A2291GLY00.0020.00633.0820.0010.0010.0000.0000.0000.000
75A2292ALA0-0.035-0.01534.1030.0010.0010.0000.0000.0000.000
76A2293LEU00.0130.01836.8370.0020.0020.0000.0000.0000.000
77A2294TRP0-0.024-0.03239.6910.0010.0010.0000.0000.0000.000
78A2295ARG10.7990.86937.4940.0720.0720.0000.0000.0000.000
79A2296ILE0-0.0550.00642.5740.0040.0040.0000.0000.0000.000
80A2297SER00.0610.03844.5600.0000.0000.0000.0000.0000.000
81A2298PRO00.0620.01248.0040.0010.0010.0000.0000.0000.000
82A2299PRO0-0.008-0.00251.0770.0000.0000.0000.0000.0000.000
83A2300SER00.0380.00746.5340.0020.0020.0000.0000.0000.000
84A2301ARG10.8020.88047.2840.0460.0460.0000.0000.0000.000
85A2302ALA0-0.008-0.00148.5750.0000.0000.0000.0000.0000.000
86A2303GLN0-0.053-0.02348.0550.0010.0010.0000.0000.0000.000
87A2304MET00.0370.03242.9560.0010.0010.0000.0000.0000.000
88A2305LYS10.8550.92247.5040.0330.0330.0000.0000.0000.000
89A2306GLN0-0.012-0.00349.9170.0000.0000.0000.0000.0000.000
90A2307GLU-1-0.831-0.89445.455-0.022-0.0220.0000.0000.0000.000
91A2308LEU0-0.0040.00743.9760.0020.0020.0000.0000.0000.000
92A2309TYR0-0.042-0.04848.0490.0010.0010.0000.0000.0000.000
93A2310ASN0-0.087-0.04951.6030.0020.0020.0000.0000.0000.000
94A2311GLY00.0020.02249.7610.0020.0020.0000.0000.0000.000
95A2312THR0-0.039-0.03450.406-0.001-0.0010.0000.0000.0000.000
96A2313ALA00.0160.01647.0060.0020.0020.0000.0000.0000.000
97A2314ASP-1-0.848-0.93142.604-0.013-0.0130.0000.0000.0000.000
98A2315ILE0-0.047-0.02541.7150.0000.0000.0000.0000.0000.000
99A2316THR0-0.014-0.01835.666-0.002-0.0020.0000.0000.0000.000
100A2317LEU0-0.038-0.01035.850-0.003-0.0030.0000.0000.0000.000
101A2318ARG10.9410.96831.2520.0570.0570.0000.0000.0000.000
102A2319PHE00.0490.02526.704-0.004-0.0040.0000.0000.0000.000
103A2320THR0-0.045-0.02926.9310.0070.0070.0000.0000.0000.000
104A2321TRP00.0290.00320.898-0.010-0.0100.0000.0000.0000.000
105A2322ASN0-0.008-0.01121.1570.0260.0260.0000.0000.0000.000
106A2323PHE00.015-0.00116.767-0.019-0.0190.0000.0000.0000.000
107A2324GLN0-0.018-0.01117.1080.0040.0040.0000.0000.0000.000
108A2325ARG10.8190.89911.8450.2710.2710.0000.0000.0000.000
109A2326ASP-1-0.775-0.87713.091-0.509-0.5090.0000.0000.0000.000
110A2327LEU00.0430.02011.657-0.117-0.1170.0000.0000.0000.000
111A2328ALA0-0.067-0.02211.6450.0310.0310.0000.0000.0000.000
112A2329LYS10.8130.8798.7330.7940.7940.0000.0000.0000.000
113A2330GLY00.0280.0006.818-0.371-0.3710.0000.0000.0000.000
114A2331GLY00.0070.0127.4330.0040.0040.0000.0000.0000.000
115A2332THR0-0.036-0.0338.9210.0160.0160.0000.0000.0000.000
116A2333VAL0-0.0050.00012.5740.0100.0100.0000.0000.0000.000
117A2334GLU-1-0.803-0.86914.145-0.233-0.2330.0000.0000.0000.000
118A2335TYR0-0.051-0.03715.703-0.050-0.0500.0000.0000.0000.000
119A2336THR0-0.037-0.02014.5560.0330.0330.0000.0000.0000.000
120A2337ASN0-0.054-0.04217.467-0.017-0.0170.0000.0000.0000.000
121A2338GLU-1-0.745-0.82520.8090.0020.0020.0000.0000.0000.000
122A2339LYS10.7240.82723.4200.0010.0010.0000.0000.0000.000
123A2340HIS00.0490.04326.8730.0060.0060.0000.0000.0000.000
124A2341THR0-0.077-0.04929.270-0.003-0.0030.0000.0000.0000.000
125A2342LEU00.0500.04432.9650.0040.0040.0000.0000.0000.000
126A2343GLU-1-0.799-0.88536.105-0.021-0.0210.0000.0000.0000.000
127A2344LEU0-0.021-0.00739.4340.0000.0000.0000.0000.0000.000
128A2345ALA00.0910.05342.0470.0010.0010.0000.0000.0000.000
129A2346PRO00.0250.02444.998-0.003-0.0030.0000.0000.0000.000
130A2347ASN0-0.046-0.03048.3460.0000.0000.0000.0000.0000.000
131A2348SER0-0.0010.00345.773-0.002-0.0020.0000.0000.0000.000
132A2349THR00.005-0.01747.234-0.001-0.0010.0000.0000.0000.000
133A2350ALA00.0960.05442.639-0.001-0.0010.0000.0000.0000.000
134A2351ARG10.7630.88844.7620.0190.0190.0000.0000.0000.000
135A2352ARG10.9180.93945.6220.0210.0210.0000.0000.0000.000
136A2353GLN00.002-0.00946.1440.0000.0000.0000.0000.0000.000
137A2354LEU00.0430.02341.534-0.002-0.0020.0000.0000.0000.000
138A2355ALA0-0.004-0.00545.160-0.001-0.0010.0000.0000.0000.000
139A2356GLN0-0.020-0.00748.275-0.001-0.0010.0000.0000.0000.000
140A2357LEU00.0090.02043.8360.0000.0000.0000.0000.0000.000
141A2358LEU0-0.0010.01245.819-0.001-0.0010.0000.0000.0000.000
142A2359GLU-1-0.829-0.88748.881-0.033-0.0330.0000.0000.0000.000
143A2360GLY0-0.026-0.01749.5400.0000.0000.0000.0000.0000.000
144A2361ARG10.8290.91450.6250.0370.0370.0000.0000.0000.000
145A2362PRO00.0060.00048.595-0.001-0.0010.0000.0000.0000.000
146A2363ASP-1-0.891-0.95047.810-0.051-0.0510.0000.0000.0000.000
147A2364GLN0-0.024-0.00948.2260.0000.0000.0000.0000.0000.000
148A2365SER00.003-0.00543.313-0.003-0.0030.0000.0000.0000.000
149A2366VAL0-0.049-0.01841.4990.0040.0040.0000.0000.0000.000
150A2367VAL00.010-0.00338.984-0.005-0.0050.0000.0000.0000.000
151A2368ILE0-0.040-0.01336.6150.0060.0060.0000.0000.0000.000
152A2369PRO00.0320.00136.355-0.006-0.0060.0000.0000.0000.000
153A2370HIS00.0110.01932.8530.0050.0050.0000.0000.0000.000
154A2371LEU00.0110.00132.1740.0030.0030.0000.0000.0000.000
155A2372PHE0-0.011-0.01926.187-0.003-0.0030.0000.0000.0000.000
156A2373PRO00.0420.03424.324-0.001-0.0010.0000.0000.0000.000
157A2374LYS10.8820.95524.1770.1740.1740.0000.0000.0000.000
158A2375TYR0-0.013-0.02420.532-0.027-0.0270.0000.0000.0000.000
159A2376ILE00.0240.01918.8070.0290.0290.0000.0000.0000.000
160A2377ARG10.8630.90411.361-0.107-0.1070.0000.0000.0000.000
161A2378ALA00.0280.00013.2120.0370.0370.0000.0000.0000.000
162A2379PRO00.0020.01111.359-0.080-0.0800.0000.0000.0000.000
163A2380ASN0-0.006-0.0256.373-0.288-0.2880.0000.0000.0000.000
164A2381GLY0-0.0050.01010.5970.0340.0340.0000.0000.0000.000
165A2382PRO00.0210.00214.391-0.052-0.0520.0000.0000.0000.000
166A2383GLU-1-0.881-0.91417.4190.0390.0390.0000.0000.0000.000
167A2384ALA0-0.0100.00417.3680.0100.0100.0000.0000.0000.000
168A2385ASN0-0.020-0.03318.399-0.017-0.0170.0000.0000.0000.000
169A2386PRO00.0260.01519.150-0.025-0.0250.0000.0000.0000.000
170A2387VAL0-0.031-0.01217.6190.0250.0250.0000.0000.0000.000
171A2388LYS10.8650.91720.264-0.024-0.0240.0000.0000.0000.000
172A2389GLN0-0.087-0.04318.4540.0130.0130.0000.0000.0000.000
173A2390LEU0-0.037-0.01619.590-0.004-0.0040.0000.0000.0000.000
174A2391GLN0-0.082-0.04022.648-0.019-0.0190.0000.0000.0000.000
175A2392PRO00.0070.00925.9000.0090.0090.0000.0000.0000.000
176A2393ASP-1-0.915-0.94727.3880.0010.0010.0000.0000.0000.000
177A2394GLU-1-0.874-0.94626.4970.0090.0090.0000.0000.0000.000
178A2395GLU-1-0.917-0.96728.630-0.034-0.0340.0000.0000.0000.000
179A2396GLU-1-0.950-0.98531.253-0.029-0.0290.0000.0000.0000.000
180A2397ASP-1-0.839-0.92628.413-0.049-0.0490.0000.0000.0000.000
181A2398TYR0-0.077-0.02826.143-0.015-0.0150.0000.0000.0000.000
182A2399LEU00.0060.00028.8210.0030.0030.0000.0000.0000.000
183A2400GLY00.0180.01131.5380.0030.0030.0000.0000.0000.000
184A2401VAL0-0.046-0.01832.527-0.008-0.0080.0000.0000.0000.000
185A2402ARG10.7850.88335.3130.0830.0830.0000.0000.0000.000
186A2403ILE00.0060.00037.177-0.005-0.0050.0000.0000.0000.000
187A2404GLN0-0.005-0.02739.6630.0020.0020.0000.0000.0000.000
188A2405LEU0-0.025-0.00641.289-0.003-0.0030.0000.0000.0000.000
189A2406ARG10.8350.91742.2920.0770.0770.0000.0000.0000.000
190A2407ARG10.8110.90244.3940.0510.0510.0000.0000.0000.000
191A2408GLU-1-0.837-0.90345.845-0.076-0.0760.0000.0000.0000.000
192A2409GLN0-0.066-0.02749.0050.0000.0000.0000.0000.0000.000
193A2410VAL0-0.023-0.01250.538-0.001-0.0010.0000.0000.0000.000
194A2424SER0-0.026-0.03651.7440.0000.0000.0000.0000.0000.000
195A2425ASP-1-0.843-0.91352.813-0.043-0.0430.0000.0000.0000.000
196A2426PHE0-0.005-0.00349.670-0.001-0.0010.0000.0000.0000.000
197A2427LEU00.0160.02445.6370.0010.0010.0000.0000.0000.000
198A2428GLU-1-0.742-0.85844.987-0.051-0.0510.0000.0000.0000.000
199A2429TRP0-0.009-0.01038.7220.0010.0010.0000.0000.0000.000
200A2430TRP00.0150.01438.4710.0020.0020.0000.0000.0000.000
201A2431VAL0-0.023-0.02037.302-0.006-0.0060.0000.0000.0000.000
202A2432ILE0-0.026-0.01131.8250.0080.0080.0000.0000.0000.000
203A2433GLU-1-0.762-0.86333.960-0.097-0.0970.0000.0000.0000.000
204A2434LEU00.0260.01129.0680.0070.0070.0000.0000.0000.000
205A2435GLN0-0.041-0.03533.5810.0030.0030.0000.0000.0000.000
206A2436ASP-1-0.806-0.89335.242-0.070-0.0700.0000.0000.0000.000
207A2437CYS0-0.095-0.03532.877-0.006-0.0060.0000.0000.0000.000
208A2438LYS10.7980.87534.9710.0960.0960.0000.0000.0000.000
209A2439ALA00.0270.01734.2260.0040.0040.0000.0000.0000.000
210A2440ASP-1-0.881-0.93431.588-0.157-0.1570.0000.0000.0000.000
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