FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 98142

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 OptHSide
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 -2774976.493337
FMO2-HF: Nuclear repulsion 2685059.232209
FMO2-HF: Total energy -89917.261129
FMO2-MP2: Total energy -90181.115616


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.
-2.9840.6341.675-2.566-2.725-0.008
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 : 0.008 / q_NPA : 0.006
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].
3A2220VAL00.0310.0203.8030.4041.886-0.012-0.761-0.7090.004
4A2221ASN0-0.035-0.0196.7050.1890.1890.0000.0000.0000.000
5A2222GLN00.0240.0158.7610.1600.1600.0000.0000.0000.000
6A2223PRO00.001-0.00212.1000.0260.0260.0000.0000.0000.000
7A2224ILE0-0.041-0.02515.320-0.036-0.0360.0000.0000.0000.000
8A2225ASP-1-0.803-0.87817.786-0.170-0.1700.0000.0000.0000.000
9A2226VAL0-0.0180.00219.3000.0020.0020.0000.0000.0000.000
10A2227THR0-0.006-0.00321.6260.0130.0130.0000.0000.0000.000
11A2228VAL0-0.017-0.00924.7330.0110.0110.0000.0000.0000.000
12A2229THR0-0.082-0.06027.0260.0030.0030.0000.0000.0000.000
13A2230LEU00.0440.03230.5200.0040.0040.0000.0000.0000.000
14A2231LYS10.8550.93333.3950.0280.0280.0000.0000.0000.000
15A2232LEU00.0620.03635.8680.0030.0030.0000.0000.0000.000
16A2233GLY00.0630.02239.0760.0000.0000.0000.0000.0000.000
17A2234GLY0-0.042-0.03438.563-0.001-0.0010.0000.0000.0000.000
18A2235TYR0-0.069-0.06540.516-0.002-0.0020.0000.0000.0000.000
19A2236GLU-1-0.807-0.91239.280-0.047-0.0470.0000.0000.0000.000
20A2237PRO0-0.038-0.01334.8990.0010.0010.0000.0000.0000.000
21A2238LEU00.0070.01337.080-0.002-0.0020.0000.0000.0000.000
22A2239PHE00.0280.00530.3210.0000.0000.0000.0000.0000.000
23A2240THR0-0.013-0.00431.4560.0050.0050.0000.0000.0000.000
24A2241MET0-0.0220.01028.152-0.005-0.0050.0000.0000.0000.000
25A2242SER00.006-0.01225.8640.0070.0070.0000.0000.0000.000
26A2243ALA0-0.0190.00423.522-0.002-0.0020.0000.0000.0000.000
27A2244GLN00.024-0.01722.099-0.024-0.0240.0000.0000.0000.000
28A2245GLN0-0.0280.00821.097-0.021-0.0210.0000.0000.0000.000
29A2246PRO0-0.015-0.01822.5110.0180.0180.0000.0000.0000.000
30A2247SER00.0440.00323.444-0.006-0.0060.0000.0000.0000.000
31A2248ILE0-0.053-0.00617.5440.0170.0170.0000.0000.0000.000
32A2249VAL0-0.022-0.01319.385-0.043-0.0430.0000.0000.0000.000
33A2250PRO00.0100.00514.8920.0200.0200.0000.0000.0000.000
34A2251PHE00.004-0.00415.7710.0610.0610.0000.0000.0000.000
35A2252THR00.0140.01516.511-0.059-0.0590.0000.0000.0000.000
36A2253PRO00.026-0.01917.1000.0150.0150.0000.0000.0000.000
37A2254GLN0-0.043-0.02018.7710.0160.0160.0000.0000.0000.000
38A2255ALA00.0510.03619.7320.0220.0220.0000.0000.0000.000
39A2256TYR0-0.032-0.02314.0740.0280.0280.0000.0000.0000.000
40A2257GLU-1-0.935-0.96118.991-0.120-0.1200.0000.0000.0000.000
41A2258GLU-1-0.846-0.91921.837-0.152-0.1520.0000.0000.0000.000
42A2259LEU0-0.035-0.01218.1690.0210.0210.0000.0000.0000.000
43A2260SER0-0.033-0.04819.9180.0300.0300.0000.0000.0000.000
44A2261GLN0-0.019-0.01121.9950.0250.0250.0000.0000.0000.000
45A2262GLN0-0.0350.00224.7730.0030.0030.0000.0000.0000.000
46A2263PHE0-0.033-0.03722.6810.0140.0140.0000.0000.0000.000
47A2264ASP-1-0.896-0.94224.758-0.003-0.0030.0000.0000.0000.000
48A2265PRO0-0.049-0.01925.7130.0130.0130.0000.0000.0000.000
49A2266TYR0-0.015-0.00325.2800.0150.0150.0000.0000.0000.000
50A2267PRO00.0220.00123.7460.0020.0020.0000.0000.0000.000
51A2268LEU00.0110.01321.8860.0110.0110.0000.0000.0000.000
52A2269ALA00.0630.03020.5090.0140.0140.0000.0000.0000.000
53A2270MET00.0260.02119.386-0.010-0.0100.0000.0000.0000.000
54A2271GLN0-0.051-0.03017.9050.0030.0030.0000.0000.0000.000
55A2272PHE00.0040.01415.0740.0340.0340.0000.0000.0000.000
56A2273ILE00.0450.00714.474-0.007-0.0070.0000.0000.0000.000
57A2274SER0-0.075-0.02714.261-0.035-0.0350.0000.0000.0000.000
58A2275GLN0-0.080-0.03910.754-0.025-0.0250.0000.0000.0000.000
59A2276TYR0-0.067-0.0429.4210.0210.0210.0000.0000.0000.000
60A2277SER00.0050.0038.7890.0240.0240.0000.0000.0000.000
61A2278PRO00.022-0.00810.954-0.023-0.0230.0000.0000.0000.000
62A2279GLU-1-0.866-0.9207.404-2.340-2.3400.0000.0000.0000.000
63A2280ASP-1-0.788-0.8807.241-1.764-1.7640.0000.0000.0000.000
64A2281ILE0-0.029-0.00310.1390.1460.1460.0000.0000.0000.000
65A2282VAL0-0.0110.00213.819-0.046-0.0460.0000.0000.0000.000
66A2283THR00.009-0.00216.6400.0650.0650.0000.0000.0000.000
67A2284ALA0-0.024-0.00820.343-0.018-0.0180.0000.0000.0000.000
68A2285GLN00.0380.00121.8460.0390.0390.0000.0000.0000.000
69A2286ILE0-0.040-0.01924.2190.0010.0010.0000.0000.0000.000
70A2287GLU-1-0.795-0.88927.164-0.130-0.1300.0000.0000.0000.000
71A2288GLY00.0670.01830.7250.0050.0050.0000.0000.0000.000
72A2289SER0-0.051-0.02133.1970.0120.0120.0000.0000.0000.000
73A2290SER0-0.035-0.02734.336-0.007-0.0070.0000.0000.0000.000
74A2291GLY00.0140.00733.351-0.001-0.0010.0000.0000.0000.000
75A2292ALA0-0.041-0.01534.3140.0000.0000.0000.0000.0000.000
76A2293LEU00.0120.00737.0960.0030.0030.0000.0000.0000.000
77A2294TRP0-0.041-0.05040.0300.0010.0010.0000.0000.0000.000
78A2295ARG10.8170.88537.9720.0590.0590.0000.0000.0000.000
79A2296ILE0-0.076-0.00242.5070.0030.0030.0000.0000.0000.000
80A2297SER00.0590.03244.7470.0000.0000.0000.0000.0000.000
81A2298PRO00.0730.01148.2230.0010.0010.0000.0000.0000.000
82A2299PRO00.0040.00451.1080.0010.0010.0000.0000.0000.000
83A2300SER00.0390.01646.4970.0010.0010.0000.0000.0000.000
84A2301ARG10.8240.89847.5190.0360.0360.0000.0000.0000.000
85A2302ALA0-0.012-0.00948.5980.0010.0010.0000.0000.0000.000
86A2303GLN0-0.039-0.01448.0030.0000.0000.0000.0000.0000.000
87A2304MET00.0310.03343.2250.0010.0010.0000.0000.0000.000
88A2305LYS10.8600.93247.6240.0240.0240.0000.0000.0000.000
89A2306GLN0-0.003-0.00749.9610.0000.0000.0000.0000.0000.000
90A2307GLU-1-0.856-0.89745.647-0.010-0.0100.0000.0000.0000.000
91A2308LEU0-0.0080.00244.1400.0020.0020.0000.0000.0000.000
92A2309TYR0-0.046-0.04248.1420.0010.0010.0000.0000.0000.000
93A2310ASN0-0.071-0.04651.6550.0010.0010.0000.0000.0000.000
94A2311GLY0-0.0100.01949.9530.0020.0020.0000.0000.0000.000
95A2312THR0-0.024-0.03150.8800.0000.0000.0000.0000.0000.000
96A2313ALA00.0070.01846.7750.0020.0020.0000.0000.0000.000
97A2314ASP-1-0.828-0.91942.6430.0030.0030.0000.0000.0000.000
98A2315ILE0-0.067-0.02741.874-0.001-0.0010.0000.0000.0000.000
99A2316THR00.000-0.00636.089-0.001-0.0010.0000.0000.0000.000
100A2317LEU0-0.052-0.02335.805-0.004-0.0040.0000.0000.0000.000
101A2318ARG10.9580.97931.1010.0320.0320.0000.0000.0000.000
102A2319PHE00.0480.01826.543-0.006-0.0060.0000.0000.0000.000
103A2320THR0-0.0060.00127.0860.0080.0080.0000.0000.0000.000
104A2321TRP00.0190.00320.981-0.015-0.0150.0000.0000.0000.000
105A2322ASN0-0.011-0.01421.4800.0260.0260.0000.0000.0000.000
106A2323PHE00.005-0.00416.893-0.022-0.0220.0000.0000.0000.000
107A2324GLN0-0.001-0.00517.7060.0120.0120.0000.0000.0000.000
108A2325ARG10.8080.90512.2430.1420.1420.0000.0000.0000.000
109A2326ASP-1-0.780-0.88413.428-0.544-0.5440.0000.0000.0000.000
110A2327LEU00.0310.00412.034-0.107-0.1070.0000.0000.0000.000
111A2328ALA0-0.055-0.01312.0150.0050.0050.0000.0000.0000.000
112A2329LYS10.8290.8958.8940.8350.8350.0000.0000.0000.000
113A2330GLY00.0210.0097.305-0.358-0.3580.0000.0000.0000.000
114A2331GLY00.0080.0107.9150.0280.0280.0000.0000.0000.000
115A2332THR0-0.037-0.0349.2550.0010.0010.0000.0000.0000.000
116A2333VAL0-0.0010.00412.720-0.003-0.0030.0000.0000.0000.000
117A2334GLU-1-0.811-0.88414.267-0.211-0.2110.0000.0000.0000.000
118A2335TYR0-0.038-0.03216.182-0.038-0.0380.0000.0000.0000.000
119A2336THR0-0.044-0.02714.8800.0340.0340.0000.0000.0000.000
120A2337ASN0-0.052-0.03317.776-0.018-0.0180.0000.0000.0000.000
121A2338GLU-1-0.733-0.82120.9710.0440.0440.0000.0000.0000.000
122A2339LYS10.7160.82123.618-0.035-0.0350.0000.0000.0000.000
123A2340HIS00.0280.03626.9070.0120.0120.0000.0000.0000.000
124A2341THR0-0.056-0.03529.196-0.006-0.0060.0000.0000.0000.000
125A2342LEU00.0280.02932.8760.0030.0030.0000.0000.0000.000
126A2343GLU-1-0.807-0.88836.041-0.001-0.0010.0000.0000.0000.000
127A2344LEU0-0.040-0.02139.4230.0000.0000.0000.0000.0000.000
128A2345ALA00.0940.04742.1000.0000.0000.0000.0000.0000.000
129A2346PRO00.0290.02445.254-0.003-0.0030.0000.0000.0000.000
130A2347ASN0-0.050-0.02948.559-0.001-0.0010.0000.0000.0000.000
131A2348SER00.0140.01345.682-0.001-0.0010.0000.0000.0000.000
132A2349THR00.014-0.01947.032-0.001-0.0010.0000.0000.0000.000
133A2350ALA00.0840.04842.608-0.002-0.0020.0000.0000.0000.000
134A2351ARG10.7970.90244.7530.0060.0060.0000.0000.0000.000
135A2352ARG10.9150.93545.7510.0090.0090.0000.0000.0000.000
136A2353GLN00.000-0.00846.288-0.001-0.0010.0000.0000.0000.000
137A2354LEU00.0380.02341.707-0.002-0.0020.0000.0000.0000.000
138A2355ALA0-0.009-0.00645.371-0.002-0.0020.0000.0000.0000.000
139A2356GLN0-0.030-0.01348.351-0.002-0.0020.0000.0000.0000.000
140A2357LEU00.0260.03143.811-0.001-0.0010.0000.0000.0000.000
141A2358LEU0-0.031-0.00845.980-0.002-0.0020.0000.0000.0000.000
142A2359GLU-1-0.852-0.91249.119-0.024-0.0240.0000.0000.0000.000
143A2360GLY0-0.027-0.01550.0040.0000.0000.0000.0000.0000.000
144A2361ARG10.8330.91751.0720.0270.0270.0000.0000.0000.000
145A2362PRO00.0210.00648.5710.0000.0000.0000.0000.0000.000
146A2363ASP-1-0.915-0.95647.563-0.040-0.0400.0000.0000.0000.000
147A2364GLN0-0.029-0.01248.0460.0000.0000.0000.0000.0000.000
148A2365SER0-0.003-0.01442.944-0.003-0.0030.0000.0000.0000.000
149A2366VAL0-0.040-0.01741.5660.0030.0030.0000.0000.0000.000
150A2367VAL00.0070.00738.850-0.004-0.0040.0000.0000.0000.000
151A2368ILE0-0.048-0.02036.7910.0050.0050.0000.0000.0000.000
152A2369PRO00.012-0.00536.529-0.004-0.0040.0000.0000.0000.000
153A2370HIS0-0.0010.01632.9700.0020.0020.0000.0000.0000.000
154A2371LEU00.012-0.00532.2990.0040.0040.0000.0000.0000.000
155A2372PHE0-0.004-0.01326.089-0.001-0.0010.0000.0000.0000.000
156A2373PRO00.0290.03224.464-0.001-0.0010.0000.0000.0000.000
157A2374LYS10.8990.95923.8000.1210.1210.0000.0000.0000.000
158A2375TYR0-0.008-0.01120.359-0.025-0.0250.0000.0000.0000.000
159A2376ILE00.0310.02218.7090.0280.0280.0000.0000.0000.000
160A2377ARG10.8520.90411.574-0.291-0.2910.0000.0000.0000.000
161A2378ALA00.001-0.00513.4660.0240.0240.0000.0000.0000.000
162A2379PRO0-0.0030.01811.275-0.051-0.0510.0000.0000.0000.000
163A2380ASN00.018-0.0186.686-0.308-0.3080.0000.0000.0000.000
164A2381GLY0-0.019-0.00210.937-0.033-0.0330.0000.0000.0000.000
165A2382PRO00.0290.00814.636-0.044-0.0440.0000.0000.0000.000
166A2383GLU-1-0.891-0.91617.6200.0860.0860.0000.0000.0000.000
167A2384ALA0-0.012-0.00417.4460.0210.0210.0000.0000.0000.000
168A2385ASN0-0.023-0.02918.414-0.028-0.0280.0000.0000.0000.000
169A2386PRO00.0400.01419.339-0.011-0.0110.0000.0000.0000.000
170A2387VAL0-0.046-0.02117.6220.0250.0250.0000.0000.0000.000
171A2388LYS10.8950.93620.263-0.084-0.0840.0000.0000.0000.000
172A2389GLN0-0.084-0.04118.4170.0110.0110.0000.0000.0000.000
173A2390LEU0-0.028-0.01119.520-0.005-0.0050.0000.0000.0000.000
174A2391GLN0-0.083-0.03522.660-0.026-0.0260.0000.0000.0000.000
175A2392PRO0-0.0030.00425.6860.0080.0080.0000.0000.0000.000
176A2393ASP-1-0.906-0.94227.1510.0370.0370.0000.0000.0000.000
177A2394GLU-1-0.873-0.95427.1290.0580.0580.0000.0000.0000.000
178A2395GLU-1-0.902-0.96128.637-0.002-0.0020.0000.0000.0000.000
179A2396GLU-1-0.952-0.97631.0280.0010.0010.0000.0000.0000.000
180A2397ASP-1-0.846-0.93328.268-0.003-0.0030.0000.0000.0000.000
181A2398TYR0-0.092-0.03926.209-0.011-0.0110.0000.0000.0000.000
182A2399LEU00.006-0.00728.6050.0000.0000.0000.0000.0000.000
183A2400GLY00.0220.01731.5420.0010.0010.0000.0000.0000.000
184A2401VAL0-0.032-0.01132.600-0.007-0.0070.0000.0000.0000.000
185A2402ARG10.7790.87935.4020.0610.0610.0000.0000.0000.000
186A2403ILE0-0.003-0.00237.427-0.005-0.0050.0000.0000.0000.000
187A2404GLN00.025-0.00439.6510.0020.0020.0000.0000.0000.000
188A2405LEU0-0.030-0.00441.322-0.003-0.0030.0000.0000.0000.000
189A2406ARG10.8700.93642.3800.0660.0660.0000.0000.0000.000
190A2407ARG10.8340.89644.5520.0410.0410.0000.0000.0000.000
191A2408GLU-1-0.860-0.91846.059-0.066-0.0660.0000.0000.0000.000
192A2409GLN0-0.068-0.02048.9850.0000.0000.0000.0000.0000.000
193A2410VAL0-0.020-0.00550.463-0.001-0.0010.0000.0000.0000.000
194A2424SER0-0.026-0.03351.8060.0000.0000.0000.0000.0000.000
195A2425ASP-1-0.867-0.92852.828-0.037-0.0370.0000.0000.0000.000
196A2426PHE00.002-0.01249.882-0.001-0.0010.0000.0000.0000.000
197A2427LEU00.0070.01745.7470.0010.0010.0000.0000.0000.000
198A2428GLU-1-0.737-0.84645.095-0.040-0.0400.0000.0000.0000.000
199A2429TRP0-0.0020.00038.9070.0000.0000.0000.0000.0000.000
200A2430TRP00.0270.01638.4460.0030.0030.0000.0000.0000.000
201A2431VAL0-0.013-0.01637.254-0.006-0.0060.0000.0000.0000.000
202A2432ILE0-0.027-0.01031.7020.0070.0070.0000.0000.0000.000
203A2433GLU-1-0.751-0.85934.140-0.076-0.0760.0000.0000.0000.000
204A2434LEU00.0260.01129.1620.0070.0070.0000.0000.0000.000
205A2435GLN0-0.014-0.02533.7300.0020.0020.0000.0000.0000.000
206A2436ASP-1-0.832-0.91635.128-0.048-0.0480.0000.0000.0000.000
207A2437CYS0-0.104-0.03332.873-0.004-0.0040.0000.0000.0000.000
208A2438LYS10.8320.89734.5480.0670.0670.0000.0000.0000.000
209A2439ALA0-0.0020.00233.4480.0030.0030.0000.0000.0000.000
210A2440ASP-1-0.872-0.93531.675-0.135-0.1350.0000.0000.0000.000
211A2442ASN0-0.047-0.02732.6640.0060.0060.0000.0000.0000.000
212A2443LEU0-0.0010.01028.457-0.006-0.0060.0000.0000.0000.000
213A2444LEU0-0.058-0.02428.8430.0090.0090.0000.0000.0000.000
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215A2446MET00.0060.01421.1810.0110.0110.0000.0000.0000.000
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218A2449PHE00.0170.01013.138-0.071-0.0710.0000.0000.0000.000
219A2450SER00.0310.00410.2220.1110.1110.0000.0000.0000.000
220A2451ASP-1-0.794-0.8437.6450.1090.1090.0000.0000.0000.000
221A2452LYS10.7760.8612.4832.6142.8961.166-0.556-0.891-0.002
222A2453VAL0-0.0130.0104.3541.1121.2830.000-0.042-0.1290.000
223A2454SER0-0.011-0.0152.879-2.425-0.8730.513-1.163-0.901-0.010
224A2455PRO00.0260.0033.429-0.559-0.4280.008-0.044-0.0950.000
225A2456PRO00.0180.0246.3270.3860.3860.0000.0000.0000.000
226A2457SER0-0.047-0.0109.9680.0370.0370.0000.0000.0000.000