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: 3JQJL

Calculation Name: 5XAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XAY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9XCC7

Base Structure: X-ray

Registration Date: 2023-09-20

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456906.920647
FMO2-HF: Nuclear repulsion 2373053.081575
FMO2-HF: Total energy -83853.839072
FMO2-MP2: Total energy -84100.819196


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-13.742-6.6993.408-4.224-6.226-0.007
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.032
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].
3A4GLN00.0420.0112.546-1.9220.3540.370-1.006-1.6400.006
4A5GLU-1-0.868-0.9182.223-9.168-6.1472.862-2.564-3.318-0.017
5A6ARG10.9270.9622.802-3.840-2.2140.177-0.647-1.1560.004
6A7ALA00.0620.0255.3120.2710.391-0.001-0.007-0.1120.000
7A8ALA00.000-0.0056.8460.1950.1950.0000.0000.0000.000
8A9GLN0-0.076-0.0548.028-0.062-0.0620.0000.0000.0000.000
9A10THR0-0.022-0.0519.7680.1180.1180.0000.0000.0000.000
10A11ARG10.9070.97911.4580.3620.3620.0000.0000.0000.000
11A12ARG10.9790.9968.8670.9290.9290.0000.0000.0000.000
12A13THR00.0150.01614.0880.0310.0310.0000.0000.0000.000
13A14ILE0-0.029-0.01015.7250.0350.0350.0000.0000.0000.000
14A15VAL00.0240.00917.1670.0260.0260.0000.0000.0000.000
15A16ALA00.0240.01218.5330.0210.0210.0000.0000.0000.000
16A17ALA0-0.022-0.00620.1210.0190.0190.0000.0000.0000.000
17A18ALA0-0.018-0.02021.6470.0160.0160.0000.0000.0000.000
18A19ALA0-0.0040.00122.9640.0100.0100.0000.0000.0000.000
19A20ALA00.0160.01524.7150.0100.0100.0000.0000.0000.000
20A21VAL00.0220.00126.3260.0090.0090.0000.0000.0000.000
21A22PHE0-0.014-0.00325.2230.0080.0080.0000.0000.0000.000
22A23ASP-1-0.879-0.94928.929-0.073-0.0730.0000.0000.0000.000
23A24GLU-1-0.907-0.93230.084-0.045-0.0450.0000.0000.0000.000
24A25LEU0-0.041-0.02931.7660.0050.0050.0000.0000.0000.000
25A26GLY0-0.0010.00933.0480.0040.0040.0000.0000.0000.000
26A27TYR00.020-0.00329.0370.0010.0010.0000.0000.0000.000
27A28GLU-1-0.904-0.95332.434-0.025-0.0250.0000.0000.0000.000
28A29ALA00.0100.00334.4360.0040.0040.0000.0000.0000.000
29A30THR00.0440.06028.1310.0030.0030.0000.0000.0000.000
30A31THR0-0.018-0.01230.0080.0020.0020.0000.0000.0000.000
31A32ILE00.0590.00424.159-0.003-0.0030.0000.0000.0000.000
32A33ALA0-0.019-0.01625.3810.0020.0020.0000.0000.0000.000
33A34GLU-1-0.883-0.94726.618-0.008-0.0080.0000.0000.0000.000
34A35ILE00.0420.02721.963-0.001-0.0010.0000.0000.0000.000
35A36LEU0-0.066-0.02720.768-0.006-0.0060.0000.0000.0000.000
36A37LYS10.9370.98322.1530.0020.0020.0000.0000.0000.000
37A38ARG10.8580.90223.9730.0580.0580.0000.0000.0000.000
38A39SER0-0.043-0.02318.532-0.001-0.0010.0000.0000.0000.000
39A40GLY00.0200.01518.692-0.001-0.0010.0000.0000.0000.000
40A41VAL0-0.0160.00215.0200.0280.0280.0000.0000.0000.000
41A42THR00.0520.03216.215-0.012-0.0120.0000.0000.0000.000
42A43LYS10.9850.97018.751-0.074-0.0740.0000.0000.0000.000
43A44GLY0-0.0210.00818.344-0.017-0.0170.0000.0000.0000.000
44A45ALA00.0520.02314.540-0.015-0.0150.0000.0000.0000.000
45A46LEU00.0260.00215.957-0.042-0.0420.0000.0000.0000.000
46A47TYR0-0.050-0.04618.565-0.013-0.0130.0000.0000.0000.000
47A48PHE0-0.071-0.00811.233-0.003-0.0030.0000.0000.0000.000
48A49HIS0-0.024-0.02011.055-0.045-0.0450.0000.0000.0000.000
49A50PHE0-0.007-0.00516.294-0.027-0.0270.0000.0000.0000.000
50A51THR0-0.019-0.01519.9450.0200.0200.0000.0000.0000.000
51A52SER0-0.001-0.01622.7950.0120.0120.0000.0000.0000.000
52A53LYS10.8730.94224.6540.0280.0280.0000.0000.0000.000
53A54GLU-1-0.812-0.90126.320-0.069-0.0690.0000.0000.0000.000
54A55GLN00.0580.04521.046-0.010-0.0100.0000.0000.0000.000
55A56LEU00.0080.00820.544-0.014-0.0140.0000.0000.0000.000
56A57ALA00.003-0.00123.090-0.012-0.0120.0000.0000.0000.000
57A58GLN0-0.026-0.03225.236-0.011-0.0110.0000.0000.0000.000
58A59GLU-1-0.907-0.93918.254-0.263-0.2630.0000.0000.0000.000
59A60VAL0-0.005-0.01022.093-0.015-0.0150.0000.0000.0000.000
60A61LEU0-0.064-0.03923.697-0.006-0.0060.0000.0000.0000.000
61A62THR0-0.0060.00023.469-0.002-0.0020.0000.0000.0000.000
62A63SER0-0.053-0.02320.555-0.012-0.0120.0000.0000.0000.000
63A64GLN0-0.016-0.00320.970-0.029-0.0290.0000.0000.0000.000
64A65LEU0-0.0070.02121.148-0.007-0.0070.0000.0000.0000.000
65A75ARG10.8790.92732.2770.1120.1120.0000.0000.0000.000
66A76LEU0-0.0190.00534.0970.0030.0030.0000.0000.0000.000
67A77VAL00.0380.03532.832-0.005-0.0050.0000.0000.0000.000
68A78LEU00.024-0.00233.869-0.004-0.0040.0000.0000.0000.000
69A79GLN0-0.067-0.03733.8760.0070.0070.0000.0000.0000.000
70A80GLN0-0.031-0.01927.1300.0010.0010.0000.0000.0000.000
71A81ILE00.0570.02031.232-0.003-0.0030.0000.0000.0000.000
72A82ILE0-0.0450.01433.1850.0010.0010.0000.0000.0000.000
73A83ASP-1-0.756-0.87029.909-0.145-0.1450.0000.0000.0000.000
74A84GLU-1-0.846-0.90927.521-0.174-0.1740.0000.0000.0000.000
75A85THR0-0.029-0.03929.6880.0010.0010.0000.0000.0000.000
76A86LEU0-0.037-0.02132.7670.0040.0040.0000.0000.0000.000
77A87LEU00.0130.00925.3280.0030.0030.0000.0000.0000.000
78A88LEU00.0290.02027.767-0.001-0.0010.0000.0000.0000.000
79A89ALA00.0180.00630.0680.0040.0040.0000.0000.0000.000
80A90GLN0-0.0130.00230.6620.0080.0080.0000.0000.0000.000
81A91LEU0-0.005-0.00725.3230.0040.0040.0000.0000.0000.000
82A92LEU0-0.037-0.02229.1560.0040.0040.0000.0000.0000.000
83A93SER0-0.029-0.00431.4580.0070.0070.0000.0000.0000.000
84A94LYS10.9040.94129.7910.1020.1020.0000.0000.0000.000
85A95GLY0-0.041-0.00130.6060.0020.0020.0000.0000.0000.000
86A96ASP-1-0.801-0.90724.097-0.183-0.1830.0000.0000.0000.000
87A97PRO00.0350.00824.1010.0050.0050.0000.0000.0000.000
88A98LEU00.0210.00819.7800.0050.0050.0000.0000.0000.000
89A99VAL0-0.005-0.00224.3420.0080.0080.0000.0000.0000.000
90A100ARG10.8770.94527.3960.0930.0930.0000.0000.0000.000
91A101GLY00.0260.02527.4850.0090.0090.0000.0000.0000.000
92A102SER0-0.015-0.00727.0050.0100.0100.0000.0000.0000.000
93A103VAL00.0210.02028.7320.0090.0090.0000.0000.0000.000
94A104ARG10.8820.95031.8900.0610.0610.0000.0000.0000.000
95A105LEU0-0.038-0.02027.9620.0070.0070.0000.0000.0000.000
96A106THR0-0.086-0.03931.8490.0040.0040.0000.0000.0000.000
97A107VAL0-0.023-0.00933.8180.0040.0040.0000.0000.0000.000
98A108GLU-1-0.882-0.93334.842-0.050-0.0500.0000.0000.0000.000
99A109PRO00.016-0.00237.874-0.002-0.0020.0000.0000.0000.000
100A110GLY00.0080.00337.7030.0020.0020.0000.0000.0000.000
101A111ALA0-0.023-0.01238.4050.0000.0000.0000.0000.0000.000
102A112PRO0-0.029-0.02439.957-0.001-0.0010.0000.0000.0000.000
103A113ARG10.7960.90037.6320.0400.0400.0000.0000.0000.000
104A114ASP-1-0.796-0.92035.986-0.046-0.0460.0000.0000.0000.000
105A115GLY0-0.055-0.02035.4740.0000.0000.0000.0000.0000.000
106A116LEU00.0170.02529.7200.0000.0000.0000.0000.0000.000
107A117ASP-1-0.878-0.94331.997-0.073-0.0730.0000.0000.0000.000
108A118ARG10.9150.93931.3890.0560.0560.0000.0000.0000.000
109A119ARG10.8860.96032.5670.0550.0550.0000.0000.0000.000
110A120ALA0-0.005-0.00229.708-0.004-0.0040.0000.0000.0000.000
111A121PRO00.0940.03727.714-0.005-0.0050.0000.0000.0000.000
112A122MET00.0050.01329.052-0.008-0.0080.0000.0000.0000.000
113A123GLN0-0.065-0.04832.1250.0070.0070.0000.0000.0000.000
114A124GLU-1-0.923-0.95125.202-0.153-0.1530.0000.0000.0000.000
115A125TRP00.0240.01729.123-0.005-0.0050.0000.0000.0000.000
116A126ILE0-0.011-0.02230.1120.0000.0000.0000.0000.0000.000
117A127GLY0-0.066-0.04731.0940.0030.0030.0000.0000.0000.000
118A128HIS00.0500.02726.5250.0030.0030.0000.0000.0000.000
119A129GLY00.0140.01129.837-0.001-0.0010.0000.0000.0000.000
120A130ARG10.8770.93333.0420.1000.1000.0000.0000.0000.000
121A131ASP-1-0.942-0.97329.790-0.128-0.1280.0000.0000.0000.000
122A132LEU0-0.024-0.02229.0110.0020.0020.0000.0000.0000.000
123A133LEU00.0120.00732.5850.0040.0040.0000.0000.0000.000
124A134ARG10.9340.96934.9620.0980.0980.0000.0000.0000.000
125A135ARG10.9400.97428.6370.1570.1570.0000.0000.0000.000
126A136ALA00.0300.01635.1240.0020.0020.0000.0000.0000.000
127A137GLU-1-1.003-0.99537.455-0.072-0.0720.0000.0000.0000.000
128A138ALA00.0130.01337.6170.0030.0030.0000.0000.0000.000
129A139GLY0-0.056-0.01738.6910.0020.0020.0000.0000.0000.000
130A140GLY0-0.033-0.01739.5470.0010.0010.0000.0000.0000.000
131A141GLU-1-0.833-0.94337.480-0.104-0.1040.0000.0000.0000.000
132A142LEU0-0.030-0.00740.2100.0010.0010.0000.0000.0000.000
133A143LEU0-0.024-0.01143.5440.0030.0030.0000.0000.0000.000
134A144PRO00.0080.00246.258-0.001-0.0010.0000.0000.0000.000
135A145ARG10.9220.94747.4360.0540.0540.0000.0000.0000.000
136A146LEU00.0430.04344.0520.0020.0020.0000.0000.0000.000
137A147ASP-1-0.827-0.91942.861-0.069-0.0690.0000.0000.0000.000
138A148VAL00.0340.00637.997-0.001-0.0010.0000.0000.0000.000
139A149ASP-1-0.845-0.92038.382-0.083-0.0830.0000.0000.0000.000
140A150ALA0-0.0020.00739.715-0.001-0.0010.0000.0000.0000.000
141A151VAL00.018-0.00439.8370.0000.0000.0000.0000.0000.000
142A152ALA0-0.003-0.00735.783-0.002-0.0020.0000.0000.0000.000
143A153ARG10.8450.91237.5890.0700.0700.0000.0000.0000.000
144A154MET0-0.0170.00139.3180.0010.0010.0000.0000.0000.000
145A155LEU00.0060.01337.0260.0000.0000.0000.0000.0000.000
146A156VAL00.0130.01833.9570.0000.0000.0000.0000.0000.000
147A157GLY00.0210.01136.4740.0010.0010.0000.0000.0000.000
148A158GLY00.0480.02139.7020.0030.0030.0000.0000.0000.000
149A159PHE00.0400.01232.9870.0020.0020.0000.0000.0000.000
150A160THR0-0.061-0.03236.5960.0000.0000.0000.0000.0000.000
151A161GLY00.0000.00037.8460.0030.0030.0000.0000.0000.000
152A162ALA0-0.018-0.01439.9680.0030.0030.0000.0000.0000.000
153A163GLN00.033-0.00435.4260.0050.0050.0000.0000.0000.000
154A164ILE0-0.022-0.00738.6900.0030.0030.0000.0000.0000.000
155A165LEU00.021-0.00540.7140.0030.0030.0000.0000.0000.000
156A166SER0-0.023-0.00940.4380.0010.0010.0000.0000.0000.000
157A167ASN0-0.042-0.03239.2560.0010.0010.0000.0000.0000.000
158A168ILE0-0.019-0.01241.1140.0030.0030.0000.0000.0000.000
159A169LEU0-0.057-0.01944.4370.0030.0030.0000.0000.0000.000
160A170THR0-0.040-0.00343.3390.0010.0010.0000.0000.0000.000
161A171GLY00.0630.03141.5840.0010.0010.0000.0000.0000.000
162A172HIS0-0.042-0.03436.179-0.003-0.0030.0000.0000.0000.000
163A173ALA0-0.042-0.01338.872-0.003-0.0030.0000.0000.0000.000
164A174ASP-1-0.800-0.89040.670-0.065-0.0650.0000.0000.0000.000
165A175LEU00.0020.02235.135-0.002-0.0020.0000.0000.0000.000
166A176LEU0-0.002-0.00735.825-0.001-0.0010.0000.0000.0000.000
167A177GLU-1-0.915-0.95538.294-0.063-0.0630.0000.0000.0000.000
168A178ARG10.9090.95441.6980.0590.0590.0000.0000.0000.000
169A179VAL00.0150.00936.1440.0010.0010.0000.0000.0000.000
170A180THR0-0.020-0.02239.181-0.002-0.0020.0000.0000.0000.000
171A181ASP-1-0.893-0.94640.449-0.064-0.0640.0000.0000.0000.000
172A182MET0-0.065-0.01241.5940.0030.0030.0000.0000.0000.000
173A183HIS00.0330.00136.4470.0040.0040.0000.0000.0000.000
174A184ARG10.9580.97840.9570.0720.0720.0000.0000.0000.000
175A185HIS0-0.033-0.01443.4290.0030.0030.0000.0000.0000.000
176A186LEU00.0080.01141.7350.0010.0010.0000.0000.0000.000
177A187MET00.0350.01439.3220.0000.0000.0000.0000.0000.000
178A188THR0-0.092-0.05142.8760.0010.0010.0000.0000.0000.000
179A189SER0-0.087-0.03845.9830.0030.0030.0000.0000.0000.000
180A190VAL00.013-0.00541.2970.0010.0010.0000.0000.0000.000
181A191ALA00.0350.02742.585-0.001-0.0010.0000.0000.0000.000
182A192VAL00.0030.00344.1270.0040.0040.0000.0000.0000.000
183A193PRO00.0610.02246.047-0.003-0.0030.0000.0000.0000.000
184A194ALA00.0060.00047.3770.0000.0000.0000.0000.0000.000
185A195VAL0-0.025-0.02241.371-0.002-0.0020.0000.0000.0000.000
186A196LEU00.0080.00343.195-0.003-0.0030.0000.0000.0000.000
187A197VAL0-0.032-0.01044.517-0.001-0.0010.0000.0000.0000.000
188A198ARG10.9250.96440.0770.0890.0890.0000.0000.0000.000
189A199LEU0-0.046-0.00138.443-0.006-0.0060.0000.0000.0000.000
190A200ASP-1-0.848-0.91637.515-0.098-0.0980.0000.0000.0000.000
191A201PHE0-0.005-0.00837.879-0.005-0.0050.0000.0000.0000.000
192A202SER0-0.047-0.01639.0220.0020.0020.0000.0000.0000.000
193A203ALA00.0770.00737.636-0.006-0.0060.0000.0000.0000.000
194A204GLU-1-0.872-0.92836.337-0.091-0.0910.0000.0000.0000.000
195A205ARG10.7990.88731.7820.1300.1300.0000.0000.0000.000
196A206SER00.0070.00332.782-0.013-0.0130.0000.0000.0000.000
197A207ILE00.024-0.00331.778-0.008-0.0080.0000.0000.0000.000
198A208THR0-0.033-0.00230.025-0.008-0.0080.0000.0000.0000.000
199A209VAL0-0.021-0.01927.771-0.012-0.0120.0000.0000.0000.000
200A210TYR00.0360.01026.828-0.016-0.0160.0000.0000.0000.000
201A211ASP-1-0.902-0.94426.576-0.151-0.1510.0000.0000.0000.000
202A212GLU-1-1.038-1.01922.295-0.299-0.2990.0000.0000.0000.000
203A213ALA00.0630.01322.585-0.024-0.0240.0000.0000.0000.000
204A214MET0-0.041-0.02721.717-0.023-0.0230.0000.0000.0000.000
205A215ARG10.8970.95220.9920.2050.2050.0000.0000.0000.000
206A216ARG10.8390.92816.6560.3610.3610.0000.0000.0000.000
207A217ARG10.7650.87516.7770.1820.1820.0000.0000.0000.000
208A218GLU-1-0.883-0.94014.669-0.385-0.3850.0000.0000.0000.000
209A219ALA0-0.035-0.00817.338-0.017-0.0170.0000.0000.0000.000
210A220PRO00.0100.03314.531-0.011-0.0110.0000.0000.0000.000
211A221LEU00.0390.01013.6210.0660.0660.0000.0000.0000.000
212A222PRO00.0570.04612.210-0.092-0.0920.0000.0000.0000.000
213A223ALA0-0.017-0.0137.6140.0610.0610.0000.0000.0000.000
214A224ALA00.005-0.0139.3880.0970.0970.0000.0000.0000.000
215A225GLY0-0.067-0.0329.702-0.017-0.0170.0000.0000.0000.000
216A226ASP-1-0.841-0.88910.8420.1110.1110.0000.0000.0000.000
217A227LEU0-0.045-0.02813.140-0.068-0.0680.0000.0000.0000.000
218A228GLU-1-0.921-0.95415.7820.1690.1690.0000.0000.0000.000
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