FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: VQ2K1

Calculation Name: 3IBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IBX

Chain ID: A

ChEMBL ID:

UniProt ID: A8KRL3

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 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2826488.811354
FMO2-HF: Nuclear repulsion 2736472.923032
FMO2-HF: Total energy -90015.888322
FMO2-MP2: Total energy -90276.630066


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:-3:ASP)


Summations of interaction energy for fragment #1(A:-3:ASP)
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.
86.03180.8935.0283.551-3.440.002
Interaction energy analysis for fragmet #1(A:-3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.933 / q_NPA : -0.974
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].
3A-1PHE0-0.048-0.0222.8180.447-4.156-0.1135.566-0.849-0.003
4A0THR0-0.0280.0012.151-8.788-9.6175.143-2.000-2.3150.005
5A1MET00.0000.0044.5941.3801.515-0.001-0.009-0.1240.000
6A2GLN00.0440.0265.1935.4115.4110.0000.0000.0000.000
7A3VAL00.0660.0117.188-4.660-4.6600.0000.0000.0000.000
8A4SER0-0.023-0.0369.021-3.598-3.5980.0000.0000.0000.000
9A5GLN0-0.016-0.0109.650-4.068-4.0680.0000.0000.0000.000
10A6TYR0-0.056-0.03811.637-2.354-2.3540.0000.0000.0000.000
11A7LEU0-0.023-0.00313.580-1.878-1.8780.0000.0000.0000.000
12A8TYR00.0200.01514.739-1.227-1.2270.0000.0000.0000.000
13A9GLN0-0.004-0.01615.324-2.188-2.1880.0000.0000.0000.000
14A10ASN0-0.093-0.05417.272-1.750-1.7500.0000.0000.0000.000
15A11ALA00.0320.03119.585-0.778-0.7780.0000.0000.0000.000
16A12GLN0-0.055-0.02119.687-1.097-1.0970.0000.0000.0000.000
17A13SER0-0.030-0.01422.393-0.561-0.5610.0000.0000.0000.000
18A14ILE00.0960.05324.922-0.342-0.3420.0000.0000.0000.000
19A15TRP00.007-0.02618.594-0.163-0.1630.0000.0000.0000.000
20A16GLY0-0.0080.00325.556-0.254-0.2540.0000.0000.0000.000
21A17ASP-1-0.877-0.94027.54910.10810.1080.0000.0000.0000.000
22A18CYS0-0.096-0.04728.002-0.368-0.3680.0000.0000.0000.000
23A19ILE0-0.016-0.00325.807-0.360-0.3600.0000.0000.0000.000
24A20SER0-0.068-0.02930.098-0.417-0.4170.0000.0000.0000.000
25A21HIS00.0540.04833.054-0.345-0.3450.0000.0000.0000.000
26A22PRO0-0.002-0.01534.982-0.001-0.0010.0000.0000.0000.000
27A23PHE00.015-0.00635.393-0.137-0.1370.0000.0000.0000.000
28A24VAL00.0440.03131.115-0.083-0.0830.0000.0000.0000.000
29A25GLN0-0.026-0.03633.199-0.268-0.2680.0000.0000.0000.000
30A26GLY0-0.015-0.00936.174-0.155-0.1550.0000.0000.0000.000
31A27ILE0-0.029-0.01434.226-0.194-0.1940.0000.0000.0000.000
32A28GLY00.0100.01135.150-0.050-0.0500.0000.0000.0000.000
33A29ARG10.8770.94435.801-8.526-8.5260.0000.0000.0000.000
34A30GLY00.0410.01339.280-0.134-0.1340.0000.0000.0000.000
35A31THR0-0.083-0.05341.160-0.150-0.1500.0000.0000.0000.000
36A32LEU0-0.0250.02338.663-0.164-0.1640.0000.0000.0000.000
37A33GLU-1-0.838-0.89442.2327.2607.2600.0000.0000.0000.000
38A34ARG10.9780.97544.040-7.045-7.0450.0000.0000.0000.000
39A35ASP-1-0.934-0.97444.4916.8826.8820.0000.0000.0000.000
40A36LYS10.9541.00042.211-7.270-7.2700.0000.0000.0000.000
41A37PHE00.0150.00736.4140.1590.1590.0000.0000.0000.000
42A38ARG10.8280.89640.267-6.780-6.7800.0000.0000.0000.000
43A39PHE0-0.012-0.00640.8880.0740.0740.0000.0000.0000.000
44A40TYR00.0330.00132.0850.0000.0000.0000.0000.0000.000
45A41ILE00.0060.00937.2210.2020.2020.0000.0000.0000.000
46A42ILE0-0.021-0.00538.1460.1050.1050.0000.0000.0000.000
47A43GLN00.000-0.00537.5230.2570.2570.0000.0000.0000.000
48A44ASP-1-0.814-0.88832.41610.23810.2380.0000.0000.0000.000
49A45TYR00.0150.00534.1690.2170.2170.0000.0000.0000.000
50A46LEU0-0.038-0.02535.8130.1150.1150.0000.0000.0000.000
51A47TYR00.006-0.00927.1790.0670.0670.0000.0000.0000.000
52A48LEU00.004-0.01229.6740.3260.3260.0000.0000.0000.000
53A49LEU0-0.0160.00431.4600.2400.2400.0000.0000.0000.000
54A50GLU-1-0.941-0.97932.5849.3549.3540.0000.0000.0000.000
55A51TYR0-0.015-0.02422.9540.1890.1890.0000.0000.0000.000
56A52ALA00.0410.01427.6580.4450.4450.0000.0000.0000.000
57A53LYS10.8840.94428.690-9.096-9.0960.0000.0000.0000.000
58A54VAL0-0.0020.00724.3480.0960.0960.0000.0000.0000.000
59A55PHE00.0380.01021.5860.4690.4690.0000.0000.0000.000
60A56ALA0-0.012-0.00725.0530.2840.2840.0000.0000.0000.000
61A57LEU0-0.024-0.02425.523-0.018-0.0180.0000.0000.0000.000
62A58GLY00.0200.01622.4560.2760.2760.0000.0000.0000.000
63A59VAL0-0.041-0.01722.7700.3800.3800.0000.0000.0000.000
64A60VAL0-0.049-0.02125.0760.0040.0040.0000.0000.0000.000
65A61LYS10.8320.91822.789-12.666-12.6660.0000.0000.0000.000
66A62ALA00.0150.02820.3080.6900.6900.0000.0000.0000.000
67A63CYS0-0.083-0.04819.626-0.629-0.6290.0000.0000.0000.000
68A64ASP-1-0.791-0.91116.85719.21019.2100.0000.0000.0000.000
69A65GLU-1-0.874-0.93919.82212.84312.8430.0000.0000.0000.000
70A66ALA0-0.023-0.00117.488-0.554-0.5540.0000.0000.0000.000
71A67VAL00.0770.03515.891-0.354-0.3540.0000.0000.0000.000
72A68MET0-0.076-0.02618.896-0.760-0.7600.0000.0000.0000.000
73A69ARG10.8670.92921.888-14.395-14.3950.0000.0000.0000.000
74A70GLU-1-0.870-0.92717.17618.57218.5720.0000.0000.0000.000
75A71PHE00.0250.00918.840-0.349-0.3490.0000.0000.0000.000
76A72SER0-0.060-0.03422.950-0.689-0.6890.0000.0000.0000.000
77A73ASN00.002-0.02023.471-1.000-1.0000.0000.0000.0000.000
78A74ALA00.0460.04123.110-0.354-0.3540.0000.0000.0000.000
79A75ILE0-0.037-0.01225.198-0.476-0.4760.0000.0000.0000.000
80A76GLN0-0.028-0.01728.443-0.641-0.6410.0000.0000.0000.000
81A77ASP-1-0.890-0.93926.55611.63311.6330.0000.0000.0000.000
82A78ILE0-0.080-0.03527.492-0.267-0.2670.0000.0000.0000.000
83A79LEU0-0.074-0.04731.077-0.369-0.3690.0000.0000.0000.000
84A80ASN0-0.066-0.02533.179-0.519-0.5190.0000.0000.0000.000
85A81ASN00.0740.04430.532-0.147-0.1470.0000.0000.0000.000
86A82GLU-1-0.905-0.94034.1968.8858.8850.0000.0000.0000.000
87A83MET0-0.030-0.02533.991-0.303-0.3030.0000.0000.0000.000
88A84SER0-0.0220.00432.3140.1390.1390.0000.0000.0000.000
89A85ILE00.005-0.01029.532-0.359-0.3590.0000.0000.0000.000
90A86HIS10.8680.90032.054-10.054-10.0540.0000.0000.0000.000
91A87ASN00.008-0.01135.760-0.431-0.4310.0000.0000.0000.000
92A88HIS0-0.0300.00037.187-0.218-0.2180.0000.0000.0000.000
93A89TYR00.014-0.04335.947-0.126-0.1260.0000.0000.0000.000
94A90ILE00.0030.01539.075-0.224-0.2240.0000.0000.0000.000
95A91ARG10.9110.97139.759-8.210-8.2100.0000.0000.0000.000
96A92GLU-1-0.944-0.96042.6447.1677.1670.0000.0000.0000.000
97A93LEU0-0.069-0.02941.939-0.171-0.1710.0000.0000.0000.000
98A94GLN0-0.058-0.04145.546-0.187-0.1870.0000.0000.0000.000
99A95ILE0-0.0130.01142.454-0.146-0.1460.0000.0000.0000.000
100A96THR0-0.005-0.00446.0150.0380.0380.0000.0000.0000.000
101A97GLN00.0750.01543.4500.1930.1930.0000.0000.0000.000
102A98LYS10.9580.97646.341-5.997-5.9970.0000.0000.0000.000
103A99GLU-1-0.829-0.90146.9656.8136.8130.0000.0000.0000.000
104A100LEU00.0000.00441.2060.0430.0430.0000.0000.0000.000
105A101GLN0-0.043-0.02543.6040.1260.1260.0000.0000.0000.000
106A102ASN0-0.024-0.01545.5480.0270.0270.0000.0000.0000.000
107A103ALA0-0.0160.02243.293-0.072-0.0720.0000.0000.0000.000
108A104CYS0-0.018-0.00843.6040.0480.0480.0000.0000.0000.000
109A105PRO00.0200.02438.7110.0080.0080.0000.0000.0000.000
110A106THR00.020-0.04039.139-0.104-0.1040.0000.0000.0000.000
111A107LEU00.026-0.00938.8520.1700.1700.0000.0000.0000.000
112A108ALA00.0120.01735.8180.1720.1720.0000.0000.0000.000
113A109ASN0-0.002-0.00734.5250.5190.5190.0000.0000.0000.000
114A110LYS10.9860.97734.173-7.615-7.6150.0000.0000.0000.000
115A111SER0-0.0410.00834.3100.1160.1160.0000.0000.0000.000
116A112TYR00.004-0.00926.3740.3010.3010.0000.0000.0000.000
117A113THR00.0230.00529.8080.3010.3010.0000.0000.0000.000
118A114SER0-0.043-0.04830.6840.1240.1240.0000.0000.0000.000
119A115TYR00.0010.01125.1740.2090.2090.0000.0000.0000.000
120A116MET00.0150.01625.3300.4280.4280.0000.0000.0000.000
121A117LEU00.0130.01026.4340.3460.3460.0000.0000.0000.000
122A118ALA0-0.044-0.01728.5340.1390.1390.0000.0000.0000.000
123A119GLU-1-0.881-0.94624.50612.25212.2520.0000.0000.0000.000
124A120GLY00.0220.01724.0570.4340.4340.0000.0000.0000.000
125A121PHE0-0.098-0.06225.1380.1490.1490.0000.0000.0000.000
126A122LYS10.8750.93227.360-11.343-11.3430.0000.0000.0000.000
127A123GLY0-0.0360.00823.2370.0430.0430.0000.0000.0000.000
128A124SER0-0.068-0.05519.734-0.092-0.0920.0000.0000.0000.000
129A125ILE00.0780.01217.270-0.161-0.1610.0000.0000.0000.000
130A126LYS10.9450.98714.892-20.322-20.3220.0000.0000.0000.000
131A127GLU-1-0.750-0.87017.04616.32316.3230.0000.0000.0000.000
132A128VAL0-0.0050.01119.999-0.264-0.2640.0000.0000.0000.000
133A129ALA0-0.006-0.00215.755-0.245-0.2450.0000.0000.0000.000
134A130ALA00.003-0.00716.8590.2170.2170.0000.0000.0000.000
135A131ALA0-0.022-0.01617.948-0.417-0.4170.0000.0000.0000.000
136A132VAL0-0.018-0.00519.790-0.659-0.6590.0000.0000.0000.000
137A133LEU00.0260.04414.699-0.258-0.2580.0000.0000.0000.000
138A134SER00.019-0.00219.1610.1670.1670.0000.0000.0000.000
139A135CYS0-0.0240.04321.378-0.255-0.2550.0000.0000.0000.000
140A136GLY00.0550.01521.786-0.311-0.3110.0000.0000.0000.000
141A137TRP00.025-0.00713.4040.0870.0870.0000.0000.0000.000
142A138SER00.019-0.00520.159-0.326-0.3260.0000.0000.0000.000
143A139TYR00.0360.01923.192-0.598-0.5980.0000.0000.0000.000
144A140LEU0-0.0110.01219.198-0.381-0.3810.0000.0000.0000.000
145A141VAL00.001-0.00420.607-0.329-0.3290.0000.0000.0000.000
146A142ILE0-0.0020.00323.275-0.505-0.5050.0000.0000.0000.000
147A143ALA0-0.012-0.00126.506-0.445-0.4450.0000.0000.0000.000
148A144GLN0-0.017-0.02620.849-0.048-0.0480.0000.0000.0000.000
149A145ASN0-0.043-0.00325.871-0.576-0.5760.0000.0000.0000.000
150A146LEU00.029-0.00627.756-0.391-0.3910.0000.0000.0000.000
151A147SER0-0.056-0.02028.409-0.360-0.3600.0000.0000.0000.000
152A148GLN0-0.090-0.04627.5370.1160.1160.0000.0000.0000.000
153A149ILE0-0.0100.04432.004-0.043-0.0430.0000.0000.0000.000
154A150PRO00.028-0.00635.271-0.120-0.1200.0000.0000.0000.000
155A151ASN0-0.049-0.05836.543-0.171-0.1710.0000.0000.0000.000
156A152ALA00.0390.03334.437-0.121-0.1210.0000.0000.0000.000
157A153LEU0-0.033-0.01831.2180.0100.0100.0000.0000.0000.000
158A154GLU-1-0.918-0.96935.2928.7758.7750.0000.0000.0000.000
159A155HIS0-0.0220.02838.758-0.223-0.2230.0000.0000.0000.000
160A156ALA00.016-0.00640.0740.1110.1110.0000.0000.0000.000
161A157PHE0-0.035-0.00841.163-0.016-0.0160.0000.0000.0000.000
162A158TYR00.007-0.04137.5280.1180.1180.0000.0000.0000.000
163A159GLY00.0600.05436.2140.2690.2690.0000.0000.0000.000
164A160HIS0-0.051-0.03134.7420.2440.2440.0000.0000.0000.000
165A161TRP00.0330.01330.3270.2870.2870.0000.0000.0000.000
166A162ILE00.0330.02730.7180.3900.3900.0000.0000.0000.000
167A163LYS10.9771.01429.789-9.172-9.1720.0000.0000.0000.000
168A164GLY0-0.002-0.00929.3120.3510.3510.0000.0000.0000.000
169A165TYR00.001-0.00626.6220.2010.2010.0000.0000.0000.000
170A166SER00.017-0.01425.1010.5190.5190.0000.0000.0000.000
171A167SER0-0.068-0.01225.1190.4340.4340.0000.0000.0000.000
172A168LYS10.9370.94322.737-11.759-11.7590.0000.0000.0000.000
173A169GLU-1-0.829-0.91721.96612.92012.9200.0000.0000.0000.000
174A170PHE00.0050.01322.5630.4560.4560.0000.0000.0000.000
175A171GLN0-0.033-0.02719.3911.2431.2430.0000.0000.0000.000
176A172ALA0-0.022-0.00218.0301.1471.1470.0000.0000.0000.000
177A173CYS0-0.0020.01017.8070.7560.7560.0000.0000.0000.000
178A174VAL00.0330.01616.6160.6810.6810.0000.0000.0000.000
179A175ASN0-0.005-0.01614.0791.6051.6050.0000.0000.0000.000
180A176TRP0-0.074-0.02113.1601.9321.9320.0000.0000.0000.000
181A177ASN0-0.008-0.01314.0060.2940.2940.0000.0000.0000.000
182A178ILE0-0.004-0.00210.3290.5630.5630.0000.0000.0000.000
183A179ASN00.012-0.0039.2164.3874.3870.0000.0000.0000.000
184A180LEU0-0.0230.0089.7032.3752.3750.0000.0000.0000.000
185A181LEU00.020-0.00111.6660.6350.6350.0000.0000.0000.000
186A182ASP-1-0.780-0.8606.36037.01937.0190.0000.0000.0000.000
187A183SER0-0.071-0.0307.5632.0562.0560.0000.0000.0000.000
188A184LEU0-0.036-0.0208.605-1.292-1.2920.0000.0000.0000.000
189A185THR0-0.062-0.0609.882-1.180-1.1800.0000.0000.0000.000
190A186LEU00.0040.0154.691-0.744-0.585-0.001-0.006-0.1520.000
191A187ALA0-0.029-0.0138.2260.0250.0250.0000.0000.0000.000
192A188SER0-0.049-0.01211.157-1.746-1.7460.0000.0000.0000.000
193A189SER0-0.0120.00212.9210.5460.5460.0000.0000.0000.000
194A190LYN00.0850.01615.4300.5330.5330.0000.0000.0000.000
195A191GLN0-0.0040.00216.730-0.082-0.0820.0000.0000.0000.000
196A192GLU-1-0.881-0.95216.50218.65918.6590.0000.0000.0000.000
197A193ILE00.0210.01211.940-0.195-0.1950.0000.0000.0000.000
198A194GLU-1-0.822-0.91015.79316.18316.1830.0000.0000.0000.000
199A195LYS10.9320.98119.157-14.715-14.7150.0000.0000.0000.000
200A196LEU0-0.002-0.01014.723-0.394-0.3940.0000.0000.0000.000
201A197LYS10.8790.94817.558-15.961-15.9610.0000.0000.0000.000
202A198GLU-1-0.932-0.96218.69512.12712.1270.0000.0000.0000.000
203A199ILE00.0010.01720.726-0.557-0.5570.0000.0000.0000.000
204A200PHE0-0.011-0.00817.828-0.375-0.3750.0000.0000.0000.000
205A201ILE00.0250.00420.654-0.268-0.2680.0000.0000.0000.000
206A202THR00.0140.01223.087-0.680-0.6800.0000.0000.0000.000
207A203THR0-0.056-0.03422.926-0.364-0.3640.0000.0000.0000.000
208A204SER00.0100.01122.528-0.264-0.2640.0000.0000.0000.000
209A205GLU-1-0.931-0.96725.19710.81110.8110.0000.0000.0000.000
210A206TYR0-0.042-0.03528.325-0.644-0.6440.0000.0000.0000.000
211A207GLU-1-0.778-0.88625.89911.26611.2660.0000.0000.0000.000
212A208TYR0-0.0030.00229.111-0.360-0.3600.0000.0000.0000.000
213A209LEU0-0.008-0.01531.065-0.397-0.3970.0000.0000.0000.000
214A210PHE0-0.046-0.01032.126-0.427-0.4270.0000.0000.0000.000
215A211TRP00.0230.00229.255-0.502-0.5020.0000.0000.0000.000
216A212ASP-1-0.873-0.93334.5728.2278.2270.0000.0000.0000.000
217A213MET0-0.0850.01136.724-0.444-0.4440.0000.0000.0000.000
218A214ALA00.0030.00137.077-0.224-0.2240.0000.0000.0000.000
219A215TYR00.009-0.00338.870-0.262-0.2620.0000.0000.0000.000
220A216GLN0-0.083-0.03940.608-0.332-0.3320.0000.0000.0000.000
221A217SER0-0.045-0.01142.743-0.184-0.1840.0000.0000.0000.000