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: J3ZJ9

Calculation Name: 5IFF-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IFF

Chain ID: B

ChEMBL ID:

UniProt ID: Q9V2B6

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2554764.697793
FMO2-HF: Nuclear repulsion 2468894.409805
FMO2-HF: Total energy -85870.287987
FMO2-MP2: Total energy -86124.783778


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(B:8:GLU)


Summations of interaction energy for fragment #1(B:8:GLU)
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.
-255.346-251.68323.761-13.9-13.5230.134
Interaction energy analysis for fragmet #1(B:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.874 / q_NPA : -0.935
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].
3B10SER0-0.027-0.0213.875-2.223-0.913-0.011-0.583-0.7160.002
4B11VAL0-0.037-0.0156.501-1.804-1.8040.0000.0000.0000.000
5B12SER0-0.049-0.0259.345-0.631-0.6310.0000.0000.0000.000
6B13PHE00.0270.00512.707-0.130-0.1300.0000.0000.0000.000
7B14GLU-1-0.739-0.84715.68216.85316.8530.0000.0000.0000.000
8B15ASN0-0.025-0.01218.7430.0580.0580.0000.0000.0000.000
9B16GLY00.0750.04521.935-0.330-0.3300.0000.0000.0000.000
10B17LYS10.8390.90518.962-13.642-13.6420.0000.0000.0000.000
11B18ILE00.0080.01013.9970.3440.3440.0000.0000.0000.000
12B19VAL0-0.031-0.00613.5980.0500.0500.0000.0000.0000.000
13B20VAL0-0.012-0.0069.0350.9580.9580.0000.0000.0000.000
14B21ARG10.8270.8968.529-21.179-21.1790.0000.0000.0000.000
15B22LEU00.0470.0205.0713.6323.6320.0000.0000.0000.000
16B23PRO0-0.0120.0012.856-5.449-4.6050.146-0.263-0.7270.001
17B24ILE00.0600.0265.7951.6071.6070.0000.0000.0000.000
18B25THR0-0.055-0.0248.459-2.758-2.7580.0000.0000.0000.000
19B26ARG10.8400.9144.724-40.226-40.084-0.001-0.005-0.1360.000
20B27PRO00.0150.0254.8349.1249.194-0.001-0.001-0.0680.000
21B28THR00.003-0.0201.677-30.318-33.62816.000-7.712-4.9780.083
22B29SER0-0.011-0.0254.906-4.446-4.440-0.001-0.0060.0000.000
23B30LYS10.8070.9102.558-63.713-61.6650.979-1.132-1.8940.015
24B31ILE00.0440.0152.232-12.214-10.4581.545-1.160-2.1410.008
25B32ALA00.0040.0094.6972.5912.754-0.001-0.008-0.1530.000
26B33VAL00.0030.0097.704-2.570-2.5700.0000.0000.0000.000
27B34LYS10.8180.89811.007-23.952-23.9520.0000.0000.0000.000
28B35LYS10.8610.93414.083-13.949-13.9490.0000.0000.0000.000
29B36ILE0-0.040-0.02016.7930.3690.3690.0000.0000.0000.000
30B37GLU-1-0.829-0.91419.65012.72512.7250.0000.0000.0000.000
31B38ASN0-0.001-0.00823.0990.0060.0060.0000.0000.0000.000
32B39GLY00.0360.03322.454-0.189-0.1890.0000.0000.0000.000
33B40VAL0-0.0120.00420.0210.8250.8250.0000.0000.0000.000
34B41GLY00.0560.02116.1870.0310.0310.0000.0000.0000.000
35B42ILE00.0250.03115.8711.3971.3970.0000.0000.0000.000
36B43PRO0-0.021-0.02213.0290.9890.9890.0000.0000.0000.000
37B44VAL00.0320.02713.561-1.503-1.5030.0000.0000.0000.000
38B45SER0-0.039-0.01713.4731.4231.4230.0000.0000.0000.000
39B46THR00.059-0.00312.059-1.698-1.6980.0000.0000.0000.000
40B47ARG10.8690.93113.311-19.586-19.5860.0000.0000.0000.000
41B48LYS10.8970.95315.910-18.353-18.3530.0000.0000.0000.000
42B49LYS10.9880.99518.713-15.332-15.3320.0000.0000.0000.000
43B50SER00.0050.00119.3560.7630.7630.0000.0000.0000.000
44B51PHE0-0.026-0.00914.8930.2650.2650.0000.0000.0000.000
45B52PRO00.0050.01320.897-0.483-0.4830.0000.0000.0000.000
46B53SER00.014-0.03223.3500.5490.5490.0000.0000.0000.000
47B54ASP-1-0.864-0.90825.90610.95410.9540.0000.0000.0000.000
48B55GLU-1-0.833-0.90225.08311.31011.3100.0000.0000.0000.000
49B56ASN0-0.005-0.01425.5560.4710.4710.0000.0000.0000.000
50B57LEU0-0.038-0.02018.7700.6010.6010.0000.0000.0000.000
51B58ARG10.9380.94720.319-10.877-10.8770.0000.0000.0000.000
52B59ASP-1-0.844-0.91021.41313.56113.5610.0000.0000.0000.000
53B60TYR0-0.069-0.04016.9060.9440.9440.0000.0000.0000.000
54B61TYR00.0080.00614.709-0.012-0.0120.0000.0000.0000.000
55B62ILE0-0.028-0.0118.1911.4581.4580.0000.0000.0000.000
56B63ALA00.0140.00610.208-1.341-1.3410.0000.0000.0000.000
57B64TRP0-0.018-0.0414.8522.6172.6170.0000.0000.0000.000
58B65GLN00.0320.0337.275-4.645-4.6450.0000.0000.0000.000
59B66ILE0-0.055-0.0217.3102.2762.2760.0000.0000.0000.000
60B67SER00.002-0.0306.238-2.225-2.2250.0000.0000.0000.000
61B68TYR0-0.019-0.0358.797-0.194-0.1940.0000.0000.0000.000
62B69ALA00.0080.01310.552-1.477-1.4770.0000.0000.0000.000
63B70ARG10.8390.8935.406-27.879-27.8790.0000.0000.0000.000
64B71ASP-1-0.816-0.8839.85123.58823.5880.0000.0000.0000.000
65B72GLY00.0440.03612.472-1.189-1.1890.0000.0000.0000.000
66B73LYS10.8620.92611.719-20.521-20.5210.0000.0000.0000.000
67B74TYR0-0.010-0.02512.3901.5931.5930.0000.0000.0000.000
68B75ASP-1-0.824-0.91412.26118.75918.7590.0000.0000.0000.000
69B76TYR0-0.051-0.0282.122-10.610-10.2785.101-2.893-2.5400.026
70B77GLU-1-0.760-0.8303.73345.47845.7800.005-0.137-0.170-0.001
71B78LEU00.1040.0457.793-1.900-1.9000.0000.0000.0000.000
72B79SER0-0.010-0.02511.273-1.220-1.2200.0000.0000.0000.000
73B80ARG10.8810.9269.432-21.980-21.9800.0000.0000.0000.000
74B81MET0-0.026-0.00110.513-0.174-0.1740.0000.0000.0000.000
75B82VAL00.0550.02613.238-1.106-1.1060.0000.0000.0000.000
76B83ARG10.8800.93915.477-16.493-16.4930.0000.0000.0000.000
77B84LEU00.0130.01513.502-0.564-0.5640.0000.0000.0000.000
78B85ALA00.0210.00717.188-0.621-0.6210.0000.0000.0000.000
79B86HIS0-0.020-0.00319.221-0.327-0.3270.0000.0000.0000.000
80B87GLU-1-0.901-0.95118.87013.92813.9280.0000.0000.0000.000
81B88HIS10.7820.88019.199-13.955-13.9550.0000.0000.0000.000
82B89GLY00.0140.01123.165-0.195-0.1950.0000.0000.0000.000
83B90ILE0-0.050-0.01020.185-0.107-0.1070.0000.0000.0000.000
84B91LEU0-0.030-0.01819.7920.1100.1100.0000.0000.0000.000
85B92THR00.021-0.02122.920-0.127-0.1270.0000.0000.0000.000
86B93TYR00.0500.00625.8330.2670.2670.0000.0000.0000.000
87B94ASN00.0370.01527.9290.1110.1110.0000.0000.0000.000
88B95ASP-1-0.791-0.85824.60111.22811.2280.0000.0000.0000.000
89B96ILE0-0.001-0.00622.6550.3170.3170.0000.0000.0000.000
90B97TYR0-0.006-0.00625.141-0.054-0.0540.0000.0000.0000.000
91B98GLU-1-0.854-0.91226.67210.84610.8460.0000.0000.0000.000
92B99LEU0-0.039-0.01321.5750.0950.0950.0000.0000.0000.000
93B100LEU0-0.017-0.01724.8380.0770.0770.0000.0000.0000.000
94B101LYS10.8060.87927.054-9.381-9.3810.0000.0000.0000.000
95B102PHE00.0160.01024.073-0.136-0.1360.0000.0000.0000.000
96B103ALA0-0.005-0.01224.906-0.004-0.0040.0000.0000.0000.000
97B104ASP-1-0.898-0.92726.6469.2259.2250.0000.0000.0000.000
98B105ASP-1-0.846-0.90130.2198.9458.9450.0000.0000.0000.000
99B106VAL0-0.030-0.00526.187-0.205-0.2050.0000.0000.0000.000
100B107LYS10.8100.87829.374-9.386-9.3860.0000.0000.0000.000
101B108SER00.0150.02429.724-0.271-0.2710.0000.0000.0000.000
102B109TYR0-0.129-0.10224.4810.3660.3660.0000.0000.0000.000
103B110LEU0-0.035-0.01721.068-0.265-0.2650.0000.0000.0000.000
104B111GLU-1-0.790-0.89520.97914.67014.6700.0000.0000.0000.000
105B112ASP-1-0.801-0.89125.02610.92010.9200.0000.0000.0000.000
106B113LYS10.8670.93627.375-10.975-10.9750.0000.0000.0000.000
107B114GLY00.0020.00927.059-0.233-0.2330.0000.0000.0000.000
108B115ILE0-0.060-0.04022.8520.3400.3400.0000.0000.0000.000
109B116ARG10.8030.87927.482-10.101-10.1010.0000.0000.0000.000
110B117ARG10.8460.88830.428-9.877-9.8770.0000.0000.0000.000
111B118GLU-1-0.825-0.87932.8739.0759.0750.0000.0000.0000.000
112B119SER00.0200.00635.7330.1090.1090.0000.0000.0000.000
113B120THR0-0.009-0.01636.850-0.103-0.1030.0000.0000.0000.000
114B121ASN0-0.035-0.02739.702-0.030-0.0300.0000.0000.0000.000
115B122GLU-1-0.923-0.94938.8778.0338.0330.0000.0000.0000.000
116B123GLU-1-0.899-0.96341.1497.2377.2370.0000.0000.0000.000
117B124LEU0-0.038-0.01536.5720.0010.0010.0000.0000.0000.000
118B125TYR0-0.051-0.04940.512-0.039-0.0390.0000.0000.0000.000
119B126GLY00.0670.04643.665-0.062-0.0620.0000.0000.0000.000
120B127PHE0-0.067-0.01839.1780.0120.0120.0000.0000.0000.000
121B128ASN0-0.019-0.01540.2610.1010.1010.0000.0000.0000.000
122B129ILE00.0150.01535.4500.2460.2460.0000.0000.0000.000
123B130TYR0-0.039-0.01134.767-0.176-0.1760.0000.0000.0000.000
124B131GLU-1-0.912-0.94931.8359.7929.7920.0000.0000.0000.000
125B132ASP-1-0.820-0.87327.91410.67310.6730.0000.0000.0000.000
126B133VAL0-0.001-0.00827.8500.4610.4610.0000.0000.0000.000
127B134TYR0-0.016-0.01522.1820.2760.2760.0000.0000.0000.000
128B135PRO0-0.0200.01224.6020.0350.0350.0000.0000.0000.000
129B136VAL0-0.025-0.03520.2410.8040.8040.0000.0000.0000.000
130B137ALA0-0.0060.00721.502-0.678-0.6780.0000.0000.0000.000
131B138LYS10.8380.91120.212-13.136-13.1360.0000.0000.0000.000
132B139LYS10.8450.91520.934-13.432-13.4320.0000.0000.0000.000
133B140GLU-1-0.867-0.94320.94613.75313.7530.0000.0000.0000.000
134B141LEU00.0100.01719.349-0.472-0.4720.0000.0000.0000.000
135B142PRO00.0240.00622.8590.1170.1170.0000.0000.0000.000
136B143SER0-0.010-0.00221.309-0.464-0.4640.0000.0000.0000.000
137B144GLY00.0350.03521.4040.1740.1740.0000.0000.0000.000
138B145GLU-1-0.847-0.90616.39316.73316.7330.0000.0000.0000.000
139B146PHE00.0050.00917.569-0.691-0.6910.0000.0000.0000.000
140B147ILE0-0.016-0.01316.3141.4581.4580.0000.0000.0000.000
141B148GLY00.0160.00416.279-1.085-1.0850.0000.0000.0000.000
142B149ILE0-0.033-0.01516.5041.1401.1400.0000.0000.0000.000
143B150VAL00.0230.01715.873-0.773-0.7730.0000.0000.0000.000
144B151LEU00.0290.02618.2600.6980.6980.0000.0000.0000.000
145B152LYS10.8550.91312.908-22.655-22.6550.0000.0000.0000.000
146B153HIS00.0900.02819.343-0.482-0.4820.0000.0000.0000.000
147B154LYS10.8950.96718.475-15.421-15.4210.0000.0000.0000.000
148B155GLN00.0430.02114.737-0.935-0.9350.0000.0000.0000.000
149B156ARG10.8700.91317.412-16.971-16.9710.0000.0000.0000.000
150B157ALA00.0060.01322.195-0.400-0.4000.0000.0000.0000.000
151B158VAL00.0560.02924.2760.2070.2070.0000.0000.0000.000
152B159GLY00.0270.02925.5300.1750.1750.0000.0000.0000.000
153B160TYR00.0260.01122.3610.2570.2570.0000.0000.0000.000
154B161GLN0-0.018-0.01915.297-0.214-0.2140.0000.0000.0000.000
155B162SER0-0.009-0.02518.3880.6270.6270.0000.0000.0000.000
156B163MET0-0.087-0.02212.7811.3141.3140.0000.0000.0000.000
157B164VAL00.0370.02413.681-0.472-0.4720.0000.0000.0000.000
158B165TYR0-0.042-0.0499.8601.7201.7200.0000.0000.0000.000
159B166VAL00.0140.02210.638-1.856-1.8560.0000.0000.0000.000
160B167CYS0-0.052-0.03111.8962.4002.4000.0000.0000.0000.000
161B168ILE00.0450.03111.077-1.355-1.3550.0000.0000.0000.000
162B169PRO00.0480.03614.0811.2881.2880.0000.0000.0000.000
163B170LEU0-0.012-0.03813.0210.2780.2780.0000.0000.0000.000
164B171THR0-0.031-0.02216.375-0.236-0.2360.0000.0000.0000.000
165B172ASN0-0.057-0.02517.003-0.912-0.9120.0000.0000.0000.000
166B173VAL0-0.047-0.02212.6560.7070.7070.0000.0000.0000.000
167B174GLU-1-0.916-0.92814.96713.96213.9620.0000.0000.0000.000
168B175PRO0-0.036-0.04214.4311.1051.1050.0000.0000.0000.000
169B176SER00.0960.03716.4200.9100.9100.0000.0000.0000.000
170B177LEU0-0.003-0.02214.2060.1790.1790.0000.0000.0000.000
171B178ALA00.0000.01518.243-0.132-0.1320.0000.0000.0000.000
172B179GLY00.0140.01021.889-0.182-0.1820.0000.0000.0000.000
173B180ARG10.7540.86716.204-17.234-17.2340.0000.0000.0000.000
174B181VAL00.0110.01418.2680.5310.5310.0000.0000.0000.000
175B182ALA00.0440.02313.461-0.153-0.1530.0000.0000.0000.000
176B183ARG10.9120.93514.935-17.088-17.0880.0000.0000.0000.000
177B184ARG10.9460.95113.601-15.476-15.4760.0000.0000.0000.000
178B185ASN00.0210.0149.6081.4231.4230.0000.0000.0000.000
179B186GLU-1-0.715-0.79410.10119.51419.5140.0000.0000.0000.000
180B187VAL00.001-0.0116.9293.3023.3020.0000.0000.0000.000
181B188VAL0-0.0040.0229.233-1.946-1.9460.0000.0000.0000.000
182B189LYS10.8340.9029.954-14.525-14.5250.0000.0000.0000.000
183B190TYR0-0.007-0.03311.834-0.240-0.2400.0000.0000.0000.000
184B191GLU-1-0.762-0.87213.52615.54715.5470.0000.0000.0000.000
185B192VAL0-0.015-0.00813.095-0.169-0.1690.0000.0000.0000.000
186B193PRO00.0350.02816.243-0.680-0.6800.0000.0000.0000.000
187B194VAL00.049-0.00218.7220.5890.5890.0000.0000.0000.000
188B195ASP-1-0.871-0.93420.52913.24513.2450.0000.0000.0000.000
189B196LEU00.0420.02414.5390.2480.2480.0000.0000.0000.000
190B197MET0-0.044-0.01515.2710.9470.9470.0000.0000.0000.000
191B198LYS10.8420.91117.259-11.359-11.3590.0000.0000.0000.000
192B199GLU-1-0.719-0.86020.15212.78612.7860.0000.0000.0000.000
193B200LEU0-0.019-0.00212.9030.3510.3510.0000.0000.0000.000
194B201LEU0-0.015-0.00516.5090.3290.3290.0000.0000.0000.000
195B202LYS10.8740.92618.104-12.389-12.3890.0000.0000.0000.000
196B203ALA00.0230.01417.470-0.379-0.3790.0000.0000.0000.000
197B204PHE0-0.003-0.02912.209-0.223-0.2230.0000.0000.0000.000
198B205ILE0-0.056-0.01818.153-0.353-0.3530.0000.0000.0000.000
199B206ILE00.0560.02321.731-0.498-0.4980.0000.0000.0000.000
200B207ALA0-0.032-0.00219.026-0.239-0.2390.0000.0000.0000.000
201B208SER00.030-0.00920.976-0.157-0.1570.0000.0000.0000.000
202B209GLU-1-0.791-0.84922.24711.15211.1520.0000.0000.0000.000
203B210THR00.0100.00319.951-0.095-0.0950.0000.0000.0000.000
204B211HIS10.8080.89615.972-17.100-17.1000.0000.0000.0000.000
205B212LYS10.8930.97019.380-10.763-10.7630.0000.0000.0000.000
206B213ASN00.0420.00722.230-0.181-0.1810.0000.0000.0000.000
207B214ASP-1-0.789-0.83317.59716.15116.1510.0000.0000.0000.000
208B215ILE0-0.028-0.01415.7720.0600.0600.0000.0000.0000.000
209B216VAL00.0240.01519.462-0.301-0.3010.0000.0000.0000.000
210B217LYS10.8880.94721.557-12.760-12.7600.0000.0000.0000.000
211B218PHE0-0.027-0.02116.487-0.063-0.0630.0000.0000.0000.000
212B219LEU00.0320.01219.864-0.256-0.2560.0000.0000.0000.000
213B220ARG10.9540.96821.933-10.893-10.8930.0000.0000.0000.000
214B221SER0-0.046-0.02621.804-0.398-0.3980.0000.0000.0000.000
215B222ILE0-0.0360.00618.8080.1070.1070.0000.0000.0000.000
216B223ILE0-0.036-0.00722.853-0.712-0.7120.0000.0000.0000.000