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

tag_button

FMODB ID: N1M5Q

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2551386.467403
FMO2-HF: Nuclear repulsion 2465516.770922
FMO2-HF: Total energy -85869.696481
FMO2-MP2: Total energy -86124.224979


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.
-229.804-219.4943.358-5.936-7.7270.056
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 : -0.936 / q_NPA : -0.977
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].
3B10SER0-0.009-0.0053.845-4.542-3.052-0.015-0.757-0.7180.003
4B11VAL0-0.023-0.0066.530-0.909-0.9090.0000.0000.0000.000
5B12SER0-0.046-0.0219.300-0.744-0.7440.0000.0000.0000.000
6B13PHE00.0350.00912.791-0.088-0.0880.0000.0000.0000.000
7B14GLU-1-0.788-0.86715.25016.88716.8870.0000.0000.0000.000
8B15ASN0-0.006-0.01018.6320.1140.1140.0000.0000.0000.000
9B16GLY00.0520.02421.890-0.216-0.2160.0000.0000.0000.000
10B17LYS10.8470.92319.345-13.441-13.4410.0000.0000.0000.000
11B18ILE00.0010.00713.9510.3800.3800.0000.0000.0000.000
12B19VAL0-0.0120.01213.1750.2610.2610.0000.0000.0000.000
13B20VAL0-0.008-0.0188.9450.9520.9520.0000.0000.0000.000
14B21ARG10.8000.8718.655-20.881-20.8810.0000.0000.0000.000
15B22LEU00.0360.0065.3583.5533.5530.0000.0000.0000.000
16B23PRO00.0120.0192.942-5.768-5.0550.118-0.178-0.6530.000
17B24ILE00.0570.0255.8722.5942.5940.0000.0000.0000.000
18B25THR0-0.045-0.0228.324-2.466-2.4660.0000.0000.0000.000
19B26ARG10.8190.9154.822-43.451-43.333-0.001-0.003-0.1130.000
20B27PRO00.0170.0205.0719.7149.778-0.0010.000-0.0630.000
21B28THR00.0130.0002.174-21.946-17.7662.055-3.191-3.0440.043
22B29SER0-0.010-0.0245.357-3.600-3.615-0.0010.0000.0170.000
23B30LYS10.8220.9133.224-62.891-61.5680.059-0.586-0.7960.005
24B31ILE00.0650.0412.314-9.088-7.6621.095-0.909-1.6100.006
25B32ALA00.0130.0155.0832.3552.478-0.001-0.002-0.1190.000
26B33VAL00.0140.0197.996-2.058-2.0580.0000.0000.0000.000
27B34LYS10.8190.90411.298-23.272-23.2720.0000.0000.0000.000
28B35LYS10.8800.92814.321-14.046-14.0460.0000.0000.0000.000
29B36ILE0-0.043-0.02817.2940.1380.1380.0000.0000.0000.000
30B37GLU-1-0.824-0.90820.11812.76712.7670.0000.0000.0000.000
31B38ASN00.010-0.00523.4780.0090.0090.0000.0000.0000.000
32B39GLY00.0120.02022.757-0.161-0.1610.0000.0000.0000.000
33B40VAL00.0030.01120.5250.9400.9400.0000.0000.0000.000
34B41GLY00.0480.02016.7500.0270.0270.0000.0000.0000.000
35B42ILE00.0060.01516.6241.1521.1520.0000.0000.0000.000
36B43PRO0-0.019-0.00713.2681.0881.0880.0000.0000.0000.000
37B44VAL00.0310.02213.597-1.493-1.4930.0000.0000.0000.000
38B45SER0-0.050-0.02213.1801.5561.5560.0000.0000.0000.000
39B46THR00.050-0.00711.931-1.705-1.7050.0000.0000.0000.000
40B47ARG10.8690.93413.378-20.358-20.3580.0000.0000.0000.000
41B48LYS10.9300.96816.065-18.738-18.7380.0000.0000.0000.000
42B49LYS11.0131.00319.130-15.365-15.3650.0000.0000.0000.000
43B50SER00.0320.01619.6240.8300.8300.0000.0000.0000.000
44B51PHE0-0.038-0.00915.1900.2340.2340.0000.0000.0000.000
45B52PRO0-0.023-0.00421.249-0.425-0.4250.0000.0000.0000.000
46B53SER00.013-0.03323.7750.4860.4860.0000.0000.0000.000
47B54ASP-1-0.875-0.91426.39010.93710.9370.0000.0000.0000.000
48B55GLU-1-0.839-0.91325.36311.36011.3600.0000.0000.0000.000
49B56ASN00.005-0.01425.8090.4250.4250.0000.0000.0000.000
50B57LEU0-0.021-0.00919.1920.6210.6210.0000.0000.0000.000
51B58ARG10.9330.95720.631-10.827-10.8270.0000.0000.0000.000
52B59ASP-1-0.850-0.91621.42713.85113.8510.0000.0000.0000.000
53B60TYR0-0.074-0.03816.7961.0031.0030.0000.0000.0000.000
54B61TYR00.0180.01515.027-0.022-0.0220.0000.0000.0000.000
55B62ILE0-0.028-0.0158.3981.6141.6140.0000.0000.0000.000
56B63ALA0-0.005-0.01810.326-1.479-1.4790.0000.0000.0000.000
57B64TRP00.011-0.0135.5622.5902.5900.0000.0000.0000.000
58B65GLN00.000-0.0027.720-3.843-3.8430.0000.0000.0000.000
59B66ILE0-0.0390.0007.9953.2183.2180.0000.0000.0000.000
60B67SER00.005-0.0287.461-1.914-1.9140.0000.0000.0000.000
61B68TYR0-0.032-0.0409.862-0.014-0.0140.0000.0000.0000.000
62B69ALA00.0050.01010.843-1.372-1.3720.0000.0000.0000.000
63B70ARG10.8520.9115.137-25.931-25.9310.0000.0000.0000.000
64B71ASP-1-0.826-0.8969.90922.41322.4130.0000.0000.0000.000
65B72GLY00.0290.02712.612-1.104-1.1040.0000.0000.0000.000
66B73LYS10.9310.97211.529-18.776-18.7760.0000.0000.0000.000
67B74TYR0-0.037-0.04212.1401.3381.3380.0000.0000.0000.000
68B75ASP-1-0.864-0.93111.71717.71417.7140.0000.0000.0000.000
69B76TYR0-0.070-0.0533.3880.3651.1370.051-0.300-0.523-0.001
70B77GLU-1-0.716-0.8154.57646.36746.483-0.001-0.010-0.1050.000
71B78LEU00.1100.0507.830-1.638-1.6380.0000.0000.0000.000
72B79SER0-0.007-0.02511.361-1.068-1.0680.0000.0000.0000.000
73B80ARG10.8700.9258.678-20.791-20.7910.0000.0000.0000.000
74B81MET0-0.031-0.00410.897-0.212-0.2120.0000.0000.0000.000
75B82VAL00.0390.01513.161-1.057-1.0570.0000.0000.0000.000
76B83ARG10.9070.95414.916-15.805-15.8050.0000.0000.0000.000
77B84LEU00.0060.01713.098-0.554-0.5540.0000.0000.0000.000
78B85ALA00.0420.00616.842-0.667-0.6670.0000.0000.0000.000
79B86HIS0-0.027-0.01219.020-0.275-0.2750.0000.0000.0000.000
80B87GLU-1-0.921-0.95418.42213.31813.3180.0000.0000.0000.000
81B88HIS10.7740.88018.856-13.598-13.5980.0000.0000.0000.000
82B89GLY00.0090.01422.694-0.181-0.1810.0000.0000.0000.000
83B90ILE0-0.054-0.01419.902-0.101-0.1010.0000.0000.0000.000
84B91LEU0-0.052-0.02719.8500.0120.0120.0000.0000.0000.000
85B92THR00.0550.00222.997-0.180-0.1800.0000.0000.0000.000
86B93TYR00.0620.00625.8320.2670.2670.0000.0000.0000.000
87B94ASN00.0190.00727.7500.0760.0760.0000.0000.0000.000
88B95ASP-1-0.769-0.85124.85911.09711.0970.0000.0000.0000.000
89B96ILE0-0.013-0.00622.4660.2420.2420.0000.0000.0000.000
90B97TYR00.004-0.00625.343-0.026-0.0260.0000.0000.0000.000
91B98GLU-1-0.841-0.89427.54610.47610.4760.0000.0000.0000.000
92B99LEU0-0.036-0.01422.0980.1040.1040.0000.0000.0000.000
93B100LEU0-0.034-0.02624.9870.1180.1180.0000.0000.0000.000
94B101LYS10.8030.88527.320-9.253-9.2530.0000.0000.0000.000
95B102PHE00.006-0.00725.021-0.092-0.0920.0000.0000.0000.000
96B103ALA00.018-0.00325.600-0.058-0.0580.0000.0000.0000.000
97B104ASP-1-0.906-0.93427.4439.0719.0710.0000.0000.0000.000
98B105ASP-1-0.833-0.90730.8178.7488.7480.0000.0000.0000.000
99B106VAL0-0.070-0.02127.077-0.126-0.1260.0000.0000.0000.000
100B107LYS10.8340.90530.258-9.165-9.1650.0000.0000.0000.000
101B108SER00.0170.02930.722-0.263-0.2630.0000.0000.0000.000
102B109TYR0-0.114-0.09425.5760.3800.3800.0000.0000.0000.000
103B110LEU0-0.039-0.02421.777-0.255-0.2550.0000.0000.0000.000
104B111GLU-1-0.840-0.92721.69714.32114.3210.0000.0000.0000.000
105B112ASP-1-0.810-0.89025.57010.64810.6480.0000.0000.0000.000
106B113LYS10.8510.92927.830-10.795-10.7950.0000.0000.0000.000
107B114GLY00.0310.02227.331-0.259-0.2590.0000.0000.0000.000
108B115ILE0-0.083-0.04923.5400.2530.2530.0000.0000.0000.000
109B116ARG10.7980.87728.176-9.989-9.9890.0000.0000.0000.000
110B117ARG10.8470.88630.852-9.811-9.8110.0000.0000.0000.000
111B118GLU-1-0.809-0.87333.5288.9708.9700.0000.0000.0000.000
112B119SER00.0210.00736.2410.0820.0820.0000.0000.0000.000
113B120THR0-0.007-0.01737.265-0.035-0.0350.0000.0000.0000.000
114B121ASN0-0.034-0.02740.234-0.058-0.0580.0000.0000.0000.000
115B122GLU-1-0.937-0.95438.8888.0988.0980.0000.0000.0000.000
116B123GLU-1-0.910-0.96941.3877.2137.2130.0000.0000.0000.000
117B124LEU0-0.030-0.02136.8330.0170.0170.0000.0000.0000.000
118B125TYR0-0.052-0.04640.765-0.052-0.0520.0000.0000.0000.000
119B126GLY00.0460.02843.666-0.029-0.0290.0000.0000.0000.000
120B127PHE0-0.056-0.00139.574-0.002-0.0020.0000.0000.0000.000
121B128ASN00.001-0.00541.0360.0430.0430.0000.0000.0000.000
122B129ILE00.0090.01435.7500.2430.2430.0000.0000.0000.000
123B130TYR0-0.044-0.00635.294-0.183-0.1830.0000.0000.0000.000
124B131GLU-1-0.905-0.95032.4819.6499.6490.0000.0000.0000.000
125B132ASP-1-0.827-0.86828.53410.57710.5770.0000.0000.0000.000
126B133VAL0-0.023-0.01828.7500.3800.3800.0000.0000.0000.000
127B134TYR0-0.010-0.01822.7720.2810.2810.0000.0000.0000.000
128B135PRO0-0.0230.00924.8660.0530.0530.0000.0000.0000.000
129B136VAL0-0.014-0.02720.6550.7710.7710.0000.0000.0000.000
130B137ALA0-0.0090.00722.046-0.574-0.5740.0000.0000.0000.000
131B138LYS10.8930.93720.633-13.213-13.2130.0000.0000.0000.000
132B139LYS10.8690.93221.667-13.226-13.2260.0000.0000.0000.000
133B140GLU-1-0.919-0.95821.57513.60313.6030.0000.0000.0000.000
134B141LEU0-0.016-0.00719.921-0.472-0.4720.0000.0000.0000.000
135B142PRO00.0460.01823.3560.0850.0850.0000.0000.0000.000
136B143SER0-0.026-0.01421.500-0.382-0.3820.0000.0000.0000.000
137B144GLY00.0490.04321.5080.3120.3120.0000.0000.0000.000
138B145GLU-1-0.844-0.90216.66116.75316.7530.0000.0000.0000.000
139B146PHE0-0.0060.00517.649-0.734-0.7340.0000.0000.0000.000
140B147ILE0-0.019-0.01316.9421.4091.4090.0000.0000.0000.000
141B148GLY00.0050.00116.806-1.065-1.0650.0000.0000.0000.000
142B149ILE0-0.041-0.01617.0151.0481.0480.0000.0000.0000.000
143B150VAL00.0120.00016.158-0.675-0.6750.0000.0000.0000.000
144B151LEU00.0460.03418.6650.6720.6720.0000.0000.0000.000
145B152LYS10.8590.91313.421-22.240-22.2400.0000.0000.0000.000
146B153HIS00.0910.03319.830-0.426-0.4260.0000.0000.0000.000
147B154LYS10.9240.97618.421-15.638-15.6380.0000.0000.0000.000
148B155GLN00.0640.03915.401-0.978-0.9780.0000.0000.0000.000
149B156ARG10.8700.91517.972-16.566-16.5660.0000.0000.0000.000
150B157ALA0-0.009-0.00122.525-0.445-0.4450.0000.0000.0000.000
151B158VAL00.0650.03624.3760.1740.1740.0000.0000.0000.000
152B159GLY00.0160.02625.4810.2480.2480.0000.0000.0000.000
153B160TYR00.0240.00722.7030.2620.2620.0000.0000.0000.000
154B161GLN0-0.022-0.01215.475-0.060-0.0600.0000.0000.0000.000
155B162SER00.016-0.01118.9680.2770.2770.0000.0000.0000.000
156B163MET0-0.112-0.04512.7731.4441.4440.0000.0000.0000.000
157B164VAL00.0490.02814.378-0.789-0.7890.0000.0000.0000.000
158B165TYR0-0.031-0.03010.2611.4301.4300.0000.0000.0000.000
159B166VAL00.0220.02311.193-1.830-1.8300.0000.0000.0000.000
160B167CYS0-0.060-0.03112.3562.3612.3610.0000.0000.0000.000
161B168ILE00.0280.01611.047-1.282-1.2820.0000.0000.0000.000
162B169PRO00.0790.05414.2341.3221.3220.0000.0000.0000.000
163B170LEU0-0.014-0.02913.1700.4080.4080.0000.0000.0000.000
164B171THR0-0.020-0.01116.325-0.126-0.1260.0000.0000.0000.000
165B172ASN0-0.065-0.03817.141-0.932-0.9320.0000.0000.0000.000
166B173VAL0-0.063-0.02612.6400.7080.7080.0000.0000.0000.000
167B174GLU-1-0.911-0.91315.17813.80413.8040.0000.0000.0000.000
168B175PRO0-0.046-0.06014.7081.1651.1650.0000.0000.0000.000
169B176SER00.0960.03116.7690.9250.9250.0000.0000.0000.000
170B177LEU0-0.055-0.04114.326-0.102-0.1020.0000.0000.0000.000
171B178ALA00.0150.01618.347-0.131-0.1310.0000.0000.0000.000
172B179GLY00.0390.02921.958-0.179-0.1790.0000.0000.0000.000
173B180ARG10.7880.88116.474-17.427-17.4270.0000.0000.0000.000
174B181VAL0-0.0050.00518.3220.6040.6040.0000.0000.0000.000
175B182ALA00.0340.01213.513-0.120-0.1200.0000.0000.0000.000
176B183ARG10.9090.93915.159-17.439-17.4390.0000.0000.0000.000
177B184ARG10.9660.95313.362-16.059-16.0590.0000.0000.0000.000
178B185ASN00.0000.0009.3591.9131.9130.0000.0000.0000.000
179B186GLU-1-0.696-0.7769.96119.66919.6690.0000.0000.0000.000
180B187VAL0-0.002-0.0137.0163.4293.4290.0000.0000.0000.000
181B188VAL0-0.0160.0089.193-2.259-2.2590.0000.0000.0000.000
182B189LYS10.9440.96910.121-14.710-14.7100.0000.0000.0000.000
183B190TYR0-0.013-0.04211.899-0.480-0.4800.0000.0000.0000.000
184B191GLU-1-0.813-0.90113.60915.04315.0430.0000.0000.0000.000
185B192VAL0-0.020-0.02013.1320.0090.0090.0000.0000.0000.000
186B193PRO00.0400.03516.205-0.734-0.7340.0000.0000.0000.000
187B194VAL00.054-0.00219.1470.5370.5370.0000.0000.0000.000
188B195ASP-1-0.873-0.94520.86612.97712.9770.0000.0000.0000.000
189B196LEU00.0180.01614.6630.2520.2520.0000.0000.0000.000
190B197MET0-0.041-0.01515.5770.7200.7200.0000.0000.0000.000
191B198LYS10.8430.90017.723-11.289-11.2890.0000.0000.0000.000
192B199GLU-1-0.707-0.84320.65112.57512.5750.0000.0000.0000.000
193B200LEU0-0.0130.00013.7670.3210.3210.0000.0000.0000.000
194B201LEU0-0.024-0.01117.0800.2120.2120.0000.0000.0000.000
195B202LYS10.8580.92018.966-12.347-12.3470.0000.0000.0000.000
196B203ALA00.0260.01418.198-0.359-0.3590.0000.0000.0000.000
197B204PHE0-0.020-0.03413.182-0.156-0.1560.0000.0000.0000.000
198B205ILE0-0.046-0.02019.185-0.337-0.3370.0000.0000.0000.000
199B206ILE00.0630.03022.633-0.422-0.4220.0000.0000.0000.000
200B207ALA0-0.033-0.00319.846-0.241-0.2410.0000.0000.0000.000
201B208SER00.013-0.00321.764-0.161-0.1610.0000.0000.0000.000
202B209GLU-1-0.770-0.84823.56510.74510.7450.0000.0000.0000.000
203B210THR00.011-0.00221.142-0.113-0.1130.0000.0000.0000.000
204B211HIS10.8070.89916.664-16.776-16.7760.0000.0000.0000.000
205B212LYS10.9020.98120.227-10.567-10.5670.0000.0000.0000.000
206B213ASN00.0260.00322.735-0.135-0.1350.0000.0000.0000.000
207B214ASP-1-0.785-0.83718.19015.36315.3630.0000.0000.0000.000
208B215ILE0-0.029-0.01716.4610.0580.0580.0000.0000.0000.000
209B216VAL00.0170.00619.893-0.248-0.2480.0000.0000.0000.000
210B217LYS10.9050.95821.775-12.173-12.1730.0000.0000.0000.000
211B218PHE0-0.004-0.00716.036-0.105-0.1050.0000.0000.0000.000
212B219LEU00.0290.00819.901-0.151-0.1510.0000.0000.0000.000
213B220ARG10.9700.97321.901-10.610-10.6100.0000.0000.0000.000
214B221SER0-0.081-0.03320.828-0.277-0.2770.0000.0000.0000.000
215B222ILE0-0.046-0.01018.372-0.097-0.0970.0000.0000.0000.000
216B223ILE0-0.0500.00022.461-0.633-0.6330.0000.0000.0000.000