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: QYY2Y

Calculation Name: 5F5U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F5U

Chain ID: A

ChEMBL ID:

UniProt ID: G0S6R0

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2152911.126409
FMO2-HF: Nuclear repulsion 2077161.495145
FMO2-HF: Total energy -75749.631264
FMO2-MP2: Total energy -75971.822645


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:22:GLY)


Summations of interaction energy for fragment #1(A:22: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.
0.3561.304-0.01-0.449-0.490.001
Interaction energy analysis for fragmet #1(A:22:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.020
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].
3A24LEU0-0.012-0.0073.840-0.8760.072-0.010-0.449-0.4900.001
4A25ALA0-0.036-0.0166.5650.4030.4030.0000.0000.0000.000
5A26PRO00.0250.0119.651-0.039-0.0390.0000.0000.0000.000
6A27ASN0-0.0310.00012.923-0.047-0.0470.0000.0000.0000.000
7A28GLY00.0450.01112.088-0.071-0.0710.0000.0000.0000.000
8A29LEU0-0.043-0.00811.278-0.109-0.1090.0000.0000.0000.000
9A30ASN00.0680.0256.417-0.207-0.2070.0000.0000.0000.000
10A31PRO00.0910.0285.9030.2550.2550.0000.0000.0000.000
11A32ALA0-0.0140.0046.8910.2030.2030.0000.0000.0000.000
12A33THR0-0.099-0.0708.6250.0710.0710.0000.0000.0000.000
13A34ILE0-0.0030.02811.1570.0450.0450.0000.0000.0000.000
14A35MET00.0010.01813.2090.0470.0470.0000.0000.0000.000
15A36GLU-1-0.751-0.85114.917-0.124-0.1240.0000.0000.0000.000
16A37LYS10.8860.92416.1390.1080.1080.0000.0000.0000.000
17A38ALA00.0450.03117.1410.0170.0170.0000.0000.0000.000
18A39VAL00.000-0.00217.8190.0160.0160.0000.0000.0000.000
19A40ARG10.9510.96912.1990.1780.1780.0000.0000.0000.000
20A41GLU-1-0.848-0.90716.277-0.039-0.0390.0000.0000.0000.000
21A42ARG10.9220.95618.6760.0370.0370.0000.0000.0000.000
22A43ILE0-0.008-0.00716.5690.0100.0100.0000.0000.0000.000
23A44VAL00.0040.02014.7630.0140.0140.0000.0000.0000.000
24A45GLU-1-0.917-0.96117.8000.0140.0140.0000.0000.0000.000
25A46SER0-0.084-0.04420.7310.0030.0030.0000.0000.0000.000
26A47TYR00.0360.00022.1550.0070.0070.0000.0000.0000.000
27A48PHE00.0300.00320.9430.0060.0060.0000.0000.0000.000
28A49TRP00.0270.00912.6610.0040.0040.0000.0000.0000.000
29A50LYS10.8550.91619.101-0.042-0.0420.0000.0000.0000.000
30A51GLU-1-0.917-0.95720.8240.0810.0810.0000.0000.0000.000
31A52GLN0-0.015-0.01122.1240.0130.0130.0000.0000.0000.000
32A53CYS0-0.043-0.00516.6080.0010.0010.0000.0000.0000.000
33A54PHE00.0310.01616.5050.0420.0420.0000.0000.0000.000
34A55GLY0-0.011-0.00916.651-0.010-0.0100.0000.0000.0000.000
35A56VAL0-0.078-0.02016.0190.0050.0050.0000.0000.0000.000
36A57ASN00.0250.00014.7540.0460.0460.0000.0000.0000.000
37A58GLU-1-0.763-0.90212.8310.3960.3960.0000.0000.0000.000
38A59ALA00.0340.01916.750-0.041-0.0410.0000.0000.0000.000
39A60ASP-1-0.761-0.88718.8580.2140.2140.0000.0000.0000.000
40A61ILE0-0.096-0.04215.506-0.025-0.0250.0000.0000.0000.000
41A62VAL0-0.031-0.02019.126-0.027-0.0270.0000.0000.0000.000
42A63ASP-1-0.889-0.93522.3430.1160.1160.0000.0000.0000.000
43A64ARG10.8590.91520.809-0.156-0.1560.0000.0000.0000.000
44A65VAL0-0.031-0.02121.457-0.017-0.0170.0000.0000.0000.000
45A66VAL0-0.010-0.00724.104-0.013-0.0130.0000.0000.0000.000
46A67GLU-1-0.852-0.89625.8850.0930.0930.0000.0000.0000.000
47A68HIS0-0.014-0.00925.041-0.015-0.0150.0000.0000.0000.000
48A69VAL0-0.064-0.00623.502-0.009-0.0090.0000.0000.0000.000
49A70ARG10.8280.89826.744-0.054-0.0540.0000.0000.0000.000
50A71PHE0-0.070-0.05127.579-0.004-0.0040.0000.0000.0000.000
51A72VAL00.0580.04625.8060.0040.0040.0000.0000.0000.000
52A73GLY00.057-0.00125.042-0.004-0.0040.0000.0000.0000.000
53A74GLY00.0600.03822.9340.0020.0020.0000.0000.0000.000
54A75VAL0-0.039-0.01422.7300.0080.0080.0000.0000.0000.000
55A76THR0-0.072-0.04125.170-0.003-0.0030.0000.0000.0000.000
56A77GLY00.0280.00828.8490.0030.0030.0000.0000.0000.000
57A78VAL00.0610.01431.527-0.003-0.0030.0000.0000.0000.000
58A79THR0-0.0030.00329.675-0.002-0.0020.0000.0000.0000.000
59A80GLN0-0.0110.00626.3060.0000.0000.0000.0000.0000.000
60A81LYS10.9740.98625.628-0.032-0.0320.0000.0000.0000.000
61A82PRO00.0210.02221.404-0.004-0.0040.0000.0000.0000.000
62A83SER0-0.043-0.02623.4960.0110.0110.0000.0000.0000.000
63A84PRO00.0730.02422.1380.0000.0000.0000.0000.0000.000
64A85PHE00.0340.01921.1320.0100.0100.0000.0000.0000.000
65A86LEU0-0.0050.00918.8020.0040.0040.0000.0000.0000.000
66A87CYS0-0.049-0.01917.638-0.003-0.0030.0000.0000.0000.000
67A88LEU00.0450.01616.3480.0170.0170.0000.0000.0000.000
68A89ALA00.0150.01615.8100.0170.0170.0000.0000.0000.000
69A90PHE0-0.012-0.01811.342-0.001-0.0010.0000.0000.0000.000
70A91LYS10.8690.95011.646-0.312-0.3120.0000.0000.0000.000
71A92LEU00.0360.02211.5140.0650.0650.0000.0000.0000.000
72A93LEU0-0.047-0.0269.6630.0210.0210.0000.0000.0000.000
73A94GLN0-0.064-0.0337.345-0.113-0.1130.0000.0000.0000.000
74A95LEU0-0.070-0.0306.8210.2170.2170.0000.0000.0000.000
75A96ALA0-0.058-0.0126.7920.1280.1280.0000.0000.0000.000
76A97PRO00.0250.0278.7120.0770.0770.0000.0000.0000.000
77A98GLY00.0740.02812.076-0.068-0.0680.0000.0000.0000.000
78A99ASP-1-0.779-0.91013.724-0.021-0.0210.0000.0000.0000.000
79A100ASP-1-0.918-0.95216.8140.1920.1920.0000.0000.0000.000
80A101ILE00.0820.03814.752-0.015-0.0150.0000.0000.0000.000
81A102LEU0-0.031-0.00514.675-0.020-0.0200.0000.0000.0000.000
82A103LYS10.8800.93718.500-0.057-0.0570.0000.0000.0000.000
83A104GLU-1-0.889-0.93521.3130.0930.0930.0000.0000.0000.000
84A105TYR0-0.060-0.05016.984-0.007-0.0070.0000.0000.0000.000
85A106LEU00.0000.01221.797-0.008-0.0080.0000.0000.0000.000
86A107TYR00.0470.02824.099-0.005-0.0050.0000.0000.0000.000
87A108PHE00.0910.05026.109-0.005-0.0050.0000.0000.0000.000
88A109GLY00.011-0.01425.198-0.002-0.0020.0000.0000.0000.000
89A110GLY00.008-0.00726.104-0.005-0.0050.0000.0000.0000.000
90A111GLU-1-0.815-0.88027.3830.0240.0240.0000.0000.0000.000
91A112LYS10.8050.93029.637-0.069-0.0690.0000.0000.0000.000
92A113PHE0-0.026-0.02827.098-0.003-0.0030.0000.0000.0000.000
93A114LYS10.9510.96627.411-0.022-0.0220.0000.0000.0000.000
94A115TYR0-0.021-0.04026.007-0.005-0.0050.0000.0000.0000.000
95A116LEU00.0160.03621.143-0.003-0.0030.0000.0000.0000.000
96A117ARG10.8070.89122.622-0.026-0.0260.0000.0000.0000.000
97A118ALA0-0.033-0.01423.597-0.007-0.0070.0000.0000.0000.000
98A119LEU0-0.019-0.01218.372-0.012-0.0120.0000.0000.0000.000
99A120ALA00.0330.01418.946-0.008-0.0080.0000.0000.0000.000
100A121ALA00.0350.01719.266-0.012-0.0120.0000.0000.0000.000
101A122PHE0-0.016-0.01918.757-0.015-0.0150.0000.0000.0000.000
102A123TYR00.0360.00910.133-0.033-0.0330.0000.0000.0000.000
103A124ILE00.0430.01915.679-0.035-0.0350.0000.0000.0000.000
104A125ARG10.8540.93017.5240.0930.0930.0000.0000.0000.000
105A126LEU0-0.074-0.04314.728-0.025-0.0250.0000.0000.0000.000
106A127THR0-0.045-0.02611.551-0.039-0.0390.0000.0000.0000.000
107A128ARG10.8760.93312.2490.0060.0060.0000.0000.0000.000
108A129PRO00.0120.00815.995-0.007-0.0070.0000.0000.0000.000
109A130ASP-1-0.721-0.84118.751-0.116-0.1160.0000.0000.0000.000
110A131LYS10.9791.00722.1060.0660.0660.0000.0000.0000.000
111A132GLU-1-0.900-0.96518.227-0.090-0.0900.0000.0000.0000.000
112A133VAL0-0.042-0.02019.8830.0160.0160.0000.0000.0000.000
113A134TYR00.008-0.00622.2140.0140.0140.0000.0000.0000.000
114A135THR0-0.008-0.02024.8060.0100.0100.0000.0000.0000.000
115A136LEU0-0.034-0.00920.6420.0110.0110.0000.0000.0000.000
116A137LEU0-0.030-0.02722.0020.0100.0100.0000.0000.0000.000
117A138GLU-1-0.769-0.86525.853-0.037-0.0370.0000.0000.0000.000
118A139PRO00.0190.01528.1820.0020.0020.0000.0000.0000.000
119A140PHE0-0.037-0.01625.6310.0050.0050.0000.0000.0000.000
120A141LEU0-0.014-0.01130.4550.0010.0010.0000.0000.0000.000
121A142GLU-1-0.903-0.94432.790-0.003-0.0030.0000.0000.0000.000
122A143ASP-1-0.823-0.87531.1440.0200.0200.0000.0000.0000.000
123A144ARG11.0561.01933.745-0.008-0.0080.0000.0000.0000.000
124A145ARG10.6720.80030.217-0.025-0.0250.0000.0000.0000.000
125A146LYS10.9640.98934.098-0.009-0.0090.0000.0000.0000.000
126A147LEU00.0060.01028.8830.0050.0050.0000.0000.0000.000
127A148ARG10.9130.95731.769-0.021-0.0210.0000.0000.0000.000
128A149ARG10.8890.94828.4280.0240.0240.0000.0000.0000.000
129A150LYS10.8770.92629.840-0.008-0.0080.0000.0000.0000.000
130A151GLY0-0.017-0.01829.396-0.002-0.0020.0000.0000.0000.000
131A152LYS10.9580.98328.9730.0470.0470.0000.0000.0000.000
132A153ASN00.0350.02132.5240.0000.0000.0000.0000.0000.000
133A154GLY00.0560.04735.2750.0020.0020.0000.0000.0000.000
134A155THR0-0.057-0.04334.1950.0010.0010.0000.0000.0000.000
135A156SER00.0410.02834.8460.0000.0000.0000.0000.0000.000
136A157LEU0-0.046-0.02835.0280.0030.0030.0000.0000.0000.000
137A158THR0-0.021-0.03631.021-0.003-0.0030.0000.0000.0000.000
138A159TYR00.004-0.00433.8190.0060.0060.0000.0000.0000.000
139A160MET0-0.058-0.01927.561-0.003-0.0030.0000.0000.0000.000
140A161ASP-1-0.801-0.90030.076-0.011-0.0110.0000.0000.0000.000
141A162GLU-1-0.757-0.86031.888-0.016-0.0160.0000.0000.0000.000
142A163PHE0-0.098-0.05023.649-0.005-0.0050.0000.0000.0000.000
143A164ILE0-0.004-0.01125.886-0.006-0.0060.0000.0000.0000.000
144A165ASP-1-0.835-0.91927.682-0.043-0.0430.0000.0000.0000.000
145A166ASP-1-0.800-0.86527.849-0.038-0.0380.0000.0000.0000.000
146A167LEU0-0.096-0.05622.071-0.009-0.0090.0000.0000.0000.000
147A168LEU0-0.0160.00124.633-0.013-0.0130.0000.0000.0000.000
148A169THR0-0.0120.00226.874-0.007-0.0070.0000.0000.0000.000
149A170LYS10.8300.91427.4800.0380.0380.0000.0000.0000.000
150A171ASP-1-0.773-0.86625.156-0.102-0.1020.0000.0000.0000.000
151A172ARG10.7570.85021.7900.0780.0780.0000.0000.0000.000
152A173VAL00.0690.03223.0600.0100.0100.0000.0000.0000.000
153A174CYS0-0.075-0.01822.116-0.002-0.0020.0000.0000.0000.000
154A175SER0-0.049-0.03321.6750.0020.0020.0000.0000.0000.000
155A176THR00.0560.02417.227-0.003-0.0030.0000.0000.0000.000
156A177SER0-0.041-0.02719.7070.0130.0130.0000.0000.0000.000
157A178LEU0-0.033-0.01118.936-0.018-0.0180.0000.0000.0000.000
158A179TRP0-0.0050.00417.428-0.006-0.0060.0000.0000.0000.000
159A180LYS10.8760.91119.8480.1190.1190.0000.0000.0000.000
160A181MET0-0.0040.01621.895-0.016-0.0160.0000.0000.0000.000
161A182ARG10.8450.89723.6290.1380.1380.0000.0000.0000.000
162A183ARG10.8870.92326.7040.0740.0740.0000.0000.0000.000
163A184ARG10.7580.81529.7940.0410.0410.0000.0000.0000.000
164A185ASP-1-0.719-0.85430.720-0.065-0.0650.0000.0000.0000.000
165A186ILE0-0.019-0.00429.839-0.002-0.0020.0000.0000.0000.000
166A187LEU0-0.058-0.03525.945-0.003-0.0030.0000.0000.0000.000
167A188GLU-1-0.856-0.92429.851-0.045-0.0450.0000.0000.0000.000
168A189ASP-1-0.893-0.92933.225-0.054-0.0540.0000.0000.0000.000
169A190LEU0-0.179-0.09228.898-0.001-0.0010.0000.0000.0000.000
170A191ASP-1-0.908-0.94831.495-0.045-0.0450.0000.0000.0000.000
171A192LEU0-0.111-0.04926.074-0.003-0.0030.0000.0000.0000.000
172A193LEU0-0.118-0.07227.8120.0000.0000.0000.0000.0000.000
173A194GLU-1-0.822-0.89830.722-0.027-0.0270.0000.0000.0000.000
174A195PRO00.0540.03133.454-0.002-0.0020.0000.0000.0000.000
175A196ARG10.9060.96832.7850.0280.0280.0000.0000.0000.000
176A197VAL00.0310.01435.3870.0000.0000.0000.0000.0000.000
177A198SER0-0.038-0.01137.9010.0030.0030.0000.0000.0000.000
178A199PRO00.0510.01239.0960.0000.0000.0000.0000.0000.000
179A200LEU0-0.011-0.02441.8630.0000.0000.0000.0000.0000.000
180A201GLY00.0170.02142.441-0.001-0.0010.0000.0000.0000.000
181A202SER00.0050.02143.5330.0000.0000.0000.0000.0000.000
182A203LEU0-0.051-0.04246.0560.0010.0010.0000.0000.0000.000
183A204GLU-1-0.904-0.97045.942-0.015-0.0150.0000.0000.0000.000
184A205ASP-1-0.921-0.94546.840-0.018-0.0180.0000.0000.0000.000
185A206ILE0-0.053-0.03349.1840.0000.0000.0000.0000.0000.000
186A207LEU0-0.119-0.05849.6120.0010.0010.0000.0000.0000.000
187A208GLU-1-0.979-0.97648.311-0.020-0.0200.0000.0000.0000.000
188A209GLU-1-1.065-1.01452.376-0.013-0.0130.0000.0000.0000.000