Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: NN4MQ

Calculation Name: 3KBG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KBG

Chain ID: A

ChEMBL ID:

UniProt ID: Q56230

Base Structure: X-ray

Registration Date: 2023-09-24

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063510.815291
FMO2-HF: Nuclear repulsion 1988580.716587
FMO2-HF: Total energy -74930.098704
FMO2-MP2: Total energy -75149.25929


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:34:LYS)


Summations of interaction energy for fragment #1(A:34:LYS)
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.
67.09771.69215.679-7.606-12.669-0.085
Interaction energy analysis for fragmet #1(A:34:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.925 / q_NPA : 0.967
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].
3A36GLN0-0.0250.0043.1621.7104.2250.015-1.139-1.3920.004
4A37SER0-0.033-0.0096.0233.7963.7960.0000.0000.0000.000
5A38VAL00.0410.0306.260-1.459-1.4590.0000.0000.0000.000
6A39THR0-0.017-0.0068.9342.5292.5290.0000.0000.0000.000
7A40LEU00.0830.04212.150-1.063-1.0630.0000.0000.0000.000
8A41LEU0-0.005-0.01114.5900.0100.0100.0000.0000.0000.000
9A42SER0-0.085-0.04910.530-0.672-0.6720.0000.0000.0000.000
10A43ILE00.1110.0669.346-0.480-0.4800.0000.0000.0000.000
11A44ILE00.0100.00411.6820.3850.3850.0000.0000.0000.000
12A45ARG10.9340.96813.66920.04920.0490.0000.0000.0000.000
13A46ASP-1-0.917-0.9578.360-31.916-31.9160.0000.0000.0000.000
14A47TYR00.005-0.00111.3350.7420.7420.0000.0000.0000.000
15A48LEU00.0180.00113.5170.7980.7980.0000.0000.0000.000
16A49LYS10.9130.94611.89823.37923.3790.0000.0000.0000.000
17A50LEU0-0.0420.00311.8560.6060.6060.0000.0000.0000.000
18A51SER0-0.058-0.01915.6471.0051.0050.0000.0000.0000.000
19A52ASP-1-0.802-0.89218.171-14.035-14.0350.0000.0000.0000.000
20A53LYS10.9460.97319.13913.66513.6650.0000.0000.0000.000
21A54GLU-1-0.833-0.91716.326-17.169-17.1690.0000.0000.0000.000
22A55ARG10.7210.83718.13515.21415.2140.0000.0000.0000.000
23A56GLU-1-0.848-0.90821.277-12.143-12.1430.0000.0000.0000.000
24A57ALA00.0150.01617.8750.2380.2380.0000.0000.0000.000
25A58ALA0-0.009-0.01319.8440.1720.1720.0000.0000.0000.000
26A59ARG10.9170.94121.76212.18512.1850.0000.0000.0000.000
27A60ILE00.0260.00221.6650.4410.4410.0000.0000.0000.000
28A61LEU00.0130.00419.4550.2610.2610.0000.0000.0000.000
29A62ALA0-0.027-0.01122.8090.4280.4280.0000.0000.0000.000
30A63ASN0-0.0040.01025.9790.6830.6830.0000.0000.0000.000
31A64GLY0-0.0030.00726.4570.2780.2780.0000.0000.0000.000
32A65LEU0-0.048-0.01625.4850.1670.1670.0000.0000.0000.000
33A66VAL00.0080.01219.374-0.327-0.3270.0000.0000.0000.000
34A67LYS10.8830.95621.92111.90311.9030.0000.0000.0000.000
35A68VAL00.0380.01617.306-0.705-0.7050.0000.0000.0000.000
36A69ASP-1-0.776-0.86819.104-14.799-14.7990.0000.0000.0000.000
37A70GLY00.0310.01621.3370.5080.5080.0000.0000.0000.000
38A71LYS10.9490.98723.43712.43212.4320.0000.0000.0000.000
39A72THR00.006-0.00423.352-0.538-0.5380.0000.0000.0000.000
40A73VAL0-0.040-0.02219.7540.2490.2490.0000.0000.0000.000
41A74ARG10.9070.93122.38711.12011.1200.0000.0000.0000.000
42A75GLU-1-0.873-0.92219.888-14.038-14.0380.0000.0000.0000.000
43A76LYS10.9900.97918.35915.46815.4680.0000.0000.0000.000
44A77LYS10.8930.92116.29013.75113.7510.0000.0000.0000.000
45A78PHE00.0140.02416.004-0.338-0.3380.0000.0000.0000.000
46A79ALA00.0100.01112.183-0.737-0.7370.0000.0000.0000.000
47A80VAL0-0.008-0.00211.1861.1281.1280.0000.0000.0000.000
48A81GLY00.0610.0059.567-2.302-2.3020.0000.0000.0000.000
49A82PHE00.0290.0189.0471.0201.0200.0000.0000.0000.000
50A83MET0-0.034-0.00310.7521.3851.3850.0000.0000.0000.000
51A84ASP-1-0.812-0.88613.823-17.465-17.4650.0000.0000.0000.000
52A85VAL00.005-0.00415.717-0.683-0.6830.0000.0000.0000.000
53A86ILE0-0.003-0.00214.2170.3550.3550.0000.0000.0000.000
54A87GLU-1-0.923-0.97618.300-11.893-11.8930.0000.0000.0000.000
55A88ILE00.0240.00417.646-0.123-0.1230.0000.0000.0000.000
56A89ASN0-0.027-0.02722.258-0.078-0.0780.0000.0000.0000.000
57A90GLY00.0350.03025.7530.2850.2850.0000.0000.0000.000
58A91GLU-1-0.855-0.92323.142-12.114-12.1140.0000.0000.0000.000
59A92SER0-0.005-0.00521.783-0.129-0.1290.0000.0000.0000.000
60A93TYR00.0020.00616.6500.1270.1270.0000.0000.0000.000
61A94ARG10.7820.88914.72516.44716.4470.0000.0000.0000.000
62A95VAL0-0.0170.0059.942-1.125-1.1250.0000.0000.0000.000
63A96VAL00.005-0.01710.7531.1971.1970.0000.0000.0000.000
64A97TYR0-0.034-0.0524.085-0.272-0.094-0.001-0.020-0.1560.000
65A98ASN00.0510.0314.474-1.383-1.246-0.001-0.004-0.1320.000
66A99ASP-1-0.780-0.9036.442-30.176-30.1760.0000.0000.0000.000
67A100GLN0-0.083-0.0372.736-3.111-1.9700.285-0.524-0.902-0.003
68A101GLY00.0340.0132.004-22.659-23.0288.541-3.476-4.695-0.055
69A102ALA0-0.072-0.0401.873-8.250-7.5746.807-2.518-4.966-0.030
70A103LEU00.0010.0103.6207.8788.1950.0330.075-0.426-0.001
71A104VAL00.0070.0036.234-1.069-1.0690.0000.0000.0000.000
72A105LEU0-0.016-0.0049.1471.8391.8390.0000.0000.0000.000
73A106MET0-0.0050.01212.905-0.653-0.6530.0000.0000.0000.000
74A107LYS10.8500.92615.24214.58614.5860.0000.0000.0000.000
75A108GLU-1-0.797-0.90118.898-15.149-15.1490.0000.0000.0000.000
76A109THR0-0.026-0.01921.0210.6570.6570.0000.0000.0000.000
77A110LYS10.9230.93824.36111.76511.7650.0000.0000.0000.000
78A111GLU-1-0.914-0.94126.755-10.351-10.3510.0000.0000.0000.000
79A112ARG10.9900.98522.48313.00513.0050.0000.0000.0000.000
80A113ALA0-0.032-0.01422.209-0.337-0.3370.0000.0000.0000.000
81A114SER0-0.0350.00123.288-0.036-0.0360.0000.0000.0000.000
82A115MET00.0150.02421.6380.3170.3170.0000.0000.0000.000
83A116LYS10.7710.86516.39115.58815.5880.0000.0000.0000.000
84A117LEU0-0.0340.01117.6160.6180.6180.0000.0000.0000.000
85A118LEU0-0.002-0.00617.253-0.894-0.8940.0000.0000.0000.000
86A119LYS10.8930.96513.01518.60318.6030.0000.0000.0000.000
87A120VAL00.0010.00017.432-0.161-0.1610.0000.0000.0000.000
88A121ARG10.9730.98012.97117.15817.1580.0000.0000.0000.000
89A122SER0-0.036-0.01317.0420.0650.0650.0000.0000.0000.000
90A123LYS10.8990.92419.89010.83510.8350.0000.0000.0000.000
91A124VAL00.0290.03423.640-0.075-0.0750.0000.0000.0000.000
92A125ILE0-0.036-0.02326.5080.1010.1010.0000.0000.0000.000
93A126ALA00.0270.02529.6300.0870.0870.0000.0000.0000.000
94A127PRO00.027-0.00832.9430.0170.0170.0000.0000.0000.000
95A128GLY00.0320.01336.393-0.038-0.0380.0000.0000.0000.000
96A129ASN0-0.038-0.01433.966-0.098-0.0980.0000.0000.0000.000
97A130ARG11.0411.03832.3058.5688.5680.0000.0000.0000.000
98A131ILE0-0.021-0.01527.475-0.174-0.1740.0000.0000.0000.000
99A132GLN0-0.0130.00326.2580.2980.2980.0000.0000.0000.000
100A133LEU0-0.005-0.01123.597-0.245-0.2450.0000.0000.0000.000
101A134GLY00.0500.02620.6780.0790.0790.0000.0000.0000.000
102A135THR00.018-0.02318.698-0.118-0.1180.0000.0000.0000.000
103A136HIS0-0.069-0.04812.2200.5610.5610.0000.0000.0000.000
104A137ASP-1-0.748-0.87013.880-15.973-15.9730.0000.0000.0000.000
105A138GLY0-0.049-0.02215.7530.1610.1610.0000.0000.0000.000
106A139ARG10.8510.92718.18114.61614.6160.0000.0000.0000.000
107A140THR0-0.022-0.01621.313-0.184-0.1840.0000.0000.0000.000
108A141PHE00.0030.00922.6450.2430.2430.0000.0000.0000.000
109A142ILE0-0.021-0.01526.742-0.074-0.0740.0000.0000.0000.000
110A143THR0-0.0060.00628.6300.2230.2230.0000.0000.0000.000
111A144ASP-1-0.841-0.92531.086-8.241-8.2410.0000.0000.0000.000
112A145ASP-1-0.806-0.88030.858-9.024-9.0240.0000.0000.0000.000
113A146LYS10.9330.95730.3097.6347.6340.0000.0000.0000.000
114A147SER0-0.120-0.09330.060-0.242-0.2420.0000.0000.0000.000
115A148ILE00.0300.02224.843-0.309-0.3090.0000.0000.0000.000
116A149LYS10.8680.94423.80110.02210.0220.0000.0000.0000.000
117A150VAL00.0240.00918.100-0.194-0.1940.0000.0000.0000.000
118A151GLY0-0.029-0.02117.7710.0310.0310.0000.0000.0000.000
119A152ASP-1-0.751-0.84518.823-11.666-11.6660.0000.0000.0000.000
120A153VAL0-0.021-0.01617.997-0.474-0.4740.0000.0000.0000.000
121A154LEU0-0.0170.00820.7930.6380.6380.0000.0000.0000.000
122A155ALA00.0310.02121.614-0.669-0.6690.0000.0000.0000.000
123A156VAL0-0.003-0.01322.0450.5390.5390.0000.0000.0000.000
124A157SER00.0210.01924.210-0.457-0.4570.0000.0000.0000.000
125A158VAL0-0.023-0.02822.285-0.027-0.0270.0000.0000.0000.000
126A159PRO0-0.039-0.02925.1240.0360.0360.0000.0000.0000.000
127A160ASP-1-0.845-0.92428.579-9.576-9.5760.0000.0000.0000.000
128A161MET0-0.061-0.02323.581-0.058-0.0580.0000.0000.0000.000
129A162LYS10.9390.99027.0818.9198.9190.0000.0000.0000.000
130A163ILE0-0.009-0.01726.016-0.302-0.3020.0000.0000.0000.000
131A164SER0-0.059-0.02527.2310.3230.3230.0000.0000.0000.000
132A165GLU-1-0.845-0.92826.467-9.648-9.6480.0000.0000.0000.000
133A166ILE00.0150.00525.078-0.390-0.3900.0000.0000.0000.000
134A167ILE0-0.054-0.03321.3370.3800.3800.0000.0000.0000.000
135A168LYS10.8510.91722.83010.20010.2000.0000.0000.0000.000
136A169MET00.013-0.00916.827-0.093-0.0930.0000.0000.0000.000
137A170GLN0-0.042-0.01822.3080.2810.2810.0000.0000.0000.000
138A171PRO00.019-0.01724.576-0.311-0.3110.0000.0000.0000.000
139A172GLY0-0.0030.00825.9670.3050.3050.0000.0000.0000.000
140A173ASN0-0.047-0.02023.5710.3080.3080.0000.0000.0000.000
141A174LYS10.9690.99019.97112.89112.8910.0000.0000.0000.000
142A175ALA0-0.020-0.02016.5790.0450.0450.0000.0000.0000.000
143A176TYR00.006-0.0169.936-0.177-0.1770.0000.0000.0000.000
144A177ILE0-0.0130.0069.9750.2050.2050.0000.0000.0000.000
145A178THR00.018-0.0027.980-0.859-0.8590.0000.0000.0000.000
146A179ALA0-0.008-0.0055.181-3.919-3.9190.0000.0000.0000.000
147A180GLY00.0120.0075.4523.0953.0950.0000.0000.0000.000
148A181SER00.010-0.0127.426-1.723-1.7230.0000.0000.0000.000
149A182HIS10.8730.9279.57019.75019.7500.0000.0000.0000.000
150A183VAL00.0000.0125.2651.0841.0840.0000.0000.0000.000
151A184ASN0-0.013-0.0028.5210.9320.9320.0000.0000.0000.000
152A185GLN00.0700.07810.3102.7712.7710.0000.0000.0000.000
153A186THR0-0.038-0.04313.5650.1750.1750.0000.0000.0000.000
154A187GLY00.0280.02216.6240.1200.1200.0000.0000.0000.000
155A188THR0-0.033-0.01719.620-0.024-0.0240.0000.0000.0000.000
156A189ILE0-0.037-0.00120.0470.0420.0420.0000.0000.0000.000
157A190SER0-0.007-0.01822.7860.4570.4570.0000.0000.0000.000
158A191LYS10.9400.97323.87411.33411.3340.0000.0000.0000.000
159A192ILE00.0100.00821.552-0.563-0.5630.0000.0000.0000.000
160A193GLU-1-0.864-0.92522.394-11.058-11.0580.0000.0000.0000.000
161A194ALA0-0.011-0.00922.157-0.517-0.5170.0000.0000.0000.000
162A195LYS10.9440.97823.36210.13910.1390.0000.0000.0000.000
163A196GLU-1-0.917-0.95623.925-9.868-9.8680.0000.0000.0000.000
164A197GLY00.0340.01323.9130.1250.1250.0000.0000.0000.000
165A198SER00.0120.00320.058-0.118-0.1180.0000.0000.0000.000
166A199SER0-0.001-0.02019.888-0.141-0.1410.0000.0000.0000.000
167A200ALA00.0760.05917.941-0.679-0.6790.0000.0000.0000.000
168A201ASN0-0.134-0.07918.3370.3200.3200.0000.0000.0000.000
169A202LEU0-0.033-0.01317.000-0.801-0.8010.0000.0000.0000.000
170A203VAL0-0.026-0.01017.4440.7520.7520.0000.0000.0000.000
171A204HIS0-0.023-0.02218.449-0.735-0.7350.0000.0000.0000.000
172A205PHE00.010-0.00316.6180.2030.2030.0000.0000.0000.000
173A206GLN00.014-0.00921.5880.0860.0860.0000.0000.0000.000
174A207GLU-1-0.840-0.91820.401-13.214-13.2140.0000.0000.0000.000
175A208GLY0-0.0060.01321.848-0.217-0.2170.0000.0000.0000.000
176A209PHE0-0.035-0.02015.258-0.538-0.5380.0000.0000.0000.000
177A210SER00.0130.00117.8650.2590.2590.0000.0000.0000.000
178A211THR00.0000.00012.634-0.905-0.9050.0000.0000.0000.000
179A212ILE00.0390.02610.6490.8780.8780.0000.0000.0000.000
180A213LYS11.0210.99713.57512.13212.1320.0000.0000.0000.000
181A214ASP-1-0.920-0.95310.851-18.018-18.0180.0000.0000.0000.000
182A215HIS0-0.022-0.0147.842-1.101-1.1010.0000.0000.0000.000
183A216VAL0-0.0040.01810.700-0.506-0.5060.0000.0000.0000.000
184A217PHE0-0.024-0.01312.7480.5960.5960.0000.0000.0000.000
185A218MET0-0.0090.00314.767-0.138-0.1380.0000.0000.0000.000
186A219ILE00.014-0.01116.612-0.103-0.1030.0000.0000.0000.000
187A220GLY0-0.0070.00119.5070.2860.2860.0000.0000.0000.000
188A221SER0-0.036-0.01723.1340.1040.1040.0000.0000.0000.000
189A222SER00.0400.00126.434-0.020-0.0200.0000.0000.0000.000
190A223LYS10.8770.96028.20910.31510.3150.0000.0000.0000.000
191A224PHE00.0460.02223.365-0.005-0.0050.0000.0000.0000.000
192A225SER0-0.003-0.01124.120-0.397-0.3970.0000.0000.0000.000
193A226PHE00.0000.00617.8050.1160.1160.0000.0000.0000.000
194A227VAL0-0.020-0.00320.3410.1210.1210.0000.0000.0000.000