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: 3J65L

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2065764.894277
FMO2-HF: Nuclear repulsion 1990833.246746
FMO2-HF: Total energy -74931.647531
FMO2-MP2: Total energy -75150.728901


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.
73.77680.4359.522-5.35-10.831-0.063
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 : 0.951 / q_NPA : 0.984
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].
3A36GLN0-0.026-0.0073.1953.7575.9980.022-0.906-1.3570.004
4A37SER0-0.023-0.0145.9144.0194.0190.0000.0000.0000.000
5A38VAL00.0140.0206.488-1.556-1.5560.0000.0000.0000.000
6A39THR0-0.006-0.0139.2402.8742.8740.0000.0000.0000.000
7A40LEU00.0550.02412.562-1.119-1.1190.0000.0000.0000.000
8A41LEU00.011-0.00515.1520.2260.2260.0000.0000.0000.000
9A42SER0-0.042-0.0029.9640.1490.1490.0000.0000.0000.000
10A43ILE00.0640.0349.728-0.121-0.1210.0000.0000.0000.000
11A44ILE00.0140.01211.6360.4470.4470.0000.0000.0000.000
12A45ARG10.8300.89713.64219.34419.3440.0000.0000.0000.000
13A46ASP-1-0.861-0.9178.745-31.041-31.0410.0000.0000.0000.000
14A47TYR00.0170.01411.3820.1490.1490.0000.0000.0000.000
15A48LEU00.0260.00113.8270.7630.7630.0000.0000.0000.000
16A49LYS10.8200.89110.99726.39426.3940.0000.0000.0000.000
17A50LEU0-0.032-0.00412.7390.6500.6500.0000.0000.0000.000
18A51SER0-0.052-0.02916.3440.9900.9900.0000.0000.0000.000
19A52ASP-1-0.793-0.86218.930-13.880-13.8800.0000.0000.0000.000
20A53LYS10.9390.96219.58913.16413.1640.0000.0000.0000.000
21A54GLU-1-0.838-0.89015.527-16.701-16.7010.0000.0000.0000.000
22A55ARG10.8020.84818.01814.82314.8230.0000.0000.0000.000
23A56GLU-1-0.793-0.87820.960-11.992-11.9920.0000.0000.0000.000
24A57ALA00.0050.01217.5290.2430.2430.0000.0000.0000.000
25A58ALA0-0.001-0.00419.5600.0920.0920.0000.0000.0000.000
26A59ARG10.8860.93821.54312.16012.1600.0000.0000.0000.000
27A60ILE00.0280.00021.6870.4600.4600.0000.0000.0000.000
28A61LEU00.0350.01118.6430.3120.3120.0000.0000.0000.000
29A62ALA0-0.0060.00822.9570.4760.4760.0000.0000.0000.000
30A63ASN0-0.009-0.01426.0680.5240.5240.0000.0000.0000.000
31A64GLY0-0.0050.00326.6760.3710.3710.0000.0000.0000.000
32A65LEU0-0.059-0.01025.5630.0840.0840.0000.0000.0000.000
33A66VAL00.0170.00820.125-0.379-0.3790.0000.0000.0000.000
34A67LYS10.8470.91822.15111.97211.9720.0000.0000.0000.000
35A68VAL00.0320.01217.340-0.702-0.7020.0000.0000.0000.000
36A69ASP-1-0.751-0.85319.078-14.597-14.5970.0000.0000.0000.000
37A70GLY00.0410.02521.3140.5020.5020.0000.0000.0000.000
38A71LYS10.9070.95823.60412.61812.6180.0000.0000.0000.000
39A72THR00.019-0.00323.469-0.598-0.5980.0000.0000.0000.000
40A73VAL0-0.038-0.01720.2240.2470.2470.0000.0000.0000.000
41A74ARG10.9170.94623.28211.17311.1730.0000.0000.0000.000
42A75GLU-1-0.813-0.87120.323-14.232-14.2320.0000.0000.0000.000
43A76LYS11.0040.99218.17715.98615.9860.0000.0000.0000.000
44A77LYS10.8310.88117.06113.07113.0710.0000.0000.0000.000
45A78PHE0-0.0100.00516.275-0.509-0.5090.0000.0000.0000.000
46A79ALA00.0200.01512.863-0.841-0.8410.0000.0000.0000.000
47A80VAL0-0.011-0.00311.6111.3331.3330.0000.0000.0000.000
48A81GLY00.0440.0009.588-2.433-2.4330.0000.0000.0000.000
49A82PHE00.0300.0219.3410.9450.9450.0000.0000.0000.000
50A83MET0-0.0060.00310.9161.3201.3200.0000.0000.0000.000
51A84ASP-1-0.810-0.87913.884-17.583-17.5830.0000.0000.0000.000
52A85VAL00.0140.01215.707-0.590-0.5900.0000.0000.0000.000
53A86ILE0-0.014-0.01314.6170.0690.0690.0000.0000.0000.000
54A87GLU-1-0.884-0.92718.668-11.633-11.6330.0000.0000.0000.000
55A88ILE00.0200.00117.952-0.059-0.0590.0000.0000.0000.000
56A89ASN0-0.044-0.03722.6260.1900.1900.0000.0000.0000.000
57A90GLY00.0360.03926.0580.3960.3960.0000.0000.0000.000
58A91GLU-1-0.784-0.88324.002-12.392-12.3920.0000.0000.0000.000
59A92SER00.0060.00322.062-0.227-0.2270.0000.0000.0000.000
60A93TYR0-0.007-0.00317.063-0.052-0.0520.0000.0000.0000.000
61A94ARG10.7660.86315.01116.01416.0140.0000.0000.0000.000
62A95VAL0-0.0170.00510.181-1.025-1.0250.0000.0000.0000.000
63A96VAL0-0.003-0.01510.6491.1731.1730.0000.0000.0000.000
64A97TYR0-0.013-0.0274.541-0.196-0.052-0.001-0.012-0.1300.000
65A98ASN00.0620.0394.651-1.952-1.814-0.001-0.006-0.1310.000
66A99ASP-1-0.791-0.9066.286-30.960-30.9600.0000.0000.0000.000
67A100GLN0-0.082-0.0333.847-1.097-0.7880.001-0.094-0.2160.000
68A101GLY00.008-0.0092.227-24.108-22.4484.918-2.728-3.849-0.040
69A102ALA0-0.048-0.0292.490-8.615-6.5554.523-1.860-4.724-0.026
70A103LEU0-0.0080.0083.3818.7328.8390.0600.256-0.424-0.001
71A104VAL0-0.017-0.0126.108-1.453-1.4530.0000.0000.0000.000
72A105LEU0-0.016-0.0089.4141.8641.8640.0000.0000.0000.000
73A106MET00.0090.02313.219-0.705-0.7050.0000.0000.0000.000
74A107LYS10.8190.89115.44014.18414.1840.0000.0000.0000.000
75A108GLU-1-0.758-0.86319.216-14.646-14.6460.0000.0000.0000.000
76A109THR0-0.023-0.02420.9530.6300.6300.0000.0000.0000.000
77A110LYS10.8500.87924.40011.73511.7350.0000.0000.0000.000
78A111GLU-1-0.884-0.92326.572-10.355-10.3550.0000.0000.0000.000
79A112ARG10.9130.96622.15512.67112.6710.0000.0000.0000.000
80A113ALA0-0.028-0.01122.311-0.330-0.3300.0000.0000.0000.000
81A114SER0-0.048-0.02523.3630.0150.0150.0000.0000.0000.000
82A115MET00.0090.01221.9440.3440.3440.0000.0000.0000.000
83A116LYS10.7540.85816.32215.60015.6000.0000.0000.0000.000
84A117LEU0-0.0040.01617.8790.6130.6130.0000.0000.0000.000
85A118LEU00.002-0.01517.578-0.900-0.9000.0000.0000.0000.000
86A119LYS10.8100.91912.83418.70018.7000.0000.0000.0000.000
87A120VAL0-0.009-0.01417.316-0.258-0.2580.0000.0000.0000.000
88A121ARG10.9270.97012.67117.59917.5990.0000.0000.0000.000
89A122SER00.0200.00116.661-0.217-0.2170.0000.0000.0000.000
90A123LYS10.8320.91519.49010.71110.7110.0000.0000.0000.000
91A124VAL00.0120.02223.307-0.075-0.0750.0000.0000.0000.000
92A125ILE0-0.022-0.02126.2580.0600.0600.0000.0000.0000.000
93A126ALA00.0280.02729.5280.0540.0540.0000.0000.0000.000
94A127PRO00.0400.00433.0530.0180.0180.0000.0000.0000.000
95A128GLY00.0470.02436.564-0.053-0.0530.0000.0000.0000.000
96A129ASN0-0.0050.00334.368-0.029-0.0290.0000.0000.0000.000
97A130ARG10.9540.98831.5128.6878.6870.0000.0000.0000.000
98A131ILE0-0.007-0.00327.637-0.207-0.2070.0000.0000.0000.000
99A132GLN00.0260.02126.1720.4100.4100.0000.0000.0000.000
100A133LEU00.005-0.00823.590-0.169-0.1690.0000.0000.0000.000
101A134GLY00.0500.03320.5760.0870.0870.0000.0000.0000.000
102A135THR00.007-0.02218.478-0.065-0.0650.0000.0000.0000.000
103A136HIS0-0.033-0.04212.2960.5230.5230.0000.0000.0000.000
104A137ASP-1-0.751-0.85313.736-16.146-16.1460.0000.0000.0000.000
105A138GLY0-0.039-0.01915.4000.0120.0120.0000.0000.0000.000
106A139ARG10.8140.88917.92814.41814.4180.0000.0000.0000.000
107A140THR0-0.038-0.03421.084-0.152-0.1520.0000.0000.0000.000
108A141PHE00.0050.01622.3640.2840.2840.0000.0000.0000.000
109A142ILE0-0.017-0.02426.750-0.071-0.0710.0000.0000.0000.000
110A143THR0-0.011-0.00428.8940.1540.1540.0000.0000.0000.000
111A144ASP-1-0.833-0.91231.487-8.258-8.2580.0000.0000.0000.000
112A145ASP-1-0.745-0.83630.978-9.114-9.1140.0000.0000.0000.000
113A146LYS10.8690.91830.0337.5827.5820.0000.0000.0000.000
114A147SER0-0.077-0.07029.937-0.272-0.2720.0000.0000.0000.000
115A148ILE00.0030.00624.701-0.318-0.3180.0000.0000.0000.000
116A149LYS10.8450.91823.57210.01710.0170.0000.0000.0000.000
117A150VAL00.0220.00917.866-0.193-0.1930.0000.0000.0000.000
118A151GLY0-0.010-0.01617.6730.0320.0320.0000.0000.0000.000
119A152ASP-1-0.751-0.85918.738-11.677-11.6770.0000.0000.0000.000
120A153VAL0-0.025-0.01417.824-0.485-0.4850.0000.0000.0000.000
121A154LEU0-0.0090.01020.5560.5590.5590.0000.0000.0000.000
122A155ALA00.0170.00721.802-0.642-0.6420.0000.0000.0000.000
123A156VAL0-0.007-0.01622.2470.4700.4700.0000.0000.0000.000
124A157SER00.014-0.01424.371-0.431-0.4310.0000.0000.0000.000
125A158VAL0-0.038-0.02422.398-0.154-0.1540.0000.0000.0000.000
126A159PRO0-0.022-0.02525.2250.0400.0400.0000.0000.0000.000
127A160ASP-1-0.787-0.86128.711-9.423-9.4230.0000.0000.0000.000
128A161MET0-0.065-0.01123.791-0.074-0.0740.0000.0000.0000.000
129A162LYS10.8780.94627.3239.0339.0330.0000.0000.0000.000
130A163ILE00.0110.00126.157-0.254-0.2540.0000.0000.0000.000
131A164SER00.000-0.00327.5990.2550.2550.0000.0000.0000.000
132A165GLU-1-0.784-0.87726.916-9.838-9.8380.0000.0000.0000.000
133A166ILE0-0.040-0.01924.914-0.386-0.3860.0000.0000.0000.000
134A167ILE0-0.0230.00321.2960.3360.3360.0000.0000.0000.000
135A168LYS10.8440.91522.49910.02410.0240.0000.0000.0000.000
136A169MET0-0.0020.00016.7010.0040.0040.0000.0000.0000.000
137A170GLN0-0.064-0.03022.1020.2900.2900.0000.0000.0000.000
138A171PRO00.037-0.00824.246-0.295-0.2950.0000.0000.0000.000
139A172GLY0-0.0030.01225.9460.2910.2910.0000.0000.0000.000
140A173ASN0-0.032-0.02023.2980.2120.2120.0000.0000.0000.000
141A174LYS10.8550.93520.24313.02713.0270.0000.0000.0000.000
142A175ALA00.007-0.01316.6420.0260.0260.0000.0000.0000.000
143A176TYR00.020-0.01010.081-0.085-0.0850.0000.0000.0000.000
144A177ILE0-0.035-0.0019.6060.3250.3250.0000.0000.0000.000
145A178THR00.0230.0027.873-0.708-0.7080.0000.0000.0000.000
146A179ALA0-0.001-0.0045.196-3.740-3.7400.0000.0000.0000.000
147A180GLY00.0280.0165.6682.9082.9080.0000.0000.0000.000
148A181SER00.009-0.0107.661-1.415-1.4150.0000.0000.0000.000
149A182HIS10.8870.9279.89820.30820.3080.0000.0000.0000.000
150A183VAL00.0080.0175.1711.1161.1160.0000.0000.0000.000
151A184ASN0-0.026-0.0128.3720.8550.8550.0000.0000.0000.000
152A185GLN00.0440.06310.2512.8852.8850.0000.0000.0000.000
153A186THR0-0.022-0.03313.4440.2070.2070.0000.0000.0000.000
154A187GLY00.0050.01416.4820.1270.1270.0000.0000.0000.000
155A188THR0-0.044-0.05719.182-0.007-0.0070.0000.0000.0000.000
156A189ILE0-0.0260.00619.9060.1130.1130.0000.0000.0000.000
157A190SER0-0.015-0.01322.6780.4540.4540.0000.0000.0000.000
158A191LYS10.8810.92323.96811.56111.5610.0000.0000.0000.000
159A192ILE0-0.016-0.01321.363-0.587-0.5870.0000.0000.0000.000
160A193GLU-1-0.796-0.86522.305-11.042-11.0420.0000.0000.0000.000
161A194ALA0-0.0020.00322.252-0.460-0.4600.0000.0000.0000.000
162A195LYS10.8860.92723.09410.38510.3850.0000.0000.0000.000
163A196GLU-1-0.900-0.93823.159-9.914-9.9140.0000.0000.0000.000
164A197GLY00.0500.02923.7830.2520.2520.0000.0000.0000.000
165A198SER0-0.009-0.01719.821-0.022-0.0220.0000.0000.0000.000
166A199SER0-0.004-0.01219.399-0.245-0.2450.0000.0000.0000.000
167A200ALA00.0670.06117.734-0.665-0.6650.0000.0000.0000.000
168A201ASN0-0.111-0.06618.5400.2510.2510.0000.0000.0000.000
169A202LEU00.0080.00516.588-0.841-0.8410.0000.0000.0000.000
170A203VAL0-0.034-0.01417.5490.7700.7700.0000.0000.0000.000
171A204HIS0-0.006-0.02818.414-0.753-0.7530.0000.0000.0000.000
172A205PHE0-0.001-0.00116.2100.2630.2630.0000.0000.0000.000
173A206GLN0-0.018-0.02121.4460.3170.3170.0000.0000.0000.000
174A207GLU-1-0.745-0.84320.623-12.893-12.8930.0000.0000.0000.000
175A208GLY00.0230.02321.357-0.391-0.3910.0000.0000.0000.000
176A209PHE0-0.043-0.02114.886-0.418-0.4180.0000.0000.0000.000
177A210SER00.0030.00017.7510.2720.2720.0000.0000.0000.000
178A211THR00.0120.00112.206-1.046-1.0460.0000.0000.0000.000
179A212ILE00.0470.03110.6400.8010.8010.0000.0000.0000.000
180A213LYS10.9980.98413.56812.22612.2260.0000.0000.0000.000
181A214ASP-1-0.905-0.93810.629-17.847-17.8470.0000.0000.0000.000
182A215HIS00.0210.0038.093-0.817-0.8170.0000.0000.0000.000
183A216VAL00.0050.03110.550-0.425-0.4250.0000.0000.0000.000
184A217PHE0-0.0030.00112.7500.4650.4650.0000.0000.0000.000
185A218MET0-0.0120.01214.745-0.134-0.1340.0000.0000.0000.000
186A219ILE00.003-0.01316.689-0.165-0.1650.0000.0000.0000.000
187A220GLY0-0.002-0.01019.5490.3000.3000.0000.0000.0000.000
188A221SER0-0.006-0.00423.1410.0270.0270.0000.0000.0000.000
189A222SER00.017-0.00726.379-0.015-0.0150.0000.0000.0000.000
190A223LYS10.8240.91228.74310.24310.2430.0000.0000.0000.000
191A224PHE00.0410.03223.9340.0320.0320.0000.0000.0000.000
192A225SER00.009-0.01124.245-0.365-0.3650.0000.0000.0000.000
193A226PHE00.0010.02318.4790.1960.1960.0000.0000.0000.000
194A227VAL00.0340.02820.4820.1690.1690.0000.0000.0000.000