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: GQKG1

Calculation Name: 2FJR-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FJR

Chain ID: A

ChEMBL ID:

UniProt ID: P08707

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 189
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1864254.579073
FMO2-HF: Nuclear repulsion 1791845.944672
FMO2-HF: Total energy -72408.634401
FMO2-MP2: Total energy -72621.728763


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:4:ASP )


Summations of interaction energy for fragment #1(A:4:ASP )
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.
32.52235.450.032-1.279-1.6810.005
Interaction energy analysis for fragmet #1(A:4:ASP )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.944 / q_NPA : -0.990
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].
3A6LEU 0-0.036-0.0483.436-10.302-7.7090.032-1.253-1.3710.005
4A7GLY 0-0.0040.0215.066-1.007-0.8630.000-0.011-0.1330.000
5A8TRP 00.0120.0005.685-0.581-0.5810.0000.0000.0000.000
6A9SER 00.0520.0487.4371.4901.4900.0000.0000.0000.000
7A10ASN 00.008-0.0338.754-0.218-0.2180.0000.0000.0000.000
8A11VAL 0-0.022-0.00710.037-1.486-1.4860.0000.0000.0000.000
9A12ASP -1-0.866-0.94512.97618.58518.5850.0000.0000.0000.000
10A13VAL 0-0.061-0.0179.411-0.531-0.5310.0000.0000.0000.000
11A14LEU 0-0.057-0.02912.833-1.053-1.0530.0000.0000.0000.000
12A15ASP -1-0.820-0.89315.11214.92314.9230.0000.0000.0000.000
13A16ARG 10.8970.96812.498-21.975-21.9750.0000.0000.0000.000
14A17ILE 0-0.011-0.00513.840-0.514-0.5140.0000.0000.0000.000
15A18CYS 0-0.076-0.04117.872-0.973-0.9730.0000.0000.0000.000
16A19GLU -1-0.940-0.96520.57613.45113.4510.0000.0000.0000.000
17A20ALA 0-0.036-0.02720.281-0.548-0.5480.0000.0000.0000.000
18A21TYR 0-0.081-0.06419.849-0.060-0.0600.0000.0000.0000.000
19A22GLY 00.0260.02924.082-0.596-0.5960.0000.0000.0000.000
20A23PHE 0-0.097-0.04522.648-0.458-0.4580.0000.0000.0000.000
21A24SER 00.0160.00324.9070.2850.2850.0000.0000.0000.000
22A25GLN 0-0.046-0.03825.8860.0080.0080.0000.0000.0000.000
23A26LYS 11.0040.99519.742-14.148-14.1480.0000.0000.0000.000
24A27ILE 0-0.009-0.00622.9070.3550.3550.0000.0000.0000.000
25A28GLN 00.0740.03425.4460.0420.0420.0000.0000.0000.000
26A29LEU 00.0610.04817.6090.0370.0370.0000.0000.0000.000
27A30ALA 0-0.078-0.04921.6790.2940.2940.0000.0000.0000.000
28A31ASN 0-0.029-0.02422.6260.1220.1220.0000.0000.0000.000
29A32HIS 0-0.030-0.00522.171-0.523-0.5230.0000.0000.0000.000
30A33PHE 0-0.049-0.03118.8020.2180.2180.0000.0000.0000.000
31A34ASP -1-0.955-0.96222.25811.95511.9550.0000.0000.0000.000
32A35ILE 0-0.054-0.00918.9400.3840.3840.0000.0000.0000.000
33A36ALA 00.0240.00523.071-0.426-0.4260.0000.0000.0000.000
34A37SER 00.0690.01122.6860.7510.7510.0000.0000.0000.000
35A38SER 0-0.002-0.00922.3060.5940.5940.0000.0000.0000.000
36A39SER 00.0300.01119.7260.3610.3610.0000.0000.0000.000
37A40LEU 00.0290.02317.3101.1081.1080.0000.0000.0000.000
38A41SER 0-0.010-0.01117.5630.6660.6660.0000.0000.0000.000
39A42ASN 0-0.014-0.01015.0040.5590.5590.0000.0000.0000.000
40A43ARG 10.7570.87313.669-18.953-18.9530.0000.0000.0000.000
41A44TYR 0-0.004-0.04112.8241.4531.4530.0000.0000.0000.000
42A45THR 0-0.0460.00014.0980.2660.2660.0000.0000.0000.000
43A46ARG 10.8240.92310.140-25.260-25.2600.0000.0000.0000.000
44A47GLY 00.0660.0257.7370.2080.2080.0000.0000.0000.000
45A48ALA 0-0.027-0.0115.9132.8942.8940.0000.0000.0000.000
46A49ILE 00.1060.0645.096-4.886-4.8860.0000.0000.0000.000
47A50SER 0-0.039-0.0177.293-0.075-0.0750.0000.0000.0000.000
48A51TYR 00.0680.0184.403-0.646-0.4550.000-0.015-0.1770.000
49A52ASP -1-0.793-0.8639.91420.84120.8410.0000.0000.0000.000
50A53PHE 00.040-0.00413.195-1.209-1.2090.0000.0000.0000.000
51A54ALA 00.0510.03111.735-1.109-1.1090.0000.0000.0000.000
52A55ALA 0-0.014-0.00512.887-1.070-1.0700.0000.0000.0000.000
53A56HIS 0-0.011-0.01914.466-1.724-1.7240.0000.0000.0000.000
54A57CYS 00.0280.05117.009-0.965-0.9650.0000.0000.0000.000
55A58ALA 00.0000.01216.091-0.930-0.9300.0000.0000.0000.000
56A59LEU 0-0.085-0.05017.307-1.035-1.0350.0000.0000.0000.000
57A60GLU -1-0.863-0.90720.39713.06013.0600.0000.0000.0000.000
58A61THR 0-0.002-0.01621.120-0.639-0.6390.0000.0000.0000.000
59A62GLY 0-0.097-0.06621.909-0.544-0.5440.0000.0000.0000.000
60A63ALA 00.0060.02819.4210.0000.0000.0000.0000.0000.000
61A64ASN 00.0160.00017.1561.6251.6250.0000.0000.0000.000
62A65LEU 00.045-0.00111.7530.5780.5780.0000.0000.0000.000
63A66GLN 00.0110.02112.6342.8092.8090.0000.0000.0000.000
64A67TRP 00.0450.04713.5291.4331.4330.0000.0000.0000.000
65A68LEU 0-0.0050.00314.1520.4450.4450.0000.0000.0000.000
66A69LEU 0-0.036-0.0368.5350.6800.6800.0000.0000.0000.000
67A70THR 0-0.031-0.01810.3110.6840.6840.0000.0000.0000.000
68A71GLY 0-0.035-0.01712.290-0.820-0.8200.0000.0000.0000.000
69A72GLU -1-0.980-0.99214.03520.59520.5950.0000.0000.0000.000
70A73GLY 0-0.050-0.02917.2040.1240.1240.0000.0000.0000.000
71A74GLU -1-0.931-0.98120.42312.00012.0000.0000.0000.0000.000
72A75ALA 0-0.0030.01420.5260.3480.3480.0000.0000.0000.000
73A76PHE 0-0.014-0.03021.5360.3360.3360.0000.0000.0000.000
74A77VAL 0-0.0170.01424.308-0.138-0.1380.0000.0000.0000.000
75A78ASN 00.0840.02726.623-0.200-0.2000.0000.0000.0000.000
76A79ASN 00.0130.00128.578-0.495-0.4950.0000.0000.0000.000
77A80ARG 10.8360.92623.586-12.379-12.3790.0000.0000.0000.000
78A81GLU -1-0.848-0.92127.12211.05111.0510.0000.0000.0000.000
79A82SER 00.0340.05226.589-0.414-0.4140.0000.0000.0000.000
80A83SER 0-0.103-0.08027.637-0.016-0.0160.0000.0000.0000.000
81A84ASP -1-0.795-0.89229.9909.4149.4140.0000.0000.0000.000
82A85ALA 0-0.0060.00529.8350.2640.2640.0000.0000.0000.000
83A86LYS 10.9090.96729.034-10.142-10.1420.0000.0000.0000.000
84A87ARG 10.8910.95026.257-11.726-11.7260.0000.0000.0000.000
85A88ILE 00.0230.03129.3660.2620.2620.0000.0000.0000.000
86A89GLU -1-0.862-0.93128.20310.92410.9240.0000.0000.0000.000
87A90GLY 00.0340.01131.500-0.277-0.2770.0000.0000.0000.000
88A91PHE 00.008-0.00832.4150.1220.1220.0000.0000.0000.000
89A92THR 0-0.0200.00237.474-0.243-0.2430.0000.0000.0000.000
90A93LEU 0-0.037-0.01341.0250.1240.1240.0000.0000.0000.000
91A94SER 0-0.045-0.03443.299-0.198-0.1980.0000.0000.0000.000
92A95GLU -1-0.942-0.97246.1266.6416.6410.0000.0000.0000.000
93A96GLU -1-0.949-0.97146.4176.5246.5240.0000.0000.0000.000
94A97ILE 00.0100.01542.2450.1750.1750.0000.0000.0000.000
95A98LEU 0-0.002-0.00737.099-0.053-0.0530.0000.0000.0000.000
96A99LYS 10.9240.95638.042-7.356-7.3560.0000.0000.0000.000
97A100SER 00.0500.02332.706-0.025-0.0250.0000.0000.0000.000
98A101ASP -1-0.873-0.92034.9808.1728.1720.0000.0000.0000.000
99A102LYS 10.8940.93533.638-8.034-8.0340.0000.0000.0000.000
100A103GLN 00.009-0.00627.893-0.112-0.1120.0000.0000.0000.000
101A104LEU 0-0.037-0.01632.924-0.232-0.2320.0000.0000.0000.000
102A105SER 0-0.050-0.03133.1650.3740.3740.0000.0000.0000.000
103A106VAL 0-0.022-0.01333.757-0.326-0.3260.0000.0000.0000.000
104A107ASP -1-0.877-0.93733.9559.2079.2070.0000.0000.0000.000
105A108ALA 00.0470.02132.308-0.120-0.1200.0000.0000.0000.000
106A109GLN 0-0.016-0.01434.325-0.300-0.3000.0000.0000.0000.000
107A110PHE 0-0.098-0.05037.486-0.282-0.2820.0000.0000.0000.000
108A111PHE 0-0.041-0.02834.961-0.209-0.2090.0000.0000.0000.000
109A112THR 00.0010.01637.0550.0180.0180.0000.0000.0000.000
110A113LYS 10.8840.94136.023-7.905-7.9050.0000.0000.0000.000
111A114PRO 00.1480.04530.716-0.082-0.0820.0000.0000.0000.000
112A115LEU 0-0.145-0.04932.072-0.128-0.1280.0000.0000.0000.000
113A116THR 00.0560.02226.8680.0350.0350.0000.0000.0000.000
114A117ASP -1-0.827-0.90927.70511.45911.4590.0000.0000.0000.000
115A118GLY 00.010-0.00829.600-0.400-0.4000.0000.0000.0000.000
116A119MET 0-0.078-0.02231.7530.1770.1770.0000.0000.0000.000
117A120ALA 0-0.0120.00534.471-0.251-0.2510.0000.0000.0000.000
118A121ILE 00.000-0.01537.0360.0270.0270.0000.0000.0000.000
119A122ARG 10.9200.97339.762-8.054-8.0540.0000.0000.0000.000
120A123SER 00.0530.00242.6250.0250.0250.0000.0000.0000.000
121A124GLU -1-0.962-0.97845.6966.3556.3550.0000.0000.0000.000
122A125GLY 00.0010.00848.162-0.089-0.0890.0000.0000.0000.000
123A126LYS 10.9290.98146.782-6.439-6.4390.0000.0000.0000.000
124A127ILE 0-0.022-0.01940.2100.1220.1220.0000.0000.0000.000
125A128TYR 00.0090.00042.060-0.080-0.0800.0000.0000.0000.000
126A129PHE 00.012-0.00536.8190.2050.2050.0000.0000.0000.000
127A130VAL 0-0.024-0.01536.796-0.171-0.1710.0000.0000.0000.000
128A131ASP -1-0.820-0.90833.5529.7109.7100.0000.0000.0000.000
129A132LYS 10.9060.92629.766-10.775-10.7750.0000.0000.0000.000
130A133GLN 0-0.0080.00429.335-0.037-0.0370.0000.0000.0000.000
131A134ALA 0-0.0450.00732.721-0.108-0.1080.0000.0000.0000.000
132A135SER 00.0060.00536.146-0.065-0.0650.0000.0000.0000.000
133A136LEU 00.009-0.00837.671-0.169-0.1690.0000.0000.0000.000
134A137SER 0-0.100-0.06440.875-0.110-0.1100.0000.0000.0000.000
135A138ASP -1-0.782-0.88243.8126.6096.6090.0000.0000.0000.000
136A139GLY 0-0.0010.00645.4860.1260.1260.0000.0000.0000.000
137A140LEU 00.0540.03545.315-0.053-0.0530.0000.0000.0000.000
138A141TRP 0-0.058-0.03338.6230.2780.2780.0000.0000.0000.000
139A142LEU 00.0080.02638.290-0.180-0.1800.0000.0000.0000.000
140A143VAL 0-0.026-0.03041.0020.1600.1600.0000.0000.0000.000
141A144ASP -1-0.865-0.92540.7667.7147.7140.0000.0000.0000.000
142A145ILE 0-0.005-0.02042.929-0.048-0.0480.0000.0000.0000.000
143A146LYS 10.9130.93845.433-6.463-6.4630.0000.0000.0000.000
144A147GLY 00.0310.01943.015-0.081-0.0810.0000.0000.0000.000
145A148ALA 0-0.0100.02543.7360.0880.0880.0000.0000.0000.000
146A149ILE 00.001-0.00739.8340.0500.0500.0000.0000.0000.000
147A150SER 0-0.021-0.01444.054-0.209-0.2090.0000.0000.0000.000
148A151ILE 00.0180.00943.5740.1750.1750.0000.0000.0000.000
149A152ARG 10.8890.94146.041-6.623-6.6230.0000.0000.0000.000
150A153GLU -1-0.878-0.93847.0996.7206.7200.0000.0000.0000.000
151A154LEU 0-0.046-0.02344.323-0.088-0.0880.0000.0000.0000.000
152A155THR 0-0.0050.00348.379-0.019-0.0190.0000.0000.0000.000
153A156LYS 10.9150.95143.610-7.179-7.1790.0000.0000.0000.000
154A157LEU 0-0.0090.00848.943-0.136-0.1360.0000.0000.0000.000
155A158PRO 0-0.003-0.01650.4820.1240.1240.0000.0000.0000.000
156A159GLY 0-0.016-0.01451.093-0.041-0.0410.0000.0000.0000.000
157A160ARG 10.9080.95945.481-6.565-6.5650.0000.0000.0000.000
158A161LYS 11.0071.01047.855-5.882-5.8820.0000.0000.0000.000
159A162LEU 00.0140.00545.0880.0880.0880.0000.0000.0000.000
160A163HIS 0-0.021-0.00749.623-0.111-0.1110.0000.0000.0000.000
161A164VAL 0-0.004-0.00249.0730.1260.1260.0000.0000.0000.000
162A165ALA 00.0470.00951.297-0.150-0.1500.0000.0000.0000.000
163A166GLY 00.0350.01051.4710.1460.1460.0000.0000.0000.000
164A167GLY 00.0000.01353.1100.0130.0130.0000.0000.0000.000
165A168LYS 10.9240.94653.966-5.630-5.6300.0000.0000.0000.000
166A169VAL 00.0130.01656.995-0.108-0.1080.0000.0000.0000.000
167A170PRO 0-0.0190.00155.2740.1040.1040.0000.0000.0000.000
168A171PHE 0-0.033-0.02349.727-0.097-0.0970.0000.0000.0000.000
169A172GLU -1-0.876-0.94052.9875.7915.7910.0000.0000.0000.000
170A173CYS 0-0.093-0.03348.228-0.062-0.0620.0000.0000.0000.000
171A174GLY 00.0390.01148.600-0.013-0.0130.0000.0000.0000.000
172A175ILE 0-0.077-0.05542.5500.0620.0620.0000.0000.0000.000
173A176ASP -1-0.930-0.96843.1887.0967.0960.0000.0000.0000.000
174A177ASP -1-0.834-0.89344.2576.6076.6070.0000.0000.0000.000
175A178ILE 0-0.072-0.04244.364-0.061-0.0610.0000.0000.0000.000
176A179LYS 10.9790.99834.625-8.841-8.8410.0000.0000.0000.000
177A180THR 0-0.023-0.01538.717-0.111-0.1110.0000.0000.0000.000
178A181LEU 0-0.050-0.03836.6060.2330.2330.0000.0000.0000.000
179A182GLY 00.0830.03435.9460.3150.3150.0000.0000.0000.000
180A183ARG 10.9190.97937.628-8.121-8.1210.0000.0000.0000.000
181A184VAL 0-0.017-0.00739.1370.1840.1840.0000.0000.0000.000
182A185VAL 0-0.071-0.04337.689-0.168-0.1680.0000.0000.0000.000
183A186GLY 00.0340.01540.912-0.079-0.0790.0000.0000.0000.000
184A187VAL 0-0.036-0.01742.2460.0870.0870.0000.0000.0000.000
185A188TYR 00.0130.01643.461-0.062-0.0620.0000.0000.0000.000
186A189SER 0-0.012-0.02545.174-0.008-0.0080.0000.0000.0000.000
187A190GLU -1-0.943-0.96147.7366.6556.6550.0000.0000.0000.000
188A191VAL 0-0.089-0.04249.758-0.063-0.0630.0000.0000.0000.000
189A192ASN -1-0.924-0.95453.4195.6735.6730.0000.0000.0000.000