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: G5181

Calculation Name: 2FJR-A-Xray372

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: 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1864458.863339
FMO2-HF: Nuclear repulsion 1792049.460675
FMO2-HF: Total energy -72409.402664
FMO2-MP2: Total energy -72622.511622


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.
27.23530.2470.027-1.305-1.7350.005
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 : -0.947 / q_NPA : -0.991
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].
3A6LEU0-0.035-0.0483.442-9.894-7.2380.029-1.280-1.4050.005
4A7GLY0-0.0050.0205.093-0.905-0.744-0.001-0.011-0.1490.000
5A8TRP00.0140.0015.685-0.584-0.5840.0000.0000.0000.000
6A9SER00.0510.0487.4371.5601.5600.0000.0000.0000.000
7A10ASN00.006-0.0338.754-0.220-0.2200.0000.0000.0000.000
8A11VAL0-0.021-0.00810.037-1.398-1.3980.0000.0000.0000.000
9A12ASP-1-0.866-0.94512.97518.60518.6050.0000.0000.0000.000
10A13VAL0-0.058-0.0179.411-0.554-0.5540.0000.0000.0000.000
11A14LEU0-0.060-0.03012.833-1.006-1.0060.0000.0000.0000.000
12A15ASP-1-0.814-0.89115.11214.97114.9710.0000.0000.0000.000
13A16ARG10.8940.96812.498-21.965-21.9650.0000.0000.0000.000
14A17ILE0-0.010-0.00513.840-0.513-0.5130.0000.0000.0000.000
15A18CYS0-0.072-0.04017.872-0.936-0.9360.0000.0000.0000.000
16A19GLU-1-0.944-0.96720.57613.47013.4700.0000.0000.0000.000
17A20ALA0-0.042-0.02920.281-0.545-0.5450.0000.0000.0000.000
18A21TYR0-0.076-0.06319.850-0.046-0.0460.0000.0000.0000.000
19A22GLY00.0220.02724.082-0.578-0.5780.0000.0000.0000.000
20A23PHE0-0.093-0.04322.648-0.456-0.4560.0000.0000.0000.000
21A24SER00.0150.00324.9070.2900.2900.0000.0000.0000.000
22A25GLN0-0.044-0.03725.8860.0000.0000.0000.0000.0000.000
23A26LYS11.0050.99619.740-14.166-14.1660.0000.0000.0000.000
24A27ILE0-0.011-0.00722.9070.3610.3610.0000.0000.0000.000
25A28GLN00.0700.03225.4460.0410.0410.0000.0000.0000.000
26A29LEU00.0650.05017.6090.0160.0160.0000.0000.0000.000
27A30ALA0-0.080-0.05021.6790.2910.2910.0000.0000.0000.000
28A31ASN0-0.027-0.02422.6260.1360.1360.0000.0000.0000.000
29A32HIS0-0.032-0.00722.171-0.531-0.5310.0000.0000.0000.000
30A33PHE0-0.048-0.03118.8020.2020.2020.0000.0000.0000.000
31A34ASP-1-0.955-0.96322.25811.96611.9660.0000.0000.0000.000
32A35ILE0-0.052-0.00718.9400.3720.3720.0000.0000.0000.000
33A36ALA00.0210.00523.071-0.411-0.4110.0000.0000.0000.000
34A37SER00.0700.01222.6860.7430.7430.0000.0000.0000.000
35A38SER0-0.003-0.01022.3060.5820.5820.0000.0000.0000.000
36A39SER00.0300.01119.7260.3350.3350.0000.0000.0000.000
37A40LEU00.0330.02417.3101.0841.0840.0000.0000.0000.000
38A41SER0-0.013-0.01217.5630.6600.6600.0000.0000.0000.000
39A42ASN0-0.015-0.01114.9740.5310.5310.0000.0000.0000.000
40A43ARG10.7570.87313.669-18.997-18.9970.0000.0000.0000.000
41A44TYR0-0.007-0.04212.8241.4401.4400.0000.0000.0000.000
42A45THR0-0.0450.00014.0980.2630.2630.0000.0000.0000.000
43A46ARG10.8260.92410.110-25.297-25.2970.0000.0000.0000.000
44A47GLY00.0660.0257.7180.1090.1090.0000.0000.0000.000
45A48ALA0-0.025-0.0105.9132.7822.7820.0000.0000.0000.000
46A49ILE00.1020.0635.096-4.867-4.8670.0000.0000.0000.000
47A50SER0-0.035-0.0167.293-0.009-0.0090.0000.0000.0000.000
48A51TYR00.0700.0194.403-0.716-0.521-0.001-0.014-0.1810.000
49A52ASP-1-0.796-0.8649.91420.92720.9270.0000.0000.0000.000
50A53PHE00.040-0.00413.195-1.173-1.1730.0000.0000.0000.000
51A54ALA00.0520.03211.735-1.121-1.1210.0000.0000.0000.000
52A55ALA0-0.017-0.00712.887-1.053-1.0530.0000.0000.0000.000
53A56HIS0-0.009-0.01814.466-1.677-1.6770.0000.0000.0000.000
54A57CYS00.0290.05117.009-0.949-0.9490.0000.0000.0000.000
55A58ALA00.0010.01116.091-0.931-0.9310.0000.0000.0000.000
56A59LEU0-0.087-0.05117.307-1.008-1.0080.0000.0000.0000.000
57A60GLU-1-0.862-0.90720.39713.08313.0830.0000.0000.0000.000
58A61THR0-0.004-0.01621.120-0.630-0.6300.0000.0000.0000.000
59A62GLY0-0.097-0.06621.909-0.549-0.5490.0000.0000.0000.000
60A63ALA00.0070.02819.420-0.019-0.0190.0000.0000.0000.000
61A64ASN00.0170.00117.1561.5911.5910.0000.0000.0000.000
62A65LEU00.0480.00111.7530.5170.5170.0000.0000.0000.000
63A66GLN00.0060.01912.6342.7712.7710.0000.0000.0000.000
64A67TRP00.0440.04613.5291.4501.4500.0000.0000.0000.000
65A68LEU0-0.0030.00414.1520.4160.4160.0000.0000.0000.000
66A69LEU0-0.034-0.0368.5350.5840.5840.0000.0000.0000.000
67A70THR0-0.028-0.01610.3110.6960.6960.0000.0000.0000.000
68A71GLY0-0.037-0.01712.290-0.739-0.7390.0000.0000.0000.000
69A72GLU-1-0.980-0.99314.03520.63020.6300.0000.0000.0000.000
70A73GLY0-0.051-0.03017.2040.1560.1560.0000.0000.0000.000
71A74GLU-1-0.931-0.98120.42312.01412.0140.0000.0000.0000.000
72A75ALA0-0.0040.01320.5260.3410.3410.0000.0000.0000.000
73A76PHE0-0.011-0.02921.5360.3470.3470.0000.0000.0000.000
74A77VAL0-0.0180.01424.308-0.121-0.1210.0000.0000.0000.000
75A78ASN00.0850.02826.623-0.182-0.1820.0000.0000.0000.000
76A79ASN00.0100.00028.578-0.493-0.4930.0000.0000.0000.000
77A80ARG10.8370.92623.586-12.390-12.3900.0000.0000.0000.000
78A81GLU-1-0.848-0.92227.12211.04511.0450.0000.0000.0000.000
79A82SER00.0330.05226.590-0.414-0.4140.0000.0000.0000.000
80A83SER0-0.099-0.07927.637-0.008-0.0080.0000.0000.0000.000
81A84ASP-1-0.799-0.89329.9909.4189.4180.0000.0000.0000.000
82A85ALA0-0.0060.00529.8350.2590.2590.0000.0000.0000.000
83A86LYS10.9120.96829.034-10.145-10.1450.0000.0000.0000.000
84A87ARG10.8920.94926.257-11.730-11.7300.0000.0000.0000.000
85A88ILE00.0190.03029.3660.2570.2570.0000.0000.0000.000
86A89GLU-1-0.859-0.92928.20310.92310.9230.0000.0000.0000.000
87A90GLY00.0350.01031.500-0.265-0.2650.0000.0000.0000.000
88A91PHE00.010-0.00632.4150.1230.1230.0000.0000.0000.000
89A92THR0-0.0210.00137.474-0.235-0.2350.0000.0000.0000.000
90A93LEU0-0.038-0.01341.0250.1260.1260.0000.0000.0000.000
91A94SER0-0.050-0.03643.299-0.190-0.1900.0000.0000.0000.000
92A95GLU-1-0.943-0.97246.1266.6456.6450.0000.0000.0000.000
93A96GLU-1-0.946-0.97046.4176.5206.5200.0000.0000.0000.000
94A97ILE00.0130.01742.2450.1670.1670.0000.0000.0000.000
95A98LEU0-0.002-0.00737.099-0.060-0.0600.0000.0000.0000.000
96A99LYS10.9250.95838.042-7.364-7.3640.0000.0000.0000.000
97A100SER00.0500.02332.706-0.034-0.0340.0000.0000.0000.000
98A101ASP-1-0.874-0.92134.9808.1738.1730.0000.0000.0000.000
99A102LYS10.8950.93633.638-8.045-8.0450.0000.0000.0000.000
100A103GLN00.014-0.00427.892-0.119-0.1190.0000.0000.0000.000
101A104LEU0-0.043-0.01932.924-0.231-0.2310.0000.0000.0000.000
102A105SER0-0.047-0.03033.1650.3670.3670.0000.0000.0000.000
103A106VAL0-0.026-0.01533.757-0.322-0.3220.0000.0000.0000.000
104A107ASP-1-0.876-0.93633.9559.2029.2020.0000.0000.0000.000
105A108ALA00.0490.02132.308-0.124-0.1240.0000.0000.0000.000
106A109GLN0-0.016-0.01434.325-0.291-0.2910.0000.0000.0000.000
107A110PHE0-0.101-0.05237.486-0.282-0.2820.0000.0000.0000.000
108A111PHE0-0.043-0.02934.962-0.212-0.2120.0000.0000.0000.000
109A112THR00.0020.01837.0550.0190.0190.0000.0000.0000.000
110A113LYS10.8860.94236.023-7.914-7.9140.0000.0000.0000.000
111A114PRO00.1490.04830.716-0.094-0.0940.0000.0000.0000.000
112A115LEU0-0.145-0.05132.071-0.133-0.1330.0000.0000.0000.000
113A116THR00.0550.02226.8680.0170.0170.0000.0000.0000.000
114A117ASP-1-0.822-0.90627.70511.45611.4560.0000.0000.0000.000
115A118GLY00.007-0.00929.600-0.387-0.3870.0000.0000.0000.000
116A119MET0-0.076-0.02131.7530.1780.1780.0000.0000.0000.000
117A120ALA0-0.0140.00434.471-0.244-0.2440.0000.0000.0000.000
118A121ILE00.005-0.01337.0360.0290.0290.0000.0000.0000.000
119A122ARG10.9160.97039.762-8.051-8.0510.0000.0000.0000.000
120A123SER00.0560.00542.6250.0280.0280.0000.0000.0000.000
121A124GLU-1-0.957-0.97645.6966.3596.3590.0000.0000.0000.000
122A125GLY0-0.0090.00248.164-0.090-0.0900.0000.0000.0000.000
123A126LYS10.9200.97546.782-6.447-6.4470.0000.0000.0000.000
124A127ILE0-0.021-0.01740.2100.1070.1070.0000.0000.0000.000
125A128TYR00.0090.00142.059-0.087-0.0870.0000.0000.0000.000
126A129PHE00.014-0.00536.8190.1860.1860.0000.0000.0000.000
127A130VAL0-0.022-0.01536.796-0.175-0.1750.0000.0000.0000.000
128A131ASP-1-0.819-0.90633.5529.6979.6970.0000.0000.0000.000
129A132LYS10.9020.92429.766-10.778-10.7780.0000.0000.0000.000
130A133GLN0-0.0020.00629.335-0.039-0.0390.0000.0000.0000.000
131A134ALA0-0.0480.00632.721-0.098-0.0980.0000.0000.0000.000
132A135SER00.0090.00636.146-0.059-0.0590.0000.0000.0000.000
133A136LEU00.011-0.00837.671-0.160-0.1600.0000.0000.0000.000
134A137SER0-0.100-0.06440.875-0.103-0.1030.0000.0000.0000.000
135A138ASP-1-0.780-0.88243.8126.6146.6140.0000.0000.0000.000
136A139GLY0-0.0030.00545.4860.1250.1250.0000.0000.0000.000
137A140LEU00.0530.03445.315-0.054-0.0540.0000.0000.0000.000
138A141TRP0-0.062-0.03338.6230.2710.2710.0000.0000.0000.000
139A142LEU00.0110.02638.289-0.182-0.1820.0000.0000.0000.000
140A143VAL0-0.031-0.03141.0020.1590.1590.0000.0000.0000.000
141A144ASP-1-0.864-0.92540.7667.7147.7140.0000.0000.0000.000
142A145ILE0-0.005-0.02042.929-0.043-0.0430.0000.0000.0000.000
143A146LYS10.9160.93945.433-6.462-6.4620.0000.0000.0000.000
144A147GLY00.0330.01943.015-0.084-0.0840.0000.0000.0000.000
145A148ALA0-0.0110.02443.7360.0900.0900.0000.0000.0000.000
146A149ILE00.003-0.00639.8340.0470.0470.0000.0000.0000.000
147A150SER0-0.020-0.01444.054-0.204-0.2040.0000.0000.0000.000
148A151ILE00.0110.00543.5740.1730.1730.0000.0000.0000.000
149A152ARG10.8920.94246.041-6.617-6.6170.0000.0000.0000.000
150A153GLU-1-0.880-0.93947.0996.7216.7210.0000.0000.0000.000
151A154LEU0-0.047-0.02444.322-0.087-0.0870.0000.0000.0000.000
152A155THR0-0.0070.00448.379-0.016-0.0160.0000.0000.0000.000
153A156LYS10.9190.95343.609-7.179-7.1790.0000.0000.0000.000
154A157LEU0-0.0080.00848.943-0.130-0.1300.0000.0000.0000.000
155A158PRO0-0.002-0.01650.4820.1240.1240.0000.0000.0000.000
156A159GLY0-0.016-0.01451.093-0.043-0.0430.0000.0000.0000.000
157A160ARG10.9090.96045.481-6.569-6.5690.0000.0000.0000.000
158A161LYS11.0061.00947.855-5.881-5.8810.0000.0000.0000.000
159A162LEU00.0140.00645.0880.0880.0880.0000.0000.0000.000
160A163HIS0-0.020-0.00649.623-0.106-0.1060.0000.0000.0000.000
161A164VAL0-0.007-0.00449.0730.1240.1240.0000.0000.0000.000
162A165ALA00.0480.01151.297-0.146-0.1460.0000.0000.0000.000
163A166GLY00.0320.00851.4710.1450.1450.0000.0000.0000.000
164A167GLY0-0.0010.01253.1100.0150.0150.0000.0000.0000.000
165A168LYS10.9250.94653.966-5.625-5.6250.0000.0000.0000.000
166A169VAL00.0140.01756.995-0.106-0.1060.0000.0000.0000.000
167A170PRO0-0.0200.00055.2740.1010.1010.0000.0000.0000.000
168A171PHE0-0.033-0.02349.727-0.096-0.0960.0000.0000.0000.000
169A172GLU-1-0.873-0.93952.9875.7895.7890.0000.0000.0000.000
170A173CYS0-0.093-0.03248.228-0.064-0.0640.0000.0000.0000.000
171A174GLY00.0380.01248.600-0.018-0.0180.0000.0000.0000.000
172A175ILE0-0.075-0.05542.5500.0560.0560.0000.0000.0000.000
173A176ASP-1-0.931-0.96943.1887.0927.0920.0000.0000.0000.000
174A177ASP-1-0.833-0.89344.2576.6096.6090.0000.0000.0000.000
175A178ILE0-0.074-0.04244.364-0.063-0.0630.0000.0000.0000.000
176A179LYS10.9790.99934.625-8.847-8.8470.0000.0000.0000.000
177A180THR0-0.021-0.01538.719-0.112-0.1120.0000.0000.0000.000
178A181LEU0-0.046-0.03636.6060.2240.2240.0000.0000.0000.000
179A182GLY00.0800.03435.9460.3120.3120.0000.0000.0000.000
180A183ARG10.9200.98037.628-8.116-8.1160.0000.0000.0000.000
181A184VAL0-0.019-0.00739.1370.1830.1830.0000.0000.0000.000
182A185VAL0-0.068-0.04237.689-0.168-0.1680.0000.0000.0000.000
183A186GLY00.0340.01640.912-0.076-0.0760.0000.0000.0000.000
184A187VAL0-0.033-0.01542.2460.0860.0860.0000.0000.0000.000
185A188TYR00.0180.01943.461-0.070-0.0700.0000.0000.0000.000
186A189SER0-0.007-0.02145.174-0.009-0.0090.0000.0000.0000.000
187A190GLU-1-0.930-0.95247.7366.6426.6420.0000.0000.0000.000
188A191VAL0-0.053-0.02349.758-0.074-0.0740.0000.0000.0000.000
189A192ASN00.0060.00653.419-0.097-0.0970.0000.0000.0000.000