FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 7J8JK

Calculation Name: 3FFV-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FFV

Chain ID: A

ChEMBL ID:

UniProt ID: P0A8U0

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 180
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2006423.102916
FMO2-HF: Nuclear repulsion 1933758.661821
FMO2-HF: Total energy -72664.441095
FMO2-MP2: Total energy -72876.751035


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:1:MET )


Summations of interaction energy for fragment #1(A:1:MET )
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.
-0.5810.933-0.014-0.573-0.928-0.001
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.069 / q_NPA : -0.050
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].
3A3ASP -1-0.820-0.9123.8231.8423.356-0.014-0.573-0.928-0.001
4A4LEU 00.027-0.0176.075-0.529-0.5290.0000.0000.0000.000
5A5THR 0-0.028-0.0079.237-0.009-0.0090.0000.0000.0000.000
6A6ALA 00.0220.0037.531-0.051-0.0510.0000.0000.0000.000
7A7GLN 0-0.064-0.0289.000-0.454-0.4540.0000.0000.0000.000
8A8ALA 00.0430.02610.5650.0920.0920.0000.0000.0000.000
9A9LEU 0-0.023-0.00212.5580.0500.0500.0000.0000.0000.000
10A10LYS 10.9530.9839.5421.6701.6700.0000.0000.0000.000
11A11ASP -1-0.845-0.91814.074-0.697-0.6970.0000.0000.0000.000
12A12PHE 0-0.051-0.02916.1570.0650.0650.0000.0000.0000.000
13A13THR 00.025-0.01016.6170.0390.0390.0000.0000.0000.000
14A14ALA 0-0.005-0.00417.5550.0320.0320.0000.0000.0000.000
15A15ARG 10.8760.94018.8430.3610.3610.0000.0000.0000.000
16A16TYR 0-0.008-0.00821.8400.0410.0410.0000.0000.0000.000
17A17CYS 0-0.016-0.02221.5650.0210.0210.0000.0000.0000.000
18A18ASP -1-0.899-0.94023.226-0.382-0.3820.0000.0000.0000.000
19A19ALA 0-0.039-0.01725.4630.0260.0260.0000.0000.0000.000
20A20TRP 00.0600.02126.9970.0160.0160.0000.0000.0000.000
21A21HIS 0-0.0320.00127.6050.0190.0190.0000.0000.0000.000
22A22GLU -1-0.978-0.98529.467-0.188-0.1880.0000.0000.0000.000
23A23GLU -1-0.933-0.96331.486-0.141-0.1410.0000.0000.0000.000
24A24HIS 0-0.062-0.03732.2730.0150.0150.0000.0000.0000.000
25A25LYS 10.7860.90432.3450.1840.1840.0000.0000.0000.000
26A26SER 0-0.039-0.03130.6800.0020.0020.0000.0000.0000.000
27A27TRP 00.0170.00521.708-0.024-0.0240.0000.0000.0000.000
28A28PRO 00.008-0.00424.4400.0210.0210.0000.0000.0000.000
29A29LEU 00.0040.00327.599-0.009-0.0090.0000.0000.0000.000
30A30SER 0-0.033-0.01928.4230.0150.0150.0000.0000.0000.000
31A31GLU -1-0.848-0.94430.388-0.146-0.1460.0000.0000.0000.000
32A32GLU -1-0.983-0.98430.251-0.147-0.1470.0000.0000.0000.000
33A33LEU 0-0.027-0.01125.3340.0000.0000.0000.0000.0000.000
34A34TYR 0-0.0210.00929.319-0.006-0.0060.0000.0000.0000.000
35A35GLY 0-0.007-0.00532.0200.0100.0100.0000.0000.0000.000
36A36VAL 0-0.051-0.01926.5690.0060.0060.0000.0000.0000.000
37A37PRO 0-0.017-0.01226.795-0.017-0.0170.0000.0000.0000.000
38A38SER 00.021-0.01621.818-0.014-0.0140.0000.0000.0000.000
39A39PRO 0-0.030-0.01319.5420.0090.0090.0000.0000.0000.000
40A40CYS 0-0.0340.00019.685-0.014-0.0140.0000.0000.0000.000
41A41ILE 0-0.0070.01422.2910.0080.0080.0000.0000.0000.000
42A42ILE 0-0.0340.00025.270-0.006-0.0060.0000.0000.0000.000
43A43SER 0-0.054-0.04527.5920.0170.0170.0000.0000.0000.000
44A44THR 0-0.004-0.01331.120-0.003-0.0030.0000.0000.0000.000
45A45THR 0-0.040-0.01033.4220.0050.0050.0000.0000.0000.000
46A46GLU -1-0.922-0.97736.697-0.132-0.1320.0000.0000.0000.000
47A47ASP -1-0.974-0.97637.216-0.135-0.1350.0000.0000.0000.000
48A48ALA 00.0640.03633.251-0.002-0.0020.0000.0000.0000.000
49A49VAL 0-0.038-0.01328.288-0.004-0.0040.0000.0000.0000.000
50A50TYR 0-0.0040.01229.1050.0000.0000.0000.0000.0000.000
51A51TRP 0-0.019-0.00820.618-0.027-0.0270.0000.0000.0000.000
52A52GLN 00.010-0.00621.4480.0120.0120.0000.0000.0000.000
53A53PRO 0-0.0090.00016.6880.0020.0020.0000.0000.0000.000
54A54GLN 0-0.017-0.00117.031-0.047-0.0470.0000.0000.0000.000
55A55PRO 0-0.034-0.03212.669-0.051-0.0510.0000.0000.0000.000
56A56PHE 00.0260.03711.1370.0970.0970.0000.0000.0000.000
57A57THR 0-0.084-0.09812.110-0.103-0.1030.0000.0000.0000.000
58A58GLY 00.0670.02813.5240.0730.0730.0000.0000.0000.000
59A59GLU -1-0.963-0.99911.668-0.256-0.2560.0000.0000.0000.000
60A60GLN 0-0.056-0.0296.766-0.171-0.1710.0000.0000.0000.000
61A61ASN 0-0.022-0.0158.7060.0540.0540.0000.0000.0000.000
62A62VAL 00.0540.02411.315-0.018-0.0180.0000.0000.0000.000
63A63ASN 00.0220.00112.1810.0870.0870.0000.0000.0000.000
64A64ALA 0-0.054-0.01815.7800.0250.0250.0000.0000.0000.000
65A65VAL 0-0.005-0.00418.2810.0150.0150.0000.0000.0000.000
66A66GLU -1-0.832-0.91415.5110.2330.2330.0000.0000.0000.000
67A67ARG 10.8940.95316.8100.0420.0420.0000.0000.0000.000
68A68ALA 0-0.060-0.01921.1320.0050.0050.0000.0000.0000.000
69A69PHE 0-0.052-0.03322.757-0.001-0.0010.0000.0000.0000.000
70A70ASP -1-0.923-0.96122.4440.1770.1770.0000.0000.0000.000
71A71ILE 0-0.074-0.03620.0900.0040.0040.0000.0000.0000.000
72A72VAL 00.0100.01716.0700.0020.0020.0000.0000.0000.000
73A73ILE 0-0.046-0.03615.2200.0110.0110.0000.0000.0000.000
74A74GLN 0-0.013-0.02814.4770.0930.0930.0000.0000.0000.000
75A75PRO 00.0310.0069.685-0.080-0.0800.0000.0000.0000.000
76A76THR 00.0300.01210.670-0.117-0.1170.0000.0000.0000.000
77A77ILE 00.0350.02712.431-0.130-0.1300.0000.0000.0000.000
78A78HIS 00.0140.01210.178-0.159-0.1590.0000.0000.0000.000
79A79THR 0-0.0170.0077.802-0.092-0.0920.0000.0000.0000.000
80A80PHE 0-0.037-0.0079.796-0.168-0.1680.0000.0000.0000.000
81A81TYR 0-0.019-0.01913.097-0.052-0.0520.0000.0000.0000.000
82A82THR 0-0.028-0.0099.882-0.062-0.0620.0000.0000.0000.000
83A83THR 0-0.024-0.0208.978-0.266-0.2660.0000.0000.0000.000
84A84GLN 0-0.112-0.08210.029-0.254-0.2540.0000.0000.0000.000
85A85PHE 0-0.0330.00213.1260.0750.0750.0000.0000.0000.000
86A86ALA 00.010-0.03516.653-0.032-0.0320.0000.0000.0000.000
87A87GLY 00.0570.02119.2090.0280.0280.0000.0000.0000.000
88A88ASP -1-0.889-0.94421.683-0.241-0.2410.0000.0000.0000.000
89A89MET 0-0.103-0.04418.631-0.015-0.0150.0000.0000.0000.000
90A90HIS 00.0780.06024.2450.0210.0210.0000.0000.0000.000
91A91ALA 0-0.001-0.01524.589-0.017-0.0170.0000.0000.0000.000
92A92GLN 0-0.026-0.01726.7140.0280.0280.0000.0000.0000.000
93A93PHE 00.0130.01224.203-0.008-0.0080.0000.0000.0000.000
94A94GLY 0-0.032-0.01827.7270.0150.0150.0000.0000.0000.000
95A95ASP -1-0.878-0.94830.859-0.057-0.0570.0000.0000.0000.000
96A96ILE 0-0.116-0.05529.7660.0010.0010.0000.0000.0000.000
97A97LYS 10.9810.99329.9870.0790.0790.0000.0000.0000.000
98A98LEU 0-0.024-0.01024.5000.0120.0120.0000.0000.0000.000
99A99THR 00.0620.04125.926-0.008-0.0080.0000.0000.0000.000
100A100LEU 0-0.087-0.04718.7990.0140.0140.0000.0000.0000.000
101A101LEU 00.0340.01721.698-0.018-0.0180.0000.0000.0000.000
102A102GLN 0-0.009-0.01216.216-0.106-0.1060.0000.0000.0000.000
103A103THR 0-0.020-0.00916.0650.0580.0580.0000.0000.0000.000
104A104TRP 00.0590.04218.172-0.069-0.0690.0000.0000.0000.000
105A105SER 00.0300.01119.748-0.016-0.0160.0000.0000.0000.000
106A106GLU -1-0.806-0.85717.784-0.390-0.3900.0000.0000.0000.000
107A107ASP -1-0.936-0.96919.757-0.181-0.1810.0000.0000.0000.000
108A108ASP -1-0.858-0.94021.984-0.192-0.1920.0000.0000.0000.000
109A109PHE 00.0100.00814.6630.0170.0170.0000.0000.0000.000
110A110ARG 10.8800.94519.5910.1670.1670.0000.0000.0000.000
111A111ARG 10.9110.94821.9660.1930.1930.0000.0000.0000.000
112A112VAL 00.0080.01418.9540.0250.0250.0000.0000.0000.000
113A113GLN 00.021-0.00817.4220.0580.0580.0000.0000.0000.000
114A114GLU -1-0.888-0.94021.189-0.071-0.0710.0000.0000.0000.000
115A115ASN 00.0110.00124.7030.0290.0290.0000.0000.0000.000
116A116LEU 0-0.0090.00419.2120.0210.0210.0000.0000.0000.000
117A117ILE 00.0050.00722.7160.0250.0250.0000.0000.0000.000
118A118GLY 0-0.006-0.00124.9320.0140.0140.0000.0000.0000.000
119A119HIS 0-0.037-0.01424.9310.0010.0010.0000.0000.0000.000
120A120LEU 00.0460.01921.9230.0140.0140.0000.0000.0000.000
121A121VAL 0-0.0070.00426.6020.0140.0140.0000.0000.0000.000
122A122THR 0-0.057-0.02229.5540.0060.0060.0000.0000.0000.000
123A123GLN 00.0440.00626.8210.0120.0120.0000.0000.0000.000
124A124LYS 10.9761.01229.341-0.089-0.0890.0000.0000.0000.000
125A125ARG 10.9180.95931.046-0.014-0.0140.0000.0000.0000.000
126A126LEU 0-0.030-0.01233.9020.0010.0010.0000.0000.0000.000
127A127LYS 10.8720.93932.937-0.069-0.0690.0000.0000.0000.000
128A128LEU 0-0.033-0.01531.2010.0050.0050.0000.0000.0000.000
129A129PRO 00.0110.00028.2910.0050.0050.0000.0000.0000.000
130A130PRO 00.0190.02624.075-0.013-0.0130.0000.0000.0000.000
131A131THR 0-0.055-0.06023.1570.0200.0200.0000.0000.0000.000
132A132LEU 00.0260.01718.125-0.009-0.0090.0000.0000.0000.000
133A133PHE 00.0380.01821.3660.0030.0030.0000.0000.0000.000
134A134ILE 0-0.030-0.01518.607-0.012-0.0120.0000.0000.0000.000
135A135ALA 00.0350.01321.263-0.031-0.0310.0000.0000.0000.000
136A136THR 00.0260.02824.3680.0170.0170.0000.0000.0000.000
137A137LEU 0-0.044-0.03828.060-0.005-0.0050.0000.0000.0000.000
138A138GLU -1-0.850-0.91931.158-0.087-0.0870.0000.0000.0000.000
139A139GLU -1-0.962-0.98634.708-0.037-0.0370.0000.0000.0000.000
140A140GLU -1-0.909-0.95934.374-0.039-0.0390.0000.0000.0000.000
141A141LEU 0-0.034-0.02534.1460.0000.0000.0000.0000.0000.000
142A142GLU -1-0.847-0.90131.9700.0060.0060.0000.0000.0000.000
143A143VAL 00.0170.01127.160-0.011-0.0110.0000.0000.0000.000
144A144ILE 0-0.0050.00823.5200.0180.0180.0000.0000.0000.000
145A145SER 00.011-0.04922.707-0.024-0.0240.0000.0000.0000.000
146A146VAL 00.0040.02917.6540.0130.0130.0000.0000.0000.000
147A154CYS 0-0.069-0.04620.9050.0000.0000.0000.0000.0000.000
148A148ASN 00.0390.00218.9340.0280.0280.0000.0000.0000.000
149A149LEU 0-0.058-0.00820.4870.0340.0340.0000.0000.0000.000
150A150SER 0-0.029-0.02921.3310.0310.0310.0000.0000.0000.000
151A151GLY 00.0340.02918.2410.0460.0460.0000.0000.0000.000
152A152GLU -1-0.891-0.92519.0490.1290.1290.0000.0000.0000.000
153A153VAL 00.0050.00720.227-0.017-0.0170.0000.0000.0000.000
154A155LYS 10.9450.99226.0720.0060.0060.0000.0000.0000.000
155A156GLU -1-0.851-0.89326.9620.0400.0400.0000.0000.0000.000
156A157THR 0-0.011-0.00230.606-0.007-0.0070.0000.0000.0000.000
157A158LEU 00.0430.00829.4660.0120.0120.0000.0000.0000.000
158A159GLY 0-0.012-0.01132.9750.0000.0000.0000.0000.0000.000
159A160THR 0-0.038-0.01634.3800.0060.0060.0000.0000.0000.000
160A161ARG 10.8480.89433.575-0.066-0.0660.0000.0000.0000.000
161A162LYS 10.8900.96533.199-0.005-0.0050.0000.0000.0000.000
162A163ARG 10.8860.93328.060-0.063-0.0630.0000.0000.0000.000
163A164THR 0-0.015-0.00830.3030.0010.0010.0000.0000.0000.000
164A165HIS 0-0.045-0.02624.308-0.015-0.0150.0000.0000.0000.000
165A166LEU 0-0.063-0.02025.633-0.010-0.0100.0000.0000.0000.000
166A167ALA 00.0460.02022.046-0.011-0.0110.0000.0000.0000.000
167A168SER 0-0.022-0.02520.2510.0210.0210.0000.0000.0000.000
168A169ASN 0-0.035-0.00916.4870.0050.0050.0000.0000.0000.000
169A170LEU 00.0450.02014.100-0.029-0.0290.0000.0000.0000.000
170A171ALA 00.0480.02613.543-0.063-0.0630.0000.0000.0000.000
171A172GLU -1-0.869-0.93015.5850.0500.0500.0000.0000.0000.000
172A173PHE 00.0310.00418.760-0.032-0.0320.0000.0000.0000.000
173A174LEU 00.0210.00815.091-0.021-0.0210.0000.0000.0000.000
174A175ASN 0-0.015-0.02015.541-0.097-0.0970.0000.0000.0000.000
175A176GLN 0-0.059-0.01919.431-0.014-0.0140.0000.0000.0000.000
176A177LEU 0-0.0560.00020.9860.0060.0060.0000.0000.0000.000
177A178LYS 10.9340.97723.5070.0940.0940.0000.0000.0000.000
178A179PRO 00.0120.00124.2320.0110.0110.0000.0000.0000.000
179A180LEU 0-0.069-0.02926.5450.0190.0190.0000.0000.0000.000
180A181LEU -1-0.894-0.93929.116-0.158-0.1580.0000.0000.0000.000