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: 1421Z

Calculation Name: 3FHF-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q58134

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2833562.029927
FMO2-HF: Nuclear repulsion 2744915.485464
FMO2-HF: Total energy -88646.544462
FMO2-MP2: Total energy -88910.337984


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:-6:GLY )


Summations of interaction energy for fragment #1(A:-6:GLY )
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.
1.3982.505-0.004-0.427-0.6760.001
Interaction energy analysis for fragmet #1(A:-6:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.000
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].
3A-4HIS 00.020-0.0063.8020.8271.934-0.004-0.427-0.6760.001
4A-3HIS 00.0720.0416.1790.4780.4780.0000.0000.0000.000
5A-2HIS 0-0.006-0.0086.0310.0190.0190.0000.0000.0000.000
6A-1HIS 00.0290.0077.8890.1420.1420.0000.0000.0000.000
7A0HIS 00.0270.06210.2740.0430.0430.0000.0000.0000.000
8A1MET 00.0160.00110.633-0.058-0.0580.0000.0000.0000.000
9A2MET 0-0.037-0.02410.8530.0480.0480.0000.0000.0000.000
10A3LEU 00.0020.02113.4820.0240.0240.0000.0000.0000.000
11A4ILE 00.0280.02015.9500.0120.0120.0000.0000.0000.000
12A5LYS 10.9480.97215.5730.0690.0690.0000.0000.0000.000
13A6LYS 10.9810.99417.532-0.061-0.0610.0000.0000.0000.000
14A7ILE 00.010-0.00619.3170.0060.0060.0000.0000.0000.000
15A8GLU -1-0.836-0.92721.210-0.058-0.0580.0000.0000.0000.000
16A9GLU -1-0.985-0.99120.4210.0270.0270.0000.0000.0000.000
17A10LEU 0-0.073-0.03123.3620.0060.0060.0000.0000.0000.000
18A11LYS 10.8410.93925.3870.0430.0430.0000.0000.0000.000
19A12ASN 0-0.066-0.01925.287-0.003-0.0030.0000.0000.0000.000
20A13SER 0-0.020-0.03227.7970.0060.0060.0000.0000.0000.000
21A14GLU -1-0.866-0.94929.7130.0210.0210.0000.0000.0000.000
22A15ILE 0-0.062-0.03128.3780.0010.0010.0000.0000.0000.000
23A16LYS 10.8950.95330.3890.0120.0120.0000.0000.0000.000
24A17ASP -1-0.850-0.92031.6540.0010.0010.0000.0000.0000.000
25A18ILE 0-0.088-0.04233.6900.0010.0010.0000.0000.0000.000
26A19ILE 0-0.030-0.02329.3120.0010.0010.0000.0000.0000.000
27A20ASP -1-0.797-0.89233.632-0.006-0.0060.0000.0000.0000.000
28A21LYS 10.8640.94135.730-0.012-0.0120.0000.0000.0000.000
29A22ARG 10.8290.91735.904-0.024-0.0240.0000.0000.0000.000
30A23ILE 00.0360.02233.7000.0000.0000.0000.0000.0000.000
31A24GLN 0-0.004-0.01637.409-0.002-0.0020.0000.0000.0000.000
32A25GLU -1-0.907-0.94940.7040.0160.0160.0000.0000.0000.000
33A26PHE 00.0220.02835.6700.0000.0000.0000.0000.0000.000
34A27LYS 10.8950.94038.9260.0070.0070.0000.0000.0000.000
35A28SER 0-0.066-0.04342.696-0.001-0.0010.0000.0000.0000.000
36A29PHE 00.004-0.00644.0210.0000.0000.0000.0000.0000.000
37A30LYS 10.9170.97746.3890.0030.0030.0000.0000.0000.000
38A31ASN 0-0.035-0.02247.989-0.001-0.0010.0000.0000.0000.000
39A32LYS 10.8650.96447.088-0.008-0.0080.0000.0000.0000.000
40A33SER 00.034-0.00751.275-0.001-0.0010.0000.0000.0000.000
41A34ASN 00.049-0.00351.9230.0010.0010.0000.0000.0000.000
42A35GLU -1-0.853-0.92152.1450.0080.0080.0000.0000.0000.000
43A36GLU -1-0.948-0.97649.8090.0140.0140.0000.0000.0000.000
44A37TRP 00.0440.00046.0850.0020.0020.0000.0000.0000.000
45A38PHE 0-0.003-0.01447.5130.0010.0010.0000.0000.0000.000
46A39LYS 10.9250.97548.746-0.012-0.0120.0000.0000.0000.000
47A40GLU -1-0.770-0.86242.9730.0220.0220.0000.0000.0000.000
48A41LEU 0-0.0100.00643.7550.0020.0020.0000.0000.0000.000
49A42CYS 0-0.052-0.02544.5860.0020.0020.0000.0000.0000.000
50A43PHE 0-0.0110.00638.8110.0030.0030.0000.0000.0000.000
51A44CYS 0-0.0330.00439.2710.0030.0030.0000.0000.0000.000
52A45ILE 0-0.0190.00340.6850.0030.0030.0000.0000.0000.000
53A46LEU 0-0.040-0.03042.7590.0030.0030.0000.0000.0000.000
54A47THR 00.0040.01136.4530.0030.0030.0000.0000.0000.000
55A48ALA 00.0280.01837.0970.0050.0050.0000.0000.0000.000
56A49ASN 0-0.097-0.05936.676-0.005-0.0050.0000.0000.0000.000
57A50PHE 00.0560.03037.5940.0000.0000.0000.0000.0000.000
58A51THR 00.0120.01936.6930.0050.0050.0000.0000.0000.000
59A52ALA 00.0780.05736.251-0.003-0.0030.0000.0000.0000.000
60A53GLU -1-0.751-0.89336.4840.0510.0510.0000.0000.0000.000
61A54GLY 0-0.013-0.03339.875-0.002-0.0020.0000.0000.0000.000
62A55GLY 0-0.002-0.01041.069-0.002-0.0020.0000.0000.0000.000
63A56ILE 00.0270.00039.865-0.003-0.0030.0000.0000.0000.000
64A57ARG 10.9210.98742.742-0.043-0.0430.0000.0000.0000.000
65A58ILE 00.0160.01645.407-0.001-0.0010.0000.0000.0000.000
66A59GLN 0-0.047-0.03644.7060.0000.0000.0000.0000.0000.000
67A60LYS 10.9250.96045.410-0.028-0.0280.0000.0000.0000.000
68A61GLU -1-0.951-0.95549.9110.0260.0260.0000.0000.0000.000
69A62ILE 0-0.059-0.01650.693-0.001-0.0010.0000.0000.0000.000
70A63GLY 00.0510.02251.584-0.001-0.0010.0000.0000.0000.000
71A64ASP -1-0.881-0.94852.9020.0130.0130.0000.0000.0000.000
72A65GLY 00.0850.03955.5840.0000.0000.0000.0000.0000.000
73A66PHE 0-0.018-0.03748.2800.0000.0000.0000.0000.0000.000
74A67LEU 0-0.082-0.05753.4700.0000.0000.0000.0000.0000.000
75A68THR 0-0.016-0.01256.3120.0000.0000.0000.0000.0000.000
76A69LEU 0-0.0090.02855.5510.0000.0000.0000.0000.0000.000
77A70PRO 00.0320.05058.1460.0000.0000.0000.0000.0000.000
78A71ARG 10.9470.96554.077-0.021-0.0210.0000.0000.0000.000
79A72GLU -1-0.844-0.93656.6700.0190.0190.0000.0000.0000.000
80A73GLU -1-0.851-0.93258.0240.0190.0190.0000.0000.0000.000
81A74LEU 0-0.071-0.02552.1390.0010.0010.0000.0000.0000.000
82A75GLU -1-0.886-0.97753.0280.0270.0270.0000.0000.0000.000
83A76GLU -1-0.858-0.92253.3160.0280.0280.0000.0000.0000.000
84A77LYS 10.9760.98853.535-0.020-0.0200.0000.0000.0000.000
85A78LEU 0-0.025-0.01348.2950.0020.0020.0000.0000.0000.000
86A79LYS 10.9420.96549.231-0.029-0.0290.0000.0000.0000.000
87A80ASN 0-0.060-0.03550.3820.0030.0030.0000.0000.0000.000
88A81LEU 0-0.0180.01048.5510.0010.0010.0000.0000.0000.000
89A82GLY 0-0.0030.00046.2810.0020.0020.0000.0000.0000.000
90A83HIS 0-0.052-0.01642.5870.0030.0030.0000.0000.0000.000
91A84ARG 10.9900.97838.281-0.059-0.0590.0000.0000.0000.000
92A85PHE 0-0.097-0.05041.056-0.001-0.0010.0000.0000.0000.000
93A86TYR 00.0390.02545.909-0.002-0.0020.0000.0000.0000.000
94A87ARG 11.0021.01248.984-0.032-0.0320.0000.0000.0000.000
95A88LYS 10.9260.95444.495-0.037-0.0370.0000.0000.0000.000
96A89ARG 10.8450.93040.768-0.040-0.0400.0000.0000.0000.000
97A90ALA 00.0810.04947.668-0.002-0.0020.0000.0000.0000.000
98A91GLU -1-0.960-0.98351.1340.0210.0210.0000.0000.0000.000
99A92TYR 0-0.033-0.02944.7320.0000.0000.0000.0000.0000.000
100A93ILE 00.0280.01748.061-0.002-0.0020.0000.0000.0000.000
101A94VAL 00.0330.01450.597-0.002-0.0020.0000.0000.0000.000
102A95LEU 0-0.018-0.00751.510-0.002-0.0020.0000.0000.0000.000
103A96ALA 0-0.018-0.00249.609-0.002-0.0020.0000.0000.0000.000
104A97ARG 10.8540.91751.602-0.017-0.0170.0000.0000.0000.000
105A98ARG 10.8070.91451.241-0.012-0.0120.0000.0000.0000.000
106A99PHE 0-0.018-0.01951.116-0.001-0.0010.0000.0000.0000.000
107A100LYS 10.9900.98952.466-0.008-0.0080.0000.0000.0000.000
108A101ASN 0-0.046-0.00553.6420.0010.0010.0000.0000.0000.000
109A102ILE 00.0400.00147.942-0.001-0.0010.0000.0000.0000.000
110A103LYS 10.8360.93049.319-0.002-0.0020.0000.0000.0000.000
111A104ASP -1-0.812-0.89850.3470.0000.0000.0000.0000.0000.000
112A105ILE 0-0.062-0.01749.627-0.001-0.0010.0000.0000.0000.000
113A106VAL 0-0.042-0.01445.100-0.001-0.0010.0000.0000.0000.000
114A107GLU -1-0.876-0.94747.267-0.004-0.0040.0000.0000.0000.000
115A108SER 0-0.077-0.03148.963-0.002-0.0020.0000.0000.0000.000
116A109PHE 0-0.032-0.02346.349-0.001-0.0010.0000.0000.0000.000
117A110GLU -1-0.859-0.92145.445-0.015-0.0150.0000.0000.0000.000
118A111ASN 0-0.006-0.01241.5140.0000.0000.0000.0000.0000.000
119A112GLU -1-0.775-0.91737.412-0.009-0.0090.0000.0000.0000.000
120A113LYS 10.8300.92634.4790.0230.0230.0000.0000.0000.000
121A114VAL 00.0460.02639.5730.0020.0020.0000.0000.0000.000
122A115ALA 00.0250.02543.0030.0020.0020.0000.0000.0000.000
123A116ARG 10.7640.84233.8740.0030.0030.0000.0000.0000.000
124A117GLU -1-0.941-0.97341.005-0.005-0.0050.0000.0000.0000.000
125A118PHE 00.0230.01642.4760.0020.0020.0000.0000.0000.000
126A119LEU 0-0.026-0.01442.2780.0020.0020.0000.0000.0000.000
127A120VAL 0-0.060-0.02939.5360.0020.0020.0000.0000.0000.000
128A121ARG 10.9070.96042.690-0.005-0.0050.0000.0000.0000.000
129A122ASN 0-0.0020.00845.5120.0000.0000.0000.0000.0000.000
130A123ILE 0-0.017-0.00145.9460.0010.0010.0000.0000.0000.000
131A124LYS 10.9600.97645.495-0.014-0.0140.0000.0000.0000.000
132A125GLY 00.006-0.01043.8330.0000.0000.0000.0000.0000.000
133A126ILE 0-0.032-0.00741.2320.0020.0020.0000.0000.0000.000
134A127GLY 00.0600.03638.594-0.002-0.0020.0000.0000.0000.000
135A128TYR 00.0650.01935.033-0.003-0.0030.0000.0000.0000.000
136A129LYS 10.9301.01632.849-0.041-0.0410.0000.0000.0000.000
137A130GLU -1-0.882-0.95534.8460.0320.0320.0000.0000.0000.000
138A131ALA 00.0180.01138.125-0.001-0.0010.0000.0000.0000.000
139A132SER 00.010-0.02034.512-0.004-0.0040.0000.0000.0000.000
140A133HIS 0-0.060-0.04235.8040.0000.0000.0000.0000.0000.000
141A134PHE 00.020-0.01236.640-0.001-0.0010.0000.0000.0000.000
142A135LEU 0-0.008-0.00638.698-0.001-0.0010.0000.0000.0000.000
143A136ARG 10.8230.92132.502-0.022-0.0220.0000.0000.0000.000
144A137ASN 0-0.022-0.03037.421-0.001-0.0010.0000.0000.0000.000
145A138VAL 0-0.061-0.01139.6730.0000.0000.0000.0000.0000.000
146A139GLY 0-0.0110.00240.476-0.002-0.0020.0000.0000.0000.000
147A140TYR 0-0.041-0.02138.885-0.003-0.0030.0000.0000.0000.000
148A141ASP -1-0.760-0.88434.743-0.006-0.0060.0000.0000.0000.000
149A142ASP -1-0.810-0.89032.516-0.028-0.0280.0000.0000.0000.000
150A143VAL 0-0.040-0.01733.388-0.001-0.0010.0000.0000.0000.000
151A144ALA 00.0550.02728.7400.0030.0030.0000.0000.0000.000
152A145ILE 0-0.0320.00630.3220.0010.0010.0000.0000.0000.000
153A146ILE 00.006-0.00326.9480.0050.0050.0000.0000.0000.000
154A147ASP -1-0.847-0.91627.6370.0690.0690.0000.0000.0000.000
155A148ARG 10.9270.93127.401-0.080-0.0800.0000.0000.0000.000
156A149HIS 0-0.041-0.02225.2130.0160.0160.0000.0000.0000.000
157A150ILE 00.0920.04721.9060.0130.0130.0000.0000.0000.000
158A151LEU 0-0.034-0.01522.2670.0040.0040.0000.0000.0000.000
159A152ARG 10.8690.93820.811-0.188-0.1880.0000.0000.0000.000
160A153GLU -1-0.757-0.84518.7660.1410.1410.0000.0000.0000.000
161A154LEU 0-0.006-0.00817.5040.0160.0160.0000.0000.0000.000
162A155TYR 0-0.034-0.01717.6450.0090.0090.0000.0000.0000.000
163A156GLU -1-0.843-0.92115.8190.2770.2770.0000.0000.0000.000
164A157ASN 0-0.112-0.05013.0350.1160.1160.0000.0000.0000.000
165A158ASN 0-0.038-0.01611.368-0.053-0.0530.0000.0000.0000.000
166A159TYR 0-0.016-0.04914.877-0.038-0.0380.0000.0000.0000.000
167A160ILE 0-0.115-0.06317.488-0.026-0.0260.0000.0000.0000.000
168A161ASP -1-0.836-0.92618.3070.0780.0780.0000.0000.0000.000
169A162GLU -1-0.940-0.96619.8290.1620.1620.0000.0000.0000.000
170A163ILE 0-0.073-0.02622.378-0.018-0.0180.0000.0000.0000.000
171A164PRO 00.0050.00524.565-0.004-0.0040.0000.0000.0000.000
172A165LYS 10.9370.98427.776-0.095-0.0950.0000.0000.0000.000
173A166THR 0-0.041-0.03930.422-0.004-0.0040.0000.0000.0000.000
174A167LEU 00.0170.01228.747-0.002-0.0020.0000.0000.0000.000
175A168SER 00.0180.01832.564-0.003-0.0030.0000.0000.0000.000
176A169ARG 10.9650.95733.6200.0050.0050.0000.0000.0000.000
177A170ARG 10.9820.98329.356-0.003-0.0030.0000.0000.0000.000
178A171LYS 10.9120.96224.622-0.024-0.0240.0000.0000.0000.000
179A172TYR 0-0.021-0.03329.1230.0030.0030.0000.0000.0000.000
180A173LEU 00.019-0.00929.972-0.001-0.0010.0000.0000.0000.000
181A174GLU -1-0.893-0.92925.656-0.014-0.0140.0000.0000.0000.000
182A175ILE 00.026-0.00124.424-0.004-0.0040.0000.0000.0000.000
183A176GLU -1-0.777-0.85625.562-0.007-0.0070.0000.0000.0000.000
184A177ASN 0-0.011-0.02526.964-0.006-0.0060.0000.0000.0000.000
185A178ILE 00.0740.07620.629-0.004-0.0040.0000.0000.0000.000
186A179LEU 0-0.041-0.02622.647-0.004-0.0040.0000.0000.0000.000
187A180ARG 10.8140.89024.2800.0290.0290.0000.0000.0000.000
188A181ASP -1-0.831-0.91222.623-0.085-0.0850.0000.0000.0000.000
189A182ILE 0-0.032-0.02119.265-0.005-0.0050.0000.0000.0000.000
190A183GLY 0-0.013-0.01321.846-0.001-0.0010.0000.0000.0000.000
191A184GLU -1-0.942-0.95424.738-0.083-0.0830.0000.0000.0000.000
192A185GLU -1-0.893-0.92717.713-0.179-0.1790.0000.0000.0000.000
193A186VAL 0-0.016-0.00521.328-0.002-0.0020.0000.0000.0000.000
194A187ASN 0-0.084-0.04223.7660.0050.0050.0000.0000.0000.000
195A188LEU 0-0.059-0.01925.5490.0090.0090.0000.0000.0000.000
196A189LYS 10.9350.97328.4050.0200.0200.0000.0000.0000.000
197A190LEU 00.012-0.00127.5770.0050.0050.0000.0000.0000.000
198A191SER 0-0.088-0.06330.0430.0060.0060.0000.0000.0000.000
199A192GLU -1-0.839-0.93530.405-0.009-0.0090.0000.0000.0000.000
200A193LEU 00.0360.02223.3150.0070.0070.0000.0000.0000.000
201A194ASP -1-0.838-0.91426.4890.0410.0410.0000.0000.0000.000
202A195LEU 0-0.002-0.00628.1630.0090.0090.0000.0000.0000.000
203A196TYR 00.0440.01425.0000.0070.0070.0000.0000.0000.000
204A197ILE 00.0040.00422.6900.0100.0100.0000.0000.0000.000
205A198TRP 0-0.026-0.01924.5120.0210.0210.0000.0000.0000.000
206A199TYR 00.0050.01025.8540.0100.0100.0000.0000.0000.000
207A200LEU 0-0.0020.00020.3850.0070.0070.0000.0000.0000.000
208A201ARG 10.7720.88123.028-0.081-0.0810.0000.0000.0000.000
209A202THR 0-0.099-0.07024.3700.0040.0040.0000.0000.0000.000
210A203GLY 00.0200.02527.249-0.001-0.0010.0000.0000.0000.000
211A204LYS 10.7860.88128.671-0.067-0.0670.0000.0000.0000.000
212A205VAL 00.0770.03430.8200.0000.0000.0000.0000.0000.000
213A206LEU 0-0.079-0.03533.256-0.002-0.0020.0000.0000.0000.000
214A207LYS 00.0700.03935.7180.0060.0060.0000.0000.0000.000