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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: J3339

Calculation Name: 5RV1-A-Xray89

Preferred Name:

Target Type:

Ligand Name: trifluoroacetic acid

ligand 3-letter code: TFA

PDB ID: 5RV1

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge TFA=-1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1797377.162929
FMO2-HF: Nuclear repulsion 1731133.075411
FMO2-HF: Total energy -66244.087517
FMO2-MP2: Total energy -66437.705284


3D Structure
Snapshot
 
Ligand structure

TFA

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.
-144.393-164.39672.185-28.814-23.366-0.249


Interactive mode: IFIE and PIEDA for fragment #210(A:201:TFA )


Summations of interaction energy for fragment #210(A:201:TFA )
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.
-144.393-164.39672.185-28.814-23.3660.249
Interaction energy analysis for fragmet #210(A:201:TFA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.750 / q_NPA : -0.827
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].
1A3VAL 00.005-0.01024.1000.0580.0580.0000.0000.0000.000
2A4ASN 0-0.012-0.01319.0400.2080.2080.0000.0000.0000.000
3A5SER 00.0280.00219.939-0.378-0.3780.0000.0000.0000.000
4A6PHE 0-0.0400.00613.5040.4990.4990.0000.0000.0000.000
5A7SER 00.0250.00816.063-0.592-0.5920.0000.0000.0000.000
6A8GLY 00.0260.00615.2151.3801.3800.0000.0000.0000.000
7A9TYR 0-0.050-0.02210.2651.6571.6570.0000.0000.0000.000
8A10LEU 00.0060.01513.302-1.860-1.8600.0000.0000.0000.000
9A11LYS 10.8150.89914.187-14.700-14.7000.0000.0000.0000.000
10A12LEU 0-0.064-0.02411.073-0.153-0.1530.0000.0000.0000.000
11A13THR 00.018-0.00615.765-0.762-0.7620.0000.0000.0000.000
12A14ASP -1-0.867-0.90718.28413.89513.8950.0000.0000.0000.000
13A15ASN 0-0.019-0.01517.414-0.381-0.3810.0000.0000.0000.000
14A16VAL 00.0110.02112.2930.9380.9380.0000.0000.0000.000
15A17TYR 00.0320.02113.308-1.140-1.1400.0000.0000.0000.000
16A18ILE 00.0160.0087.3152.5332.5330.0000.0000.0000.000
17A19LYS 10.8350.9078.536-28.525-28.5250.0000.0000.0000.000
18A20ASN 0-0.058-0.0255.4970.6230.6230.0000.0000.0000.000
19A21ALA 0-0.034-0.0276.478-6.279-6.2790.0000.0000.0000.000
20A22ASP -1-0.790-0.8966.06043.08243.0820.0000.0000.0000.000
21A23ILE 00.025-0.0066.416-5.167-5.1670.0000.0000.0000.000
22A24VAL 00.0080.0098.169-4.160-4.1600.0000.0000.0000.000
23A25GLU -1-0.830-0.90011.06819.05919.0590.0000.0000.0000.000
24A26GLU -1-0.780-0.85510.54222.22322.2230.0000.0000.0000.000
25A27ALA 0-0.012-0.01412.088-1.974-1.9740.0000.0000.0000.000
26A28LYS 10.8120.89313.896-21.912-21.9120.0000.0000.0000.000
27A29LYS 10.8240.91414.314-22.305-22.3050.0000.0000.0000.000
28A30VAL 0-0.053-0.03415.296-0.983-0.9830.0000.0000.0000.000
29A31LYS 10.8750.96317.181-16.709-16.7090.0000.0000.0000.000
30A32PRO 0-0.0040.01314.357-0.802-0.8020.0000.0000.0000.000
31A33THR 00.035-0.00317.657-0.306-0.3060.0000.0000.0000.000
32A34VAL 0-0.023-0.01715.417-0.474-0.4740.0000.0000.0000.000
33A35VAL 00.0200.01511.3730.9290.9290.0000.0000.0000.000
34A36VAL 00.004-0.00210.472-1.297-1.2970.0000.0000.0000.000
35A37ASN 0-0.003-0.02210.0544.8364.8360.0000.0000.0000.000
36A38ALA 00.0080.0237.071-1.225-1.2250.0000.0000.0000.000
37A39ALA 00.0320.0339.119-0.336-0.3360.0000.0000.0000.000
38A40ASN 0-0.003-0.02012.164-0.802-0.8020.0000.0000.0000.000
39A41VAL 00.0450.02114.376-0.245-0.2450.0000.0000.0000.000
40A42TYR 0-0.003-0.00317.859-0.582-0.5820.0000.0000.0000.000
41A43LEU 0-0.0040.01016.643-0.281-0.2810.0000.0000.0000.000
42A44LYS 10.9791.00817.067-14.972-14.9720.0000.0000.0000.000
43A45HIS 00.0170.01014.1102.5552.5550.0000.0000.0000.000
44A46GLY 00.0400.03414.294-0.225-0.2250.0000.0000.0000.000
45A47GLY 00.0560.01911.304-0.531-0.5310.0000.0000.0000.000
46A48GLY 00.0250.0217.2200.2850.2850.0000.0000.0000.000
47A49VAL 00.0770.0325.284-1.613-1.6130.0000.0000.0000.000
48A50ALA 00.0220.0277.881-2.981-2.9810.0000.0000.0000.000
49A51GLY 0-0.026-0.00211.047-2.135-2.1350.0000.0000.0000.000
50A52ALA 00.0200.0149.649-2.058-2.0580.0000.0000.0000.000
51A53LEU 00.0280.00110.317-1.925-1.9250.0000.0000.0000.000
52A54ASN 00.0570.00712.792-2.192-2.1920.0000.0000.0000.000
53A55LYS 10.9640.99615.131-20.710-20.7100.0000.0000.0000.000
54A56ALA 0-0.040-0.01014.745-1.231-1.2310.0000.0000.0000.000
55A57THR 0-0.055-0.01716.690-1.090-1.0900.0000.0000.0000.000
56A58ASN 0-0.037-0.02219.206-0.806-0.8060.0000.0000.0000.000
57A59ASN 0-0.006-0.00219.907-0.144-0.1440.0000.0000.0000.000
58A60ALA 00.0340.02721.219-0.371-0.3710.0000.0000.0000.000
59A61MET 00.0050.01214.8300.1510.1510.0000.0000.0000.000
60A62GLN 0-0.051-0.02818.5730.8640.8640.0000.0000.0000.000
61A63VAL 00.0270.02420.643-0.391-0.3910.0000.0000.0000.000
62A64GLU -1-0.731-0.84321.56714.17914.1790.0000.0000.0000.000
63A65SER 00.005-0.00819.5990.0670.0670.0000.0000.0000.000
64A66ASP -1-0.811-0.89221.85813.37913.3790.0000.0000.0000.000
65A67ASP -1-0.841-0.87724.32010.62410.6240.0000.0000.0000.000
66A68TYR 00.0420.01022.497-0.280-0.2800.0000.0000.0000.000
67A69ILE 0-0.040-0.02420.978-0.272-0.2720.0000.0000.0000.000
68A70ALA 0-0.034-0.00724.924-0.317-0.3170.0000.0000.0000.000
69A71THR 0-0.037-0.00428.273-0.518-0.5180.0000.0000.0000.000
70A72ASN 0-0.092-0.05625.874-0.523-0.5230.0000.0000.0000.000
71A73GLY 00.0130.02326.356-0.071-0.0710.0000.0000.0000.000
72A74PRO 0-0.057-0.03521.9220.4120.4120.0000.0000.0000.000
73A75LEU 0-0.009-0.00117.425-0.319-0.3190.0000.0000.0000.000
74A76LYS 10.9700.97620.500-12.342-12.3420.0000.0000.0000.000
75A77VAL 00.0370.01315.2040.6320.6320.0000.0000.0000.000
76A78GLY 00.0150.01715.776-0.708-0.7080.0000.0000.0000.000
77A79GLY 0-0.032-0.00716.836-0.225-0.2250.0000.0000.0000.000
78A80SER 0-0.010-0.03816.5390.9980.9980.0000.0000.0000.000
79A81CYS 0-0.0430.00518.114-0.756-0.7560.0000.0000.0000.000
80A82VAL 00.0080.00718.7831.0691.0690.0000.0000.0000.000
81A83LEU 00.0070.01119.759-0.775-0.7750.0000.0000.0000.000
82A84SER 00.0230.00820.5940.5240.5240.0000.0000.0000.000
83A85GLY 0-0.0080.00918.1290.8470.8470.0000.0000.0000.000
84A86HIS 0-0.040-0.04118.5820.3930.3930.0000.0000.0000.000
85A87ASN 0-0.020-0.02219.362-0.035-0.0350.0000.0000.0000.000
86A88LEU 0-0.008-0.01414.0690.1810.1810.0000.0000.0000.000
87A89ALA 0-0.011-0.00516.1590.7170.7170.0000.0000.0000.000
88A90LYS 10.8520.94718.265-13.334-13.3340.0000.0000.0000.000
89A91HIS 00.0220.01019.543-1.063-1.0630.0000.0000.0000.000
90A92CYS 0-0.012-0.00315.1311.6291.6290.0000.0000.0000.000
91A93LEU 0-0.0320.00415.276-1.067-1.0670.0000.0000.0000.000
92A94HIS 00.0470.00614.1983.0493.0490.0000.0000.0000.000
93A95VAL 00.010-0.00212.213-1.619-1.6190.0000.0000.0000.000
94A96VAL 0-0.0390.00412.0031.8501.8500.0000.0000.0000.000
95A97GLY 00.0610.03710.621-1.071-1.0710.0000.0000.0000.000
96A98PRO 0-0.0140.00311.639-0.230-0.2300.0000.0000.0000.000
97A99ASN 0-0.030-0.01410.9222.1272.1270.0000.0000.0000.000
98A100VAL 00.0680.02711.019-1.727-1.7270.0000.0000.0000.000
99A101ASN 0-0.058-0.03010.284-2.215-2.2150.0000.0000.0000.000
100A102LYS 10.8150.90913.783-19.328-19.3280.0000.0000.0000.000
101A103GLY 0-0.0010.01315.989-0.870-0.8700.0000.0000.0000.000
102A104GLU -1-0.793-0.84814.95917.72117.7210.0000.0000.0000.000
103A105ASP -1-0.817-0.91516.05815.54715.5470.0000.0000.0000.000
104A106ILE 00.0540.01711.3050.6750.6750.0000.0000.0000.000
105A107GLN 00.0070.00514.8081.0111.0110.0000.0000.0000.000
106A108LEU 0-0.056-0.03316.1490.0120.0120.0000.0000.0000.000
107A109LEU 0-0.025-0.0199.4850.4560.4560.0000.0000.0000.000
108A110LYS 10.8780.93813.668-15.199-15.1990.0000.0000.0000.000
109A111SER 00.0240.00615.936-0.040-0.0400.0000.0000.0000.000
110A112ALA 00.0340.01513.034-0.142-0.1420.0000.0000.0000.000
111A113TYR 00.020-0.0057.8270.7230.7230.0000.0000.0000.000
112A114GLU -1-0.864-0.91914.40714.52214.5220.0000.0000.0000.000
113A115ASN 0-0.050-0.01916.301-1.425-1.4250.0000.0000.0000.000
114A116PHE 00.039-0.00410.457-0.232-0.2320.0000.0000.0000.000
115A117ASN 0-0.032-0.00816.710-0.429-0.4290.0000.0000.0000.000
116A118GLN 0-0.0290.01120.040-1.080-1.0800.0000.0000.0000.000
117A119HIS 0-0.040-0.02718.303-0.370-0.3700.0000.0000.0000.000
118A120GLU -1-0.878-0.93419.50113.36313.3630.0000.0000.0000.000
119A121VAL 00.011-0.00816.9380.3260.3260.0000.0000.0000.000
120A122LEU 0-0.0370.02413.740-0.308-0.3080.0000.0000.0000.000
121A123LEU 0-0.0150.0139.7210.3870.3870.0000.0000.0000.000
122A124ALA 00.017-0.0078.952-1.276-1.2760.0000.0000.0000.000
123A125PRO 0-0.0390.0074.5722.8363.015-0.001-0.017-0.1610.000
124A126LEU 00.0270.0093.102-9.391-8.0260.108-0.635-0.8380.004
125A127LEU 00.0290.0254.5453.6133.702-0.001-0.001-0.0870.000
126A128SER 00.001-0.0346.939-0.334-0.3340.0000.0000.0000.000
127A129ALA 00.0190.0412.754-3.479-2.3050.683-0.821-1.0360.007
128A130GLY 00.0180.0023.072-0.8040.6520.371-0.739-1.0880.003
129A131ILE 00.020-0.0053.580-6.135-5.5970.078-0.219-0.3960.003
130A132PHE 0-0.044-0.0036.180-4.013-4.0130.0000.0000.0000.000
131A133GLY 00.0270.0157.168-2.599-2.5990.0000.0000.0000.000
132A134ALA 0-0.018-0.0107.775-2.229-2.2290.0000.0000.0000.000
133A135ASP -1-0.815-0.9126.91230.70030.7000.0000.0000.0000.000
134A136PRO 0-0.010-0.0213.073-1.075-0.3900.063-0.326-0.4230.002
135A137ILE 0-0.007-0.0065.1080.0500.107-0.001-0.001-0.0550.000
136A138HIS 00.0490.0238.308-1.284-1.2840.0000.0000.0000.000
137A139SER 0-0.011-0.0235.983-1.354-1.3540.0000.0000.0000.000
138A140LEU 0-0.019-0.0047.253-0.714-0.7140.0000.0000.0000.000
139A141ARG 10.8520.9238.682-20.398-20.3980.0000.0000.0000.000
140A142VAL 00.0170.01311.513-1.434-1.4340.0000.0000.0000.000
141A143CYS 0-0.0070.0069.998-1.158-1.1580.0000.0000.0000.000
142A144VAL 0-0.0230.00212.077-1.361-1.3610.0000.0000.0000.000
143A145ASP -1-0.796-0.88614.42016.07916.0790.0000.0000.0000.000
144A146THR 0-0.085-0.03415.322-1.653-1.6530.0000.0000.0000.000
145A147VAL 0-0.059-0.01913.767-0.934-0.9340.0000.0000.0000.000
146A148ARG 10.9740.99716.830-14.421-14.4210.0000.0000.0000.000
147A149THR 0-0.042-0.00118.526-0.318-0.3180.0000.0000.0000.000
148A150ASN 0-0.0120.00217.5640.8710.8710.0000.0000.0000.000
149A151VAL 00.0130.00211.1940.2230.2230.0000.0000.0000.000
150A152TYR 00.0140.02011.847-0.501-0.5010.0000.0000.0000.000
151A153LEU 00.014-0.0117.0121.3391.3390.0000.0000.0000.000
152A154ALA 00.0190.0036.054-2.008-2.0080.0000.0000.0000.000
153A155VAL 00.0060.0312.67111.29813.9872.002-1.857-2.8340.021
154A156PHE 0-0.001-0.0022.002-23.809-27.35811.696-3.490-4.6560.042
155A157ASP -1-0.882-0.9481.86721.15718.5427.718-2.335-2.7680.027
156A158LYS 10.8650.9233.850-29.257-29.0980.006-0.002-0.1630.001
157A159ASN 0-0.003-0.0017.098-1.685-1.6850.0000.0000.0000.000
158A160LEU 0-0.012-0.0162.672-5.830-3.8211.803-1.644-2.1680.018
159A161TYR 00.003-0.0015.596-3.324-3.3240.0000.0000.0000.000
160A162ASP -1-0.791-0.8816.75523.59823.5980.0000.0000.0000.000
161A163LYS 10.9550.9988.536-29.773-29.7730.0000.0000.0000.000
162A164LEU 0-0.039-0.0074.306-1.813-1.742-0.001-0.005-0.0650.000
163A165VAL 00.0220.0168.931-2.180-2.1800.0000.0000.0000.000
164A166SER 0-0.039-0.02812.049-2.158-2.1580.0000.0000.0000.000
165A167SER 0-0.087-0.06011.232-1.139-1.1390.0000.0000.0000.000
166A168PHE 00.0110.01211.967-0.196-0.1960.0000.0000.0000.000
167A169LEU -1-0.839-0.87913.83115.93115.9310.0000.0000.0000.000
168A303HOH 0-0.051-0.03930.168-0.143-0.1430.0000.0000.0000.000
169A321HOH 0-0.074-0.06125.4650.0860.0860.0000.0000.0000.000
170A323HOH 00.001-0.01010.5590.3390.3390.0000.0000.0000.000
171A324HOH 0-0.051-0.03717.308-0.247-0.2470.0000.0000.0000.000
172A330HOH 0-0.029-0.00811.886-0.512-0.5120.0000.0000.0000.000
173A341HOH 0-0.028-0.02513.277-0.562-0.5620.0000.0000.0000.000
174A344HOH 0-0.021-0.02324.780-0.034-0.0340.0000.0000.0000.000
175A345HOH 0-0.029-0.0153.022-6.032-5.2400.070-0.481-0.3810.002
176A346HOH 0-0.053-0.04319.999-0.253-0.2530.0000.0000.0000.000
177A347HOH 0-0.030-0.03712.939-0.018-0.0180.0000.0000.0000.000
178A349HOH 0-0.013-0.03519.0340.3940.3940.0000.0000.0000.000
179A353HOH 0-0.007-0.01410.1720.9470.9470.0000.0000.0000.000
180A355HOH 00.011-0.00513.0930.9590.9590.0000.0000.0000.000
181A357HOH 0-0.058-0.03825.176-0.147-0.1470.0000.0000.0000.000
182A363HOH 0-0.028-0.01717.1850.2270.2270.0000.0000.0000.000
183A366HOH 0-0.061-0.04610.904-0.237-0.2370.0000.0000.0000.000
184A372HOH 0-0.021-0.02816.077-0.311-0.3110.0000.0000.0000.000
185A375HOH 00.0150.00320.072-0.077-0.0770.0000.0000.0000.000
186A381HOH 0-0.030-0.0253.196-8.381-7.3630.048-0.664-0.4020.004
187A383HOH 00.004-0.0171.568-21.547-34.63625.044-8.906-3.0490.063
188A388HOH 0-0.008-0.01519.099-0.323-0.3230.0000.0000.0000.000
189A389HOH 0-0.012-0.01419.8730.0330.0330.0000.0000.0000.000
190A390HOH 0-0.079-0.06717.794-0.306-0.3060.0000.0000.0000.000
191A391HOH 0-0.016-0.0224.302-3.659-3.6160.000-0.011-0.0310.000
192A392HOH 0-0.030-0.0511.601-17.825-30.92522.499-6.659-2.7400.052
193A393HOH 00.002-0.0057.0060.2290.2290.0000.0000.0000.000
194A394HOH 00.003-0.00221.1180.2230.2230.0000.0000.0000.000
195A395HOH 0-0.027-0.04123.0530.2200.2200.0000.0000.0000.000
196A396HOH 00.0040.0018.3871.5871.5870.0000.0000.0000.000
197A404HOH 0-0.008-0.01015.620-0.558-0.5580.0000.0000.0000.000
198A405HOH 0-0.004-0.00611.2380.9060.9060.0000.0000.0000.000
199A408HOH 00.0340.01921.1690.2350.2350.0000.0000.0000.000
200A410HOH 0-0.059-0.04718.181-0.373-0.3730.0000.0000.0000.000
201A414HOH 0-0.015-0.00815.1810.0020.0020.0000.0000.0000.000
202A420HOH 00.012-0.01213.9670.4280.4280.0000.0000.0000.000
203A423HOH 0-0.021-0.0138.107-0.277-0.2770.0000.0000.0000.000
204A424HOH 0-0.039-0.03010.483-0.522-0.5220.0000.0000.0000.000
205A425HOH 00.0290.01220.7390.0770.0770.0000.0000.0000.000
206A426HOH 0-0.061-0.05815.047-0.143-0.1430.0000.0000.0000.000
207A436HOH 0-0.029-0.0284.477-3.196-3.1700.000-0.001-0.0250.000
208A454HOH 0-0.038-0.02623.7370.1500.1500.0000.0000.0000.000
209A478HOH 0-0.032-0.02717.767-0.010-0.0100.0000.0000.0000.000