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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: 22K6R

Calculation Name: 5RV1-B-Xray89

Preferred Name:

Target Type:

Ligand Name: trifluoroacetic acid

ligand 3-letter code: TFA

PDB ID: 5RV1

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-27

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 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1789501.510346
FMO2-HF: Nuclear repulsion 1723043.237191
FMO2-HF: Total energy -66458.273155
FMO2-MP2: Total energy -66652.050331


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(B:1:SER )


Summations of interaction energy for fragment #1(B:1:SER )
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.
-1.7850.855-0.004-1.221-1.4150.006
Interaction energy analysis for fragmet #1(B:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.005
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].
3B3VAL 00.0370.0133.621-0.8031.837-0.004-1.221-1.4150.006
4B4ASN 0-0.004-0.0095.900-0.579-0.5790.0000.0000.0000.000
5B5SER 00.0170.0188.223-0.237-0.2370.0000.0000.0000.000
6B6PHE 0-0.013-0.01210.1670.1190.1190.0000.0000.0000.000
7B7SER 00.012-0.00413.877-0.046-0.0460.0000.0000.0000.000
8B8GLY 00.0230.01015.8670.0470.0470.0000.0000.0000.000
9B9TYR 0-0.082-0.06316.5480.0320.0320.0000.0000.0000.000
10B10LEU 00.0120.01920.998-0.021-0.0210.0000.0000.0000.000
11B11LYS 10.8630.92423.1360.1920.1920.0000.0000.0000.000
12B12LEU 0-0.042-0.00824.9920.0060.0060.0000.0000.0000.000
13B13THR 00.034-0.00726.5410.0010.0010.0000.0000.0000.000
14B14ASP -1-0.870-0.93725.388-0.159-0.1590.0000.0000.0000.000
15B15ASN 0-0.040-0.02022.461-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0190.02222.2790.0090.0090.0000.0000.0000.000
17B17TYR 0-0.0010.00020.610-0.023-0.0230.0000.0000.0000.000
18B18ILE 00.0060.00622.6740.0200.0200.0000.0000.0000.000
19B19LYS 10.8470.90617.8370.1060.1060.0000.0000.0000.000
20B20ASN 0-0.040-0.01122.7540.0120.0120.0000.0000.0000.000
21B21ALA 00.002-0.01519.879-0.009-0.0090.0000.0000.0000.000
22B22ASP -1-0.810-0.88720.9250.0830.0830.0000.0000.0000.000
23B23ILE 00.0340.00418.6020.0010.0010.0000.0000.0000.000
24B24VAL 00.0160.01617.3730.0250.0250.0000.0000.0000.000
25B25GLU -1-0.815-0.89516.0760.1630.1630.0000.0000.0000.000
26B26GLU -1-0.764-0.85515.071-0.098-0.0980.0000.0000.0000.000
27B27ALA 00.0000.00213.314-0.013-0.0130.0000.0000.0000.000
28B28LYS 10.8470.91011.371-0.128-0.1280.0000.0000.0000.000
29B29LYS 10.7720.88310.3490.1560.1560.0000.0000.0000.000
30B30VAL 0-0.069-0.0309.584-0.078-0.0780.0000.0000.0000.000
31B31LYS 10.9440.9885.144-0.333-0.3330.0000.0000.0000.000
32B32PRO 00.0230.0307.8690.1500.1500.0000.0000.0000.000
33B33THR 00.0100.00110.1720.2400.2400.0000.0000.0000.000
34B34VAL 0-0.005-0.00510.8920.0300.0300.0000.0000.0000.000
35B35VAL 0-0.0140.00114.596-0.052-0.0520.0000.0000.0000.000
36B36VAL 0-0.007-0.00216.5400.0120.0120.0000.0000.0000.000
37B37ASN 00.002-0.03120.300-0.016-0.0160.0000.0000.0000.000
38B38ALA 0-0.0160.01522.724-0.008-0.0080.0000.0000.0000.000
39B39ALA 00.0410.03825.9770.0000.0000.0000.0000.0000.000
40B40ASN 00.014-0.00927.739-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0400.01630.4520.0080.0080.0000.0000.0000.000
42B42TYR 00.0380.01332.3460.0030.0030.0000.0000.0000.000
43B43LEU 0-0.031-0.00326.3150.0060.0060.0000.0000.0000.000
44B44LYS 10.8540.93328.839-0.100-0.1000.0000.0000.0000.000
45B45HIS 00.0030.00025.525-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0310.02528.3100.0030.0030.0000.0000.0000.000
47B47GLY 00.0240.00030.2970.0010.0010.0000.0000.0000.000
48B48GLY 00.0090.00228.9040.0040.0040.0000.0000.0000.000
49B49VAL 00.0620.02622.9400.0070.0070.0000.0000.0000.000
50B50ALA 00.0150.02424.0810.0140.0140.0000.0000.0000.000
51B51GLY 0-0.0080.00724.8990.0140.0140.0000.0000.0000.000
52B52ALA 0-0.036-0.02823.4270.0090.0090.0000.0000.0000.000
53B53LEU 00.011-0.00418.6950.0140.0140.0000.0000.0000.000
54B54ASN 00.0680.02320.6690.0360.0360.0000.0000.0000.000
55B55LYS 10.9290.97022.704-0.101-0.1010.0000.0000.0000.000
56B56ALA 00.0220.02618.4230.0070.0070.0000.0000.0000.000
57B57THR 0-0.046-0.01417.7990.0240.0240.0000.0000.0000.000
58B58ASN 0-0.025-0.02019.627-0.007-0.0070.0000.0000.0000.000
59B59ASN 0-0.017-0.00822.706-0.011-0.0110.0000.0000.0000.000
60B60ALA 00.0560.04220.320-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0380.03519.628-0.011-0.0110.0000.0000.0000.000
62B62GLN 0-0.046-0.03522.293-0.014-0.0140.0000.0000.0000.000
63B63VAL 00.0150.01925.252-0.009-0.0090.0000.0000.0000.000
64B64GLU -1-0.701-0.82320.3810.2840.2840.0000.0000.0000.000
65B65SER 00.001-0.00524.601-0.010-0.0100.0000.0000.0000.000
66B66ASP -1-0.806-0.88026.4180.1100.1100.0000.0000.0000.000
67B67ASP -1-0.875-0.91327.2360.1590.1590.0000.0000.0000.000
68B68TYR 00.0570.01825.967-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.051-0.02628.228-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.030-0.00131.546-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.036-0.00630.039-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.088-0.05528.557-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0190.00432.334-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.058-0.03232.5590.0060.0060.0000.0000.0000.000
75B75LEU 0-0.026-0.01227.606-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9820.98132.135-0.056-0.0560.0000.0000.0000.000
77B77VAL 00.0270.00032.6060.0040.0040.0000.0000.0000.000
78B78GLY 0-0.009-0.00132.041-0.004-0.0040.0000.0000.0000.000
79B79GLY 0-0.0100.01329.980-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.045-0.05224.7590.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0170.02224.665-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0160.01618.2030.0030.0030.0000.0000.0000.000
83B83LEU 00.0060.01319.972-0.004-0.0040.0000.0000.0000.000
84B84SER 00.0420.02016.2450.0580.0580.0000.0000.0000.000
85B85GLY 00.0150.01914.441-0.057-0.0570.0000.0000.0000.000
86B86HIS 0-0.044-0.03714.7280.0110.0110.0000.0000.0000.000
87B87ASN 0-0.038-0.02912.4740.0940.0940.0000.0000.0000.000
88B88LEU 0-0.029-0.01012.567-0.018-0.0180.0000.0000.0000.000
89B89ALA 00.0340.02010.847-0.029-0.0290.0000.0000.0000.000
90B90LYS 10.9210.9909.515-0.765-0.7650.0000.0000.0000.000
91B91HIS 00.016-0.00611.387-0.027-0.0270.0000.0000.0000.000
92B92CYS 0-0.031-0.01515.021-0.021-0.0210.0000.0000.0000.000
93B93LEU 0-0.0320.00417.969-0.009-0.0090.0000.0000.0000.000
94B94HIS 00.0500.00620.558-0.037-0.0370.0000.0000.0000.000
95B95VAL 00.004-0.00423.718-0.006-0.0060.0000.0000.0000.000
96B96VAL 0-0.0290.01326.303-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0240.01029.944-0.006-0.0060.0000.0000.0000.000
98B98PRO 0-0.0170.00331.6210.0040.0040.0000.0000.0000.000
99B99ASN 0-0.008-0.00334.456-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0820.04236.3580.0000.0000.0000.0000.0000.000
101B101ASN 0-0.034-0.01537.312-0.004-0.0040.0000.0000.0000.000
102B102LYS 10.7630.87836.276-0.050-0.0500.0000.0000.0000.000
103B103GLY 0-0.0010.00540.9950.0000.0000.0000.0000.0000.000
104B104GLU -1-0.824-0.87536.7820.0450.0450.0000.0000.0000.000
105B105ASP -1-0.822-0.91140.4990.0130.0130.0000.0000.0000.000
106B106ILE 00.035-0.00136.3760.0020.0020.0000.0000.0000.000
107B107GLN 0-0.028-0.01637.3500.0010.0010.0000.0000.0000.000
108B108LEU 00.0230.00535.665-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.029-0.01531.3340.0040.0040.0000.0000.0000.000
110B110LYS 10.8870.93031.8170.0130.0130.0000.0000.0000.000
111B111SER 00.0330.01631.391-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0270.01029.7280.0040.0040.0000.0000.0000.000
113B113TYR 00.028-0.01126.2790.0080.0080.0000.0000.0000.000
114B114GLU -1-0.840-0.87426.5600.0040.0040.0000.0000.0000.000
115B115ASN 0-0.029-0.00524.9280.0060.0060.0000.0000.0000.000
116B116PHE 00.033-0.00622.2430.0130.0130.0000.0000.0000.000
117B117ASN 0-0.039-0.02021.630-0.013-0.0130.0000.0000.0000.000
118B118GLN 0-0.0400.00422.092-0.008-0.0080.0000.0000.0000.000
119B119HIS 00.0010.00217.2140.0330.0330.0000.0000.0000.000
120B120GLU -1-0.829-0.89515.513-0.089-0.0890.0000.0000.0000.000
121B121VAL 0-0.015-0.01312.758-0.043-0.0430.0000.0000.0000.000
122B122LEU 0-0.0130.02515.1780.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0050.01414.701-0.044-0.0440.0000.0000.0000.000
124B124ALA 00.001-0.01117.0580.0350.0350.0000.0000.0000.000
125B125PRO 00.0030.01520.648-0.018-0.0180.0000.0000.0000.000
126B126LEU 00.0050.00323.810-0.001-0.0010.0000.0000.0000.000
127B127LEU 00.0200.02025.7670.0070.0070.0000.0000.0000.000
128B128SER 00.010-0.02328.707-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0170.02729.966-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0320.01231.6690.0070.0070.0000.0000.0000.000
131B131ILE 00.005-0.00131.336-0.002-0.0020.0000.0000.0000.000
132B132PHE 0-0.067-0.02330.7120.0010.0010.0000.0000.0000.000
133B133GLY 00.0240.01034.485-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.0200.00034.730-0.003-0.0030.0000.0000.0000.000
135B135ASP -1-0.813-0.90935.768-0.006-0.0060.0000.0000.0000.000
136B136PRO 0-0.023-0.02132.249-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.0160.00032.618-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0500.02734.527-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.026-0.02730.626-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.019-0.01228.2800.0000.0000.0000.0000.0000.000
141B141ARG 10.8210.87930.7980.0340.0340.0000.0000.0000.000
142B142VAL 00.0260.01531.817-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0210.00426.4730.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0020.00928.407-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.759-0.83229.627-0.041-0.0410.0000.0000.0000.000
146B146THR 0-0.114-0.06129.2300.0030.0030.0000.0000.0000.000
147B147VAL 0-0.052-0.01423.4240.0030.0030.0000.0000.0000.000
148B148ARG 10.8960.95625.4060.0220.0220.0000.0000.0000.000
149B149THR 0-0.0120.02219.870-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.041-0.01217.546-0.012-0.0120.0000.0000.0000.000
151B151VAL 00.0370.01618.3870.0230.0230.0000.0000.0000.000
152B152TYR 0-0.016-0.00816.584-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.015-0.00319.4090.0310.0310.0000.0000.0000.000
154B154ALA 00.002-0.00119.841-0.017-0.0170.0000.0000.0000.000
155B155VAL 0-0.019-0.01221.9290.0140.0140.0000.0000.0000.000
156B156PHE 00.0230.01224.532-0.010-0.0100.0000.0000.0000.000
157B157ASP -1-0.791-0.89226.065-0.008-0.0080.0000.0000.0000.000
158B158LYS 10.8710.91828.9970.0460.0460.0000.0000.0000.000
159B159ASN 0-0.015-0.02930.029-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0020.00630.476-0.002-0.0020.0000.0000.0000.000
161B161TYR 0-0.018-0.01625.450-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.767-0.85729.823-0.052-0.0520.0000.0000.0000.000
163B163LYS 10.9481.01332.6840.0120.0120.0000.0000.0000.000
164B164LEU 0-0.0320.00329.419-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0320.00628.879-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.072-0.04731.769-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.016-0.02335.3470.0000.0000.0000.0000.0000.000
168B168PHE 0-0.0090.00731.2850.0020.0020.0000.0000.0000.000
169B169LEU -1-0.911-0.93134.183-0.056-0.0560.0000.0000.0000.000
170B212HOH 0-0.063-0.04011.8560.0400.0400.0000.0000.0000.000
171B213HOH 0-0.038-0.03238.7810.0010.0010.0000.0000.0000.000
172B218HOH 0-0.005-0.01731.544-0.003-0.0030.0000.0000.0000.000
173B220HOH 0-0.007-0.01233.6780.0010.0010.0000.0000.0000.000
174B228HOH 0-0.035-0.03011.344-0.024-0.0240.0000.0000.0000.000
175B233HOH 0-0.043-0.03427.6650.0000.0000.0000.0000.0000.000
176B245HOH 0-0.030-0.02331.1830.0020.0020.0000.0000.0000.000
177B249HOH 0-0.010-0.03419.397-0.014-0.0140.0000.0000.0000.000
178B252HOH 0-0.080-0.06525.2790.0050.0050.0000.0000.0000.000
179B254HOH 0-0.025-0.03513.7110.0010.0010.0000.0000.0000.000
180B260HOH 00.0250.00029.502-0.002-0.0020.0000.0000.0000.000
181B264HOH 0-0.010-0.01328.402-0.004-0.0040.0000.0000.0000.000
182B265HOH 00.0150.00324.0330.0060.0060.0000.0000.0000.000
183B267HOH 0-0.018-0.02122.6820.0040.0040.0000.0000.0000.000
184B269HOH 0-0.001-0.00322.1670.0030.0030.0000.0000.0000.000
185B270HOH 0-0.067-0.05029.029-0.003-0.0030.0000.0000.0000.000
186B271HOH 0-0.031-0.03022.9990.0060.0060.0000.0000.0000.000
187B272HOH 0-0.025-0.02428.4050.0010.0010.0000.0000.0000.000
188B278HOH 0-0.019-0.03012.5010.0320.0320.0000.0000.0000.000
189B279HOH 0-0.022-0.00927.495-0.002-0.0020.0000.0000.0000.000
190B281HOH 0-0.033-0.02922.8060.0000.0000.0000.0000.0000.000
191B283HOH 0-0.085-0.06337.052-0.002-0.0020.0000.0000.0000.000
192B284HOH 00.0200.01427.994-0.002-0.0020.0000.0000.0000.000
193B291HOH 0-0.037-0.03128.631-0.002-0.0020.0000.0000.0000.000
194B301HOH 00.008-0.01527.895-0.003-0.0030.0000.0000.0000.000
195B310HOH 0-0.018-0.01215.3450.0140.0140.0000.0000.0000.000
196B315HOH 0-0.042-0.03333.975-0.002-0.0020.0000.0000.0000.000
197B323HOH 0-0.019-0.00229.5260.0030.0030.0000.0000.0000.000
198B324HOH 0-0.023-0.01531.7600.0010.0010.0000.0000.0000.000
199B326HOH 0-0.030-0.03234.7030.0020.0020.0000.0000.0000.000
200B329HOH 0-0.012-0.01230.1360.0020.0020.0000.0000.0000.000
201B332HOH 00.0360.02433.7280.0020.0020.0000.0000.0000.000
202B333HOH 00.000-0.01815.7800.0180.0180.0000.0000.0000.000
203B340HOH 00.005-0.00630.551-0.003-0.0030.0000.0000.0000.000
204B342HOH 00.0270.01831.6200.0010.0010.0000.0000.0000.000
205B343HOH 00.0150.00628.326-0.003-0.0030.0000.0000.0000.000
206B347HOH 0-0.016-0.02828.591-0.001-0.0010.0000.0000.0000.000
207B358HOH 0-0.027-0.01829.0500.0000.0000.0000.0000.0000.000