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: 6639Z

Calculation Name: 5RUR-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 6-fluoro-1,3-benzothiazol-2-amine

ligand 3-letter code: FBB

PDB ID: 5RUR

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 203
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1776827.695669
FMO2-HF: Nuclear repulsion 1710673.55476
FMO2-HF: Total energy -66154.140909
FMO2-MP2: Total energy -66347.128978


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.
-1.9320.780.001-1.241-1.4730.006
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 : 0.004 / q_NPA : 0.004
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 00.0410.0163.522-0.8561.8560.001-1.241-1.4730.006
4B4ASN 0-0.004-0.0105.952-0.632-0.6320.0000.0000.0000.000
5B5SER 0-0.0030.0018.035-0.150-0.1500.0000.0000.0000.000
6B6PHE 0-0.014-0.00410.0760.0660.0660.0000.0000.0000.000
7B7SER 00.0270.00313.911-0.053-0.0530.0000.0000.0000.000
8B8GLY 00.0180.00915.8290.0490.0490.0000.0000.0000.000
9B9TYR 0-0.081-0.06116.5820.0300.0300.0000.0000.0000.000
10B10LEU 00.0140.02020.944-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8560.92222.9670.1900.1900.0000.0000.0000.000
12B12LEU 0-0.045-0.01024.9420.0060.0060.0000.0000.0000.000
13B13THR 00.040-0.00426.4500.0010.0010.0000.0000.0000.000
14B14ASP -1-0.871-0.94225.339-0.158-0.1580.0000.0000.0000.000
15B15ASN 0-0.048-0.02322.356-0.022-0.0220.0000.0000.0000.000
16B16VAL 00.0160.01922.1940.0100.0100.0000.0000.0000.000
17B17TYR 00.0030.00620.597-0.022-0.0220.0000.0000.0000.000
18B18ILE 00.0120.00922.6970.0210.0210.0000.0000.0000.000
19B19LYS 10.8450.90517.8220.0760.0760.0000.0000.0000.000
20B20ASN 0-0.046-0.01322.8110.0120.0120.0000.0000.0000.000
21B21ALA 00.006-0.01419.907-0.007-0.0070.0000.0000.0000.000
22B22ASP -1-0.814-0.89020.9660.1020.1020.0000.0000.0000.000
23B23ILE 00.0370.00318.6560.0040.0040.0000.0000.0000.000
24B24VAL 00.0250.02217.4170.0280.0280.0000.0000.0000.000
25B25GLU -1-0.818-0.89816.1250.2000.2000.0000.0000.0000.000
26B26GLU -1-0.776-0.85915.102-0.054-0.0540.0000.0000.0000.000
27B27ALA 0-0.0020.00013.345-0.006-0.0060.0000.0000.0000.000
28B28LYS 10.8380.90611.407-0.148-0.1480.0000.0000.0000.000
29B29LYS 10.7770.88510.3810.1200.1200.0000.0000.0000.000
30B30VAL 0-0.072-0.0339.579-0.064-0.0640.0000.0000.0000.000
31B31LYS 10.9741.0075.114-0.455-0.4550.0000.0000.0000.000
32B32PRO 00.0160.0267.9440.1640.1640.0000.0000.0000.000
33B33THR 00.0190.00310.1180.2410.2410.0000.0000.0000.000
34B34VAL 0-0.017-0.01210.8310.0240.0240.0000.0000.0000.000
35B35VAL 0-0.0110.00414.537-0.049-0.0490.0000.0000.0000.000
36B36VAL 0-0.009-0.00416.5950.0100.0100.0000.0000.0000.000
37B37ASN 00.001-0.03120.358-0.014-0.0140.0000.0000.0000.000
38B38ALA 0-0.0120.01822.793-0.010-0.0100.0000.0000.0000.000
39B39ALA 00.0300.03126.0600.0000.0000.0000.0000.0000.000
40B40ASN 00.022-0.00227.820-0.010-0.0100.0000.0000.0000.000
41B41VAL 00.0380.01130.5080.0080.0080.0000.0000.0000.000
42B42TYR 00.0380.01532.4290.0020.0020.0000.0000.0000.000
43B43LEU 0-0.037-0.00726.3780.0060.0060.0000.0000.0000.000
44B44LYS 10.8650.94228.931-0.103-0.1030.0000.0000.0000.000
45B45HIS 00.0020.00025.591-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0290.02228.3680.0030.0030.0000.0000.0000.000
47B47GLY 00.0240.00230.3650.0010.0010.0000.0000.0000.000
48B48GLY 00.0080.00328.9450.0050.0050.0000.0000.0000.000
49B49VAL 00.0580.02422.9970.0080.0080.0000.0000.0000.000
50B50ALA 00.0180.02424.1290.0150.0150.0000.0000.0000.000
51B51GLY 0-0.0110.00724.9520.0140.0140.0000.0000.0000.000
52B52ALA 0-0.035-0.02823.4930.0100.0100.0000.0000.0000.000
53B53LEU 00.011-0.00318.7390.0160.0160.0000.0000.0000.000
54B54ASN 00.0630.01920.7250.0370.0370.0000.0000.0000.000
55B55LYS 10.9310.97322.747-0.112-0.1120.0000.0000.0000.000
56B56ALA 00.0140.02318.4520.0070.0070.0000.0000.0000.000
57B57THR 0-0.042-0.01517.8240.0260.0260.0000.0000.0000.000
58B58ASN 0-0.023-0.01719.658-0.009-0.0090.0000.0000.0000.000
59B59ASN 0-0.018-0.00922.748-0.012-0.0120.0000.0000.0000.000
60B60ALA 00.0380.02720.363-0.010-0.0100.0000.0000.0000.000
61B61MET 00.0170.02219.681-0.013-0.0130.0000.0000.0000.000
62B62GLN 0-0.043-0.03422.346-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.0090.00125.289-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.718-0.83720.4750.2860.2860.0000.0000.0000.000
65B65SER 0-0.017-0.02024.661-0.011-0.0110.0000.0000.0000.000
66B66ASP -1-0.823-0.89226.4930.1120.1120.0000.0000.0000.000
67B67ASP -1-0.914-0.94627.3020.1500.1500.0000.0000.0000.000
68B68TYR 00.0520.01325.991-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.036-0.02028.243-0.012-0.0120.0000.0000.0000.000
70B70ALA 0-0.033-0.00331.580-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.036-0.00730.069-0.008-0.0080.0000.0000.0000.000
72B72ASN 0-0.090-0.05628.580-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0210.00432.332-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.059-0.03332.5440.0060.0060.0000.0000.0000.000
75B75LEU 0-0.025-0.01327.607-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9970.99332.137-0.053-0.0530.0000.0000.0000.000
77B77VAL 00.0280.00432.5820.0040.0040.0000.0000.0000.000
78B78GLY 00.0000.00831.967-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0010.01929.909-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.044-0.05024.7210.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0160.02324.643-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0160.01518.1920.0040.0040.0000.0000.0000.000
83B83LEU 0-0.0030.00919.945-0.006-0.0060.0000.0000.0000.000
84B84SER 00.0350.01516.3220.0590.0590.0000.0000.0000.000
85B85GLY 00.0220.02314.440-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.042-0.03414.7620.0180.0180.0000.0000.0000.000
87B87ASN 0-0.039-0.03012.5150.0940.0940.0000.0000.0000.000
88B88LEU 0-0.026-0.00612.621-0.011-0.0110.0000.0000.0000.000
89B89ALA 00.0350.02010.901-0.021-0.0210.0000.0000.0000.000
90B90LYS 10.9180.9919.472-0.754-0.7540.0000.0000.0000.000
91B91HIS 00.016-0.00611.351-0.031-0.0310.0000.0000.0000.000
92B92CYS 0-0.032-0.01414.978-0.016-0.0160.0000.0000.0000.000
93B93LEU 0-0.0260.00518.032-0.011-0.0110.0000.0000.0000.000
94B94HIS 00.0510.00820.518-0.035-0.0350.0000.0000.0000.000
95B95VAL 00.003-0.00623.673-0.008-0.0080.0000.0000.0000.000
96B96VAL 0-0.0290.01026.2590.0000.0000.0000.0000.0000.000
97B97GLY 00.0200.00829.953-0.007-0.0070.0000.0000.0000.000
98B98PRO 0-0.0140.00631.6740.0040.0040.0000.0000.0000.000
99B99ASN 00.0000.00134.609-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0880.04336.468-0.001-0.0010.0000.0000.0000.000
101B101ASN 0-0.041-0.01737.416-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7580.87236.433-0.052-0.0520.0000.0000.0000.000
103B103GLY 00.0050.01241.0620.0000.0000.0000.0000.0000.000
104B104GLU -1-0.830-0.87936.8670.0470.0470.0000.0000.0000.000
105B105ASP -1-0.817-0.91340.5670.0140.0140.0000.0000.0000.000
106B106ILE 00.0350.00236.4770.0020.0020.0000.0000.0000.000
107B107GLN 0-0.034-0.01937.3130.0010.0010.0000.0000.0000.000
108B108LEU 00.0200.00435.640-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.034-0.01931.3580.0040.0040.0000.0000.0000.000
110B110LYS 10.8750.93031.7580.0130.0130.0000.0000.0000.000
111B111SER 00.0280.01731.328-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0270.00829.6620.0040.0040.0000.0000.0000.000
113B113TYR 00.024-0.01326.2290.0080.0080.0000.0000.0000.000
114B114GLU -1-0.877-0.91926.5020.0050.0050.0000.0000.0000.000
115B115ASN 0-0.018-0.00224.8850.0050.0050.0000.0000.0000.000
116B116PHE 00.030-0.00822.1670.0130.0130.0000.0000.0000.000
117B117ASN 0-0.043-0.02021.556-0.013-0.0130.0000.0000.0000.000
118B118GLN 0-0.0350.00722.056-0.011-0.0110.0000.0000.0000.000
119B119HIS 00.0010.00117.1360.0310.0310.0000.0000.0000.000
120B120GLU -1-0.840-0.90315.475-0.112-0.1120.0000.0000.0000.000
121B121VAL 0-0.015-0.01312.654-0.041-0.0410.0000.0000.0000.000
122B122LEU 0-0.0120.02615.1090.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0020.01514.752-0.044-0.0440.0000.0000.0000.000
124B124ALA 00.001-0.01217.1130.0330.0330.0000.0000.0000.000
125B125PRO 00.0010.01620.722-0.017-0.0170.0000.0000.0000.000
126B126LEU 00.0130.00623.871-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0210.02025.8230.0070.0070.0000.0000.0000.000
128B128SER 00.007-0.02728.762-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0210.02930.005-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0340.01331.7260.0070.0070.0000.0000.0000.000
131B131ILE 0-0.003-0.00431.387-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.066-0.02530.7810.0000.0000.0000.0000.0000.000
133B133GLY 00.0300.01534.560-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.024-0.00334.773-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.811-0.91135.827-0.001-0.0010.0000.0000.0000.000
136B136PRO 0-0.026-0.02032.294-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.014-0.00232.677-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0540.03234.598-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.025-0.03030.680-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.021-0.01028.3520.0000.0000.0000.0000.0000.000
141B141ARG 10.8550.90130.7420.0300.0300.0000.0000.0000.000
142B142VAL 00.0220.01631.753-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0130.00726.3870.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0070.00428.319-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.765-0.83329.522-0.041-0.0410.0000.0000.0000.000
146B146THR 0-0.110-0.06129.0800.0020.0020.0000.0000.0000.000
147B147VAL 0-0.054-0.01623.3460.0020.0020.0000.0000.0000.000
148B148ARG 10.9200.96825.3340.0270.0270.0000.0000.0000.000
149B149THR 0-0.0160.02019.794-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.030-0.00917.489-0.008-0.0080.0000.0000.0000.000
151B151VAL 00.0360.01518.3060.0240.0240.0000.0000.0000.000
152B152TYR 0-0.019-0.00816.458-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.021-0.00119.4580.0320.0320.0000.0000.0000.000
154B154ALA 00.000-0.00119.899-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.021-0.01321.9870.0120.0120.0000.0000.0000.000
156B156PHE 00.0200.00824.584-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.790-0.89126.1220.0020.0020.0000.0000.0000.000
158B158LYS 10.8690.91629.0330.0350.0350.0000.0000.0000.000
159B159ASN 0-0.016-0.02830.069-0.009-0.0090.0000.0000.0000.000
160B160LEU 00.0000.00730.556-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.019-0.01825.501-0.004-0.0040.0000.0000.0000.000
162B162ASP -1-0.761-0.85829.872-0.043-0.0430.0000.0000.0000.000
163B163LYS 10.9491.01332.7220.0070.0070.0000.0000.0000.000
164B164LEU 0-0.0390.00129.468-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0340.00428.928-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.067-0.04031.819-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.023-0.02935.386-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0140.00131.2600.0020.0020.0000.0000.0000.000
169B169LEU -1-0.910-0.93034.140-0.053-0.0530.0000.0000.0000.000
170B209HOH 0-0.006-0.01133.7330.0010.0010.0000.0000.0000.000
171B221HOH 0-0.066-0.04411.8580.0390.0390.0000.0000.0000.000
172B224HOH 0-0.037-0.03138.8330.0010.0010.0000.0000.0000.000
173B229HOH 0-0.043-0.03427.6600.0000.0000.0000.0000.0000.000
174B233HOH 0-0.034-0.02911.389-0.026-0.0260.0000.0000.0000.000
175B246HOH 0-0.020-0.02122.7200.0040.0040.0000.0000.0000.000
176B253HOH 0-0.036-0.02931.0270.0020.0020.0000.0000.0000.000
177B254HOH 0-0.023-0.03313.6190.0030.0030.0000.0000.0000.000
178B260HOH 00.0160.00324.0200.0060.0060.0000.0000.0000.000
179B261HOH 0-0.010-0.03419.436-0.014-0.0140.0000.0000.0000.000
180B262HOH 0-0.010-0.01228.464-0.004-0.0040.0000.0000.0000.000
181B264HOH 0-0.041-0.02934.7840.0010.0010.0000.0000.0000.000
182B271HOH 0-0.030-0.02923.0570.0060.0060.0000.0000.0000.000
183B275HOH 00.0250.00129.563-0.002-0.0020.0000.0000.0000.000
184B277HOH 0-0.085-0.06237.063-0.001-0.0010.0000.0000.0000.000
185B278HOH 0-0.067-0.04929.118-0.003-0.0030.0000.0000.0000.000
186B279HOH 0-0.021-0.00727.396-0.002-0.0020.0000.0000.0000.000
187B286HOH 00.001-0.00322.1290.0030.0030.0000.0000.0000.000
188B290HOH 0-0.024-0.02228.3130.0010.0010.0000.0000.0000.000
189B295HOH 0-0.019-0.03012.4280.0320.0320.0000.0000.0000.000
190B298HOH 00.0200.01328.057-0.002-0.0020.0000.0000.0000.000
191B299HOH 00.007-0.01627.949-0.003-0.0030.0000.0000.0000.000
192B309HOH 0-0.017-0.01015.2880.0150.0150.0000.0000.0000.000
193B315HOH 0-0.040-0.03134.092-0.002-0.0020.0000.0000.0000.000
194B318HOH 0-0.020-0.00329.5810.0030.0030.0000.0000.0000.000
195B325HOH 00.0020.00331.5960.0030.0030.0000.0000.0000.000
196B328HOH 0-0.027-0.02934.8080.0020.0020.0000.0000.0000.000
197B335HOH 00.001-0.01815.7360.0200.0200.0000.0000.0000.000
198B343HOH 00.0170.00830.0050.0020.0020.0000.0000.0000.000
199B347HOH 00.0280.01831.8490.0010.0010.0000.0000.0000.000
200B349HOH 00.006-0.00530.545-0.002-0.0020.0000.0000.0000.000
201B350HOH 00.0150.00528.318-0.003-0.0030.0000.0000.0000.000
202B359HOH 0-0.017-0.02828.6560.0000.0000.0000.0000.0000.000
203B371HOH 0-0.029-0.02028.8250.0000.0000.0000.0000.0000.000