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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: 4333N

Calculation Name: 5RUF-A-Xray89

Preferred Name:

Target Type:

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

ligand 3-letter code: 54T

PDB ID: 5RUF

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 208
LigandCharge 54T=1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1802069.759504
FMO2-HF: Nuclear repulsion 1735267.325155
FMO2-HF: Total energy -66802.434349
FMO2-MP2: Total energy -66996.010292


3D Structure
Snapshot
 
Ligand structure

54T

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.
-79.315-74.44149.787-19.413-35.2480.148


Interactive mode: IFIE and PIEDA for fragment #208(A:201:54T )


Summations of interaction energy for fragment #208(A:201:54T )
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.
-79.315-74.44149.787-19.413-35.248-0.148
Interaction energy analysis for fragmet #208(A:201:54T )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.953
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 00.014-0.00524.3360.0020.0020.0000.0000.0000.000
2A4ASN 0-0.014-0.01719.702-0.477-0.4770.0000.0000.0000.000
3A5SER 00.0290.00417.5260.1840.1840.0000.0000.0000.000
4A6PHE 0-0.0410.00512.834-0.955-0.9550.0000.0000.0000.000
5A7SER 00.0280.01115.6710.8520.8520.0000.0000.0000.000
6A8GLY 00.011-0.00515.503-1.460-1.4600.0000.0000.0000.000
7A9TYR 0-0.060-0.04211.757-1.131-1.1310.0000.0000.0000.000
8A10LEU 00.0040.01315.8861.0591.0590.0000.0000.0000.000
9A11LYS 10.8090.89717.06012.14412.1440.0000.0000.0000.000
10A12LEU 0-0.049-0.01515.2530.2270.2270.0000.0000.0000.000
11A13THR 00.0350.00719.5030.4980.4980.0000.0000.0000.000
12A14ASP -1-0.858-0.89021.847-11.544-11.5440.0000.0000.0000.000
13A15ASN 0-0.004-0.00819.8170.1990.1990.0000.0000.0000.000
14A16VAL 00.0080.01615.249-0.819-0.8190.0000.0000.0000.000
15A17TYR 00.0340.02415.7980.6710.6710.0000.0000.0000.000
16A18ILE 00.0230.01211.162-1.392-1.3920.0000.0000.0000.000
17A19LYS 10.8320.90211.04025.71225.7120.0000.0000.0000.000
18A20ASN 0-0.042-0.0188.567-0.597-0.5970.0000.0000.0000.000
19A21ALA 0-0.002-0.0107.8401.2721.2720.0000.0000.0000.000
20A22ASP -1-0.761-0.8691.852-136.644-143.11326.447-10.335-9.644-0.124
21A23ILE 00.0330.0012.8361.9532.6531.944-0.646-1.998-0.003
22A24VAL 00.0260.0212.4176.4478.1091.106-0.737-2.030-0.004
23A25GLU -1-0.832-0.9034.152-33.766-33.6070.000-0.033-0.1250.000
24A26GLU -1-0.774-0.8526.239-20.641-20.6410.0000.0000.0000.000
25A27ALA 0-0.011-0.0137.4613.8313.8310.0000.0000.0000.000
26A28LYS 10.8320.9066.63339.48339.4830.0000.0000.0000.000
27A29LYS 10.8300.91410.07126.77226.7720.0000.0000.0000.000
28A30VAL 0-0.041-0.02911.9371.6071.6070.0000.0000.0000.000
29A31LYS 10.8750.96312.73921.39321.3930.0000.0000.0000.000
30A32PRO 00.0050.01712.3231.3301.3300.0000.0000.0000.000
31A33THR 00.035-0.00215.323-0.180-0.1800.0000.0000.0000.000
32A34VAL 0-0.016-0.01414.6700.1770.1770.0000.0000.0000.000
33A35VAL 00.0030.0078.915-0.643-0.6430.0000.0000.0000.000
34A36VAL 00.0080.00310.0360.9600.9600.0000.0000.0000.000
35A37ASN 0-0.011-0.0308.460-5.553-5.5530.0000.0000.0000.000
36A38ALA 0-0.0120.0166.7492.1952.1950.0000.0000.0000.000
37A39ALA 00.0490.0438.631-0.979-0.9790.0000.0000.0000.000
38A40ASN 0-0.003-0.01911.8121.7421.7420.0000.0000.0000.000
39A41VAL 00.0450.02214.041-0.108-0.1080.0000.0000.0000.000
40A42TYR 00.0090.00617.2770.4470.4470.0000.0000.0000.000
41A43LEU 0-0.0050.00915.278-0.086-0.0860.0000.0000.0000.000
42A44LYS 10.9811.00715.59716.30816.3080.0000.0000.0000.000
43A45HIS 00.0260.01610.882-2.281-2.2810.0000.0000.0000.000
44A46GLY 00.0460.03511.159-1.106-1.1060.0000.0000.0000.000
45A47GLY 00.0450.0107.128-0.840-0.8400.0000.0000.0000.000
46A48GLY 0-0.0010.0093.5331.1441.6850.054-0.188-0.4070.001
47A49VAL 00.001-0.0192.198-9.275-7.7902.912-0.747-3.650-0.005
48A50ALA 00.0270.0294.290-1.939-1.6380.0130.003-0.3180.000
49A51GLY 0-0.0140.0047.5301.1711.1710.0000.0000.0000.000
50A52ALA 0-0.024-0.0122.724-0.3580.5001.908-0.674-2.0920.002
51A53LEU 00.016-0.0054.8531.1841.481-0.001-0.019-0.2770.000
52A54ASN 00.0670.0136.6143.8853.8850.0000.0000.0000.000
53A55LYS 10.9580.9886.96536.85636.8560.0000.0000.0000.000
54A56ALA 0-0.031-0.0056.0132.5012.5010.0000.0000.0000.000
55A57THR 0-0.044-0.0118.0932.9202.9200.0000.0000.0000.000
56A58ASN 0-0.031-0.02011.2061.7031.7030.0000.0000.0000.000
57A59ASN 0-0.0050.00012.4430.5410.5410.0000.0000.0000.000
58A60ALA 00.0400.03014.2501.0461.0460.0000.0000.0000.000
59A61MET 0-0.0010.00710.6970.0980.0980.0000.0000.0000.000
60A62GLN 0-0.061-0.03314.484-0.723-0.7230.0000.0000.0000.000
61A63VAL 00.0340.02816.0460.8600.8600.0000.0000.0000.000
62A64GLU -1-0.722-0.83717.424-16.427-16.4270.0000.0000.0000.000
63A65SER 00.004-0.01016.4430.3890.3890.0000.0000.0000.000
64A66ASP -1-0.818-0.90018.856-15.599-15.5990.0000.0000.0000.000
65A67ASP -1-0.816-0.85621.460-11.724-11.7240.0000.0000.0000.000
66A68TYR 00.0370.00621.0830.5220.5220.0000.0000.0000.000
67A69ILE 0-0.041-0.02619.9900.5200.5200.0000.0000.0000.000
68A70ALA 0-0.0250.00223.5190.4940.4940.0000.0000.0000.000
69A71THR 0-0.037-0.00726.4680.6290.6290.0000.0000.0000.000
70A72ASN 0-0.090-0.05224.8640.7270.7270.0000.0000.0000.000
71A73GLY 00.0130.02125.8020.2330.2330.0000.0000.0000.000
72A74PRO 0-0.062-0.03721.853-0.474-0.4740.0000.0000.0000.000
73A75LEU 0-0.011-0.00317.1250.4290.4290.0000.0000.0000.000
74A76LYS 10.9810.98321.00411.22011.2200.0000.0000.0000.000
75A77VAL 00.0360.00916.488-0.595-0.5950.0000.0000.0000.000
76A78GLY 00.0100.01717.0540.6480.6480.0000.0000.0000.000
77A79GLY 0-0.028-0.00618.3950.2420.2420.0000.0000.0000.000
78A80SER 0-0.018-0.04417.106-0.848-0.8480.0000.0000.0000.000
79A81CYS 0-0.0350.01017.5260.5770.5770.0000.0000.0000.000
80A82VAL 00.0120.00917.526-1.093-1.0930.0000.0000.0000.000
81A83LEU 00.0030.00917.1040.7070.7070.0000.0000.0000.000
82A84SER 00.0330.01417.686-0.482-0.4820.0000.0000.0000.000
83A85GLY 0-0.0130.00714.022-1.074-1.0740.0000.0000.0000.000
84A86HIS 0-0.029-0.03213.220-1.667-1.6670.0000.0000.0000.000
85A87ASN 0-0.021-0.02411.0830.5430.5430.0000.0000.0000.000
86A88LEU 0-0.022-0.0227.774-0.917-0.9170.0000.0000.0000.000
87A89ALA 0-0.009-0.00511.298-0.571-0.5710.0000.0000.0000.000
88A90LYS 10.8550.94714.06414.20914.2090.0000.0000.0000.000
89A91HIS 00.0360.01616.8881.0201.0200.0000.0000.0000.000
90A92CYS 0-0.023-0.00912.477-1.947-1.9470.0000.0000.0000.000
91A93LEU 0-0.0260.00914.0521.1531.1530.0000.0000.0000.000
92A94HIS 00.0530.00312.954-2.485-2.4850.0000.0000.0000.000
93A95VAL 00.0160.00312.5091.5591.5590.0000.0000.0000.000
94A96VAL 0-0.0430.00612.415-1.460-1.4600.0000.0000.0000.000
95A97GLY 00.0540.03412.2241.0271.0270.0000.0000.0000.000
96A98PRO 0-0.0040.00513.185-0.359-0.3590.0000.0000.0000.000
97A99ASN 0-0.024-0.01011.663-0.702-0.7020.0000.0000.0000.000
98A100VAL 00.0690.02712.7020.8860.8860.0000.0000.0000.000
99A101ASN 0-0.056-0.02710.8811.5071.5070.0000.0000.0000.000
100A102LYS 10.8130.90614.51717.01317.0130.0000.0000.0000.000
101A103GLY 00.0040.01117.1350.5640.5640.0000.0000.0000.000
102A104GLU -1-0.787-0.84216.016-15.023-15.0230.0000.0000.0000.000
103A105ASP -1-0.809-0.90818.008-11.876-11.8760.0000.0000.0000.000
104A106ILE 00.0480.01014.531-0.465-0.4650.0000.0000.0000.000
105A107GLN 00.0020.00217.710-0.499-0.4990.0000.0000.0000.000
106A108LEU 0-0.037-0.02118.214-0.050-0.0500.0000.0000.0000.000
107A109LEU 0-0.037-0.02612.468-0.472-0.4720.0000.0000.0000.000
108A110LYS 10.8810.93716.26311.53411.5340.0000.0000.0000.000
109A111SER 00.0310.01018.979-0.062-0.0620.0000.0000.0000.000
110A112ALA 00.0160.00614.890-0.108-0.1080.0000.0000.0000.000
111A113TYR 00.027-0.00511.485-0.838-0.8380.0000.0000.0000.000
112A114GLU -1-0.849-0.91016.641-11.823-11.8230.0000.0000.0000.000
113A115ASN 0-0.059-0.02217.1650.5960.5960.0000.0000.0000.000
114A116PHE 00.033-0.01011.516-0.267-0.2670.0000.0000.0000.000
115A117ASN 0-0.023-0.00317.6080.1420.1420.0000.0000.0000.000
116A118GLN 0-0.0330.01020.7860.7030.7030.0000.0000.0000.000
117A119HIS 0-0.041-0.03018.610-0.091-0.0910.0000.0000.0000.000
118A120GLU -1-0.869-0.92820.245-12.128-12.1280.0000.0000.0000.000
119A121VAL 00.008-0.01017.440-0.060-0.0600.0000.0000.0000.000
120A122LEU 0-0.0360.02514.016-0.335-0.3350.0000.0000.0000.000
121A123LEU 0-0.0210.0129.0200.0170.0170.0000.0000.0000.000
122A124ALA 00.028-0.0039.145-0.438-0.4380.0000.0000.0000.000
123A125PRO 0-0.047-0.0054.640-1.395-1.295-0.001-0.010-0.0890.000
124A126LEU 00.0440.0176.4722.3962.3960.0000.0000.0000.000
125A127LEU 00.0020.0207.043-1.558-1.5580.0000.0000.0000.000
126A128SER 00.035-0.0129.0210.9530.9530.0000.0000.0000.000
127A129ALA 0-0.0020.0215.6820.6590.679-0.001-0.004-0.0150.000
128A130GLY 00.0160.0153.598-1.660-1.2500.090-0.144-0.3550.000
129A131ILE 00.011-0.0164.5211.5511.7250.002-0.021-0.1560.000
130A132PHE 0-0.070-0.0236.8651.5851.5850.0000.0000.0000.000
131A133GLY 00.0300.0238.3631.4361.4360.0000.0000.0000.000
132A134ALA 00.0070.0089.9221.1751.1750.0000.0000.0000.000
133A135ASP -1-0.795-0.89810.014-17.408-17.4080.0000.0000.0000.000
134A136PRO 0-0.020-0.0238.0040.1290.1290.0000.0000.0000.000
135A137ILE 00.0300.01110.061-0.131-0.1310.0000.0000.0000.000
136A138HIS 00.0370.02413.5760.4860.4860.0000.0000.0000.000
137A139SER 0-0.011-0.02410.4120.3760.3760.0000.0000.0000.000
138A140LEU 0-0.018-0.00512.382-0.029-0.0290.0000.0000.0000.000
139A141ARG 10.8530.92213.63413.09313.0930.0000.0000.0000.000
140A142VAL 00.0170.01615.6880.4680.4680.0000.0000.0000.000
141A143CYS 0-0.040-0.00413.3120.4880.4880.0000.0000.0000.000
142A144VAL 00.0150.01516.0490.3870.3870.0000.0000.0000.000
143A145ASP -1-0.806-0.89318.796-11.727-11.7270.0000.0000.0000.000
144A146THR 0-0.115-0.06318.8030.7860.7860.0000.0000.0000.000
145A147VAL 0-0.060-0.01816.0540.3250.3250.0000.0000.0000.000
146A148ARG 10.9450.98119.50511.67611.6760.0000.0000.0000.000
147A149THR 0-0.0370.00419.6780.2450.2450.0000.0000.0000.000
148A150ASN 0-0.0120.00419.284-0.238-0.2380.0000.0000.0000.000
149A151VAL 00.0160.00313.085-0.628-0.6280.0000.0000.0000.000
150A152TYR 00.0260.02613.3400.6940.6940.0000.0000.0000.000
151A153LEU 00.021-0.0069.817-1.876-1.8760.0000.0000.0000.000
152A154ALA 0-0.007-0.0066.5290.5090.5090.0000.0000.0000.000
153A155VAL 00.0030.0115.650-2.713-2.7130.0000.0000.0000.000
154A156PHE 0-0.012-0.0282.813-11.641-4.2945.491-2.658-10.180-0.018
155A157ASP -1-0.845-0.9224.938-28.192-27.9970.000-0.025-0.1700.000
156A158LYS 10.8850.9277.46321.97921.9790.0000.0000.0000.000
157A159ASN 00.000-0.00210.9932.0872.0870.0000.0000.0000.000
158A160LEU 0-0.008-0.0086.5121.3401.3400.0000.0000.0000.000
159A161TYR 0-0.008-0.00710.0381.2821.2820.0000.0000.0000.000
160A162ASP -1-0.768-0.86011.295-17.845-17.8450.0000.0000.0000.000
161A163LYS 10.9520.99313.02617.83817.8380.0000.0000.0000.000
162A164LEU 0-0.045-0.0199.4120.7750.7750.0000.0000.0000.000
163A165VAL 00.0100.01013.8870.7230.7230.0000.0000.0000.000
164A166SER 0-0.043-0.02916.6640.9190.9190.0000.0000.0000.000
165A167SER 0-0.104-0.07116.3940.6440.6440.0000.0000.0000.000
166A168PHE 0-0.016-0.00417.1450.1410.1410.0000.0000.0000.000
167A169LEU -1-0.879-0.92519.159-11.655-11.6550.0000.0000.0000.000
168A302HOH 0-0.064-0.05026.999-0.017-0.0170.0000.0000.0000.000
169A339HOH 0-0.075-0.06122.213-0.049-0.0490.0000.0000.0000.000
170A342HOH 0-0.049-0.03613.1680.4270.4270.0000.0000.0000.000
171A345HOH 0-0.014-0.0154.205-0.456-0.3420.005-0.032-0.0880.000
172A346HOH 0-0.054-0.04422.0070.1260.1260.0000.0000.0000.000
173A347HOH 00.007-0.0058.0620.1560.1560.0000.0000.0000.000
174A348HOH 0-0.020-0.02224.661-0.015-0.0150.0000.0000.0000.000
175A359HOH 0-0.057-0.03825.2490.1650.1650.0000.0000.0000.000
176A360HOH 00.008-0.00723.0830.1470.1470.0000.0000.0000.000
177A362HOH 0-0.011-0.01410.799-0.240-0.2400.0000.0000.0000.000
178A363HOH 0-0.014-0.03615.344-0.423-0.4230.0000.0000.0000.000
179A364HOH 0-0.030-0.01012.0480.1790.1790.0000.0000.0000.000
180A365HOH 00.0160.00319.835-0.019-0.0190.0000.0000.0000.000
181A370HOH 0-0.064-0.04910.0070.1970.1970.0000.0000.0000.000
182A372HOH 0-0.025-0.01110.084-0.015-0.0150.0000.0000.0000.000
183A374HOH 0-0.031-0.03813.790-0.239-0.2390.0000.0000.0000.000
184A378HOH 0-0.028-0.0227.766-0.582-0.5820.0000.0000.0000.000
185A381HOH 0-0.027-0.01720.996-0.098-0.0980.0000.0000.0000.000
186A383HOH 0-0.031-0.0334.5821.4371.4970.000-0.023-0.0370.000
187A389HOH 0-0.007-0.01519.0930.3010.3010.0000.0000.0000.000
188A392HOH 0-0.048-0.0379.2011.1081.1080.0000.0000.0000.000
189A403HOH 0-0.018-0.02615.6190.1180.1180.0000.0000.0000.000
190A404HOH 00.003-0.00220.675-0.185-0.1850.0000.0000.0000.000
191A405HOH 0-0.020-0.02021.7530.2190.2190.0000.0000.0000.000
192A409HOH 00.005-0.0055.011-0.253-0.2230.000-0.003-0.0270.000
193A410HOH 00.0290.0207.102-1.333-1.3330.0000.0000.0000.000
194A412HOH 00.0000.00224.065-0.099-0.0990.0000.0000.0000.000
195A414HOH 0-0.021-0.03925.601-0.142-0.1420.0000.0000.0000.000
196A416HOH 00.014-0.01012.5170.0270.0270.0000.0000.0000.000
197A419HOH 0-0.061-0.05815.518-0.091-0.0910.0000.0000.0000.000
198A421HOH 00.0300.01321.0350.0030.0030.0000.0000.0000.000
199A424HOH 0-0.019-0.01915.9080.1090.1090.0000.0000.0000.000
200A428HOH 00.0240.01314.005-0.752-0.7520.0000.0000.0000.000
201A431HOH 0-0.007-0.01124.487-0.105-0.1050.0000.0000.0000.000
202A447HOH 0-0.010-0.0282.267-0.453-3.5816.873-1.814-1.9310.004
203A448HOH 00.0440.0242.4661.0130.9142.940-1.275-1.566-0.001
204A451HOH 0-0.013-0.0174.635-1.670-1.5530.005-0.028-0.0930.000
205A455HOH 0-0.032-0.02418.991-0.309-0.3090.0000.0000.0000.000
206A457HOH 00.0210.01123.3940.0680.0680.0000.0000.0000.000
207A484HOH 00.0120.00810.465-0.747-0.7470.0000.0000.0000.000