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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: VR2M1

Calculation Name: 5RUF-B-Xray89

Preferred Name:

Target Type:

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

ligand 3-letter code: 54T

PDB ID: 5RUF

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 205
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1783821.597447
FMO2-HF: Nuclear repulsion 1717515.366728
FMO2-HF: Total energy -66306.23072
FMO2-MP2: Total energy -66499.619739


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.
-1.9030.753-0.004-1.218-1.4330.006
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 : 0.003 / 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 00.0370.0133.593-0.7851.871-0.004-1.218-1.4330.006
4B4ASN 0-0.001-0.0095.951-0.611-0.6110.0000.0000.0000.000
5B5SER 00.0200.0198.144-0.252-0.2520.0000.0000.0000.000
6B6PHE 0-0.016-0.01310.0960.1190.1190.0000.0000.0000.000
7B7SER 00.016-0.00113.863-0.052-0.0520.0000.0000.0000.000
8B8GLY 00.0200.00715.8030.0490.0490.0000.0000.0000.000
9B9TYR 0-0.080-0.05916.5660.0310.0310.0000.0000.0000.000
10B10LEU 00.0170.02120.931-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8510.91822.9580.1930.1930.0000.0000.0000.000
12B12LEU 0-0.043-0.00824.9280.0060.0060.0000.0000.0000.000
13B13THR 00.034-0.00726.4860.0010.0010.0000.0000.0000.000
14B14ASP -1-0.865-0.93925.360-0.160-0.1600.0000.0000.0000.000
15B15ASN 0-0.043-0.02022.394-0.022-0.0220.0000.0000.0000.000
16B16VAL 00.0200.02122.2270.0100.0100.0000.0000.0000.000
17B17TYR 00.0010.00420.619-0.023-0.0230.0000.0000.0000.000
18B18ILE 00.0140.01122.6750.0210.0210.0000.0000.0000.000
19B19LYS 10.8460.90417.8050.0870.0870.0000.0000.0000.000
20B20ASN 0-0.050-0.01622.7780.0120.0120.0000.0000.0000.000
21B21ALA 00.009-0.01119.876-0.008-0.0080.0000.0000.0000.000
22B22ASP -1-0.816-0.89120.9370.0960.0960.0000.0000.0000.000
23B23ILE 00.0360.00218.6210.0030.0030.0000.0000.0000.000
24B24VAL 00.0220.02117.3730.0270.0270.0000.0000.0000.000
25B25GLU -1-0.814-0.89716.0870.1890.1890.0000.0000.0000.000
26B26GLU -1-0.775-0.85615.062-0.070-0.0700.0000.0000.0000.000
27B27ALA 0-0.001-0.00213.308-0.008-0.0080.0000.0000.0000.000
28B28LYS 10.8450.91311.370-0.141-0.1410.0000.0000.0000.000
29B29LYS 10.7750.88310.3450.1360.1360.0000.0000.0000.000
30B30VAL 0-0.070-0.0319.509-0.069-0.0690.0000.0000.0000.000
31B31LYS 10.9570.9975.111-0.465-0.4650.0000.0000.0000.000
32B32PRO 00.0160.0267.9160.1620.1620.0000.0000.0000.000
33B33THR 00.0170.00410.1610.2440.2440.0000.0000.0000.000
34B34VAL 0-0.014-0.01210.8780.0280.0280.0000.0000.0000.000
35B35VAL 0-0.0080.00514.571-0.049-0.0490.0000.0000.0000.000
36B36VAL 0-0.009-0.00316.5750.0100.0100.0000.0000.0000.000
37B37ASN 00.005-0.02820.349-0.014-0.0140.0000.0000.0000.000
38B38ALA 0-0.0110.01922.756-0.009-0.0090.0000.0000.0000.000
39B39ALA 00.0280.03026.0230.0000.0000.0000.0000.0000.000
40B40ASN 00.019-0.00227.783-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0280.01030.4760.0080.0080.0000.0000.0000.000
42B42TYR 00.0370.01532.4290.0030.0030.0000.0000.0000.000
43B43LEU 0-0.037-0.00826.3780.0060.0060.0000.0000.0000.000
44B44LYS 10.8610.94028.898-0.103-0.1030.0000.0000.0000.000
45B45HIS 00.000-0.00325.565-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0300.02328.3340.0030.0030.0000.0000.0000.000
47B47GLY 00.0250.00430.2730.0010.0010.0000.0000.0000.000
48B48GLY 00.0080.00128.9160.0050.0050.0000.0000.0000.000
49B49VAL 00.0610.02622.9570.0080.0080.0000.0000.0000.000
50B50ALA 00.0160.02124.0990.0150.0150.0000.0000.0000.000
51B51GLY 0-0.0100.00924.9100.0150.0150.0000.0000.0000.000
52B52ALA 0-0.040-0.03223.4430.0100.0100.0000.0000.0000.000
53B53LEU 00.0150.00118.7000.0160.0160.0000.0000.0000.000
54B54ASN 00.0600.01520.6920.0370.0370.0000.0000.0000.000
55B55LYS 10.9300.97222.717-0.109-0.1090.0000.0000.0000.000
56B56ALA 00.0160.02418.4160.0070.0070.0000.0000.0000.000
57B57THR 0-0.038-0.01117.7920.0260.0260.0000.0000.0000.000
58B58ASN 0-0.030-0.02119.611-0.008-0.0080.0000.0000.0000.000
59B59ASN 0-0.011-0.00622.717-0.011-0.0110.0000.0000.0000.000
60B60ALA 00.0360.02620.332-0.010-0.0100.0000.0000.0000.000
61B61MET 00.0190.02419.630-0.013-0.0130.0000.0000.0000.000
62B62GLN 0-0.043-0.03622.317-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.0090.00125.286-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.717-0.83720.4770.2860.2860.0000.0000.0000.000
65B65SER 0-0.021-0.02124.665-0.011-0.0110.0000.0000.0000.000
66B66ASP -1-0.820-0.89226.4820.1120.1120.0000.0000.0000.000
67B67ASP -1-0.911-0.94227.3150.1510.1510.0000.0000.0000.000
68B68TYR 00.0480.00826.036-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.038-0.02028.289-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.0250.00231.624-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.039-0.00830.118-0.008-0.0080.0000.0000.0000.000
72B72ASN 0-0.088-0.05528.608-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0220.00332.360-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.055-0.03232.5620.0060.0060.0000.0000.0000.000
75B75LEU 0-0.028-0.01327.637-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9940.99032.171-0.053-0.0530.0000.0000.0000.000
77B77VAL 00.0310.00532.6040.0040.0040.0000.0000.0000.000
78B78GLY 0-0.0020.00832.018-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0020.01829.942-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.046-0.05224.7540.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0110.02524.686-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0120.01218.2280.0040.0040.0000.0000.0000.000
83B83LEU 0-0.0020.01019.978-0.005-0.0050.0000.0000.0000.000
84B84SER 00.0350.01616.3240.0580.0580.0000.0000.0000.000
85B85GLY 00.0140.01914.424-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.032-0.02714.7300.0170.0170.0000.0000.0000.000
87B87ASN 0-0.039-0.03012.5040.0950.0950.0000.0000.0000.000
88B88LEU 0-0.026-0.00712.584-0.012-0.0120.0000.0000.0000.000
89B89ALA 00.0320.01910.905-0.024-0.0240.0000.0000.0000.000
90B90LYS 10.9220.9909.515-0.759-0.7590.0000.0000.0000.000
91B91HIS 00.013-0.00411.382-0.029-0.0290.0000.0000.0000.000
92B92CYS 0-0.030-0.01515.015-0.018-0.0180.0000.0000.0000.000
93B93LEU 0-0.0310.00418.006-0.011-0.0110.0000.0000.0000.000
94B94HIS 00.0530.00720.549-0.036-0.0360.0000.0000.0000.000
95B95VAL 00.006-0.00123.694-0.007-0.0070.0000.0000.0000.000
96B96VAL 0-0.0250.01426.278-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0310.01729.972-0.007-0.0070.0000.0000.0000.000
98B98PRO 00.0000.01531.6630.0050.0050.0000.0000.0000.000
99B99ASN 00.0040.00334.588-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0850.04336.4400.0000.0000.0000.0000.0000.000
101B101ASN 0-0.045-0.02037.359-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7650.87936.228-0.052-0.0520.0000.0000.0000.000
103B103GLY 00.0070.01141.0220.0000.0000.0000.0000.0000.000
104B104GLU -1-0.820-0.86436.8160.0470.0470.0000.0000.0000.000
105B105ASP -1-0.818-0.91340.5210.0130.0130.0000.0000.0000.000
106B106ILE 00.0320.00136.4650.0020.0020.0000.0000.0000.000
107B107GLN 0-0.033-0.01937.3350.0010.0010.0000.0000.0000.000
108B108LEU 00.0230.00535.671-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.034-0.01831.3850.0040.0040.0000.0000.0000.000
110B110LYS 10.8930.93531.7930.0140.0140.0000.0000.0000.000
111B111SER 00.0220.01231.364-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0280.00829.6910.0040.0040.0000.0000.0000.000
113B113TYR 00.029-0.01026.2550.0080.0080.0000.0000.0000.000
114B114GLU -1-0.838-0.87026.5360.0030.0030.0000.0000.0000.000
115B115ASN 0-0.025-0.00524.9160.0050.0050.0000.0000.0000.000
116B116PHE 00.034-0.00822.2170.0130.0130.0000.0000.0000.000
117B117ASN 0-0.034-0.01321.584-0.013-0.0130.0000.0000.0000.000
118B118GLN 0-0.0410.00422.097-0.010-0.0100.0000.0000.0000.000
119B119HIS 0-0.002-0.00117.1870.0320.0320.0000.0000.0000.000
120B120GLU -1-0.835-0.90115.513-0.106-0.1060.0000.0000.0000.000
121B121VAL 0-0.016-0.01212.707-0.042-0.0420.0000.0000.0000.000
122B122LEU 0-0.0080.02915.1460.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0090.01114.715-0.045-0.0450.0000.0000.0000.000
124B124ALA 00.005-0.00817.0870.0340.0340.0000.0000.0000.000
125B125PRO 00.0000.01720.693-0.018-0.0180.0000.0000.0000.000
126B126LEU 00.0110.00323.836-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0210.02125.8440.0070.0070.0000.0000.0000.000
128B128SER 00.008-0.02728.736-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0160.02529.939-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0340.01631.6820.0070.0070.0000.0000.0000.000
131B131ILE 00.002-0.00431.306-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.070-0.02330.6420.0000.0000.0000.0000.0000.000
133B133GLY 00.0310.01434.496-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.027-0.00534.738-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.814-0.91135.818-0.003-0.0030.0000.0000.0000.000
136B136PRO 0-0.022-0.01832.264-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.012-0.00432.650-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0560.03334.582-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.030-0.03230.655-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.016-0.00828.3130.0000.0000.0000.0000.0000.000
141B141ARG 10.8550.90130.7750.0320.0320.0000.0000.0000.000
142B142VAL 00.0210.01631.783-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0100.01226.4200.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0120.00228.358-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.753-0.82929.548-0.042-0.0420.0000.0000.0000.000
146B146THR 0-0.114-0.06029.1780.0020.0020.0000.0000.0000.000
147B147VAL 0-0.050-0.01423.3750.0030.0030.0000.0000.0000.000
148B148ARG 10.9070.96225.3840.0250.0250.0000.0000.0000.000
149B149THR 0-0.0180.02019.825-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.037-0.01017.507-0.010-0.0100.0000.0000.0000.000
151B151VAL 00.0370.01418.3490.0240.0240.0000.0000.0000.000
152B152TYR 0-0.021-0.01016.517-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.021-0.00319.4290.0320.0320.0000.0000.0000.000
154B154ALA 0-0.001-0.00119.877-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.024-0.01621.9630.0130.0130.0000.0000.0000.000
156B156PHE 00.0210.01124.556-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.793-0.89326.087-0.002-0.0020.0000.0000.0000.000
158B158LYS 10.8700.91629.0020.0400.0400.0000.0000.0000.000
159B159ASN 0-0.011-0.02630.038-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0080.00430.523-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.016-0.01725.473-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.764-0.85929.849-0.047-0.0470.0000.0000.0000.000
163B163LYS 10.9501.01332.6810.0100.0100.0000.0000.0000.000
164B164LEU 0-0.0360.00229.435-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0330.00428.906-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.066-0.03931.787-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.022-0.02935.353-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0180.00031.3050.0020.0020.0000.0000.0000.000
169B169LEU -1-0.907-0.92834.193-0.055-0.0550.0000.0000.0000.000
170B215HOH 0-0.066-0.04611.8030.0410.0410.0000.0000.0000.000
171B217HOH 0-0.006-0.01133.7020.0010.0010.0000.0000.0000.000
172B220HOH 0-0.017-0.02731.945-0.003-0.0030.0000.0000.0000.000
173B223HOH 0-0.038-0.03138.8010.0010.0010.0000.0000.0000.000
174B231HOH 0-0.043-0.03427.6220.0000.0000.0000.0000.0000.000
175B234HOH 0-0.035-0.03011.391-0.025-0.0250.0000.0000.0000.000
176B255HOH 0-0.031-0.02531.1260.0020.0020.0000.0000.0000.000
177B256HOH 0-0.050-0.05133.9000.0020.0020.0000.0000.0000.000
178B257HOH 0-0.019-0.02222.7450.0040.0040.0000.0000.0000.000
179B260HOH 0-0.025-0.03413.7220.0000.0000.0000.0000.0000.000
180B261HOH 00.0160.00424.0470.0060.0060.0000.0000.0000.000
181B263HOH 0-0.011-0.01328.431-0.004-0.0040.0000.0000.0000.000
182B268HOH 0-0.041-0.02934.8150.0010.0010.0000.0000.0000.000
183B270HOH 0-0.011-0.03419.419-0.014-0.0140.0000.0000.0000.000
184B277HOH 0-0.030-0.02923.0240.0060.0060.0000.0000.0000.000
185B279HOH 00.000-0.00322.1640.0030.0030.0000.0000.0000.000
186B281HOH 00.0230.00129.509-0.002-0.0020.0000.0000.0000.000
187B283HOH 0-0.069-0.05129.035-0.003-0.0030.0000.0000.0000.000
188B284HOH 0-0.021-0.00827.418-0.002-0.0020.0000.0000.0000.000
189B293HOH 0-0.085-0.06237.077-0.001-0.0010.0000.0000.0000.000
190B300HOH 0-0.024-0.02328.3580.0010.0010.0000.0000.0000.000
191B301HOH 0-0.016-0.01015.3550.0150.0150.0000.0000.0000.000
192B303HOH 0-0.018-0.03012.4770.0320.0320.0000.0000.0000.000
193B304HOH 00.0220.01328.027-0.002-0.0020.0000.0000.0000.000
194B308HOH 00.008-0.01427.929-0.003-0.0030.0000.0000.0000.000
195B311HOH 0-0.041-0.03134.063-0.002-0.0020.0000.0000.0000.000
196B319HOH 0-0.020-0.00229.4850.0030.0030.0000.0000.0000.000
197B333HOH 00.001-0.01434.6770.0020.0020.0000.0000.0000.000
198B335HOH 0-0.004-0.00832.1410.0010.0010.0000.0000.0000.000
199B336HOH 00.001-0.01815.8110.0190.0190.0000.0000.0000.000
200B342HOH 0-0.027-0.02030.1010.0010.0010.0000.0000.0000.000
201B348HOH 00.0280.01831.7370.0010.0010.0000.0000.0000.000
202B352HOH 00.0150.00428.354-0.003-0.0030.0000.0000.0000.000
203B355HOH 00.006-0.00530.581-0.002-0.0020.0000.0000.0000.000
204B360HOH 0-0.015-0.02728.6090.0000.0000.0000.0000.0000.000
205B369HOH 0-0.027-0.01928.9580.0000.0000.0000.0000.0000.000