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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 14JRZ

Calculation Name: 5RSK-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-[(3-methoxy-1,2-oxazol-5-yl)methyl]-3h-purin-6-amine

ligand 3-letter code: W57

PDB ID: 5RSK

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 -1783709.752176
FMO2-HF: Nuclear repulsion 1717403.515568
FMO2-HF: Total energy -66306.236608
FMO2-MP2: Total energy -66499.636984


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.
-1.4350.963-0.013-1.036-1.3490.006
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 : 0.003
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 00.0400.0153.777-0.6391.759-0.013-1.036-1.3490.006
4B4ASN 0-0.004-0.0115.979-0.529-0.5290.0000.0000.0000.000
5B5SER 0-0.0040.0037.963-0.128-0.1280.0000.0000.0000.000
6B6PHE 0-0.017-0.00810.0640.0640.0640.0000.0000.0000.000
7B7SER 00.0360.00913.861-0.040-0.0400.0000.0000.0000.000
8B8GLY 00.0160.00515.7690.0480.0480.0000.0000.0000.000
9B9TYR 0-0.076-0.05616.5580.0300.0300.0000.0000.0000.000
10B10LEU 00.0190.02220.889-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8550.92523.7130.1890.1890.0000.0000.0000.000
12B12LEU 0-0.033-0.00424.9340.0060.0060.0000.0000.0000.000
13B13THR 00.038-0.00626.6240.0020.0020.0000.0000.0000.000
14B14ASP -1-0.878-0.95325.446-0.160-0.1600.0000.0000.0000.000
15B15ASN 0-0.035-0.01122.608-0.020-0.0200.0000.0000.0000.000
16B16VAL 00.0150.01922.4860.0090.0090.0000.0000.0000.000
17B17TYR 00.0010.00320.654-0.020-0.0200.0000.0000.0000.000
18B18ILE 00.0160.01422.6800.0190.0190.0000.0000.0000.000
19B19LYS 10.8300.89417.7970.1010.1010.0000.0000.0000.000
20B20ASN 0-0.038-0.00822.7780.0120.0120.0000.0000.0000.000
21B21ALA 00.007-0.01319.917-0.008-0.0080.0000.0000.0000.000
22B22ASP -1-0.812-0.88820.9970.0810.0810.0000.0000.0000.000
23B23ILE 00.0360.00418.6570.0010.0010.0000.0000.0000.000
24B24VAL 00.0180.01517.3920.0230.0230.0000.0000.0000.000
25B25GLU -1-0.815-0.89516.0940.1620.1620.0000.0000.0000.000
26B26GLU -1-0.767-0.85315.074-0.097-0.0970.0000.0000.0000.000
27B27ALA 0-0.0010.00313.330-0.016-0.0160.0000.0000.0000.000
28B28LYS 10.8480.91011.403-0.128-0.1280.0000.0000.0000.000
29B29LYS 10.7790.88510.3650.1520.1520.0000.0000.0000.000
30B30VAL 0-0.083-0.0439.466-0.077-0.0770.0000.0000.0000.000
31B31LYS 10.9691.0065.191-0.227-0.2270.0000.0000.0000.000
32B32PRO 00.0120.0237.9450.1250.1250.0000.0000.0000.000
33B33THR 00.0190.00410.3570.2330.2330.0000.0000.0000.000
34B34VAL 0-0.010-0.01111.0680.0330.0330.0000.0000.0000.000
35B35VAL 0-0.0110.00314.766-0.050-0.0500.0000.0000.0000.000
36B36VAL 0-0.011-0.00616.6070.0130.0130.0000.0000.0000.000
37B37ASN 00.009-0.02420.375-0.015-0.0150.0000.0000.0000.000
38B38ALA 0-0.0140.01722.790-0.008-0.0080.0000.0000.0000.000
39B39ALA 00.0370.03426.0480.0000.0000.0000.0000.0000.000
40B40ASN 00.017-0.00427.804-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0240.00930.5030.0080.0080.0000.0000.0000.000
42B42TYR 00.0380.01432.4460.0030.0030.0000.0000.0000.000
43B43LEU 0-0.033-0.00326.4160.0060.0060.0000.0000.0000.000
44B44LYS 10.8560.93328.936-0.097-0.0970.0000.0000.0000.000
45B45HIS 00.0070.00425.596-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0270.02028.3670.0030.0030.0000.0000.0000.000
47B47GLY 00.0290.00430.2950.0010.0010.0000.0000.0000.000
48B48GLY 00.0060.00128.9460.0040.0040.0000.0000.0000.000
49B49VAL 00.0620.02322.9930.0070.0070.0000.0000.0000.000
50B50ALA 00.0100.01924.1120.0140.0140.0000.0000.0000.000
51B51GLY 0-0.0060.01224.9510.0140.0140.0000.0000.0000.000
52B52ALA 0-0.041-0.03323.4700.0090.0090.0000.0000.0000.000
53B53LEU 00.013-0.00218.7280.0150.0150.0000.0000.0000.000
54B54ASN 00.0720.02520.7210.0360.0360.0000.0000.0000.000
55B55LYS 10.9230.96722.745-0.100-0.1000.0000.0000.0000.000
56B56ALA 00.0210.02618.4310.0070.0070.0000.0000.0000.000
57B57THR 0-0.048-0.01717.8450.0250.0250.0000.0000.0000.000
58B58ASN 0-0.024-0.01719.678-0.007-0.0070.0000.0000.0000.000
59B59ASN 0-0.022-0.01322.747-0.010-0.0100.0000.0000.0000.000
60B60ALA 00.0420.03020.369-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0170.02319.651-0.012-0.0120.0000.0000.0000.000
62B62GLN 0-0.045-0.03822.348-0.014-0.0140.0000.0000.0000.000
63B63VAL 00.0000.00625.302-0.009-0.0090.0000.0000.0000.000
64B64GLU -1-0.720-0.83620.4930.2740.2740.0000.0000.0000.000
65B65SER 0-0.025-0.02524.684-0.010-0.0100.0000.0000.0000.000
66B66ASP -1-0.816-0.88826.5120.1070.1070.0000.0000.0000.000
67B67ASP -1-0.920-0.94927.3090.1470.1470.0000.0000.0000.000
68B68TYR 00.0550.01326.105-0.007-0.0070.0000.0000.0000.000
69B69ILE 0-0.041-0.02128.365-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.0230.00331.652-0.008-0.0080.0000.0000.0000.000
71B71THR 0-0.039-0.01030.157-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.090-0.05628.695-0.008-0.0080.0000.0000.0000.000
73B73GLY 0-0.026-0.00232.459-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.051-0.02832.6670.0060.0060.0000.0000.0000.000
75B75LEU 0-0.034-0.01627.765-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9940.98932.297-0.051-0.0510.0000.0000.0000.000
77B77VAL 00.0290.00232.7610.0040.0040.0000.0000.0000.000
78B78GLY 00.0020.01132.190-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0030.02030.118-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.045-0.05124.9170.0050.0050.0000.0000.0000.000
81B81CYS 0-0.0080.02724.823-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0050.00918.3290.0030.0030.0000.0000.0000.000
83B83LEU 00.0020.01120.131-0.003-0.0030.0000.0000.0000.000
84B84SER 00.0430.01816.3390.0540.0540.0000.0000.0000.000
85B85GLY 00.0130.01714.451-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.037-0.03114.7310.0130.0130.0000.0000.0000.000
87B87ASN 0-0.037-0.02712.5070.0910.0910.0000.0000.0000.000
88B88LEU 0-0.025-0.00512.594-0.018-0.0180.0000.0000.0000.000
89B89ALA 00.0330.01810.924-0.033-0.0330.0000.0000.0000.000
90B90LYS 10.9130.9879.650-0.741-0.7410.0000.0000.0000.000
91B91HIS 00.015-0.00411.491-0.020-0.0200.0000.0000.0000.000
92B92CYS 0-0.025-0.00915.145-0.022-0.0220.0000.0000.0000.000
93B93LEU 0-0.0290.00418.028-0.008-0.0080.0000.0000.0000.000
94B94HIS 00.0470.00420.696-0.036-0.0360.0000.0000.0000.000
95B95VAL 00.007-0.00223.856-0.006-0.0060.0000.0000.0000.000
96B96VAL 0-0.0330.01326.385-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0310.01430.013-0.006-0.0060.0000.0000.0000.000
98B98PRO 00.0080.01831.7030.0050.0050.0000.0000.0000.000
99B99ASN 0-0.008-0.00134.623-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0910.04636.4710.0000.0000.0000.0000.0000.000
101B101ASN 0-0.045-0.01937.387-0.004-0.0040.0000.0000.0000.000
102B102LYS 10.7630.87736.280-0.047-0.0470.0000.0000.0000.000
103B103GLY 00.0020.00841.0500.0000.0000.0000.0000.0000.000
104B104GLU -1-0.815-0.86336.8310.0430.0430.0000.0000.0000.000
105B105ASP -1-0.826-0.91440.5490.0110.0110.0000.0000.0000.000
106B106ILE 00.0270.00036.5020.0020.0020.0000.0000.0000.000
107B107GLN 0-0.020-0.01437.4950.0010.0010.0000.0000.0000.000
108B108LEU 00.0200.00535.892-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.038-0.02031.4310.0040.0040.0000.0000.0000.000
110B110LYS 10.8780.93132.0010.0150.0150.0000.0000.0000.000
111B111SER 00.0210.01231.568-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0310.01329.9090.0040.0040.0000.0000.0000.000
113B113TYR 00.026-0.01326.3250.0070.0070.0000.0000.0000.000
114B114GLU -1-0.875-0.92026.7430.0030.0030.0000.0000.0000.000
115B115ASN 0-0.023-0.00325.1000.0060.0060.0000.0000.0000.000
116B116PHE 00.032-0.00722.4140.0120.0120.0000.0000.0000.000
117B117ASN 0-0.048-0.02221.790-0.013-0.0130.0000.0000.0000.000
118B118GLN 0-0.0270.01122.275-0.008-0.0080.0000.0000.0000.000
119B119HIS 00.0020.00217.3670.0310.0310.0000.0000.0000.000
120B120GLU -1-0.835-0.90015.731-0.098-0.0980.0000.0000.0000.000
121B121VAL 0-0.017-0.01012.947-0.043-0.0430.0000.0000.0000.000
122B122LEU 0-0.0110.02715.3550.0690.0690.0000.0000.0000.000
123B123LEU 0-0.0070.01414.744-0.042-0.0420.0000.0000.0000.000
124B124ALA 00.004-0.00917.1150.0340.0340.0000.0000.0000.000
125B125PRO 00.0030.01520.713-0.017-0.0170.0000.0000.0000.000
126B126LEU 0-0.0010.00023.859-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0230.02025.8790.0070.0070.0000.0000.0000.000
128B128SER 00.012-0.02228.762-0.007-0.0070.0000.0000.0000.000
129B129ALA 00.0150.02330.011-0.003-0.0030.0000.0000.0000.000
130B130GLY 00.0300.01531.7020.0070.0070.0000.0000.0000.000
131B131ILE 00.008-0.00231.329-0.002-0.0020.0000.0000.0000.000
132B132PHE 0-0.071-0.02530.6660.0010.0010.0000.0000.0000.000
133B133GLY 00.0270.01234.525-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.0180.00034.762-0.003-0.0030.0000.0000.0000.000
135B135ASP -1-0.811-0.90935.829-0.007-0.0070.0000.0000.0000.000
136B136PRO 0-0.032-0.02432.265-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.008-0.00532.667-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0610.03334.579-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.020-0.02630.667-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.023-0.01128.3050.0000.0000.0000.0000.0000.000
141B141ARG 10.8200.87730.8490.0350.0350.0000.0000.0000.000
142B142VAL 00.0230.01631.984-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0080.00926.5770.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0060.00528.570-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.767-0.83529.779-0.043-0.0430.0000.0000.0000.000
146B146THR 0-0.111-0.06029.3520.0030.0030.0000.0000.0000.000
147B147VAL 0-0.064-0.02323.6070.0030.0030.0000.0000.0000.000
148B148ARG 10.9150.96725.5910.0270.0270.0000.0000.0000.000
149B149THR 0-0.0150.01920.041-0.019-0.0190.0000.0000.0000.000
150B150ASN 0-0.047-0.01317.690-0.011-0.0110.0000.0000.0000.000
151B151VAL 00.0430.01618.5800.0220.0220.0000.0000.0000.000
152B152TYR 0-0.020-0.00816.756-0.027-0.0270.0000.0000.0000.000
153B153LEU 00.024-0.00119.4460.0300.0300.0000.0000.0000.000
154B154ALA 0-0.006-0.00619.895-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.019-0.01421.9760.0130.0130.0000.0000.0000.000
156B156PHE 00.0180.01124.577-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.790-0.89326.100-0.008-0.0080.0000.0000.0000.000
158B158LYS 10.8690.91728.9920.0450.0450.0000.0000.0000.000
159B159ASN 0-0.010-0.02630.036-0.008-0.0080.0000.0000.0000.000
160B160LEU 0-0.0070.00330.545-0.002-0.0020.0000.0000.0000.000
161B161TYR 0-0.019-0.01625.463-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.762-0.85729.851-0.051-0.0510.0000.0000.0000.000
163B163LYS 10.9431.01132.6710.0130.0130.0000.0000.0000.000
164B164LEU 0-0.0310.00429.462-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0300.00428.882-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.063-0.03831.770-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.023-0.02735.3270.0000.0000.0000.0000.0000.000
168B168PHE 0-0.0110.00531.3730.0020.0020.0000.0000.0000.000
169B169LEU -1-0.910-0.92934.137-0.056-0.0560.0000.0000.0000.000
170B217HOH 0-0.066-0.04511.8240.0420.0420.0000.0000.0000.000
171B221HOH 0-0.039-0.03238.8130.0020.0020.0000.0000.0000.000
172B222HOH 0-0.033-0.02811.529-0.023-0.0230.0000.0000.0000.000
173B229HOH 0-0.006-0.01233.7120.0010.0010.0000.0000.0000.000
174B236HOH 0-0.050-0.05133.9250.0020.0020.0000.0000.0000.000
175B242HOH 0-0.040-0.03127.851-0.001-0.0010.0000.0000.0000.000
176B245HOH 0-0.036-0.02931.2640.0020.0020.0000.0000.0000.000
177B247HOH 0-0.011-0.01328.466-0.004-0.0040.0000.0000.0000.000
178B253HOH 0-0.027-0.03613.975-0.003-0.0030.0000.0000.0000.000
179B256HOH 0-0.019-0.02122.9180.0040.0040.0000.0000.0000.000
180B260HOH 0-0.010-0.03419.443-0.014-0.0140.0000.0000.0000.000
181B261HOH 0-0.040-0.02935.0010.0010.0010.0000.0000.0000.000
182B267HOH 00.000-0.00322.3250.0030.0030.0000.0000.0000.000
183B268HOH 00.0230.00029.529-0.002-0.0020.0000.0000.0000.000
184B269HOH 0-0.024-0.02328.5810.0010.0010.0000.0000.0000.000
185B270HOH 00.0160.00424.1990.0060.0060.0000.0000.0000.000
186B271HOH 0-0.022-0.00927.638-0.002-0.0020.0000.0000.0000.000
187B279HOH 0-0.068-0.05129.071-0.003-0.0030.0000.0000.0000.000
188B286HOH 0-0.029-0.02923.0470.0060.0060.0000.0000.0000.000
189B289HOH 0-0.019-0.03212.6830.0310.0310.0000.0000.0000.000
190B298HOH 00.0360.02433.8000.0020.0020.0000.0000.0000.000
191B299HOH 00.0220.01428.058-0.002-0.0020.0000.0000.0000.000
192B302HOH 0-0.086-0.06337.055-0.001-0.0010.0000.0000.0000.000
193B305HOH 00.009-0.01327.952-0.003-0.0030.0000.0000.0000.000
194B311HOH 0-0.016-0.01115.5250.0130.0130.0000.0000.0000.000
195B321HOH 0-0.041-0.03234.002-0.002-0.0020.0000.0000.0000.000
196B323HOH 00.0030.00431.8570.0030.0030.0000.0000.0000.000
197B324HOH 0-0.019-0.00229.5080.0030.0030.0000.0000.0000.000
198B327HOH 00.001-0.01434.7160.0020.0020.0000.0000.0000.000
199B328HOH 0-0.001-0.01916.0450.0170.0170.0000.0000.0000.000
200B333HOH 00.0160.00730.2660.0020.0020.0000.0000.0000.000
201B337HOH 00.0230.01731.3000.0000.0000.0000.0000.0000.000
202B341HOH 00.006-0.00530.706-0.002-0.0020.0000.0000.0000.000
203B343HOH 00.0150.00628.492-0.003-0.0030.0000.0000.0000.000
204B356HOH 0-0.015-0.02728.638-0.001-0.0010.0000.0000.0000.000
205B369HOH 0-0.030-0.02029.0630.0000.0000.0000.0000.0000.000