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About

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: K3RN3

Calculation Name: 5RTV-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-hydroxy-2-methylbenzoic acid

ligand 3-letter code: PF0

PDB ID: 5RTV

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 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1786820.889887
FMO2-HF: Nuclear repulsion 1720438.633043
FMO2-HF: Total energy -66382.256843
FMO2-MP2: Total energy -66575.845684


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.
-1.8840.684-0.008-1.14-1.420.006
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 : 0.000 / q_NPA : 0.002
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 00.0370.0143.640-0.6881.880-0.008-1.140-1.4200.006
4B4ASN 0-0.001-0.0096.001-0.625-0.6250.0000.0000.0000.000
5B5SER 00.0210.0208.069-0.257-0.2570.0000.0000.0000.000
6B6PHE 0-0.014-0.01310.0710.1210.1210.0000.0000.0000.000
7B7SER 00.018-0.00113.831-0.056-0.0560.0000.0000.0000.000
8B8GLY 00.0190.00615.7580.0510.0510.0000.0000.0000.000
9B9TYR 0-0.081-0.05916.6260.0290.0290.0000.0000.0000.000
10B10LEU 00.0180.02120.868-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8570.92422.9540.1930.1930.0000.0000.0000.000
12B12LEU 0-0.043-0.01024.9000.0060.0060.0000.0000.0000.000
13B13THR 00.035-0.00626.4940.0010.0010.0000.0000.0000.000
14B14ASP -1-0.868-0.94425.396-0.161-0.1610.0000.0000.0000.000
15B15ASN 0-0.046-0.02122.412-0.022-0.0220.0000.0000.0000.000
16B16VAL 00.0170.02022.2520.0100.0100.0000.0000.0000.000
17B17TYR 00.0030.00620.657-0.021-0.0210.0000.0000.0000.000
18B18ILE 00.0110.00922.7510.0210.0210.0000.0000.0000.000
19B19LYS 10.8380.90117.7640.0690.0690.0000.0000.0000.000
20B20ASN 0-0.041-0.01022.8410.0120.0120.0000.0000.0000.000
21B21ALA 00.006-0.01319.952-0.006-0.0060.0000.0000.0000.000
22B22ASP -1-0.814-0.89120.9930.1070.1070.0000.0000.0000.000
23B23ILE 00.0380.00618.7290.0050.0050.0000.0000.0000.000
24B24VAL 00.0200.01717.4480.0290.0290.0000.0000.0000.000
25B25GLU -1-0.815-0.89816.1630.2120.2120.0000.0000.0000.000
26B26GLU -1-0.775-0.85615.134-0.046-0.0460.0000.0000.0000.000
27B27ALA 00.0000.00213.392-0.003-0.0030.0000.0000.0000.000
28B28LYS 10.8430.91011.447-0.154-0.1540.0000.0000.0000.000
29B29LYS 10.7790.88510.4190.1170.1170.0000.0000.0000.000
30B30VAL 0-0.072-0.0339.566-0.058-0.0580.0000.0000.0000.000
31B31LYS 10.9570.9975.160-0.548-0.5480.0000.0000.0000.000
32B32PRO 00.0140.0248.0390.1600.1600.0000.0000.0000.000
33B33THR 00.0180.00310.2000.2450.2450.0000.0000.0000.000
34B34VAL 0-0.012-0.01210.9110.0270.0270.0000.0000.0000.000
35B35VAL 0-0.0070.00614.596-0.047-0.0470.0000.0000.0000.000
36B36VAL 0-0.011-0.00516.6680.0090.0090.0000.0000.0000.000
37B37ASN 00.003-0.02920.440-0.012-0.0120.0000.0000.0000.000
38B38ALA 0-0.0140.01722.849-0.010-0.0100.0000.0000.0000.000
39B39ALA 00.0320.03326.1180.0000.0000.0000.0000.0000.000
40B40ASN 00.022-0.00127.872-0.010-0.0100.0000.0000.0000.000
41B41VAL 00.0270.00830.5660.0080.0080.0000.0000.0000.000
42B42TYR 00.0320.01332.4880.0020.0020.0000.0000.0000.000
43B43LEU 0-0.036-0.00626.4600.0060.0060.0000.0000.0000.000
44B44LYS 10.8610.93928.987-0.104-0.1040.0000.0000.0000.000
45B45HIS 00.004-0.00125.650-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0340.02628.4140.0030.0030.0000.0000.0000.000
47B47GLY 00.0320.00530.3410.0010.0010.0000.0000.0000.000
48B48GLY 00.0080.00628.9950.0040.0040.0000.0000.0000.000
49B49VAL 00.0720.03123.0440.0080.0080.0000.0000.0000.000
50B50ALA 00.0140.01924.1660.0150.0150.0000.0000.0000.000
51B51GLY 0-0.0080.01125.0010.0140.0140.0000.0000.0000.000
52B52ALA 0-0.036-0.03023.4990.0100.0100.0000.0000.0000.000
53B53LEU 00.014-0.00118.7700.0170.0170.0000.0000.0000.000
54B54ASN 00.0640.01820.7530.0380.0380.0000.0000.0000.000
55B55LYS 10.9250.96922.762-0.115-0.1150.0000.0000.0000.000
56B56ALA 00.0180.02618.4790.0070.0070.0000.0000.0000.000
57B57THR 0-0.042-0.01517.8500.0270.0270.0000.0000.0000.000
58B58ASN 0-0.024-0.01819.667-0.009-0.0090.0000.0000.0000.000
59B59ASN 0-0.018-0.00822.747-0.012-0.0120.0000.0000.0000.000
60B60ALA 00.0580.04420.398-0.010-0.0100.0000.0000.0000.000
61B61MET 00.0350.03619.702-0.014-0.0140.0000.0000.0000.000
62B62GLN 0-0.041-0.03422.389-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.0050.00525.326-0.011-0.0110.0000.0000.0000.000
64B64GLU -1-0.732-0.84720.5390.2870.2870.0000.0000.0000.000
65B65SER 0-0.021-0.01924.722-0.011-0.0110.0000.0000.0000.000
66B66ASP -1-0.817-0.88926.5540.1130.1130.0000.0000.0000.000
67B67ASP -1-0.913-0.94527.3770.1490.1490.0000.0000.0000.000
68B68TYR 00.0470.00826.033-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.031-0.01428.304-0.012-0.0120.0000.0000.0000.000
70B70ALA 0-0.030-0.00231.625-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.038-0.00730.108-0.008-0.0080.0000.0000.0000.000
72B72ASN 0-0.091-0.05828.615-0.010-0.0100.0000.0000.0000.000
73B73GLY 0-0.0200.00432.369-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.057-0.03332.5910.0060.0060.0000.0000.0000.000
75B75LEU 0-0.028-0.01327.654-0.003-0.0030.0000.0000.0000.000
76B76LYS 11.0000.99432.190-0.051-0.0510.0000.0000.0000.000
77B77VAL 00.024-0.00132.6190.0040.0040.0000.0000.0000.000
78B78GLY 00.0020.01032.031-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0020.02029.970-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.045-0.05124.7660.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0130.02524.691-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0170.01518.2400.0050.0050.0000.0000.0000.000
83B83LEU 0-0.0090.00619.982-0.006-0.0060.0000.0000.0000.000
84B84SER 00.0410.01816.3780.0580.0580.0000.0000.0000.000
85B85GLY 00.0150.02014.490-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.036-0.02914.7830.0210.0210.0000.0000.0000.000
87B87ASN 0-0.040-0.03112.5230.0970.0970.0000.0000.0000.000
88B88LEU 0-0.028-0.00812.613-0.008-0.0080.0000.0000.0000.000
89B89ALA 00.0350.02110.961-0.022-0.0220.0000.0000.0000.000
90B90LYS 10.9180.9889.527-0.752-0.7520.0000.0000.0000.000
91B91HIS 00.016-0.00411.380-0.029-0.0290.0000.0000.0000.000
92B92CYS 0-0.032-0.01515.019-0.015-0.0150.0000.0000.0000.000
93B93LEU 0-0.0240.00718.086-0.012-0.0120.0000.0000.0000.000
94B94HIS 00.0470.00420.556-0.035-0.0350.0000.0000.0000.000
95B95VAL 00.007-0.00123.719-0.008-0.0080.0000.0000.0000.000
96B96VAL 0-0.0260.01326.3020.0000.0000.0000.0000.0000.000
97B97GLY 00.0300.01629.992-0.007-0.0070.0000.0000.0000.000
98B98PRO 00.0010.01531.7180.0050.0050.0000.0000.0000.000
99B99ASN 00.0030.00534.698-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0860.04236.548-0.001-0.0010.0000.0000.0000.000
101B101ASN 0-0.047-0.02137.467-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7650.87936.373-0.053-0.0530.0000.0000.0000.000
103B103GLY 00.0060.01241.1380.0000.0000.0000.0000.0000.000
104B104GLU -1-0.818-0.86336.9070.0470.0470.0000.0000.0000.000
105B105ASP -1-0.818-0.91540.6070.0130.0130.0000.0000.0000.000
106B106ILE 00.0330.00236.5540.0020.0020.0000.0000.0000.000
107B107GLN 0-0.031-0.01737.3640.0010.0010.0000.0000.0000.000
108B108LEU 00.0220.00635.705-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.036-0.02031.4060.0040.0040.0000.0000.0000.000
110B110LYS 10.8770.93131.8100.0150.0150.0000.0000.0000.000
111B111SER 00.0240.01331.386-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0250.00929.7080.0040.0040.0000.0000.0000.000
113B113TYR 00.026-0.01126.2690.0080.0080.0000.0000.0000.000
114B114GLU -1-0.877-0.91926.5560.0020.0020.0000.0000.0000.000
115B115ASN 0-0.023-0.00624.9230.0040.0040.0000.0000.0000.000
116B116PHE 00.028-0.01022.2300.0120.0120.0000.0000.0000.000
117B117ASN 0-0.038-0.01621.617-0.014-0.0140.0000.0000.0000.000
118B118GLN 0-0.0360.00822.113-0.012-0.0120.0000.0000.0000.000
119B119HIS 00.000-0.00117.1990.0290.0290.0000.0000.0000.000
120B120GLU -1-0.835-0.90015.542-0.129-0.1290.0000.0000.0000.000
121B121VAL 0-0.018-0.01412.753-0.040-0.0400.0000.0000.0000.000
122B122LEU 0-0.0070.02815.1680.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0080.01414.812-0.043-0.0430.0000.0000.0000.000
124B124ALA 00.005-0.01017.1780.0330.0330.0000.0000.0000.000
125B125PRO 00.0000.01520.781-0.017-0.0170.0000.0000.0000.000
126B126LEU 00.0090.00523.923-0.003-0.0030.0000.0000.0000.000
127B127LEU 00.0180.01925.9010.0080.0080.0000.0000.0000.000
128B128SER 00.014-0.02328.822-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0120.02230.051-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0340.01731.7700.0070.0070.0000.0000.0000.000
131B131ILE 00.000-0.00631.397-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.072-0.02430.7260.0000.0000.0000.0000.0000.000
133B133GLY 00.0280.01134.592-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.022-0.00234.815-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.811-0.90935.877-0.001-0.0010.0000.0000.0000.000
136B136PRO 0-0.028-0.02232.332-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.003-0.00632.726-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0680.04134.663-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.027-0.03030.735-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.019-0.01328.3830.0000.0000.0000.0000.0000.000
141B141ARG 10.7980.86130.7840.0320.0320.0000.0000.0000.000
142B142VAL 00.0220.01731.802-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0160.00526.4270.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0070.00528.369-0.005-0.0050.0000.0000.0000.000
145B145ASP -1-0.765-0.83329.573-0.042-0.0420.0000.0000.0000.000
146B146THR 0-0.115-0.06429.1430.0020.0020.0000.0000.0000.000
147B147VAL 0-0.055-0.01923.3990.0020.0020.0000.0000.0000.000
148B148ARG 10.9200.97025.4030.0300.0300.0000.0000.0000.000
149B149THR 0-0.0200.01719.854-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.027-0.00617.564-0.006-0.0060.0000.0000.0000.000
151B151VAL 00.0340.01218.3760.0240.0240.0000.0000.0000.000
152B152TYR 0-0.022-0.01016.541-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.0220.00019.5080.0320.0320.0000.0000.0000.000
154B154ALA 00.0030.00119.944-0.015-0.0150.0000.0000.0000.000
155B155VAL 0-0.022-0.01722.0300.0120.0120.0000.0000.0000.000
156B156PHE 00.0200.01224.610-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.794-0.89326.1630.0040.0040.0000.0000.0000.000
158B158LYS 10.8720.91629.0090.0330.0330.0000.0000.0000.000
159B159ASN 0-0.011-0.02530.099-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0080.00430.634-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.016-0.01625.538-0.004-0.0040.0000.0000.0000.000
162B162ASP -1-0.762-0.85829.917-0.042-0.0420.0000.0000.0000.000
163B163LYS 10.9501.01232.7410.0060.0060.0000.0000.0000.000
164B164LEU 0-0.0400.00329.503-0.002-0.0020.0000.0000.0000.000
165B165VAL 00.0380.00728.958-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.068-0.03731.843-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.012-0.02435.406-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.022-0.00231.2890.0020.0020.0000.0000.0000.000
169B169LEU -1-0.906-0.92934.115-0.053-0.0530.0000.0000.0000.000
170B213HOH 0-0.067-0.04611.8610.0390.0390.0000.0000.0000.000
171B218HOH 0-0.038-0.03138.8630.0010.0010.0000.0000.0000.000
172B226HOH 0-0.006-0.01333.7470.0010.0010.0000.0000.0000.000
173B235HOH 0-0.034-0.02911.435-0.028-0.0280.0000.0000.0000.000
174B236HOH 0-0.043-0.03427.6710.0000.0000.0000.0000.0000.000
175B241HOH 0-0.019-0.02122.7390.0040.0040.0000.0000.0000.000
176B248HOH 0-0.051-0.05133.9930.0020.0020.0000.0000.0000.000
177B253HOH 0-0.042-0.03034.8600.0010.0010.0000.0000.0000.000
178B255HOH 0-0.026-0.03513.752-0.001-0.0010.0000.0000.0000.000
179B256HOH 0-0.011-0.03419.495-0.014-0.0140.0000.0000.0000.000
180B259HOH 00.0160.00424.0570.0060.0060.0000.0000.0000.000
181B263HOH 0-0.010-0.01228.527-0.004-0.0040.0000.0000.0000.000
182B264HOH 0-0.035-0.02931.0940.0020.0020.0000.0000.0000.000
183B267HOH 0-0.069-0.05229.116-0.003-0.0030.0000.0000.0000.000
184B271HOH 0-0.031-0.02923.1010.0060.0060.0000.0000.0000.000
185B275HOH 0-0.033-0.03022.9150.0020.0020.0000.0000.0000.000
186B276HOH 00.0230.00029.600-0.002-0.0020.0000.0000.0000.000
187B279HOH 0-0.022-0.00827.461-0.002-0.0020.0000.0000.0000.000
188B281HOH 0-0.024-0.02328.3800.0010.0010.0000.0000.0000.000
189B282HOH 0-0.084-0.06237.037-0.001-0.0010.0000.0000.0000.000
190B297HOH 00.0220.01228.096-0.002-0.0020.0000.0000.0000.000
191B298HOH 0-0.018-0.03112.4990.0330.0330.0000.0000.0000.000
192B300HOH 00.001-0.00322.1760.0030.0030.0000.0000.0000.000
193B310HOH 0-0.019-0.01334.237-0.002-0.0020.0000.0000.0000.000
194B314HOH 0-0.015-0.00915.3610.0150.0150.0000.0000.0000.000
195B317HOH 00.008-0.01428.014-0.003-0.0030.0000.0000.0000.000
196B321HOH 00.0020.00331.6520.0030.0030.0000.0000.0000.000
197B324HOH 0-0.018-0.00229.5690.0030.0030.0000.0000.0000.000
198B326HOH 00.0350.02433.8140.0020.0020.0000.0000.0000.000
199B330HOH 00.002-0.01334.8000.0020.0020.0000.0000.0000.000
200B331HOH 00.000-0.01915.8020.0200.0200.0000.0000.0000.000
201B339HOH 00.0170.00830.0660.0020.0020.0000.0000.0000.000
202B341HOH 0-0.001-0.00535.4510.0000.0000.0000.0000.0000.000
203B345HOH 00.0150.00428.373-0.003-0.0030.0000.0000.0000.000
204B350HOH 00.006-0.00530.595-0.002-0.0020.0000.0000.0000.000
205B354HOH 0-0.015-0.02728.7000.0000.0000.0000.0000.0000.000
206B363HOH 0-0.029-0.02028.8970.0000.0000.0000.0000.0000.000