Manual

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: JLLV9

Calculation Name: 4RZA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZA

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAV1

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2121353.093834
FMO2-HF: Nuclear repulsion 2046470.118177
FMO2-HF: Total energy -74882.975656
FMO2-MP2: Total energy -75098.221477


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-29.726-33.31923.276-9.227-10.4550.035
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.022
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].
3A3ASN00.0400.0422.165-5.237-4.1888.786-4.084-5.751-0.003
4A4ARG10.8880.9301.896-22.965-27.78514.492-5.127-4.5440.038
5A5THR00.017-0.0054.923-0.700-0.667-0.001-0.009-0.0230.000
6A6VAL00.0000.0248.2830.3250.3250.0000.0000.0000.000
7A7LYS10.8990.9307.316-0.730-0.7300.0000.0000.0000.000
8A8ASP-1-0.857-0.92510.8630.3030.3030.0000.0000.0000.000
9A9ALA0-0.0030.02313.278-0.038-0.0380.0000.0000.0000.000
10A10HIS10.8450.92415.000-0.261-0.2610.0000.0000.0000.000
11A11SER0-0.035-0.02416.6010.0380.0380.0000.0000.0000.000
12A12ILE00.0140.02317.568-0.045-0.0450.0000.0000.0000.000
13A13HIS0-0.020-0.01419.2960.0280.0280.0000.0000.0000.000
14A14GLY0-0.0090.00421.085-0.002-0.0020.0000.0000.0000.000
15A15THR0-0.036-0.01716.5930.0580.0580.0000.0000.0000.000
16A16ASN00.0310.0309.505-0.110-0.1100.0000.0000.0000.000
17A17PRO00.1000.05213.3780.0010.0010.0000.0000.0000.000
18A18GLN00.0280.0017.5480.0070.0070.0000.0000.0000.000
19A19TYR0-0.131-0.0819.8550.1130.1130.0000.0000.0000.000
20A20LEU00.0490.04214.295-0.065-0.0650.0000.0000.0000.000
21A21VAL0-0.0010.01813.923-0.064-0.0640.0000.0000.0000.000
22A22GLU-1-0.758-0.88714.4210.6040.6040.0000.0000.0000.000
23A23LYS10.9520.97110.774-0.400-0.4000.0000.0000.0000.000
24A24ILE0-0.028-0.02711.4810.0970.0970.0000.0000.0000.000
25A25ILE00.0140.01713.366-0.011-0.0110.0000.0000.0000.000
26A26ARG10.8770.9409.482-1.185-1.1850.0000.0000.0000.000
27A27THR0-0.057-0.0238.1650.1800.1800.0000.0000.0000.000
28A28ARG10.8540.8999.432-0.296-0.2960.0000.0000.0000.000
29A29ILE00.0080.00910.535-0.085-0.0850.0000.0000.0000.000
30A30TYR0-0.035-0.0285.8370.1460.291-0.001-0.007-0.1370.000
31A31GLU-1-0.815-0.8827.9540.2980.2980.0000.0000.0000.000
32A32SER0-0.042-0.0149.995-0.255-0.2550.0000.0000.0000.000
33A33LYS10.8210.87112.0030.0550.0550.0000.0000.0000.000
34A34TYR00.040-0.00313.934-0.019-0.0190.0000.0000.0000.000
35A35TRP00.021-0.0155.983-0.049-0.0490.0000.0000.0000.000
36A36LYS10.8190.8948.807-0.318-0.3180.0000.0000.0000.000
37A37GLU-1-0.830-0.88110.464-0.206-0.2060.0000.0000.0000.000
38A38GLU-1-0.820-0.89213.797-0.034-0.0340.0000.0000.0000.000
39A39CYS0-0.039-0.00411.1360.0380.0380.0000.0000.0000.000
40A40PHE00.0000.0046.976-0.086-0.0860.0000.0000.0000.000
41A41GLY0-0.042-0.0249.5250.0370.0370.0000.0000.0000.000
42A42LEU0-0.033-0.00211.4810.0400.0400.0000.0000.0000.000
43A43THR00.0540.01813.1000.0310.0310.0000.0000.0000.000
44A44ALA00.0450.00515.3640.0250.0250.0000.0000.0000.000
45A45GLU-1-0.899-0.94017.723-0.008-0.0080.0000.0000.0000.000
46A46LEU00.0070.00416.8220.0040.0040.0000.0000.0000.000
47A47VAL0-0.025-0.01916.2080.0100.0100.0000.0000.0000.000
48A48VAL00.0320.01418.6230.0150.0150.0000.0000.0000.000
49A49ASP-1-0.878-0.94021.039-0.016-0.0160.0000.0000.0000.000
50A50LYS10.7910.87417.7700.0170.0170.0000.0000.0000.000
51A51ALA0-0.005-0.01020.5820.0170.0170.0000.0000.0000.000
52A52MET0-0.030-0.01122.1910.0050.0050.0000.0000.0000.000
53A53GLU-1-0.831-0.88322.6230.0030.0030.0000.0000.0000.000
54A54LEU0-0.066-0.00620.7260.0070.0070.0000.0000.0000.000
55A55ARG10.8240.88824.405-0.043-0.0430.0000.0000.0000.000
56A56PHE0-0.073-0.04223.432-0.007-0.0070.0000.0000.0000.000
57A57VAL00.0360.03624.7340.0090.0090.0000.0000.0000.000
58A58GLY00.0930.02924.187-0.013-0.0130.0000.0000.0000.000
59A59GLY00.0210.01820.8040.0180.0180.0000.0000.0000.000
60A60VAL0-0.068-0.03217.8430.0180.0180.0000.0000.0000.000
61A61TYR00.0310.01720.662-0.019-0.0190.0000.0000.0000.000
62A62GLY00.0460.02321.9140.0070.0070.0000.0000.0000.000
63A63GLY0-0.018-0.02022.9030.0160.0160.0000.0000.0000.000
64A64ASN0-0.017-0.01116.5620.0160.0160.0000.0000.0000.000
65A65ILE0-0.014-0.00316.6550.0270.0270.0000.0000.0000.000
66A66LYS10.9130.95617.506-0.137-0.1370.0000.0000.0000.000
67A67PRO00.0330.01814.396-0.026-0.0260.0000.0000.0000.000
68A68THR0-0.016-0.00317.709-0.027-0.0270.0000.0000.0000.000
69A69PRO00.0360.01117.7970.0400.0400.0000.0000.0000.000
70A70PHE00.0760.03817.8860.0210.0210.0000.0000.0000.000
71A71LEU00.0040.02416.1550.0220.0220.0000.0000.0000.000
72A72CYS0-0.072-0.03613.8350.0780.0780.0000.0000.0000.000
73A73LEU00.0500.02013.6530.0580.0580.0000.0000.0000.000
74A74THR00.009-0.00515.7110.0040.0040.0000.0000.0000.000
75A75LEU0-0.031-0.02010.1800.0250.0250.0000.0000.0000.000
76A76LYS10.8340.9208.064-0.078-0.0780.0000.0000.0000.000
77A77MET00.0280.02112.294-0.017-0.0170.0000.0000.0000.000
78A78LEU0-0.038-0.01713.9840.0110.0110.0000.0000.0000.000
79A79GLN0-0.096-0.0526.1400.1730.1730.0000.0000.0000.000
80A80ILE0-0.008-0.02910.9330.0420.0420.0000.0000.0000.000
81A81GLN0-0.046-0.00913.106-0.062-0.0620.0000.0000.0000.000
82A82PRO00.0430.02016.388-0.023-0.0230.0000.0000.0000.000
83A83GLU-1-0.850-0.90419.0710.1290.1290.0000.0000.0000.000
84A84LYS10.8810.90522.309-0.188-0.1880.0000.0000.0000.000
85A85ASP-1-0.895-0.95625.0200.1030.1030.0000.0000.0000.000
86A86ILE00.1110.06721.895-0.006-0.0060.0000.0000.0000.000
87A87ILE0-0.046-0.02021.0300.0010.0010.0000.0000.0000.000
88A88VAL0-0.051-0.02824.920-0.004-0.0040.0000.0000.0000.000
89A89GLU-1-0.901-0.95127.4940.0550.0550.0000.0000.0000.000
90A90PHE0-0.052-0.04421.183-0.002-0.0020.0000.0000.0000.000
91A91ILE0-0.060-0.02526.954-0.003-0.0030.0000.0000.0000.000
92A92LYS10.8920.94429.380-0.104-0.1040.0000.0000.0000.000
93A93ASN0-0.0020.00630.185-0.005-0.0050.0000.0000.0000.000
94A94GLU-1-0.821-0.89032.1700.0700.0700.0000.0000.0000.000
95A95ASP-1-0.878-0.92132.8550.0450.0450.0000.0000.0000.000
96A96PHE00.0170.00128.4600.0010.0010.0000.0000.0000.000
97A97LYS10.8950.94129.312-0.059-0.0590.0000.0000.0000.000
98A98TYR0-0.006-0.02326.0320.0070.0070.0000.0000.0000.000
99A99VAL00.0450.04024.8010.0160.0160.0000.0000.0000.000
100A100ARG10.8000.88925.637-0.068-0.0680.0000.0000.0000.000
101A101MET0-0.062-0.01926.6530.0120.0120.0000.0000.0000.000
102A102LEU0-0.0030.00119.1910.0160.0160.0000.0000.0000.000
103A103GLY00.0310.01122.7040.0230.0230.0000.0000.0000.000
104A104ALA00.0100.00024.4770.0130.0130.0000.0000.0000.000
105A105LEU00.0140.00521.3990.0100.0100.0000.0000.0000.000
106A106TYR00.0660.01417.3450.0390.0390.0000.0000.0000.000
107A107MET00.0250.02821.8110.0210.0210.0000.0000.0000.000
108A108ARG10.8170.89824.985-0.219-0.2190.0000.0000.0000.000
109A109LEU0-0.066-0.03519.2820.0100.0100.0000.0000.0000.000
110A110THR0-0.071-0.05919.5950.0220.0220.0000.0000.0000.000
111A111GLY00.0270.03522.376-0.005-0.0050.0000.0000.0000.000
112A112THR0-0.038-0.04726.0710.0040.0040.0000.0000.0000.000
113A113ALA00.000-0.01429.011-0.003-0.0030.0000.0000.0000.000
114A114ILE00.0220.01132.012-0.007-0.0070.0000.0000.0000.000
115A115ASP-1-0.794-0.86528.8640.1680.1680.0000.0000.0000.000
116A116CYS0-0.023-0.00729.285-0.002-0.0020.0000.0000.0000.000
117A117TYR00.0080.00131.372-0.004-0.0040.0000.0000.0000.000
118A118LYS10.9180.96833.418-0.119-0.1190.0000.0000.0000.000
119A119TYR0-0.025-0.02330.550-0.010-0.0100.0000.0000.0000.000
120A120LEU00.0110.00928.702-0.005-0.0050.0000.0000.0000.000
121A121GLU-1-0.846-0.91632.7750.1090.1090.0000.0000.0000.000
122A122PRO0-0.045-0.02735.600-0.006-0.0060.0000.0000.0000.000
123A123LEU0-0.0140.00031.856-0.006-0.0060.0000.0000.0000.000
124A124TYR0-0.038-0.05436.0900.0000.0000.0000.0000.0000.000
125A125ASN0-0.061-0.03238.590-0.007-0.0070.0000.0000.0000.000
126A126ASP-1-0.756-0.83735.2510.0740.0740.0000.0000.0000.000
127A127TYR0-0.0140.00037.2370.0020.0020.0000.0000.0000.000
128A128ARG10.7290.83434.533-0.072-0.0720.0000.0000.0000.000
129A129LYS10.8990.94135.983-0.057-0.0570.0000.0000.0000.000
130A130ILE0-0.028-0.00930.239-0.004-0.0040.0000.0000.0000.000
131A131LYS10.9540.98330.268-0.063-0.0630.0000.0000.0000.000
132A132SER00.0270.01128.3800.0120.0120.0000.0000.0000.000
133A133GLN0-0.055-0.03824.3490.0030.0030.0000.0000.0000.000
134A134ASN00.0070.00425.9540.0230.0230.0000.0000.0000.000
135A135ARG10.8570.88822.510-0.224-0.2240.0000.0000.0000.000
136A136ASN0-0.045-0.04626.1400.0070.0070.0000.0000.0000.000
137A137GLY0-0.0030.00126.446-0.006-0.0060.0000.0000.0000.000
138A138GLU-1-0.889-0.91127.3860.0670.0670.0000.0000.0000.000
139A139PHE0-0.063-0.05026.6770.0080.0080.0000.0000.0000.000
140A140GLU-1-0.813-0.88231.2000.0950.0950.0000.0000.0000.000
141A141LEU0-0.091-0.06332.8090.0010.0010.0000.0000.0000.000
142A142MET00.0190.03831.5620.0010.0010.0000.0000.0000.000
143A143HIS00.014-0.00235.341-0.009-0.0090.0000.0000.0000.000
144A144VAL00.011-0.00332.2290.0080.0080.0000.0000.0000.000
145A145ASP-1-0.813-0.92733.6240.0930.0930.0000.0000.0000.000
146A146GLU-1-0.831-0.90835.3850.0960.0960.0000.0000.0000.000
147A147PHE00.018-0.00425.6930.0110.0110.0000.0000.0000.000
148A148ILE0-0.022-0.01730.8520.0140.0140.0000.0000.0000.000
149A149ASP-1-0.759-0.83932.6020.1200.1200.0000.0000.0000.000
150A150GLU-1-0.917-0.96230.4130.1550.1550.0000.0000.0000.000
151A151LEU0-0.042-0.02826.1620.0140.0140.0000.0000.0000.000
152A152LEU0-0.034-0.01429.5600.0130.0130.0000.0000.0000.000
153A153HIS10.7530.85832.453-0.124-0.1240.0000.0000.0000.000
154A154SER00.0210.02530.130-0.006-0.0060.0000.0000.0000.000
155A155GLU-1-0.956-0.97728.2320.1910.1910.0000.0000.0000.000
156A156ARG10.8750.92623.627-0.214-0.2140.0000.0000.0000.000
157A157VAL00.1140.07124.647-0.017-0.0170.0000.0000.0000.000
158A158CYS0-0.073-0.01021.8400.0170.0170.0000.0000.0000.000
159A159ASP-1-0.807-0.89820.7220.2740.2740.0000.0000.0000.000
160A160ILE0-0.0240.00318.3670.0270.0270.0000.0000.0000.000
161A161ILE0-0.017-0.01320.818-0.034-0.0340.0000.0000.0000.000
162A162LEU00.0090.01822.3660.0310.0310.0000.0000.0000.000
163A163PRO00.0060.02122.610-0.014-0.0140.0000.0000.0000.000
164A164ARG10.9430.95924.883-0.235-0.2350.0000.0000.0000.000
165A165LEU00.0670.03927.6690.0080.0080.0000.0000.0000.000
166A166GLN00.0110.01228.390-0.024-0.0240.0000.0000.0000.000
167A167LYS10.9940.98230.202-0.140-0.1400.0000.0000.0000.000
168A168ARG10.9040.95732.783-0.155-0.1550.0000.0000.0000.000
169A169TYR00.0580.01332.2850.0120.0120.0000.0000.0000.000
170A170VAL0-0.052-0.03227.636-0.001-0.0010.0000.0000.0000.000
171A171LEU00.0320.02827.8160.0020.0020.0000.0000.0000.000
172A172GLU-1-0.911-0.97222.1350.3400.3400.0000.0000.0000.000
173A173GLU-1-0.815-0.89021.6960.2730.2730.0000.0000.0000.000
174A174ALA0-0.024-0.02524.514-0.014-0.0140.0000.0000.0000.000
175A175GLU-1-0.909-0.93824.9200.1140.1140.0000.0000.0000.000
176A176GLN0-0.115-0.07124.355-0.016-0.0160.0000.0000.0000.000
177A177LEU00.0200.00628.222-0.006-0.0060.0000.0000.0000.000
178A178GLU-1-0.919-0.95831.8280.1180.1180.0000.0000.0000.000
179A179PRO0-0.077-0.01733.567-0.007-0.0070.0000.0000.0000.000