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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: 2J2YR

Calculation Name: 3RK6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RK6

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H074

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2638354.375712
FMO2-HF: Nuclear repulsion 2550508.297025
FMO2-HF: Total energy -87846.078688
FMO2-MP2: Total energy -88099.403216


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:78:THR)


Summations of interaction energy for fragment #1(A:78:THR)
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.
-58.542-71.27247.601-20.498-14.373-0.075
Interaction energy analysis for fragmet #1(A:78:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.061
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].
3A80SER0-0.008-0.0171.836-9.762-11.2168.860-3.661-3.7450.033
4A81GLU-1-0.847-0.8771.596-52.019-63.95238.737-16.641-10.163-0.108
5A82TYR0-0.006-0.0113.7100.4250.9590.005-0.159-0.3800.000
6A83VAL0-0.016-0.0165.4830.5860.5860.0000.0000.0000.000
7A84GLN0-0.056-0.0336.8800.1800.1800.0000.0000.0000.000
8A85ASP-1-0.840-0.9298.070-1.556-1.5560.0000.0000.0000.000
9A86PHE0-0.026-0.0109.7310.1900.1900.0000.0000.0000.000
10A87LEU0-0.033-0.01810.7600.1180.1180.0000.0000.0000.000
11A88ASN0-0.0120.00410.7090.2110.2110.0000.0000.0000.000
12A89HIS0-0.013-0.01513.8230.0620.0620.0000.0000.0000.000
13A90LEU0-0.015-0.01415.6730.0680.0680.0000.0000.0000.000
14A91THR0-0.091-0.06816.6410.0640.0640.0000.0000.0000.000
15A92GLU-1-0.989-0.99017.211-0.401-0.4010.0000.0000.0000.000
16A93GLN0-0.047-0.02218.8420.0470.0470.0000.0000.0000.000
17A94PRO0-0.011-0.00521.0480.0040.0040.0000.0000.0000.000
18A95GLY0-0.031-0.01822.2820.0120.0120.0000.0000.0000.000
19A96SER00.0110.01318.1750.0230.0230.0000.0000.0000.000
20A97PHE00.0460.00419.325-0.003-0.0030.0000.0000.0000.000
21A98GLU-1-0.791-0.87720.351-0.109-0.1090.0000.0000.0000.000
22A99THR0-0.055-0.01820.7700.0150.0150.0000.0000.0000.000
23A100GLU-1-0.840-0.91115.950-0.376-0.3760.0000.0000.0000.000
24A101ILE0-0.033-0.01116.530-0.021-0.0210.0000.0000.0000.000
25A102GLU-1-0.821-0.88716.974-0.062-0.0620.0000.0000.0000.000
26A103GLN0-0.0060.00213.8540.0130.0130.0000.0000.0000.000
27A104PHE00.0400.0359.8060.0240.0240.0000.0000.0000.000
28A105ALA00.014-0.01312.499-0.001-0.0010.0000.0000.0000.000
29A106GLU-1-0.885-0.92814.5840.0270.0270.0000.0000.0000.000
30A107THR0-0.029-0.0158.7240.0080.0080.0000.0000.0000.000
31A108LEU0-0.003-0.0028.8890.0610.0610.0000.0000.0000.000
32A109ASN00.0170.01011.1410.1190.1190.0000.0000.0000.000
33A110GLY0-0.0240.00912.0870.0460.0460.0000.0000.0000.000
34A111CYS0-0.108-0.0646.8690.0020.0020.0000.0000.0000.000
35A112VAL0-0.0110.0068.4160.1410.1410.0000.0000.0000.000
36A113THR0-0.004-0.01010.239-0.022-0.0220.0000.0000.0000.000
37A114THR00.011-0.00110.824-0.021-0.0210.0000.0000.0000.000
38A115ASP-1-0.801-0.89112.6650.3000.3000.0000.0000.0000.000
39A116ASP-1-0.943-0.9629.6000.7730.7730.0000.0000.0000.000
40A117ALA00.0730.0408.1890.0560.0560.0000.0000.0000.000
41A118LEU0-0.022-0.0179.132-0.034-0.0340.0000.0000.0000.000
42A119GLN0-0.035-0.02412.092-0.027-0.0270.0000.0000.0000.000
43A120GLU-1-0.821-0.9224.2942.7462.869-0.001-0.037-0.0850.000
44A121LEU00.0040.0029.038-0.008-0.0080.0000.0000.0000.000
45A122VAL0-0.044-0.02410.070-0.081-0.0810.0000.0000.0000.000
46A123GLU-1-0.784-0.86811.2220.2750.2750.0000.0000.0000.000
47A124LEU0-0.0140.0006.385-0.092-0.0920.0000.0000.0000.000
48A125ILE00.0340.01010.758-0.129-0.1290.0000.0000.0000.000
49A126TYR0-0.044-0.03713.647-0.067-0.0670.0000.0000.0000.000
50A127GLN00.002-0.00313.163-0.102-0.1020.0000.0000.0000.000
51A128GLN00.0410.06113.533-0.021-0.0210.0000.0000.0000.000
52A129ALA0-0.012-0.01215.349-0.035-0.0350.0000.0000.0000.000
53A130THR0-0.071-0.03818.222-0.012-0.0120.0000.0000.0000.000
54A131SER0-0.054-0.04517.2090.0040.0040.0000.0000.0000.000
55A132ILE00.0010.01416.299-0.013-0.0130.0000.0000.0000.000
56A133PRO00.003-0.01319.5620.0090.0090.0000.0000.0000.000
57A134ASN0-0.057-0.03922.742-0.003-0.0030.0000.0000.0000.000
58A135PHE00.0900.05316.5260.0070.0070.0000.0000.0000.000
59A136SER0-0.032-0.00621.1810.0040.0040.0000.0000.0000.000
60A137TYR00.0420.02523.2250.0040.0040.0000.0000.0000.000
61A138MET0-0.0030.02218.9970.0100.0100.0000.0000.0000.000
62A139GLY00.0680.02918.6030.0000.0000.0000.0000.0000.000
63A140ALA0-0.0080.00219.6430.0150.0150.0000.0000.0000.000
64A141ARG10.7580.85622.4110.0950.0950.0000.0000.0000.000
65A142LEU00.0310.01614.8160.0050.0050.0000.0000.0000.000
66A143CYS0-0.040-0.02618.5270.0200.0200.0000.0000.0000.000
67A144ASN0-0.005-0.02019.5250.0200.0200.0000.0000.0000.000
68A145TYR0-0.012-0.02518.4440.0080.0080.0000.0000.0000.000
69A146LEU00.0410.01014.7000.0040.0040.0000.0000.0000.000
70A147SER0-0.106-0.06518.5260.0170.0170.0000.0000.0000.000
71A148HIS0-0.059-0.03920.7220.0160.0160.0000.0000.0000.000
72A149HIS10.8420.92719.3630.0280.0280.0000.0000.0000.000
73A150LEU0-0.0140.01413.965-0.003-0.0030.0000.0000.0000.000
74A151THR0-0.035-0.03617.0500.0180.0180.0000.0000.0000.000
75A152ILE0-0.0330.00914.3960.0030.0030.0000.0000.0000.000
76A153SER0-0.020-0.03017.604-0.012-0.0120.0000.0000.0000.000
77A154PRO0-0.0160.00016.297-0.008-0.0080.0000.0000.0000.000
78A155GLN0-0.020-0.01519.084-0.013-0.0130.0000.0000.0000.000
79A156SER0-0.076-0.06118.234-0.013-0.0130.0000.0000.0000.000
80A157GLY00.0070.00320.348-0.011-0.0110.0000.0000.0000.000
81A158ASN00.0300.00718.6700.0170.0170.0000.0000.0000.000
82A159PHE00.0920.03714.2800.0000.0000.0000.0000.0000.000
83A160ARG10.8490.91518.025-0.060-0.0600.0000.0000.0000.000
84A161GLN0-0.004-0.00221.5840.0030.0030.0000.0000.0000.000
85A162LEU00.0260.02015.623-0.005-0.0050.0000.0000.0000.000
86A163LEU00.0590.02918.0440.0050.0050.0000.0000.0000.000
87A164LEU0-0.017-0.01219.447-0.009-0.0090.0000.0000.0000.000
88A165GLN0-0.017-0.00320.8510.0000.0000.0000.0000.0000.000
89A166ARG10.8470.91016.464-0.245-0.2450.0000.0000.0000.000
90A167CYS0-0.058-0.03320.339-0.016-0.0160.0000.0000.0000.000
91A168ARG10.8220.89423.247-0.097-0.0970.0000.0000.0000.000
92A169THR0-0.0110.00620.8060.0000.0000.0000.0000.0000.000
93A170GLU-1-0.738-0.85420.8740.1340.1340.0000.0000.0000.000
94A171TYR0-0.050-0.01524.689-0.015-0.0150.0000.0000.0000.000
95A172GLU-1-0.896-0.94427.5380.0670.0670.0000.0000.0000.000
96A173VAL0-0.0090.00026.760-0.004-0.0040.0000.0000.0000.000
97A174LYS10.8470.91529.742-0.051-0.0510.0000.0000.0000.000
98A175ASP-1-0.829-0.90130.9930.0350.0350.0000.0000.0000.000
99A176GLN0-0.021-0.01431.460-0.009-0.0090.0000.0000.0000.000
100A177ALA0-0.0010.00128.331-0.005-0.0050.0000.0000.0000.000
101A178ALA00.0090.01130.139-0.006-0.0060.0000.0000.0000.000
102A179LYS10.8170.89833.168-0.029-0.0290.0000.0000.0000.000
103A180GLY00.0350.02931.846-0.003-0.0030.0000.0000.0000.000
104A181ASP-1-0.789-0.87930.682-0.012-0.0120.0000.0000.0000.000
105A182GLU-1-0.831-0.89931.574-0.028-0.0280.0000.0000.0000.000
106A183VAL0-0.054-0.02726.978-0.004-0.0040.0000.0000.0000.000
107A184THR00.001-0.03826.7740.0030.0030.0000.0000.0000.000
108A185ARG10.7780.85626.9600.0070.0070.0000.0000.0000.000
109A186LYS10.7920.88326.3340.0350.0350.0000.0000.0000.000
110A187ARG10.8610.93517.654-0.100-0.1000.0000.0000.0000.000
111A188PHE00.0390.01524.1580.0060.0060.0000.0000.0000.000
112A189HIS10.8430.89526.8150.0020.0020.0000.0000.0000.000
113A190ALA00.0270.03622.759-0.002-0.0020.0000.0000.0000.000
114A191PHE00.0530.01522.780-0.001-0.0010.0000.0000.0000.000
115A192VAL0-0.029-0.01324.3370.0010.0010.0000.0000.0000.000
116A193LEU0-0.022-0.01827.045-0.001-0.0010.0000.0000.0000.000
117A194PHE0-0.0010.01019.741-0.004-0.0040.0000.0000.0000.000
118A195LEU00.005-0.00424.0010.0020.0020.0000.0000.0000.000
119A196GLY00.002-0.00326.4570.0000.0000.0000.0000.0000.000
120A197GLU-1-0.830-0.94125.808-0.024-0.0240.0000.0000.0000.000
121A198LEU0-0.020-0.00422.467-0.002-0.0020.0000.0000.0000.000
122A199TYR0-0.053-0.04825.9600.0020.0020.0000.0000.0000.000
123A200LEU0-0.037-0.01829.5350.0000.0000.0000.0000.0000.000
124A201ASN0-0.062-0.03626.420-0.005-0.0050.0000.0000.0000.000
125A202LEU0-0.0200.00423.3460.0000.0000.0000.0000.0000.000
126A203GLU-1-0.843-0.88326.5580.0090.0090.0000.0000.0000.000
127A204ILE0-0.040-0.02627.2180.0090.0090.0000.0000.0000.000
128A205LYS10.8980.94529.397-0.041-0.0410.0000.0000.0000.000
129A206GLY00.0540.02231.7700.0060.0060.0000.0000.0000.000
130A207THR00.006-0.01134.444-0.001-0.0010.0000.0000.0000.000
131A208ASN00.0160.01136.5410.0010.0010.0000.0000.0000.000
132A209GLY0-0.018-0.00635.902-0.003-0.0030.0000.0000.0000.000
133A210GLN00.0140.01536.036-0.002-0.0020.0000.0000.0000.000
134A211VAL00.0240.02232.6040.0040.0040.0000.0000.0000.000
135A212THR0-0.019-0.01232.907-0.002-0.0020.0000.0000.0000.000
136A213ARG10.9210.96130.870-0.011-0.0110.0000.0000.0000.000
137A214ALA00.0470.01627.8190.0030.0030.0000.0000.0000.000
138A215ASP-1-0.820-0.90729.9220.0390.0390.0000.0000.0000.000
139A216ILE0-0.0020.00227.600-0.002-0.0020.0000.0000.0000.000
140A217LEU0-0.001-0.00325.7850.0020.0020.0000.0000.0000.000
141A218GLN0-0.0050.01529.897-0.007-0.0070.0000.0000.0000.000
142A219VAL00.007-0.00433.646-0.003-0.0030.0000.0000.0000.000
143A220GLY00.0030.00230.867-0.001-0.0010.0000.0000.0000.000
144A221LEU00.014-0.00230.209-0.002-0.0020.0000.0000.0000.000
145A222ARG10.7250.83933.320-0.026-0.0260.0000.0000.0000.000
146A223GLU-1-0.820-0.91034.4810.0300.0300.0000.0000.0000.000
147A224LEU0-0.034-0.01729.256-0.001-0.0010.0000.0000.0000.000
148A225LEU0-0.003-0.00233.597-0.004-0.0040.0000.0000.0000.000
149A226ASN0-0.017-0.01336.626-0.006-0.0060.0000.0000.0000.000
150A227ALA00.0080.02734.737-0.002-0.0020.0000.0000.0000.000
151A228LEU0-0.051-0.01732.698-0.003-0.0030.0000.0000.0000.000
152A229PHE00.017-0.01036.601-0.003-0.0030.0000.0000.0000.000
153A230SER0-0.043-0.03239.669-0.001-0.0010.0000.0000.0000.000
154A231ASN0-0.032-0.00537.2730.0010.0010.0000.0000.0000.000
155A232PRO00.0460.04638.561-0.002-0.0020.0000.0000.0000.000
156A233MET00.0340.00837.542-0.002-0.0020.0000.0000.0000.000
157A234ASP-1-0.720-0.84838.465-0.014-0.0140.0000.0000.0000.000
158A235ASP-1-0.777-0.86233.435-0.009-0.0090.0000.0000.0000.000
159A236ASN0-0.035-0.03633.9710.0020.0020.0000.0000.0000.000
160A237LEU00.0110.02035.4850.0010.0010.0000.0000.0000.000
161A238ILE00.0190.00134.6130.0000.0000.0000.0000.0000.000
162A239CYS0-0.063-0.01831.374-0.002-0.0020.0000.0000.0000.000
163A240ALA00.0410.02233.7010.0010.0010.0000.0000.0000.000
164A241VAL00.018-0.00336.1740.0000.0000.0000.0000.0000.000
165A242LYS10.9000.94931.2450.0280.0280.0000.0000.0000.000
166A243LEU00.0490.03531.357-0.001-0.0010.0000.0000.0000.000
167A244LEU00.0300.02334.0580.0010.0010.0000.0000.0000.000
168A245LYS10.8930.94536.9040.0200.0200.0000.0000.0000.000
169A246LEU0-0.0370.00530.065-0.001-0.0010.0000.0000.0000.000
170A247THR0-0.006-0.03032.4800.0020.0020.0000.0000.0000.000
171A248GLY00.0160.01435.5540.0030.0030.0000.0000.0000.000
172A249SER00.0200.01039.1260.0020.0020.0000.0000.0000.000
173A250VAL0-0.008-0.00135.6330.0010.0010.0000.0000.0000.000
174A251LEU0-0.0050.00035.2120.0030.0030.0000.0000.0000.000
175A252GLU-1-0.815-0.89538.8600.0030.0030.0000.0000.0000.000
176A253ASP-1-0.843-0.92642.0910.0060.0060.0000.0000.0000.000
177A254ALA0-0.023-0.00238.8710.0010.0010.0000.0000.0000.000
178A255TRP0-0.034-0.03538.0260.0010.0010.0000.0000.0000.000
179A256LYS10.9040.95142.607-0.005-0.0050.0000.0000.0000.000
180A257GLU-1-0.863-0.90242.2030.0240.0240.0000.0000.0000.000
181A258LYS10.7690.86141.294-0.026-0.0260.0000.0000.0000.000
182A259GLY0-0.0110.00044.9740.0010.0010.0000.0000.0000.000
183A260LYS10.7830.88741.031-0.027-0.0270.0000.0000.0000.000
184A261MET00.0550.02245.622-0.001-0.0010.0000.0000.0000.000
185A262ASP-1-0.780-0.86541.5360.0230.0230.0000.0000.0000.000
186A263MET00.0110.00542.8900.0000.0000.0000.0000.0000.000
187A264GLU-1-0.897-0.94644.8060.0080.0080.0000.0000.0000.000
188A265GLU-1-0.809-0.87644.8420.0200.0200.0000.0000.0000.000
189A266ILE0-0.063-0.03340.069-0.001-0.0010.0000.0000.0000.000
190A267ILE00.0120.01343.843-0.002-0.0020.0000.0000.0000.000
191A268GLN00.0090.01546.859-0.001-0.0010.0000.0000.0000.000
192A269ARG10.9130.95542.298-0.018-0.0180.0000.0000.0000.000
193A270ILE0-0.020-0.00842.541-0.001-0.0010.0000.0000.0000.000
194A271GLU-1-0.904-0.95345.4680.0000.0000.0000.0000.0000.000
195A272ASN0-0.033-0.03448.008-0.001-0.0010.0000.0000.0000.000
196A273VAL0-0.015-0.00243.103-0.001-0.0010.0000.0000.0000.000
197A274VAL0-0.008-0.02146.442-0.002-0.0020.0000.0000.0000.000
198A275LEU0-0.042-0.00348.758-0.001-0.0010.0000.0000.0000.000
199A276ASP-1-0.865-0.93149.3850.0020.0020.0000.0000.0000.000
200A277ALA0-0.043-0.00845.1430.0000.0000.0000.0000.0000.000
201A278ASN0-0.051-0.02946.564-0.001-0.0010.0000.0000.0000.000
202A279CYS0-0.051-0.00743.1750.0000.0000.0000.0000.0000.000
203A280SER00.012-0.02443.223-0.001-0.0010.0000.0000.0000.000
204A281ARG10.9590.96545.3470.0160.0160.0000.0000.0000.000
205A282ASP-1-0.874-0.94742.797-0.022-0.0220.0000.0000.0000.000
206A283VAL00.0210.01040.9350.0000.0000.0000.0000.0000.000
207A284LYS10.8340.91643.3290.0070.0070.0000.0000.0000.000
208A285GLN00.0120.01146.5020.0020.0020.0000.0000.0000.000
209A286MET0-0.092-0.05940.4020.0000.0000.0000.0000.0000.000
210A287LEU00.0080.00941.6310.0010.0010.0000.0000.0000.000
211A288LEU00.0460.02244.5810.0010.0010.0000.0000.0000.000
212A289LYS10.7370.84245.4870.0140.0140.0000.0000.0000.000
213A290LEU0-0.037-0.01540.2910.0000.0000.0000.0000.0000.000
214A291VAL00.0260.01544.7580.0010.0010.0000.0000.0000.000
215A292GLU-1-0.836-0.89848.015-0.011-0.0110.0000.0000.0000.000
216A293LEU0-0.074-0.03344.0530.0000.0000.0000.0000.0000.000
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