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: MV35Z

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 OptH
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 -2630012.520674
FMO2-HF: Nuclear repulsion 2542168.485994
FMO2-HF: Total energy -87844.034679
FMO2-MP2: Total energy -88097.381491


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.
-35.515-25.3569.146-9.008-10.298-0.036
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 : -0.006 / q_NPA : -0.017
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].
3A80SER00.014-0.0052.871-0.5551.7470.188-1.099-1.3910.002
4A81GLU-1-0.890-0.9362.052-35.548-28.5128.933-7.755-8.215-0.039
5A82TYR00.0370.0233.619-0.4150.2320.027-0.143-0.5310.001
6A83VAL0-0.005-0.0105.3070.3610.475-0.001-0.009-0.1040.000
7A84GLN0-0.057-0.0266.8630.0830.0830.0000.0000.0000.000
8A85ASP-1-0.900-0.9457.647-1.822-1.8220.0000.0000.0000.000
9A86PHE0-0.005-0.0099.5620.1810.1810.0000.0000.0000.000
10A87LEU0-0.014-0.01510.9260.0860.0860.0000.0000.0000.000
11A88ASN00.0060.01711.1270.1460.1460.0000.0000.0000.000
12A89HIS00.008-0.00613.6880.0140.0140.0000.0000.0000.000
13A90LEU0-0.034-0.01115.5620.0580.0580.0000.0000.0000.000
14A91THR0-0.106-0.08716.5270.0470.0470.0000.0000.0000.000
15A92GLU-1-0.996-0.99017.675-0.331-0.3310.0000.0000.0000.000
16A93GLN0-0.034-0.01319.6030.0360.0360.0000.0000.0000.000
17A94PRO00.0060.00420.8610.0050.0050.0000.0000.0000.000
18A95GLY0-0.058-0.04222.6810.0120.0120.0000.0000.0000.000
19A96SER00.0160.01919.1790.0070.0070.0000.0000.0000.000
20A97PHE00.0330.00019.5780.0000.0000.0000.0000.0000.000
21A98GLU-1-0.871-0.92620.438-0.082-0.0820.0000.0000.0000.000
22A99THR0-0.014-0.01520.9290.0110.0110.0000.0000.0000.000
23A100GLU-1-0.852-0.90315.855-0.309-0.3090.0000.0000.0000.000
24A101ILE0-0.047-0.00916.282-0.013-0.0130.0000.0000.0000.000
25A102GLU-1-0.952-0.98116.870-0.039-0.0390.0000.0000.0000.000
26A103GLN00.0160.00613.5470.0300.0300.0000.0000.0000.000
27A104PHE00.0530.0379.8250.0390.0390.0000.0000.0000.000
28A105ALA0-0.011-0.02012.6110.0200.0200.0000.0000.0000.000
29A106GLU-1-0.972-0.97314.6890.1030.1030.0000.0000.0000.000
30A107THR0-0.015-0.0158.7590.0390.0390.0000.0000.0000.000
31A108LEU0-0.012-0.0229.1570.0850.0850.0000.0000.0000.000
32A109ASN0-0.0050.00311.3290.1010.1010.0000.0000.0000.000
33A110GLY0-0.0340.00612.4720.0310.0310.0000.0000.0000.000
34A111CYS0-0.064-0.0396.8210.0710.0710.0000.0000.0000.000
35A112VAL0-0.0080.0038.6810.1180.1180.0000.0000.0000.000
36A113THR00.0140.00010.404-0.042-0.0420.0000.0000.0000.000
37A114THR0-0.001-0.00710.833-0.037-0.0370.0000.0000.0000.000
38A115ASP-1-0.829-0.89113.0650.2640.2640.0000.0000.0000.000
39A116ASP-1-0.933-0.96710.1200.5420.5420.0000.0000.0000.000
40A117ALA00.0580.0428.6520.0320.0320.0000.0000.0000.000
41A118LEU0-0.022-0.0209.574-0.035-0.0350.0000.0000.0000.000
42A119GLN0-0.029-0.03512.583-0.012-0.0120.0000.0000.0000.000
43A120GLU-1-0.879-0.9335.0561.4931.553-0.001-0.002-0.0570.000
44A121LEU0-0.0080.0039.7290.0090.0090.0000.0000.0000.000
45A122VAL0-0.040-0.02310.439-0.058-0.0580.0000.0000.0000.000
46A123GLU-1-0.776-0.86411.4670.1830.1830.0000.0000.0000.000
47A124LEU00.0170.0126.783-0.046-0.0460.0000.0000.0000.000
48A125ILE00.0150.00311.254-0.089-0.0890.0000.0000.0000.000
49A126TYR0-0.024-0.01614.036-0.045-0.0450.0000.0000.0000.000
50A127GLN00.0160.00313.434-0.068-0.0680.0000.0000.0000.000
51A128GLN00.0520.07213.865-0.002-0.0020.0000.0000.0000.000
52A129ALA0-0.048-0.02915.611-0.027-0.0270.0000.0000.0000.000
53A130THR0-0.090-0.05018.548-0.010-0.0100.0000.0000.0000.000
54A131SER0-0.083-0.06017.244-0.002-0.0020.0000.0000.0000.000
55A132ILE0-0.017-0.02116.364-0.006-0.0060.0000.0000.0000.000
56A133PRO00.0190.01519.5390.0090.0090.0000.0000.0000.000
57A134ASN0-0.061-0.04022.394-0.001-0.0010.0000.0000.0000.000
58A135PHE00.1340.06216.826-0.002-0.0020.0000.0000.0000.000
59A136SER0-0.021-0.00421.2800.0060.0060.0000.0000.0000.000
60A137TYR00.0440.01623.6170.0030.0030.0000.0000.0000.000
61A138MET00.0100.02619.4110.0090.0090.0000.0000.0000.000
62A139GLY00.0690.03118.9020.0010.0010.0000.0000.0000.000
63A140ALA0-0.0040.00619.9580.0130.0130.0000.0000.0000.000
64A141ARG10.8260.90522.6970.0740.0740.0000.0000.0000.000
65A142LEU00.0310.01114.9100.0070.0070.0000.0000.0000.000
66A143CYS0-0.038-0.02119.0170.0190.0190.0000.0000.0000.000
67A144ASN00.003-0.00619.9960.0190.0190.0000.0000.0000.000
68A145TYR00.0310.02518.9610.0100.0100.0000.0000.0000.000
69A146LEU00.0470.00615.0620.0070.0070.0000.0000.0000.000
70A147SER0-0.125-0.05918.8050.0190.0190.0000.0000.0000.000
71A148HIS0-0.052-0.03421.2240.0130.0130.0000.0000.0000.000
72A149HIS10.8530.92819.889-0.011-0.0110.0000.0000.0000.000
73A150LEU00.0060.02814.3680.0000.0000.0000.0000.0000.000
74A151THR0-0.005-0.00817.5460.0040.0040.0000.0000.0000.000
75A152ILE0-0.0320.00714.119-0.004-0.0040.0000.0000.0000.000
76A153SER0-0.026-0.02917.672-0.021-0.0210.0000.0000.0000.000
77A154PRO0-0.0010.01217.042-0.006-0.0060.0000.0000.0000.000
78A155GLN0-0.021-0.02519.824-0.008-0.0080.0000.0000.0000.000
79A156SER0-0.067-0.06519.197-0.013-0.0130.0000.0000.0000.000
80A157GLY00.0070.00821.216-0.008-0.0080.0000.0000.0000.000
81A158ASN00.0380.00919.5120.0120.0120.0000.0000.0000.000
82A159PHE00.0850.03414.882-0.001-0.0010.0000.0000.0000.000
83A160ARG10.9810.99518.632-0.073-0.0730.0000.0000.0000.000
84A161GLN0-0.065-0.01721.9470.0040.0040.0000.0000.0000.000
85A162LEU00.0580.01916.115-0.005-0.0050.0000.0000.0000.000
86A163LEU00.0390.03518.5700.0000.0000.0000.0000.0000.000
87A164LEU0-0.025-0.03119.963-0.008-0.0080.0000.0000.0000.000
88A165GLN0-0.016-0.00721.3540.0000.0000.0000.0000.0000.000
89A166ARG10.8350.90916.487-0.171-0.1710.0000.0000.0000.000
90A167CYS0-0.034-0.02420.709-0.010-0.0100.0000.0000.0000.000
91A168ARG10.8780.93423.427-0.066-0.0660.0000.0000.0000.000
92A169THR00.0160.01821.596-0.003-0.0030.0000.0000.0000.000
93A170GLU-1-0.865-0.93122.0530.0770.0770.0000.0000.0000.000
94A171TYR0-0.099-0.05524.729-0.009-0.0090.0000.0000.0000.000
95A172GLU-1-0.921-0.95527.6530.0460.0460.0000.0000.0000.000
96A173VAL0-0.0160.00326.885-0.005-0.0050.0000.0000.0000.000
97A174LYS10.9000.95029.714-0.036-0.0360.0000.0000.0000.000
98A175ASP-1-0.894-0.94831.3090.0210.0210.0000.0000.0000.000
99A176GLN0-0.064-0.03631.697-0.007-0.0070.0000.0000.0000.000
100A177ALA00.0240.01729.079-0.004-0.0040.0000.0000.0000.000
101A178ALA0-0.0230.00530.825-0.005-0.0050.0000.0000.0000.000
102A179LYS10.9300.96633.738-0.015-0.0150.0000.0000.0000.000
103A180GLY00.0600.04332.626-0.001-0.0010.0000.0000.0000.000
104A181ASP-1-0.863-0.94731.554-0.020-0.0200.0000.0000.0000.000
105A182GLU-1-0.904-0.95931.830-0.029-0.0290.0000.0000.0000.000
106A183VAL0-0.028-0.01827.582-0.002-0.0020.0000.0000.0000.000
107A184THR0-0.034-0.01927.2080.0020.0020.0000.0000.0000.000
108A185ARG10.8320.89927.2860.0150.0150.0000.0000.0000.000
109A186LYS10.9020.95826.5930.0510.0510.0000.0000.0000.000
110A187ARG10.9931.00918.297-0.049-0.0490.0000.0000.0000.000
111A188PHE00.0430.02124.7060.0060.0060.0000.0000.0000.000
112A189HIS10.8160.86727.2390.0140.0140.0000.0000.0000.000
113A190ALA00.0270.04223.2470.0000.0000.0000.0000.0000.000
114A191PHE00.0360.00823.3100.0020.0020.0000.0000.0000.000
115A192VAL0-0.021-0.01424.8840.0020.0020.0000.0000.0000.000
116A193LEU0-0.011-0.01827.3760.0010.0010.0000.0000.0000.000
117A194PHE0-0.0050.01520.435-0.001-0.0010.0000.0000.0000.000
118A195LEU00.004-0.00724.8710.0030.0030.0000.0000.0000.000
119A196GLY0-0.003-0.00526.9180.0010.0010.0000.0000.0000.000
120A197GLU-1-0.855-0.95426.137-0.021-0.0210.0000.0000.0000.000
121A198LEU0-0.016-0.00322.9430.0000.0000.0000.0000.0000.000
122A199TYR0-0.060-0.03526.4530.0010.0010.0000.0000.0000.000
123A200LEU0-0.069-0.03329.9100.0010.0010.0000.0000.0000.000
124A201ASN0-0.038-0.03526.958-0.002-0.0020.0000.0000.0000.000
125A202LEU0-0.0260.00623.8980.0020.0020.0000.0000.0000.000
126A203GLU-1-0.915-0.94427.0310.0150.0150.0000.0000.0000.000
127A204ILE0-0.044-0.03627.6600.0080.0080.0000.0000.0000.000
128A205LYS10.9520.97929.770-0.049-0.0490.0000.0000.0000.000
129A206GLY00.0400.00832.0690.0040.0040.0000.0000.0000.000
130A207THR00.000-0.01634.8580.0010.0010.0000.0000.0000.000
131A208ASN00.0120.01336.8820.0020.0020.0000.0000.0000.000
132A209GLY0-0.027-0.01836.025-0.002-0.0020.0000.0000.0000.000
133A210GLN0-0.0120.00036.440-0.002-0.0020.0000.0000.0000.000
134A211VAL00.0110.02133.0110.0040.0040.0000.0000.0000.000
135A212THR00.0060.00532.905-0.004-0.0040.0000.0000.0000.000
136A213ARG10.9420.98331.711-0.011-0.0110.0000.0000.0000.000
137A214ALA00.0420.00928.6380.0030.0030.0000.0000.0000.000
138A215ASP-1-0.865-0.93630.7170.0350.0350.0000.0000.0000.000
139A216ILE0-0.004-0.01328.111-0.003-0.0030.0000.0000.0000.000
140A217LEU0-0.028-0.01126.4510.0000.0000.0000.0000.0000.000
141A218GLN00.0760.05330.553-0.005-0.0050.0000.0000.0000.000
142A219VAL0-0.010-0.00233.928-0.003-0.0030.0000.0000.0000.000
143A220GLY0-0.026-0.02531.273-0.001-0.0010.0000.0000.0000.000
144A221LEU00.0530.02030.778-0.003-0.0030.0000.0000.0000.000
145A222ARG10.7890.89633.593-0.018-0.0180.0000.0000.0000.000
146A223GLU-1-0.928-0.97234.4290.0220.0220.0000.0000.0000.000
147A224LEU0-0.021-0.01229.593-0.001-0.0010.0000.0000.0000.000
148A225LEU00.0110.00934.051-0.003-0.0030.0000.0000.0000.000
149A226ASN00.0050.01237.002-0.005-0.0050.0000.0000.0000.000
150A227ALA00.0200.01334.866-0.002-0.0020.0000.0000.0000.000
151A228LEU0-0.042-0.01633.015-0.002-0.0020.0000.0000.0000.000
152A229PHE0-0.001-0.02236.889-0.002-0.0020.0000.0000.0000.000
153A230SER0-0.030-0.00939.885-0.001-0.0010.0000.0000.0000.000
154A231ASN0-0.061-0.02137.6320.0000.0000.0000.0000.0000.000
155A232PRO00.0420.03438.921-0.002-0.0020.0000.0000.0000.000
156A233MET00.0310.00937.911-0.001-0.0010.0000.0000.0000.000
157A234ASP-1-0.707-0.84239.040-0.019-0.0190.0000.0000.0000.000
158A235ASP-1-0.780-0.87933.880-0.017-0.0170.0000.0000.0000.000
159A236ASN0-0.031-0.01334.2290.0000.0000.0000.0000.0000.000
160A237LEU00.0350.02335.8770.0020.0020.0000.0000.0000.000
161A238ILE00.0250.00734.9320.0000.0000.0000.0000.0000.000
162A239CYS0-0.068-0.02231.859-0.001-0.0010.0000.0000.0000.000
163A240ALA00.0350.02334.0070.0010.0010.0000.0000.0000.000
164A241VAL00.0190.00936.4760.0010.0010.0000.0000.0000.000
165A242LYS10.9020.94932.1120.0310.0310.0000.0000.0000.000
166A243LEU00.0470.03131.660-0.001-0.0010.0000.0000.0000.000
167A244LEU00.0230.01434.1790.0020.0020.0000.0000.0000.000
168A245LYS10.8980.94836.9620.0220.0220.0000.0000.0000.000
169A246LEU0-0.0320.00130.2830.0000.0000.0000.0000.0000.000
170A247THR0-0.006-0.01432.6980.0020.0020.0000.0000.0000.000
171A248GLY00.0160.01035.6940.0030.0030.0000.0000.0000.000
172A249SER0-0.001-0.00539.3090.0010.0010.0000.0000.0000.000
173A250VAL00.0350.02135.8900.0010.0010.0000.0000.0000.000
174A251LEU0-0.030-0.01835.7990.0030.0030.0000.0000.0000.000
175A252GLU-1-0.880-0.94239.2290.0030.0030.0000.0000.0000.000
176A253ASP-1-0.905-0.95641.7630.0060.0060.0000.0000.0000.000
177A254ALA0-0.032-0.01139.2540.0010.0010.0000.0000.0000.000
178A255TRP0-0.030-0.03738.7390.0010.0010.0000.0000.0000.000
179A256LYS11.0001.00643.204-0.006-0.0060.0000.0000.0000.000
180A257GLU-1-0.885-0.92543.6640.0210.0210.0000.0000.0000.000
181A258LYS10.8090.89642.018-0.023-0.0230.0000.0000.0000.000
182A259GLY0-0.023-0.00345.5180.0010.0010.0000.0000.0000.000
183A260LYS10.8630.93540.898-0.022-0.0220.0000.0000.0000.000
184A261MET00.0460.02446.448-0.001-0.0010.0000.0000.0000.000
185A262ASP-1-0.837-0.91742.1290.0170.0170.0000.0000.0000.000
186A263MET00.0100.01043.574-0.001-0.0010.0000.0000.0000.000
187A264GLU-1-0.862-0.93945.1650.0060.0060.0000.0000.0000.000
188A265GLU-1-0.899-0.93545.4560.0130.0130.0000.0000.0000.000
189A266ILE0-0.079-0.04140.586-0.001-0.0010.0000.0000.0000.000
190A267ILE00.0180.00844.348-0.002-0.0020.0000.0000.0000.000
191A268GLN00.0360.03047.176-0.001-0.0010.0000.0000.0000.000
192A269ARG10.8990.94242.543-0.011-0.0110.0000.0000.0000.000
193A270ILE0-0.020-0.00542.906-0.001-0.0010.0000.0000.0000.000
194A271GLU-1-0.900-0.96545.843-0.003-0.0030.0000.0000.0000.000
195A272ASN00.0220.00248.362-0.001-0.0010.0000.0000.0000.000
196A273VAL0-0.0080.00343.683-0.001-0.0010.0000.0000.0000.000
197A274VAL0-0.025-0.01746.975-0.001-0.0010.0000.0000.0000.000
198A275LEU0-0.043-0.00749.129-0.001-0.0010.0000.0000.0000.000
199A276ASP-1-0.901-0.94349.758-0.002-0.0020.0000.0000.0000.000
200A277ALA0-0.086-0.02545.6050.0000.0000.0000.0000.0000.000
201A278ASN0-0.039-0.03546.864-0.001-0.0010.0000.0000.0000.000
202A279CYS0-0.0640.00243.510-0.001-0.0010.0000.0000.0000.000
203A280SER00.015-0.03043.4320.0000.0000.0000.0000.0000.000
204A281ARG10.9630.96845.7730.0180.0180.0000.0000.0000.000
205A282ASP-1-0.891-0.96243.475-0.024-0.0240.0000.0000.0000.000
206A283VAL00.0420.02141.1440.0000.0000.0000.0000.0000.000
207A284LYS10.8480.90843.6440.0110.0110.0000.0000.0000.000
208A285GLN0-0.019-0.01046.7180.0020.0020.0000.0000.0000.000
209A286MET0-0.068-0.02840.3340.0010.0010.0000.0000.0000.000
210A287LEU00.014-0.00241.8260.0010.0010.0000.0000.0000.000
211A288LEU00.0190.00744.8110.0010.0010.0000.0000.0000.000
212A289LYS10.8370.91745.5090.0150.0150.0000.0000.0000.000
213A290LEU0-0.044-0.01840.9460.0000.0000.0000.0000.0000.000
214A291VAL0-0.006-0.00245.1540.0010.0010.0000.0000.0000.000
215A292GLU-1-0.912-0.94248.274-0.011-0.0110.0000.0000.0000.000
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