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: 72G9K

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 OptHSide
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 -2631349.807542
FMO2-HF: Nuclear repulsion 2543504.354748
FMO2-HF: Total energy -87845.452794
FMO2-MP2: Total energy -88098.763439


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.
-55.876-58.89734.141-17.293-13.826-0.079
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 : -0.035 / q_NPA : -0.068
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].
3A80SER00.0120.0032.325-7.257-3.9011.399-2.086-2.6690.018
4A81GLU-1-0.868-0.8981.646-50.792-57.94132.731-15.012-10.569-0.097
5A82TYR00.0100.0043.6710.0430.6580.013-0.183-0.4460.000
6A83VAL0-0.002-0.0045.3350.4570.576-0.001-0.009-0.1080.000
7A84GLN0-0.066-0.0416.9830.1480.1480.0000.0000.0000.000
8A85ASP-1-0.885-0.9397.925-1.830-1.8300.0000.0000.0000.000
9A86PHE0-0.022-0.0149.6200.2230.2230.0000.0000.0000.000
10A87LEU0-0.014-0.01510.9400.1140.1140.0000.0000.0000.000
11A88ASN00.0150.02111.0850.1890.1890.0000.0000.0000.000
12A89HIS00.004-0.00913.8510.0410.0410.0000.0000.0000.000
13A90LEU0-0.020-0.00315.6160.0700.0700.0000.0000.0000.000
14A91THR0-0.100-0.07716.6920.0570.0570.0000.0000.0000.000
15A92GLU-1-0.992-0.98717.524-0.401-0.4010.0000.0000.0000.000
16A93GLN0-0.051-0.02619.1270.0480.0480.0000.0000.0000.000
17A94PRO00.0120.01020.8970.0060.0060.0000.0000.0000.000
18A95GLY0-0.055-0.03722.7210.0130.0130.0000.0000.0000.000
19A96SER00.0130.01418.3620.0220.0220.0000.0000.0000.000
20A97PHE00.028-0.00419.584-0.002-0.0020.0000.0000.0000.000
21A98GLU-1-0.811-0.89220.431-0.107-0.1070.0000.0000.0000.000
22A99THR0-0.024-0.01920.7990.0130.0130.0000.0000.0000.000
23A100GLU-1-0.852-0.90715.950-0.384-0.3840.0000.0000.0000.000
24A101ILE0-0.043-0.00716.258-0.022-0.0220.0000.0000.0000.000
25A102GLU-1-0.864-0.90416.835-0.056-0.0560.0000.0000.0000.000
26A103GLN00.0090.00613.5140.0240.0240.0000.0000.0000.000
27A104PHE00.0640.0439.7720.0420.0420.0000.0000.0000.000
28A105ALA00.000-0.01512.5590.0160.0160.0000.0000.0000.000
29A106GLU-1-0.944-0.96014.6200.0630.0630.0000.0000.0000.000
30A107THR0-0.017-0.0158.6890.0180.0180.0000.0000.0000.000
31A108LEU00.014-0.0079.1010.0890.0890.0000.0000.0000.000
32A109ASN0-0.0060.00811.2910.1280.1280.0000.0000.0000.000
33A110GLY0-0.0390.00412.4190.0430.0430.0000.0000.0000.000
34A111CYS0-0.104-0.0587.0170.0160.0160.0000.0000.0000.000
35A112VAL0-0.0050.0028.6620.1590.1590.0000.0000.0000.000
36A113THR00.0170.00010.393-0.042-0.0420.0000.0000.0000.000
37A114THR00.004-0.00110.776-0.044-0.0440.0000.0000.0000.000
38A115ASP-1-0.822-0.89712.9040.3260.3260.0000.0000.0000.000
39A116ASP-1-0.941-0.9749.6780.7960.7960.0000.0000.0000.000
40A117ALA00.0560.0388.5010.0560.0560.0000.0000.0000.000
41A118LEU0-0.013-0.0169.428-0.039-0.0390.0000.0000.0000.000
42A119GLN0-0.037-0.03112.465-0.025-0.0250.0000.0000.0000.000
43A120GLU-1-0.844-0.9254.9752.3042.342-0.001-0.003-0.0340.000
44A121LEU00.0060.0059.680-0.005-0.0050.0000.0000.0000.000
45A122VAL0-0.030-0.01710.397-0.083-0.0830.0000.0000.0000.000
46A123GLU-1-0.801-0.87311.4250.2380.2380.0000.0000.0000.000
47A124LEU0-0.0090.0036.754-0.089-0.0890.0000.0000.0000.000
48A125ILE00.0180.00611.200-0.113-0.1130.0000.0000.0000.000
49A126TYR0-0.050-0.04514.027-0.059-0.0590.0000.0000.0000.000
50A127GLN00.007-0.00813.406-0.092-0.0920.0000.0000.0000.000
51A128GLN00.0300.04313.835-0.019-0.0190.0000.0000.0000.000
52A129ALA0-0.033-0.02315.634-0.030-0.0300.0000.0000.0000.000
53A130THR0-0.081-0.04118.532-0.011-0.0110.0000.0000.0000.000
54A131SER0-0.070-0.03617.2980.0000.0000.0000.0000.0000.000
55A132ILE00.000-0.00716.243-0.004-0.0040.0000.0000.0000.000
56A133PRO00.0150.00919.5980.0100.0100.0000.0000.0000.000
57A134ASN0-0.067-0.04022.485-0.002-0.0020.0000.0000.0000.000
58A135PHE00.1300.06216.905-0.002-0.0020.0000.0000.0000.000
59A136SER0-0.031-0.00821.3390.0070.0070.0000.0000.0000.000
60A137TYR00.0520.02723.6600.0040.0040.0000.0000.0000.000
61A138MET00.0020.02119.5150.0110.0110.0000.0000.0000.000
62A139GLY00.0680.03018.9540.0000.0000.0000.0000.0000.000
63A140ALA00.0000.01220.0060.0150.0150.0000.0000.0000.000
64A141ARG10.7850.88322.7880.0980.0980.0000.0000.0000.000
65A142LEU00.0280.01015.0430.0070.0070.0000.0000.0000.000
66A143CYS0-0.050-0.03319.0000.0220.0220.0000.0000.0000.000
67A144ASN0-0.004-0.01919.9870.0240.0240.0000.0000.0000.000
68A145TYR0-0.026-0.04018.8750.0110.0110.0000.0000.0000.000
69A146LEU00.0360.00414.9940.0080.0080.0000.0000.0000.000
70A147SER0-0.120-0.06318.8050.0230.0230.0000.0000.0000.000
71A148HIS0-0.050-0.03921.1570.0190.0190.0000.0000.0000.000
72A149HIS10.8680.94019.6940.0130.0130.0000.0000.0000.000
73A150LEU0-0.0100.02214.311-0.002-0.0020.0000.0000.0000.000
74A151THR0-0.002-0.01117.5220.0090.0090.0000.0000.0000.000
75A152ILE0-0.0340.00414.0620.0000.0000.0000.0000.0000.000
76A153SER0-0.015-0.02517.663-0.021-0.0210.0000.0000.0000.000
77A154PRO0-0.0130.00816.948-0.009-0.0090.0000.0000.0000.000
78A155GLN0-0.026-0.02819.773-0.010-0.0100.0000.0000.0000.000
79A156SER0-0.074-0.05518.813-0.017-0.0170.0000.0000.0000.000
80A157GLY00.0100.00821.094-0.009-0.0090.0000.0000.0000.000
81A158ASN00.0350.00519.3880.0140.0140.0000.0000.0000.000
82A159PHE00.0810.03414.7540.0010.0010.0000.0000.0000.000
83A160ARG10.9430.96818.549-0.072-0.0720.0000.0000.0000.000
84A161GLN0-0.068-0.02021.8800.0060.0060.0000.0000.0000.000
85A162LEU00.0560.01916.167-0.006-0.0060.0000.0000.0000.000
86A163LEU00.0440.03318.4940.0010.0010.0000.0000.0000.000
87A164LEU0-0.019-0.02119.927-0.009-0.0090.0000.0000.0000.000
88A165GLN0-0.015-0.00921.3260.0020.0020.0000.0000.0000.000
89A166ARG10.8270.89916.757-0.217-0.2170.0000.0000.0000.000
90A167CYS0-0.038-0.02720.693-0.012-0.0120.0000.0000.0000.000
91A168ARG10.8480.92323.430-0.084-0.0840.0000.0000.0000.000
92A169THR00.0260.01821.548-0.003-0.0030.0000.0000.0000.000
93A170GLU-1-0.774-0.86221.4260.1120.1120.0000.0000.0000.000
94A171TYR0-0.065-0.03324.762-0.014-0.0140.0000.0000.0000.000
95A172GLU-1-0.922-0.95427.6730.0640.0640.0000.0000.0000.000
96A173VAL0-0.032-0.00926.869-0.005-0.0050.0000.0000.0000.000
97A174LYS10.8520.91529.755-0.046-0.0460.0000.0000.0000.000
98A175ASP-1-0.837-0.90531.3000.0310.0310.0000.0000.0000.000
99A176GLN0-0.009-0.01531.613-0.009-0.0090.0000.0000.0000.000
100A177ALA00.0030.00629.000-0.005-0.0050.0000.0000.0000.000
101A178ALA0-0.0040.01330.735-0.006-0.0060.0000.0000.0000.000
102A179LYS10.8390.91833.668-0.024-0.0240.0000.0000.0000.000
103A180GLY00.0510.03532.552-0.002-0.0020.0000.0000.0000.000
104A181ASP-1-0.824-0.90631.224-0.019-0.0190.0000.0000.0000.000
105A182GLU-1-0.848-0.92631.791-0.036-0.0360.0000.0000.0000.000
106A183VAL0-0.020-0.01827.412-0.003-0.0030.0000.0000.0000.000
107A184THR00.000-0.02427.1600.0020.0020.0000.0000.0000.000
108A185ARG10.7860.86927.2430.0120.0120.0000.0000.0000.000
109A186LYS10.8040.90226.7540.0470.0470.0000.0000.0000.000
110A187ARG10.9250.97217.956-0.074-0.0740.0000.0000.0000.000
111A188PHE00.0430.01524.6800.0060.0060.0000.0000.0000.000
112A189HIS10.8200.88127.1920.0110.0110.0000.0000.0000.000
113A190ALA00.0310.04323.274-0.001-0.0010.0000.0000.0000.000
114A191PHE00.0340.00623.1800.0000.0000.0000.0000.0000.000
115A192VAL0-0.016-0.01224.8490.0020.0020.0000.0000.0000.000
116A193LEU0-0.026-0.02427.3700.0010.0010.0000.0000.0000.000
117A194PHE00.0070.01920.332-0.003-0.0030.0000.0000.0000.000
118A195LEU00.008-0.00124.6240.0030.0030.0000.0000.0000.000
119A196GLY0-0.004-0.01126.8880.0010.0010.0000.0000.0000.000
120A197GLU-1-0.843-0.94826.188-0.028-0.0280.0000.0000.0000.000
121A198LEU0-0.0150.00122.990-0.001-0.0010.0000.0000.0000.000
122A199TYR0-0.054-0.03826.4470.0010.0010.0000.0000.0000.000
123A200LEU0-0.044-0.02029.9130.0010.0010.0000.0000.0000.000
124A201ASN0-0.060-0.04526.984-0.004-0.0040.0000.0000.0000.000
125A202LEU0-0.0100.01323.8000.0010.0010.0000.0000.0000.000
126A203GLU-1-0.888-0.91327.0100.0110.0110.0000.0000.0000.000
127A204ILE0-0.036-0.02727.6140.0090.0090.0000.0000.0000.000
128A205LYS10.9020.94929.707-0.047-0.0470.0000.0000.0000.000
129A206GLY00.0500.01131.9880.0050.0050.0000.0000.0000.000
130A207THR00.006-0.01334.7790.0010.0010.0000.0000.0000.000
131A208ASN00.0110.01136.7880.0020.0020.0000.0000.0000.000
132A209GLY0-0.026-0.01435.941-0.002-0.0020.0000.0000.0000.000
133A210GLN00.0270.02336.393-0.002-0.0020.0000.0000.0000.000
134A211VAL00.0100.02032.6660.0050.0050.0000.0000.0000.000
135A212THR00.0020.00333.096-0.004-0.0040.0000.0000.0000.000
136A213ARG10.9100.96431.674-0.010-0.0100.0000.0000.0000.000
137A214ALA00.0390.01028.5900.0040.0040.0000.0000.0000.000
138A215ASP-1-0.832-0.92630.6820.0400.0400.0000.0000.0000.000
139A216ILE00.0120.00328.015-0.003-0.0030.0000.0000.0000.000
140A217LEU0-0.019-0.01426.4370.0000.0000.0000.0000.0000.000
141A218GLN00.0430.04830.546-0.008-0.0080.0000.0000.0000.000
142A219VAL0-0.007-0.00633.908-0.003-0.0030.0000.0000.0000.000
143A220GLY0-0.014-0.01431.283-0.001-0.0010.0000.0000.0000.000
144A221LEU00.0320.01130.667-0.003-0.0030.0000.0000.0000.000
145A222ARG10.7590.87333.595-0.024-0.0240.0000.0000.0000.000
146A223GLU-1-0.849-0.93234.6410.0280.0280.0000.0000.0000.000
147A224LEU0-0.025-0.01429.565-0.001-0.0010.0000.0000.0000.000
148A225LEU00.0030.00633.983-0.004-0.0040.0000.0000.0000.000
149A226ASN0-0.028-0.01836.953-0.006-0.0060.0000.0000.0000.000
150A227ALA00.0160.02534.838-0.002-0.0020.0000.0000.0000.000
151A228LEU0-0.046-0.01132.996-0.003-0.0030.0000.0000.0000.000
152A229PHE0-0.004-0.02336.840-0.003-0.0030.0000.0000.0000.000
153A230SER0-0.046-0.03539.818-0.001-0.0010.0000.0000.0000.000
154A231ASN0-0.0140.00537.6210.0010.0010.0000.0000.0000.000
155A232PRO00.0480.04338.877-0.002-0.0020.0000.0000.0000.000
156A233MET00.0160.00237.884-0.002-0.0020.0000.0000.0000.000
157A234ASP-1-0.704-0.84539.026-0.020-0.0200.0000.0000.0000.000
158A235ASP-1-0.786-0.86733.919-0.015-0.0150.0000.0000.0000.000
159A236ASN0-0.038-0.03434.3250.0000.0000.0000.0000.0000.000
160A237LEU00.0270.02435.8600.0020.0020.0000.0000.0000.000
161A238ILE00.0210.00734.926-0.001-0.0010.0000.0000.0000.000
162A239CYS0-0.078-0.02531.738-0.001-0.0010.0000.0000.0000.000
163A240ALA00.0480.03034.0140.0010.0010.0000.0000.0000.000
164A241VAL00.0110.00436.4690.0000.0000.0000.0000.0000.000
165A242LYS10.9120.95031.5320.0360.0360.0000.0000.0000.000
166A243LEU00.0560.04031.670-0.001-0.0010.0000.0000.0000.000
167A244LEU00.0200.01434.1870.0020.0020.0000.0000.0000.000
168A245LYS10.8880.94537.0130.0250.0250.0000.0000.0000.000
169A246LEU0-0.034-0.00130.3270.0000.0000.0000.0000.0000.000
170A247THR0-0.005-0.01632.7270.0020.0020.0000.0000.0000.000
171A248GLY00.0230.01635.7050.0030.0030.0000.0000.0000.000
172A249SER00.0040.00239.3140.0020.0020.0000.0000.0000.000
173A250VAL00.0190.01035.8610.0020.0020.0000.0000.0000.000
174A251LEU0-0.018-0.01435.7340.0030.0030.0000.0000.0000.000
175A252GLU-1-0.828-0.89939.2090.0020.0020.0000.0000.0000.000
176A253ASP-1-0.925-0.96241.7070.0050.0050.0000.0000.0000.000
177A254ALA0-0.027-0.00939.2250.0020.0020.0000.0000.0000.000
178A255TRP0-0.025-0.03938.5590.0010.0010.0000.0000.0000.000
179A256LYS11.0061.01143.196-0.006-0.0060.0000.0000.0000.000
180A257GLU-1-0.850-0.89242.9080.0250.0250.0000.0000.0000.000
181A258LYS10.7630.85841.944-0.027-0.0270.0000.0000.0000.000
182A259GLY0-0.0170.00045.4890.0010.0010.0000.0000.0000.000
183A260LYS10.8160.90741.335-0.026-0.0260.0000.0000.0000.000
184A261MET00.0480.02346.438-0.001-0.0010.0000.0000.0000.000
185A262ASP-1-0.794-0.88741.9320.0220.0220.0000.0000.0000.000
186A263MET00.0100.01443.130-0.001-0.0010.0000.0000.0000.000
187A264GLU-1-0.893-0.95245.1290.0070.0070.0000.0000.0000.000
188A265GLU-1-0.847-0.90345.2800.0180.0180.0000.0000.0000.000
189A266ILE0-0.074-0.04440.477-0.001-0.0010.0000.0000.0000.000
190A267ILE00.0220.01644.306-0.002-0.0020.0000.0000.0000.000
191A268GLN00.0070.01547.148-0.001-0.0010.0000.0000.0000.000
192A269ARG10.9140.95442.609-0.016-0.0160.0000.0000.0000.000
193A270ILE0-0.027-0.01242.735-0.001-0.0010.0000.0000.0000.000
194A271GLU-1-0.899-0.95745.818-0.002-0.0020.0000.0000.0000.000
195A272ASN00.009-0.00248.296-0.002-0.0020.0000.0000.0000.000
196A273VAL00.0070.00843.613-0.001-0.0010.0000.0000.0000.000
197A274VAL0-0.019-0.01946.945-0.002-0.0020.0000.0000.0000.000
198A275LEU0-0.0350.00049.118-0.002-0.0020.0000.0000.0000.000
199A276ASP-1-0.919-0.95449.681-0.001-0.0010.0000.0000.0000.000
200A277ALA0-0.075-0.02145.5950.0000.0000.0000.0000.0000.000
201A278ASN0-0.036-0.02846.950-0.001-0.0010.0000.0000.0000.000
202A279CYS0-0.060-0.00743.506-0.001-0.0010.0000.0000.0000.000
203A280SER00.008-0.02443.5570.0000.0000.0000.0000.0000.000
204A281ARG10.9750.96845.7930.0190.0190.0000.0000.0000.000
205A282ASP-1-0.877-0.95543.211-0.026-0.0260.0000.0000.0000.000
206A283VAL00.0280.01941.2560.0000.0000.0000.0000.0000.000
207A284LYS10.8330.91343.6710.0110.0110.0000.0000.0000.000
208A285GLN0-0.002-0.00346.7340.0020.0020.0000.0000.0000.000
209A286MET0-0.089-0.04540.7760.0000.0000.0000.0000.0000.000
210A287LEU00.016-0.00141.7910.0010.0010.0000.0000.0000.000
211A288LEU00.0230.01244.8260.0010.0010.0000.0000.0000.000
212A289LYS10.7730.86045.6890.0160.0160.0000.0000.0000.000
213A290LEU0-0.043-0.01640.7180.0000.0000.0000.0000.0000.000
214A291VAL00.0200.00545.1750.0010.0010.0000.0000.0000.000
215A292GLU-1-0.842-0.88648.283-0.013-0.0130.0000.0000.0000.000
216A293LEU0-0.082-0.03644.4800.0000.0000.0000.0000.0000.000
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