Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5JJKZ

Calculation Name: 2J5U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J5U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y6Y4

Base Structure: X-ray

Registration Date: 2023-09-21

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2198028.79845
FMO2-HF: Nuclear repulsion 2118183.641615
FMO2-HF: Total energy -79845.156835
FMO2-MP2: Total energy -80079.541471


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:74:THR)


Summations of interaction energy for fragment #1(A:74: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.
-7.357-2.2177.393-5.213-7.319-0.011
Interaction energy analysis for fragmet #1(A:74:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.012
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].
3A76ASN0-0.034-0.0413.228-2.760-0.0310.005-1.182-1.5510.001
4A77GLN0-0.0240.0132.029-3.293-1.5876.762-3.734-4.734-0.012
5A78HIS00.029-0.0042.309-1.358-0.6530.626-0.297-1.0340.000
6A79LEU00.0360.0295.5180.0840.0840.0000.0000.0000.000
7A80LYS10.9050.9677.185-0.918-0.9180.0000.0000.0000.000
8A81GLU-1-0.941-0.9848.7710.0300.0300.0000.0000.0000.000
9A82ARG10.9851.0116.7730.7320.7320.0000.0000.0000.000
10A83LEU0-0.018-0.01610.785-0.013-0.0130.0000.0000.0000.000
11A84GLU-1-0.930-0.96212.6720.3920.3920.0000.0000.0000.000
12A85GLU-1-0.929-0.98014.001-0.049-0.0490.0000.0000.0000.000
13A86LEU0-0.100-0.02814.240-0.040-0.0400.0000.0000.0000.000
14A87ALA00.0630.01816.169-0.005-0.0050.0000.0000.0000.000
15A88GLN0-0.0160.00818.3420.0090.0090.0000.0000.0000.000
16A89LEU00.007-0.00118.576-0.006-0.0060.0000.0000.0000.000
17A90GLU-1-0.975-0.98919.507-0.095-0.0950.0000.0000.0000.000
18A91SER0-0.035-0.01922.2100.0040.0040.0000.0000.0000.000
19A92GLU-1-0.866-0.92324.220-0.030-0.0300.0000.0000.0000.000
20A93VAL0-0.049-0.04124.112-0.005-0.0050.0000.0000.0000.000
21A94ALA0-0.042-0.02126.4900.0010.0010.0000.0000.0000.000
22A95ASP-1-0.858-0.91328.4820.0120.0120.0000.0000.0000.000
23A96LEU00.0170.01328.219-0.003-0.0030.0000.0000.0000.000
24A97LYS10.8230.90626.8520.0760.0760.0000.0000.0000.000
25A98LYS10.9220.96531.8750.0020.0020.0000.0000.0000.000
26A99GLU-1-0.892-0.94034.345-0.015-0.0150.0000.0000.0000.000
27A100ASN0-0.066-0.05334.670-0.003-0.0030.0000.0000.0000.000
28A101LYS10.8680.94236.2500.0280.0280.0000.0000.0000.000
29A102ASP-1-0.803-0.90437.954-0.010-0.0100.0000.0000.0000.000
30A103LEU0-0.036-0.01438.3960.0000.0000.0000.0000.0000.000
31A104LYS10.8330.90236.6330.0530.0530.0000.0000.0000.000
32A105GLU-1-0.858-0.92641.828-0.021-0.0210.0000.0000.0000.000
33A106SER0-0.095-0.03844.1700.0030.0030.0000.0000.0000.000
34A107LEU0-0.091-0.03743.8350.0010.0010.0000.0000.0000.000
35A108ASP-1-0.882-0.94146.479-0.025-0.0250.0000.0000.0000.000
36A109ILE0-0.120-0.05742.272-0.003-0.0030.0000.0000.0000.000
37A110THR00.0460.01843.3260.0010.0010.0000.0000.0000.000
38A111ASP-1-0.935-0.96040.846-0.054-0.0540.0000.0000.0000.000
39A112SER00.0000.00838.075-0.003-0.0030.0000.0000.0000.000
40A113ILE0-0.001-0.02236.500-0.004-0.0040.0000.0000.0000.000
41A114ARG10.8970.92729.5990.0850.0850.0000.0000.0000.000
42A115ASP-1-0.866-0.90633.695-0.068-0.0680.0000.0000.0000.000
43A116TYR0-0.017-0.03828.456-0.006-0.0060.0000.0000.0000.000
44A117ASP-1-0.875-0.90534.218-0.071-0.0710.0000.0000.0000.000
45A118PRO0-0.064-0.04029.993-0.005-0.0050.0000.0000.0000.000
46A119LEU00.0210.01731.7280.0070.0070.0000.0000.0000.000
47A120ASN0-0.006-0.00227.072-0.016-0.0160.0000.0000.0000.000
48A121ALA0-0.040-0.03328.4980.0120.0120.0000.0000.0000.000
49A122SER00.0280.01827.090-0.012-0.0120.0000.0000.0000.000
50A123VAL0-0.032-0.00926.6580.0150.0150.0000.0000.0000.000
51A124ILE0-0.019-0.02528.979-0.003-0.0030.0000.0000.0000.000
52A125SER0-0.055-0.03331.5260.0020.0020.0000.0000.0000.000
53A126ARG10.8550.91925.0040.2720.2720.0000.0000.0000.000
54A127ASN00.0230.03131.432-0.008-0.0080.0000.0000.0000.000
55A128PRO00.0550.00330.863-0.004-0.0040.0000.0000.0000.000
56A129THR0-0.058-0.02832.042-0.002-0.0020.0000.0000.0000.000
57A130ASN00.0300.00734.273-0.003-0.0030.0000.0000.0000.000
58A131TRP00.0120.02525.1840.0130.0130.0000.0000.0000.000
59A132ASN00.0040.00227.445-0.022-0.0220.0000.0000.0000.000
60A133ASP-1-0.777-0.86829.834-0.173-0.1730.0000.0000.0000.000
61A134GLN0-0.021-0.03132.5020.0080.0080.0000.0000.0000.000
62A135VAL0-0.0070.01128.240-0.010-0.0100.0000.0000.0000.000
63A136GLU-1-0.938-0.95731.682-0.124-0.1240.0000.0000.0000.000
64A137ILE0-0.013-0.00630.332-0.010-0.0100.0000.0000.0000.000
65A138ASP-1-0.851-0.93831.911-0.136-0.1360.0000.0000.0000.000
66A139LYS10.8870.95933.0100.1290.1290.0000.0000.0000.000
67A140GLY0-0.001-0.01535.872-0.004-0.0040.0000.0000.0000.000
68A141SER00.0070.01039.1030.0040.0040.0000.0000.0000.000
69A142SER0-0.131-0.06942.1580.0030.0030.0000.0000.0000.000
70A143ASP-1-0.848-0.92437.626-0.091-0.0910.0000.0000.0000.000
71A144GLY0-0.027-0.01938.735-0.001-0.0010.0000.0000.0000.000
72A145VAL0-0.033-0.01136.161-0.001-0.0010.0000.0000.0000.000
73A146LYS10.9430.94638.6700.0780.0780.0000.0000.0000.000
74A147PRO00.005-0.00638.948-0.005-0.0050.0000.0000.0000.000
75A148ASP-1-0.892-0.96438.332-0.098-0.0980.0000.0000.0000.000
76A149MET0-0.0380.01635.393-0.001-0.0010.0000.0000.0000.000
77A150ALA00.0180.00831.477-0.007-0.0070.0000.0000.0000.000
78A151VAL00.0280.01328.2730.0040.0040.0000.0000.0000.000
79A152THR0-0.064-0.03625.453-0.009-0.0090.0000.0000.0000.000
80A153THR00.0550.03721.317-0.009-0.0090.0000.0000.0000.000
81A154PRO00.0530.00618.6370.0080.0080.0000.0000.0000.000
82A155SER00.0020.00617.0230.0220.0220.0000.0000.0000.000
83A156GLY0-0.017-0.01319.128-0.005-0.0050.0000.0000.0000.000
84A157LEU0-0.028-0.02022.6610.0050.0050.0000.0000.0000.000
85A158ILE00.010-0.00724.092-0.014-0.0140.0000.0000.0000.000
86A159GLY00.0520.01226.7260.0000.0000.0000.0000.0000.000
87A160LYS10.9070.97530.5110.1390.1390.0000.0000.0000.000
88A161VAL00.0040.01333.841-0.003-0.0030.0000.0000.0000.000
89A162THR00.0000.00536.1290.0060.0060.0000.0000.0000.000
90A163THR00.0170.00538.9370.0060.0060.0000.0000.0000.000
91A164THR0-0.019-0.00839.617-0.004-0.0040.0000.0000.0000.000
92A165GLY00.0550.03841.0360.0050.0050.0000.0000.0000.000
93A166ALA0-0.025-0.04242.3780.0000.0000.0000.0000.0000.000
94A167LYS10.9590.95939.8470.0800.0800.0000.0000.0000.000
95A168SER00.0440.06537.230-0.001-0.0010.0000.0000.0000.000
96A169ALA00.032-0.00236.4620.0080.0080.0000.0000.0000.000
97A170THR00.0390.05135.603-0.007-0.0070.0000.0000.0000.000
98A171VAL0-0.019-0.00930.7590.0060.0060.0000.0000.0000.000
99A172GLU-1-0.928-0.96333.019-0.150-0.1500.0000.0000.0000.000
100A173LEU00.007-0.00927.664-0.002-0.0020.0000.0000.0000.000
101A174LEU0-0.027-0.03226.6360.0090.0090.0000.0000.0000.000
102A175THR0-0.098-0.07126.0840.0020.0020.0000.0000.0000.000
103A176SER0-0.0100.01229.2670.0020.0020.0000.0000.0000.000
104A177SER0-0.054-0.02732.8310.0030.0030.0000.0000.0000.000
105A178ASP-1-0.860-0.92235.398-0.114-0.1140.0000.0000.0000.000
106A179VAL00.027-0.00437.507-0.001-0.0010.0000.0000.0000.000
107A180LYS10.8840.94339.2680.1100.1100.0000.0000.0000.000
108A181ASN0-0.0190.00233.3830.0100.0100.0000.0000.0000.000
109A182ARG10.9100.95535.6960.1000.1000.0000.0000.0000.000
110A183VAL00.0130.01532.0450.0020.0020.0000.0000.0000.000
111A184SER0-0.0140.00634.909-0.001-0.0010.0000.0000.0000.000
112A185ALA00.002-0.00231.529-0.004-0.0040.0000.0000.0000.000
113A186LYS10.9120.95632.0950.1060.1060.0000.0000.0000.000
114A187VAL00.0160.02229.415-0.012-0.0120.0000.0000.0000.000
115A188GLN0-0.038-0.02926.8820.0070.0070.0000.0000.0000.000
116A189GLY00.0560.00729.205-0.009-0.0090.0000.0000.0000.000
117A190LYS10.9090.95931.0190.0520.0520.0000.0000.0000.000
118A191GLU-1-0.899-0.94033.194-0.051-0.0510.0000.0000.0000.000
119A192ASN0-0.029-0.01633.231-0.010-0.0100.0000.0000.0000.000
120A193ALA00.0600.03934.4010.0050.0050.0000.0000.0000.000
121A194PHE0-0.043-0.04334.919-0.007-0.0070.0000.0000.0000.000
122A195GLY00.0810.04536.1670.0030.0030.0000.0000.0000.000
123A196ILE0-0.073-0.02536.3670.0000.0000.0000.0000.0000.000
124A197ILE00.0030.01030.119-0.003-0.0030.0000.0000.0000.000
125A198ASN0-0.069-0.08133.6320.0090.0090.0000.0000.0000.000
126A199GLY00.0960.05633.9650.0050.0050.0000.0000.0000.000
127A200TYR00.0180.00925.299-0.017-0.0170.0000.0000.0000.000
128A201ASP-1-0.824-0.89229.191-0.201-0.2010.0000.0000.0000.000
129A202SER00.002-0.02827.885-0.018-0.0180.0000.0000.0000.000
130A203ASP-1-0.911-0.93826.625-0.243-0.2430.0000.0000.0000.000
131A204THR0-0.114-0.06725.447-0.024-0.0240.0000.0000.0000.000
132A205LYS10.9150.95621.5100.3610.3610.0000.0000.0000.000
133A206LEU0-0.057-0.02323.624-0.011-0.0110.0000.0000.0000.000
134A207LEU0-0.005-0.01126.3640.0130.0130.0000.0000.0000.000
135A208GLU-1-0.896-0.94128.945-0.145-0.1450.0000.0000.0000.000
136A209LEU0-0.052-0.02031.1490.0050.0050.0000.0000.0000.000
137A210LYS10.9360.96433.1240.1310.1310.0000.0000.0000.000
138A211GLN0-0.018-0.02536.856-0.001-0.0010.0000.0000.0000.000
139A212LEU00.0000.02833.2070.0030.0030.0000.0000.0000.000
140A213PRO00.0290.00137.6600.0020.0020.0000.0000.0000.000
141A214TYR00.0570.00439.037-0.003-0.0030.0000.0000.0000.000
142A215ASP-1-0.940-0.94840.688-0.065-0.0650.0000.0000.0000.000
143A216MET00.0090.02936.1820.0000.0000.0000.0000.0000.000
144A217LYS10.9340.96933.9260.0660.0660.0000.0000.0000.000
145A218PHE00.0350.00530.644-0.001-0.0010.0000.0000.0000.000
146A219LYS10.9000.94026.5870.0960.0960.0000.0000.0000.000
147A220LYS10.9510.97420.2880.2660.2660.0000.0000.0000.000
148A221GLY00.000-0.01022.0240.0030.0030.0000.0000.0000.000
149A222GLN0-0.0170.01622.8750.0000.0000.0000.0000.0000.000
150A223LYS11.0051.00419.9120.2010.2010.0000.0000.0000.000
151A224VAL00.0280.02625.2270.0200.0200.0000.0000.0000.000
152A225VAL0-0.025-0.01526.634-0.012-0.0120.0000.0000.0000.000
153A226THR00.0600.03828.8690.0060.0060.0000.0000.0000.000
154A227SER0-0.001-0.00531.7960.0050.0050.0000.0000.0000.000
155A228GLY00.0360.02335.0910.0060.0060.0000.0000.0000.000
156A229LEU0-0.013-0.02536.9810.0040.0040.0000.0000.0000.000
157A230GLY00.0310.03738.8040.0030.0030.0000.0000.0000.000
158A231GLY0-0.037-0.02140.3910.0010.0010.0000.0000.0000.000
159A232LYS10.9740.98738.4550.0970.0970.0000.0000.0000.000
160A233PHE0-0.030-0.00133.214-0.004-0.0040.0000.0000.0000.000
161A234PRO00.0670.05632.3950.0060.0060.0000.0000.0000.000
162A235ALA0-0.012-0.02833.303-0.008-0.0080.0000.0000.0000.000
163A236GLY0-0.091-0.05730.0150.0030.0030.0000.0000.0000.000
164A237ILE00.0180.02126.704-0.007-0.0070.0000.0000.0000.000
165A238PHE0-0.003-0.00120.2910.0060.0060.0000.0000.0000.000
166A239ILE00.0310.01225.002-0.009-0.0090.0000.0000.0000.000
167A240GLY00.0630.01322.527-0.024-0.0240.0000.0000.0000.000
168A241THR0-0.069-0.01621.1800.0180.0180.0000.0000.0000.000
169A242ILE0-0.0090.01623.342-0.007-0.0070.0000.0000.0000.000
170A243GLU-1-0.920-0.96921.401-0.313-0.3130.0000.0000.0000.000
171A244LYS10.9230.96024.7220.1860.1860.0000.0000.0000.000
172A245VAL0-0.009-0.01028.0280.0000.0000.0000.0000.0000.000
173A246GLU-1-0.944-0.95931.545-0.134-0.1340.0000.0000.0000.000
174A247THR00.0030.00334.9920.0030.0030.0000.0000.0000.000
175A248ASP-1-0.823-0.91338.693-0.093-0.0930.0000.0000.0000.000
176A249LYS10.9660.96140.7610.0940.0940.0000.0000.0000.000
177A250MET0-0.057-0.02343.9030.0030.0030.0000.0000.0000.000
178A251GLY00.0500.03443.8340.0040.0040.0000.0000.0000.000
179A252LEU0-0.050-0.02644.7020.0030.0030.0000.0000.0000.000
180A253SER0-0.099-0.03440.5850.0010.0010.0000.0000.0000.000
181A254GLN0-0.050-0.04435.943-0.005-0.0050.0000.0000.0000.000
182A255THR00.000-0.00733.8920.0030.0030.0000.0000.0000.000
183A256ALA0-0.028-0.00330.059-0.002-0.0020.0000.0000.0000.000
184A257PHE00.0260.01128.365-0.004-0.0040.0000.0000.0000.000
185A258ILE00.005-0.03225.217-0.006-0.0060.0000.0000.0000.000
186A259LYS11.0141.02315.8450.5000.5000.0000.0000.0000.000
187A260PRO0-0.020-0.00122.1170.0020.0020.0000.0000.0000.000
188A261GLY0-0.006-0.02219.350-0.032-0.0320.0000.0000.0000.000
189A262ALA0-0.0230.00818.420-0.045-0.0450.0000.0000.0000.000
190A263ASP-1-0.880-0.95117.577-0.496-0.4960.0000.0000.0000.000
191A264MET0-0.041-0.00719.6120.0150.0150.0000.0000.0000.000
192A265TYR0-0.0230.00020.4490.0300.0300.0000.0000.0000.000
193A266ASP-1-0.922-0.95619.541-0.411-0.4110.0000.0000.0000.000
194A267LEU0-0.040-0.00520.878-0.008-0.0080.0000.0000.0000.000
195A268ASN00.0490.01722.1870.0340.0340.0000.0000.0000.000
196A269HIS0-0.002-0.00421.6000.0320.0320.0000.0000.0000.000
197A270VAL00.003-0.00523.529-0.020-0.0200.0000.0000.0000.000
198A271THR0-0.013-0.00726.0220.0100.0100.0000.0000.0000.000
199A272VAL0-0.017-0.00528.172-0.004-0.0040.0000.0000.0000.000
200A273LEU0-0.039-0.02429.0950.0080.0080.0000.0000.0000.000
201A274LYS10.9690.99032.9580.0720.0720.0000.0000.0000.000
202A275ARG10.7550.85436.2470.0820.0820.0000.0000.0000.000
203A276SER0-0.007-0.00537.6810.0010.0010.0000.0000.0000.000
204A277ALA0-0.0040.01039.4790.0030.0030.0000.0000.0000.000
205A278GLU-1-0.837-0.91541.460-0.059-0.0590.0000.0000.0000.000
206A279ALA0-0.039-0.01043.503-0.004-0.0040.0000.0000.0000.000
207A280GLY0-0.013-0.00243.9140.0030.0030.0000.0000.0000.000
208A281THR00.041-0.00645.520-0.002-0.0020.0000.0000.0000.000
209A282THR0-0.097-0.03646.3510.0010.0010.0000.0000.0000.000
210A283ASP-1-0.926-0.95142.695-0.091-0.0910.0000.0000.0000.000