FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: J2QN9

Calculation Name: 2OPT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OPT

Chain ID: A

ChEMBL ID:

UniProt ID: Q53901

Base Structure: X-ray

Registration Date: 2023-09-27

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

DOI:

Apendix: None


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 209
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2083431.024527
FMO2-HF: Nuclear repulsion 2003669.525825
FMO2-HF: Total energy -79761.498702
FMO2-MP2: Total energy -79992.783577


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:27:ALA)


Summations of interaction energy for fragment #1(A:27:ALA)
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.
-0.6760.8150.025-0.686-0.829-0.001
Interaction energy analysis for fragmet #1(A:27:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.027
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].
3A29ALA00.0470.0393.668-0.6110.8800.025-0.686-0.829-0.001
4A30PRO0-0.010-0.0186.5340.3650.3650.0000.0000.0000.000
5A31LEU00.0010.0069.957-0.109-0.1090.0000.0000.0000.000
6A32THR00.0270.01811.3600.0280.0280.0000.0000.0000.000
7A33GLN00.0630.00914.1530.0030.0030.0000.0000.0000.000
8A34ASP-1-0.855-0.92915.831-0.294-0.2940.0000.0000.0000.000
9A35ARG10.9410.9899.6320.5870.5870.0000.0000.0000.000
10A36ILE0-0.011-0.01713.0290.0270.0270.0000.0000.0000.000
11A37VAL00.0530.02914.4770.0270.0270.0000.0000.0000.000
12A38VAL00.0190.02714.5690.0140.0140.0000.0000.0000.000
13A39THR0-0.075-0.05112.2850.0060.0060.0000.0000.0000.000
14A40ALA0-0.014-0.01714.5620.0280.0280.0000.0000.0000.000
15A41LEU00.0210.01717.8440.0180.0180.0000.0000.0000.000
16A42GLY00.0410.03017.1050.0080.0080.0000.0000.0000.000
17A43ILE0-0.053-0.03015.7840.0170.0170.0000.0000.0000.000
18A44LEU00.0260.01419.0660.0110.0110.0000.0000.0000.000
19A45ASP-1-0.823-0.89121.282-0.091-0.0910.0000.0000.0000.000
20A46ALA0-0.060-0.02320.3910.0060.0060.0000.0000.0000.000
21A47GLU-1-0.891-0.93419.7740.0070.0070.0000.0000.0000.000
22A48GLY0-0.057-0.01823.7190.0080.0080.0000.0000.0000.000
23A49LEU00.010-0.04024.6140.0020.0020.0000.0000.0000.000
24A50ASP-1-0.966-0.99225.924-0.005-0.0050.0000.0000.0000.000
25A51ALA0-0.028-0.00122.4350.0070.0070.0000.0000.0000.000
26A52LEU00.0150.03119.6500.0070.0070.0000.0000.0000.000
27A53SER00.0240.02821.2950.0030.0030.0000.0000.0000.000
28A54MET00.0940.03219.7800.0000.0000.0000.0000.0000.000
29A55ARG10.9230.96018.167-0.088-0.0880.0000.0000.0000.000
30A56ARG10.7430.86016.2370.0060.0060.0000.0000.0000.000
31A57LEU00.0750.04414.7940.0100.0100.0000.0000.0000.000
32A58ALA00.008-0.00713.866-0.010-0.0100.0000.0000.0000.000
33A59GLN0-0.041-0.02412.4860.0200.0200.0000.0000.0000.000
34A60GLU-1-0.912-0.96211.5950.0580.0580.0000.0000.0000.000
35A61LEU0-0.024-0.0109.429-0.024-0.0240.0000.0000.0000.000
36A62LYS10.8410.9426.849-0.243-0.2430.0000.0000.0000.000
37A63THR00.0300.0248.8900.1110.1110.0000.0000.0000.000
38A64GLY0-0.015-0.00711.1480.0100.0100.0000.0000.0000.000
39A65HIS00.047-0.01414.603-0.027-0.0270.0000.0000.0000.000
40A66ALA0-0.0070.01317.706-0.019-0.0190.0000.0000.0000.000
41A67SER00.0370.01413.188-0.016-0.0160.0000.0000.0000.000
42A68LEU00.0320.02315.351-0.032-0.0320.0000.0000.0000.000
43A69TYR00.0140.00116.638-0.017-0.0170.0000.0000.0000.000
44A70ALA0-0.039-0.02718.677-0.007-0.0070.0000.0000.0000.000
45A71HIS0-0.084-0.03915.423-0.037-0.0370.0000.0000.0000.000
46A72VAL0-0.023-0.02418.271-0.015-0.0150.0000.0000.0000.000
47A73GLY00.0480.06120.8780.0010.0010.0000.0000.0000.000
48A74ASN0-0.048-0.04522.5030.0030.0030.0000.0000.0000.000
49A75ARG10.8700.88923.8760.0090.0090.0000.0000.0000.000
50A76ASP-1-0.891-0.94724.923-0.025-0.0250.0000.0000.0000.000
51A77GLU-1-0.834-0.89825.266-0.033-0.0330.0000.0000.0000.000
52A78LEU0-0.029-0.01719.356-0.010-0.0100.0000.0000.0000.000
53A79LEU00.004-0.01923.125-0.011-0.0110.0000.0000.0000.000
54A80ASP-1-0.804-0.86725.432-0.053-0.0530.0000.0000.0000.000
55A81LEU0-0.057-0.03721.258-0.008-0.0080.0000.0000.0000.000
56A82VAL0-0.047-0.02321.081-0.012-0.0120.0000.0000.0000.000
57A83PHE00.0310.00523.384-0.005-0.0050.0000.0000.0000.000
58A84ASP-1-0.742-0.88025.895-0.104-0.1040.0000.0000.0000.000
59A85ILE0-0.034-0.01519.761-0.005-0.0050.0000.0000.0000.000
60A86VAL00.0150.00023.985-0.008-0.0080.0000.0000.0000.000
61A87LEU00.003-0.00325.6470.0040.0040.0000.0000.0000.000
62A88THR0-0.041-0.00424.3360.0000.0000.0000.0000.0000.000
63A89GLU-1-0.896-0.92925.298-0.113-0.1130.0000.0000.0000.000
64A90VAL0-0.057-0.01028.7180.0060.0060.0000.0000.0000.000
65A91GLU-1-0.963-0.98630.947-0.109-0.1090.0000.0000.0000.000
66A92VAL0-0.045-0.01434.2120.0060.0060.0000.0000.0000.000
67A93PRO00.0020.00537.351-0.003-0.0030.0000.0000.0000.000
68A94GLU-1-0.879-0.95339.394-0.068-0.0680.0000.0000.0000.000
69A95PRO0-0.010-0.01141.1640.0010.0010.0000.0000.0000.000
70A96GLU-1-0.863-0.92343.711-0.057-0.0570.0000.0000.0000.000
71A97PRO0-0.023-0.02546.9580.0020.0020.0000.0000.0000.000
72A98GLY0-0.020-0.01050.7510.0000.0000.0000.0000.0000.000
73A99ARG10.8650.93643.5200.0540.0540.0000.0000.0000.000
74A100TRP00.0150.00647.8690.0000.0000.0000.0000.0000.000
75A101ALA00.0540.01647.473-0.001-0.0010.0000.0000.0000.000
76A102GLU-1-0.914-0.98346.721-0.042-0.0420.0000.0000.0000.000
77A103GLN00.0450.03743.0370.0000.0000.0000.0000.0000.000
78A104VAL00.0450.03442.673-0.003-0.0030.0000.0000.0000.000
79A105LYS10.9150.95842.8330.0370.0370.0000.0000.0000.000
80A106GLU-1-0.935-0.97338.949-0.066-0.0660.0000.0000.0000.000
81A107MET00.0450.01838.395-0.003-0.0030.0000.0000.0000.000
82A108CYS0-0.054-0.01037.946-0.001-0.0010.0000.0000.0000.000
83A109ARG10.8330.89638.5510.0470.0470.0000.0000.0000.000
84A110SER0-0.025-0.00334.277-0.003-0.0030.0000.0000.0000.000
85A111LEU00.0710.04533.551-0.003-0.0030.0000.0000.0000.000
86A112ARG10.8000.88933.9670.0440.0440.0000.0000.0000.000
87A113ARG10.9240.95831.7750.0720.0720.0000.0000.0000.000
88A114MET00.0210.04028.703-0.002-0.0020.0000.0000.0000.000
89A115PHE00.024-0.01129.524-0.001-0.0010.0000.0000.0000.000
90A116LEU0-0.077-0.03030.9080.0020.0020.0000.0000.0000.000
91A117ALA0-0.046-0.00127.2590.0020.0020.0000.0000.0000.000
92A118HIS10.7420.83623.4190.1000.1000.0000.0000.0000.000
93A119ARG11.0191.01326.1220.0350.0350.0000.0000.0000.000
94A120ASP-1-0.830-0.91527.109-0.031-0.0310.0000.0000.0000.000
95A121LEU00.0120.01526.6710.0030.0030.0000.0000.0000.000
96A122ALA00.0410.01229.3520.0000.0000.0000.0000.0000.000
97A123ARG10.8670.93631.3610.0230.0230.0000.0000.0000.000
98A124ILE0-0.048-0.00726.4770.0020.0020.0000.0000.0000.000
99A125ALA00.0270.00130.7870.0010.0010.0000.0000.0000.000
100A126ILE0-0.062-0.00432.7970.0010.0010.0000.0000.0000.000
101A127ASP-1-0.911-0.95534.023-0.031-0.0310.0000.0000.0000.000
102A128ARG10.8030.88529.3110.0410.0410.0000.0000.0000.000
103A129VAL00.0290.01234.4960.0000.0000.0000.0000.0000.000
104A130PRO00.0000.01032.468-0.003-0.0030.0000.0000.0000.000
105A131LEU0-0.035-0.03433.095-0.001-0.0010.0000.0000.0000.000
106A132GLY00.0240.03229.0500.0010.0010.0000.0000.0000.000
107A133PRO0-0.041-0.02626.1450.0030.0030.0000.0000.0000.000
108A134ASN0-0.001-0.02325.2460.0010.0010.0000.0000.0000.000
109A135GLY00.0050.00229.3910.0050.0050.0000.0000.0000.000
110A136MET0-0.038-0.02932.1080.0040.0040.0000.0000.0000.000
111A137VAL0-0.0050.01331.5420.0040.0040.0000.0000.0000.000
112A138GLY00.0410.02133.5170.0030.0030.0000.0000.0000.000
113A139MET00.0030.00635.0130.0060.0060.0000.0000.0000.000
114A140GLU-1-0.926-0.96237.521-0.054-0.0540.0000.0000.0000.000
115A141ARG10.8270.92035.3840.0800.0800.0000.0000.0000.000
116A142THR0-0.002-0.01338.3290.0030.0030.0000.0000.0000.000
117A143MET0-0.036-0.01640.8040.0040.0040.0000.0000.0000.000
118A144ASN0-0.0110.00142.4510.0050.0050.0000.0000.0000.000
119A145LEU00.0190.00842.3280.0030.0030.0000.0000.0000.000
120A146LEU0-0.0140.01744.1850.0030.0030.0000.0000.0000.000
121A147ARG10.9860.98646.9730.0420.0420.0000.0000.0000.000
122A148SER0-0.098-0.05247.4120.0020.0020.0000.0000.0000.000
123A149GLY0-0.009-0.01349.3770.0010.0010.0000.0000.0000.000
124A150GLY0-0.051-0.02351.3960.0020.0020.0000.0000.0000.000
125A151LEU0-0.043-0.01449.4880.0020.0020.0000.0000.0000.000
126A152HIS00.0390.01952.287-0.001-0.0010.0000.0000.0000.000
127A153ASP-1-0.863-0.95651.079-0.034-0.0340.0000.0000.0000.000
128A154GLU-1-0.933-0.97150.311-0.026-0.0260.0000.0000.0000.000
129A155LEU0-0.0280.00650.8680.0000.0000.0000.0000.0000.000
130A156ALA0-0.035-0.01748.052-0.001-0.0010.0000.0000.0000.000
131A157ALA00.011-0.00246.096-0.002-0.0020.0000.0000.0000.000
132A158TYR00.0210.00645.891-0.001-0.0010.0000.0000.0000.000
133A159GLY00.0240.01046.9800.0000.0000.0000.0000.0000.000
134A160GLY00.027-0.00243.728-0.001-0.0010.0000.0000.0000.000
135A161ASP-1-0.925-0.94542.504-0.037-0.0370.0000.0000.0000.000
136A162LEU0-0.024-0.00743.1010.0000.0000.0000.0000.0000.000
137A163LEU0-0.014-0.02742.7580.0000.0000.0000.0000.0000.000
138A164SER0-0.026-0.00438.532-0.001-0.0010.0000.0000.0000.000
139A165THR00.0430.02739.6030.0000.0000.0000.0000.0000.000
140A166PHE0-0.035-0.00941.6900.0010.0010.0000.0000.0000.000
141A167VAL00.001-0.01037.4390.0010.0010.0000.0000.0000.000
142A168THR0-0.021-0.02335.812-0.002-0.0020.0000.0000.0000.000
143A169ALA0-0.015-0.00637.9480.0010.0010.0000.0000.0000.000
144A170GLU-1-0.859-0.94240.540-0.029-0.0290.0000.0000.0000.000
145A171ALA0-0.0070.01435.2650.0010.0010.0000.0000.0000.000
146A172LEU0-0.025-0.01735.5380.0010.0010.0000.0000.0000.000
147A173GLU-1-0.933-0.98637.199-0.022-0.0220.0000.0000.0000.000
148A174GLN00.0250.00536.7900.0010.0010.0000.0000.0000.000
149A175SER0-0.025-0.01833.9620.0000.0000.0000.0000.0000.000
150A176SER0-0.086-0.01835.9250.0030.0030.0000.0000.0000.000
151A177ARG10.8710.95837.6980.0290.0290.0000.0000.0000.000
152A188ALA00.0310.01441.5610.0010.0010.0000.0000.0000.000
153A189GLY00.027-0.00443.5700.0000.0000.0000.0000.0000.000
154A190VAL00.0140.00845.7710.0010.0010.0000.0000.0000.000
155A191PHE00.014-0.00346.5570.0000.0000.0000.0000.0000.000
156A192ALA00.0830.04447.9520.0010.0010.0000.0000.0000.000
157A193ASP-1-0.841-0.92449.679-0.014-0.0140.0000.0000.0000.000
158A194GLN0-0.076-0.02750.7230.0010.0010.0000.0000.0000.000
159A195LEU00.0290.02151.4550.0010.0010.0000.0000.0000.000
160A196HIS0-0.028-0.01253.4900.0000.0000.0000.0000.0000.000
161A197GLY0-0.0010.00255.2920.0000.0000.0000.0000.0000.000
162A198TYR0-0.006-0.00556.7640.0010.0010.0000.0000.0000.000
163A199LEU00.000-0.00856.5050.0000.0000.0000.0000.0000.000
164A200LYS10.9470.96459.0900.0120.0120.0000.0000.0000.000
165A201SER0-0.118-0.05460.9990.0000.0000.0000.0000.0000.000
166A202LEU00.0370.03261.2130.0010.0010.0000.0000.0000.000
167A203PRO0-0.002-0.00664.4620.0000.0000.0000.0000.0000.000
168A204ALA00.0490.02267.7230.0000.0000.0000.0000.0000.000
169A205THR0-0.038-0.02068.6700.0000.0000.0000.0000.0000.000
170A206SER0-0.037-0.01568.5780.0000.0000.0000.0000.0000.000
171A207PHE00.011-0.00264.2270.0000.0000.0000.0000.0000.000
172A208PRO00.0410.03565.2080.0000.0000.0000.0000.0000.000
173A209ASN0-0.003-0.01963.2970.0000.0000.0000.0000.0000.000
174A210LEU00.0360.02259.346-0.001-0.0010.0000.0000.0000.000
175A211VAL00.0160.01360.5820.0000.0000.0000.0000.0000.000
176A212HIS0-0.062-0.03261.9050.0000.0000.0000.0000.0000.000
177A213LEU0-0.019-0.02158.512-0.001-0.0010.0000.0000.0000.000
178A214ALA00.0180.02857.346-0.001-0.0010.0000.0000.0000.000
179A215GLY00.0610.02555.2660.0000.0000.0000.0000.0000.000
180A216PRO0-0.010-0.00453.702-0.001-0.0010.0000.0000.0000.000
181A217ILE0-0.020-0.01752.748-0.001-0.0010.0000.0000.0000.000
182A218THR0-0.022-0.01051.1490.0000.0000.0000.0000.0000.000
183A219SER0-0.119-0.05249.8740.0000.0000.0000.0000.0000.000
184A220LEU0-0.032-0.02648.478-0.001-0.0010.0000.0000.0000.000
185A221ASP-1-0.840-0.91445.016-0.030-0.0300.0000.0000.0000.000
186A222SER00.038-0.00941.3200.0000.0000.0000.0000.0000.000
187A223ASP-1-0.818-0.88741.417-0.042-0.0420.0000.0000.0000.000
188A224ARG10.9100.97943.7860.0280.0280.0000.0000.0000.000
189A225ARG10.8490.92445.1020.0260.0260.0000.0000.0000.000
190A226PHE00.0390.01840.5960.0000.0000.0000.0000.0000.000
191A227GLU-1-0.801-0.91143.835-0.043-0.0430.0000.0000.0000.000
192A228LEU0-0.029-0.00846.8100.0010.0010.0000.0000.0000.000
193A229GLY00.0140.00247.7950.0010.0010.0000.0000.0000.000
194A230LEU00.0100.00443.5990.0000.0000.0000.0000.0000.000
195A231GLU-1-1.006-1.00947.191-0.031-0.0310.0000.0000.0000.000
196A232ILE0-0.044-0.01950.6810.0010.0010.0000.0000.0000.000
197A233ILE00.0100.01446.7880.0010.0010.0000.0000.0000.000
198A234ILE00.0130.00746.5720.0000.0000.0000.0000.0000.000
199A235ALA0-0.021-0.00850.5570.0000.0000.0000.0000.0000.000
200A236GLY0-0.005-0.00153.6330.0010.0010.0000.0000.0000.000
201A237LEU00.006-0.00148.3420.0000.0000.0000.0000.0000.000
202A238LEU00.004-0.00653.0240.0000.0000.0000.0000.0000.000
203A239ALA0-0.064-0.02355.0920.0010.0010.0000.0000.0000.000
204A240GLY00.0510.02756.5740.0010.0010.0000.0000.0000.000
205A241ALA0-0.021-0.02454.8050.0000.0000.0000.0000.0000.000
206A242GLY0-0.044-0.03456.8840.0000.0000.0000.0000.0000.000
207A243GLU-1-0.994-0.98360.096-0.022-0.0220.0000.0000.0000.000
208A244ALA0-0.035-0.01458.8050.0000.0000.0000.0000.0000.000
209A245ALA0-0.075-0.01660.1530.0010.0010.0000.0000.0000.000