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: 537QZ

Calculation Name: 1J1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J1J

Chain ID: A

ChEMBL ID:

UniProt ID: Q15631

Base Structure: X-ray

Registration Date: 2023-06-20

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 -2577767.105661
FMO2-HF: Nuclear repulsion 2491708.398058
FMO2-HF: Total energy -86058.707603
FMO2-MP2: Total energy -86316.111779


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-18.228-7.1394.918-6.557-9.449-0.047
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.013
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].
3A3VAL00.038-0.0113.290-1.9970.5480.051-1.445-1.1510.005
4A4SER00.0230.0135.9030.5030.5030.0000.0000.0000.000
5A5GLU-1-0.813-0.8682.467-9.594-5.0182.457-3.190-3.842-0.032
6A6ILE00.0370.0262.502-1.919-0.1071.233-0.588-2.457-0.001
7A7PHE0-0.009-0.0183.6100.3330.4730.0120.057-0.2090.000
8A8VAL0-0.0170.0016.5810.3040.3040.0000.0000.0000.000
9A9GLU-1-0.908-0.9582.539-7.237-5.2211.165-1.391-1.790-0.019
10A10LEU0-0.020-0.0185.9730.4960.4960.0000.0000.0000.000
11A11GLN0-0.033-0.0108.2740.2150.2150.0000.0000.0000.000
12A12GLY00.0290.0219.6020.1460.1460.0000.0000.0000.000
13A13PHE0-0.034-0.0226.3730.2110.2110.0000.0000.0000.000
14A14LEU0-0.028-0.01811.2830.1070.1070.0000.0000.0000.000
15A15ALA0-0.0160.00013.7830.0620.0620.0000.0000.0000.000
16A16ALA00.0690.03514.3960.0530.0530.0000.0000.0000.000
17A17GLU-1-0.826-0.89615.601-0.119-0.1190.0000.0000.0000.000
18A18GLN0-0.025-0.02117.4140.0390.0390.0000.0000.0000.000
19A19ASP-1-0.874-0.92918.698-0.197-0.1970.0000.0000.0000.000
20A20ILE0-0.028-0.00918.5210.0260.0260.0000.0000.0000.000
21A21ARG10.8160.89619.0310.1730.1730.0000.0000.0000.000
22A22GLU-1-0.778-0.86623.722-0.142-0.1420.0000.0000.0000.000
23A23GLU-1-0.829-0.91324.936-0.062-0.0620.0000.0000.0000.000
24A24ILE0-0.0320.00224.7300.0140.0140.0000.0000.0000.000
25A25ARG10.8240.88424.5620.1300.1300.0000.0000.0000.000
26A26LYS10.9000.96128.5990.0920.0920.0000.0000.0000.000
27A27VAL0-0.0130.00730.9330.0050.0050.0000.0000.0000.000
28A28VAL00.0040.00231.2730.0060.0060.0000.0000.0000.000
29A29GLN00.0350.00733.7580.0060.0060.0000.0000.0000.000
30A30SER0-0.0070.00735.6390.0030.0030.0000.0000.0000.000
31A31LEU0-0.010-0.00135.4180.0040.0040.0000.0000.0000.000
32A32GLU-1-0.818-0.91536.461-0.047-0.0470.0000.0000.0000.000
33A33GLN0-0.124-0.05939.533-0.001-0.0010.0000.0000.0000.000
34A34THR00.0190.00641.1620.0030.0030.0000.0000.0000.000
35A35ALA00.0500.02041.5610.0030.0030.0000.0000.0000.000
36A36ARG10.8450.91439.3940.0460.0460.0000.0000.0000.000
37A37GLU-1-0.798-0.86544.993-0.026-0.0260.0000.0000.0000.000
38A38ILE0-0.004-0.00945.0280.0010.0010.0000.0000.0000.000
39A39LEU0-0.0080.00547.5100.0020.0020.0000.0000.0000.000
40A40THR0-0.026-0.01849.3350.0010.0010.0000.0000.0000.000
41A41LEU0-0.074-0.03050.4980.0010.0010.0000.0000.0000.000
42A42LEU00.0090.00750.7320.0010.0010.0000.0000.0000.000
43A43GLN0-0.017-0.03351.929-0.001-0.0010.0000.0000.0000.000
44A44GLY00.004-0.00654.9800.0000.0000.0000.0000.0000.000
45A45VAL00.006-0.00457.2360.0000.0000.0000.0000.0000.000
46A46HIS0-0.093-0.03355.3430.0010.0010.0000.0000.0000.000
47A47GLN0-0.065-0.03758.612-0.001-0.0010.0000.0000.0000.000
48A48GLY0-0.0020.00163.0490.0000.0000.0000.0000.0000.000
49A49ALA00.0120.01266.1750.0000.0000.0000.0000.0000.000
50A50GLY0-0.030-0.01168.4950.0000.0000.0000.0000.0000.000
51A51PHE00.006-0.00362.5480.0000.0000.0000.0000.0000.000
52A52GLN0-0.006-0.01364.3820.0010.0010.0000.0000.0000.000
53A53ASP-1-0.820-0.89761.224-0.008-0.0080.0000.0000.0000.000
54A54ILE00.0480.03859.1900.0000.0000.0000.0000.0000.000
55A55PRO00.0530.02858.8270.0000.0000.0000.0000.0000.000
56A56LYS10.9480.97658.7000.0070.0070.0000.0000.0000.000
57A57ARG10.8350.90956.3670.0120.0120.0000.0000.0000.000
58A58CYS00.0140.00454.523-0.001-0.0010.0000.0000.0000.000
59A59LEU0-0.0230.00053.7450.0000.0000.0000.0000.0000.000
60A60LYS10.9920.99353.4740.0110.0110.0000.0000.0000.000
61A61ALA0-0.020-0.00250.543-0.001-0.0010.0000.0000.0000.000
62A62ARG10.8190.87249.188-0.003-0.0030.0000.0000.0000.000
63A63GLU-1-0.903-0.95349.046-0.005-0.0050.0000.0000.0000.000
64A64HIS10.8040.88145.3480.0180.0180.0000.0000.0000.000
65A65PHE00.0820.00843.860-0.002-0.0020.0000.0000.0000.000
66A66GLY00.0290.02543.8050.0010.0010.0000.0000.0000.000
67A67THR0-0.028-0.01241.7750.0000.0000.0000.0000.0000.000
68A68VAL00.0030.01240.153-0.002-0.0020.0000.0000.0000.000
69A69LYS10.8940.95338.968-0.007-0.0070.0000.0000.0000.000
70A70THR0-0.0310.00038.0790.0020.0020.0000.0000.0000.000
71A71HIS0-0.002-0.00936.212-0.001-0.0010.0000.0000.0000.000
72A72LEU00.0200.00634.491-0.003-0.0030.0000.0000.0000.000
73A73THR0-0.004-0.00733.3640.0030.0030.0000.0000.0000.000
74A74SER0-0.009-0.00532.2950.0000.0000.0000.0000.0000.000
75A75LEU0-0.019-0.01829.269-0.003-0.0030.0000.0000.0000.000
76A76LYS10.8130.88028.634-0.023-0.0230.0000.0000.0000.000
77A77THR0-0.062-0.02027.8080.0070.0070.0000.0000.0000.000
78A78LYS10.7540.86625.5540.0500.0500.0000.0000.0000.000
79A79PHE00.0030.00322.468-0.014-0.0140.0000.0000.0000.000
80A80PRO00.0480.02319.2570.0110.0110.0000.0000.0000.000
81A81ALA00.0480.02522.506-0.002-0.0020.0000.0000.0000.000
82A82GLU-1-0.932-0.95519.4240.1170.1170.0000.0000.0000.000
83A83GLN0-0.033-0.03117.138-0.026-0.0260.0000.0000.0000.000
84A84TYR00.004-0.00722.675-0.018-0.0180.0000.0000.0000.000
85A85TYR0-0.055-0.07225.789-0.008-0.0080.0000.0000.0000.000
86A86ARG10.7720.89314.8150.0720.0720.0000.0000.0000.000
87A87PHE00.0390.00819.677-0.016-0.0160.0000.0000.0000.000
88A88HIS00.0410.04025.228-0.004-0.0040.0000.0000.0000.000
89A89GLU-1-0.866-0.93826.179-0.052-0.0520.0000.0000.0000.000
90A90HIS0-0.055-0.03924.792-0.016-0.0160.0000.0000.0000.000
91A91TRP00.0570.01427.4070.0010.0010.0000.0000.0000.000
92A92ARG10.8670.94329.3360.0310.0310.0000.0000.0000.000
93A93PHE0-0.0060.00334.1740.0040.0040.0000.0000.0000.000
94A94VAL00.0410.01335.2420.0030.0030.0000.0000.0000.000
95A95LEU00.0170.01334.1010.0030.0030.0000.0000.0000.000
96A96GLN00.022-0.00137.5420.0010.0010.0000.0000.0000.000
97A97ARG10.8100.89340.2090.0270.0270.0000.0000.0000.000
98A98LEU00.0010.00838.8970.0000.0000.0000.0000.0000.000
99A99VAL00.0090.01440.6700.0020.0020.0000.0000.0000.000
100A100PHE0-0.0170.00043.3240.0010.0010.0000.0000.0000.000
101A101LEU0-0.023-0.00744.7550.0010.0010.0000.0000.0000.000
102A102ALA00.0080.00645.2520.0010.0010.0000.0000.0000.000
103A103ALA00.028-0.00347.2190.0020.0020.0000.0000.0000.000
104A104PHE0-0.020-0.01849.2940.0000.0000.0000.0000.0000.000
105A105VAL0-0.009-0.00949.9550.0000.0000.0000.0000.0000.000
106A106VAL00.0260.01650.5680.0010.0010.0000.0000.0000.000
107A107TYR00.0070.02653.1670.0000.0000.0000.0000.0000.000
108A108LEU0-0.033-0.03055.0170.0000.0000.0000.0000.0000.000
109A109GLU-1-0.865-0.89755.5020.0030.0030.0000.0000.0000.000
110A110THR0-0.081-0.05856.0530.0010.0010.0000.0000.0000.000
111A111GLU-1-0.858-0.91558.0920.0000.0000.0000.0000.0000.000
112A112THR00.0180.01254.3980.0000.0000.0000.0000.0000.000
113A113LEU0-0.010-0.00949.271-0.002-0.0020.0000.0000.0000.000
114A114VAL0-0.0090.01947.4740.0020.0020.0000.0000.0000.000
115A115THR00.0630.03546.747-0.001-0.0010.0000.0000.0000.000
116A116ARG10.7630.85137.920-0.027-0.0270.0000.0000.0000.000
117A117GLU-1-0.792-0.90942.3460.0230.0230.0000.0000.0000.000
118A118ALA00.0700.04243.7760.0000.0000.0000.0000.0000.000
119A119VAL0-0.036-0.02642.162-0.002-0.0020.0000.0000.0000.000
120A120THR0-0.028-0.03039.045-0.003-0.0030.0000.0000.0000.000
121A121GLU-1-0.901-0.94041.2930.0190.0190.0000.0000.0000.000
122A122ILE0-0.057-0.03543.881-0.002-0.0020.0000.0000.0000.000
123A123LEU0-0.033-0.02639.378-0.002-0.0020.0000.0000.0000.000
124A124GLY0-0.069-0.02839.965-0.002-0.0020.0000.0000.0000.000
125A125ILE0-0.047-0.01634.940-0.001-0.0010.0000.0000.0000.000
126A126GLU-1-0.711-0.80234.1050.0280.0280.0000.0000.0000.000
127A127PRO00.0570.03536.474-0.001-0.0010.0000.0000.0000.000
128A128ASP-1-0.821-0.88535.3420.0380.0380.0000.0000.0000.000
129A129ARG10.8290.89935.226-0.062-0.0620.0000.0000.0000.000
130A130GLU-1-0.859-0.93235.6690.0420.0420.0000.0000.0000.000
131A131LYS10.8890.94328.568-0.100-0.1000.0000.0000.0000.000
132A132GLY00.0740.03730.4930.0040.0040.0000.0000.0000.000
133A133PHE00.0030.01230.064-0.006-0.0060.0000.0000.0000.000
134A134HIS0-0.040-0.03331.6220.0080.0080.0000.0000.0000.000
135A135LEU00.0170.02534.247-0.006-0.0060.0000.0000.0000.000
136A136ASP-1-0.771-0.87133.6670.0170.0170.0000.0000.0000.000
137A137VAL00.0450.01636.203-0.003-0.0030.0000.0000.0000.000
138A138GLU-1-0.841-0.93736.7120.0030.0030.0000.0000.0000.000
139A139ASP-1-0.807-0.89535.377-0.015-0.0150.0000.0000.0000.000
140A140TYR0-0.039-0.04338.735-0.002-0.0020.0000.0000.0000.000
141A141LEU00.0400.01741.725-0.002-0.0020.0000.0000.0000.000
142A142SER0-0.040-0.03740.283-0.003-0.0030.0000.0000.0000.000
143A143GLY00.011-0.00442.652-0.002-0.0020.0000.0000.0000.000
144A144VAL00.001-0.00444.138-0.001-0.0010.0000.0000.0000.000
145A145LEU0-0.025-0.00545.033-0.001-0.0010.0000.0000.0000.000
146A146ILE0-0.047-0.01943.334-0.001-0.0010.0000.0000.0000.000
147A147LEU0-0.0210.00247.830-0.001-0.0010.0000.0000.0000.000
148A148ALA00.0540.02850.2470.0000.0000.0000.0000.0000.000
149A149SER0-0.019-0.03150.8960.0000.0000.0000.0000.0000.000
150A150GLU-1-0.803-0.85851.782-0.017-0.0170.0000.0000.0000.000
151A151LEU0-0.001-0.01253.6230.0000.0000.0000.0000.0000.000
152A152SER00.000-0.03255.8470.0000.0000.0000.0000.0000.000
153A153ARG10.8080.90154.3480.0170.0170.0000.0000.0000.000
154A154LEU00.0080.00057.2700.0000.0000.0000.0000.0000.000
155A155SER00.0220.00959.4920.0000.0000.0000.0000.0000.000
156A156VAL00.0570.02561.9630.0000.0000.0000.0000.0000.000
157A157ASN0-0.009-0.01359.8190.0000.0000.0000.0000.0000.000
158A158SER0-0.018-0.02563.5650.0000.0000.0000.0000.0000.000
159A159VAL0-0.023-0.01265.1700.0000.0000.0000.0000.0000.000
160A160THR0-0.053-0.03466.2730.0000.0000.0000.0000.0000.000
161A161ALA0-0.0180.00566.1450.0000.0000.0000.0000.0000.000
162A162GLY00.0170.01168.2160.0000.0000.0000.0000.0000.000
163A163ASP-1-0.846-0.91666.735-0.003-0.0030.0000.0000.0000.000
164A164TYR00.0430.01267.8400.0000.0000.0000.0000.0000.000
165A165SER0-0.0110.00468.3130.0010.0010.0000.0000.0000.000
166A166ARG10.8470.89961.9350.0030.0030.0000.0000.0000.000
167A167PRO00.0000.01563.7010.0000.0000.0000.0000.0000.000
168A168LEU00.0290.02064.1890.0000.0000.0000.0000.0000.000
169A169HIS10.8730.95062.7080.0000.0000.0000.0000.0000.000
170A170ILE00.0380.01958.5020.0010.0010.0000.0000.0000.000
171A171SER00.002-0.00259.5780.0000.0000.0000.0000.0000.000
172A172THR0-0.030-0.01660.8130.0000.0000.0000.0000.0000.000
173A173PHE00.0420.02253.3700.0000.0000.0000.0000.0000.000
174A174ILE0-0.020-0.01755.3150.0000.0000.0000.0000.0000.000
175A175ASN0-0.023-0.01556.0190.0010.0010.0000.0000.0000.000
176A176GLU-1-0.912-0.94856.6680.0060.0060.0000.0000.0000.000
177A177LEU0-0.026-0.01450.9330.0010.0010.0000.0000.0000.000
178A178ASP-1-0.771-0.86352.249-0.001-0.0010.0000.0000.0000.000
179A179SER0-0.045-0.03353.4310.0010.0010.0000.0000.0000.000
180A180GLY0-0.0010.00351.9320.0010.0010.0000.0000.0000.000
181A181PHE0-0.003-0.03145.3690.0010.0010.0000.0000.0000.000
182A182ARG10.7930.88849.259-0.001-0.0010.0000.0000.0000.000
183A183LEU0-0.0160.00350.0920.0010.0010.0000.0000.0000.000
184A184LEU0-0.037-0.00645.1630.0020.0020.0000.0000.0000.000
185A185ASN0-0.012-0.00444.106-0.003-0.0030.0000.0000.0000.000
186A186LEU00.011-0.00842.2770.0010.0010.0000.0000.0000.000
187A187LYS10.8890.94537.715-0.013-0.0130.0000.0000.0000.000
188A188ASN00.0570.04635.784-0.007-0.0070.0000.0000.0000.000
189A189ASP-1-0.751-0.87337.305-0.028-0.0280.0000.0000.0000.000
190A190SER0-0.052-0.01337.557-0.002-0.0020.0000.0000.0000.000
191A191LEU0-0.0190.00339.483-0.001-0.0010.0000.0000.0000.000
192A192ARG10.9720.98141.3740.0070.0070.0000.0000.0000.000
193A193LYS10.8310.88640.4650.0260.0260.0000.0000.0000.000
194A194ARG10.8840.95441.0910.0200.0200.0000.0000.0000.000
195A195TYR0-0.032-0.02445.4010.0000.0000.0000.0000.0000.000
196A196ASP-1-0.859-0.92147.317-0.012-0.0120.0000.0000.0000.000
197A197GLY0-0.0030.01548.811-0.001-0.0010.0000.0000.0000.000
198A198LEU00.0110.01050.5140.0000.0000.0000.0000.0000.000
199A199LYS10.8590.89251.7060.0130.0130.0000.0000.0000.000
200A200TYR0-0.040-0.00954.5140.0000.0000.0000.0000.0000.000
201A201ASP-1-0.739-0.84753.161-0.013-0.0130.0000.0000.0000.000
202A202VAL0-0.013-0.00155.9380.0010.0010.0000.0000.0000.000
203A203LYS10.9140.95158.2860.0100.0100.0000.0000.0000.000
204A204LYS10.8340.93356.5060.0150.0150.0000.0000.0000.000
205A205VAL0-0.039-0.00559.5000.0000.0000.0000.0000.0000.000
206A206GLU-1-0.852-0.92462.244-0.004-0.0040.0000.0000.0000.000
207A207GLU-1-0.875-0.93564.337-0.010-0.0100.0000.0000.0000.000
208A208VAL0-0.0100.00264.3010.0000.0000.0000.0000.0000.000
209A209VAL0-0.006-0.00965.6270.0000.0000.0000.0000.0000.000
210A210TYR0-0.008-0.00368.2390.0010.0010.0000.0000.0000.000
211A211ASP-1-0.846-0.89369.810-0.009-0.0090.0000.0000.0000.000
212A212LEU00.002-0.01269.0900.0000.0000.0000.0000.0000.000
213A213SER0-0.0240.00272.3270.0000.0000.0000.0000.0000.000
214A214ILE0-0.055-0.02774.2250.0000.0000.0000.0000.0000.000
215A215ARG10.7790.85873.4460.0080.0080.0000.0000.0000.000
216A216GLY0-0.0220.00877.5580.0000.0000.0000.0000.0000.000
217A217PHE0-0.052-0.02573.7290.0000.0000.0000.0000.0000.000