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: 3Q5RL

Calculation Name: 5DAJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DAJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HY46

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2305172.4628
FMO2-HF: Nuclear repulsion 2222326.914988
FMO2-HF: Total energy -82845.547812
FMO2-MP2: Total energy -83084.158357


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:5:LYS)


Summations of interaction energy for fragment #1(A:5:LYS)
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.
-49.723-47.6130.113-0.307-1.9160
Interaction energy analysis for fragmet #1(A:5:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.893
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].
3A7ASP-1-0.899-0.9673.196-27.897-26.3950.115-0.239-1.3780.000
4A8SER0-0.005-0.0114.3460.8541.078-0.001-0.026-0.1970.000
5A9GLU-1-0.798-0.8963.932-42.061-41.677-0.001-0.042-0.3410.000
6A10LYS10.8530.9416.18139.54439.5440.0000.0000.0000.000
7A11THR0-0.017-0.0108.5563.8073.8070.0000.0000.0000.000
8A12ARG10.8840.9477.95131.59931.5990.0000.0000.0000.000
9A13THR0-0.007-0.0078.6152.1722.1720.0000.0000.0000.000
10A14ALA0-0.0080.00511.3131.9831.9830.0000.0000.0000.000
11A15ILE0-0.004-0.00413.6591.7071.7070.0000.0000.0000.000
12A16LEU0-0.005-0.00312.4321.2761.2760.0000.0000.0000.000
13A17LEU0-0.003-0.00314.7500.9970.9970.0000.0000.0000.000
14A18ALA00.0290.02617.2001.0351.0350.0000.0000.0000.000
15A19ALA00.002-0.01319.1630.8950.8950.0000.0000.0000.000
16A20GLU-1-0.840-0.89818.589-15.614-15.6140.0000.0000.0000.000
17A21GLU-1-0.949-0.98621.148-12.512-12.5120.0000.0000.0000.000
18A22LEU00.014-0.00723.4220.7140.7140.0000.0000.0000.000
19A23PHE0-0.025-0.02221.8930.5470.5470.0000.0000.0000.000
20A24LEU0-0.0140.00125.0580.5270.5270.0000.0000.0000.000
21A25GLU-1-0.915-0.94527.081-10.271-10.2710.0000.0000.0000.000
22A26LYS10.8180.90828.54910.90410.9040.0000.0000.0000.000
23A27GLY00.0290.03329.3710.3950.3950.0000.0000.0000.000
24A28VAL0-0.015-0.00325.908-0.167-0.1670.0000.0000.0000.000
25A29SER00.0010.00228.230-0.264-0.2640.0000.0000.0000.000
26A30HIS0-0.0080.00531.113-0.083-0.0830.0000.0000.0000.000
27A31THR0-0.026-0.02825.210-0.020-0.0200.0000.0000.0000.000
28A32SER0-0.025-0.02126.785-0.243-0.2430.0000.0000.0000.000
29A33LEU00.0820.00920.613-0.275-0.2750.0000.0000.0000.000
30A34GLU-1-0.984-0.99022.298-11.225-11.2250.0000.0000.0000.000
31A35GLN0-0.021-0.01924.039-0.306-0.3060.0000.0000.0000.000
32A36ILE00.0570.04519.763-0.046-0.0460.0000.0000.0000.000
33A37ALA0-0.009-0.00319.514-0.500-0.5000.0000.0000.0000.000
34A38ARG10.9280.96120.31010.85910.8590.0000.0000.0000.000
35A39ALA0-0.0030.00122.772-0.023-0.0230.0000.0000.0000.000
36A40ALA00.0150.01917.470-0.238-0.2380.0000.0000.0000.000
37A41GLY0-0.0440.00417.935-0.732-0.7320.0000.0000.0000.000
38A42VAL0-0.008-0.01214.737-0.656-0.6560.0000.0000.0000.000
39A43THR00.0250.01316.6520.6570.6570.0000.0000.0000.000
40A44ARG11.0150.97917.94410.93710.9370.0000.0000.0000.000
41A45GLY00.0160.00518.263-0.009-0.0090.0000.0000.0000.000
42A46ALA00.0510.02713.639-0.338-0.3380.0000.0000.0000.000
43A47VAL00.0210.01314.226-0.916-0.9160.0000.0000.0000.000
44A48TYR0-0.038-0.03216.218-0.191-0.1910.0000.0000.0000.000
45A49TRP0-0.065-0.01610.0700.5100.5100.0000.0000.0000.000
46A50HIS0-0.006-0.0019.367-1.796-1.7960.0000.0000.0000.000
47A51PHE00.0350.01112.663-0.733-0.7330.0000.0000.0000.000
48A52GLN00.0160.03314.9330.2220.2220.0000.0000.0000.000
49A53ASN0-0.036-0.03618.2870.7670.7670.0000.0000.0000.000
50A54LYS10.8960.94720.37510.72210.7220.0000.0000.0000.000
51A55ALA00.0250.02722.301-0.341-0.3410.0000.0000.0000.000
52A56HIS00.0040.00315.804-1.032-1.0320.0000.0000.0000.000
53A57LEU0-0.017-0.00617.653-0.723-0.7230.0000.0000.0000.000
54A58PHE00.004-0.00918.289-0.706-0.7060.0000.0000.0000.000
55A59ASN00.001-0.01019.515-0.400-0.4000.0000.0000.0000.000
56A60GLU-1-0.873-0.93813.446-22.596-22.5960.0000.0000.0000.000
57A61MET0-0.050-0.01015.332-0.679-0.6790.0000.0000.0000.000
58A62LEU0-0.031-0.02117.224-0.177-0.1770.0000.0000.0000.000
59A63ASN00.0120.00115.2071.2351.2350.0000.0000.0000.000
60A64GLN0-0.043-0.01712.5990.8910.8910.0000.0000.0000.000
61A65VAL0-0.017-0.00215.079-0.188-0.1880.0000.0000.0000.000
62A66ARG10.8630.95418.05216.13916.1390.0000.0000.0000.000
63A67LEU00.0160.01717.921-0.787-0.7870.0000.0000.0000.000
64A68PRO0-0.0010.01015.9520.5000.5000.0000.0000.0000.000
65A69PRO00.036-0.00418.6800.5410.5410.0000.0000.0000.000
66A70GLU-1-0.876-0.93918.599-15.657-15.6570.0000.0000.0000.000
67A71GLN00.0520.01316.1490.6380.6380.0000.0000.0000.000
68A72LEU0-0.014-0.00121.0440.6350.6350.0000.0000.0000.000
69A73THR0-0.014-0.02623.9130.4630.4630.0000.0000.0000.000
70A74GLU-1-0.962-0.95021.855-13.808-13.8080.0000.0000.0000.000
71A75ARG10.8080.88524.72212.24412.2440.0000.0000.0000.000
72A76LEU0-0.023-0.01426.3860.4910.4910.0000.0000.0000.000
73A77SER0-0.057-0.05228.2230.4440.4440.0000.0000.0000.000
74A78GLY0-0.007-0.00230.5140.2920.2920.0000.0000.0000.000
75A79CYS0-0.0240.03331.060-0.049-0.0490.0000.0000.0000.000
76A80ASP-1-0.870-0.92728.637-11.177-11.1770.0000.0000.0000.000
77A81GLY0-0.042-0.04331.3630.2990.2990.0000.0000.0000.000
78A82SER0-0.082-0.04634.8630.1000.1000.0000.0000.0000.000
79A83ASP-1-0.798-0.90335.521-8.393-8.3930.0000.0000.0000.000
80A84PRO00.0670.03833.943-0.183-0.1830.0000.0000.0000.000
81A85LEU0-0.056-0.03834.449-0.150-0.1500.0000.0000.0000.000
82A86ARG10.9280.97635.1468.6358.6350.0000.0000.0000.000
83A87SER00.045-0.02030.453-0.066-0.0660.0000.0000.0000.000
84A88LEU0-0.0100.00730.918-0.306-0.3060.0000.0000.0000.000
85A89TYR00.0080.00532.204-0.128-0.1280.0000.0000.0000.000
86A90ASP-1-0.858-0.93630.617-9.746-9.7460.0000.0000.0000.000
87A91LEU0-0.028-0.01425.538-0.266-0.2660.0000.0000.0000.000
88A92CYS0-0.084-0.04928.555-0.243-0.2430.0000.0000.0000.000
89A93LEU00.0500.02031.011-0.067-0.0670.0000.0000.0000.000
90A94GLU-1-0.765-0.85026.148-11.996-11.9960.0000.0000.0000.000
91A95ALA0-0.058-0.01726.560-0.365-0.3650.0000.0000.0000.000
92A96VAL0-0.0040.01627.628-0.210-0.2100.0000.0000.0000.000
93A97GLN00.0440.01729.468-0.307-0.3070.0000.0000.0000.000
94A98SER0-0.123-0.09424.291-0.283-0.2830.0000.0000.0000.000
95A99LEU0-0.026-0.00725.679-0.450-0.4500.0000.0000.0000.000
96A100LEU00.0130.01527.973-0.144-0.1440.0000.0000.0000.000
97A101THR00.0030.00125.196-0.369-0.3690.0000.0000.0000.000
98A102GLN0-0.007-0.00120.992-0.901-0.9010.0000.0000.0000.000
99A103GLU-1-0.903-0.95222.603-12.961-12.9610.0000.0000.0000.000
100A104LYS10.9190.96314.81219.65119.6510.0000.0000.0000.000
101A105LYS10.9880.99220.51513.39613.3960.0000.0000.0000.000
102A106ARG10.9150.97222.06212.07012.0700.0000.0000.0000.000
103A107ARG10.8790.93221.82714.15514.1550.0000.0000.0000.000
104A108ILE00.0390.01018.2630.4220.4220.0000.0000.0000.000
105A109LEU0-0.003-0.00522.8090.2840.2840.0000.0000.0000.000
106A110THR00.0130.00225.6560.5760.5760.0000.0000.0000.000
107A111ILE0-0.030-0.02523.1200.3890.3890.0000.0000.0000.000
108A112LEU0-0.056-0.02625.3830.3340.3340.0000.0000.0000.000
109A113MET0-0.040-0.01027.1270.4090.4090.0000.0000.0000.000
110A114GLN0-0.0070.00830.1690.2830.2830.0000.0000.0000.000
111A115ARG10.8560.94428.58210.43610.4360.0000.0000.0000.000
112A116CYS0-0.041-0.02228.202-0.297-0.2970.0000.0000.0000.000
113A117GLU-1-0.852-0.91130.321-8.824-8.8240.0000.0000.0000.000
114A118PHE0-0.033-0.02627.665-0.210-0.2100.0000.0000.0000.000
115A119THR00.0360.01832.2570.1850.1850.0000.0000.0000.000
116A120GLU-1-0.903-0.97231.787-9.394-9.3940.0000.0000.0000.000
117A121GLU-1-0.907-0.95228.693-10.894-10.8940.0000.0000.0000.000
118A122LEU0-0.015-0.00926.173-0.576-0.5760.0000.0000.0000.000
119A123ARG10.9720.99128.0869.2589.2580.0000.0000.0000.000
120A124GLU-1-0.858-0.94221.041-14.189-14.1890.0000.0000.0000.000
121A125ALA0-0.032-0.02124.221-0.316-0.3160.0000.0000.0000.000
122A126GLN00.0100.00425.203-0.075-0.0750.0000.0000.0000.000
123A127GLU-1-0.944-0.96827.208-10.824-10.8240.0000.0000.0000.000
124A128ARG10.9800.97818.77615.17215.1720.0000.0000.0000.000
125A129ASN0-0.0330.00024.852-0.671-0.6710.0000.0000.0000.000
126A130ASN0-0.008-0.01826.3080.1210.1210.0000.0000.0000.000
127A131ALA0-0.0040.00925.4740.1890.1890.0000.0000.0000.000
128A132PHE00.0120.00622.6720.0520.0520.0000.0000.0000.000
129A133VAL00.0040.00225.5950.1100.1100.0000.0000.0000.000
130A134GLN0-0.055-0.02528.9070.3200.3200.0000.0000.0000.000
131A135MET00.0360.01924.3510.0520.0520.0000.0000.0000.000
132A136PHE00.0220.00927.5140.1460.1460.0000.0000.0000.000
133A137ILE0-0.018-0.02028.8770.3230.3230.0000.0000.0000.000
134A138GLU-1-0.886-0.95031.220-9.710-9.7100.0000.0000.0000.000
135A139LEU0-0.014-0.00126.6880.2290.2290.0000.0000.0000.000
136A140CYS0-0.024-0.00131.1830.2730.2730.0000.0000.0000.000
137A141GLU-1-0.913-0.94933.700-8.172-8.1720.0000.0000.0000.000
138A142GLN0-0.005-0.02031.4030.3030.3030.0000.0000.0000.000
139A143LEU00.0010.00733.1710.1990.1990.0000.0000.0000.000
140A144PHE00.027-0.01835.5760.2320.2320.0000.0000.0000.000
141A145ALA0-0.067-0.04438.5130.2810.2810.0000.0000.0000.000
142A146ARG10.9230.98832.2089.5169.5160.0000.0000.0000.000
143A147ASP-1-0.901-0.94140.022-7.176-7.1760.0000.0000.0000.000
144A148GLU-1-0.915-0.97838.883-7.991-7.9910.0000.0000.0000.000
145A149CYS0-0.076-0.02537.8790.0820.0820.0000.0000.0000.000
146A150ARG10.9981.00141.5167.3377.3370.0000.0000.0000.000
147A151VAL0-0.040-0.01743.8020.1600.1600.0000.0000.0000.000
148A152ARG10.8790.93941.3737.6637.6630.0000.0000.0000.000
149A153LEU0-0.0130.01542.029-0.007-0.0070.0000.0000.0000.000
150A154HIS0-0.0050.00845.9550.3000.3000.0000.0000.0000.000
151A155PRO0-0.020-0.03848.921-0.052-0.0520.0000.0000.0000.000
152A156GLY0-0.0110.00350.5820.0300.0300.0000.0000.0000.000
153A157MET0-0.0080.02344.009-0.041-0.0410.0000.0000.0000.000
154A158THR0-0.028-0.02144.766-0.075-0.0750.0000.0000.0000.000
155A159PRO00.0730.02439.912-0.032-0.0320.0000.0000.0000.000
156A160ARG10.9911.01039.6747.1827.1820.0000.0000.0000.000
157A161ILE0-0.036-0.02139.989-0.151-0.1510.0000.0000.0000.000
158A162ALA00.0560.03340.482-0.068-0.0680.0000.0000.0000.000
159A163SER00.0200.01135.560-0.113-0.1130.0000.0000.0000.000
160A164ARG10.8260.91136.1828.2978.2970.0000.0000.0000.000
161A165ALA0-0.0050.00438.153-0.058-0.0580.0000.0000.0000.000
162A166LEU00.0390.01534.582-0.034-0.0340.0000.0000.0000.000
163A167HIS00.0170.00230.4280.1220.1220.0000.0000.0000.000
164A168ALA00.0120.00634.402-0.164-0.1640.0000.0000.0000.000
165A169LEU00.0020.01436.874-0.020-0.0200.0000.0000.0000.000
166A170ILE00.0140.00630.767-0.053-0.0530.0000.0000.0000.000
167A171LEU0-0.027-0.01631.473-0.189-0.1890.0000.0000.0000.000
168A172GLY00.018-0.00133.360-0.077-0.0770.0000.0000.0000.000
169A173LEU00.0190.01734.5910.0310.0310.0000.0000.0000.000
170A174PHE0-0.021-0.01526.891-0.191-0.1910.0000.0000.0000.000
171A175ASN0-0.029-0.03032.3600.1250.1250.0000.0000.0000.000
172A176ASP-1-0.852-0.90434.255-8.062-8.0620.0000.0000.0000.000
173A177TRP0-0.033-0.00430.186-0.197-0.1970.0000.0000.0000.000
174A178LEU0-0.049-0.04128.949-0.085-0.0850.0000.0000.0000.000
175A179ARG10.8220.90932.7718.1628.1620.0000.0000.0000.000
176A180ASP-1-0.913-0.96935.849-7.822-7.8220.0000.0000.0000.000
177A181PRO00.0460.02234.2550.1060.1060.0000.0000.0000.000
178A182ARG10.8210.90236.3287.7127.7120.0000.0000.0000.000
179A183LEU0-0.083-0.02239.1860.1940.1940.0000.0000.0000.000
180A184PHE0-0.013-0.01635.0220.1470.1470.0000.0000.0000.000
181A185ASP-1-0.752-0.85035.825-9.185-9.1850.0000.0000.0000.000
182A186PRO0-0.088-0.05332.1270.0350.0350.0000.0000.0000.000
183A187ASP-1-0.962-0.96933.125-9.652-9.6520.0000.0000.0000.000
184A188THR0-0.032-0.05634.0070.1210.1210.0000.0000.0000.000
185A189ASP-1-0.808-0.90537.566-7.798-7.7980.0000.0000.0000.000
186A190ALA0-0.049-0.02134.3230.1190.1190.0000.0000.0000.000
187A191GLU-1-0.915-0.96836.283-8.305-8.3050.0000.0000.0000.000
188A192HIS00.010-0.00138.1680.2150.2150.0000.0000.0000.000
189A193LEU0-0.038-0.01137.7020.1830.1830.0000.0000.0000.000
190A194LEU0-0.032-0.01434.1730.0600.0600.0000.0000.0000.000
191A195GLU-1-0.837-0.91438.825-7.398-7.3980.0000.0000.0000.000
192A196PRO0-0.028-0.01041.7140.1210.1210.0000.0000.0000.000
193A197MET0-0.0100.00639.3570.1560.1560.0000.0000.0000.000
194A198PHE00.025-0.00535.4270.0310.0310.0000.0000.0000.000
195A199ARG10.8930.95041.4676.9456.9450.0000.0000.0000.000
196A200GLY0-0.028-0.01444.9230.1560.1560.0000.0000.0000.000
197A201LEU0-0.051-0.02140.3270.0920.0920.0000.0000.0000.000
198A202VAL0-0.027-0.02741.4380.0830.0830.0000.0000.0000.000
199A203ARG10.9120.95344.7726.3886.3880.0000.0000.0000.000
200A204ASP-1-0.936-0.95246.550-6.524-6.5240.0000.0000.0000.000
201A205TRP0-0.074-0.02538.1110.0210.0210.0000.0000.0000.000