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: 22K8R

Calculation Name: 5BNF-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BNF

Chain ID: A

ChEMBL ID:

UniProt ID: F1S5D9

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2698241.314351
FMO2-HF: Nuclear repulsion 2608047.389253
FMO2-HF: Total energy -90193.925098
FMO2-MP2: Total energy -90452.468157


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:54:TRP )


Summations of interaction energy for fragment #1(A:54:TRP )
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.
-31.149-17.99722.744-10.479-25.42-0.02
Interaction energy analysis for fragmet #1(A:54:TRP )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.015
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].
3A56GLY 00.0240.0182.578-2.0680.6600.185-1.326-1.588-0.001
4A57LYS 10.9650.9734.144-1.250-1.1160.001-0.042-0.0930.000
5A58GLY 00.0600.0445.979-0.277-0.2770.0000.0000.0000.000
6A59SER 0-0.045-0.0656.8140.9480.9480.0000.0000.0000.000
7A60THR 0-0.036-0.0149.6980.0620.0620.0000.0000.0000.000
8A61VAL 00.0480.00912.986-0.022-0.0220.0000.0000.0000.000
9A62ASP -1-0.842-0.91115.180-0.622-0.6220.0000.0000.0000.000
10A63PHE 0-0.033-0.00814.1950.0860.0860.0000.0000.0000.000
11A64GLN 00.035-0.00315.6090.1020.1020.0000.0000.0000.000
12A65GLU -1-0.873-0.94918.829-0.501-0.5010.0000.0000.0000.000
13A66ILE 0-0.034-0.01017.8070.0830.0830.0000.0000.0000.000
14A67ILE 00.0090.00018.3490.0710.0710.0000.0000.0000.000
15A68LEU 0-0.036-0.01321.3490.0490.0490.0000.0000.0000.000
16A69ARG 10.9580.98124.0470.3900.3900.0000.0000.0000.000
17A70ARG 10.8030.90619.7100.3900.3900.0000.0000.0000.000
18A87CYS 00.0850.03625.1450.0320.0320.0000.0000.0000.000
19A72TYR 00.037-0.00126.7220.0210.0210.0000.0000.0000.000
20A73THR 0-0.045-0.03328.7230.0190.0190.0000.0000.0000.000
21A74TYR 00.038-0.00628.2340.0190.0190.0000.0000.0000.000
22A75ILE 0-0.0060.00230.3270.0130.0130.0000.0000.0000.000
23A76ARG 10.9240.97032.8920.1960.1960.0000.0000.0000.000
24A77VAL 0-0.044-0.01633.6870.0070.0070.0000.0000.0000.000
25A78VAL 0-0.0510.00229.9980.0090.0090.0000.0000.0000.000
26A79GLN 0-0.064-0.03432.8040.0140.0140.0000.0000.0000.000
27A80PRO 00.0100.02234.914-0.003-0.0030.0000.0000.0000.000
28A81GLU -1-0.887-0.95236.874-0.085-0.0850.0000.0000.0000.000
29A82LEU 0-0.040-0.02931.7450.0040.0040.0000.0000.0000.000
30A83GLY 00.0090.00334.217-0.012-0.0120.0000.0000.0000.000
31A84ASP -1-0.928-0.95436.093-0.113-0.1130.0000.0000.0000.000
32A85ARG 10.8260.92530.5740.1100.1100.0000.0000.0000.000
33A86ASP -1-0.864-0.95430.190-0.226-0.2260.0000.0000.0000.000
34A88GLN 00.0340.02724.675-0.036-0.0360.0000.0000.0000.000
35A89LYS 10.9370.96125.4080.1560.1560.0000.0000.0000.000
36A90ILE 0-0.0040.00823.194-0.013-0.0130.0000.0000.0000.000
37A91LYS 10.9840.99420.8900.4380.4380.0000.0000.0000.000
38A92LYS 10.8350.92720.4010.3850.3850.0000.0000.0000.000
39A93ALA 00.0500.03020.433-0.029-0.0290.0000.0000.0000.000
40A94PHE 0-0.009-0.01115.650-0.011-0.0110.0000.0000.0000.000
41A95THR 0-0.018-0.02315.930-0.051-0.0510.0000.0000.0000.000
42A96ASP -1-0.862-0.93915.600-0.517-0.5170.0000.0000.0000.000
43A97ALA 0-0.0170.00116.147-0.007-0.0070.0000.0000.0000.000
44A98PHE 0-0.008-0.00310.7200.0280.0280.0000.0000.0000.000
45A99ILE 00.0280.01610.969-0.238-0.2380.0000.0000.0000.000
46A100SER 0-0.077-0.04511.0720.1650.1650.0000.0000.0000.000
47A101LYS 10.8550.94310.1520.5600.5600.0000.0000.0000.000
48A102ASP -1-0.844-0.9205.111-1.693-1.5930.000-0.002-0.0990.000
49A103PRO 0-0.002-0.0042.875-0.3870.6810.137-0.304-0.9010.001
50A184CYS 0-0.011-0.0223.6100.2452.5671.330-0.826-2.8270.005
51A105SER 0-0.043-0.0115.865-0.103-0.1030.0000.0000.0000.000
52A106ALA 0-0.0120.0149.102-0.137-0.1370.0000.0000.0000.000
53A107ARG 10.9560.96011.4350.0640.0640.0000.0000.0000.000
54A108GLU -1-0.896-0.96614.9520.1260.1260.0000.0000.0000.000
55A109GLU -1-0.835-0.93118.1550.0640.0640.0000.0000.0000.000
56A110ASP -1-0.908-0.92514.370-0.132-0.1320.0000.0000.0000.000
57A111TYR 0-0.046-0.06614.089-0.113-0.1130.0000.0000.0000.000
58A112ASP -1-0.875-0.93219.647-0.036-0.0360.0000.0000.0000.000
59A113LEU 0-0.033-0.02122.575-0.002-0.0020.0000.0000.0000.000
60A114LEU 00.023-0.00119.4130.0010.0010.0000.0000.0000.000
61A115MET 0-0.009-0.00321.472-0.003-0.0030.0000.0000.0000.000
62A116LYS 10.9040.96324.7350.1020.1020.0000.0000.0000.000
63A117LEU 0-0.050-0.03625.6700.0040.0040.0000.0000.0000.000
64A118GLY 00.0420.01526.277-0.007-0.0070.0000.0000.0000.000
65A119HIS 0-0.0100.02027.3090.0080.0080.0000.0000.0000.000
66A120GLN 00.0460.01129.493-0.018-0.0180.0000.0000.0000.000
67A121THR 0-0.0220.00231.1910.0100.0100.0000.0000.0000.000
68A122VAL 0-0.0120.00831.553-0.006-0.0060.0000.0000.0000.000
69A123PRO 0-0.021-0.00734.3370.0070.0070.0000.0000.0000.000
70A205CYS 00.024-0.02433.5590.0060.0060.0000.0000.0000.000
71A125ASP -1-0.892-0.95238.1920.0000.0000.0000.0000.0000.000
72A126LYS 10.8580.91735.7040.0230.0230.0000.0000.0000.000
73A127THR 00.0160.01730.582-0.004-0.0040.0000.0000.0000.000
74A128VAL 0-0.048-0.02730.3480.0090.0090.0000.0000.0000.000
75A129PHE 00.0260.00526.199-0.004-0.0040.0000.0000.0000.000
76A130TRP 0-0.054-0.02720.3610.0140.0140.0000.0000.0000.000
77A131SER 00.0280.01124.0940.0130.0130.0000.0000.0000.000
78A132LYS 10.9240.95820.480-0.094-0.0940.0000.0000.0000.000
79A133THR 0-0.021-0.03623.349-0.005-0.0050.0000.0000.0000.000
80A134LYS 10.9150.99019.6760.1100.1100.0000.0000.0000.000
81A135GLU -1-0.961-0.98022.122-0.096-0.0960.0000.0000.0000.000
82A136NME 00.0250.03124.6090.0060.0060.0000.0000.0000.000
83A144ACE 00.0240.00234.9540.0020.0020.0000.0000.0000.000
84A145LYS 10.9500.95635.1920.0680.0680.0000.0000.0000.000
85A146GLY 00.0420.04635.9920.0050.0050.0000.0000.0000.000
86A147LEU 0-0.075-0.03134.1400.0060.0060.0000.0000.0000.000
87A148PHE 00.0390.01530.802-0.005-0.0050.0000.0000.0000.000
88A149THR 00.0180.01227.0770.0120.0120.0000.0000.0000.000
89A150LEU 00.0590.03121.534-0.013-0.0130.0000.0000.0000.000
90A151GLU -1-0.744-0.87721.921-0.051-0.0510.0000.0000.0000.000
91A152ASN 0-0.050-0.00524.423-0.006-0.0060.0000.0000.0000.000
92A153THR 0-0.044-0.01725.635-0.006-0.0060.0000.0000.0000.000
93A154LEU 00.0450.00126.258-0.016-0.0160.0000.0000.0000.000
94A155LEU 0-0.001-0.01522.255-0.024-0.0240.0000.0000.0000.000
95A156GLY 00.0270.01321.482-0.022-0.0220.0000.0000.0000.000
96A157TYR 0-0.0290.00021.813-0.027-0.0270.0000.0000.0000.000
97A158ILE 0-0.050-0.04620.975-0.028-0.0280.0000.0000.0000.000
98A159ALA 00.0090.00417.326-0.051-0.0510.0000.0000.0000.000
99A160ASP -1-0.880-0.94017.122-0.232-0.2320.0000.0000.0000.000
100A161ASP -1-0.916-0.94416.292-0.318-0.3180.0000.0000.0000.000
101A162LEU 0-0.123-0.04114.564-0.103-0.1030.0000.0000.0000.000
102A163SER 0-0.056-0.0368.9900.0720.0720.0000.0000.0000.000
103A164TRP 0-0.0170.00210.005-0.146-0.1460.0000.0000.0000.000
104A178CYS 0-0.033-0.0153.115-4.000-1.5040.335-1.041-1.790-0.008
105A166GLY 00.0380.0377.978-0.283-0.2830.0000.0000.0000.000
106A167LYS 10.9780.9786.2691.8781.8780.0000.0000.0000.000
107A168VAL 00.0530.0407.4060.5170.5170.0000.0000.0000.000
108A169GLY 0-0.003-0.0019.597-0.089-0.0890.0000.0000.0000.000
109A170SER 0-0.042-0.01010.3270.1590.1590.0000.0000.0000.000
110A171SER 00.0240.00012.2760.0200.0200.0000.0000.0000.000
111A172GLU -1-0.983-0.98713.123-0.978-0.9780.0000.0000.0000.000
112A173ILE 0-0.029-0.02010.449-0.175-0.1750.0000.0000.0000.000
113A174ASN 00.0270.0214.8330.5000.5000.0000.0000.0000.000
114A175LEU 00.0340.0047.328-0.238-0.2380.0000.0000.0000.000
115A176GLU -1-0.939-0.9524.604-5.300-5.1130.000-0.012-0.1750.000
116A177SER 0-0.038-0.0222.166-6.854-6.1795.008-2.570-3.112-0.020
117A179PRO 0-0.0100.0122.008-4.621-1.87910.388-4.071-9.0590.011
118A180ASP -1-0.817-0.9202.9081.209-0.9300.1712.750-0.7820.001
119A181ARG 10.9300.9415.6050.1620.1620.0000.0000.0000.000
120A182ARG 10.9020.9427.627-1.100-1.1000.0000.0000.0000.000
121A183ASN 00.0050.0082.402-5.091-2.2525.189-3.035-4.994-0.009
122A185ASN 00.010-0.0035.663-0.381-0.3810.0000.0000.0000.000
123A186SER 0-0.066-0.0308.475-0.167-0.1670.0000.0000.0000.000
124A187ASN 00.0510.0537.193-0.644-0.6440.0000.0000.0000.000
125A188PHE 00.069-0.0068.801-0.273-0.2730.0000.0000.0000.000
126A189VAL 00.0450.0649.755-0.110-0.1100.0000.0000.0000.000
127A190SER 0-0.035-0.03910.3940.0260.0260.0000.0000.0000.000
128A191VAL 00.0180.02212.443-0.076-0.0760.0000.0000.0000.000
129A192PHE 00.0160.02214.428-0.065-0.0650.0000.0000.0000.000
130A193TRP 00.0260.01514.0010.0210.0210.0000.0000.0000.000
131A194ASN 0-0.075-0.04315.557-0.037-0.0370.0000.0000.0000.000
132A195LEU 00.0140.02218.112-0.018-0.0180.0000.0000.0000.000
133A196LEU 0-0.005-0.00720.000-0.019-0.0190.0000.0000.0000.000
134A197SER 00.0170.00120.446-0.013-0.0130.0000.0000.0000.000
135A198LYS 10.8940.96422.267-0.163-0.1630.0000.0000.0000.000
136A199ARG 10.8970.93424.375-0.055-0.0550.0000.0000.0000.000
137A200PHE 0-0.048-0.02325.650-0.010-0.0100.0000.0000.0000.000
138A201ALA 0-0.010-0.00826.926-0.004-0.0040.0000.0000.0000.000
139A202GLU -1-0.864-0.92028.1710.0690.0690.0000.0000.0000.000
140A203ASN 0-0.070-0.04429.706-0.004-0.0040.0000.0000.0000.000
141A204ALA 00.0110.02731.860-0.009-0.0090.0000.0000.0000.000
142A206GLY 00.0020.00837.349-0.004-0.0040.0000.0000.0000.000
143A207MET 0-0.049-0.01838.8790.0080.0080.0000.0000.0000.000
144A208VAL 00.0540.03533.237-0.005-0.0050.0000.0000.0000.000
145A209GLN 00.0330.01033.7560.0060.0060.0000.0000.0000.000
146A210VAL 00.0280.01428.7560.0000.0000.0000.0000.0000.000
147A211PHE 0-0.032-0.01530.007-0.001-0.0010.0000.0000.0000.000
148A212LEU 00.010-0.01228.5050.0080.0080.0000.0000.0000.000
149A213ASN 00.0850.07127.298-0.017-0.0170.0000.0000.0000.000
150A214GLY 00.0760.02230.0560.0120.0120.0000.0000.0000.000
151A215SER 0-0.017-0.04830.4700.0050.0050.0000.0000.0000.000
152A216ILE 0-0.064-0.03926.0670.0060.0060.0000.0000.0000.000
153A217SER 0-0.019-0.02929.130-0.003-0.0030.0000.0000.0000.000
154A218ASN 00.0430.02927.645-0.015-0.0150.0000.0000.0000.000
155A219ALA 0-0.018-0.00327.6160.0090.0090.0000.0000.0000.000
156A220PHE 0-0.026-0.00527.8250.0000.0000.0000.0000.0000.000
157A221ASP -1-0.774-0.85922.5540.2900.2900.0000.0000.0000.000
158A222LYS 11.0210.98524.810-0.199-0.1990.0000.0000.0000.000
159A223THR 0-0.077-0.05319.5170.0290.0290.0000.0000.0000.000
160A224SER 0-0.045-0.02119.5500.0320.0320.0000.0000.0000.000
161A225THR 00.027-0.01118.4640.0310.0310.0000.0000.0000.000
162A226PHE 00.0710.03920.736-0.004-0.0040.0000.0000.0000.000
163A227GLY 0-0.004-0.00224.242-0.009-0.0090.0000.0000.0000.000
164A228ARG 10.8860.95217.344-0.410-0.4100.0000.0000.0000.000
165A229VAL 0-0.049-0.03020.2980.0060.0060.0000.0000.0000.000
166A230GLU -1-0.839-0.93223.4880.0840.0840.0000.0000.0000.000
167A231VAL 00.0010.01025.965-0.014-0.0140.0000.0000.0000.000
168A232HIS 0-0.038-0.03225.946-0.022-0.0220.0000.0000.0000.000
169A233SER 0-0.002-0.00126.296-0.004-0.0040.0000.0000.0000.000
170A234LEU 0-0.0350.01028.895-0.016-0.0160.0000.0000.0000.000
171A235GLN 00.0600.02032.1340.0130.0130.0000.0000.0000.000
172A236PRO 00.0460.02235.014-0.008-0.0080.0000.0000.0000.000
173A237SER 0-0.024-0.00638.034-0.004-0.0040.0000.0000.0000.000
174A238LYS 10.8650.94535.235-0.028-0.0280.0000.0000.0000.000
175A239VAL 0-0.0250.01034.767-0.006-0.0060.0000.0000.0000.000
176A240HIS 00.0480.04238.0950.0090.0090.0000.0000.0000.000
177A241THR 0-0.035-0.03539.7990.0040.0040.0000.0000.0000.000
178A242LEU 00.0110.01732.369-0.003-0.0030.0000.0000.0000.000
179A243LYS 10.8370.90336.542-0.024-0.0240.0000.0000.0000.000
180A244ALA 00.0210.00334.1400.0000.0000.0000.0000.0000.000
181A245TRP 0-0.039-0.03034.199-0.003-0.0030.0000.0000.0000.000
182A246VAL 00.0110.01133.5800.0030.0030.0000.0000.0000.000
183A247ILE 0-0.036-0.02332.655-0.006-0.0060.0000.0000.0000.000
184A248HIS 0-0.059-0.03733.9560.0070.0070.0000.0000.0000.000
185A249ASP -1-0.829-0.91334.1540.0110.0110.0000.0000.0000.000
186A250SER 0-0.049-0.03836.7270.0050.0050.0000.0000.0000.000
187A251GLY 00.0030.01338.4030.0010.0010.0000.0000.0000.000
188A252LYS 10.8650.95035.472-0.063-0.0630.0000.0000.0000.000
189A253THR 00.005-0.01838.1780.0000.0000.0000.0000.0000.000
190A254PRO 00.0370.01536.4840.0040.0040.0000.0000.0000.000
191A255ARG 10.8190.92530.950-0.112-0.1120.0000.0000.0000.000
192A256ASP -1-0.791-0.89332.4810.1230.1230.0000.0000.0000.000
193A257THR 00.016-0.00534.669-0.010-0.0100.0000.0000.0000.000
194A279CYS 0-0.013-0.00936.6690.0080.0080.0000.0000.0000.000
195A259SER 0-0.053-0.03038.4090.0010.0010.0000.0000.0000.000
196A260GLY 00.0050.03736.4020.0030.0030.0000.0000.0000.000
197A261SER 00.025-0.01033.959-0.002-0.0020.0000.0000.0000.000
198A262SER 00.0520.04230.0170.0010.0010.0000.0000.0000.000
199A263ILE 00.0550.01232.3780.0020.0020.0000.0000.0000.000
200A264ASN 0-0.0110.00234.368-0.010-0.0100.0000.0000.0000.000
201A265GLU -1-0.952-0.98030.1900.1860.1860.0000.0000.0000.000
202A266LEU 0-0.048-0.00630.9620.0020.0020.0000.0000.0000.000
203A267GLN 00.0600.02033.006-0.008-0.0080.0000.0000.0000.000
204A268LEU 0-0.012-0.01535.341-0.005-0.0050.0000.0000.0000.000
205A269ILE 0-0.049-0.00329.5680.0010.0010.0000.0000.0000.000
206A270LEU 0-0.017-0.00933.754-0.004-0.0040.0000.0000.0000.000
207A271ARG 10.9400.95936.146-0.077-0.0770.0000.0000.0000.000
208A272GLY 0-0.0020.02236.909-0.004-0.0040.0000.0000.0000.000
209A273LYS 10.8370.92531.568-0.110-0.1100.0000.0000.0000.000
210A274ASN 0-0.043-0.02638.163-0.007-0.0070.0000.0000.0000.000
211A275ILE 0-0.0270.00435.994-0.006-0.0060.0000.0000.0000.000
212A276LYS 10.9290.96639.926-0.036-0.0360.0000.0000.0000.000
213A277PHE 00.0610.01835.2060.0010.0010.0000.0000.0000.000
214A278THR 0-0.046-0.01939.023-0.005-0.0050.0000.0000.0000.000
215A280GLN 00.0120.00038.553-0.003-0.0030.0000.0000.0000.000
216A281GLU -1-0.753-0.87538.2310.0600.0600.0000.0000.0000.000
217A282ASN 0-0.072-0.05038.105-0.010-0.0100.0000.0000.0000.000
218A283TYR 00.0250.04437.6220.0010.0010.0000.0000.0000.000
219A284ARG 10.9630.96435.3620.0060.0060.0000.0000.0000.000
220A1NME 00.0270.03037.4190.0010.0010.0000.0000.0000.000