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: VR191

Calculation Name: 5BNF-A-Xray372

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: 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2685427.214466
FMO2-HF: Nuclear repulsion 2595423.35379
FMO2-HF: Total energy -90003.860676
FMO2-MP2: Total energy -90261.769409


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.
-31.204-18.19822.951-10.435-25.518-0.019
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 : -0.022 / q_NPA : -0.017
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].
3A56GLY00.0220.0182.578-2.0990.6890.177-1.341-1.6230.000
4A57LYS10.9640.9734.144-1.220-1.0840.000-0.040-0.0950.000
5A58GLY00.0600.0455.979-0.259-0.2590.0000.0000.0000.000
6A59SER0-0.042-0.0646.8140.9110.9110.0000.0000.0000.000
7A60THR0-0.033-0.0139.6980.0500.0500.0000.0000.0000.000
8A61VAL00.0420.00712.986-0.023-0.0230.0000.0000.0000.000
9A62ASP-1-0.841-0.91015.180-0.616-0.6160.0000.0000.0000.000
10A63PHE0-0.037-0.01114.1950.0850.0850.0000.0000.0000.000
11A64GLN00.041-0.00215.6100.0980.0980.0000.0000.0000.000
12A65GLU-1-0.876-0.94918.830-0.495-0.4950.0000.0000.0000.000
13A66ILE0-0.033-0.01017.8070.0810.0810.0000.0000.0000.000
14A67ILE00.0130.00218.3500.0680.0680.0000.0000.0000.000
15A68LEU0-0.040-0.01421.3490.0470.0470.0000.0000.0000.000
16A69ARG10.9570.98124.0470.3820.3820.0000.0000.0000.000
17A70ARG10.8030.90519.7100.3820.3820.0000.0000.0000.000
18A71CYS00.0890.03925.1460.0310.0310.0000.0000.0000.000
19A72TYR00.037-0.00126.7230.0200.0200.0000.0000.0000.000
20A73THR0-0.045-0.03428.7230.0180.0180.0000.0000.0000.000
21A74TYR00.037-0.00628.2340.0180.0180.0000.0000.0000.000
22A75ILE0-0.0050.00130.3270.0120.0120.0000.0000.0000.000
23A76ARG10.9250.97032.8920.1920.1920.0000.0000.0000.000
24A77VAL0-0.045-0.01733.6870.0060.0060.0000.0000.0000.000
25A78VAL0-0.0530.00229.9980.0080.0080.0000.0000.0000.000
26A79GLN0-0.062-0.03232.8040.0130.0130.0000.0000.0000.000
27A80PRO00.0110.02234.914-0.003-0.0030.0000.0000.0000.000
28A81GLU-1-0.889-0.95336.874-0.083-0.0830.0000.0000.0000.000
29A82LEU0-0.042-0.02831.7460.0040.0040.0000.0000.0000.000
30A83GLY00.0100.00334.217-0.011-0.0110.0000.0000.0000.000
31A84ASP-1-0.929-0.95536.094-0.110-0.1100.0000.0000.0000.000
32A85ARG10.8260.92530.5750.1070.1070.0000.0000.0000.000
33A86ASP-1-0.862-0.95330.191-0.221-0.2210.0000.0000.0000.000
34A88GLN00.0300.02524.675-0.035-0.0350.0000.0000.0000.000
35A89LYS10.9360.96125.4080.1530.1530.0000.0000.0000.000
36A90ILE0-0.0050.00723.194-0.013-0.0130.0000.0000.0000.000
37A91LYS10.9870.99520.8900.4320.4320.0000.0000.0000.000
38A92LYS10.8340.92620.4020.3790.3790.0000.0000.0000.000
39A93ALA00.0470.02920.432-0.028-0.0280.0000.0000.0000.000
40A94PHE0-0.010-0.01115.651-0.010-0.0100.0000.0000.0000.000
41A95THR0-0.009-0.02015.931-0.047-0.0470.0000.0000.0000.000
42A96ASP-1-0.867-0.94115.599-0.508-0.5080.0000.0000.0000.000
43A97ALA0-0.0150.00116.145-0.008-0.0080.0000.0000.0000.000
44A98PHE0-0.014-0.00510.7190.0320.0320.0000.0000.0000.000
45A99ILE00.0350.01910.968-0.228-0.2280.0000.0000.0000.000
46A100SER0-0.079-0.04611.0720.1650.1650.0000.0000.0000.000
47A101LYS10.8540.94310.1510.5470.5470.0000.0000.0000.000
48A102ASP-1-0.843-0.9185.111-1.650-1.552-0.001-0.001-0.0950.000
49A103PRO0-0.003-0.0062.875-0.4190.6530.136-0.304-0.9030.001
50A104CYS0-0.008-0.0213.6100.2142.5361.327-0.819-2.8300.005
51A105SER0-0.042-0.0115.865-0.084-0.0840.0000.0000.0000.000
52A106ALA0-0.0140.0139.102-0.136-0.1360.0000.0000.0000.000
53A107ARG10.9560.96211.4350.0580.0580.0000.0000.0000.000
54A108GLU-1-0.896-0.96514.9520.1310.1310.0000.0000.0000.000
55A109GLU-1-0.835-0.93118.1550.0700.0700.0000.0000.0000.000
56A110ASP-1-0.910-0.92714.370-0.123-0.1230.0000.0000.0000.000
57A111TYR0-0.045-0.06514.090-0.111-0.1110.0000.0000.0000.000
58A112ASP-1-0.874-0.93219.645-0.033-0.0330.0000.0000.0000.000
59A113LEU0-0.036-0.02322.573-0.002-0.0020.0000.0000.0000.000
60A114LEU00.022-0.00219.4140.0010.0010.0000.0000.0000.000
61A115MET0-0.005-0.00221.472-0.005-0.0050.0000.0000.0000.000
62A116LYS10.9010.96224.7340.0980.0980.0000.0000.0000.000
63A117LEU0-0.052-0.03725.6690.0040.0040.0000.0000.0000.000
64A118GLY00.0450.01626.277-0.008-0.0080.0000.0000.0000.000
65A119HIS0-0.0080.02127.3090.0070.0070.0000.0000.0000.000
66A120GLN00.0450.01129.493-0.018-0.0180.0000.0000.0000.000
67A121THR0-0.0220.00231.1910.0100.0100.0000.0000.0000.000
68A122VAL0-0.0120.00831.553-0.006-0.0060.0000.0000.0000.000
69A123PRO0-0.021-0.00734.3370.0060.0060.0000.0000.0000.000
70A124CYS00.022-0.02533.5590.0060.0060.0000.0000.0000.000
71A125ASP-1-0.892-0.95338.1930.0000.0000.0000.0000.0000.000
72A126LYS10.8610.91935.7040.0210.0210.0000.0000.0000.000
73A127THR00.0140.01630.582-0.004-0.0040.0000.0000.0000.000
74A128VAL0-0.045-0.02530.3480.0090.0090.0000.0000.0000.000
75A129PHE00.0220.00426.199-0.004-0.0040.0000.0000.0000.000
76A130TRP0-0.052-0.02720.3610.0140.0140.0000.0000.0000.000
77A131SER00.0280.01124.0930.0120.0120.0000.0000.0000.000
78A132LYS10.9250.95920.479-0.094-0.0940.0000.0000.0000.000
79A133THR0-0.022-0.03523.349-0.004-0.0040.0000.0000.0000.000
80A134LYS10.9110.99419.6750.1080.1080.0000.0000.0000.000
81A135GLU-1-0.931-0.95422.122-0.090-0.0900.0000.0000.0000.000
82A145LYS10.9750.96235.1920.0740.0740.0000.0000.0000.000
83A146GLY00.0350.03735.9710.0040.0040.0000.0000.0000.000
84A147LEU0-0.064-0.02434.1410.0060.0060.0000.0000.0000.000
85A148PHE00.0360.01430.802-0.005-0.0050.0000.0000.0000.000
86A149THR00.0150.01127.0770.0120.0120.0000.0000.0000.000
87A150LEU00.0600.03121.534-0.013-0.0130.0000.0000.0000.000
88A151GLU-1-0.740-0.87621.921-0.047-0.0470.0000.0000.0000.000
89A152ASN0-0.057-0.00924.423-0.006-0.0060.0000.0000.0000.000
90A153THR0-0.041-0.01525.635-0.006-0.0060.0000.0000.0000.000
91A154LEU00.037-0.00126.258-0.015-0.0150.0000.0000.0000.000
92A155LEU00.007-0.01322.256-0.023-0.0230.0000.0000.0000.000
93A156GLY00.0250.01421.482-0.022-0.0220.0000.0000.0000.000
94A157TYR0-0.031-0.00221.813-0.026-0.0260.0000.0000.0000.000
95A158ILE0-0.053-0.04720.976-0.027-0.0270.0000.0000.0000.000
96A159ALA00.0150.00617.326-0.049-0.0490.0000.0000.0000.000
97A160ASP-1-0.887-0.94217.122-0.227-0.2270.0000.0000.0000.000
98A161ASP-1-0.913-0.94316.293-0.310-0.3100.0000.0000.0000.000
99A162LEU0-0.123-0.04114.564-0.097-0.0970.0000.0000.0000.000
100A163SER0-0.056-0.0368.9900.0730.0730.0000.0000.0000.000
101A164TRP0-0.0130.00310.005-0.138-0.1380.0000.0000.0000.000
102A165CYS0-0.031-0.0133.115-3.972-1.4860.331-1.025-1.792-0.007
103A166GLY00.0370.0367.978-0.270-0.2700.0000.0000.0000.000
104A167LYS10.9780.9796.2691.8931.8930.0000.0000.0000.000
105A168VAL00.0510.0397.4060.4910.4910.0000.0000.0000.000
106A169GLY0-0.002-0.0019.597-0.095-0.0950.0000.0000.0000.000
107A170SER0-0.040-0.01010.3270.1580.1580.0000.0000.0000.000
108A171SER00.0250.00012.2760.0160.0160.0000.0000.0000.000
109A172GLU-1-0.983-0.98713.123-0.962-0.9620.0000.0000.0000.000
110A173ILE0-0.029-0.01910.449-0.164-0.1640.0000.0000.0000.000
111A174ASN00.0250.0214.8290.5050.5050.0000.0000.0000.000
112A175LEU00.0330.0037.328-0.235-0.2350.0000.0000.0000.000
113A176GLU-1-0.939-0.9524.581-5.237-5.049-0.001-0.011-0.1760.000
114A177SER0-0.034-0.0202.134-6.923-6.4385.332-2.662-3.155-0.021
115A179PRO0-0.0120.0122.008-4.849-2.10010.307-3.992-9.0630.011
116A180ASP-1-0.823-0.9222.9081.321-0.8370.1622.782-0.7860.001
117A181ARG10.9360.9425.6050.1540.1540.0000.0000.0000.000
118A182ARG10.9000.9417.627-1.084-1.0840.0000.0000.0000.000
119A183ASN00.0060.0082.402-5.137-2.2975.181-3.022-5.000-0.009
120A185ASN00.005-0.0045.663-0.342-0.3420.0000.0000.0000.000
121A186SER0-0.066-0.0308.475-0.161-0.1610.0000.0000.0000.000
122A187ASN00.0550.0557.193-0.637-0.6370.0000.0000.0000.000
123A188PHE00.064-0.0078.801-0.253-0.2530.0000.0000.0000.000
124A189VAL00.0470.0649.755-0.110-0.1100.0000.0000.0000.000
125A190SER0-0.033-0.03810.3950.0180.0180.0000.0000.0000.000
126A191VAL00.0120.02012.443-0.074-0.0740.0000.0000.0000.000
127A192PHE00.0170.02314.428-0.060-0.0600.0000.0000.0000.000
128A193TRP00.0270.01514.0010.0190.0190.0000.0000.0000.000
129A194ASN0-0.079-0.04515.557-0.040-0.0400.0000.0000.0000.000
130A195LEU00.0150.02318.112-0.017-0.0170.0000.0000.0000.000
131A196LEU00.003-0.00520.000-0.018-0.0180.0000.0000.0000.000
132A197SER00.005-0.00320.446-0.014-0.0140.0000.0000.0000.000
133A198LYS10.8960.96522.267-0.165-0.1650.0000.0000.0000.000
134A199ARG10.8990.93424.375-0.057-0.0570.0000.0000.0000.000
135A200PHE0-0.045-0.02225.650-0.010-0.0100.0000.0000.0000.000
136A201ALA0-0.012-0.00926.926-0.005-0.0050.0000.0000.0000.000
137A202GLU-1-0.861-0.91928.1710.0700.0700.0000.0000.0000.000
138A203ASN0-0.071-0.04529.706-0.004-0.0040.0000.0000.0000.000
139A204ALA00.0160.02831.860-0.009-0.0090.0000.0000.0000.000
140A206GLY0-0.0010.00837.349-0.004-0.0040.0000.0000.0000.000
141A207MET0-0.049-0.01938.8790.0070.0070.0000.0000.0000.000
142A208VAL00.0590.03733.237-0.005-0.0050.0000.0000.0000.000
143A209GLN00.0270.00833.7560.0060.0060.0000.0000.0000.000
144A210VAL00.0260.01328.7560.0000.0000.0000.0000.0000.000
145A211PHE0-0.024-0.01230.007-0.001-0.0010.0000.0000.0000.000
146A212LEU00.010-0.01128.5050.0080.0080.0000.0000.0000.000
147A213ASN00.0790.06827.300-0.017-0.0170.0000.0000.0000.000
148A214GLY00.0770.02330.0560.0120.0120.0000.0000.0000.000
149A215SER0-0.018-0.04930.4700.0040.0040.0000.0000.0000.000
150A216ILE0-0.061-0.03826.0670.0050.0050.0000.0000.0000.000
151A217SER0-0.018-0.02929.130-0.003-0.0030.0000.0000.0000.000
152A218ASN00.0390.02827.645-0.015-0.0150.0000.0000.0000.000
153A219ALA0-0.016-0.00227.6160.0090.0090.0000.0000.0000.000
154A220PHE0-0.025-0.00527.8250.0000.0000.0000.0000.0000.000
155A221ASP-1-0.774-0.85822.5540.2860.2860.0000.0000.0000.000
156A222LYS11.0200.98424.810-0.198-0.1980.0000.0000.0000.000
157A223THR0-0.081-0.05519.5170.0270.0270.0000.0000.0000.000
158A224SER0-0.040-0.01919.5500.0320.0320.0000.0000.0000.000
159A225THR00.027-0.01018.4630.0310.0310.0000.0000.0000.000
160A226PHE00.0680.03820.736-0.003-0.0030.0000.0000.0000.000
161A227GLY0-0.003-0.00324.240-0.009-0.0090.0000.0000.0000.000
162A228ARG10.8860.95117.344-0.409-0.4090.0000.0000.0000.000
163A229VAL0-0.050-0.03120.2980.0060.0060.0000.0000.0000.000
164A230GLU-1-0.838-0.93023.4880.0860.0860.0000.0000.0000.000
165A231VAL00.0030.01025.965-0.014-0.0140.0000.0000.0000.000
166A232HIS0-0.039-0.03225.946-0.022-0.0220.0000.0000.0000.000
167A233SER0-0.0020.00026.295-0.004-0.0040.0000.0000.0000.000
168A234LEU0-0.0360.01028.895-0.015-0.0150.0000.0000.0000.000
169A235GLN00.0610.02132.1340.0130.0130.0000.0000.0000.000
170A236PRO00.0440.02135.014-0.007-0.0070.0000.0000.0000.000
171A237SER0-0.024-0.00838.034-0.004-0.0040.0000.0000.0000.000
172A238LYS10.8650.94635.235-0.029-0.0290.0000.0000.0000.000
173A239VAL0-0.0210.01234.767-0.006-0.0060.0000.0000.0000.000
174A240HIS00.0460.04138.0950.0090.0090.0000.0000.0000.000
175A241THR0-0.036-0.03539.7990.0040.0040.0000.0000.0000.000
176A242LEU00.0120.01832.369-0.003-0.0030.0000.0000.0000.000
177A243LYS10.8350.90236.542-0.024-0.0240.0000.0000.0000.000
178A244ALA00.0190.00334.1400.0000.0000.0000.0000.0000.000
179A245TRP0-0.034-0.02834.199-0.002-0.0020.0000.0000.0000.000
180A246VAL00.0060.01033.5800.0030.0030.0000.0000.0000.000
181A247ILE0-0.035-0.02432.655-0.006-0.0060.0000.0000.0000.000
182A248HIS0-0.058-0.03633.9560.0060.0060.0000.0000.0000.000
183A249ASP-1-0.831-0.91434.1540.0110.0110.0000.0000.0000.000
184A250SER0-0.052-0.04036.7270.0050.0050.0000.0000.0000.000
185A251GLY00.0040.01238.4030.0010.0010.0000.0000.0000.000
186A252LYS10.8670.95235.473-0.063-0.0630.0000.0000.0000.000
187A253THR00.006-0.01638.1780.0000.0000.0000.0000.0000.000
188A254PRO00.0320.01336.4840.0040.0040.0000.0000.0000.000
189A255ARG10.8230.92630.949-0.111-0.1110.0000.0000.0000.000
190A256ASP-1-0.788-0.89332.4810.1220.1220.0000.0000.0000.000
191A257THR00.013-0.00434.669-0.009-0.0090.0000.0000.0000.000
192A258CYS0-0.012-0.00936.6690.0080.0080.0000.0000.0000.000
193A259SER0-0.055-0.03138.4090.0010.0010.0000.0000.0000.000
194A260GLY00.0050.03736.4010.0020.0020.0000.0000.0000.000
195A261SER00.024-0.00933.972-0.003-0.0030.0000.0000.0000.000
196A262SER00.0530.04230.0160.0010.0010.0000.0000.0000.000
197A263ILE00.0560.01332.3780.0020.0020.0000.0000.0000.000
198A264ASN0-0.0130.00134.368-0.010-0.0100.0000.0000.0000.000
199A265GLU-1-0.950-0.98030.1900.1840.1840.0000.0000.0000.000
200A266LEU0-0.049-0.00630.9610.0020.0020.0000.0000.0000.000
201A267GLN00.0640.02133.006-0.008-0.0080.0000.0000.0000.000
202A268LEU0-0.010-0.01435.341-0.005-0.0050.0000.0000.0000.000
203A269ILE0-0.052-0.00429.5680.0010.0010.0000.0000.0000.000
204A270LEU0-0.017-0.00933.754-0.004-0.0040.0000.0000.0000.000
205A271ARG10.9410.95936.146-0.077-0.0770.0000.0000.0000.000
206A272GLY0-0.0040.02036.909-0.004-0.0040.0000.0000.0000.000
207A273LYS10.8370.92631.568-0.110-0.1100.0000.0000.0000.000
208A274ASN0-0.042-0.02638.163-0.007-0.0070.0000.0000.0000.000
209A275ILE0-0.0260.00535.994-0.006-0.0060.0000.0000.0000.000
210A276LYS10.9270.96639.926-0.036-0.0360.0000.0000.0000.000
211A277PHE00.0630.01835.2060.0010.0010.0000.0000.0000.000
212A278THR0-0.046-0.01839.023-0.005-0.0050.0000.0000.0000.000
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