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: R8ZN8

Calculation Name: 1VOL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VOL

Chain ID: A

ChEMBL ID:

UniProt ID: P28147

Base Structure: X-ray

Registration Date: 2023-09-24

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2246636.050834
FMO2-HF: Nuclear repulsion 2165950.046528
FMO2-HF: Total energy -80686.004306
FMO2-MP2: Total energy -80917.044769


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:113:ALA)


Summations of interaction energy for fragment #1(A:113: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.
-6.838-2.3191.361-2.239-3.642-0.009
Interaction energy analysis for fragmet #1(A:113:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.003
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].
3A115MET00.0330.0153.817-3.472-1.483-0.018-1.003-0.9680.001
4A116ASN0-0.016-0.0492.907-0.991-0.2770.051-0.208-0.5570.000
5A117ALA00.0660.0394.202-0.491-0.2240.000-0.081-0.1860.000
6A118PHE00.040-0.0045.5060.2610.2610.0000.0000.0000.000
7A119LYS10.8750.9806.123-0.768-0.7680.0000.0000.0000.000
8A120GLU-1-0.866-0.9208.527-0.436-0.4360.0000.0000.0000.000
9A121ILE0-0.047-0.0119.6690.0620.0620.0000.0000.0000.000
10A122THR0-0.032-0.01111.7360.0450.0450.0000.0000.0000.000
11A123THR00.0760.04213.126-0.005-0.0050.0000.0000.0000.000
12A124MET0-0.091-0.06111.5600.0290.0290.0000.0000.0000.000
13A125ALA0-0.012-0.02415.7080.0240.0240.0000.0000.0000.000
14A126ASP-1-0.881-0.94017.742-0.033-0.0330.0000.0000.0000.000
15A127ARG10.9100.96117.8270.1640.1640.0000.0000.0000.000
16A128ILE0-0.063-0.02520.2940.0070.0070.0000.0000.0000.000
17A129ASN0-0.026-0.01722.3540.0050.0050.0000.0000.0000.000
18A130LEU0-0.057-0.02619.2210.0090.0090.0000.0000.0000.000
19A131PRO00.0160.01821.5130.0050.0050.0000.0000.0000.000
20A132ARG11.0200.98317.594-0.046-0.0460.0000.0000.0000.000
21A133ASN00.0620.03620.2040.0000.0000.0000.0000.0000.000
22A134LYS10.9610.98320.0210.0270.0270.0000.0000.0000.000
23A135VAL0-0.018-0.00916.154-0.012-0.0120.0000.0000.0000.000
24A136ASP-1-0.907-0.95015.6430.1700.1700.0000.0000.0000.000
25A137ARG10.9610.97615.729-0.008-0.0080.0000.0000.0000.000
26A138THR0-0.060-0.03113.776-0.009-0.0090.0000.0000.0000.000
27A139ASN00.0180.01311.470-0.067-0.0670.0000.0000.0000.000
28A140ASN00.0130.00211.7880.0250.0250.0000.0000.0000.000
29A141LEU0-0.0060.01313.9960.0040.0040.0000.0000.0000.000
30A142PHE00.008-0.0144.867-0.005-0.0050.0000.0000.0000.000
31A143ARG10.8470.9108.709-0.736-0.7360.0000.0000.0000.000
32A144GLN00.0980.0539.9600.0350.0350.0000.0000.0000.000
33A145ALA0-0.0190.01010.021-0.007-0.0070.0000.0000.0000.000
34A146TYR0-0.172-0.1142.864-0.5460.0540.147-0.218-0.5300.000
35A147GLU-1-0.801-0.9008.3350.5700.5700.0000.0000.0000.000
36A148GLN00.0700.05111.337-0.038-0.0380.0000.0000.0000.000
37A149LYS10.8330.9277.0130.2240.2240.0000.0000.0000.000
38A150SER00.0520.01511.523-0.018-0.0180.0000.0000.0000.000
39A151LEU0-0.032-0.0269.763-0.021-0.0210.0000.0000.0000.000
40A152LYS10.9320.9409.4140.0920.0920.0000.0000.0000.000
41A153GLY00.0610.0478.796-0.075-0.0750.0000.0000.0000.000
42A154ARG10.7960.9089.9120.2950.2950.0000.0000.0000.000
43A155ALA00.0980.0387.925-0.117-0.1170.0000.0000.0000.000
44A156ASN00.0720.0292.484-2.361-1.4121.181-0.729-1.401-0.010
45A157ASP-1-0.753-0.8965.846-0.742-0.7420.0000.0000.0000.000
46A158ALA0-0.048-0.0098.3680.1890.1890.0000.0000.0000.000
47A159ILE0-0.027-0.0236.5850.1290.1290.0000.0000.0000.000
48A160ALA00.0400.0388.4610.1170.1170.0000.0000.0000.000
49A161SER00.0340.01510.3030.1260.1260.0000.0000.0000.000
50A162ALA0-0.020-0.01713.5020.0560.0560.0000.0000.0000.000
51A163CYS00.0830.05311.8740.0620.0620.0000.0000.0000.000
52A164LEU0-0.0070.00814.2610.0520.0520.0000.0000.0000.000
53A165TYR0-0.088-0.04116.1960.0040.0040.0000.0000.0000.000
54A166ILE0-0.054-0.03716.5740.0170.0170.0000.0000.0000.000
55A167ALA00.0470.03017.5020.0190.0190.0000.0000.0000.000
56A168CYS0-0.088-0.03219.4300.0140.0140.0000.0000.0000.000
57A169ARG10.9450.94622.2540.0790.0790.0000.0000.0000.000
58A170GLN0-0.0140.01420.9370.0090.0090.0000.0000.0000.000
59A171GLU-1-0.884-0.94122.4530.0250.0250.0000.0000.0000.000
60A172GLY00.0250.02925.2220.0040.0040.0000.0000.0000.000
61A173VAL0-0.032-0.01226.316-0.002-0.0020.0000.0000.0000.000
62A174PRO00.0520.03124.702-0.008-0.0080.0000.0000.0000.000
63A175ARG10.9600.94721.7350.0760.0760.0000.0000.0000.000
64A176THR00.0160.01424.267-0.011-0.0110.0000.0000.0000.000
65A177PHE00.011-0.01320.029-0.004-0.0040.0000.0000.0000.000
66A178LYS10.8760.90221.8560.0830.0830.0000.0000.0000.000
67A179GLU-1-0.753-0.85523.186-0.087-0.0870.0000.0000.0000.000
68A180ILE00.0160.02017.230-0.002-0.0020.0000.0000.0000.000
69A181CYS0-0.028-0.02818.437-0.018-0.0180.0000.0000.0000.000
70A182ALA0-0.0170.01119.033-0.021-0.0210.0000.0000.0000.000
71A183VAL0-0.051-0.00417.0560.0130.0130.0000.0000.0000.000
72A184SER0-0.054-0.03614.182-0.027-0.0270.0000.0000.0000.000
73A185ARG10.9861.0129.8500.5500.5500.0000.0000.0000.000
74A186ILE0-0.042-0.01211.2780.0250.0250.0000.0000.0000.000
75A187SER00.0430.00415.2590.0380.0380.0000.0000.0000.000
76A188LYS11.0591.01518.3050.1190.1190.0000.0000.0000.000
77A189LYS10.9070.95220.0990.1740.1740.0000.0000.0000.000
78A190GLU-1-0.748-0.86514.495-0.293-0.2930.0000.0000.0000.000
79A191ILE00.0640.06915.702-0.004-0.0040.0000.0000.0000.000
80A192GLY00.014-0.00416.9060.0240.0240.0000.0000.0000.000
81A193ARG10.8290.90217.4820.2040.2040.0000.0000.0000.000
82A194CYS00.025-0.00813.0610.0060.0060.0000.0000.0000.000
83A195PHE00.0500.04215.1560.0140.0140.0000.0000.0000.000
84A196LYS10.9110.94717.4290.1460.1460.0000.0000.0000.000
85A197LEU0-0.051-0.03114.5720.0110.0110.0000.0000.0000.000
86A198ILE00.0360.01412.4840.0090.0090.0000.0000.0000.000
87A199LEU0-0.0340.00415.8960.0190.0190.0000.0000.0000.000
88A200LYS10.9070.94919.4680.0950.0950.0000.0000.0000.000
89A201ALA0-0.0260.00615.5090.0100.0100.0000.0000.0000.000
90A202LEU00.0200.00514.8090.0110.0110.0000.0000.0000.000
91A203GLU-1-0.916-0.93118.1770.0300.0300.0000.0000.0000.000
92A204THR0-0.038-0.01920.7060.0070.0070.0000.0000.0000.000
93A205SER0-0.033-0.04522.176-0.017-0.0170.0000.0000.0000.000
94A206VAL0-0.077-0.06222.8900.0040.0040.0000.0000.0000.000
95A207ASP-1-0.791-0.90325.625-0.017-0.0170.0000.0000.0000.000
96A208LEU0-0.053-0.02328.3980.0000.0000.0000.0000.0000.000
97A209ILE0-0.114-0.01526.188-0.006-0.0060.0000.0000.0000.000
98A210THR00.010-0.00830.4400.0010.0010.0000.0000.0000.000
99A211THR00.0580.00633.799-0.002-0.0020.0000.0000.0000.000
100A212GLY0-0.0100.01035.533-0.002-0.0020.0000.0000.0000.000
101A213ASP-1-0.822-0.91930.958-0.034-0.0340.0000.0000.0000.000
102A214PHE0-0.074-0.04828.009-0.003-0.0030.0000.0000.0000.000
103A215MET0-0.041-0.00232.315-0.002-0.0020.0000.0000.0000.000
104A216SER00.0220.03233.3030.0000.0000.0000.0000.0000.000
105A217ARG10.8430.90627.5120.0600.0600.0000.0000.0000.000
106A218PHE00.0260.02329.696-0.001-0.0010.0000.0000.0000.000
107A219CYS00.0210.01033.7140.0000.0000.0000.0000.0000.000
108A220SER0-0.001-0.00833.5020.0020.0020.0000.0000.0000.000
109A221ASN0-0.040-0.01729.5950.0040.0040.0000.0000.0000.000
110A222LEU00.0060.00233.891-0.001-0.0010.0000.0000.0000.000
111A223CYS0-0.0360.00437.0010.0020.0020.0000.0000.0000.000
112A224LEU0-0.0230.00738.9250.0020.0020.0000.0000.0000.000
113A225PRO00.0400.02340.8560.0010.0010.0000.0000.0000.000
114A226LYS10.9960.98842.3110.0120.0120.0000.0000.0000.000
115A227GLN0-0.019-0.02243.3280.0010.0010.0000.0000.0000.000
116A228VAL00.0900.04742.5620.0000.0000.0000.0000.0000.000
117A229GLN00.0380.01538.439-0.002-0.0020.0000.0000.0000.000
118A230MET0-0.022-0.02540.774-0.001-0.0010.0000.0000.0000.000
119A231ALA00.0550.03043.7880.0000.0000.0000.0000.0000.000
120A232ALA00.0360.02841.383-0.001-0.0010.0000.0000.0000.000
121A233THR0-0.061-0.06040.030-0.001-0.0010.0000.0000.0000.000
122A234HIS0-0.031-0.01541.6500.0020.0020.0000.0000.0000.000
123A235ILE0-0.0020.02844.7270.0000.0000.0000.0000.0000.000
124A236ALA0-0.011-0.02340.1640.0000.0000.0000.0000.0000.000
125A237ARG10.9280.96741.9090.0160.0160.0000.0000.0000.000
126A238LYS10.9490.98242.7620.0160.0160.0000.0000.0000.000
127A239ALA00.0000.00243.2220.0000.0000.0000.0000.0000.000
128A240VAL0-0.057-0.03639.9240.0000.0000.0000.0000.0000.000
129A241GLU-1-0.900-0.94643.103-0.015-0.0150.0000.0000.0000.000
130A242LEU0-0.048-0.03445.7170.0010.0010.0000.0000.0000.000
131A243ASP-1-0.914-0.95844.359-0.028-0.0280.0000.0000.0000.000
132A244LEU0-0.0250.00645.932-0.001-0.0010.0000.0000.0000.000
133A245VAL0-0.097-0.06041.516-0.002-0.0020.0000.0000.0000.000
134A246PRO00.0860.03941.366-0.003-0.0030.0000.0000.0000.000
135A247GLY00.0430.03038.9370.0000.0000.0000.0000.0000.000
136A248ARG10.8380.93137.6050.0400.0400.0000.0000.0000.000
137A249SER00.0170.01031.9560.0010.0010.0000.0000.0000.000
138A250PRO00.1280.04932.2520.0000.0000.0000.0000.0000.000
139A251ILE00.0000.01329.5630.0020.0020.0000.0000.0000.000
140A252SER0-0.056-0.03433.5140.0010.0010.0000.0000.0000.000
141A253VAL00.0410.03336.4200.0020.0020.0000.0000.0000.000
142A254ALA00.0380.01335.6520.0020.0020.0000.0000.0000.000
143A255ALA00.0230.00535.8040.0020.0020.0000.0000.0000.000
144A256ALA0-0.029-0.02537.7410.0020.0020.0000.0000.0000.000
145A257ALA00.005-0.00541.1170.0020.0020.0000.0000.0000.000
146A258ILE00.010-0.01137.1420.0020.0020.0000.0000.0000.000
147A259TYR0-0.021-0.02341.2980.0010.0010.0000.0000.0000.000
148A260MET0-0.0010.00143.3950.0020.0020.0000.0000.0000.000
149A261ALA00.0020.00644.1610.0010.0010.0000.0000.0000.000
150A262SER0-0.021-0.00743.5040.0010.0010.0000.0000.0000.000
151A263GLN0-0.026-0.02145.5980.0020.0020.0000.0000.0000.000
152A264ALA00.0390.02748.1850.0010.0010.0000.0000.0000.000
153A265SER0-0.061-0.03747.7980.0020.0020.0000.0000.0000.000
154A266ALA00.0620.05349.7860.0000.0000.0000.0000.0000.000
155A267GLU-1-0.901-0.99544.912-0.027-0.0270.0000.0000.0000.000
156A268LYS10.8470.99045.5790.0230.0230.0000.0000.0000.000
157A269ARG10.8850.93540.5340.0330.0330.0000.0000.0000.000
158A270THR0-0.004-0.02142.1210.0000.0000.0000.0000.0000.000
159A271GLN0-0.007-0.01340.848-0.003-0.0030.0000.0000.0000.000
160A272LYS10.9220.96635.5970.0630.0630.0000.0000.0000.000
161A273GLU-1-0.732-0.85337.178-0.044-0.0440.0000.0000.0000.000
162A274ILE0-0.021-0.00536.545-0.002-0.0020.0000.0000.0000.000
163A275GLY0-0.022-0.03635.364-0.003-0.0030.0000.0000.0000.000
164A276ASP-1-0.891-0.95133.146-0.074-0.0740.0000.0000.0000.000
165A277ILE0-0.0120.00731.583-0.005-0.0050.0000.0000.0000.000
166A278ALA0-0.033-0.02130.876-0.003-0.0030.0000.0000.0000.000
167A279GLY00.0080.01829.554-0.005-0.0050.0000.0000.0000.000
168A280VAL0-0.111-0.06830.511-0.006-0.0060.0000.0000.0000.000
169A281ALA00.0410.01933.287-0.001-0.0010.0000.0000.0000.000
170A282ASP-1-0.781-0.88935.933-0.055-0.0550.0000.0000.0000.000
171A283VAL00.0040.00839.2650.0030.0030.0000.0000.0000.000
172A284THR0-0.025-0.03136.1490.0020.0020.0000.0000.0000.000
173A285ILE0-0.0120.02437.5390.0020.0020.0000.0000.0000.000
174A286ARG10.9660.98540.0860.0430.0430.0000.0000.0000.000
175A287GLN0-0.039-0.03741.5430.0020.0020.0000.0000.0000.000
176A288SER00.0550.02540.1740.0020.0020.0000.0000.0000.000
177A289TYR0-0.0140.00242.7620.0020.0020.0000.0000.0000.000
178A290ARG10.9250.94844.9590.0380.0380.0000.0000.0000.000
179A291LEU0-0.054-0.01943.6090.0010.0010.0000.0000.0000.000
180A292ILE00.015-0.00243.9670.0010.0010.0000.0000.0000.000
181A293TYR00.0170.01547.7630.0010.0010.0000.0000.0000.000
182A294PRO0-0.010-0.01150.3360.0010.0010.0000.0000.0000.000
183A295ARG10.8910.95950.7010.0200.0200.0000.0000.0000.000
184A296ALA0-0.003-0.01050.8870.0010.0010.0000.0000.0000.000
185A297PRO0-0.016-0.00951.9500.0000.0000.0000.0000.0000.000
186A298ASP-1-0.823-0.91652.793-0.017-0.0170.0000.0000.0000.000
187A299LEU0-0.066-0.01547.1920.0000.0000.0000.0000.0000.000
188A300PHE0-0.008-0.01948.8800.0000.0000.0000.0000.0000.000
189A301PRO0-0.040-0.02448.2940.0000.0000.0000.0000.0000.000
190A302THR00.0370.04750.7250.0010.0010.0000.0000.0000.000
191A303ASP-1-0.895-0.94252.343-0.012-0.0120.0000.0000.0000.000
192A304PHE0-0.093-0.06948.4790.0000.0000.0000.0000.0000.000
193A305LYS10.8790.94149.4100.0150.0150.0000.0000.0000.000
194A306PHE00.016-0.02652.4750.0000.0000.0000.0000.0000.000
195A307ASP-1-0.916-0.92952.820-0.019-0.0190.0000.0000.0000.000
196A308THR0-0.029-0.01353.2560.0000.0000.0000.0000.0000.000
197A309PRO00.0220.02754.2060.0000.0000.0000.0000.0000.000
198A310VAL00.0930.01853.659-0.001-0.0010.0000.0000.0000.000
199A311ASP-1-0.913-0.95255.553-0.019-0.0190.0000.0000.0000.000
200A312LYS10.9120.94356.8220.0180.0180.0000.0000.0000.000
201A313LEU0-0.0430.00250.475-0.001-0.0010.0000.0000.0000.000
202A314PRO0-0.024-0.00249.2220.0000.0000.0000.0000.0000.000
203A315GLN00.0070.00450.258-0.002-0.0020.0000.0000.0000.000