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

tag_button

FMODB ID: QVR7Y

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 OptHSide
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 -2243082.258649
FMO2-HF: Nuclear repulsion 2162393.981506
FMO2-HF: Total energy -80688.277143
FMO2-MP2: Total energy -80919.007881


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.
-5.655-0.9351.147-2.24-3.627-0.009
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 : 0.011 / q_NPA : -0.001
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].
3A115MET00.0540.0263.817-3.272-1.295-0.017-0.980-0.9800.001
4A116ASN00.014-0.0072.861-0.887-0.2070.065-0.196-0.5490.000
5A117ALA00.0570.0484.091-0.258-0.0100.000-0.072-0.1760.000
6A118PHE00.0470.0025.5260.3340.3340.0000.0000.0000.000
7A119LYS10.8840.9466.307-0.341-0.3410.0000.0000.0000.000
8A120GLU-1-0.884-0.9258.478-0.440-0.4400.0000.0000.0000.000
9A121ILE0-0.023-0.0109.7510.0860.0860.0000.0000.0000.000
10A122THR0-0.033-0.01811.7570.0640.0640.0000.0000.0000.000
11A123THR00.0440.03212.6930.0440.0440.0000.0000.0000.000
12A124MET0-0.097-0.06111.5650.0310.0310.0000.0000.0000.000
13A125ALA0-0.004-0.02315.7280.0300.0300.0000.0000.0000.000
14A126ASP-1-0.818-0.90417.778-0.054-0.0540.0000.0000.0000.000
15A127ARG10.9130.97017.6050.1970.1970.0000.0000.0000.000
16A128ILE0-0.067-0.03320.3850.0110.0110.0000.0000.0000.000
17A129ASN0-0.047-0.02222.3690.0120.0120.0000.0000.0000.000
18A130LEU0-0.050-0.01319.0450.0110.0110.0000.0000.0000.000
19A131PRO00.0610.03121.4800.0030.0030.0000.0000.0000.000
20A132ARG10.8890.91018.1530.0090.0090.0000.0000.0000.000
21A133ASN00.1030.06820.204-0.009-0.0090.0000.0000.0000.000
22A134LYS10.9370.97320.0240.0420.0420.0000.0000.0000.000
23A135VAL0-0.024-0.01516.253-0.015-0.0150.0000.0000.0000.000
24A136ASP-1-0.883-0.92715.6430.1280.1280.0000.0000.0000.000
25A137ARG10.9220.93715.7290.0060.0060.0000.0000.0000.000
26A138THR0-0.002-0.01713.184-0.013-0.0130.0000.0000.0000.000
27A139ASN0-0.017-0.00311.474-0.102-0.1020.0000.0000.0000.000
28A140ASN0-0.016-0.01811.8540.0270.0270.0000.0000.0000.000
29A141LEU00.0020.01514.0570.0100.0100.0000.0000.0000.000
30A142PHE0-0.004-0.0205.030-0.009-0.0090.0000.0000.0000.000
31A143ARG10.8170.8818.772-0.726-0.7260.0000.0000.0000.000
32A144GLN00.0860.0469.9630.0550.0550.0000.0000.0000.000
33A145ALA0-0.0100.01310.1390.0010.0010.0000.0000.0000.000
34A146TYR0-0.122-0.1012.729-0.5000.1710.134-0.248-0.5570.000
35A147GLU-1-0.731-0.8428.3660.6400.6400.0000.0000.0000.000
36A148GLN00.0640.05711.347-0.040-0.0400.0000.0000.0000.000
37A149LYS10.7580.8996.1260.1460.1460.0000.0000.0000.000
38A150SER00.0040.00011.554-0.028-0.0280.0000.0000.0000.000
39A151LEU0-0.002-0.0179.878-0.024-0.0240.0000.0000.0000.000
40A152LYS10.9620.9529.8730.0190.0190.0000.0000.0000.000
41A153GLY00.0430.0408.809-0.067-0.0670.0000.0000.0000.000
42A154ARG10.8280.91610.0410.2660.2660.0000.0000.0000.000
43A155ALA00.0810.0317.968-0.107-0.1070.0000.0000.0000.000
44A156ASN00.0740.0272.548-2.284-1.1400.965-0.744-1.365-0.010
45A157ASP-1-0.718-0.8675.919-0.798-0.7980.0000.0000.0000.000
46A158ALA0-0.059-0.0168.3890.1960.1960.0000.0000.0000.000
47A159ILE0-0.021-0.0206.7880.1110.1110.0000.0000.0000.000
48A160ALA00.0410.0418.4780.1140.1140.0000.0000.0000.000
49A161SER00.0340.01510.3910.1260.1260.0000.0000.0000.000
50A162ALA0-0.032-0.01413.5920.0550.0550.0000.0000.0000.000
51A163CYS00.0560.04311.9810.0610.0610.0000.0000.0000.000
52A164LEU00.0200.02714.3470.0530.0530.0000.0000.0000.000
53A165TYR0-0.087-0.06216.2200.0050.0050.0000.0000.0000.000
54A166ILE0-0.054-0.03616.6600.0180.0180.0000.0000.0000.000
55A167ALA00.0400.02917.5670.0200.0200.0000.0000.0000.000
56A168CYS0-0.066-0.03619.5140.0150.0150.0000.0000.0000.000
57A169ARG10.9520.96222.3400.0860.0860.0000.0000.0000.000
58A170GLN00.0140.02521.1310.0090.0090.0000.0000.0000.000
59A171GLU-1-0.874-0.91022.3980.0090.0090.0000.0000.0000.000
60A172GLY00.0150.02225.3040.0040.0040.0000.0000.0000.000
61A173VAL0-0.046-0.02226.496-0.002-0.0020.0000.0000.0000.000
62A174PRO00.0160.02024.786-0.010-0.0100.0000.0000.0000.000
63A175ARG10.9340.95721.8620.0900.0900.0000.0000.0000.000
64A176THR00.015-0.00424.290-0.011-0.0110.0000.0000.0000.000
65A177PHE0-0.001-0.01520.468-0.005-0.0050.0000.0000.0000.000
66A178LYS10.8830.92021.8780.0880.0880.0000.0000.0000.000
67A179GLU-1-0.727-0.82023.206-0.098-0.0980.0000.0000.0000.000
68A180ILE00.0250.02417.270-0.003-0.0030.0000.0000.0000.000
69A181CYS0-0.021-0.01618.458-0.022-0.0220.0000.0000.0000.000
70A182ALA00.0040.01519.051-0.022-0.0220.0000.0000.0000.000
71A183VAL0-0.062-0.02317.0510.0130.0130.0000.0000.0000.000
72A184SER0-0.043-0.02114.216-0.025-0.0250.0000.0000.0000.000
73A185ARG10.9610.99010.0250.5590.5590.0000.0000.0000.000
74A186ILE0-0.059-0.02311.2960.0300.0300.0000.0000.0000.000
75A187SER00.0380.00915.2750.0420.0420.0000.0000.0000.000
76A188LYS11.0851.01718.3380.1240.1240.0000.0000.0000.000
77A189LYS10.9060.95420.1730.1710.1710.0000.0000.0000.000
78A190GLU-1-0.761-0.86414.913-0.271-0.2710.0000.0000.0000.000
79A191ILE00.0750.05315.537-0.001-0.0010.0000.0000.0000.000
80A192GLY00.0300.00816.9830.0240.0240.0000.0000.0000.000
81A193ARG10.7880.88717.5830.2120.2120.0000.0000.0000.000
82A194CYS00.0330.01413.1960.0030.0030.0000.0000.0000.000
83A195PHE00.0530.04015.2240.0130.0130.0000.0000.0000.000
84A196LYS10.8610.91517.5050.1490.1490.0000.0000.0000.000
85A197LEU0-0.033-0.02415.1740.0110.0110.0000.0000.0000.000
86A198ILE00.0330.00712.2540.0100.0100.0000.0000.0000.000
87A199LEU0-0.045-0.00115.9610.0190.0190.0000.0000.0000.000
88A200LYS10.9300.95819.5340.0880.0880.0000.0000.0000.000
89A201ALA0-0.0230.00615.5460.0110.0110.0000.0000.0000.000
90A202LEU00.004-0.00414.4650.0130.0130.0000.0000.0000.000
91A203GLU-1-0.911-0.92918.2300.0360.0360.0000.0000.0000.000
92A204THR0-0.046-0.02420.6230.0070.0070.0000.0000.0000.000
93A205SER0-0.028-0.04022.244-0.017-0.0170.0000.0000.0000.000
94A206VAL0-0.057-0.04622.8870.0030.0030.0000.0000.0000.000
95A207ASP-1-0.824-0.91225.702-0.021-0.0210.0000.0000.0000.000
96A208LEU0-0.034-0.02528.4350.0000.0000.0000.0000.0000.000
97A209ILE0-0.112-0.02126.305-0.006-0.0060.0000.0000.0000.000
98A210THR00.014-0.00630.5250.0020.0020.0000.0000.0000.000
99A211THR00.0530.00133.886-0.002-0.0020.0000.0000.0000.000
100A212GLY00.0020.01735.614-0.003-0.0030.0000.0000.0000.000
101A213ASP-1-0.859-0.94430.732-0.044-0.0440.0000.0000.0000.000
102A214PHE0-0.021-0.02228.031-0.004-0.0040.0000.0000.0000.000
103A215MET0-0.0340.00632.338-0.002-0.0020.0000.0000.0000.000
104A216SER00.0230.03033.5000.0000.0000.0000.0000.0000.000
105A217ARG10.8410.88027.4740.0710.0710.0000.0000.0000.000
106A218PHE00.0430.02629.8140.0000.0000.0000.0000.0000.000
107A219CYS00.0240.00933.7360.0000.0000.0000.0000.0000.000
108A220SER0-0.008-0.00633.5100.0020.0020.0000.0000.0000.000
109A221ASN0-0.043-0.02529.7520.0020.0020.0000.0000.0000.000
110A222LEU00.0130.00833.912-0.001-0.0010.0000.0000.0000.000
111A223CYS0-0.051-0.00236.8940.0020.0020.0000.0000.0000.000
112A224LEU0-0.0070.01738.9450.0030.0030.0000.0000.0000.000
113A225PRO00.0460.02140.8780.0010.0010.0000.0000.0000.000
114A226LYS10.9750.97542.3360.0170.0170.0000.0000.0000.000
115A227GLN00.016-0.00943.3500.0000.0000.0000.0000.0000.000
116A228VAL00.0870.05242.7550.0000.0000.0000.0000.0000.000
117A229GLN00.009-0.00338.107-0.002-0.0020.0000.0000.0000.000
118A230MET0-0.008-0.00840.533-0.001-0.0010.0000.0000.0000.000
119A231ALA00.0570.03643.8110.0010.0010.0000.0000.0000.000
120A232ALA00.0390.02541.3660.0000.0000.0000.0000.0000.000
121A233THR0-0.061-0.07239.723-0.001-0.0010.0000.0000.0000.000
122A234HIS0-0.043-0.01541.6740.0020.0020.0000.0000.0000.000
123A235ILE00.0120.03044.6870.0000.0000.0000.0000.0000.000
124A236ALA0-0.003-0.02440.2200.0000.0000.0000.0000.0000.000
125A237ARG10.8440.91041.6550.0190.0190.0000.0000.0000.000
126A238LYS10.9120.94942.8490.0190.0190.0000.0000.0000.000
127A239ALA0-0.009-0.00143.3760.0000.0000.0000.0000.0000.000
128A240VAL0-0.039-0.02939.8370.0000.0000.0000.0000.0000.000
129A241GLU-1-0.784-0.84943.188-0.018-0.0180.0000.0000.0000.000
130A242LEU0-0.052-0.04045.8010.0010.0010.0000.0000.0000.000
131A243ASP-1-0.908-0.95444.363-0.030-0.0300.0000.0000.0000.000
132A244LEU0-0.0090.00846.014-0.001-0.0010.0000.0000.0000.000
133A245VAL0-0.115-0.06841.730-0.002-0.0020.0000.0000.0000.000
134A246PRO00.0730.03641.447-0.003-0.0030.0000.0000.0000.000
135A247GLY00.0490.03639.0160.0000.0000.0000.0000.0000.000
136A248ARG10.7970.89937.6830.0430.0430.0000.0000.0000.000
137A249SER00.0300.01331.8350.0010.0010.0000.0000.0000.000
138A250PRO00.1080.04832.3250.0010.0010.0000.0000.0000.000
139A251ILE0-0.0020.00529.7320.0020.0020.0000.0000.0000.000
140A252SER0-0.053-0.02833.5890.0000.0000.0000.0000.0000.000
141A253VAL00.0390.03236.4740.0020.0020.0000.0000.0000.000
142A254ALA00.0360.01335.6540.0020.0020.0000.0000.0000.000
143A255ALA00.0190.00535.8550.0020.0020.0000.0000.0000.000
144A256ALA0-0.030-0.02437.7630.0020.0020.0000.0000.0000.000
145A257ALA00.008-0.00341.1120.0020.0020.0000.0000.0000.000
146A258ILE00.015-0.01137.0630.0020.0020.0000.0000.0000.000
147A259TYR0-0.029-0.01841.3210.0010.0010.0000.0000.0000.000
148A260MET0-0.0050.00743.4170.0020.0020.0000.0000.0000.000
149A261ALA00.0080.00444.1600.0010.0010.0000.0000.0000.000
150A262SER0-0.010-0.00443.4800.0010.0010.0000.0000.0000.000
151A263GLN0-0.030-0.01645.6200.0020.0020.0000.0000.0000.000
152A264ALA00.0030.01648.2060.0010.0010.0000.0000.0000.000
153A265SER0-0.052-0.03847.7850.0020.0020.0000.0000.0000.000
154A266ALA00.0760.05949.8400.0000.0000.0000.0000.0000.000
155A267GLU-1-0.854-0.94944.958-0.032-0.0320.0000.0000.0000.000
156A268LYS10.8230.96445.6000.0260.0260.0000.0000.0000.000
157A269ARG10.8210.88440.5070.0370.0370.0000.0000.0000.000
158A270THR0-0.009-0.04642.1690.0000.0000.0000.0000.0000.000
159A271GLN00.0240.01540.868-0.003-0.0030.0000.0000.0000.000
160A272LYS10.8570.91435.3470.0680.0680.0000.0000.0000.000
161A273GLU-1-0.725-0.83737.197-0.049-0.0490.0000.0000.0000.000
162A274ILE0-0.025-0.00736.565-0.003-0.0030.0000.0000.0000.000
163A275GLY0-0.013-0.03235.385-0.003-0.0030.0000.0000.0000.000
164A276ASP-1-0.819-0.89533.107-0.081-0.0810.0000.0000.0000.000
165A277ILE0-0.0400.00231.603-0.006-0.0060.0000.0000.0000.000
166A278ALA0-0.030-0.02430.897-0.003-0.0030.0000.0000.0000.000
167A279GLY00.0160.02229.576-0.005-0.0050.0000.0000.0000.000
168A280VAL0-0.111-0.06230.532-0.005-0.0050.0000.0000.0000.000
169A281ALA00.0450.01833.307-0.001-0.0010.0000.0000.0000.000
170A282ASP-1-0.793-0.90835.953-0.059-0.0590.0000.0000.0000.000
171A283VAL00.0180.01839.3130.0030.0030.0000.0000.0000.000
172A284THR0-0.006-0.01936.0700.0030.0030.0000.0000.0000.000
173A285ILE0-0.0110.02437.4810.0020.0020.0000.0000.0000.000
174A286ARG10.9050.94740.1070.0460.0460.0000.0000.0000.000
175A287GLN00.004-0.00441.5270.0030.0030.0000.0000.0000.000
176A288SER00.0360.01940.3410.0020.0020.0000.0000.0000.000
177A289TYR0-0.018-0.01742.8450.0020.0020.0000.0000.0000.000
178A290ARG10.9340.95644.9810.0400.0400.0000.0000.0000.000
179A291LEU0-0.034-0.01643.9670.0010.0010.0000.0000.0000.000
180A292ILE0-0.001-0.00444.0900.0010.0010.0000.0000.0000.000
181A293TYR00.0440.02647.8470.0020.0020.0000.0000.0000.000
182A294PRO0-0.007-0.00550.3580.0010.0010.0000.0000.0000.000
183A295ARG10.8360.89450.8440.0220.0220.0000.0000.0000.000
184A296ALA0-0.004-0.00850.9190.0010.0010.0000.0000.0000.000
185A297PRO0-0.001-0.00551.9720.0000.0000.0000.0000.0000.000
186A298ASP-1-0.801-0.86652.762-0.019-0.0190.0000.0000.0000.000
187A299LEU0-0.047-0.01247.0230.0000.0000.0000.0000.0000.000
188A300PHE0-0.004-0.01748.931-0.001-0.0010.0000.0000.0000.000
189A301PRO0-0.036-0.01448.2710.0010.0010.0000.0000.0000.000
190A302THR00.0140.02650.7490.0010.0010.0000.0000.0000.000
191A303ASP-1-0.827-0.89552.089-0.016-0.0160.0000.0000.0000.000
192A304PHE0-0.091-0.07448.2640.0000.0000.0000.0000.0000.000
193A305LYS10.8250.90751.0010.0180.0180.0000.0000.0000.000
194A306PHE00.015-0.01652.3880.0000.0000.0000.0000.0000.000
195A307ASP-1-0.881-0.91752.951-0.023-0.0230.0000.0000.0000.000
196A308THR0-0.028-0.01153.2500.0000.0000.0000.0000.0000.000
197A309PRO00.0470.03454.2280.0000.0000.0000.0000.0000.000
198A310VAL00.1070.03053.666-0.001-0.0010.0000.0000.0000.000
199A311ASP-1-0.886-0.91755.575-0.021-0.0210.0000.0000.0000.000
200A312LYS10.8400.88856.9130.0200.0200.0000.0000.0000.000
201A313LEU0-0.0320.00950.098-0.001-0.0010.0000.0000.0000.000
202A314PRO0-0.0090.00549.2460.0000.0000.0000.0000.0000.000
203A315GLN0-0.023-0.00151.017-0.002-0.0020.0000.0000.0000.000