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: KGY73

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 OptAll
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 -2237343.771893
FMO2-HF: Nuclear repulsion 2156653.959837
FMO2-HF: Total energy -80689.812057
FMO2-MP2: Total energy -80920.175184


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.
-2.7341.721.615-2.263-3.805-0.009
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 : 0.053 / 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].
3A115MET00.0510.0233.885-2.432-0.962-0.001-0.684-0.7850.002
4A116ASN00.0120.0023.3480.0360.6390.009-0.169-0.4420.000
5A117ALA00.0310.0214.2270.2720.604-0.001-0.140-0.1920.000
6A118PHE00.0530.0115.9620.4250.4250.0000.0000.0000.000
7A119LYS10.8840.9586.7820.3430.3430.0000.0000.0000.000
8A120GLU-1-0.893-0.9418.832-0.462-0.4620.0000.0000.0000.000
9A121ILE0-0.019-0.0159.7850.1030.1030.0000.0000.0000.000
10A122THR0-0.026-0.01312.0010.0940.0940.0000.0000.0000.000
11A123THR00.0290.02013.1150.0640.0640.0000.0000.0000.000
12A124MET0-0.097-0.05911.4070.0560.0560.0000.0000.0000.000
13A125ALA00.009-0.00715.9430.0370.0370.0000.0000.0000.000
14A126ASP-1-0.801-0.88417.958-0.108-0.1080.0000.0000.0000.000
15A127ARG10.8830.93617.4540.2430.2430.0000.0000.0000.000
16A128ILE0-0.060-0.01820.2170.0140.0140.0000.0000.0000.000
17A129ASN0-0.038-0.02222.3320.0170.0170.0000.0000.0000.000
18A130LEU0-0.0180.00519.1090.0140.0140.0000.0000.0000.000
19A131PRO00.0470.02822.029-0.001-0.0010.0000.0000.0000.000
20A132ARG10.8600.87018.8890.0790.0790.0000.0000.0000.000
21A133ASN00.0590.07020.113-0.009-0.0090.0000.0000.0000.000
22A134LYS10.9430.96619.9960.0590.0590.0000.0000.0000.000
23A135VAL0-0.032-0.01716.059-0.016-0.0160.0000.0000.0000.000
24A136ASP-1-0.859-0.92215.4950.0610.0610.0000.0000.0000.000
25A137ARG10.9070.94315.6410.0110.0110.0000.0000.0000.000
26A138THR0-0.001-0.01012.7810.0070.0070.0000.0000.0000.000
27A139ASN00.0250.01211.298-0.095-0.0950.0000.0000.0000.000
28A140ASN0-0.038-0.02911.4640.0510.0510.0000.0000.0000.000
29A141LEU00.0200.00913.1910.0340.0340.0000.0000.0000.000
30A142PHE0-0.005-0.0234.746-0.113-0.026-0.001-0.007-0.0780.000
31A143ARG10.8240.8798.642-0.669-0.6690.0000.0000.0000.000
32A144GLN00.0460.0279.7230.0690.0690.0000.0000.0000.000
33A145ALA0-0.024-0.0039.8590.0190.0190.0000.0000.0000.000
34A146TYR0-0.093-0.0762.518-0.6820.1230.585-0.472-0.918-0.001
35A147GLU-1-0.724-0.8417.9050.7640.7640.0000.0000.0000.000
36A148GLN00.0400.03410.961-0.047-0.0470.0000.0000.0000.000
37A149LYS10.7840.9305.767-0.237-0.2370.0000.0000.0000.000
38A150SER00.0530.02111.132-0.058-0.0580.0000.0000.0000.000
39A151LEU0-0.016-0.02010.001-0.031-0.0310.0000.0000.0000.000
40A152LYS10.9200.9359.689-0.113-0.1130.0000.0000.0000.000
41A153GLY00.0370.0289.668-0.003-0.0030.0000.0000.0000.000
42A154ARG10.8250.91210.0730.1630.1630.0000.0000.0000.000
43A155ALA00.0600.0288.242-0.046-0.0460.0000.0000.0000.000
44A156ASN00.0350.0042.585-1.739-0.5821.024-0.791-1.390-0.010
45A157ASP-1-0.698-0.8426.005-0.734-0.7340.0000.0000.0000.000
46A158ALA0-0.023-0.0078.8300.1400.1400.0000.0000.0000.000
47A159ILE0-0.002-0.0066.5780.0900.0900.0000.0000.0000.000
48A160ALA00.0270.0308.6290.0890.0890.0000.0000.0000.000
49A161SER00.031-0.00610.1980.0790.0790.0000.0000.0000.000
50A162ALA0-0.063-0.02913.1710.0540.0540.0000.0000.0000.000
51A163CYS0-0.041-0.00211.3360.0520.0520.0000.0000.0000.000
52A164LEU00.0790.03813.8450.0390.0390.0000.0000.0000.000
53A165TYR0-0.0310.00015.9290.0330.0330.0000.0000.0000.000
54A166ILE0-0.020-0.01516.3720.0150.0150.0000.0000.0000.000
55A167ALA00.0250.01616.9770.0180.0180.0000.0000.0000.000
56A168CYS0-0.064-0.03518.9590.0130.0130.0000.0000.0000.000
57A169ARG10.8270.91021.7680.0700.0700.0000.0000.0000.000
58A170GLN00.0260.01321.1440.0090.0090.0000.0000.0000.000
59A171GLU-1-0.866-0.90722.197-0.004-0.0040.0000.0000.0000.000
60A172GLY00.0280.02525.0550.0020.0020.0000.0000.0000.000
61A173VAL0-0.056-0.02426.202-0.001-0.0010.0000.0000.0000.000
62A174PRO00.0500.03224.483-0.011-0.0110.0000.0000.0000.000
63A175ARG10.8820.92821.9880.0970.0970.0000.0000.0000.000
64A176THR0-0.002-0.01624.277-0.005-0.0050.0000.0000.0000.000
65A177PHE00.002-0.02420.456-0.008-0.0080.0000.0000.0000.000
66A178LYS10.8860.93621.7710.0840.0840.0000.0000.0000.000
67A179GLU-1-0.712-0.80623.125-0.106-0.1060.0000.0000.0000.000
68A180ILE00.0390.02617.273-0.009-0.0090.0000.0000.0000.000
69A181CYS0-0.058-0.04018.506-0.023-0.0230.0000.0000.0000.000
70A182ALA0-0.0030.00319.322-0.022-0.0220.0000.0000.0000.000
71A183VAL0-0.048-0.00617.3060.0020.0020.0000.0000.0000.000
72A184SER00.0400.05613.872-0.019-0.0190.0000.0000.0000.000
73A185ARG10.9370.94710.5200.5050.5050.0000.0000.0000.000
74A186ILE0-0.070-0.02911.8000.0300.0300.0000.0000.0000.000
75A187SER00.0420.01515.8340.0390.0390.0000.0000.0000.000
76A188LYS11.0671.00418.5180.1060.1060.0000.0000.0000.000
77A189LYS10.9110.96620.6470.1450.1450.0000.0000.0000.000
78A190GLU-1-0.767-0.86315.107-0.196-0.1960.0000.0000.0000.000
79A191ILE00.0680.04515.6420.0050.0050.0000.0000.0000.000
80A192GLY00.0400.01516.8260.0160.0160.0000.0000.0000.000
81A193ARG10.8110.91017.4940.1610.1610.0000.0000.0000.000
82A194CYS00.0200.00813.1580.0080.0080.0000.0000.0000.000
83A195PHE00.0560.02715.0420.0170.0170.0000.0000.0000.000
84A196LYS10.8910.93017.3970.1080.1080.0000.0000.0000.000
85A197LEU0-0.0090.00615.1690.0120.0120.0000.0000.0000.000
86A198ILE00.0550.01312.1220.0140.0140.0000.0000.0000.000
87A199LEU0-0.034-0.01015.6520.0170.0170.0000.0000.0000.000
88A200LYS10.8670.93618.9820.0440.0440.0000.0000.0000.000
89A201ALA0-0.017-0.00514.8650.0080.0080.0000.0000.0000.000
90A202LEU0-0.010-0.00213.7840.0190.0190.0000.0000.0000.000
91A203GLU-1-0.941-0.94117.7040.0720.0720.0000.0000.0000.000
92A204THR0-0.002-0.00720.122-0.001-0.0010.0000.0000.0000.000
93A205SER0-0.037-0.04122.206-0.012-0.0120.0000.0000.0000.000
94A206VAL0-0.032-0.03222.597-0.001-0.0010.0000.0000.0000.000
95A207ASP-1-0.830-0.89825.486-0.017-0.0170.0000.0000.0000.000
96A208LEU0-0.017-0.01328.498-0.003-0.0030.0000.0000.0000.000
97A209ILE0-0.085-0.04125.970-0.008-0.0080.0000.0000.0000.000
98A210THR0-0.020-0.03130.1470.0020.0020.0000.0000.0000.000
99A211THR0-0.010-0.02633.309-0.004-0.0040.0000.0000.0000.000
100A212GLY00.0320.01535.863-0.002-0.0020.0000.0000.0000.000
101A213ASP-1-0.811-0.89030.243-0.042-0.0420.0000.0000.0000.000
102A214PHE0-0.029-0.02728.044-0.006-0.0060.0000.0000.0000.000
103A215MET0-0.0260.02132.546-0.002-0.0020.0000.0000.0000.000
104A216SER00.0330.02334.193-0.001-0.0010.0000.0000.0000.000
105A217ARG10.8660.92427.4990.0770.0770.0000.0000.0000.000
106A218PHE00.0520.02030.146-0.002-0.0020.0000.0000.0000.000
107A219CYS0-0.0060.00734.1250.0010.0010.0000.0000.0000.000
108A220SER00.009-0.00233.7610.0020.0020.0000.0000.0000.000
109A221ASN0-0.038-0.02730.0510.0000.0000.0000.0000.0000.000
110A222LEU0-0.028-0.00233.985-0.001-0.0010.0000.0000.0000.000
111A223CYS00.0020.01137.1980.0020.0020.0000.0000.0000.000
112A224LEU0-0.0050.01139.1120.0030.0030.0000.0000.0000.000
113A225PRO00.0530.03040.9010.0000.0000.0000.0000.0000.000
114A226LYS10.9700.96842.4750.0220.0220.0000.0000.0000.000
115A227GLN00.0330.00043.4640.0010.0010.0000.0000.0000.000
116A228VAL00.0580.04042.8130.0010.0010.0000.0000.0000.000
117A229GLN00.0440.00838.407-0.002-0.0020.0000.0000.0000.000
118A230MET0-0.028-0.00840.1040.0000.0000.0000.0000.0000.000
119A231ALA00.0340.02843.7040.0010.0010.0000.0000.0000.000
120A232ALA00.0380.01641.2810.0000.0000.0000.0000.0000.000
121A233THR0-0.031-0.04539.590-0.001-0.0010.0000.0000.0000.000
122A234HIS0-0.048-0.03041.4650.0020.0020.0000.0000.0000.000
123A235ILE00.0060.01644.5150.0000.0000.0000.0000.0000.000
124A236ALA00.014-0.01639.8410.0000.0000.0000.0000.0000.000
125A237ARG10.8220.90041.5830.0180.0180.0000.0000.0000.000
126A238LYS10.8840.92742.6290.0180.0180.0000.0000.0000.000
127A239ALA00.012-0.00142.9750.0010.0010.0000.0000.0000.000
128A240VAL0-0.037-0.01539.6350.0000.0000.0000.0000.0000.000
129A241GLU-1-0.801-0.86543.039-0.016-0.0160.0000.0000.0000.000
130A242LEU0-0.038-0.01745.8350.0010.0010.0000.0000.0000.000
131A243ASP-1-0.878-0.94244.191-0.024-0.0240.0000.0000.0000.000
132A244LEU0-0.0110.00845.983-0.001-0.0010.0000.0000.0000.000
133A245VAL0-0.077-0.05941.359-0.002-0.0020.0000.0000.0000.000
134A246PRO00.0640.04041.090-0.003-0.0030.0000.0000.0000.000
135A247GLY00.0080.01638.7070.0000.0000.0000.0000.0000.000
136A248ARG10.7890.89737.7410.0380.0380.0000.0000.0000.000
137A249SER00.0140.00931.9130.0010.0010.0000.0000.0000.000
138A250PRO00.0960.03932.2830.0000.0000.0000.0000.0000.000
139A251ILE0-0.0020.00429.6540.0010.0010.0000.0000.0000.000
140A252SER0-0.021-0.01733.5550.0000.0000.0000.0000.0000.000
141A253VAL00.0280.02436.5170.0010.0010.0000.0000.0000.000
142A254ALA00.0270.01135.7180.0020.0020.0000.0000.0000.000
143A255ALA00.0120.00436.2920.0010.0010.0000.0000.0000.000
144A256ALA0-0.028-0.01738.1810.0010.0010.0000.0000.0000.000
145A257ALA00.0240.00841.0780.0020.0020.0000.0000.0000.000
146A258ILE00.016-0.01037.3750.0020.0020.0000.0000.0000.000
147A259TYR0-0.049-0.01841.6320.0010.0010.0000.0000.0000.000
148A260MET00.0130.00843.6640.0020.0020.0000.0000.0000.000
149A261ALA00.0010.00244.3020.0010.0010.0000.0000.0000.000
150A262SER0-0.044-0.03843.5600.0010.0010.0000.0000.0000.000
151A263GLN0-0.013-0.01045.6940.0020.0020.0000.0000.0000.000
152A264ALA00.0110.02148.5500.0010.0010.0000.0000.0000.000
153A265SER0-0.077-0.05847.7860.0020.0020.0000.0000.0000.000
154A266ALA00.1050.05050.176-0.001-0.0010.0000.0000.0000.000
155A267GLU-1-0.864-0.90045.076-0.037-0.0370.0000.0000.0000.000
156A268LYS10.8120.91445.4450.0280.0280.0000.0000.0000.000
157A269ARG10.7960.88440.9770.0420.0420.0000.0000.0000.000
158A270THR0-0.018-0.05542.3190.0010.0010.0000.0000.0000.000
159A271GLN00.0470.01141.193-0.002-0.0020.0000.0000.0000.000
160A272LYS10.8300.91435.6000.0690.0690.0000.0000.0000.000
161A273GLU-1-0.729-0.82837.261-0.054-0.0540.0000.0000.0000.000
162A274ILE0-0.005-0.00136.311-0.004-0.0040.0000.0000.0000.000
163A275GLY0-0.001-0.00835.636-0.002-0.0020.0000.0000.0000.000
164A276ASP-1-0.837-0.90632.867-0.082-0.0820.0000.0000.0000.000
165A277ILE0-0.046-0.00831.460-0.007-0.0070.0000.0000.0000.000
166A278ALA0-0.009-0.00631.122-0.003-0.0030.0000.0000.0000.000
167A279GLY00.0000.00929.656-0.003-0.0030.0000.0000.0000.000
168A280VAL0-0.104-0.05830.541-0.003-0.0030.0000.0000.0000.000
169A281ALA00.0590.03733.5540.0000.0000.0000.0000.0000.000
170A282ASP-1-0.785-0.90736.329-0.057-0.0570.0000.0000.0000.000
171A283VAL00.0230.01139.7490.0030.0030.0000.0000.0000.000
172A284THR0-0.025-0.02235.8200.0020.0020.0000.0000.0000.000
173A285ILE00.0160.02237.5000.0030.0030.0000.0000.0000.000
174A286ARG10.8680.92640.4120.0440.0440.0000.0000.0000.000
175A287GLN00.0260.00341.4300.0030.0030.0000.0000.0000.000
176A288SER00.0130.01140.0570.0020.0020.0000.0000.0000.000
177A289TYR0-0.013-0.02742.5880.0020.0020.0000.0000.0000.000
178A290ARG10.9130.95845.0810.0360.0360.0000.0000.0000.000
179A291LEU0-0.0200.00444.1090.0010.0010.0000.0000.0000.000
180A292ILE00.0170.01143.9440.0010.0010.0000.0000.0000.000
181A293TYR00.0270.01547.6550.0010.0010.0000.0000.0000.000
182A294PRO0-0.023-0.01750.3320.0010.0010.0000.0000.0000.000
183A295ARG10.8420.89950.8430.0200.0200.0000.0000.0000.000
184A296ALA00.0220.00650.9360.0000.0000.0000.0000.0000.000
185A297PRO0-0.018-0.01951.9840.0000.0000.0000.0000.0000.000
186A298ASP-1-0.792-0.85652.176-0.018-0.0180.0000.0000.0000.000
187A299LEU0-0.028-0.00146.6030.0000.0000.0000.0000.0000.000
188A300PHE00.0300.01348.464-0.001-0.0010.0000.0000.0000.000
189A301PRO0-0.028-0.01047.9550.0010.0010.0000.0000.0000.000
190A302THR0-0.032-0.00350.5080.0020.0020.0000.0000.0000.000
191A303ASP-1-0.802-0.90251.830-0.018-0.0180.0000.0000.0000.000
192A304PHE0-0.089-0.05248.5400.0000.0000.0000.0000.0000.000
193A305LYS10.8130.89651.3810.0200.0200.0000.0000.0000.000
194A306PHE0-0.014-0.01252.9180.0000.0000.0000.0000.0000.000
195A307ASP-1-0.821-0.88552.835-0.026-0.0260.0000.0000.0000.000
196A308THR0-0.039-0.01453.267-0.001-0.0010.0000.0000.0000.000
197A309PRO00.0590.04054.236-0.001-0.0010.0000.0000.0000.000
198A310VAL00.0780.01353.683-0.001-0.0010.0000.0000.0000.000
199A311ASP-1-0.851-0.91155.659-0.021-0.0210.0000.0000.0000.000
200A312LYS10.8180.88657.1230.0210.0210.0000.0000.0000.000
201A313LEU0-0.0140.01950.550-0.001-0.0010.0000.0000.0000.000
202A314PRO00.0070.02249.5350.0000.0000.0000.0000.0000.000
203A315GLN0-0.056-0.03550.333-0.002-0.0020.0000.0000.0000.000