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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: V24Y1

Calculation Name: 4YO2-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YO2

Chain ID: A

ChEMBL ID:

UniProt ID: A0AVK6

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2072581.082888
FMO2-HF: Nuclear repulsion 1996625.801378
FMO2-HF: Total energy -75955.28151
FMO2-MP2: Total energy -76177.12589


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:110:GLN )


Summations of interaction energy for fragment #1(A:110:GLN )
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.
-13.833-8.8970.486-2.628-2.793-0.019
Interaction energy analysis for fragmet #1(A:110:GLN )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.009
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].
3A112SER 0-0.0020.0063.274-0.5091.453-0.001-0.902-1.0590.002
4A113ARG 11.0310.9995.091-0.746-0.7050.000-0.008-0.0320.000
5A114LYS 10.9160.9377.6050.9930.9930.0000.0000.0000.000
6A115GLU -1-0.868-0.9272.630-13.070-10.1370.487-1.718-1.702-0.021
7A116LYS 10.9690.9875.232-0.663-0.6630.0000.0000.0000.000
8A117SER 0-0.047-0.0188.9330.3790.3790.0000.0000.0000.000
9A118LEU 00.0380.00911.995-0.030-0.0300.0000.0000.0000.000
10A119GLY 00.0650.02115.2880.0140.0140.0000.0000.0000.000
11A120LEU 00.0040.0389.7760.0140.0140.0000.0000.0000.000
12A121LEU 00.0290.01313.3540.0460.0460.0000.0000.0000.000
13A122CYS 0-0.040-0.00415.4540.0660.0660.0000.0000.0000.000
14A123HIS 00.002-0.01516.5720.0560.0560.0000.0000.0000.000
15A124LYS 10.8100.90515.6340.3900.3900.0000.0000.0000.000
16A125PHE 0-0.016-0.00918.2700.0390.0390.0000.0000.0000.000
17A126LEU 0-0.031-0.03221.0500.0270.0270.0000.0000.0000.000
18A127ALA 0-0.041-0.01120.4670.0120.0120.0000.0000.0000.000
19A128ARG 10.7410.86921.1970.2050.2050.0000.0000.0000.000
20A129TYR 00.0210.01023.7450.0160.0160.0000.0000.0000.000
21A130PRO 00.0270.03027.100-0.008-0.0080.0000.0000.0000.000
22A131ASN 00.0250.00027.5410.0030.0030.0000.0000.0000.000
23A132TYR 0-0.043-0.03830.6490.0100.0100.0000.0000.0000.000
24A133PRO 00.0110.02632.8310.0000.0000.0000.0000.0000.000
25A134ASN 0-0.012-0.01435.0180.0100.0100.0000.0000.0000.000
26A135PRO 0-0.013-0.02437.636-0.003-0.0030.0000.0000.0000.000
27A136ALA 00.0810.05836.5730.0020.0020.0000.0000.0000.000
28A137VAL 0-0.024-0.00534.8280.0070.0070.0000.0000.0000.000
29A138ASN 0-0.030-0.01332.174-0.011-0.0110.0000.0000.0000.000
30A139ASN 0-0.058-0.04231.8620.0060.0060.0000.0000.0000.000
31A140ASP -1-0.818-0.89527.320-0.104-0.1040.0000.0000.0000.000
32A141ILE 0-0.010-0.00826.6240.0210.0210.0000.0000.0000.000
33A142CYS 0-0.051-0.01523.5130.0030.0030.0000.0000.0000.000
34A143LEU 0-0.015-0.03722.2980.0070.0070.0000.0000.0000.000
35A144ASP -1-0.792-0.90922.277-0.014-0.0140.0000.0000.0000.000
36A145GLU -1-0.853-0.90320.587-0.184-0.1840.0000.0000.0000.000
37A146VAL 0-0.137-0.06717.346-0.012-0.0120.0000.0000.0000.000
38A147ALA 0-0.029-0.01017.6730.0070.0070.0000.0000.0000.000
39A148GLU -1-0.878-0.91519.299-0.199-0.1990.0000.0000.0000.000
40A149GLU -1-0.845-0.90914.620-0.389-0.3890.0000.0000.0000.000
41A150LEU 0-0.0150.0019.2810.0530.0530.0000.0000.0000.000
42A151ASN 0-0.087-0.04411.4590.1380.1380.0000.0000.0000.000
43A152VAL 00.1050.02111.831-0.013-0.0130.0000.0000.0000.000
44A153GLU -1-0.902-0.94014.4810.5310.5310.0000.0000.0000.000
45A154ARG 10.9900.97216.416-0.205-0.2050.0000.0000.0000.000
46A155ARG 10.8570.92519.041-0.153-0.1530.0000.0000.0000.000
47A156ARG 10.9570.98215.011-0.139-0.1390.0000.0000.0000.000
48A157ILE 00.1040.06318.465-0.024-0.0240.0000.0000.0000.000
49A158TYR 0-0.033-0.01220.763-0.003-0.0030.0000.0000.0000.000
50A159ASP -1-0.884-0.95920.276-0.010-0.0100.0000.0000.0000.000
51A160ILE 00.0820.04118.188-0.008-0.0080.0000.0000.0000.000
52A161VAL 00.0370.02822.660-0.007-0.0070.0000.0000.0000.000
53A162ASN 0-0.116-0.07325.7220.0170.0170.0000.0000.0000.000
54A163VAL 00.0220.00124.1500.0040.0040.0000.0000.0000.000
55A164LEU 00.0460.05124.697-0.004-0.0040.0000.0000.0000.000
56A165GLU -1-0.785-0.88627.948-0.003-0.0030.0000.0000.0000.000
57A166SER 0-0.117-0.07329.8590.0050.0050.0000.0000.0000.000
58A167LEU 00.017-0.00129.6610.0030.0030.0000.0000.0000.000
59A168HIS 0-0.088-0.04233.363-0.001-0.0010.0000.0000.0000.000
60A169MET 0-0.023-0.00127.658-0.007-0.0070.0000.0000.0000.000
61A170VAL 00.0130.02928.656-0.003-0.0030.0000.0000.0000.000
62A171SER 0-0.011-0.01431.9950.0070.0070.0000.0000.0000.000
63A172ARG 10.8340.91430.909-0.017-0.0170.0000.0000.0000.000
64A173LEU 00.0120.02333.955-0.001-0.0010.0000.0000.0000.000
65A174ALA 00.0320.00034.2750.0060.0060.0000.0000.0000.000
66A175LYS 10.9720.98330.858-0.075-0.0750.0000.0000.0000.000
67A176ASN 0-0.055-0.05226.358-0.011-0.0110.0000.0000.0000.000
68A177ARG 10.9871.01429.7730.0070.0070.0000.0000.0000.000
69A178TYR 00.003-0.00829.0690.0130.0130.0000.0000.0000.000
70A179THR 00.0430.02431.210-0.002-0.0020.0000.0000.0000.000
71A180TRP 00.0490.00527.5010.0030.0030.0000.0000.0000.000
72A181HIS 0-0.097-0.04630.964-0.005-0.0050.0000.0000.0000.000
73A182GLY 00.0730.03832.048-0.010-0.0100.0000.0000.0000.000
74A183ARG 10.8870.94429.2680.1490.1490.0000.0000.0000.000
75A184HIS 00.0200.01334.1660.0020.0020.0000.0000.0000.000
76A185ASN 00.0230.00437.4910.0080.0080.0000.0000.0000.000
77A186LEU 00.0470.03332.8050.0020.0020.0000.0000.0000.000
78A187ASN 0-0.006-0.02036.2420.0020.0020.0000.0000.0000.000
79A188LYS 11.0071.00939.0360.0450.0450.0000.0000.0000.000
80A189THR 0-0.037-0.00736.1690.0070.0070.0000.0000.0000.000
81A190LEU 00.0350.02035.7550.0050.0050.0000.0000.0000.000
82A191GLY 00.0190.01438.6380.0040.0040.0000.0000.0000.000
83A192THR 0-0.041-0.05141.5200.0050.0050.0000.0000.0000.000
84A193LEU 0-0.014-0.01236.4610.0050.0050.0000.0000.0000.000
85A194LYS 10.9690.96640.8960.0500.0500.0000.0000.0000.000
86A195SER 0-0.054-0.01643.1100.0030.0030.0000.0000.0000.000
87A196ILE 0-0.076-0.03442.0810.0030.0030.0000.0000.0000.000
88A197GLY 00.0210.00342.4200.0030.0030.0000.0000.0000.000
89A198GLU -1-0.886-0.93642.930-0.002-0.0020.0000.0000.0000.000
90A199GLU -1-0.882-0.95842.871-0.020-0.0200.0000.0000.0000.000
91A200ASN 00.006-0.00843.924-0.002-0.0020.0000.0000.0000.000
92A201LYS 10.9470.98044.5060.0000.0000.0000.0000.0000.000
93A202TYR 0-0.040-0.01940.0760.0050.0050.0000.0000.0000.000
94A203ALA 00.0570.02141.7340.0000.0000.0000.0000.0000.000
95A204GLU -1-0.899-0.95143.2750.0020.0020.0000.0000.0000.000
96A205GLN 0-0.001-0.01340.2660.0040.0040.0000.0000.0000.000
97A206ILE 0-0.020-0.01339.4870.0020.0020.0000.0000.0000.000
98A207MET 0-0.082-0.03741.3030.0000.0000.0000.0000.0000.000
99A208MET 0-0.0470.00143.6510.0030.0030.0000.0000.0000.000
100A209ILE 00.0210.00737.7680.0020.0020.0000.0000.0000.000
101A210LYS 10.9070.97940.6830.0100.0100.0000.0000.0000.000
102A211LYS 10.8730.90041.734-0.001-0.0010.0000.0000.0000.000
103A212LYS 10.9280.97944.109-0.009-0.0090.0000.0000.0000.000
104A213NME 00.0950.06745.0540.0030.0030.0000.0000.0000.000
105A258ACE 0-0.002-0.01140.6430.0000.0000.0000.0000.0000.000
106A259ASN 00.0410.01041.522-0.004-0.0040.0000.0000.0000.000
107A260SER 00.0250.02240.6760.0020.0020.0000.0000.0000.000
108A261ARG 11.0221.01541.115-0.060-0.0600.0000.0000.0000.000
109A262LYS 10.8760.92435.646-0.097-0.0970.0000.0000.0000.000
110A263ASP -1-0.884-0.90836.3800.0340.0340.0000.0000.0000.000
111A264LYS 10.9640.96233.408-0.089-0.0890.0000.0000.0000.000
112A265SER 00.008-0.02031.388-0.001-0.0010.0000.0000.0000.000
113A266LEU 0-0.0260.00025.995-0.004-0.0040.0000.0000.0000.000
114A267ARG 11.0131.01029.807-0.028-0.0280.0000.0000.0000.000
115A268VAL 00.0990.07331.567-0.009-0.0090.0000.0000.0000.000
116A269MET 0-0.056-0.02628.638-0.002-0.0020.0000.0000.0000.000
117A270SER 0-0.020-0.02328.975-0.007-0.0070.0000.0000.0000.000
118A271GLN 00.0230.00930.820-0.003-0.0030.0000.0000.0000.000
119A272LYS 10.9530.97034.340-0.012-0.0120.0000.0000.0000.000
120A273PHE 0-0.052-0.00527.971-0.001-0.0010.0000.0000.0000.000
121A274VAL 00.0580.01231.587-0.005-0.0050.0000.0000.0000.000
122A275MET 0-0.0920.00333.765-0.002-0.0020.0000.0000.0000.000
123A276LEU 0-0.017-0.02033.2140.0010.0010.0000.0000.0000.000
124A277PHE 00.0110.01329.283-0.006-0.0060.0000.0000.0000.000
125A278LEU 0-0.085-0.02935.236-0.004-0.0040.0000.0000.0000.000
126A279VAL 00.0310.01838.3570.0060.0060.0000.0000.0000.000
127A280SER 00.014-0.00240.280-0.005-0.0050.0000.0000.0000.000
128A281THR 0-0.045-0.02840.361-0.002-0.0020.0000.0000.0000.000
129A282PRO 0-0.003-0.00735.4660.0040.0040.0000.0000.0000.000
130A283GLN 0-0.005-0.00535.6800.0020.0020.0000.0000.0000.000
131A284ILE 00.0290.07131.4170.0050.0050.0000.0000.0000.000
132A285VAL 00.018-0.01428.2380.0030.0030.0000.0000.0000.000
133A286SER 0-0.010-0.02729.6420.0040.0040.0000.0000.0000.000
134A287LEU 00.0700.04431.7060.0110.0110.0000.0000.0000.000
135A288GLU -1-0.747-0.89232.944-0.032-0.0320.0000.0000.0000.000
136A289VAL 0-0.078-0.03429.7230.0060.0060.0000.0000.0000.000
137A290ALA 00.0410.02032.8770.0100.0100.0000.0000.0000.000
138A291ALA 00.0720.03936.1610.0040.0040.0000.0000.0000.000
139A292LYS 10.8080.89332.4740.0060.0060.0000.0000.0000.000
140A293ILE 0-0.066-0.03933.2370.0080.0080.0000.0000.0000.000
141A294LEU 00.0990.05136.7710.0030.0030.0000.0000.0000.000
142A295ILE 0-0.058-0.02036.518-0.001-0.0010.0000.0000.0000.000
143A296GLY 0-0.140-0.07337.3840.0020.0020.0000.0000.0000.000
144A297GLU -1-0.971-0.97938.3920.0790.0790.0000.0000.0000.000
145A298ASP -1-0.970-0.98440.5940.0320.0320.0000.0000.0000.000
146A299HIS 00.0300.00543.528-0.001-0.0010.0000.0000.0000.000
147A300VAL 0-0.042-0.00344.254-0.001-0.0010.0000.0000.0000.000
148A301GLU -1-0.923-0.94941.5340.0730.0730.0000.0000.0000.000
149A302ASP -1-0.912-0.97239.3710.0690.0690.0000.0000.0000.000
150A303LEU 0-0.054-0.03436.5070.0070.0070.0000.0000.0000.000
151A304ASP -1-0.784-0.85636.3100.0690.0690.0000.0000.0000.000
152A305LYS 10.9140.98133.187-0.100-0.1000.0000.0000.0000.000
153A306SER 0-0.118-0.10630.5980.0090.0090.0000.0000.0000.000
154A307LYS 10.9961.01530.374-0.137-0.1370.0000.0000.0000.000
155A308PHE 00.1130.02729.9340.0000.0000.0000.0000.0000.000
156A309LYS 11.0101.00126.092-0.164-0.1640.0000.0000.0000.000
157A310THR 0-0.069-0.05524.9290.0030.0030.0000.0000.0000.000
158A311LYS 10.9160.96626.050-0.059-0.0590.0000.0000.0000.000
159A312ILE 00.0640.04224.734-0.012-0.0120.0000.0000.0000.000
160A313ARG 10.8850.95721.318-0.185-0.1850.0000.0000.0000.000
161A314ARG 10.9190.95420.713-0.144-0.1440.0000.0000.0000.000
162A315LEU 00.0400.03424.500-0.014-0.0140.0000.0000.0000.000
163A316TYR 0-0.007-0.01220.814-0.014-0.0140.0000.0000.0000.000
164A317ASP -1-0.942-0.96720.066-0.026-0.0260.0000.0000.0000.000
165A318ILE 0-0.007-0.02221.340-0.022-0.0220.0000.0000.0000.000
166A319ALA 00.0080.01922.780-0.014-0.0140.0000.0000.0000.000
167A320ASN 0-0.002-0.01816.7780.0070.0070.0000.0000.0000.000
168A321VAL 0-0.045-0.01820.129-0.036-0.0360.0000.0000.0000.000
169A322LEU 00.003-0.00721.451-0.004-0.0040.0000.0000.0000.000
170A323SER 0-0.074-0.03020.2810.0010.0010.0000.0000.0000.000
171A324SER 0-0.031-0.01319.508-0.052-0.0520.0000.0000.0000.000
172A325LEU 0-0.0110.00621.4240.0240.0240.0000.0000.0000.000
173A326ASP -1-0.800-0.91624.218-0.182-0.1820.0000.0000.0000.000
174A327LEU 0-0.166-0.08526.927-0.003-0.0030.0000.0000.0000.000
175A328ILE 00.0930.05124.7960.0150.0150.0000.0000.0000.000
176A329LYS 10.8600.93326.2310.1150.1150.0000.0000.0000.000
177A330LYS 10.9810.99619.4800.2150.2150.0000.0000.0000.000
178A331VAL 0-0.067-0.02824.047-0.002-0.0020.0000.0000.0000.000
179A332HIS 00.0510.02525.3770.0020.0020.0000.0000.0000.000
180A333VAL 00.0090.00324.294-0.008-0.0080.0000.0000.0000.000
181A334THR 0-0.093-0.06026.4010.0100.0100.0000.0000.0000.000
182A335GLU -1-0.809-0.91124.335-0.169-0.1690.0000.0000.0000.000
183A336GLU -1-0.791-0.89928.704-0.063-0.0630.0000.0000.0000.000
184A337ARG 10.8010.89928.6820.1480.1480.0000.0000.0000.000
185A338GLY 00.1520.07231.158-0.001-0.0010.0000.0000.0000.000
186A339ARG 10.8540.93330.4770.1530.1530.0000.0000.0000.000
187A340LYS 10.9320.95933.4350.1170.1170.0000.0000.0000.000
188A341PRO -1-0.790-0.86535.813-0.072-0.0720.0000.0000.0000.000