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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: G5YV1

Calculation Name: 3KV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KV0

Chain ID: A

ChEMBL ID:

UniProt ID: Q01494

Base Structure: X-ray

Registration Date: 2023-09-22

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 195
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2315573.560921
FMO2-HF: Nuclear repulsion 2237236.400623
FMO2-HF: Total energy -78337.160298
FMO2-MP2: Total energy -78567.364844


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:14:THR)


Summations of interaction energy for fragment #1(A:14:THR)
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.
-52.712-41.62320.488-15.009-16.569-0.087
Interaction energy analysis for fragmet #1(A:14:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.027
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].
3A16LEU0-0.0290.0122.797-3.2300.3690.529-1.894-2.2340.011
4A17GLU-1-0.878-0.9292.375-19.191-13.2714.763-4.458-6.225-0.007
5A18THR0-0.116-0.0804.192-1.040-0.6330.005-0.095-0.3170.000
6A19PHE0-0.081-0.0456.3460.0120.0120.0000.0000.0000.000
7A20MLY10.9430.9788.763-0.010-0.0100.0000.0000.0000.000
8A21MLY10.9300.97311.9320.3600.3600.0000.0000.0000.000
9A22SER00.0920.0548.7200.0670.0670.0000.0000.0000.000
10A23PHE00.003-0.03010.6870.0890.0890.0000.0000.0000.000
11A24VAL0-0.021-0.0149.6490.0870.0870.0000.0000.0000.000
12A25ASP-1-0.906-0.94111.413-0.798-0.7980.0000.0000.0000.000
13A26VAL0-0.061-0.02414.3030.0880.0880.0000.0000.0000.000
14A27PRO0-0.026-0.00617.158-0.008-0.0080.0000.0000.0000.000
15A28ILE0-0.020-0.02619.7100.0220.0220.0000.0000.0000.000
16A29ASP-1-0.850-0.92922.669-0.213-0.2130.0000.0000.0000.000
17A30ALA0-0.018-0.03026.0560.0130.0130.0000.0000.0000.000
18A31GLU-1-0.934-0.96227.562-0.171-0.1710.0000.0000.0000.000
19A32MLY10.8510.94029.8110.1750.1750.0000.0000.0000.000
20A33GLY0-0.0010.00230.6800.0020.0020.0000.0000.0000.000
21A34ASN0-0.027-0.02625.580-0.010-0.0100.0000.0000.0000.000
22A35ALA00.0340.03725.884-0.008-0.0080.0000.0000.0000.000
23A36ILE00.0050.00321.369-0.019-0.0190.0000.0000.0000.000
24A37SER0-0.011-0.00521.8140.0320.0320.0000.0000.0000.000
25A38THR0-0.011-0.03121.998-0.019-0.0190.0000.0000.0000.000
26A39ALA00.0300.01322.321-0.003-0.0030.0000.0000.0000.000
27A40GLU-1-0.796-0.89617.685-0.258-0.2580.0000.0000.0000.000
28A41PHE00.0320.01517.371-0.023-0.0230.0000.0000.0000.000
29A42LEU0-0.049-0.03018.457-0.001-0.0010.0000.0000.0000.000
30A43GLU-1-0.904-0.96116.284-0.213-0.2130.0000.0000.0000.000
31A44ALA00.0010.00713.9910.0070.0070.0000.0000.0000.000
32A45ALA0-0.017-0.01114.314-0.008-0.0080.0000.0000.0000.000
33A46GLU-1-0.878-0.93616.350-0.065-0.0650.0000.0000.0000.000
34A47SER00.0000.00511.0910.0530.0530.0000.0000.0000.000
35A48LEU00.0140.05011.9700.0270.0270.0000.0000.0000.000
36A49THR0-0.066-0.05813.1170.0450.0450.0000.0000.0000.000
37A50THR0-0.026-0.03911.1900.0480.0480.0000.0000.0000.000
38A51MET00.0470.0218.2050.1170.1170.0000.0000.0000.000
39A52PHE0-0.039-0.02411.5580.0330.0330.0000.0000.0000.000
40A53ASP-1-0.836-0.92413.5610.1320.1320.0000.0000.0000.000
41A54VAL0-0.0370.0058.7810.0490.0490.0000.0000.0000.000
42A55LEU0-0.030-0.01511.9410.0320.0320.0000.0000.0000.000
43A56GLY00.029-0.00114.3400.0140.0140.0000.0000.0000.000
44A57SER0-0.0330.00417.125-0.027-0.0270.0000.0000.0000.000
45A58ILE00.0200.00818.382-0.022-0.0220.0000.0000.0000.000
46A59ALA00.0020.01920.548-0.018-0.0180.0000.0000.0000.000
47A60PHE00.051-0.01118.371-0.025-0.0250.0000.0000.0000.000
48A61SER0-0.034-0.00820.468-0.020-0.0200.0000.0000.0000.000
49A62PRO0-0.008-0.00222.019-0.012-0.0120.0000.0000.0000.000
50A63VAL00.0100.01020.267-0.009-0.0090.0000.0000.0000.000
51A64MLY10.9500.98517.656-0.079-0.0790.0000.0000.0000.000
52A65THR0-0.042-0.02720.419-0.007-0.0070.0000.0000.0000.000
53A66ASP-1-0.937-0.96423.901-0.080-0.0800.0000.0000.0000.000
54A67MET0-0.041-0.00918.687-0.012-0.0120.0000.0000.0000.000
55A68LEU00.0320.00318.934-0.011-0.0110.0000.0000.0000.000
56A69GLY00.0170.01722.588-0.001-0.0010.0000.0000.0000.000
57A70ASN0-0.040-0.03424.9320.0040.0040.0000.0000.0000.000
58A71VAL00.0300.01120.439-0.006-0.0060.0000.0000.0000.000
59A72GLU-1-0.891-0.93023.863-0.063-0.0630.0000.0000.0000.000
60A73MLY10.8800.94226.4210.0690.0690.0000.0000.0000.000
61A74ILE0-0.0110.00024.8220.0020.0020.0000.0000.0000.000
62A75ARG10.9140.94321.4290.0930.0930.0000.0000.0000.000
63A76MLY10.9650.98927.1160.0490.0490.0000.0000.0000.000
64A77ARG10.9300.96730.6740.0870.0870.0000.0000.0000.000
65A78MET00.018-0.00125.524-0.003-0.0030.0000.0000.0000.000
66A79LEU0-0.024-0.01328.0820.0010.0010.0000.0000.0000.000
67A80ALA0-0.045-0.01431.2530.0040.0040.0000.0000.0000.000
68A81ALA0-0.039-0.01233.7280.0050.0050.0000.0000.0000.000
69A82PRO00.0670.03831.583-0.007-0.0070.0000.0000.0000.000
70A83LEU0-0.022-0.02031.772-0.009-0.0090.0000.0000.0000.000
71A84GLU-1-0.952-0.97533.992-0.086-0.0860.0000.0000.0000.000
72A85SER0-0.013-0.01230.330-0.003-0.0030.0000.0000.0000.000
73A86GLN00.0390.02228.404-0.012-0.0120.0000.0000.0000.000
74A87ASN0-0.0060.00826.432-0.015-0.0150.0000.0000.0000.000
75A88ILE00.0070.00424.0240.0170.0170.0000.0000.0000.000
76A89GLN00.0430.01226.6510.0140.0140.0000.0000.0000.000
77A90ASP-1-0.825-0.91530.156-0.125-0.1250.0000.0000.0000.000
78A91LEU0-0.068-0.01528.2060.0110.0110.0000.0000.0000.000
79A92VAL0-0.026-0.01730.2060.0100.0100.0000.0000.0000.000
80A93ARG10.7920.86232.5080.1450.1450.0000.0000.0000.000
81A94ASN0-0.033-0.04335.0150.0110.0110.0000.0000.0000.000
82A95GLU-1-0.775-0.85334.253-0.082-0.0820.0000.0000.0000.000
83A96LEU0-0.041-0.02935.8700.0070.0070.0000.0000.0000.000
84A97MLY10.9021.00338.6490.0850.0850.0000.0000.0000.000
85A98THR0-0.014-0.04439.8950.0020.0020.0000.0000.0000.000
86A99MLY10.9230.96742.1460.0400.0400.0000.0000.0000.000
87A100SER0-0.0160.00636.8060.0020.0020.0000.0000.0000.000
88A101HIS10.9860.99636.3500.0650.0650.0000.0000.0000.000
89A102THR0-0.029-0.01333.207-0.003-0.0030.0000.0000.0000.000
90A103ALA00.0290.01430.399-0.002-0.0020.0000.0000.0000.000
91A104THR0-0.001-0.02729.998-0.010-0.0100.0000.0000.0000.000
92A105GLU-1-0.987-0.99331.008-0.077-0.0770.0000.0000.0000.000
93A106GLY0-0.011-0.01529.098-0.002-0.0020.0000.0000.0000.000
94A107LEU00.0320.02225.120-0.007-0.0070.0000.0000.0000.000
95A108LEU0-0.020-0.00526.415-0.012-0.0120.0000.0000.0000.000
96A109TRP0-0.032-0.03727.433-0.009-0.0090.0000.0000.0000.000
97A110LEU00.0250.02320.710-0.002-0.0020.0000.0000.0000.000
98A111VAL00.0180.00622.404-0.018-0.0180.0000.0000.0000.000
99A112ARG10.9350.97822.9840.1010.1010.0000.0000.0000.000
100A113GLY00.0080.00922.371-0.003-0.0030.0000.0000.0000.000
101A114LEU00.003-0.00317.231-0.009-0.0090.0000.0000.0000.000
102A115GLU-1-0.811-0.90818.631-0.243-0.2430.0000.0000.0000.000
103A116PHE0-0.048-0.02720.594-0.009-0.0090.0000.0000.0000.000
104A117THR00.0210.00914.8370.0100.0100.0000.0000.0000.000
105A118CYS00.0140.02415.804-0.043-0.0430.0000.0000.0000.000
106A119ILE00.0100.01816.863-0.033-0.0330.0000.0000.0000.000
107A120ALA0-0.029-0.01117.5820.0000.0000.0000.0000.0000.000
108A121LEU00.0290.00511.4360.0190.0190.0000.0000.0000.000
109A122SER00.015-0.00514.387-0.060-0.0600.0000.0000.0000.000
110A123MLY10.8630.94216.0400.1780.1780.0000.0000.0000.000
111A124ASN0-0.0150.03214.8760.0010.0010.0000.0000.0000.000
112A125ILE00.0430.01911.2130.0510.0510.0000.0000.0000.000
113A126GLY0-0.062-0.01414.330-0.012-0.0120.0000.0000.0000.000
114A127SER0-0.068-0.03217.5420.0530.0530.0000.0000.0000.000
115A128THR00.016-0.00317.966-0.014-0.0140.0000.0000.0000.000
116A129GLU-1-0.801-0.88619.923-0.116-0.1160.0000.0000.0000.000
117A130GLU-1-0.731-0.87219.0090.0120.0120.0000.0000.0000.000
118A131LEU00.0180.00313.822-0.026-0.0260.0000.0000.0000.000
119A132ALA00.0100.00818.148-0.019-0.0190.0000.0000.0000.000
120A133ASP-1-0.885-0.95021.341-0.055-0.0550.0000.0000.0000.000
121A134SER0-0.021-0.02618.641-0.014-0.0140.0000.0000.0000.000
122A135PHE00.0280.00215.559-0.012-0.0120.0000.0000.0000.000
123A136ARG10.8830.92820.8820.0270.0270.0000.0000.0000.000
124A137GLY0-0.065-0.04324.0470.0020.0020.0000.0000.0000.000
125A138SER00.0360.01020.9670.0010.0010.0000.0000.0000.000
126A139TYR00.007-0.01823.4160.0070.0070.0000.0000.0000.000
127A140ARG10.8620.91725.3450.0970.0970.0000.0000.0000.000
128A141VAL0-0.007-0.00325.7620.0080.0080.0000.0000.0000.000
129A142THR00.0310.03823.500-0.002-0.0020.0000.0000.0000.000
130A143LEU00.007-0.00623.9770.0090.0090.0000.0000.0000.000
131A144MLY10.9260.98227.7740.0700.0700.0000.0000.0000.000
132A145PRO0-0.048-0.03930.1990.0100.0100.0000.0000.0000.000
133A146HIS0-0.0060.00430.3950.0090.0090.0000.0000.0000.000
134A147HIS00.0610.07227.2080.0070.0070.0000.0000.0000.000
135A148SER00.0280.00432.8010.0020.0020.0000.0000.0000.000
136A149PHE00.010-0.02934.670-0.001-0.0010.0000.0000.0000.000
137A150LEU00.0400.02235.8250.0020.0020.0000.0000.0000.000
138A151VAL00.0360.02429.9470.0040.0040.0000.0000.0000.000
139A152MLY10.8850.96530.3790.0540.0540.0000.0000.0000.000
140A153PRO0-0.005-0.01030.133-0.001-0.0010.0000.0000.0000.000
141A154ILE00.0220.02927.0480.0050.0050.0000.0000.0000.000
142A155PHE00.0570.01823.8240.0050.0050.0000.0000.0000.000
143A156SER0-0.051-0.02425.4350.0000.0000.0000.0000.0000.000
144A157ALA00.0150.00726.6220.0030.0030.0000.0000.0000.000
145A158ALA00.0100.01122.4780.0090.0090.0000.0000.0000.000
146A159MET0-0.028-0.01021.635-0.001-0.0010.0000.0000.0000.000
147A160SER0-0.061-0.03822.219-0.001-0.0010.0000.0000.0000.000
148A161ALA0-0.0260.00522.5810.0080.0080.0000.0000.0000.000
149A162CYS0-0.077-0.02218.3470.0110.0110.0000.0000.0000.000
150A163PRO00.0090.03014.7850.0090.0090.0000.0000.0000.000
151A164TYR00.0160.00917.496-0.044-0.0440.0000.0000.0000.000
152A165ARG10.8380.89814.4340.2040.2040.0000.0000.0000.000
153A166MLY10.8980.95412.828-0.021-0.0210.0000.0000.0000.000
154A167ASP-1-0.821-0.91712.4270.3610.3610.0000.0000.0000.000
155A168PHE0-0.063-0.03910.2130.1080.1080.0000.0000.0000.000
156A169TYR0-0.033-0.0848.3290.0240.0240.0000.0000.0000.000
157A170ALA00.0470.0367.2330.0670.0670.0000.0000.0000.000
158A171MLY10.8770.9427.196-0.057-0.0570.0000.0000.0000.000
159A172LEU0-0.058-0.0314.2990.0030.174-0.001-0.032-0.1370.000
160A173GLY00.0420.0122.598-1.6290.4591.369-1.474-1.983-0.015
161A174ASP-1-0.935-0.9543.6531.9471.9890.013-0.004-0.0510.000
162A175ASP-1-0.915-0.9624.538-0.753-0.765-0.001-0.0110.0240.000
163A176GLU-1-0.971-0.9965.497-0.634-0.6340.0000.0000.0000.000
164A177GLN0-0.010-0.0097.685-0.334-0.3340.0000.0000.0000.000
165A178MLY11.0451.0282.9033.1873.7340.088-0.111-0.5240.000
166A179VAL00.0060.0112.937-2.107-1.3690.153-0.185-0.7060.000
167A180GLN0-0.028-0.0174.263-0.263-0.254-0.001-0.0110.0020.000
168A181GLU-1-0.976-0.9837.518-1.095-1.0950.0000.0000.0000.000
169A182GLU-1-0.840-0.9051.724-29.865-32.28513.571-6.734-4.418-0.076
170A183LEU00.004-0.0036.1210.6770.6770.0000.0000.0000.000
171A184ARG10.9150.9457.6521.1851.1850.0000.0000.0000.000
172A185GLU-1-0.916-0.9438.654-1.618-1.6180.0000.0000.0000.000
173A186TYR0-0.010-0.0137.9290.3510.3510.0000.0000.0000.000
174A187LEU0-0.015-0.0169.9610.2420.2420.0000.0000.0000.000
175A188VAL00.0040.00512.8760.1490.1490.0000.0000.0000.000
176A189ALA00.0000.01013.0370.1080.1080.0000.0000.0000.000
177A190LEU0-0.037-0.02213.9840.0980.0980.0000.0000.0000.000
178A191ASP-1-0.893-0.96215.634-0.306-0.3060.0000.0000.0000.000
179A192MLY10.9540.98718.0170.4810.4810.0000.0000.0000.000
180A193ILE00.0130.00016.8320.0520.0520.0000.0000.0000.000
181A194VAL00.0080.00319.2620.0440.0440.0000.0000.0000.000
182A195ASN0-0.014-0.01721.6000.0540.0540.0000.0000.0000.000
183A196ILE0-0.071-0.02822.2820.0290.0290.0000.0000.0000.000
184A197LEU00.0150.00022.4660.0260.0260.0000.0000.0000.000
185A198MLY10.8710.95525.0490.2220.2220.0000.0000.0000.000
186A199ARG10.9680.99025.8170.2480.2480.0000.0000.0000.000
187A200PHE00.0140.01128.9000.0120.0120.0000.0000.0000.000
188A201LEU0-0.020-0.01227.5540.0150.0150.0000.0000.0000.000
189A202GLU-1-0.980-0.97830.885-0.145-0.1450.0000.0000.0000.000
190A203SER0-0.062-0.03933.6190.0120.0120.0000.0000.0000.000
191A204MLY10.9420.93635.6600.0960.0960.0000.0000.0000.000
192A205GLU-1-0.808-0.87735.236-0.125-0.1250.0000.0000.0000.000
193A206ALA00.0130.03433.2710.0030.0030.0000.0000.0000.000
194A207MLY10.8810.94635.2660.1020.1020.0000.0000.0000.000
195A208TRP00.0210.01234.1570.0040.0040.0000.0000.0000.000