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: VKRM1

Calculation Name: 3WKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WKM

Chain ID: A

ChEMBL ID:

UniProt ID: O67776

Base Structure: X-ray

Registration Date: 2023-09-26

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1708246.899857
FMO2-HF: Nuclear repulsion 1641598.428454
FMO2-HF: Total energy -66648.471402
FMO2-MP2: Total energy -66848.817322


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:116:VAL)


Summations of interaction energy for fragment #1(A:116:VAL)
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.
-2.5840.0669999999999990.407-0.862-2.196-0.001
Interaction energy analysis for fragmet #1(A:116:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.002
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].
3A118LYS10.9820.9913.831-0.6240.7680.007-0.561-0.8370.001
4A119TYR00.0600.0304.735-0.0350.142-0.001-0.008-0.1680.000
5A120LEU0-0.015-0.0012.508-0.4270.2380.374-0.221-0.818-0.002
6A121LYS10.8530.8973.1431.5801.9970.027-0.072-0.3730.000
7A122GLU-1-0.934-0.9647.123-0.647-0.6470.0000.0000.0000.000
8A123PRO00.0490.0109.9800.0160.0160.0000.0000.0000.000
9A124VAL0-0.0010.01613.2720.0050.0050.0000.0000.0000.000
10A125VAL00.0020.00315.0470.0460.0460.0000.0000.0000.000
11A126VAL0-0.021-0.01016.441-0.008-0.0080.0000.0000.0000.000
12A127GLY0-0.015-0.02317.3710.0110.0110.0000.0000.0000.000
13A128TYR0-0.036-0.02617.6470.0280.0280.0000.0000.0000.000
14A129VAL00.0310.01118.789-0.020-0.0200.0000.0000.0000.000
15A130GLN00.0020.01018.4360.0020.0020.0000.0000.0000.000
16A131ARG10.8900.91621.821-0.022-0.0220.0000.0000.0000.000
17A132ASP-1-0.827-0.88424.9830.0090.0090.0000.0000.0000.000
18A133SER0-0.021-0.00522.291-0.006-0.0060.0000.0000.0000.000
19A134ILE00.0110.00622.6580.0010.0010.0000.0000.0000.000
20A135ALA00.0430.02221.307-0.002-0.0020.0000.0000.0000.000
21A136GLN00.0100.00623.4480.0040.0040.0000.0000.0000.000
22A137LYS10.8580.91826.1140.0230.0230.0000.0000.0000.000
23A138ILE00.0050.01824.7800.0010.0010.0000.0000.0000.000
24A139GLY00.0310.02927.818-0.003-0.0030.0000.0000.0000.000
25A140ILE0-0.0100.00321.415-0.002-0.0020.0000.0000.0000.000
26A141LYS10.8230.89724.1880.0770.0770.0000.0000.0000.000
27A142PRO0-0.033-0.02421.469-0.013-0.0130.0000.0000.0000.000
28A143GLY00.0060.00821.3760.0110.0110.0000.0000.0000.000
29A144ASP-1-0.747-0.82022.073-0.114-0.1140.0000.0000.0000.000
30A145LYS10.7920.87518.4160.1910.1910.0000.0000.0000.000
31A146ILE0-0.025-0.01717.7860.0130.0130.0000.0000.0000.000
32A147ILE00.0230.00918.354-0.028-0.0280.0000.0000.0000.000
33A148LYS10.8190.91520.2730.1780.1780.0000.0000.0000.000
34A149ILE00.0050.00719.1530.0130.0130.0000.0000.0000.000
35A150ASN00.0420.01822.073-0.015-0.0150.0000.0000.0000.000
36A151GLY00.0170.00324.1440.0040.0040.0000.0000.0000.000
37A152TYR0-0.047-0.02318.645-0.015-0.0150.0000.0000.0000.000
38A153GLU-1-0.786-0.88318.474-0.229-0.2290.0000.0000.0000.000
39A154VAL0-0.050-0.02415.256-0.026-0.0260.0000.0000.0000.000
40A155ARG10.8580.92614.1620.3690.3690.0000.0000.0000.000
41A156THR0-0.056-0.0419.669-0.050-0.0500.0000.0000.0000.000
42A157TRP0-0.004-0.0249.0980.1020.1020.0000.0000.0000.000
43A158GLU-1-0.834-0.8875.584-1.492-1.4920.0000.0000.0000.000
44A159ASP-1-0.793-0.8779.340-0.440-0.4400.0000.0000.0000.000
45A160LEU00.0060.00112.8510.0630.0630.0000.0000.0000.000
46A161ARG10.8180.8869.3150.2440.2440.0000.0000.0000.000
47A162ASP-1-0.841-0.93011.104-0.399-0.3990.0000.0000.0000.000
48A163ALA0-0.0040.00513.6850.0460.0460.0000.0000.0000.000
49A164LEU0-0.032-0.02015.7980.0390.0390.0000.0000.0000.000
50A165ILE0-0.017-0.01013.0850.0340.0340.0000.0000.0000.000
51A166ARG10.8140.88616.7870.1910.1910.0000.0000.0000.000
52A167LEU00.0330.00919.0240.0210.0210.0000.0000.0000.000
53A168SER0-0.059-0.04820.6600.0200.0200.0000.0000.0000.000
54A169LEU0-0.069-0.03418.2930.0140.0140.0000.0000.0000.000
55A170ASP-1-0.822-0.87422.383-0.132-0.1320.0000.0000.0000.000
56A171GLY00.0170.01424.6600.0060.0060.0000.0000.0000.000
57A172VAL00.0180.02925.3840.0080.0080.0000.0000.0000.000
58A173LYS10.8170.88626.5080.0680.0680.0000.0000.0000.000
59A174GLU-1-0.897-0.94827.835-0.058-0.0580.0000.0000.0000.000
60A175THR0-0.015-0.01524.269-0.006-0.0060.0000.0000.0000.000
61A176THR00.0140.02526.8550.0040.0040.0000.0000.0000.000
62A177LEU0-0.017-0.00920.450-0.014-0.0140.0000.0000.0000.000
63A178PHE0-0.008-0.00623.1640.0120.0120.0000.0000.0000.000
64A179LEU0-0.003-0.00822.308-0.020-0.0200.0000.0000.0000.000
65A180GLU-1-0.793-0.87223.214-0.171-0.1710.0000.0000.0000.000
66A181ARG10.8130.84624.2120.0880.0880.0000.0000.0000.000
67A182ASN0-0.022-0.02026.9610.0020.0020.0000.0000.0000.000
68A183GLY00.0280.02427.6480.0050.0050.0000.0000.0000.000
69A184GLU-1-0.932-0.94528.813-0.082-0.0820.0000.0000.0000.000
70A185VAL0-0.018-0.02026.804-0.008-0.0080.0000.0000.0000.000
71A186LEU0-0.027-0.01027.5820.0090.0090.0000.0000.0000.000
72A187HIS00.0220.00327.237-0.012-0.0120.0000.0000.0000.000
73A188LEU00.001-0.00626.6170.0090.0090.0000.0000.0000.000
74A189THR00.0200.01427.265-0.010-0.0100.0000.0000.0000.000
75A190ILE0-0.035-0.01322.2960.0050.0050.0000.0000.0000.000
76A191LYS10.8420.90325.3670.0470.0470.0000.0000.0000.000
77A192VAL00.0180.00722.291-0.007-0.0070.0000.0000.0000.000
78A193PRO0-0.0270.00219.5460.0140.0140.0000.0000.0000.000
79A194ASN00.0440.02721.813-0.011-0.0110.0000.0000.0000.000
80A195VAL00.0770.02017.9180.0120.0120.0000.0000.0000.000
81A196GLN0-0.0010.01019.9050.0220.0220.0000.0000.0000.000
82A197LYS10.8600.92422.2530.0040.0040.0000.0000.0000.000
83A198GLY00.0170.01918.4710.0120.0120.0000.0000.0000.000
84A199GLU-1-0.821-0.87918.852-0.036-0.0360.0000.0000.0000.000
85A200GLU-1-0.831-0.90514.060-0.099-0.0990.0000.0000.0000.000
86A201LEU00.0170.00617.7660.0110.0110.0000.0000.0000.000
87A202GLY00.0250.01417.9540.0100.0100.0000.0000.0000.000
88A203ILE0-0.006-0.01016.0650.0110.0110.0000.0000.0000.000
89A204ALA00.0100.01213.803-0.010-0.0100.0000.0000.0000.000
90A205PRO00.1040.06410.8910.0260.0260.0000.0000.0000.000
91A206LEU00.0280.01514.2290.0530.0530.0000.0000.0000.000
92A207VAL0-0.0250.00412.2940.0000.0000.0000.0000.0000.000
93A208LYS11.0010.99615.3720.0980.0980.0000.0000.0000.000
94A209PRO00.0190.02817.9500.0270.0270.0000.0000.0000.000
95A210VAL0-0.006-0.01419.0140.0010.0010.0000.0000.0000.000
96A211VAL00.0000.00118.2810.0250.0250.0000.0000.0000.000
97A212GLY0-0.021-0.01716.292-0.034-0.0340.0000.0000.0000.000
98A213GLY00.0200.01017.0950.0110.0110.0000.0000.0000.000
99A214VAL0-0.012-0.01617.968-0.009-0.0090.0000.0000.0000.000
100A215LYS10.8990.97219.415-0.333-0.3330.0000.0000.0000.000
101A216LYS11.0301.01020.805-0.220-0.2200.0000.0000.0000.000
102A217GLY00.0130.00424.2350.0090.0090.0000.0000.0000.000
103A218SER0-0.062-0.01423.214-0.012-0.0120.0000.0000.0000.000
104A219PRO00.0550.01725.146-0.009-0.0090.0000.0000.0000.000
105A220ALA00.0340.00723.911-0.013-0.0130.0000.0000.0000.000
106A221ASP-1-0.846-0.91424.9130.1760.1760.0000.0000.0000.000
107A222GLN0-0.035-0.02426.546-0.021-0.0210.0000.0000.0000.000
108A223VAL00.0180.02728.909-0.010-0.0100.0000.0000.0000.000
109A224GLY00.0070.01029.601-0.011-0.0110.0000.0000.0000.000
110A225ILE0-0.0150.00024.197-0.006-0.0060.0000.0000.0000.000
111A226LYS10.7860.87624.520-0.142-0.1420.0000.0000.0000.000
112A227PRO0-0.004-0.01120.138-0.007-0.0070.0000.0000.0000.000
113A228GLY0-0.015-0.00521.933-0.014-0.0140.0000.0000.0000.000
114A229ASP-1-0.751-0.82523.2760.0940.0940.0000.0000.0000.000
115A230LEU00.0010.00823.0060.0100.0100.0000.0000.0000.000
116A231ILE0-0.012-0.01522.554-0.005-0.0050.0000.0000.0000.000
117A232LEU00.0200.01124.994-0.006-0.0060.0000.0000.0000.000
118A233GLU-1-0.815-0.88927.8240.0310.0310.0000.0000.0000.000
119A234VAL00.0110.00225.4550.0100.0100.0000.0000.0000.000
120A235ASN00.008-0.00628.933-0.004-0.0040.0000.0000.0000.000
121A236GLY00.0590.04732.265-0.003-0.0030.0000.0000.0000.000
122A237LYS10.8280.91526.325-0.043-0.0430.0000.0000.0000.000
123A238LYS10.9290.94129.266-0.019-0.0190.0000.0000.0000.000
124A239ILE0-0.091-0.02522.8320.0010.0010.0000.0000.0000.000
125A240ASN00.010-0.00623.555-0.007-0.0070.0000.0000.0000.000
126A241THR0-0.055-0.04818.648-0.006-0.0060.0000.0000.0000.000
127A242TRP00.017-0.00115.7190.0110.0110.0000.0000.0000.000
128A243TYR0-0.001-0.02513.3360.0390.0390.0000.0000.0000.000
129A244GLU-1-0.702-0.83618.0780.0350.0350.0000.0000.0000.000
130A245LEU00.0020.01519.5590.0040.0040.0000.0000.0000.000
131A246VAL0-0.009-0.01116.4130.0090.0090.0000.0000.0000.000
132A247GLU-1-0.858-0.91719.8500.0600.0600.0000.0000.0000.000
133A248GLU-1-0.845-0.92122.3670.0650.0650.0000.0000.0000.000
134A249VAL0-0.017-0.00622.1000.0010.0010.0000.0000.0000.000
135A250ARG10.8850.95819.506-0.170-0.1700.0000.0000.0000.000
136A251LYS10.7970.86723.889-0.075-0.0750.0000.0000.0000.000
137A252SER0-0.020-0.00826.596-0.007-0.0070.0000.0000.0000.000
138A253GLN00.0150.00828.547-0.007-0.0070.0000.0000.0000.000
139A254GLY00.0140.01028.9420.0000.0000.0000.0000.0000.000
140A255LYS10.8980.95529.847-0.076-0.0760.0000.0000.0000.000
141A256ALA00.008-0.00531.0140.0070.0070.0000.0000.0000.000
142A257ILE0-0.023-0.00626.459-0.004-0.0040.0000.0000.0000.000
143A258LYS10.8830.92131.142-0.060-0.0600.0000.0000.0000.000
144A259LEU0-0.031-0.02126.1580.0020.0020.0000.0000.0000.000
145A260LYS10.8630.93629.601-0.045-0.0450.0000.0000.0000.000
146A261ILE0-0.022-0.01326.4590.0030.0030.0000.0000.0000.000
147A262LEU00.0020.01128.046-0.006-0.0060.0000.0000.0000.000
148A263ARG10.8350.86327.850-0.090-0.0900.0000.0000.0000.000
149A264ASN0-0.016-0.02329.1760.0010.0010.0000.0000.0000.000
150A265GLY00.0450.02830.888-0.004-0.0040.0000.0000.0000.000
151A266LYS10.9500.98132.791-0.036-0.0360.0000.0000.0000.000
152A267MET00.0140.01132.6830.0060.0060.0000.0000.0000.000
153A268ILE0-0.017-0.00731.6310.0000.0000.0000.0000.0000.000
154A269GLU-1-0.850-0.93732.0680.0530.0530.0000.0000.0000.000
155A270LYS10.8190.90129.643-0.086-0.0860.0000.0000.0000.000
156A271GLU-1-0.797-0.88332.0370.0690.0690.0000.0000.0000.000
157A272LEU0-0.0180.00126.1790.0040.0040.0000.0000.0000.000
158A273ILE00.0600.02330.195-0.005-0.0050.0000.0000.0000.000
159A274PRO0-0.063-0.02625.1920.0120.0120.0000.0000.0000.000
160A275ALA00.0730.04925.248-0.008-0.0080.0000.0000.0000.000
161A276LYS10.9360.96024.437-0.137-0.1370.0000.0000.0000.000
162A277ASP-1-0.865-0.92920.1000.3460.3460.0000.0000.0000.000
163A278PRO00.0620.00821.1490.0130.0130.0000.0000.0000.000
164A279LYS10.9390.97616.810-0.454-0.4540.0000.0000.0000.000
165A280THR0-0.048-0.02416.2260.0300.0300.0000.0000.0000.000
166A281GLY00.0310.02818.128-0.020-0.0200.0000.0000.0000.000
167A282THR0-0.053-0.03419.425-0.034-0.0340.0000.0000.0000.000
168A283TYR0-0.046-0.01122.2360.0120.0120.0000.0000.0000.000
169A284PHE00.0170.00717.1830.0110.0110.0000.0000.0000.000
170A285ILE00.0560.02121.522-0.010-0.0100.0000.0000.0000.000
171A286GLY00.027-0.01220.977-0.013-0.0130.0000.0000.0000.000
172A287LEU0-0.0370.00819.3280.0170.0170.0000.0000.0000.000
173A288PHE00.0310.00714.0220.0350.0350.0000.0000.0000.000
174A289PRO00.0620.03812.313-0.040-0.0400.0000.0000.0000.000
175A290LYS10.8890.93013.902-0.059-0.0590.0000.0000.0000.000
176A291THR0-0.0170.0108.810-0.043-0.0430.0000.0000.0000.000