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: YNY32

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1708115.887854
FMO2-HF: Nuclear repulsion 1641467.788227
FMO2-HF: Total energy -66648.099627
FMO2-MP2: Total energy -66848.448353


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.
-3.236-0.5930.342-1.007-1.977-0.001
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 : 0.012 / q_NPA : -0.003
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].
3A118LYS10.9850.9753.496-1.2230.3610.024-0.763-0.8450.001
4A119TYR00.0790.0455.0590.0050.178-0.001-0.008-0.1630.000
5A120LEU0-0.034-0.0092.559-0.4320.2110.317-0.207-0.753-0.002
6A121LYS10.8730.9023.6111.7131.9560.002-0.029-0.2160.000
7A122GLU-1-0.956-0.9707.538-0.561-0.5610.0000.0000.0000.000
8A123PRO00.0510.01610.3440.0190.0190.0000.0000.0000.000
9A124VAL0-0.0060.01013.289-0.003-0.0030.0000.0000.0000.000
10A125VAL0-0.0040.00615.1530.0470.0470.0000.0000.0000.000
11A126VAL0-0.032-0.01316.357-0.005-0.0050.0000.0000.0000.000
12A127GLY0-0.009-0.01917.1360.0110.0110.0000.0000.0000.000
13A128TYR0-0.059-0.04317.6240.0280.0280.0000.0000.0000.000
14A129VAL00.0230.01518.793-0.017-0.0170.0000.0000.0000.000
15A130GLN00.0220.00618.8590.0030.0030.0000.0000.0000.000
16A131ARG10.8610.91821.721-0.036-0.0360.0000.0000.0000.000
17A132ASP-1-0.825-0.89425.2000.0210.0210.0000.0000.0000.000
18A133SER0-0.013-0.00822.185-0.005-0.0050.0000.0000.0000.000
19A134ILE00.010-0.00723.067-0.001-0.0010.0000.0000.0000.000
20A135ALA00.0340.02221.323-0.003-0.0030.0000.0000.0000.000
21A136GLN00.0480.02223.4660.0020.0020.0000.0000.0000.000
22A137LYS10.8430.92226.0560.0160.0160.0000.0000.0000.000
23A138ILE00.0060.01925.0240.0010.0010.0000.0000.0000.000
24A139GLY0-0.0120.00528.120-0.003-0.0030.0000.0000.0000.000
25A140ILE0-0.017-0.01321.641-0.003-0.0030.0000.0000.0000.000
26A141LYS10.8850.93924.7840.0660.0660.0000.0000.0000.000
27A142PRO0-0.016-0.02721.661-0.012-0.0120.0000.0000.0000.000
28A143GLY0-0.018-0.00521.2710.0080.0080.0000.0000.0000.000
29A144ASP-1-0.730-0.80522.260-0.110-0.1100.0000.0000.0000.000
30A145LYS10.8020.88618.7180.1980.1980.0000.0000.0000.000
31A146ILE0-0.010-0.01317.8240.0140.0140.0000.0000.0000.000
32A147ILE00.0190.00618.422-0.031-0.0310.0000.0000.0000.000
33A148LYS10.8510.92120.4790.1770.1770.0000.0000.0000.000
34A149ILE00.0090.01118.9460.0160.0160.0000.0000.0000.000
35A150ASN00.0510.03722.023-0.017-0.0170.0000.0000.0000.000
36A151GLY0-0.011-0.01124.4160.0030.0030.0000.0000.0000.000
37A152TYR0-0.029-0.02118.962-0.012-0.0120.0000.0000.0000.000
38A153GLU-1-0.813-0.89319.105-0.230-0.2300.0000.0000.0000.000
39A154VAL0-0.046-0.01715.238-0.027-0.0270.0000.0000.0000.000
40A155ARG10.8860.92914.5600.3700.3700.0000.0000.0000.000
41A156THR0-0.044-0.0329.986-0.050-0.0500.0000.0000.0000.000
42A157TRP0-0.007-0.0219.1850.0920.0920.0000.0000.0000.000
43A158GLU-1-0.827-0.8905.767-1.565-1.5650.0000.0000.0000.000
44A159ASP-1-0.753-0.8489.384-0.463-0.4630.0000.0000.0000.000
45A160LEU0-0.033-0.00913.0140.0680.0680.0000.0000.0000.000
46A161ARG10.8590.9179.3820.2540.2540.0000.0000.0000.000
47A162ASP-1-0.863-0.94111.286-0.443-0.4430.0000.0000.0000.000
48A163ALA0-0.009-0.00813.8320.0480.0480.0000.0000.0000.000
49A164LEU0-0.044-0.02415.7130.0400.0400.0000.0000.0000.000
50A165ILE0-0.005-0.00913.2760.0360.0360.0000.0000.0000.000
51A166ARG10.8500.92417.2150.1960.1960.0000.0000.0000.000
52A167LEU00.0200.01019.2160.0220.0220.0000.0000.0000.000
53A168SER0-0.041-0.03420.9240.0200.0200.0000.0000.0000.000
54A169LEU0-0.081-0.04118.3900.0150.0150.0000.0000.0000.000
55A170ASP-1-0.839-0.89622.459-0.133-0.1330.0000.0000.0000.000
56A171GLY0-0.054-0.02224.9870.0070.0070.0000.0000.0000.000
57A172VAL0-0.003-0.00125.4900.0070.0070.0000.0000.0000.000
58A173LYS10.9060.95326.3320.0610.0610.0000.0000.0000.000
59A174GLU-1-0.908-0.94627.680-0.057-0.0570.0000.0000.0000.000
60A175THR0-0.007-0.01523.997-0.008-0.0080.0000.0000.0000.000
61A176THR00.0170.02827.1740.0060.0060.0000.0000.0000.000
62A177LEU0-0.037-0.02120.633-0.015-0.0150.0000.0000.0000.000
63A178PHE00.000-0.00723.4830.0120.0120.0000.0000.0000.000
64A179LEU0-0.022-0.01622.305-0.019-0.0190.0000.0000.0000.000
65A180GLU-1-0.788-0.87323.517-0.176-0.1760.0000.0000.0000.000
66A181ARG10.7990.84024.6300.0840.0840.0000.0000.0000.000
67A182ASN0-0.023-0.01927.3410.0020.0020.0000.0000.0000.000
68A183GLY00.0140.00827.8240.0050.0050.0000.0000.0000.000
69A184GLU-1-0.915-0.92929.038-0.079-0.0790.0000.0000.0000.000
70A185VAL0-0.013-0.02527.121-0.007-0.0070.0000.0000.0000.000
71A186LEU0-0.036-0.00427.7350.0100.0100.0000.0000.0000.000
72A187HIS00.0280.00227.486-0.013-0.0130.0000.0000.0000.000
73A188LEU0-0.006-0.00326.6120.0090.0090.0000.0000.0000.000
74A189THR00.0410.02227.429-0.011-0.0110.0000.0000.0000.000
75A190ILE0-0.044-0.01422.4590.0060.0060.0000.0000.0000.000
76A191LYS10.8670.91825.5120.0400.0400.0000.0000.0000.000
77A192VAL00.004-0.00922.135-0.006-0.0060.0000.0000.0000.000
78A193PRO0-0.051-0.01619.7530.0120.0120.0000.0000.0000.000
79A194ASN00.0260.00721.911-0.012-0.0120.0000.0000.0000.000
80A195VAL00.0770.02618.1210.0130.0130.0000.0000.0000.000
81A196GLN00.0080.01119.6870.0210.0210.0000.0000.0000.000
82A197LYS10.8660.93822.2620.0020.0020.0000.0000.0000.000
83A198GLY00.0130.01018.3650.0140.0140.0000.0000.0000.000
84A199GLU-1-0.831-0.88718.517-0.028-0.0280.0000.0000.0000.000
85A200GLU-1-0.863-0.93313.980-0.065-0.0650.0000.0000.0000.000
86A201LEU00.0230.00617.6620.0080.0080.0000.0000.0000.000
87A202GLY00.0220.00917.8980.0090.0090.0000.0000.0000.000
88A203ILE0-0.0040.00716.0990.0120.0120.0000.0000.0000.000
89A204ALA00.0020.00113.942-0.006-0.0060.0000.0000.0000.000
90A205PRO00.0900.06510.6510.0180.0180.0000.0000.0000.000
91A206LEU00.0270.01113.9860.0610.0610.0000.0000.0000.000
92A207VAL00.0040.01812.388-0.015-0.0150.0000.0000.0000.000
93A208LYS10.9940.98715.4440.0710.0710.0000.0000.0000.000
94A209PRO00.0330.04017.7420.0290.0290.0000.0000.0000.000
95A210VAL0-0.024-0.03218.7230.0020.0020.0000.0000.0000.000
96A211VAL00.0070.00617.9420.0330.0330.0000.0000.0000.000
97A212GLY0-0.035-0.03016.179-0.038-0.0380.0000.0000.0000.000
98A213GLY00.0210.01016.9530.0090.0090.0000.0000.0000.000
99A214VAL00.002-0.00617.831-0.004-0.0040.0000.0000.0000.000
100A215LYS10.9340.98919.034-0.374-0.3740.0000.0000.0000.000
101A216LYS11.0381.01920.545-0.238-0.2380.0000.0000.0000.000
102A217GLY0-0.0050.00123.9230.0130.0130.0000.0000.0000.000
103A218SER0-0.071-0.02622.693-0.014-0.0140.0000.0000.0000.000
104A219PRO00.0720.02324.425-0.010-0.0100.0000.0000.0000.000
105A220ALA00.0340.01123.388-0.017-0.0170.0000.0000.0000.000
106A221ASP-1-0.869-0.95324.6510.1940.1940.0000.0000.0000.000
107A222GLN0-0.058-0.03026.259-0.023-0.0230.0000.0000.0000.000
108A223VAL00.0100.02528.436-0.012-0.0120.0000.0000.0000.000
109A224GLY0-0.0030.00529.308-0.011-0.0110.0000.0000.0000.000
110A225ILE0-0.018-0.00423.817-0.008-0.0080.0000.0000.0000.000
111A226LYS10.8460.92224.662-0.162-0.1620.0000.0000.0000.000
112A227PRO00.014-0.00320.062-0.003-0.0030.0000.0000.0000.000
113A228GLY0-0.040-0.02521.347-0.018-0.0180.0000.0000.0000.000
114A229ASP-1-0.737-0.81122.7610.1090.1090.0000.0000.0000.000
115A230LEU0-0.018-0.00922.7260.0110.0110.0000.0000.0000.000
116A231ILE00.0150.00521.909-0.006-0.0060.0000.0000.0000.000
117A232LEU0-0.0090.00024.702-0.007-0.0070.0000.0000.0000.000
118A233GLU-1-0.805-0.90027.4480.0410.0410.0000.0000.0000.000
119A234VAL00.0100.00324.8840.0100.0100.0000.0000.0000.000
120A235ASN00.0210.00228.351-0.005-0.0050.0000.0000.0000.000
121A236GLY00.0280.02931.697-0.004-0.0040.0000.0000.0000.000
122A237LYS10.8970.95926.634-0.059-0.0590.0000.0000.0000.000
123A238LYS10.9110.93728.852-0.028-0.0280.0000.0000.0000.000
124A239ILE0-0.078-0.01622.4400.0000.0000.0000.0000.0000.000
125A240ASN0-0.002-0.01523.426-0.005-0.0050.0000.0000.0000.000
126A241THR0-0.042-0.02718.443-0.004-0.0040.0000.0000.0000.000
127A242TRP00.0240.00815.4310.0070.0070.0000.0000.0000.000
128A243TYR00.008-0.02313.0650.0450.0450.0000.0000.0000.000
129A244GLU-1-0.748-0.87117.7990.0510.0510.0000.0000.0000.000
130A245LEU00.0090.01619.4560.0030.0030.0000.0000.0000.000
131A246VAL0-0.023-0.01716.0280.0080.0080.0000.0000.0000.000
132A247GLU-1-0.866-0.92019.4700.0820.0820.0000.0000.0000.000
133A248GLU-1-0.846-0.92621.9720.0860.0860.0000.0000.0000.000
134A249VAL0-0.021-0.00221.680-0.002-0.0020.0000.0000.0000.000
135A250ARG10.8940.95519.049-0.200-0.2000.0000.0000.0000.000
136A251LYS10.7830.86323.300-0.097-0.0970.0000.0000.0000.000
137A252SER0-0.015-0.00726.203-0.010-0.0100.0000.0000.0000.000
138A253GLN00.0110.00028.260-0.010-0.0100.0000.0000.0000.000
139A254GLY0-0.025-0.00928.700-0.003-0.0030.0000.0000.0000.000
140A255LYS10.9060.96429.818-0.090-0.0900.0000.0000.0000.000
141A256ALA00.004-0.01330.6210.0070.0070.0000.0000.0000.000
142A257ILE0-0.019-0.00125.834-0.004-0.0040.0000.0000.0000.000
143A258LYS10.9040.93230.503-0.073-0.0730.0000.0000.0000.000
144A259LEU0-0.031-0.01625.6810.0020.0020.0000.0000.0000.000
145A260LYS10.8790.94529.357-0.055-0.0550.0000.0000.0000.000
146A261ILE0-0.031-0.02725.9950.0050.0050.0000.0000.0000.000
147A262LEU0-0.0040.00327.782-0.008-0.0080.0000.0000.0000.000
148A263ARG10.8270.86727.568-0.104-0.1040.0000.0000.0000.000
149A264ASN0-0.006-0.01728.8090.0000.0000.0000.0000.0000.000
150A265GLY00.0340.01830.625-0.004-0.0040.0000.0000.0000.000
151A266LYS10.9520.97932.584-0.044-0.0440.0000.0000.0000.000
152A267MET00.0010.01232.4010.0070.0070.0000.0000.0000.000
153A268ILE0-0.003-0.00131.5050.0000.0000.0000.0000.0000.000
154A269GLU-1-0.863-0.94032.0900.0640.0640.0000.0000.0000.000
155A270LYS10.8310.91329.293-0.103-0.1030.0000.0000.0000.000
156A271GLU-1-0.824-0.90031.7160.0820.0820.0000.0000.0000.000
157A272LEU0-0.0100.00125.6420.0040.0040.0000.0000.0000.000
158A273ILE00.0560.02629.899-0.003-0.0030.0000.0000.0000.000
159A274PRO0-0.046-0.01625.0030.0130.0130.0000.0000.0000.000
160A275ALA00.0490.03325.134-0.012-0.0120.0000.0000.0000.000
161A276LYS10.9510.97124.169-0.145-0.1450.0000.0000.0000.000
162A277ASP-1-0.879-0.94519.4180.3870.3870.0000.0000.0000.000
163A278PRO00.011-0.00821.1930.0100.0100.0000.0000.0000.000
164A279LYS10.9440.98116.842-0.496-0.4960.0000.0000.0000.000
165A280THR0-0.027-0.01215.5840.0150.0150.0000.0000.0000.000
166A281GLY00.0290.02917.607-0.016-0.0160.0000.0000.0000.000
167A282THR0-0.054-0.04019.095-0.040-0.0400.0000.0000.0000.000
168A283TYR0-0.0220.00221.7070.0150.0150.0000.0000.0000.000
169A284PHE00.0250.01716.6650.0180.0180.0000.0000.0000.000
170A285ILE00.0630.01821.079-0.016-0.0160.0000.0000.0000.000
171A286GLY00.003-0.01119.932-0.012-0.0120.0000.0000.0000.000
172A287LEU0-0.0190.00018.853-0.001-0.0010.0000.0000.0000.000
173A288PHE00.0160.00413.7040.0390.0390.0000.0000.0000.000
174A289PRO00.0700.04712.167-0.048-0.0480.0000.0000.0000.000
175A290LYS10.9000.94413.667-0.086-0.0860.0000.0000.0000.000
176A291THR00.0030.0148.603-0.002-0.0020.0000.0000.0000.000