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: 5N3MZ

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1705371.219922
FMO2-HF: Nuclear repulsion 1638724.208053
FMO2-HF: Total energy -66647.011869
FMO2-MP2: Total energy -66847.340496


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.
-2.2430.3780.399-1.027-1.992-0.003
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 : 0.029 / 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].
3A118LYS10.9930.9753.391-0.6430.9550.038-0.774-0.8620.000
4A119TYR00.0740.0435.0000.0910.264-0.001-0.008-0.1640.000
5A120LEU0-0.015-0.0042.548-0.4070.2520.362-0.227-0.793-0.003
6A121LYS10.9310.9573.8451.8222.0130.000-0.018-0.1730.000
7A122GLU-1-0.979-0.9767.484-0.711-0.7110.0000.0000.0000.000
8A123PRO00.0270.00210.2800.0410.0410.0000.0000.0000.000
9A124VAL00.0000.01213.377-0.015-0.0150.0000.0000.0000.000
10A125VAL0-0.0120.00415.1380.0560.0560.0000.0000.0000.000
11A126VAL0-0.028-0.01116.334-0.014-0.0140.0000.0000.0000.000
12A127GLY0-0.013-0.02117.1080.0100.0100.0000.0000.0000.000
13A128TYR0-0.059-0.03817.6470.0300.0300.0000.0000.0000.000
14A129VAL00.0250.01418.750-0.017-0.0170.0000.0000.0000.000
15A130GLN00.005-0.00519.0790.0080.0080.0000.0000.0000.000
16A131ARG10.9380.97221.670-0.030-0.0300.0000.0000.0000.000
17A132ASP-1-0.916-0.96625.1460.0150.0150.0000.0000.0000.000
18A133SER0-0.045-0.01322.113-0.004-0.0040.0000.0000.0000.000
19A134ILE00.006-0.01222.656-0.003-0.0030.0000.0000.0000.000
20A135ALA00.0400.01621.297-0.004-0.0040.0000.0000.0000.000
21A136GLN00.0410.02423.4210.0030.0030.0000.0000.0000.000
22A137LYS10.9020.95526.0110.0240.0240.0000.0000.0000.000
23A138ILE0-0.0070.00725.0260.0020.0020.0000.0000.0000.000
24A139GLY0-0.0110.00728.099-0.004-0.0040.0000.0000.0000.000
25A140ILE0-0.028-0.01321.663-0.005-0.0050.0000.0000.0000.000
26A141LYS10.9060.94524.7780.0900.0900.0000.0000.0000.000
27A142PRO0-0.022-0.02521.620-0.014-0.0140.0000.0000.0000.000
28A143GLY0-0.020-0.00521.2460.0110.0110.0000.0000.0000.000
29A144ASP-1-0.726-0.80722.295-0.139-0.1390.0000.0000.0000.000
30A145LYS10.9620.98317.7620.3060.3060.0000.0000.0000.000
31A146ILE0-0.012-0.01917.8210.0180.0180.0000.0000.0000.000
32A147ILE00.0160.00618.409-0.037-0.0370.0000.0000.0000.000
33A148LYS10.9110.97120.4460.1830.1830.0000.0000.0000.000
34A149ILE00.0050.00918.9680.0160.0160.0000.0000.0000.000
35A150ASN00.0900.07122.001-0.016-0.0160.0000.0000.0000.000
36A151GLY0-0.065-0.04524.591-0.001-0.0010.0000.0000.0000.000
37A152TYR00.008-0.02218.905-0.005-0.0050.0000.0000.0000.000
38A153GLU-1-0.894-0.94319.345-0.262-0.2620.0000.0000.0000.000
39A154VAL0-0.029-0.00715.280-0.026-0.0260.0000.0000.0000.000
40A155ARG10.8770.92514.5690.3910.3910.0000.0000.0000.000
41A156THR0-0.009-0.0029.919-0.024-0.0240.0000.0000.0000.000
42A157TRP00.010-0.0139.1970.1060.1060.0000.0000.0000.000
43A158GLU-1-0.891-0.9455.826-1.553-1.5530.0000.0000.0000.000
44A159ASP-1-0.762-0.8669.367-0.489-0.4890.0000.0000.0000.000
45A160LEU0-0.045-0.01612.9810.0800.0800.0000.0000.0000.000
46A161ARG10.9260.9599.3730.2390.2390.0000.0000.0000.000
47A162ASP-1-0.872-0.94011.233-0.470-0.4700.0000.0000.0000.000
48A163ALA00.001-0.00613.8080.0540.0540.0000.0000.0000.000
49A164LEU0-0.040-0.02415.8610.0440.0440.0000.0000.0000.000
50A165ILE0-0.005-0.00813.2330.0380.0380.0000.0000.0000.000
51A166ARG10.9130.96117.3370.1710.1710.0000.0000.0000.000
52A167LEU0-0.0010.01219.1890.0240.0240.0000.0000.0000.000
53A168SER0-0.0200.00120.7870.0200.0200.0000.0000.0000.000
54A169LEU0-0.071-0.04518.3880.0150.0150.0000.0000.0000.000
55A170ASP-1-0.896-0.94022.422-0.114-0.1140.0000.0000.0000.000
56A171GLY0-0.062-0.02324.9580.0050.0050.0000.0000.0000.000
57A172VAL0-0.020-0.00325.4060.0060.0060.0000.0000.0000.000
58A173LYS10.9200.95326.2940.0480.0480.0000.0000.0000.000
59A174GLU-1-0.906-0.94827.640-0.060-0.0600.0000.0000.0000.000
60A175THR00.008-0.00423.850-0.008-0.0080.0000.0000.0000.000
61A176THR00.0240.02427.1330.0080.0080.0000.0000.0000.000
62A177LEU0-0.034-0.01620.609-0.015-0.0150.0000.0000.0000.000
63A178PHE0-0.003-0.01023.4540.0130.0130.0000.0000.0000.000
64A179LEU0-0.028-0.01822.125-0.022-0.0220.0000.0000.0000.000
65A180GLU-1-0.888-0.94323.493-0.207-0.2070.0000.0000.0000.000
66A181ARG10.7790.83524.5760.1070.1070.0000.0000.0000.000
67A182ASN0-0.040-0.02827.2550.0030.0030.0000.0000.0000.000
68A183GLY00.0200.01427.7430.0060.0060.0000.0000.0000.000
69A184GLU-1-0.917-0.93228.963-0.097-0.0970.0000.0000.0000.000
70A185VAL0-0.006-0.01927.098-0.008-0.0080.0000.0000.0000.000
71A186LEU0-0.0320.00127.7160.0120.0120.0000.0000.0000.000
72A187HIS00.021-0.00127.464-0.013-0.0130.0000.0000.0000.000
73A188LEU0-0.004-0.00526.2660.0100.0100.0000.0000.0000.000
74A189THR00.0260.01927.398-0.009-0.0090.0000.0000.0000.000
75A190ILE0-0.048-0.01622.4880.0060.0060.0000.0000.0000.000
76A191LYS10.9210.95625.9180.0330.0330.0000.0000.0000.000
77A192VAL00.004-0.01221.998-0.008-0.0080.0000.0000.0000.000
78A193PRO0-0.065-0.02419.7480.0130.0130.0000.0000.0000.000
79A194ASN0-0.004-0.02021.866-0.010-0.0100.0000.0000.0000.000
80A195VAL00.0810.02918.0920.0150.0150.0000.0000.0000.000
81A196GLN00.0120.01219.6540.0280.0280.0000.0000.0000.000
82A197LYS10.8620.93222.231-0.011-0.0110.0000.0000.0000.000
83A198GLY00.0090.01018.3220.0140.0140.0000.0000.0000.000
84A199GLU-1-0.870-0.91818.468-0.020-0.0200.0000.0000.0000.000
85A200GLU-1-0.931-0.97414.167-0.013-0.0130.0000.0000.0000.000
86A201LEU00.016-0.00117.6210.0060.0060.0000.0000.0000.000
87A202GLY00.0300.01217.8630.0090.0090.0000.0000.0000.000
88A203ILE0-0.0120.00516.0950.0090.0090.0000.0000.0000.000
89A204ALA00.0120.00713.861-0.005-0.0050.0000.0000.0000.000
90A205PRO00.0840.05810.6450.0220.0220.0000.0000.0000.000
91A206LEU00.0250.01113.9550.0640.0640.0000.0000.0000.000
92A207VAL00.0050.01712.340-0.032-0.0320.0000.0000.0000.000
93A208LYS10.9880.98415.4210.1690.1690.0000.0000.0000.000
94A209PRO00.0390.03817.7200.0200.0200.0000.0000.0000.000
95A210VAL0-0.019-0.02918.6870.0070.0070.0000.0000.0000.000
96A211VAL00.0060.00717.9220.0220.0220.0000.0000.0000.000
97A212GLY0-0.070-0.05415.848-0.041-0.0410.0000.0000.0000.000
98A213GLY00.0170.01416.7170.0060.0060.0000.0000.0000.000
99A214VAL00.0210.00517.5810.0010.0010.0000.0000.0000.000
100A215LYS10.9330.98218.940-0.384-0.3840.0000.0000.0000.000
101A216LYS11.0271.01220.537-0.223-0.2230.0000.0000.0000.000
102A217GLY0-0.023-0.01823.9020.0180.0180.0000.0000.0000.000
103A218SER0-0.070-0.03022.679-0.011-0.0110.0000.0000.0000.000
104A219PRO00.0650.02024.412-0.012-0.0120.0000.0000.0000.000
105A220ALA00.0340.01023.393-0.018-0.0180.0000.0000.0000.000
106A221ASP-1-0.866-0.93324.6700.1730.1730.0000.0000.0000.000
107A222GLN0-0.059-0.02126.248-0.024-0.0240.0000.0000.0000.000
108A223VAL00.0060.02628.513-0.012-0.0120.0000.0000.0000.000
109A224GLY00.000-0.00329.295-0.012-0.0120.0000.0000.0000.000
110A225ILE0-0.044-0.02323.798-0.011-0.0110.0000.0000.0000.000
111A226LYS10.9210.96024.515-0.110-0.1100.0000.0000.0000.000
112A227PRO00.002-0.01119.807-0.005-0.0050.0000.0000.0000.000
113A228GLY0-0.039-0.02121.030-0.016-0.0160.0000.0000.0000.000
114A229ASP-1-0.741-0.84022.4400.0710.0710.0000.0000.0000.000
115A230LEU0-0.014-0.00922.7070.0040.0040.0000.0000.0000.000
116A231ILE00.0060.00321.6790.0000.0000.0000.0000.0000.000
117A232LEU0-0.010-0.00624.681-0.009-0.0090.0000.0000.0000.000
118A233GLU-1-0.865-0.94727.4270.0240.0240.0000.0000.0000.000
119A234VAL00.0200.01024.9110.0100.0100.0000.0000.0000.000
120A235ASN00.004-0.00928.332-0.005-0.0050.0000.0000.0000.000
121A236GLY00.0280.02531.679-0.003-0.0030.0000.0000.0000.000
122A237LYS10.9470.98428.830-0.037-0.0370.0000.0000.0000.000
123A238LYS10.9560.96728.831-0.001-0.0010.0000.0000.0000.000
124A239ILE0-0.058-0.00722.2500.0020.0020.0000.0000.0000.000
125A240ASN00.014-0.00623.531-0.001-0.0010.0000.0000.0000.000
126A241THR0-0.072-0.04718.376-0.011-0.0110.0000.0000.0000.000
127A242TRP00.0250.00615.1380.0030.0030.0000.0000.0000.000
128A243TYR00.009-0.02013.2410.0520.0520.0000.0000.0000.000
129A244GLU-1-0.753-0.86517.7800.0260.0260.0000.0000.0000.000
130A245LEU00.0030.01319.2780.0080.0080.0000.0000.0000.000
131A246VAL0-0.026-0.01816.0130.0140.0140.0000.0000.0000.000
132A247GLU-1-0.891-0.95719.4530.0770.0770.0000.0000.0000.000
133A248GLU-1-0.909-0.96821.9550.0760.0760.0000.0000.0000.000
134A249VAL0-0.0140.00121.6630.0010.0010.0000.0000.0000.000
135A250ARG10.8970.94619.222-0.204-0.2040.0000.0000.0000.000
136A251LYS10.8240.91223.287-0.090-0.0900.0000.0000.0000.000
137A252SER00.0070.01826.422-0.009-0.0090.0000.0000.0000.000
138A253GLN0-0.029-0.02328.250-0.011-0.0110.0000.0000.0000.000
139A254GLY0-0.029-0.00828.702-0.002-0.0020.0000.0000.0000.000
140A255LYS10.9480.98729.808-0.090-0.0900.0000.0000.0000.000
141A256ALA00.009-0.00830.6080.0070.0070.0000.0000.0000.000
142A257ILE0-0.0140.00625.980-0.005-0.0050.0000.0000.0000.000
143A258LYS10.9900.99030.487-0.058-0.0580.0000.0000.0000.000
144A259LEU0-0.027-0.01625.5550.0010.0010.0000.0000.0000.000
145A260LYS10.9130.96329.339-0.033-0.0330.0000.0000.0000.000
146A261ILE0-0.023-0.02126.3740.0020.0020.0000.0000.0000.000
147A262LEU0-0.0150.00027.760-0.006-0.0060.0000.0000.0000.000
148A263ARG10.8410.89927.548-0.073-0.0730.0000.0000.0000.000
149A264ASN0-0.007-0.01728.4700.0030.0030.0000.0000.0000.000
150A265GLY00.0370.01930.387-0.002-0.0020.0000.0000.0000.000
151A266LYS10.9490.97532.383-0.016-0.0160.0000.0000.0000.000
152A267MET00.0010.01832.3810.0050.0050.0000.0000.0000.000
153A268ILE00.000-0.00431.7790.0020.0020.0000.0000.0000.000
154A269GLU-1-0.902-0.95032.0710.0460.0460.0000.0000.0000.000
155A270LYS10.8260.91629.384-0.084-0.0840.0000.0000.0000.000
156A271GLU-1-0.900-0.95831.6930.0760.0760.0000.0000.0000.000
157A272LEU0-0.0100.00325.6250.0050.0050.0000.0000.0000.000
158A273ILE00.0600.02429.885-0.003-0.0030.0000.0000.0000.000
159A274PRO0-0.057-0.02025.0820.0140.0140.0000.0000.0000.000
160A275ALA00.0550.03725.102-0.010-0.0100.0000.0000.0000.000
161A276LYS10.9640.97124.161-0.163-0.1630.0000.0000.0000.000
162A277ASP-1-0.854-0.93018.9150.4300.4300.0000.0000.0000.000
163A278PRO0-0.002-0.00921.1890.0120.0120.0000.0000.0000.000
164A279LYS10.9330.97416.770-0.544-0.5440.0000.0000.0000.000
165A280THR0-0.026-0.01915.3870.0180.0180.0000.0000.0000.000
166A281GLY00.0170.02617.603-0.016-0.0160.0000.0000.0000.000
167A282THR0-0.050-0.03719.143-0.046-0.0460.0000.0000.0000.000
168A283TYR0-0.034-0.00221.6990.0150.0150.0000.0000.0000.000
169A284PHE00.0270.01517.0880.0190.0190.0000.0000.0000.000
170A285ILE00.0610.01521.068-0.015-0.0150.0000.0000.0000.000
171A286GLY0-0.008-0.00819.941-0.013-0.0130.0000.0000.0000.000
172A287LEU0-0.0100.00318.838-0.005-0.0050.0000.0000.0000.000
173A288PHE00.002-0.00313.3650.0420.0420.0000.0000.0000.000
174A289PRO00.0710.04912.221-0.047-0.0470.0000.0000.0000.000
175A290LYS10.9330.96313.649-0.005-0.0050.0000.0000.0000.000
176A291THR0-0.0040.0088.378-0.028-0.0280.0000.0000.0000.000